Autologous co-culture of human liver organoids with immune cells

Abstract

Embodiments of the disclosure include co-culture media compositions for co-culturing human liver organoids (HLOs) with immune cells, wherein the co-culture media composition comprises a first culture media comprising hepatocyte basal medium (HBM) comprising transferrin, ascorbic acid, insulin, and bovine serum albumin (BSA), and a second culture media comprising X-VIVO15 or RPMI, and uses thereof. Further embodiments include compositions of HLOs with immune cells, and uses thereof. Further embodiments include primed immune cell populations, and methods of making and using the same.

Description

Attorney Docket No.: CHMC.P0025WO PCT AUTOLOGOUS CO-CULTURE OF HUMAN LIVER ORGANOIDS WITH IMMUNE CELLS CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] The present application claims the benefit of priority under 35 U.S.C. § 119(e) to U.S. Provisional Application No. 63 / 656,015, AUTOLOGOUS CO-CULTURE OF HUMAN LIVER ORGANOIDS WITH IMMUNE CELLS, filed on filed June 4, 2024, which is currently co-pending herewith and which is incorporated by reference in its entirety. FIELD OF THE DISCLOSURE

[0002] Aspects of the present disclosure generally relate to co-cultures of human liver organoids (HLOs) with immune cells, and compositions including the same, as well as uses thereof. BACKGROUND

[0003] Three-dimensional (3D) cell cultures including organoids have great promise as model systems for studying biological function, development, and disease, as compared to traditional two-dimensional culture systems. These 3D cultures have the potential to more accurately reflect characteristics of organs found in vivo for various applications, such as studying pharmacological behavior, cell signaling, and other features.

[0004] While organoid systems are helpful models, organoid monoculture models have various limitations and may not completely recapitulate in vivo functionality and behavior. Thus, there is a need for improved model systems, such as co-culture models, which include different cell types, such as immune cells, for using as an investigational tool in various settings, such as studying disease and evaluating potential treatments.

[0005] Modeling adaptive immune responses in vitro remains a critical unmet need in liver research and drug development. Immune-mediated liver injuries - including autoimmune hepatitis, drug hypersensitivity reactions, and immune-related adverse events from cancer immunotherapies - are driven by complex, patient-specific mechanisms that current in vitro systems fail to recapitulate.SUMMARY OF THE DISCLOSURE

[0006] Embodiments of the disclosure include co-culture media compositions for co- culturing human liver organoids (HLOs) with immune cells, wherein the co-culture media composition comprises a first culture media comprising hepatocyte basal medium (HBM) comprising transferrin, ascorbic acid, insulin, and bovine serum albumin (BSA), and a second culture media comprising X-VIVO15 or RPMI. In some embodiments, the first culture media is an HLO culture media. In some embodiments, the second culture media is an immune cell culture media. In some embodiments, the first culture media is an HLO culture media, and the second culture media is an immune cell culture media.

[0007] In some embodiments, the co-culture media composition further includes oncostatin M (OSM) and hepatocyte growth factor (HGF). In some embodiments, the co-culture media composition further includes Penicillin / Streptomycin (Pen / Strep), human serum, IL-2, IL- 7, IL-15, and / or IL-21, and the co-culture media composition does not include epidermal growth factor (EGF). In some embodiments, the co-culture media composition further includes Penicillin / Streptomycin (Pen / Strep), human serum, IL-2, IL-7, IL-15, and IL-21, and the co- culture media composition does not include epidermal growth factor (EGF). In some embodiments, the co-culture media composition includes IL-15 and IL-21 and does not include EGF. In some embodiments, the first culture media and / or the second culture media is prepared without immunomodulators. In some embodiments, immunomodulators include hydrocortisone, hEGF, HGF, and / or dexamethasone. In some embodiments, the second culture media further includes glutamine.

[0008] In some embodiments, the co-culture media composition includes, by volume, about 10%-90%, 30%-70%, 40%-60%, or any intermediate or intervening ratio between these ratios, of the first culture media; and the co-culture media composition further includes about 10%-90%, 30%-70%, 40%-60%, or any intermediate or intervening ratio between these ratios, of the second culture media. In some embodiments, the co-culture media composition includes, by volume, about 30%-70%, or any intermediate or intervening ratio between these ratios, of the first culture media; and the co-culture media composition further includes about 30%-70%, or any intermediate or intervening ratio between these ratios, of the second culture media. In some embodiments, the co-culture media composition includes, by volume, about 45%-55% of thefirst culture media; and the co-culture media composition further includes about 45%-55% or any intermediate or intervening ratio between these ratios, of the second culture media; optionally wherein the co-culture media composition includes, by volume, about 50% of the first culture media; and wherein the co-culture media composition further includes about 50% of the second culture media. In some embodiments, the co-culture media composition includes the first culture media and the second culture media in a ratio, by volume, of about 1 / 99, 10 / 90, 20 / 80, 30 / 70, 40 / 60, 50 / 50, 60 / 40, 70 / 30, 80 / 20, 90 / 10, or 99 / 1, or any intermediate or intervening ratio between these ratios. In some embodiments, the co-culture media composition includes the first culture media and the second culture media in about a 40 / 60, 50 / 50, or 60 / 40 ratio, or any intermediate or intervening ratio between these ratios. In some embodiments, the co-culture media composition includes the first culture media and the second culture media in a ratio, by volume, of about 1 / 99, 10 / 90, 20 / 80, 30 / 70, 40 / 60, 50 / 50, 60 / 40, 70 / 30, 80 / 20, 90 / 10, or 99 / 1, or any intermediate or intervening ratio between these ratios, and further includes about 0.01-1000 ng / ml OSM, about 0.01-1000 ng / ml HGF, about 0.1-1000 IU / ml IL-2, about 0.1-1000 IU / ml IL- 7, about 0.1-1000 IU / ml IL-15, and / or about 0.1-1000 IU / ml IL-21, or any intermediate or intervening ratio between these ratios. In some embodiments, the co-culture media composition includes the first culture media and the second culture media in about a 40 / 60, 50 / 50, or 60 / 40 ratio, or any intermediate or intervening ratio between these ratios, and further includes about 0.1-50 ng / ml OSM, about 0.1-50 ng / ml HGF, about 1-100 IU / ml IL-2, about 1-100 IU / ml IL-7, about 1-100 IU / ml IL-15, and / or about 1-100 IU / ml IL-21, or any intermediate or intervening ratio between these ratios. In some embodiments, the co-culture media composition includes about 10-1000 IU / mL, 50-500 IU / mL, or 80-300 IU / mL IL-2, and / or about 0.01%-10%, 0.1%- 5%, or 0.5%-2% Pen / Strep. In some embodiments, the co-culture media composition includes about 100-250 IU / mL IL-2, and / or about 0.5-2% Pen / Strep. In some embodiments, the co-culture media composition includes about 45-55% of the first culture media, about 45-55% of the second culture media, and further includes about 1-40 ng / ml OSM, about 1-40 ng / ml HGF, about 1-50 IU / ml IL-2, about 1-50 IU / ml IL-7, about 1-50 IU / ml IL-15, and / or about 1-50 IU / ml IL-21; optionally wherein the co-culture media further includes about 0.5-2% Pen / Strep.

[0009] Additional embodiments of the disclosure include compositions, including the co-culture media compositions as described herein, and further including one or more humanliver organoid (HLO), and immune cells, thereby providing a HLO:immune cell composition in culture media. In some embodiments, the HLO and the immune cells are co-cultured in the culture media.

[0010] Additional embodiments of the disclosure include compositions, including one or more human liver organoid (HLO), and immune cells, thereby providing a HLO:immune cell composition. In some embodiments, the HLO and the immune cells are co-cultured in a culture media, such as the co-culture media compositions as described herein.

[0011] In some embodiments, the immune cells include peripheral blood mononuclear cells (PBMCs). In some embodiments, the immune cells include CD8 T cells, CD4 T cells, NK cells, monocytes, macrophages, and / or dendritic cells.

[0012] In some embodiments, the HLO and / or immune cells are derived from pluripotent stem cells. In some embodiments, the pluripotent stem cells include embryonic stem cells or induced pluripotent stem cells. In some embodiments, the HLO and / or immune cells are derived from primary cells. In some embodiments, the immune cells include T cells and / or monocyte-derived dendritic cells (mDCs). In some embodiments, the immune cells include CD4 and / or CD8 T cells. In some embodiments, the immune cells include CD8 T lymphocytes, including effector CD8 cells, proliferating effector CD8 cells, antigen-activated CD8 cells, cytotoxic CD8 cells, effector memory CD8 cells, and / or regulatory CD8 cells.

[0013] In some embodiments, the one or more HLO and the immune cells can be derived from a single subject. In some embodiments, the one or more HLO and the immune cells can be derived from different subjects. . In some embodiments, the HLO and / or immune cells are derived from a universal donor and / or from hypoimmune stem cells.

[0014] In some embodiments, the immune cells have been primed with one or more exogenous agent prior to co-culturing with the HLO. In some embodiments, the HLO has been pre-treated with one or more exogenous agent prior to co-culturing with the immune cells.

[0015] In some embodiments, the immune cells and HLOs are co-cultured in a ratio of about 1:1, 5:1, 10:1, 50:1, 100:1, 200:1, 300:1, 400:1, 500:1, 600:1, 700:1, 800:1, 900:1, 1000:1, 1500:1, 2000:1, 5000:1, 10,000:1, or greater, or any value between these ratios, immune cells to HLOs; optionally about 50-5000:1 immune cells to HLOs. In some embodiments, the immune cells and HLOs are co-cultured in a ratio of about 1:10, 1:5, 1:4,1:3, 1:2, 1:1, 2:1, 3:1,4:1, 5:1, 10:1, 20:1, 30:1, 40:1, 50:1, 100:1, or any value between these ratios, immune cells to liver cells; optionally about 1-50:1 immune cells to liver cells.

[0016] In some embodiments, the HLOs and immune cells have been co-cultured in the culture media for a time period selected from about 12 hours to about 10 days, or longer. In some embodiments, the HLOs and immune cells have been co-cultured in the culture media for about 3 days, + / - 1 day, to about 7 days, + / - 1 day.

[0017] In some embodiments, the composition is co-cultured via a droplet, multi-well plate, microcavity array culture platform, and / or organ-on-chip device. In some embodiments, the microcavity array culture platform includes one or more Gri3D® plate; AggreWell™ plate; Elplasia® plate; ultra-low attachment (ULA), or ultra-low adhesion, plate; micro-patterned hydrogel plate; SmartSphero plate; Acura plate; Sphericalplate 5D; microfluidic culture device; and / or hanging drop plate. In some embodiments, the composition and / or culture platform do not include a basement membrane matrix.

[0018] In some embodiments, the HLOs and the immune cells self-assemble. In some embodiments, the HLOs and the immune cells self-assemble into a three-dimensional form. In some embodiments, the immune cells spontaneously migrate toward the HLO. In some embodiments, the immune cells infiltrate the HLO.

[0019] In some embodiments, the HLO includes endothelial cells, mesenchymal cells, and cholangiocytes. In some embodiments, HLO includes one or more additional cell type selected from hepatoblasts, epithelial cells, Kupffer cells, stellate cells. In some embodiments, the HLO includes epithelial cells including hepatocytes, and mesenchymal cells including hepatic stellate cells. In some embodiments, the HLO includes a luminal structure. In some embodiments, the luminal structure includes internalized microvilli. In some embodiments, the HLO includes a structure with a single lumen. In some embodiments, the HLO is an artificial liver organoid, and / or is generated in vitro. In some embodiments, the HLO is three-dimensional. In some embodiments, the HLO is a mature liver organoid.

[0020] Additional embodiments of the disclosure include in vitro methods for co- culturing one or more human liver organoid (HLO) with immune cells, the method including: differentiating and / or culturing the one or more HLO in a co-culture media composition described herein for a first period of time; suspending the immune cells in a co-culture mediacomposition described herein for a second period of time; and co-culturing the one or more HLO with the immune cells in a co-culture media composition described herein for a third period of time, to provide an HLO:immune cell co-culture system; wherein the HLO and / or immune cells are derived from pluripotent stem cells; optionally wherein the pluripotent stem cells are embryonic stem cells or induced pluripotent stem cells.

[0021] In some embodiments of the methods, the immune cells include peripheral blood mononuclear cells (PBMCs). In some embodiments, the immune cells include CD8 T cells, CD4 T cells, NK cells, monocytes, macrophages, and / or dendritic cells. In some embodiments, the HLO and / or immune cells are derived from primary cells. In some embodiments, the immune cells include T cells and / or monocyte-derived dendritic cells (mDCs). In some embodiments, the T cells include CD8 T lymphocytes, including effector CD8 cells, proliferating effector CD8 cells, antigen-activated CD8 cells, cytotoxic CD8 cells, effector memory CD8 cells, and / or regulatory CD8 cells.

[0022] In some embodiments of the methods, the one or more HLO and the immune cells are derived from a single subject. In some embodiments, the one or more HLO and the immune cells are derived from different subjects. In some embodiments, the HLO and / or immune cells are derived from a universal donor and / or from hypoimmune stem cells.

[0023] In some embodiments of the methods, the HLOs and immune cells have been co-cultured in the culture media for a time period selected from about 12 hours to about 10 days, or longer. In some embodiments, the HLOs and immune cells have been co-cultured in the culture media for about 3 days, + / - 1 day, to about 7 days, + / - 1 day.

[0024] In some embodiments of the methods, the one or more HLO is co-cultured with the immune cells in a droplet or microcavity array culture platform. In some embodiments, the droplet or microcavity array culture platform includes one or more Gri3D® plate; AggreWell™ plate; Elplasia® plate; ultra-low attachment (ULA), or ultra-low adhesion, plate; micro-patterned hydrogel plate; SmartSphero plate; Acura plate; Sphericalplate 5D; microfluidic culture device; and / or hanging drop plate. In some embodiments, the composition and / or culture platform do not include a basement membrane matrix.

[0025] In some embodiments of the methods, the HLOs and the immune cells self- assemble into a three-dimensional form. In some embodiments, the immune cells spontaneously migrate toward the HLO. In some embodiments, the immune cells infiltrate the HLO.

[0026] In some embodiments of the methods, the first period of time is between about 12 hours to about 10 days, or longer; and / or the second period of time is between about 0 days to about 10 days, or longer; and / or the third period of time is between about 12 hours to about 10 days, or longer. In some embodiments, the immune cells and HLOs are co-cultured in a ratio of about 1:1, 5:1, 10:1, 50:1, 100:1, 200:1, 300:1, 400:1, 500:1, 600:1, 700:1, 800:1, 900:1, 1000:1, 1500:1, 2000:1, 5000:1, 10,000:1, or greater, or any value between these ratios, immune cells to HLOs; optionally about 50-5000:1 immune cells to HLOs. In some embodiments, the immune cells and HLOs are co-cultured in a ratio of about 1:10, 1:5, 1:4,1:3, 1:2, 1:1, 2:1, 3:1, 4:1, 5:1, 10:1, 20:1, 30:1, 40:1, 50:1, 100:1, or any value between these ratios, immune cells to liver cells; optionally about 1-50:1 immune cells to liver cells. In some embodiments, posterior foregut cells for forming the HLOs are seeded at a density of greater than about 1×104cells / well, greater than about 0.5×105cells / well, greater than about 1×105cells / well, greater than about 2×105cells / well, greater than about 3×105cells / well, greater than about 4×105cells / well, greater than about 5×105cells / well, or higher. In some embodiments, the HLOs for co-culturing are present in a well density of about 1-500 organoids per well; optionally about 5-200 organoids per well. In some embodiments, the HLOs for co-culturing are in a microcavity array culture platform in a well density of about 5-200 organoids per well; optionally about 30-100 organoids per well. In some embodiments, the HLOs for co-culturing are in a droplet culture platform in a well density of about 5-200 organoids per well; optionally about 10-70 organoids per well.

[0027] In some embodiments of the methods, the co-culture media composition includes a first culture media comprising hepatocyte basal medium (HBM) comprising transferrin, ascorbic acid, insulin, and bovine serum albumin (BSA), and a second culture media comprising X-VIVO15 or RPMI, and optionally further includes further includes Penicillin / Streptomycin (Pen / Strep), human serum, IL-2, IL-7, IL-15, and / or IL-21. In some embodiments of the methods, the co-culture media composition includes a first culture media comprising hepatocyte basal medium (HBM) comprising transferrin, ascorbic acid, insulin, andbovine serum albumin (BSA), and a second culture media comprising X-VIVO15 or RPMI, and further includes Penicillin / Streptomycin (Pen / Strep), human serum, IL-2, IL-7, IL-15, and IL-21.

[0028] In some embodiments of the methods, the HLO includes endothelial cells, mesenchymal cells, and cholangiocytes. In some embodiments, the epithelial cells include one or more additional cell type selected from hepatoblasts, epithelial cells, Kupffer cells, stellate cells. In some embodiments, the HLO includes epithelial cells including hepatocytes, and mesenchymal cells including hepatic stellate cells. In some embodiments, the luminal structure includes internalized microvilli. In some embodiments, the HLO includes a structure with a single lumen. In some embodiments, the HLO is an artificial liver organoid and / or is generated in vitro. In some embodiments, the HLO is three-dimensional. In some embodiments, the HLO is a mature liver organoid.

[0029] Additional embodiments of the disclosure include methods of priming immune cells. In some embodiments, the immune cells are primed with one or more exogenous agent, and / or pre-treating the HLO with one or more exogenous agent, prior to co-culturing with the one or more HLO. In some embodiments, the methods further include analyzing the composition to assess liver cell viability and / or function, and / or to assess immune cell maturation, proliferation, and / or activation, following treatment with the one or more exogenous agent.

[0030] In some embodiments of the methods, the immune cells primed with one or more exogenous agent include CD8 T cells. In some embodiments, priming the immune cells with one or more exogenous agent prior to co-culturing includes: differentiating monocyte- derived dendritic cells (mDCs) and / or autologous antigen presenting cells (APCs), in the presence of the one or more exogenous agent, to provide pre-stimulated mDCs and / or pre- stimulated APCs; culturing naïve immune cells with the pre-stimulated mDCs and / or pre- stimulated APCs; and stimulating the naïve immune cells and pre-stimulated mDCs and / or pre- stimulated APCs with the one or more exogenous agent, to provide stimulated immune cells.

[0031] In some embodiments of the methods, the naïve immune cells include naïve CD8 T cells. In some embodiments, the mDCs and / or naïve immune cells are derived from peripheral blood mononuclear cells (PBMCs). In some embodiments, the APCs include a B cell lymphoblastoid line, and / or Kupffer cells; optionally wherein said APCs are primary or derivedfrom hPSCs, or wherein said APCs are derived from the HLO. In some embodiments, the mDCs and / or APCs are differentiated via EBV transformation.

[0032] In some embodiments of the methods, culturing naïve immune cells with the pre-stimulated mDCs and / or pre-stimulated APCs can be via an antigen presentation assay, wherein: sub-populations of the DCs and CD8 T cells are re-stimulated with the first exogenous agent for one or more additional period of time, at one or more different concentrations; and / or sub-populations of the DCs and CD8 T cells are stimulated with a control exogenous agent for one or more additional period of time, at the same or different concentrations.

[0033] In some embodiments, the methods can further include one, two, three, four, five, or more additional steps of re-stimulating the naïve immune cells and pre-stimulated mDCs and / or pre-stimulated APCs with the one or more exogenous agent. In some embodiments, the one or more exogenous agent is provided in different concentrations in two or more of the stimulation and re-stimulation steps. In some embodiments, the method further includes culturing the stimulated immune cells with a fresh population of pre-stimulated mDCs and / or pre-stimulated APCs. In some embodiments, the step of culturing naïve immune cells with the pre-stimulated mDCs and / or pre-stimulated APCs is in the presence of IL-21 and / or b- mercaptoethanol. In some embodiments, the stimulation and / or re-stimulation steps are in the presence of IL-7 and / or IL-15.

[0034] In some embodiments, the methods can further include analyzing the composition to profile immune cells, and / or to assess viability, following treatment with the one or more exogenous agent. In some embodiments, profiling immune cells includes assessing CD8 cell maturation, proliferation, and / or antigen-specific activation, and / or assessing viability includes detecting potential liver damage profile. In some embodiments, pre-treating the one or more HLO with one or more exogenous agent prior to co-culturing with the immune cells includes stimulating the one or more HLO with the one or more exogenous agent, to provide a stimulated HLO.

[0035] Additional embodiments of the disclosure include methods of priming immune cells, the methods including: differentiating monocyte-derived dendritic cells (mDCs) and / or autologous antigen presenting cells (APC) (e.g. a B cell lymphoblastoid line, and / or Kupffer cells; optionally wherein said APCs are primary or derived from hPSCs, or wherein saidAPCs are derived from the HLO) via EBV transformation, in the presence of the one or more exogenous agent, to provide pre-stimulated mDCs and / or pre-stimulated APCs; culturing naïve immune cells with the pre-stimulated mDCs and / or pre-stimulated APCs; and stimulating the naïve immune cells and pre-stimulated mDCs and / or pre-stimulated APCs with the one or more exogenous agent, to provide primed immune cells.

[0036] In some embodiments of the methods, the naïve immune cells include naïve CD8 T cells. In some embodiments, the mDCs and / or naïve immune cells are derived from peripheral blood mononuclear cells (PBMCs). In some embodiments, the APCs include a B cell lymphoblastoid line, and / or Kupffer cells; optionally wherein said APCs are primary or derived from hPSCs, or wherein said APCs are derived from the HLO. In some embodiments, the mDCs and / or APCs can be differentiated via EBV transformation.

[0037] In some embodiments of the methods, culturing naïve immune cells with the pre-stimulated mDCs and / or pre-stimulated APCs is via an antigen presentation assay, wherein: sub-populations of the DCs and CD8 T cells are re-stimulated with the first exogenous agent for one or more additional period of time, at one or more different concentrations; and / or sub- populations of the DCs and CD8 T cells are stimulated with a control exogenous agent for one or more additional period of time, at the same or different concentrations.

[0038] In some embodiments, the methods can further include one, two, three, four, five, or more additional steps of re-stimulating the naïve immune cells and pre-stimulated mDCs and / or pre-stimulated APCs with the one or more exogenous agent.

[0039] In some embodiments of the methods, the one or more exogenous agent is provided in different concentrations in two or more of the stimulation and re-stimulation steps.

[0040] In some embodiments, the methods further include culturing the stimulated immune cells with a fresh population of pre-stimulated mDCs and / or pre-stimulated APCs. In some embodiments, the step of culturing naïve immune cells with the pre-stimulated mDCs and / or pre-stimulated APCs is in the presence of GM-CSF, IFNγ, IL-4, IL-12, and / or IL-21. In some embodiments, the stimulation and / or re-stimulation steps are in the presence of IL-7 and / or IL-15.

[0041] In some embodiments, the methods further include analyzing the composition to profile immune cells, and / or to assess viability, following treatment with the one or moreexogenous agent. In some embodiments, profiling immune cells includes assessing CD8 cell maturation, proliferation, and / or antigen-specific activation, and / or assessing viability includes detecting potential liver damage profile.

[0042] In some embodiments of the methods, the first exogenous agent is a therapeutic or a therapeutic candidate. In some embodiments, the primed immune cell population is enriched with CD8 T cells which are reactive to the therapeutic or therapeutic candidate.

[0043] Additional embodiments of the disclosure include primed immune cell populations, prepared by the methods as described herein.

[0044] Additional embodiments of the disclosure include methods for screening a compound or composition, wherein the compound or composition to be screened includes one or more exogenous agent, the method including: culturing immune cells primed with the compound or composition, with one or more human liver organoid (HLO) in a co-culture media composition as described herein; adding the compound or composition to the co-culture of one or more HLO and primed immune cells; culturing the HLO and immune cells with the compound or composition; and assessing one or more effects of the compound or composition on the HLO and / or immune cells, thereby screening the compound or composition

[0045] Additional embodiments of the disclosure include methods for screening a compound or composition, including the methods as described herein, wherein the compound or composition to be screened includes the one or more exogenous agent, the methods further including: co-culturing immune cells primed with the one or more compound to be screened, with one or more human liver organoid (HLO) in the co-culture media composition as described herein; adding the compound or composition to be screened to the co-culture of one or more HLO and primed immune cells; co-culturing the HLO and immune cells with the compound or composition; and assessing one or more effects of the compound or composition on the HLO and / or immune cells, thereby screening the compound or composition.

[0046] In some embodiments of the methods, the screening of the compound or composition includes conducting one or more translational studies, predicting risk of immune- mediated adverse drug reaction (ADR), assessing toxicity, and / or modeling immune-driven drug- induced liver injury (DILI), following culturing with the compound or composition to be screened. In some embodiments, the screening includes determining one or more genetic riskfactors for a subject from whom the HLO and / or immune cells are derived. In some embodiments, the screening includes evaluating an HLA type for a subject from whom the HLO and / or immune cells are derived; optionally wherein evaluating an HLA type includes determining HLA type contribution to one or more effect of the compound or composition on the HLO and / or immune cells; optionally wherein the effect of the compound or composition on the HLO and / or immune cells includes an adverse drug reaction and / or drug-induced liver injury.

[0047] In some embodiments of the methods, the screening includes providing a prognosis for a subject from whom the HLO and / or immune cells are derived. In some embodiments, the screening includes providing a prognosis based on an HLA type, or based on one or more biomarker indicating genetic susceptibility to immune-driven drug-induced liver injury (DILI), for a subject from whom the HLO and / or immune cells are derived. In some embodiments, providing a prognosis includes predicting risk of immune-mediated adverse drug reaction (ADR), toxicity, and / or immune-driven drug-induced liver injury (DILI). In some embodiments, assessing toxicity includes assessing liver toxicity. In some embodiments, assessing toxicity includes assessing cell viability (live / dead), morphology, HLO functionality, immune cell functionality, albumin release and expression, CYP3A4 expression, and / or immune cell infiltration. In some embodiments, assessing HLO functionality includes determining levels of one or more HLO markers (e.g. CK18 (M65), albumin, and / or AST / ALT), and / or wherein assessing immune cell functionality includes determining levels of one or more immune cell markers (e.g. IFNg, TNFa, and / or Granzyme B). In some embodiments, toxicity includes increasing expression of one or more chemokines and / or NKG2D ligands, inducing chemotaxis, promoting differentiation and / or multiplication of leukocytes, causing tissue extravasation, and / or contributing to CD8 T cell immune-mediated liver injury. In some embodiments, assessing one or more effects of the compound or composition on the HLO and immune cells includes detecting toxicity of the compound or composition; studying hepatocyte function and developmental divergence; studying liver-related disease; identifying therapeutic targets; identifying compounds and / or compositions which induce immune-driven liver toxicity, and / or identifying therapeutic compounds and / or compositions effective in treating a liver-related disease or disorder, optionally wherein the therapeutic compound or composition comprises an immunotherapy.

[0048] In some embodiments of the methods, one or more effect of the compound or composition to be screened is compared to a corresponding effect of a compound or composition associated with immune-driven drug-induced liver injury (DILI). In some embodiments, the compound or composition associated with DILI includes abacavir, carbamazepine, allopurinol, dapsone, phenytoin, lamotrigine, nevirapine, sulphamethoxazole, methazolamide, amoxicillin- clavulanate, flucloxacillin, lumiracoxib, ticlopidine, terbinafine, fenofibrate, trimethoprim- sulfamethoxazole, Polygonum multiflorum (green tea), minocycline, infliximab, pazopanib, methimazole, ximelagatran, nitrofurantoin, lumiracoxib, flupirtine, and / or one or more antithyroid, anti-HIV, and / or anti-TB therapeutic; optionally wherein the compound or composition includes flucloxacillin.

[0049] In some embodiments of the methods, the HLO and immune cells are derived from a single subject. In some embodiments, the screening is to determine an effect of the compound or composition in a subject from whose cells the HLO and immune cells are derived.

[0050] In some embodiments of the methods, the subject is a carrier of one or more genetic, acquired, or other risk factors to develop an adverse drug reaction (ADR) and / or immune-driven drug-induced liver injury (DILI). In some embodiments, ADR risk is determined by scanning confocal microscopy-based HLO morphological and killing profile assessment; CK18 and albumin secretion; CYP3A4 expression; and / or assaying and / or quantifying chemokine production (e.g. CXCL9), NKG2D ligand expression (e.g. ULBP1), and / or associated CD8 T cell HLO infiltration and activation. In some embodiments, the screening provides a differential response between a carrier and a non-carrier of one or more risk factors to develop an ADR and / or immune-driven DILI.

[0051] In some embodiments of the methods, the screening is used for one or more translational studies. In some embodiments, the screening is used for patient or treatment selection in a clinical trial. In some embodiments, the screening is used for predicting risk of developing an adverse drug reaction (ADR) and / or immune-driven drug-induced liver injury (DILI). In some embodiments, the ADR includes drug-induced activation of T cells and / or immune-mediated damage of liver cells.

[0052] Additional embodiments of the disclosure include uses of the compositions as described herein, as an in vitro human model system for predicting risk for develop an adversedrug reaction (ADR) and / or immune-driven drug-induced liver injury (DILI); studying hepatocyte function and developmental divergence; studying liver-related disease; detecting toxicity of a compound or composition; identifying therapeutic targets; identifying therapeutic compounds and / or compositions with a favorable safety profile and / or which are effective in treating a liver-related disease or disorder, optionally wherein the therapeutic compound or composition comprises an immunotherapy; identifying compounds and / or compositions which induce immune-driven liver toxicity; identifying and / or validating mechanisms of immune- mediated drug toxicity in a physiologically relevant setting; identifying and / or validating drug mechanism of action (MOA); and / or correlating patient genotype with one or more phenotypic drug response.

[0053] In some embodiments of the methods, the liver-related disease or disorder includes an adverse drug reaction (ADR) and / or immune-driven drug-induced liver injury (DILI). In some embodiments, the ADR includes drug-induced activation of T cells and / or immune-mediated damage of liver cells. In some embodiments, the subject is a carrier of one or more genetic, acquired, or other risk factors to develop an adverse drug reaction (ADR) and / or immune-driven drug-induced liver injury (DILI). In some embodiments, ADR risk is determined by scanning confocal microscopy-based HLO morphological and killing profile assessment; CK18 and albumin secretion; CYP3A4 expression; and / or assaying and / or quantifying chemokine production (e.g. CXCL9), NKG2D ligand expression (e.g. ULBP1), and / or associated CD8 T cell HLO infiltration and activation.

[0054] In some embodiments of the methods, the liver-related disease or disorder includes one or more types of liver dysfunction and / or failure, hepatitis, viral hepatitis, hepatitis triggered by one or more checkpoint inhibitor, cholangitis, fibrosis, hepatic encephalopathy, hepatic porphyria, cirrhosis, cancer, drug-induced cholestasis, metabolic disease, autoimmune liver disease, biologic drug immunogenicity, Wilson’s disease, metabolic-associated fatty liver disease, hyperammonemia, hyperbilirubinemia, Crigler-Najjar Syndrome, urea cycle disorders, Wolman disease, hepatic cancer, hepatoblastoma, metabolic dysfunction–associated liver disease (MASLD), MetALD, metabolic dysfunction-associated steatohepatitis (MASH), drug-induced liver injury (DILI), glycogen storage disease, hemorrhagic disease, hepatic cyst, and / or alcohol- associated liver disease.

[0055] Additional embodiments of the disclosure include uses of compositions as described herein, for treating a liver-related disease or disorder. Additional embodiments of the disclosure include compositions as described herein, for use in the manufacture of a medicament for the treatment of a liver-related disease or disorder.

[0056] Additional embodiments of the disclosure include methods and / or compositions and / or uses as described herein, wherein the HLO is made according to a method including: a) activating an FGF signaling pathway and a Wnt signaling pathway in definitive endoderm cells (DE) for a first period of time; b) activating an FGF signaling pathway, a Wnt signaling pathway, and a RA signaling pathway in the cells of step a) for a second period of time, thereby differentiating the DE to posterior foregut cells; and c) culturing the posterior foregut spheroids for a third period of time to differentiate the posterior foregut cells to the HLO. Optionally, frozen posterior foregut cells can be used in accordance with various methods, rather than freshly generating posterior foregut cells each time, to render the process more scalable.

[0057] In some embodiments, the culturing the posterior foregut cells under conditions to induce expression from the heterologous expression system occurs on or about day 17 of culture of the progenitor cell population. In some embodiments, the posterior foregut spheroids are seeded for culturing on a droplet or microcavity array culture platform. In some embodiments, the posterior foregut spheroids are cultured in the absence of a basement membrane matrix.

[0058] Additional embodiments of the disclosure include kits including means for preparing any of the compositions, performing any of the methods, or for any of the uses, as described herein. Additional embodiments of the disclosure include kits including the co-culture media composition and / or the composition as described herein.

[0059] In some embodiments, one or more of the co-culture media components or composition components are provided in separate vials. In some embodiments, one or more of the co-culture media components or composition components are pre-loaded onto one or more assay platform. In some embodiments, the one or more assay platform includes a droplet or microcavity array culture platform. In some embodiments, the droplet or microcavity array culture platform includes one or more Gri3D® plate; AggreWell™ plate; Elplasia® plate; ultra- low attachment (ULA), or ultra-low adhesion, plate; micro-patterned hydrogel plate;SmartSphero plate; Acura plate; Sphericalplate 5D; microfluidic culture device; and / or hanging drop plate. In some embodiments, one or more of the co-culture media components, composition components, and / or assay platform are pre-frozen. BRIEF DESCRIPTION OF THE DRAWINGS

[0060] Those of skill in the art will understand that the drawings, described below, are for illustrative purposes only. The drawings are not intended to limit the scope of the present teachings in any way.

[0061] FIGURE 1. Testing of various exemplary HLO:immune cell co-culture media systems in PBMC monoculture.

[0062] FIG. 1A) The compositions of exemplary media compositions assessed. FIG. 1B) Morphology and viability after 7 days in PBMC monoculture. FIG. 1C) LDH release observed over 7 days of growth in all media formulations tested. FIG. 1D) LDH release observed over 7 days of growth in all media formulations tested, with and without CD3 / CD28 stimulation. FIG. 1E) ATP ratio relative to standard PBMC media observed over 7 days of growth in all media formulations tested, with and without CD3 / CD28 stimulation. FIG. 1F) ATP ratio relative to standard PBMC media observed over 7 days of growth in all media formulations tested upon stimulation with CD3 / CD28. FIG. 1G) Granzyme B observed over 3 days of growth in all media formulations tested, with and without CD3 / CD28 stimulation. FIG. 1H) Granzyme B observed over 7 days of growth in all media formulations tested, with and without CD3 / CD28 stimulation. FIG. 1I) IFN-γ observed over 3 days of growth in all media formulations tested, with and without CD3 / CD28 stimulation. FIG. 1J) IFN-γ observed over 7 days of growth in all media formulations tested, with and without CD3 / CD28 stimulation.

[0063] FIGURE 2. Testing of various exemplary HLO:immune cell co-culture media systems in HLO monoculture.

[0064] FIG. 2A) Morphology and viability after 7 days in HLO monoculture. FIG. 2B) LDH release observed over 7 days of growth in all media formulations tested. FIG. 2C) Albumin secretion observed over 7 days of growth in all media formulations tested.

[0065] FIGURE 3. Final media testing in HLO:immune cell co-culture.

[0066] FIG. 3A) The composition of the types of media assessed. FIG. 3B) Morphology and viability after 3 days in HLO:immune cell co-culture. FIG. 3C) Morphologyand viability after 7 days in HLO:immune cell co-culture. FIG. 3D) Granzyme B observed over 3 days of growth in all media formulations tested, with and without CD3 / CD28 stimulation. FIG. 3E) Granzyme B observed over 7 days of growth in all media formulations tested, with and without CD3 / CD28 stimulation. FIG. 3F) Albumin secretion observed over 3 and 7 days of growth in all media formulations tested, with and without CD3 / CD28 stimulation. FIG. 3G) GLDH activity after 7 days of growth in all media formulations tested, with and without CD3 / CD28 stimulation.

[0067] FIGURE 4. Establishment of exemplary autologous co-culture model of HLOs with immune cells.

[0068] FIG. 4A) Exemplary experimental design for comparing autologous and allogenic HLO:immune cell co-cultures. FIG. 4B) Cell morphology after 7 days of co-culture, at various effector:target (E:T) ratios. FIG. 4C) Cell viability after 7 days of co-culture, with and without CD3 / CD28 stimulation, at various E:T ratios, as observed via Hoechst staining. FIG. 4D) Cell death after 7 days of co-culture, at various E:T ratios, with and without CD3 / CD28 stimulation. FIG. 4E) Cytokine (IFN-γ and TNFα) and granzyme B secretion after 7 days of co- culture, at various E:T ratios, with and without CD3 / CD28 stimulation. FIG. 4F) Chemokine (CXCL9 and CXCL10) secretion after 7 days of co-culture, at various E:T ratios, with and without CD3 / CD28 stimulation.

[0069] FIGURE 5. Evaluation of toxicity profile of Flucloxacillin (Flux) in exemplary autologous co-culture model of HLO:immune cell composition.

[0070] FIG. 5A) Exemplary experimental design for testing Flucloxacillin in exemplary autologous HLO:immune cell co-culture. FIG. 5B) Varying compound concentrations in mono-culture and co-culture. FIG. 5C) Effect of Flucloxacillin on HLO morphology and PBMC migration, with and without CD28. FIG. 5D) Imaging results of effect of various concentrations of Flucloxacillin on HLO viability, with and without CD28. FIG. 5E) Effect of various concentrations of Flucloxacillin on HLO viability, with and without CD28. FIG. 5F) Effect of various concentrations of Flucloxacillin on albumin secretion, with and without CD28. FIG. 5G) Effect of various concentrations of Flucloxacillin on cytokeratin 18 (CK18) release, with and without CD28. FIG. 5H) Exemplary experimental design for testing the effect of Flucloxacillin on immune cells. FIG. 5I) Effect of Flucloxacillin on immune cells atDay 0 for Control Donor (Donor 459). FIG. 5J) Effect of Flucloxacillin on immune cells at Day 0 for B*57-01 Carrier (Donor 622). FIG. 5K) Effect of Flucloxacillin on immune cells at Day 7 for Control Donor (Donor 459), with various concentrations of Flucloxacillin, measuring total CD8 cells (top row) and proliferating CD8 cells (bottom row). FIG. 5L) Direct effect of Flucloxacillin on immune cells at Day 7 for Control Donor (Donor 459), with various concentrations of Flucloxacillin, measuring total CD8 cells by FSC-A (top row) and proliferating CD8 cells (bottom row). FIG. 5M) Effect of Flucloxacillin on immune cells at Day 7 for Control Donor (Donor 459) by FSC-A, with various concentrations of Flucloxacillin, measuring activated effector CD8 cells (top row), regulatory effector CD8 cells (middle row), and cytotoxic CD8 cells (bottom row). FIG. 5N) Effect of Flucloxacillin on immune cells at Day 7 for B*57- 01 Carrier (Donor 622), with various concentrations of Flucloxacillin, measuring total CD8 cells (top row) and proliferating CD8 cells (bottom row). FIG. 5O) Direct effect of Flucloxacillin on immune cells at Day 7 for B*57-01 Carrier (Donor 622), with various concentrations of Flucloxacillin, measuring total CD8 cells by FSC-A (top row) and proliferating CD8 cells (bottom row). FIG. 5P) Effect of Flucloxacillin on immune cells at Day 7 for B*57-01 Carrier (Donor 622) by FSC-A, with various concentrations of Flucloxacillin, measuring activated effector CD8 cells (top row), regulatory effector CD8 cells (middle row), and cytotoxic CD8 cells (bottom row).

[0071] FIGURE 6. T cell priming for use in exemplary autologous co-culture model of HLOs with PBMCs.

[0072] FIG. 6A) Exemplary experimental design for using primed CD8 T cells for use in exemplary autologous HLO:immune cell co-culture. FIG. 6B) Exemplary experimental design for priming CD8 T cells. FIG. 6C) Exemplary experimental design and timeline for CD8 T cell priming. FIG. 6D) Immature PBMC monocyte-derived dendritic cells (DCs) (left) at Day 2 and mature DCs (right) at Day 4, for B*57-01 Carrier (Donor 622). FIG. 6E) DC-mediated priming 2μM pp65, 0.1 mM Flux, and 1 mM Flux, for B*57-01 Carrier (Donor 622). FIG. 6F) CD8 T cell mediated responses to pp65, at Day 14, showing total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, regulatory CD8 cells, antigen-specific activated CD8 cells, and cytotoxic CD8 cells. FIG. 6G) CD8 T cell mediated responses to 0.1 mM Flux, at Day 14, showing total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, regulatory CD8cells, antigen-specific activated CD8 cells, and cytotoxic CD8 cells. FIG. 6H) CD8 T cell mediated responses to 1 mM Flux, at Day 14, showing total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, regulatory CD8 cells, antigen-specific activated CD8 cells, and cytotoxic CD8 cells. FIG. 6I) CD8 T cell mediated responses to repeated stimulation for an additional 48 hours with pp65, showing total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, regulatory CD8 cells, antigen-specific activated CD8 cells, and cytotoxic CD8 cells. FIG. 6J) CD8 T cell mediated responses to repeated stimulation for an additional 48 hours with 0.1 mM Flux, showing total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, regulatory CD8 cells, antigen-specific activated CD8 cells, and cytotoxic CD8 cells. FIG. 6K) CD8 T cell mediated responses to repeated stimulation for an additional 48 hours with 1 mM Flux, showing total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, regulatory CD8 cells, antigen-specific activated CD8 cells, and cytotoxic CD8 cells. FIG. 6L) CD8 T cell mediated responses to repeated stimulation for an additional 48 hours with mock 0.1 mM Flux and 1 mM Flux showing total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, regulatory CD8 cells, antigen-specific activated CD8 cells, and cytotoxic CD8 cells. FIG. 6M) CD8 T cell mediated responses to repeated stimulation for an additional 48 hours with 0.1 mM Flux and mock 1 mM Flux showing total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, regulatory CD8 cells, antigen-specific activated CD8 cells, and cytotoxic CD8 cells.

[0073] FIGURE 7. Exemplary co-culture of HLOs with PBMCs in an exemplary microcavity platform (Gri3D®).

[0074] FIG. 7A) Exemplary depiction of HLOs and immune cells grown in Gri3D® hydrogel-based microwells. FIG. 7B) Experimental design for establishment of autologous co- culture model of HLOs with PBMCs. FIG. 7C) Cell morphology after 7 days of co-culture of autologous and allogenic HLO:immune cell compositions, at various E:T ratios. FIG. 7D) Albumin secretion after 7 days of co-culture of autologous and allogenic HLO:immune cell compositions, at various E:T ratios. FIG. 7E) Effect of CD3 / CD28 stimulation on albumin secretion, in droplet and Gri3D® systems, at various E:T ratios and with and without CD3 / CD28 stimulation. FIG. 7F) Live cells (left) and CD4+ and CD8+ cells (by CD4 BV711) after CD3 / CD28 stimulation. FIG. 7G) IFN-γ, Granzyme B, and CD107 expression from CD8+ cells for cells without (left) and with (middle) CD3 / CD28 stimulation, and with PMA / Iono (right)stimulation. FIG. 7H) CD8 T cell infiltration in HLO co-culture at 24, 48, and 72 hours, comparing allogenic CD8 T cells with HLO monoculture. FIG. 7I) HLO damage (death) in HLO co-culture at 24, 48, and 72 hours, comparing allogenic CD8 T cells with HLO monoculture. FIG. 7J) Measurement of immune soluble markers TNFα (left), IFN-γ (middle), and Granzyme B (right), in HLO co-culture at 24, 48, and 72 hours, comparing allogenic CD8 T cells with HLO monoculture. FIG. 7K) HLO damage (death) in HLO co-culture for different donors (P622 and P522), with autologous and allogenic CD8 T cells, with and without MHC class I and MHC class II blocking with antibodies, or HLO monoculture. FIG. 7L) P values via Dunnett’s multiple comparisons test for model systems, for different donors (P622 and P522), with autologous and allogenic CD8 T cells, with and without MHC class I and MHC class II blocking with antibodies, or HLO monoculture.

[0075] FIGURE 8. Use of the exemplary autologous HLO:T cell co-culture for assessing an effect of an exogenous component, e.g. a test compound or condition.

[0076] FIG. 8A) Exemplary protocol for assessment of immune-driven drug-induced liver injury (DILI) in autologous HLO:T cell co-culture. FIG. 8B) Flow cytometry results from CD8 T cell proliferation / activation read out details, with CFSE labeling. FIG. 8C) CD8 T cell- mediated responses with pp65, for Carrier Donor (Donor 534), assessing lymphocytes, total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, antigen-activated CD8 cells, cytotoxic CD8 cells, and regulatory CD8 cells. FIG. 8D) CD8 T cell-mediated responses with Flux, for Carrier Donor (Donor 534), assessing lymphocytes, total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, antigen-activated CD8 cells, cytotoxic CD8 cells, and regulatory CD8 cells. FIG. 8E) HLO killing with autologous Flux-primed CD8 T cells, for Carrier Donor (Donor 534). FIG. 8F) Effect of various concentrations of Flux (1000, 100, 10, and 0 uM) on HLO monoculture, unprimed HLO:immune cell co-culture, and pp65- and Flux-primed HLO:immune cell co-culture, showing HLO nuclei, dead HLOs, and CD8 T cells, for Carrier Donor (Donor 534). FIG. 8G) Measurement of immune soluble markers IFN-γ, in unprimed and Flux-primed co- HLO:immune cell co-culture, for Carrier Donor (Donor 534). FIG. 8H) Measurement of immune soluble markers Granzyme B, in unprimed and Flux-primed co- HLO:immune cell co-culture, for Carrier Donor (Donor 534). FIG. 8I) CD8 T cell-mediated responses with pp65, for Non-Carrier Donor (Donor 461), assessing lymphocytes, total CD8cells, effector CD8 cells, proliferating effector CD8 cells, antigen-activated CD8 cells, cytotoxic CD8 cells, and regulatory CD8 cells, in Round II of testing. FIG. 8J) CD8 T cell-mediated responses with Flux, for Non-Carrier Donor (Donor 461), assessing lymphocytes, total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, antigen-activated CD8 cells, cytotoxic CD8 cells, and regulatory CD8 cells, in Round II of testing. FIG. 8K) HLO killing with autologous Flux-primed CD8 T cells, for Non-Carrier Donor (Donor 461).

[0077] FIGURE 9. Exemplary assessment of immune-driven DILI in exemplary autologous HLO:T cell co-culture model.

[0078] FIG. 9A) Exemplary experimental design for HLA typing with Flux in multiple experimental rounds in HLO co-culture. FIG. 9B) CD8 T cell activation in monoculture, assessing proliferating effector CD8 cells (via CFSE marker), regulatory effector CD8 cells (via HLA-DR marker), antigen-activated CD8 cells (via CD137 marker), cytotoxic CD8 cells (via CD107a marker), and effector memory CD8 cells (via CD69 marker). FIG. 9C) CD8 T cell activation in monoculture, for three controls (P522, P524, and P646) and three B*57:01 carriers (P534, P622, and P650). FIG. 9D) HLO damage in co-culture for HLOs in monoculture, with unprimed CD8 T cells, pp65-primed CD8 T cells, and Flux-primed T cells.

[0079] FIGURE 10. Exemplary assessment of T cell activity and cell death in exemplary non-carrier donor 522, on treatment with pp65 and Flux.

[0080] FIG. 10A) CD8 T cell-mediated responses with pp65, for Non-Carrier Donor (Donor 522), assessing lymphocytes, total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, antigen-activated CD8 cells, cytotoxic CD8 cells, and regulatory CD8 cells. FIG. 10B) CD8 T cell-mediated responses with Flux, for Non-Carrier Donor (Donor 522), assessing lymphocytes, total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, antigen- activated CD8 cells, cytotoxic CD8 cells, and regulatory CD8 cells. FIG. 10C) HLO killing with HLO monoculture, unprimed HLO:immune cell co-culture, pp65-primed, Flux-primed, and Triton X CD8 T cells, for Non-Carrier Donor (Donor 522), showing CD8 T cells, dead cells, and nuclei. FIG. 10D) Relative HLO death with HLO monoculture, unprimed HLO:immune cell co- culture, pp65-primed, Flux-primed, and Triton X CD8 T cells, for Non-Carrier Donor (Donor 522). FIG. 10E) HLO damage measured by CK18 and TNFα release with HLO monoculture, unprimed HLO:immune cell co-culture, pp65-primed, and Flux-primed CD8 T cells, for Non-Carrier Donor (Donor 522). FIG. 10F) T cell activity measured by IFN-γ and Granzyme B release with HLO monoculture, unprimed HLO:immune cell co-culture, pp65-primed, and Flux- primed CD8 T cells, for Non-Carrier Donor (Donor 522).

[0081] FIGURE 11. Exemplary assessment of T cell activity and cell death in exemplary non-carrier donor 524, on treatment with pp65 and Flux.

[0082] FIG. 11A) CD8 T cell-mediated responses with pp65, for Non-Carrier Donor (Donor 524), assessing lymphocytes, total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, antigen-activated CD8 cells, cytotoxic CD8 cells, and regulatory CD8 cells. FIG. 11B) CD8 T cell-mediated responses with Flux, for Non-Carrier Donor (Donor 524), assessing lymphocytes, total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, antigen- activated CD8 cells, cytotoxic CD8 cells, and regulatory CD8 cells. FIG. 11C) HLO killing with HLO monoculture, unprimed HLO:immune cell co-culture, pp65-primed, and Flux-primed CD8 T cells, for Non-Carrier Donor (Donor 524), showing CD8 T cells, dead cells, and nuclei. FIG. 11D) Relative HLO death with HLO monoculture, unprimed HLO:immune cell co-culture, pp65-primed, and Flux-primed CD8 T cells, for Non-Carrier Donor (Donor 524). FIG. 11E) HLO damage measured by CK18 and TNFα release with HLO monoculture, unprimed HLO:immune cell co-culture, pp65-primed, and Flux-primed CD8 T cells, for Non-Carrier Donor (Donor 524). FIG. 11F) T cell activity measured by IFN-γ and Granzyme B release with HLO monoculture, unprimed HLO:immune cell co-culture, pp65-primed, and Flux-primed CD8 T cells, for Non-Carrier Donor (Donor 524).

[0083] FIGURE 12. Exemplary assessment of T cell activity and cell death in exemplary non-carrier donor 646, on treatment with pp65 and Flux.

[0084] FIG. 12A) CD8 T cell-mediated responses with pp65, for Non-Carrier Donor (Donor 646), assessing lymphocytes, total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, antigen-activated CD8 cells, cytotoxic CD8 cells, and regulatory CD8 cells. FIG. 12B) CD8 T cell-mediated responses with Flux, for Non-Carrier Donor (Donor 646), assessing lymphocytes, total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, antigen- activated CD8 cells, cytotoxic CD8 cells, and regulatory CD8 cells. FIG. 12C) HLO killing with HLO monoculture, unprimed HLO:immune cell co-culture, pp65-primed, Flux-primed, and Triton X CD8 T cells, for Non-Carrier Donor (Donor 646), showing CD8 T cells, dead cells, andnuclei. FIG. 12D) Relative HLO death with HLO monoculture, unprimed HLO:immune cell co- culture, pp65-primed, Flux-primed, and Triton X CD8 T cells, for Non-Carrier Donor (Donor 646). FIG. 12E) HLO damage measured by CK18 and TNFα release with HLO monoculture, unprimed HLO:immune cell co-culture, pp65-primed, and Flux-primed CD8 T cells, for Non- Carrier Donor (Donor 646). FIG. 12F) T cell activity measured by IFN-γ and Granzyme B release with HLO monoculture, unprimed HLO:immune cell co-culture, pp65-primed, and Flux- primed CD8 T cells, for Non-Carrier Donor (Donor 646).

[0085] FIGURE 13. Exemplary assessment of T cell activity and cell death in exemplary carrier donor 622, on treatment with pp65 and Flux.

[0086] FIG. 13A) CD8 T cell-mediated responses with pp65, for Carrier Donor (Donor 622), assessing lymphocytes, total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, antigen-activated CD8 cells, cytotoxic CD8 cells, and regulatory CD8 cells. FIG. 13B) CD8 T cell-mediated responses with Flux, for Carrier Donor (Donor 622), assessing lymphocytes, total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, antigen- activated CD8 cells, cytotoxic CD8 cells, and regulatory CD8 cells. FIG. 13C) HLO killing with HLO monoculture, unprimed HLO:immune cell co-culture, pp65-primed, and Flux-primed CD8 T cells, for Carrier Donor (Donor 622), showing CD8 T cells, dead cells, and nuclei. FIG. 13D) Relative HLO death with HLO monoculture, unprimed HLO:immune cell co-culture, pp65- primed, and Flux-primed CD8 T cells, for Carrier Donor (Donor 622). FIG. 13E) HLO damage measured by CK18 and TNFα release with HLO monoculture, unprimed HLO:immune cell co- culture, pp65-primed, and Flux-primed CD8 T cells, for Carrier Donor (Donor 622). FIG. 13F) T cell activity measured by IFN-γ and Granzyme B release with HLO monoculture, unprimed HLO:immune cell co-culture, pp65-primed, and Flux-primed CD8 T cells, for Carrier Donor (Donor 622).

[0087] FIGURE 14. Exemplary assessment of T cell activity and cell death in exemplary carrier donor 534, on treatment with pp65 and Flux.

[0088] FIG. 14A) CD8 T cell-mediated responses with pp65, for Carrier Donor (Donor 534), assessing lymphocytes, total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, antigen-activated CD8 cells, cytotoxic CD8 cells, and regulatory CD8 cells. FIG. 14B) CD8 T cell-mediated responses with Flux, for Carrier Donor (Donor 534), assessinglymphocytes, total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, antigen- activated CD8 cells, cytotoxic CD8 cells, and regulatory CD8 cells. FIG. 14C) HLO killing with HLO monoculture, unprimed HLO:immune cell co-culture, pp65-primed, and Flux-primed CD8 T cells, for Carrier Donor (Donor 534), showing CD8 T cells, dead cells, and nuclei. FIG. 14D) Relative HLO death with HLO monoculture, unprimed HLO:immune cell co-culture, pp65- primed, and Flux-primed CD8 T cells, for Carrier Donor (Donor 534). FIG. 14E) HLO damage measured by CK18 and TNFα release with HLO monoculture, unprimed HLO:immune cell co- culture, pp65-primed, and Flux-primed CD8 T cells, for Carrier Donor (Donor 534). FIG. 14F) T cell activity measured by IFN-γ and Granzyme B release with HLO monoculture, unprimed HLO:immune cell co-culture, pp65-primed, and Flux-primed CD8 T cells, for Carrier Donor (Donor 534).

[0089] FIGURE 15. Exemplary assessment of T cell activity and cell death in exemplary carrier donor 650, on treatment with pp65 and Flux.

[0090] FIG. 15A) CD8 T cell-mediated responses with pp65, for Carrier Donor (Donor 650), assessing lymphocytes, total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, antigen-activated CD8 cells, cytotoxic CD8 cells, and regulatory CD8 cells. FIG. 15B) CD8 T cell-mediated responses with Flux, for Carrier Donor (Donor 650), assessing lymphocytes, total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, antigen- activated CD8 cells, cytotoxic CD8 cells, and regulatory CD8 cells. FIG. 15C) HLO killing with HLO monoculture, unprimed HLO:immune cell co-culture, pp65-primed, Flux-primed, and Triton X CD8 T cells, for Carrier Donor (Donor 650), showing CD8 T cells, dead cells, and nuclei. FIG. 15D) Relative HLO death with HLO monoculture, unprimed HLO:immune cell co- culture, pp65-primed, Flux-primed, and Triton X CD8 T cells, for Carrier Donor (Donor 650). FIG. 15E) HLO damage measured by CK18 and TNFα release with HLO monoculture, unprimed HLO:immune cell co-culture, pp65-primed, and Flux-primed CD8 T cells, for Carrier Donor (Donor 650). FIG. 15F) T cell activity measured by IFN-γ and Granzyme B release with HLO monoculture, unprimed HLO:immune cell co-culture, pp65-primed, and Flux-primed CD8 T cells, for Carrier Donor (Donor 650). FIG. 15G) CD8 T cell-mediated responses with pp65, for Carrier Donor (Donor 650), assessing lymphocytes, total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, antigen-activated CD8 cells, cytotoxic CD8 cells, and regulatoryCD8 cells. FIG. 15H) CD8 T cell-mediated responses with Flux, for Carrier Donor (Donor 650), assessing lymphocytes, total CD8 cells, effector CD8 cells, proliferating effector CD8 cells, antigen-activated CD8 cells, cytotoxic CD8 cells, and regulatory CD8 cells.

[0091] FIGURE 16. Proof of mechanism in exemplary B*57:01 carrier.

[0092] FIG. 16A) Reactive compound inactivation by thiol-catalyzed cyclization with 2β-mercaptoethanol (2βME) reduces protein haptenization. FIG. 16B) Marker relative expression (fold change) for control and with 2βME on treatment with Flux. FIG. 16C) Relative HLO death (fold change) for control and with 2βME, both without (control) and with treatment with Flux. FIG. 16D) Relative gene expression of Albumin, ULBP1, CXCL10, CXCL9, and CYP3A4, on treatment with Flux. FIG. 16E) Schematic showing the interaction between Flux and MHC-I leading to a CD8-mediated immune response.

[0093] FIGURE 17. High-throughput HLO microarrays enable uniform and scalable culture.

[0094] FIG. 17A) Schematic overview of the generation of HLO microarrayed cultures from iPSCs. FIG. 17B) Representative image of Day 23 HLOs in a microarray format, showing albumin-positive hepatocytes surrounded by vimentin-positive mesenchymal cells. Scale bar, 100 µm. FIGs. 17C-D) Quantification of the organoid count (FIG. 17C), and organoid diameter (FIG. 17D) on day 23 in HLO microarrays (Gri3D) versus Matrigel-grown HLOs across three donors. Each data point represents an individual organoid; n = 32-36, ****P < 0.0001; ANOVA, Sidak’s post hoc test. FIG. 17E) Expression of early and late (developmentally) hepatocyte markers at day 23 relative to D6. (mean ± SEM, n = 3 biological replicates) ns =non-significant, P > 0.05; (two-way ANOVA). FIG. 17F) Albumin secretion levels in HLOs grown on Gri3D or embedded in Matrigel from three donors, each data point represents one technical replicate (n=4); Two-way ANOVA ***, P ≤ 0.0001. FIG. 17G) Immunohistochemistry characterization of HLO microarrays, showing expression of hepatic (HNF4α, ALB, ASGR1), mesenchymal (VIM, αSMA), endothelial (CD31), and cholangiocyte (CK7) markers.

[0095] FIGURE 18. Microarrays enhance culture homogeneity compared to Matrigel dome cultures.

[0096] FIG. 18A) Representative brightfield images of organoid cultures grown as Matrigel domes and exemplary microarrays (Gri3D) across three iPSC donors at day 23. Scale bar, 500 µm. FIG. 18B) Quantification of intra-donor variability in organoid count and diameter, expressed as the coefficient of variation (CV), demonstrating improved uniformity of parallel samples from the same line in Gri3D cultures compared to Matrigel domes. (n = 32-36). FIG. 18C) Quantification of inter-donor variability in organoid count and diameter, showing reduced line-to-line variation in Gri3D-grown HLOs compared to Matrigel-based cultures (n = 3 donors).

[0097] FIGURE 19. Flucloxacillin does not induce direct hepatotoxicity in HLO microarrays.

[0098] FIG. 19A) Experimental workflow schematic. FIG. 19B) Representative images of HLO microarrays treated for seven days with Chlorpromazine or Flucloxacillin at different concentrations. Scale bar, 100 µm. FIGs. 19C-E) Quantification of cell death (% DRAQ7-positive cells) (FIG. 19C), cell viability (% relative to the viability of vehicle-treated controls) (FIG. 19D), and albumin secretion (% relative to the release from vehicle-treated controls) (FIG. 19E) following treatment with Chlorpromazine (open black circles) or Flucloxacillin (closed purple circles) across five concentrations (n = 8 technical replicates). Data represent mean± SEM. Representative of three biologically independent experiments is shown.

[0099] FIGURE 20. Integration of autologous CD8+T cells restores immune competence in HLO co-cultures.

[0100] FIG. 20A) Schematic overview of the experimental workflow. FIG. 20B) Representative images of microarrayed HLO and their co-cultures with autologous or allogeneic CD8+T cells at different effector-to-target (E:T) ratios, with (+) or without (-) anti-CD3 / CD28 stimulation. Scale bar, 100 µm. FIGs. 20C-E) Quantification of cell death (FIG. 20C), albumin release (FIG. 20D), and Granzyme B secretion (FIG. 20E) across different mono and co-culture conditions. *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001, ANOVA and Tukey’s tests. Only statistically significant (P ≤ 0.05) comparisons are shown. Data represent mean ± SEM, n= 3.

[0101] FIGURE 21. Flucloxacillin-induced CD8+T cell activation occurs exclusively in HLA-B*57:01 carriers.

[0102] FIG. 21A) Schematics of the experimental workflow followed in this study. FIG. 21B) HLA class I genotypes of healthy donors, classified as HLA-B*57:01 carriers andnon-carriers (controls). FIG. 21C) Stimulation index of CD8⁺ T cell activation markers following Flucloxacillin priming in control and HLA-B*57:01 carrier groups. *P ≤ 0.05, ***P ≤ 0.001, ANOVA and Tukey’s tests vs average marker expression in non-carrier control group. Representative of three independent assay repeats.

[0103] FIGURE 22. Flucloxacillin-induced CD8⁺ T cell activation is specific to HLA-B*57:01 carriers.

[0104] Representative flow cytometry plots illustrating the expression of CD8⁺ T cell activation markers in response to dendritic cell (mDC) priming with Flucloxacillin (Flux) or mock (media alone). Data are shown for one HLA*B57:01 carrier and one HLA*B57:01 non- donor (control).

[0105] FIGURE 23. HLA-B*57:01-dependent CD8+T cell responses drive immune- mediated hepatotoxicity in HLOs.

[0106] FIG. 23A) Schematic overview of the experimental workflow. FIGs. 23B and 23D) Representative images of HLO-CD8+T cell co-cultures from HLA-B*57:01 non- carriers (FIG. 23B) and HLA-B*57:01 carriers (FIG. 23D) after three days of co-culture at a 5:1 effector-to-target ratio. Culture conditions: unprimed (HLO + unprimed CD8+T cells), flux- primed (HLO + Flucloxacillin-primed CD8+T cells). Scale bar, 100 µm. (FIGs. 23C and 23E) Quantification of HLO death, cytokeratin-18 (CK18) release, TNFα, and Granzyme B (GzmB) secretion across experimental conditions.: *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001, ANOVA and Dunnett’s tests. Only statistically significant (P ≤ 0.05) comparisons are shown. Data represent mean ± SEM, n= 5. DETAILED DESCRIPTION OF THE DISCLOSURE

[0107] In the following detailed description, reference is made to the accompanying drawings, which form a part hereof. In the drawings, similar symbols typically identify similar components, unless context dictates otherwise. The illustrative embodiments described in the detailed description, drawings, and claims are not meant to be limiting. Other embodiments may be utilized, and other changes may be made, without departing from the spirit or scope of the subject matter presented herein. It will be readily understood that the aspects of the present disclosure, as generally described herein, and illustrated in the Figures, can be arranged,substituted, combined, separated, and designed in a wide variety of different configurations, all of which are explicitly contemplated herein.

[0108] The following description of various embodiments is exemplary and explanatory only and is not to be construed as limiting or restrictive in any way. Other embodiments, features, objects, and advantages of the present teachings will be apparent from the description and accompanying drawings, and from the claims.

[0109] The disclosure herein uses affirmative language to describe the numerous embodiments. The disclosure also includes embodiments in which subject matter is excluded, in full or in part, such as substances or materials, method steps and conditions, protocols, or procedures.

[0110] It should be understood that any use of subheadings herein are for organizational purposes, and should not be read to limit the application of those subheaded features to the various embodiments herein. Each and every feature described herein is applicable and usable in all the various embodiments discussed herein and that all features described herein can be used in any contemplated combination, regardless of the specific example embodiments that are described herein. It should further be noted that exemplary description of specific features are used, largely for informational purposes, and not in any way to limit the design, subfeature, and functionality of the specifically described feature. Overview

[0111] As described herein, various embodiments of the disclosure include methods for developing co-culture media compositions, and methods for developing compositions including human liver organoids (HLOs) and immune cells, as well as the co-culture media composition and compositions themselves, and uses involving the same. In some embodiments, the HLOs and immune cells are co-cultured together in a co-culture media composition as described herein. For example, the composition can include HLOs in combination with immune cells, such as peripheral blood mononuclear cells (PBMCs) and / or T cells, such as, for example, CD8 T lymphocytes. In particular embodiments, the composition is autologous.

[0112] The disclosure also encompasses high-throughput HLO microarray platforms co-cultured with autologous CD8+ T cells to model immune-mediated hepatotoxicity. This co- culture model can be applied as an investigational tool in various settings. For example, thismodel can be used as an in vitro human model system for predicting risk for develop an immune- mediated adverse drug reaction (ADR) and / or immune-driven drug-induced liver injury (DILI). This model can also be used for translational studies for specific patients of interest; for example, the model can be used to identify carriers of a genetic risk factor predisposing the subject to one or more ADRs within a clinical trial. The model also can be used for studying hepatocyte function and developmental divergence and / or studying liver-related disease. Screening assays utilizing the model can be used for detecting toxicity of a compound or composition; identifying therapeutic targets; identifying therapeutic compounds and / or compositions with a favorable safety profile and / or which are effective in treating a liver-related disease or disorder, optionally wherein the therapeutic compound or composition comprises an immunotherapy; identifying compounds and / or compositions which induce immune-driven liver toxicity; identifying and / or validating mechanisms of immune-mediated drug toxicity in a physiologically relevant setting; identifying and / or validating drug mechanism of action (MOA); and / or correlating patient genotype with one or more phenotypic drug response. This model can also be used to identify or validate mechanisms of immune-mediated drug toxicity in a physiologically relevant setting. One skilled in the art can contemplate other possible uses for the co-culture system, in various studies and methods.

[0113] As an exemplary use of the compositions and methods described herein, samples can be obtained from patients who develop an ADR, or who may be at risk of developing an ADR, during a clinical trial. Mechanisms of drug toxicity in these patients can be determined based on more descriptive clinical and omics datasets (such as, for example, genome sequencing). These mechanisms can then be validated using the co-culture of HLOs and CD8 T cells as described herein; this can enable direct correlation of the patient’s genotype with phenotypic drug responses.

[0114] As another exemplary use of the compositions and methods described herein, an immune cell population primed with an exogenous agent can be prepared from naïve immune cells, via a single or multiple stimulation steps. The primed immune cell population can then be co-cultured with an HLO, to allow for assessment of liver cell viability and / or function, and / or to assess immune cell maturation, proliferation, and / or activation, following treatment with the one or more exogenous agent, in an assay to screen a compound or composition for therapeuticefficacy and / or safety. This can be particularly beneficial for subjects who are carriers of one or more genetic, acquired, or other risk factors to develop an ADR and / or immune-driven drug- induced liver injury (iDILI).

[0115] The persistent translational gap between existing in vitro platforms, animal studies, and the human immune responses that ultimately drive patient outcomes arises in part from the limitations of conventional hepatotoxicity assays which rely on direct measures of cytotoxicity and lack the antigen presentation machinery and T cell compartments required to model HLA-restricted, cytotoxic CD8⁺ T cell responses – mechanisms known to underlie conditions such as iDILI in clinical settings. While recent advances in iPSC-derived hepatocyte systems and liver-on-chip technologies have improved physiological fidelity for hepatic metabolism and innate immunity, they still fail to recapitulate the antigen specificity, T cell priming, and adaptive effector functions essential for modeling immune-mediated hepatotoxicity. Notably, hepatocyte death in iDILI is not triggered directly by the drug, but by CD8⁺ T cells activated through HLA-restricted pathways - a mechanism that current models fail to represent. This mirrors the immune-mediated injury seen in viral hepatitis, where adaptive immune responses, not the pathogen itself, drive tissue damage, further underscoring the need for models that replicate these dynamics. In addition, reliance on primary cells or Matrigel scaffolds hampers scalability, standardization, and the incorporation of genetic diversity, which are all factors important for investigating patient-specific risk.

[0116] To overcome these barriers, a fully human, matrix-free liver organoid (HLO) microarray platform was developed as described herein that integrates iPSC-derived hepatocytes with autologous CD8⁺ T cells in a genetically defined context. This scalable co-culture system enables controlled, reproducible assessment of antigen-specific immune responses and immune- mediated hepatotoxicity.

[0117] This approach and model has been validated by interrogating the platform with an exemplary compound associated with immune-driven DILI, namely Flucloxacillin (Flux). Flux is a β-lactam antibiotic which is a clinically relevant and mechanistically well- characterized example of HLA-B*57:01-linked, T cell–mediated hepatotoxicity, reported to cause immune-driven DILI in HLA-B∗57:01 carriers. Despite the strong genetic association, most carriers of the risk allele do not develop liver injury, highlighting the limitations of geneticscreening alone and the importance of functional assays that capture donor-specific immune activation.

[0118] The platform developed as described herein faithfully recapitulates key features of the immune response, including CD8⁺ T cell activation, cytokine secretion, and hepatocyte apoptosis, without relying on supra-physiological stimuli or surrogate animal models. By bridging the gap between genetic susceptibility and functional immune outcomes, this system provides a broadly applicable tool for studying immune-mediated toxicities, validating HLA- associated risks, and enabling precision safety assessment in drug development.

[0119] The experimental procedures described herein, including immune cell priming (e.g. CD8 T cell priming) and assays involving co-cultures of HLOs with immune cells, can be used for, e.g., quantitative assessment of drug (e.g., Flux)-induced activation of T cells and / or immune-mediated damage of liver cells (e.g. scanning confocal microscopy-based HLO morphological and killing profile assessment; CK18 and albumin secretion; CYP3A4 expression), as described herein using an exemplary autologous CD8 T cell and HLO co-culture model.

[0120] Using HLA-genotyped donor-derived cells, the data herein demonstrate that this system accurately recapitulates Flucloxacillin-induced liver injury in an HLA-B*57:01- dependent manner, characterized by antigen-specific CD8+ T cell activation and hepatocyte apoptosis. This platform bridges genetic susceptibility with functional immune responses, offering a scalable and physiologically relevant tool for patient-specific risk assessment, mechanistic investigations of iDILI, and preclinical drug safety evaluation.

[0121] As another exemplary use of the compositions and methods described herein, a drug induced “danger signal” can be assessed by assaying and / or quantifying chemokine (e.g. CXCL9) production, NKG2D ligand expression (e.g. ULBP1), and / or associated CD8 T cell HLO infiltration and activation correspondingly. T cells isolated from the blood of carriers and non-carriers of one or more genetic risk factors for development of an ADR (e.g., HLA-B∗57:01) can be compared in this assay, thereby assessing the impact of patient’s genotype on the reactivity of the CD8 T cells to a given drug (e.g., Flux) and the efficiency of the killing of autologous HLOs.

[0122] The development of in vitro platforms that can recapitulate key components of adaptive immune responses - particularly antigen-specific T cell activation and effector function - in genetically defined, human-relevant context remains a longstanding challenge in toxicology and regenerative medicine. The immune-competent, matrix-free liver organoid–T cell co-culture platform described herein addresses this need by enabling systematic evaluation of HLA- restricted, CD8⁺ T cell–mediated hepatotoxicity using a fully autologous and scalable system. Unlike previous models that rely on indirect cytokine stimulation or conditioned media transfer, the approach described herein supports direct, antigen-specific interactions between primed T cells and hepatocytes under physiologically relevant, defined and reproducible conditions.

[0123] This methodological advancement confers several advantages. First, it enables functional modeling of genetic risk alleles - such as HLA-B*57:01 - in a context that reflects true clinical heterogeneity. Second, the use of micropatterned hydrogel arrays and matrix-free differentiation supports scalable, miniaturized culture compatible with high-content analysis. Unlike conventional organoid models that rely on Matrigel - a murine-derived basement membrane matrix known to hinder immune cell function – the matrix-free design of the disclosure enables unrestricted T cell–hepatocyte interactions in a physiologically relevant environment. This feature enhances immune compatibility and makes the system particularly well-suited for modeling antigen-specific responses in immunotoxicity. Third, by incorporating clinically relevant immune readouts - including cytokeratin-18 release, TNF-α and Granzyme B secretion, and DRAQ7⁺ hepatocyte death - the platform captures core features of CD8⁺ T cell– mediated liver injury.

[0124] In the proof-of-concept studies described herein, the platform was found to effectively model both antigen-specific CD8⁺ T cell activation and subsequent hepatocyte injury in a controlled, autologous in vitro setting. This dual capability enables linkage of T cell activation with downstream liver injury and highlights inter-individual variability in immune responses. It also underscores that genetic predisposition alone is insufficient to predict adverse outcomes, positioning this platform as a critical tool for functional immunotoxicology assays and patient-specific risk assessment.

[0125] Beyond flucloxacillin, which was used in various examples herein, the modular design of this platform enables broad application to other forms of immune liver injury -including hepatitis triggered by checkpoint inhibitors, autoimmune disease, or biologic drug immunogenicity. Additionally, its autologous configuration makes it well-suited for dissecting inter-individual variability in T cell priming, effector function, and hepatocyte susceptibility - all key contributors to idiosyncratic drug toxicity.

[0126] This system constitutes a much-needed infrastructure for the field by enabling immune-liver modeling with greater physiological relevance, genetic definition, and functional resolution than existing approaches. As toxicology increasingly shifts toward mechanistically grounded, patient-relevant platforms, such models will be essential for assessing immunogenic risk early in development.

[0127] The platform can be further scaled for automation, increasing donor diversity to support population-level analysis, and integrating single-cell profiling to uncover transcriptional correlates of immune response heterogeneity. The use of iPSC-derived T cells can further extend its utility by offering a renewable, standardized immune component suitable for screening applications.

[0128] A key advantage of this platform is its high-throughput microarray format, which enables the generation of uniform, scalable liver organoid cultures for systematic immune- toxicity assessment and rapid hypothesis testing. By integrating micropatterned hydrogels and patient-matched T cells, this system builds upon previously established HLO technology, while enhancing its applicability and scalability. Unlike traditional organoid culture systems that rely on murine basement membrane extracts (e.g. Matrigel), which can interfere with immune cell interactions, the presently described matrix-free model provides an optimal microenvironment for antigen-specific T cell responses. This feature makes it particularly well-suited for modeling immune-mediated hepatotoxicity.

[0129] There are various important applications and uses of this platform contemplated in accordance with various embodiments of the disclosure. For example, this platform provides a physiologically relevant system for dissecting the mechanisms driving antigen-specific T cell responses and hepatocyte injury in immune-mediated DILI. In addition, this platform offers a clinically actionable preclinical model for identifying individuals at heightened risk of immune-related drug toxicity. The ability to generate liver organoid cultures from iPSC-derived cells, combined with the capacity to expand and prime antigen-specific CD8+T cells, creates a controlled and reproducible system for investigating HLA-restricted immune responses in hepatoxicity. This model facilitates functional validation of genetic risk factors, T cell activation pathways, and immune effector mechanisms underlying iDILI pathogenesis.

[0130] From a translational perspective, this platform offers a personalized approach to iDILI risk assessment by integrating genetic predisposition with functional immune assays. While genetic screening can identify individuals carrying risk-associated HLA alleles, its low positive predictive value underscores the need for complementary functional assessments to capture individual variability in immune responses. By leveraging patient-derived iPSCs and autologous immune cells, this system has the potential to refine individual risk stratification before drug administration. Moreover, integrating HLA typing with functional immune assays represents a critical step in bridging genetic susceptibility and with immune-driven liver toxicity, advancing personalized medicine in drug safety evaluation.

[0131] Automating patient-specific liver organoid–T cell co-cultures in high- throughput systems can enhance the prediction and mitigation of immune-mediated toxicities. Integrating this approach into drug development pipelines can provide a transformative tool for identifying immunogenic risks, improving drug safety, and addressing iDILI-related challenges in ongoing clinical studies.

[0132] In summary, a scalable, modular, and autologous liver organoid - T cell co- culture platform has been developed for modeling immune-mediated hepatotoxicity. By integrating genetic risk with functional immune assessment, this system addresses a key gap in preclinical drug safety and provides a translationally relevant framework for mechanistic discovery and patient-specific toxicity profiling.

[0133] Further detail is provided in the sections that follow, including Examples 1- 16. Definitions of Terms

[0134] Unless otherwise noted, terms are to be understood according to conventional usage by those of ordinary skill in the relevant art. For purposes of the present disclosure, the following terms are explained below.

[0135] The disclosure herein uses affirmative language to describe the numerous embodiments. The disclosure also includes embodiments in which subject matter is excluded, infull or in part, such as substances or materials, method steps and conditions, protocols, or procedures.

[0136] As used herein the specification, “a” or “an” may mean one or more. As used herein in the claim(s), when used in conjunction with the word “comprising,” the words “a” or “an” may mean one or more than one. Some embodiments of the disclosure may consist of or consist essentially of one or more elements, method steps, and / or methods of the disclosure. It is contemplated that any method or composition described herein can be implemented with respect to any other method or composition described herein and that different embodiments may be combined.

[0137] By “about” is meant a quantity, level, value, number, frequency, percentage, dimension, size, amount, weight or length that varies by as much as 10% to a reference quantity, level, value, number, frequency, percentage, dimension, size, amount, weight or length.

[0138] The use of the term “or” in the claims is used to mean “and / or” unless explicitly indicated to refer to alternatives only or the alternatives are mutually exclusive, although the disclosure supports a definition that refers to only alternatives and “and / or.” For example, “x, y, and / or z” can refer to “x” alone, “y” alone, “z” alone, “x, y, and z,” “(x and y) or z,” “x or (y and z),” or “x or y or z.” It is specifically contemplated that x, y, or z may be specifically excluded from an embodiment. As used herein “another” may mean at least a second or more.

[0139] The term “ones” means more than one.

[0140] As used herein, the term “plurality” may be 2, 3, 4, 5, 6, 7, 8, 9, 10, or more.

[0141] As used herein, the term “set of” means one or more. For example, a set of items includes one or more items.

[0142] As used herein, the phrase “at least one of,” when used with a list of items, means different combinations of one or more of the listed items may be used and only one of the items in the list may be needed. The item may be a particular object, thing, step, operation, process, or category. In other words, “at least one of” means any combination of items or number of items may be used from the list, but not all of the items in the list may be required. For example, without limitation, “at least one of item A, item B, or item C” means item A; item A and item B; item B; item A, item B, and item C; item B and item C; or item A and C. In somecases, “at least one of item A, item B, or item C” means, but is not limited to, two of item A, one of item B, and ten of item C; four of item B and seven of item C; or some other suitable combination.

[0143] As used herein, “substantially” means sufficient to work for the intended purpose. The term “substantially” thus allows for minor, insignificant variations from an absolute or perfect state, dimension, measurement, result, or the like such as would be expected by a person of ordinary skill in the field but that do not appreciably affect overall performance. When used with respect to numerical values or parameters or characteristics that can be expressed as numerical values, “substantially” means within ten percent.

[0144] Throughout this specification, unless the context requires otherwise, the words “comprise”, “comprises” and “comprising” will be understood to imply the inclusion of a stated step or element or group of steps or elements but not the exclusion of any other step or element or group of steps or elements. By “consisting of” is meant including, and limited to, whatever follows the phrase “consisting of.” Thus, the phrase “consisting of” indicates that the listed elements are required or mandatory, and that no other elements may be present. By “consisting essentially of” is meant including any elements listed after the phrase, and limited to other elements that do not interfere with or contribute to the activity or action specified in the disclosure for the listed elements. Thus, the phrase “consisting essentially of” indicates that the listed elements are required or mandatory, but that no other elements are optional and may or may not be present depending upon whether or not they affect the activity or action of the listed elements.

[0145] Reference throughout this specification to “one embodiment,” “an embodiment,” “a particular embodiment,” “a related embodiment,” “a certain embodiment,” “an additional embodiment,” or “a further embodiment” or combinations thereof means that a particular feature, structure or characteristic described in connection with the embodiment is included in at least one embodiment of the present disclosure. Thus, the appearances of the foregoing phrases in various places throughout this specification are not necessarily all referring to the same embodiment. Furthermore, the particular features, structures, or characteristics may be combined in any suitable manner in various embodiments.

[0146] The terms “individual”, “subject”, or “patient” as used herein have their plain and ordinary meaning as understood in light of the specification, and mean a human or a non- human mammal, e.g., a dog, a cat, a mouse, a rat, a cow, a sheep, a pig, a goat, a non-human primate, or a bird, e.g., a chicken, as well as any other vertebrate or invertebrate. The term “mammal” is used in its usual biological sense. Thus, it specifically includes, but is not limited to, primates, including simians (chimpanzees, apes, monkeys) and humans, cattle, horses, sheep, goats, swine, rabbits, dogs, cats, rodents, rats, mice, guinea pigs, or the like.

[0147] As used herein, the terms “treatment,” “treating,” “treat,” and the like, with respect to a disease or condition, can refer to obtaining a desired pharmacologic and / or physiologic effect. The effect can be prophylactic in terms of completely or partially preventing a disease or symptom thereof and / or can be therapeutic in terms of a partial or complete cure for a disease and / or adverse effect attributable to the disease. For example, a treatment can include executing a protocol, which may include administering one or more drugs to a patient, in an effort to alleviate signs or symptoms of the disease. Desirable effects of treatment include decreasing the rate of disease progression, ameliorating or palliating the disease state, and remission or improved prognosis. Alleviation can occur prior to signs or symptoms of the disease or condition appearing, as well as after their appearance. Thus, “treating” or “treatment” may include “preventing” or “prevention” of disease or undesirable condition. In addition, “treating” or “treatment” does not require complete alleviation of signs or symptoms, does not require a cure, and specifically includes protocols that have only a marginal effect on the patient.

[0148] “Treatment,” as used herein, thus can cover any treatment of a disease in a subject, particularly in a human, and includes: (a) preventing the disease from occurring in a subject which may be predisposed to the disease but has not yet been diagnosed as having it; (b) inhibiting the disease, i.e., arresting its development; and (c) relieving the disease, i.e., causing regression of the disease and / or relieving one or more disease symptoms. “Treatment” can also encompass delivery of an agent or administration of a therapy in order to provide for a pharmacologic effect, even in the absence of a disease or condition.

[0149] The term “therapeutically effective” or “therapeutically effective amount” as used throughout this application can refer to an amount effective to achieve a desired and / or beneficial effect, and / or anything that promotes or enhances the well-being of the subject withrespect to the medical treatment of a condition. This includes, but is not limited to, a reduction in the frequency or severity of one or more signs or symptoms of a disease. An effective amount can be administered in one or more administrations. In the methods, a therapeutically effective amount is an amount appropriate to treat an indication. By treating an indication is meant achieving any desirable effect, such as one or more of palliate, ameliorate, stabilize, reverse, slow, or delay disease progression, increase the quality of life, or to prolong life. Such achievement can be measured by any suitable method, such as measurement of tumor size or blood cell count, or any other suitable measurement.

[0150] The terms “effective amount” or “effective dose” as used herein have their plain and ordinary meaning as understood in light of the specification, and can refer to that amount of a recited composition or compound that, results in an observable effect. Actual dosage levels of active ingredients in an active composition of the presently disclosed subject matter can be varied so as to administer an amount of the active composition or compound that, is effective to achieve the desired response for a particular subject and / or application. The selected dosage level wall depend upon a variety of factors including, but not limited to, the activity of the composition, formulation, route of administration, combination with other drugs or treatments, severity of the condition being treated, and the physical condition and prior medical history of the subject being treated. In some embodiments, a minimal dose is administered, and dose is escalated in the absence of dose-limiting toxicity to a minimally effective amount. Determination and adjustment of an effective dose, as well as evaluation of when and how to make such adjustments, are contemplated herein.

[0151] The term “disease state” as used herein, can generally refer to a condition that affects the structure or function of an organism. Disease states can include, for example, stages of a disease progression.

[0152] As used herein, the term “assessing” can include any form of measurement, and includes determining if an element is present or not. The terms “determining,” “measuring,” “evaluating,” “assessing” and “assaying” can be used interchangeably and can include quantitative and / or qualitative determinations.

[0153] As used herein, the terms “modulated” or “modulation,” or “regulated” or “regulation” and “differentially regulated” can refer to both up regulation (i.e., activation orstimulation, e.g., by agonizing or potentiating) and down regulation (i.e., inhibition or suppression, e.g., by antagonizing, decreasing or inhibiting), unless otherwise specified or clear from the context of a specific usage.

[0154] As used herein, the term “marker” or “biomarker” can refer to any measurable substance taken as a sample from a subject whose presence is indicative of some phenomenon. Non-limiting examples of such phenomenon can include a disease state, a condition, or exposure to a compound or environmental condition. In various embodiments described herein, biomarkers may be used for diagnostic purposes (e.g., to diagnose a disease state, a health state, an asymptomatic state, a symptomatic state, etc.). The term “biomarker” may be used interchangeably with the term “marker”. The term “marker” or “biomarker” can include a biological molecule, such as, for example, a nucleic acid, peptide, protein, hormone, and the like, whose presence or concentration can be detected and correlated with a known condition, such as a disease state. It can also be used to refer to a differentially expressed gene whose expression pattern can be utilized as part of a predictive, prognostic or diagnostic process in healthy conditions or a disease state, or which, alternatively, can be used in methods for identifying a useful treatment or prevention therapy.

[0155] As used herein, the term “cellular phenotype” can refer to any determinable, observable, and / or measurable characteristic associated with a cell population.

[0156] As used herein, a “model” can include one or more in vitro or in vivo disease models; a model can also include algorithms, one or more mathematical techniques, one or more machine learning algorithms, or a combination thereof. A model can be used in a process and / or applied to an assay, in accordance with various embodiments as disclosed herein.

[0157] As used herein, a “process” can include one or more steps involving one or more features of one or more model as disclosed herein.

[0158] The terms “function” and “functional” as used herein have their plain and ordinary meaning as understood in light of the specification, and can refer to a biological, enzymatic, or therapeutic function.

[0159] The term “inhibit” as used herein has its plain and ordinary meaning as understood in light of the specification, and can refer to the reduction or prevention of a biological activity. The reduction can be by a percentage that is, is about, is at least, is at leastabout, is not more than, or is not more than about, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%, or an amount that is within a range defined by any two of the aforementioned values. As used herein, the term “delay” has its plain and ordinary meaning as understood in light of the specification, and refers to a slowing, postponement, or deferment of a biological event, to a time which is later than would otherwise be expected. The delay can be a delay of a percentage that is, is about, is at least, is at least about, is not more than, or is not more than about, 0%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or an amount within a range defined by any two of the aforementioned values. The terms inhibit and delay may not necessarily indicate a 100% inhibition or delay, A partial inhibition or delay may be realized.

[0160] As used herein, the term “isolated” has its plain and ordinary meaning as understood in light of the specification, and can refer to a substance and / or entity that has been (1) separated from at least some of the components with which it was associated when initially produced (whether in nature and / or in an experimental setting), and / or (2) produced, prepared, and / or manufactured by the hand of man. Isolated substances and / or entities may be separated from equal to, about, at least, at least about, not more than, or not more than about, 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 95%, about 98%, about 99%, substantially 100%, or 100% of the other components with which they were initially associated (or ranges including and / or spanning the aforementioned values). In some embodiments, isolated agents are, are about, are at least, are at least about, are not more than, or are not more than about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, substantially 100%, or 100% pure (or ranges including and / or spanning the aforementioned values). As used herein, a substance that is “isolated” may be “pure” (e.g., substantially free of other components). As used herein, the term “isolated cell” can refer to a cell not contained in a multi - cellular organism or tissue.

[0161] As used herein, “in vivo” is given its plain and ordinary meaning as understood in light of the specification and can refer to the performance of a method inside living organisms, usually animals, mammals, including humans, and plants, as opposed to a tissue extract or dead organism.

[0162] As used herein, “ex vivo” is given its plain and ordinary meaning as understood in light of the specification and can refer to the performance of a method outside a living organism with little alteration of natural conditions.

[0163] As used herein, “in vitro” is given its plain and ordinary' meaning as understood in light of the specification and can refer to the performance of a method outside of biological conditions, e.g., in a petri dish or test tube.

[0164] The terms “nucleic acid” or “nucleic acid molecule” as used herein have their plain and ordinary meaning as understood in light of the specification, and can refer to polynucleotides, such as deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), oligonucleotides, those that appear in a cell naturally, fragments generated by the polymerase chain reaction (PCR), and fragments generated by any of ligation, scission, endonuclease action, and exonuclease action. Nucleic acid molecules can be composed of monomers that are naturally-occurring nucleotides (such as DNA and RNA), or analogs of naturally-occurring nucleotides (e.g., enantiomeric forms of naturally-occurring nucleotides), or a combination of both. Modified nucleotides can have alterations in sugar moieties and / or in pyrimidine or purine base moieties. Sugar modifications include, for example, replacement of one or more hydroxyl groups with halogens, alkyl groups, amines, and azido groups, or sugars can be functionalized as ethers or esters. Moreover, the entire sugar moiety can be replaced with statically and electronically similar structures, such as aza- sugars and carbocyclic sugar analogs. Examples of modifications in a base moiety include alkylated purines and pyrimidines, acylated purines or pyrimidines, or other well-known heterocyclic substitutes. Nucleic acid monomers can be linked by phosphodiester bonds or analogs of such linkages. Analogs of phosphodiester linkages include phosphorothioate, phosphorodithioate, phosphoroselenoate, phosphorodiselenoate, phosphoroanilothioate, phosphoramlidate, or phosphoramidate. The term “nucleic acid molecule” also includes so-called “peptide nucleic acids,” which comprise naturally-occurring or modified nucleic acid bases attached to a polyamide backbone. Nucleic acids can be either single stranded or double stranded. “Oligonucleotide” can be used interchangeable with nucleic acid and can refer to either double stranded or single stranded DNA or RNA. A nucleic acid or nucleic acids can be contained in a nucleic acid vector or nucleic acid construct (e.g. plasmid, virus, retrovirus, lentivirus, bacteriophage, cosmid, fosmid, phagemid, bacterial artificialchromosome (BAG), yeast artificial chromosome (YAC), or human artificial chromosome (HAG)) that can be used for amplification and / or expression of the nucleic acid or nucleic acids in various biological systems. Typically, the vector or construct will also contain elements including but not limited to promoters, enhancers, terminators, inducers, ribosome binding sites, translation initiation sites, start codons, stop codons, polyadenylation signals, origins of replication, cloning sites, multiple cloning sites, restriction enzyme sites, epitopes, reporter genes, selection markers, antibiotic selection markers, targeting sequences, peptide purification tags, or accessory genes, or any combination thereof.

[0165] A nucleic acid or nucleic acid molecule can comprise one or more sequences encoding different peptides, polypeptides, or proteins. These one or more sequences can be joined in the same nucleic acid or nucleic acid molecule adjacently, or with extra nucleic acids in between, e.g. linkers, repeats or restriction enzyme sites, or any other sequence that is, is about, is at least, is at least about, is not more than, or is not more than about, I, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, or 300 bases long, or any length in a range defined by any two of the aforementioned lengths. The term “downstream” on a nucleic acid as used herein has its plain and ordinary meaning as understood in light of the specification and refers to a sequence being after the 3’-end of a previous sequence, on the strand containing the encoding sequence (sense strand) if the nucleic acid is double stranded. The term “upstream” on a nucleic acid as used herein has its plain and ordinary meaning as understood in light of the specification and refers to a sequence being before the 5’- end of a subsequent sequence, on the strand containing the encoding sequence (sense strand) if the nucleic acid is double stranded. The term “grouped” on a nucleic acid as used herein has its plain and ordinary meaning as understood in light of the specification and refers to two or more sequences that occur in proximity either directly or with extra nucleic acids in between, e.g. linkers, repeats, or restriction enzyme sites, or any other sequence that is, is about, is at least, is at least about, is not more than, or is not more than about, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, or 300 bases long, or any length in a range defined by any two of the aforementioned lengths, but generally not with a sequence in between that encodes for a functioning or catalytic polypeptide, protein, or protein domain.

[0166] The nucleic acids described herein comprise nucleobases. Primary, canonical, natural, or unmodified bases are adenine, cytosine, guanine, thymine, and uracil. Other nucleobases include but are not limited to purines, pyrimidines, modified nucleobases, 5- methylcytosine, pseudouridine, dihydrouridine, inosine, 7-methylguanosine, hypoxanthine, xanthine, 5,6-dihydrouracil, 5-hydroxymethylcytosine, 5-bromouracil, isoguanine, isocytosine, aminoallyl bases, dye-labeled bases, fluorescent bases, or biotin-labeled bases.

[0167] The terms “peptide”, “polypeptide”, and “protein” as used herein have their plain and ordinary meaning as understood in light of the specification and refer to macromolecules comprised of amino acids linked by peptide bonds. The numerous functions of peptides, polypeptides, and proteins are known in the art, and include but are not limited to enzymes, structure, transport, defense, hormones, or signaling. Peptides, polypeptides, and proteins are often, but not always, produced biologically by a ribosomal complex using a nucleic acid template, although chemical syntheses are also available. By manipulating the nucleic acid template, peptide, polypeptide, and protein mutations such as substitutions, deletions, truncations, additions, duplications, or fusions of more than one peptide, polypeptide, or protein can be performed. These fusions of more than one peptide, polypeptide, or protein can be joined in the same molecule adjacently, or with extra amino acids in between, e.g. linkers, repeats, epitopes, or tags, or any other sequence that is, is about, is at least, is at least about, is not more than, or is not more than about, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, or 300 bases long, or any length in a range defined by any two of the aforementioned lengths. The term “downstream” on a polypeptide as used herein has its plain and ordinary meaning as understood in light of the specification and refers to a sequence being after the C-terminus of a previous sequence. The term “upstream” on a polypeptide as used herein has its plain and ordinary meaning as understood in light of the specification and refers to a sequence being before the N- terminus of a subsequent sequence.

[0168] The term “purity” of any given substance, compound, or material as used herein has its plain and ordinary meaning as understood in light of the specification and can refer to the actual abundance of the substance, compound, or material relative to the expected abundance. For example, the substance, compound, or material may be at least 80, 85, 90, 91, 92,93, 94, 95, 96, 97, 98, 99, or 100% pure, including all decimals in between. Purity may be affected by unwanted impurities, including but not limited to nucleic acids, DNA, RNA, nucleotides, proteins, polypeptides, peptides, amino acids, lipids, cell membrane, cell debris, small molecules, degradation products, solvent, carrier, vehicle, or contaminants, or any combination thereof. In some embodiments, the substance, compound, or material is substantially free of host cell proteins, host cell nucleic acids, plasmid DNA, contaminating viruses, proteasomes, host cell culture components, process related components, mycoplasma, pyrogens, bacterial endotoxins, and adventitious agents. Purity' can be measured using technologies including but not limited to electrophoresis, SDS-PAGE, capillary electrophoresis, PCR, rtPCR, qPCR, chromatography, liquid chromatography, gas chromatography, thin layer chromatography, enzyme-linked immunosorbent assay (ELISA), spectroscopy, UV-visible spectrometry, infrared spectrometry, mass spectrometry, nuclear magnetic resonance, gravimetry, or titration, or any combination thereof.

[0169] The term “yield” of any given substance, compound, or material as used herein has its plain and ordinary meaning as understood in light of the specification and can refer to the actual overall amount of the substance, compound, or material relative to the expected overall amount. For example, the yield of the substance, compound, or material is, is about, is at least, is at least about, is not more than, or is not more than about 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% of the expected overall amount, including ail decimals in between. Yield may be affected by the efficiency of a reaction or process, unwanted side reactions, degradation, quality of the input substances, compounds, or materials, or loss of the desired substance, compound, or material during any step of the production.

[0170] As used herein, “pharmaceutically acceptable” has its plain and ordinary meaning as understood in light of the specification and refers to carriers, excipients, and / or stabilizers that are nontoxic to the cell or mammal being exposed thereto at the dosages and concentrations employed or that have an acceptable level of toxicity. A “pharmaceutically acceptable” “diluent,” “excipient,” and / or “carrier” as used herein have their plain and ordinary meaning as understood in light of the specification and are intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with administration to humans, cats, dogs, or othervertebrate hosts. Typically, a pharmaceutically acceptable diluent, excipient, and / or carrier is a diluent, excipient, and / or carrier approved by a regulatory agency of a Federal, a state government, or other regulatory agency, or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, including humans as well as non-human mammals, such as cats and dogs. The term diluent, excipient, and / or “carrier” can refer to a diluent, adjuvant, excipient, or vehicle with which the pharmaceutical composition is administered. Such pharmaceutical diluent, excipient, and / or carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin. Water, saline solutions and aqueous dextrose and glycerol solutions can be employed as liquid diluents, excipients, and / or carriers, particularly for injectable solutions. Suitable pharmaceutical diluents and / or excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like. A non-limiting example of a physiologically acceptable carrier is an aqueous pH buffered solution. The physiologically acceptable carrier may also comprise one or more of the following: antioxidants, such as ascorbic acid, low molecular weight (less than about 10 residues) polypeptides, proteins, such as serum albumin, gelatin, immunoglobulins, hydrophilic polymers such as polyvinylpyrrolidone, amino acids, carbohydrates such as glucose, mannose, or dextrins, chelating agents such as EDTA, sugar alcohols such as mannitol or sorbitol, salt-forming counterions such as sodium, and nonionic surfactants such as TWEEN®, polyethylene glycol (PEG), and PLURONICS®. The composition, if desired, can also contain minor amounts of wetting, bulking, emulsifying agents, or pH buffering agents. These compositions can take the form of solutions, suspensions, emulsion, sustained release formulations and the like. The formulation should suit the mode of administration.

[0171] Cryoprotectants are cell composition additives to improve efficiency and yield of low temperature cryopreservation by preventing formation of large ice crystals. Cryoprotectants include but are not limited to DMSO, ethylene glycol, glycerol, propylene glycol, trehalose, formamide, methyl-formamide, dimethyl-formamide, glycerol 3-phosphate, proline, sorbitol, diethyl glycol, sucrose, triethylene glycol, polyvinyl alcohol, polyethylene glycol, or hydroxyethyl starch. Cryoprotectants can be used as part of a cryopreservationmedium, which include other components such as nutrients (e.g. albumin, serum, bovine serum, fetal calf serum [FCS]) to enhance post-thawing survivability of the cells. In these cryopreservation media, at least one cryoprotectant may be found at a concentration that is, is about, is at least, is at least about, is not more than, or is not more than about, 0.01%, 0.05%, 0.1%, 0.5%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90%, or any percentage within a range defined by any two of the aforementioned numbers.

[0172] Additional excipients with desirable properties include but are not limited to preservatives, adjuvants, stabilizers, solvents, buffers, diluents, solubilizing agents, detergents, surfactants, chelating agents, antioxidants, alcohols, ketones, aldehydes, ethylenediaminetetraacetic acid (EDTA), citric acid, salts, sodium cHLOride, sodium bicarbonate, sodium phosphate, sodium borate, sodium citrate, potassium cHLOride, potassium phosphate, magnesium sulfate sugars, dextrose, fructose, mannose, lactose, galactose, sucrose, sorbitol, cellulose, serum, amino acids, polysorbate 20, polysorbate 80, sodium deoxycholate, sodium taurodeoxycholate, magnesium stearate, octylphenol ethoxylate, benzethonium cHLOride, thimerosal, gelatin, esters, ethers, 2-phenoxyethanol, urea, or vitamins, or any combination thereof. Some excipients may be in residual amounts or contaminants from the process of manufacturing, including but not limited to serum, albumin, ovalbumin, antibiotics, inactivating agents, formaldehyde, glutaraldehyde, β-propiolactone, gelatin, cell debris, nucleic acids, peptides, amino acids, or growth medium components or any combination thereof. The amount of the excipient may be found in composition at a percentage that is, is about, is at least, is at least about, is not more than, or is not more than about, 0%, 0.1%, 0.2%, 0.3%, 0.4%, 0.5%, 0.6%, 0.7%, 0.8%, 0.9%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 100% w / w or any percentage by weight in a range defined by any two of the aforementioned numbers.

[0173] The term “pharmaceutically acceptable salts” has its plain and ordinary meaning as understood in light of the specification and includes relatively non-toxic, inorganic and organic acid, or base addition salts of compositions or excipients, including without limitation, analgesic agents, therapeutic agents, other materials, and the like. Examples of pharmaceutically acceptable salts include those derived from mineral acids, such as hydrochloricacid and sulfuric acid, and those derived from organic acids, such as ethanesulfonic acid, benzenesulfonic acid, p-toluenesulfonic acid, and the like. Examples of suitable inorganic bases for the formation of salts include the hydroxides, carbonates, and bicarbonates of ammonia, sodium, lithium, potassium, calcium, magnesium, aluminum, zinc, and the like. Salts may also be formed with suitable organic bases, including those that are non-toxic and strong enough to form such salts. For example, the class of such organic bases may include but are not limited to mono-, di-, and trialkylamines, including methylamine, dimethylamine, and triethylamine; mono-, di-, or trihydroxyalkylamines including mono-, di-, and triethanolamine; amino acids, including glycine, arginine and lysine; guanidine; N-methylglucosamine; N-methylglucamine; L- glutamine; N-methylpiperazine; morpholine; ethylenediamine; N-benzylphenethylamine; trihydroxymethyl aminoethane.

[0174] Proper formulation is dependent upon the route of administration chosen. Techniques for formulation and administration of the compounds described herein are known to those skilled in the art. Multiple techniques of administering a compound exist in the art including, but not limited to, enteral, oral, rectal, topical, sublingual, buccal, intraaural, epidural, epicutaneous, aerosol, parenteral delivery, including intramuscular, subcutaneous, intra-arterial, intravenous, intraportal, intra-articular, intradermal, peritoneal, intramedullary injections, intrathecal, direct intraventricular, intraperitoneal, intranasal or intraocular injections. Pharmaceutical compositions will generally be tailored to the specific intended route of administration.

[0175] As used herein, a “carrier” has its plain and ordinary meaning as understood in light of the specification and refers to a compound, particle, solid, semi-solid, liquid, or diluent that facilitates the passage, delivery and / or incorporation of a compound to cells, tissues and / or bodily organs.

[0176] As used herein, a “diluent” has its plain and ordinary meaning as understood in light of the specification and refers to an ingredient in a pharmaceutical composition that lacks pharmacological activity but may be pharmaceutically necessary or desirable. For example, a diluent may be used to increase the bulk of a potent drug whose mass is too small for manufacture and / or administration. It may also be a liquid for the dissolution of a drug to be administered by injection, ingestion or inhalation. A common form of diluent in the art is abuffered aqueous solution such as, without limitation, phosphate buffered saline that mimics the composition of human blood.

[0177] The term “% w / w” or “% wt / wt” as used herein has its plain and ordinary meaning as understood in light of the specification and refers to a percentage expressed in terms of the weight of the ingredient or agent over the total weight of the composition multiplied by 100. The term “% v / v” or “% vol / vol” as used herein has its plain and ordinary meaning as understood in the light of the specification and refers to a percentage expressed in terms of the liquid volume of the compound, substance, ingredient, or agent over the total liquid volume of the composition multiplied by 100.

[0178] The term “basement membrane matrix” or “extracellular matrix” as used herein has its plain and ordinary meaning in light of the specification and refers to any biological or synthetic compound, substance, or composition that enhances cell attachment and / or growth. Any extracellular matrix, as well as any mimetic or derivative thereof, known in the art can be used for the methods disclosed herein. Some examples of extracellular matrices, or mimetics or derivative thereof, include but are not limited to cell-based feeder layers, polymers, proteins, polypeptides, nucleic acids, sugars, lipids, poly-lysine, poly-ornithine, collagen, collagen IV, gelatin, fibronectin, vitronectin, laminin, laminin-511 elastin, tenascin, heparan sulfate, entactin, nidogen, osteopontin, perlecan, fibrin, basement membrane, Matrigel®, hydrogel, PEI, WGA, or hyaluronic acid, or any combination thereof. A common basement membrane matrix that is used in laboratories are those isolated from murine Engelbreth-Holm-Swarm (EHS) sarcoma cells. However, these basement membrane matrices are derived from non-human animals and therefore contain xenogeneic components that prevent its use towards humans. They are also not defined, which can lead to variability in manufacturing, as well as potentially harbor pathogens. Accordingly, in some embodiments, the methods for culturing cells may involve the use of synthetic and / or defined alternatives to these xenogeneic basement membrane matrices. The use of non-xenogeneic basement membrane matrices or mimetics or derivatives thereof enables manufacturing of biological products better suited for human use.

[0179] The terms “passage” and “passaging” as used herein have their plain and ordinary meaning as understood in light of the specification, and refer to the conventional approaches performed in biological cell culture methods to maintain a viable population of cellsfor prolonged periods of time. As cells are generally proliferative in cell culture, they undergo multiple cycles of mitosis until occupying the available space, which is typically a surface of a cell culture container (e.g., a plate, dish, or flask) submerged under culture medium. For example, the cells may grow out as a monolayer on a cell culture container surface. If the growing cells occupy the entire available space of surface, they cannot proliferate further and may exhibit senescent behavior. In order to continue growth of the cells, which may be performed to maintain the viability and proliferative nature of the cells and / or to expand the number of cells for downstream purposes, the cells may be passaged by taking a fraction of the cells and seeding this fraction onto a fresh surface (e.g., of a cell culture container) in culture medium. This fraction of the cells will continue to proliferate and multiply until they occupy the available space of the new surface, upon which this passaging can be repeated successively.

[0180] The microscopic architecture of the liver is made up of polygonal structures called “hepatic lobules”. Classically, these lobules take on a hexagonal structure, although other geometric shapes are observed depending on tissue specification. Each lobule unit comprises plates or layers of hepatocytes surrounding an internal central vein and encapsulated by bundles of vessels called portal triads, which are made up of a portal vein, hepatic artery, and bile duct. Hepatic activity occurs as blood flows from the portal triads at the periphery, across the hepatocytes, and into the central vein to return to the circulatory system. Due to the asymmetric organization of these lobules, the layers of hepatocytes are divided into three zones. Cells in the “periportal zone” (zone 1) are closest to the portal triad and receive the most oxygenated blood, the pericentral zone (zone 3) are closest to the central vein and therefore receive the least amount of oxygenated blood, and the transition zone (zone 2) is in between zone 1 and 3.

[0181] The term “bilirubin” as used herein has its plain and ordinary meaning as understood in light of the specification and refers to the naturally occurring metabolite created by normal catabolic degradation of heme. Bilirubin arises from the catalysis of biliverdin by biliverdin reductase. In the liver, bilirubin is conjugated with glucuronic acid by a family of enzymes called UDT-glucuronosyltransferases (UGTs). This conjugation renders bilirubin water soluble, enabling it to be carried in bile to the small intestine and colon, whereby it is further metabolized to waste products. Dysfunctional bilirubin metabolism, particularly due to abnormal function of UGTs preventing conjugation of bilirubin, leads to accumulation of bilirubin and isassociated with various diseases characterized by hyperbilirubinemia. Notably, however, while excessive bilirubin is detrimental, bilirubin also has antioxidant capabilities and therefore may have beneficial effects in reducing oxidative damage in cells.

[0182] The term “L-gulonolactone oxidase” and “GULO” as used herein has its plain and ordinary meaning as understood in light of the specification and refers to the enzyme that catalyzes L-gulonolactone to produce L-xylo-hex-3-gulonolactone and hydrogen peroxide. The L-xylo-hex-3-gulonolactone then spontaneously converts to ascorbate (vitamin C). Accordingly, this enzyme is involved in the biosynthesis of vitamin C, which is an essential nutrient that is involved in many biological functions such as use as a cofactor for several important enzymes and as an antioxidant. Notably, humans, as well as other haplorrhine primates, certain species of bats, and Guinea pigs have evolved to harbor a non-functional GULO gene. Therefore, these organisms are unable to synthesize ascorbate and require vitamin C intake from diet or supplementation, where a deficiency of vitamin C can lead to scurvy. As applied to the disclosure herein, a “functional GULO protein” is a GULO protein that has L-gulonolactone catalytic activity to result in the production of ascorbate. Conversely, an “inactive” GULO protein or “non-functional” GULO protein is one that does not have the catalytic activity to produce ascorbate. Humans and cells that are derived from humans comprise a non-functional GULO protein and do not have the ability to synthesize ascorbate. However, as disclosed herein, human cells may be engineered to express a functional GULO protein to enable ascorbate synthesis ability. These functional GULO proteins may be expressed in human cells (or other cells that are unable to normally synthesize ascorbate) through conventional methods of cloning, such as genetically engineering cells to have genetic sequences that encode for a functional GULO protein.

[0183] The term “exogenous” as used herein has its plain and ordinary meaning as understood in light of the specification and refers to external factors that originate outside of a biological specimen (e.g., a cell, population of cells, organoid, etc.), as opposed to being naturally occurring and / or produced by the biological specimen itself. As used herein, exogenous components, reagents, agents, and / or conditions, are components, reagents, agents, and / or conditions that are added to compositions described herein, although this does not necessarilypreclude the possibility of the same components, reagents, and / or conditions also being present through a function endogenous to a biological specimen.

[0184] The terms “liver organoid”, or “human liver organoid” (HLO), are used interchangeably herein, and refer to populations of cells differentiated in vitro to form self- organizing structures, which generally are three-dimensional (3D), and include one or more functional cell types. Liver organoids differ from naturally occurring liver tissue in a number of ways. For example, as compared with naturally occurring liver tissue, liver organoids can have a structure having a single lumen and generally a spherical shape, and can include a basement membrane which is unnatural. The single lumen of a liver organoid contains 3D tissues but generally does not make any hepatic lobular structure nor cord-like structure, as with naturally occurring liver tissue. Liver organoids also generally do not contain hematopoietic tissue and acquired immune cell subsets, such as T cell lineages. Further, as compared with naturally occurring liver tissue, liver organoids can have different efflux mechanisms, as a liver organoid can have a three-dimensional structure with a luminal structure but no ejection mechanism. In addition, liver organoids generally cannot receive dietary inputs, as they lack a gut and connected vascular channel. In some embodiments, a liver organoid can include a functional GULO protein or can have been genetically modified to produce a functional GULO protein.

[0185] Liver organoids can be derived from pluripotent stem cells (PSCs), including at least embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs). Liver organoids may also be formed from liver-derived stem cells. In general, liver organoids can self-organize through cell sorting and spatially restricted lineage commitment in a manner similar to that which occurs in vivo, but as directed in vitro by thoughtful introduction of exogenous and / or endogenous differentiating factors and / or conditions as described herein, optionally through one or more directed steps, optionally involving introduction of one or more components.

[0186] The term “mature liver organoid” as used herein refers to liver organoids which have continued to develop from a liver organoid to include, in various embodiments, luminal projections that resemble bile canaliculi, and / or a structure having a single lumen and generally a spherical shape. Mature liver organoids may exhibit lumens with smaller sizes and reduced circularity when compared to lumens of liver organoids. In some embodiments, mature liver organoids may be generated through addition of exogenous bilirubin and / or amino acidsupplementation as described herein. In some embodiments, a mature liver organoid may be characterized as expressing reduced levels of AFP, CDX2, and / or NANOG relative to liver organoids, and / or as expressing increased levels of ALB, SLC4A2 and / or HO-1 relative to liver organoids. In some embodiments, a mature liver organoid may be characterized as expressing CYP2E1, CYP7A1, PROX1, MRP3, MRP3, and / or OATP2. In some embodiments, a mature liver organoid may exhibit increased CYP3A4 and / or CYP1A2 protein levels and / or enzymatic activity relative to liver organoids.

[0187] The term “tissue culture surface”, or “surface” with respect to a plate or multi- well plate used for culturing cells or tissues, as used herein has its plain and ordinary meaning as understood in light of the specification and refers to a substrate surface on which cells may aggregate and / or adhere to facilitate cell growth, differentiation, and / or function.

[0188] The term “engineered” as used herein refers to an entity that is generated by the hand of man, including a cell, nucleic acid, polypeptide, vector, and so forth. In at least some cases, an engineered entity is synthetic and comprises elements that are not naturally present or configured in the manner in which it is utilized in the disclosure. In certain embodiments, a construct and / or vector is engineered through recombinant nucleic acid technologies, and a cell is engineered through transfection or transduction of an engineered vector. Cells may be engineered to express heterologous proteins that are not naturally expressed by the cells, either because the heterologous proteins are recombinant or synthetic or because the cells do not naturally express the proteins. HLO:Immune Cell Compositions and Exemplary Uses Thereof

[0189] As described herein, including in Examples 1-16, exemplary HLO:immune cell co-culture media compositions and compositions were conceived, methods for preparing versions of the exemplary HLO:immune cell co-culture media compositions and compositions were developed. Non-limiting methods of using the exemplary HLO:immune cell co-culture media compositions and compositions are described herein as well. One skilled in the art will appreciate that there will be various uses and applications of the exemplary HLO:immune cell co-culture media compositions and compositions, in addition to the specific embodiments described herein.

[0190] The establishment of a co-culture media that maintains functionality of both liver organoids and CD8 T cells over a prolonged time has been described. This allows for the development of a liver organoid-based screening, e.g. high throughput screening, model. For example, such screening models can be capable of detecting differential responses between carriers and non-carriers of genetic risk factors to develop ADR and immune-driven DILI. This platform provides an unbiased strategy for the enrichment of drug-reactive immune cells, e.g. CD8 T cells, and provides a means by which to assess the sensitivity of liver cells to autoimmune, e.g. CD8 T cell-mediated, attack at the level of the individual patient. Co-culture media and HLO:immune cell compositions

[0191] An appropriate media composition was determined, and HLO:immune cell co- culture media composition and co-cultured compositions were established. Various compositions of cell culture media were evaluated for their ability to support the viability and function of liver as well as immune cells, independently as well as in combination. Versions of HLO and PBMC media were tested, along with mixtures thereof. Of the compositions tested, a 50 / 50 mixture of a comprising hepatocyte basal medium (HBM) comprising transferrin, ascorbic acid, insulin, and bovine serum albumin (BSA), and a second culture media comprising X-VIVO15 or RPMI, without immunomodulators, was found to best support the HLO:immune cell co-culture system, though other compositions had some success as well, as described herein.

[0192] Embodiments of the disclosure can include media compositions for culturing HLOs, immune cells, and combinations thereof. Embodiments of the disclosure can also include compositions of co-cultured HLOs and immune cells. In some embodiments, the compositions provided herein are ex vivo compositions. In some embodiments, also provided herein are compositions for performing any of the methods disclosed herein. In some embodiments, also provided herein are compositions produced according to processes provided in any of the methods disclosed herein. It is expressly contemplated that, in certain embodiments, any method or composition described herein can be implemented with respect to any other method or composition described herein and that different embodiments may be combined.

[0193] Co-culture media compositions in accordance with the disclosure can include comprising hepatocyte basal medium (HBM) comprising transferrin, ascorbic acid, insulin, and bovine serum albumin (BSA), and a second culture media comprising X-VIVO15 or RPMI. Insome embodiments, the first culture media is an HLO culture media. In some embodiments, the second culture media is an immune cell culture media. In some embodiments, the first culture media is an HLO culture media, and the second culture media is an immune cell culture media. In some embodiments, the second culture media can include, for example, PBMC media.

[0194] As described herein, the first culture media can include hepatocyte basal medium (HBM), including transferrin, ascorbic acid, insulin, and bovine serum albumin (BSA), and the second culture media can include X-VIVO15 or RPMI. In particular embodiments, the co-culture media composition can further include oncostatin M (OSM) and hepatocyte growth factor (HGF). Additional components which can be present in any combination in further embodiments can include Penicillin / Streptomycin (Pen / Strep), human serum, IL-2, IL-7, IL-15, and / or IL-21. In addition, in particular embodiments, the co-culture media composition does not include epidermal growth factor (EGF). In some embodiments, the co-culture media composition can includes Penicillin / Streptomycin (Pen / Strep), human serum, IL-2, IL-7, IL-15, and IL-21, and does not include epidermal growth factor (EGF). In some embodiments, the co-culture media composition includes IL-15 and IL-21 and does not include EGF. The first culture media and the second culture media can each, independently or when used in combination, be modified. For example, the first culture media and the second culture media can be modified with immunomodulators and / or other active or inactive components (e.g. transferrin, ascorbic acid, insulin, hydrocortisone, BSA, OSM, HGF, dexamethasone, GA-1000, hEGF, glutamine, and the like). In some embodiments, the second culture media can be modified with transferrin, ascorbic acid, insulin, hydrocortisone, and BSA, and without GA-1000 and epidermal growth factor (hEGF). In some embodiments, the first culture media is prepared without immunomodulators (e.g. hydrocortisone, hEGF, HGF, and / or dexamethasone, and the like). In some embodiments, the second culture media further includes glutamine.

[0195] In some embodiments, the co-culture media composition includes, by volume, about 10%-90%, 20%-80%, 30%-70%, 40%-60%, 50%-50%, or any intermediate or intervening ratio between these ratios, of the first culture media; and the co-culture media composition further includes about 10%-90%, 20%-80%, 30%-70%, 40%-60%, 50%-50%, or any intermediate or intervening ratio between these ratios, of the second culture media. In some embodiments, the co-culture media composition includes, by volume, about 30%-70%, or anyintermediate or intervening ratio between these ratios, of the first culture media; and the co- culture media composition further includes about 30%-70%, or any intermediate or intervening ratio between these ratios, of the second culture media. In some embodiments, the co-culture media composition includes, by volume, about 45%-55% of the first culture media; and the co- culture media composition further includes about 45%-55% or any intermediate or intervening ratio between these ratios, of the second culture media. In some embodiments, the co-culture media composition includes, by volume, about 50% of the first culture media; and the co-culture media composition further includes about 50% of the second culture media.

[0196] In various embodiments, the composition and / or co-culture media composition can include a mixture of the first culture media and the second culture media, including the first culture media and the second culture media in a ratio of about 1 / 99, 10 / 90, 20 / 80, 30 / 70, 40 / 60, 50 / 50, 60 / 40, 70 / 30, 80 / 20, 90 / 10, or 99 / 1, or any intermediate or intervening ratio between these ratios. In some embodiments, the co-culture media composition includes the first culture media and the second culture media in about a 40 / 60, 50 / 50, or 60 / 40 ratio, or any intermediate or intervening ratio between these ratios. In some embodiments, the co-culture media includes the first culture media and the second culture media in about a 50 / 50 ratio. In some embodiments, the co-culture media composition includes the first culture media and the second culture media in a ratio, by volume, of about 1 / 99, 10 / 90, 20 / 80, 30 / 70, 40 / 60, 50 / 50, 60 / 40, 70 / 30, 80 / 20, 90 / 10, or 99 / 1, or any intermediate or intervening ratio between these ratios, and further includes about 0.01-1000 ng / ml OSM, about 0.01-1000 ng / ml HGF, about 0.1- 1000 IU / ml IL-2, about 0.1-1000 IU / ml IL-7, about 0.1-1000 IU / ml IL-15, and / or about 0.1-1000 IU / ml IL-21, or any intermediate or intervening ratio between these ratios. In some embodiments, the co-culture media composition includes the first culture media and the second culture media in about a 40 / 60, 50 / 50, or 60 / 40 ratio, or any intermediate or intervening ratio between these ratios, and further includes about 0.1-50 ng / ml OSM, about 0.1-50 ng / ml HGF, about 1-100 IU / ml IL-2, about 1-100 IU / ml IL-7, about 1-100 IU / ml IL-15, and / or about 1-100 IU / ml IL-21, or any intermediate or intervening ratio between these ratios. In some embodiments, the co-culture media composition includes about 10-1000 IU / mL, 50-500 IU / mL, or 80-300 IU / mL IL-2, and / or about 0.01%-10%, 0.1%-5%, or 0.5%-2% Pen / Strep. In some embodiments, the co-culture media composition includes about 100-250 IU / mL IL-2, and / orabout 0.5-2% Pen / Strep. In some embodiments, the co-culture media composition includes about 45-55% of the first culture media, about 45-55% of the second culture media, and further includes about 1-40 ng / ml OSM, about 1-40 ng / ml HGF, about 1-50 IU / ml IL-2, about 1-50 IU / ml IL-7, about 1-50 IU / ml IL-15, and / or about 1-50 IU / ml IL-21; optionally wherein the co- culture media further includes about 0.5-2% Pen / Strep.

[0197] In some embodiments, provided herein are cell compositions in the form of a three-dimensional liver organoid, which has been co-cultured with immune cells. In some embodiments, provided herein are ex vivo compositions including a three-dimensional liver organoid, and additionally including one or more types of immune cells, such as, for example, T cells. In some embodiments, provided herein are ex vivo compositions including a three- dimensional liver organoid, and additionally including CD8 T lymphocytes.

[0198] In some embodiments, provided herein are compositions, such as cell compositions and / or liver organoids, that optionally further include culture media. In some embodiments, the compositions, such as compositions which include immune cell compositions and liver organoids, further include co-culture media.

[0199] Additional embodiments of the disclosure include compositions, including the co-culture media compositions as described above, and further including one or more HLO, and immune cells, wherein the HLO and the immune cells are co-cultured in the culture media, thereby providing a HLO:immune cell composition. Additional embodiments of the disclosure include compositions, including one or more HLO and immune cells, wherein the HLO and the immune cells are co-cultured in the culture media, thereby providing a HLO:immune cell composition, wherein the compositions optionally may or may not include culture media, such as the co-culture media composition described herein.

[0200] In some embodiments, the immune cells of compositions disclosed herein can include peripheral blood mononuclear cells (PBMCs). In some embodiments, the immune cells include CD8 T cells, CD4 T cells, NK cells, monocytes, macrophages, and / or dendritic cells.

[0201] In some embodiments, the HLO and / or immune cells are derived from pluripotent stem cells. In some embodiments, the pluripotent stem cells include embryonic stem cells or induced pluripotent stem cells. In some embodiments, the HLO and / or immune cells are derived from primary cells. In some embodiments, the immune cells include T cells and / ormonocyte-derived dendritic cells (mDCs). In some embodiments, the immune cells include CD4 and / or CD8 T cells. In some embodiments, the immune cells include CD8 T lymphocytes, including effector CD8 cells, proliferating effector CD8 cells, antigen-activated CD8 cells, cytotoxic CD8 cells, effector memory CD8 cells, and / or regulatory CD8 cells. In some embodiments, the immune cells are CD8 T cells.

[0202] In some embodiments of compositions disclosed herein, the one or more HLO and the immune cells can be derived from a single subject. In some embodiments, the one or more HLO and the immune cells can be derived from different subjects. . In some embodiments, the HLO and / or immune cells are derived from a universal donor and / or from hypoimmune stem cells.

[0203] In some embodiments of compositions disclosed herein, the immune cells have been primed with one or more exogenous agent prior to co-culturing with the HLO. In some embodiments, the HLO has been pre-treated with one or more exogenous agent prior to co- culturing with the immune cells.

[0204] In some embodiments of compositions disclosed herein, the immune cells and HLOs are co-cultured in a ratio of about 1:1, 5:1, 10:1, 50:1, 100:1, 200:1, 300:1, 400:1, 500:1, 600:1, 700:1, 800:1, 900:1, 1000:1, 1500:1, 2000:1, 5000:1, 10,000:1, or greater, or any value between these ratios, immune cells to HLOs; optionally about 50-5000:1 immune cells to HLOs. In some embodiments, the immune cells and HLOs are co-cultured in a ratio of about 1:10, 1:5, 1:4,1:3, 1:2, 1:1, 2:1, 3:1, 4:1, 5:1, 10:1, 20:1, 30:1, 40:1, 50:1, 100:1, or any value between these ratios, immune cells to liver cells; optionally about 1-50:1 immune cells to liver cells.

[0205] In some embodiments of compositions disclosed herein, the HLOs and immune cells have been co-cultured in the culture media for a time period selected from about 12 hours to about 10 days, or longer. In some embodiments, the HLOs and immune cells have been co-cultured in the culture media for about 3 days, + / - 1 day, to about 7 days, + / - 1 day.

[0206] In some embodiments of compositions disclosed herein, the composition is co-cultured via a droplet, multi-well plate, microcavity array culture platform, and / or organ-on- chip device. One skilled in the art will appreciate that various types of plates, platforms, devices, etc., can be used in accordance with the present disclosure. In some embodiments, the composition and / or culture platform do not include a basement membrane matrix.

[0207] Such microcavity array plates contemplated in accordance with various embodiments of the disclosure include Gri3D® plates, which are specialized microstructured culture plates designed to support the formation, growth, and controlled differentiation of 3D cellular aggregates, such as spheroids and organoids. The distinguishing feature of these plates is their patterned, microcavity-based surface. The plate surface is composed of an array of uniform, microwell-like cavities that are precisely defined in geometry, size, and spacing. The cavities typically have a rounded or hemispherical bottom, which promotes consistent aggregate formation by minimizing cell adherence to flat surfaces and encouraging cell–cell interactions within each microwell.

[0208] These plates can be fabricated from biocompatible hydrogel materials. The non-adhesive or low-adhesive nature of the microwell walls prevents unwanted cell attachment to the substrate, supporting the reproducible formation of uniform spheroids or organoids across the entire plate. The open cavity design also facilitates easy diffusion of nutrients, gases, and soluble factors, supporting prolonged culture and maturation of complex 3D structures. Gri3D® plates are compatible with high-content imaging and automated liquid handling, making them suitable for scalable and reproducible 3D cell culture applications.

[0209] Other exemplary commercial or custom plate formats can serve similar functions for the generation and maintenance of uniform spheroids or organoids, including: AggreWell™ Plates (STEMCELL Technologies), which contain microwells with conical or rounded geometry designed to enable rapid and uniform spheroid or aggregate formation; Elplasia® Plates (Corning), which are microcavity plates featuring arrays of ultra-low attachment microwells that promote consistent spheroid formation; ULA (Ultra-Low Attachment) Plates (Corning, Thermo Fisher Scientific), which are flat-bottom or round-bottom plates with chemically modified non-adhesive surfaces that promote spontaneous aggregation and spheroid formation; micro-patterned hydrogel plates (custom or commercial), which are plates where hydrogel substrates are patterned with microwells or microstructures to control 3D culture geometry; microfluidic culture devices, which are chips or plates with engineered microchambers or microchannels for dynamic culture and analysis of 3D cellular models; hanging drop plates (InSphero, Greiner Bio-One), which are plates that use gravity-assisted droplet formation to create hanging drops, allowing cells to aggregate into spheroids.

[0210] One skilled in the art will appreciate that various times of droplet or microcavity array culture platform can be used in accordance with various embodiments of the disclosure. These include, for example, Gri3D® plates; AggreWell™ plates; Elplasia® plates; ultra-low attachment (ULA), or ultra-low adhesion, plates; micro-patterned hydrogel plates; SmartSphero plates; Acura plates; Sphericalplates 5D; microfluidic culture devices; hanging drop plates; and the like. One skilled in the art can select an appropriate platform in order to achieve the desired outcome. Certain platforms, such as Gri3D® plates, lend themselves to automation more easily than others.

[0211] In some embodiments of compositions disclosed herein, the HLOs and the immune cells self-assemble. In some embodiments, the HLOs and the immune cells self- assemble into a three-dimensional form. In some embodiments, the immune cells spontaneously migrate toward the HLO. In some embodiments, the immune cells infiltrate the HLO.

[0212] In some embodiments of compositions disclosed herein, the HLO includes epithelial cells and mesenchymal cells. In some embodiments, the epithelial cells include hepatocytes, and the mesenchymal cells include hepatic stellate cells. In some embodiments, the HLO includes one or more additional cell type selected from hepatoblasts, cholangiocytes, endothelial cells, Kupffer cells, and / or stellate cells. In some embodiments, the HLO includes a luminal structure. In some embodiments, the luminal structure includes internalized microvilli. In some embodiments, the HLO includes a structure with a single lumen. In some embodiments, the HLO is an artificial liver organoid, and / or is generated in vitro. In some embodiments, the HLO is three-dimensional. In some embodiments, the HLO is a mature liver organoid.

[0213] Methods for preparing the co-culture media composition and composition are described herein, including in vitro methods for co-culturing one or more human liver organoid (HLO) with immune cells, by differentiating and / or culturing the one or more HLO in a co- culture media composition as described herein for a first period of time; suspending the immune cells in a co-culture media composition as described herein for a second period of time; and co- culturing the one or more HLO with the immune cells in a co-culture media composition as described herein for a third period of time, to provide an HLO:immune cell composition. The HLO and / or immune cells can be derived from pluripotent stem cells; such as embryonic stemcells or induced pluripotent stem cells. The HLO and / or immune cells can also be derived from primary cells.

[0214] In various embodiments of the methods, the immune cells can include peripheral blood mononuclear cells (PBMCs). In some embodiments, the immune cells can include CD8 T cells, CD4 T cells, NK cells, monocytes, macrophages, and / or dendritic cells. In various embodiments, the immune cells include T cells and / or monocyte-derived dendritic cells (mDCs). In various embodiments, the T cells include CD8 T cells. In various embodiments, the T cells include CD8 T lymphocytes, including effector CD8 cells, proliferating effector CD8 cells, antigen-activated CD8 cells, cytotoxic CD8 cells, effector memory CD8 cells, and / or regulatory CD8 cells.

[0215] In some embodiments of the methods, the one or more HLO and the immune cells can be derived from a single subject, i.e. the composition is autologous. In some embodiments, the one or more HLO and the immune cells can be derived from different subjects, i.e. the composition is allogenic. In some embodiments, the HLO and / or immune cells can be derived from a universal donor and / or from hypoimmune stem cells.

[0216] In some embodiments of the methods, the HLOs and immune cells have been co-cultured in the culture media for a time period selected from about 12 hours to about 10 days, or longer. In some embodiments, the HLOs and immune cells have been co-cultured in the culture media for about 3 days, + / - 1 day, to about 7 days, + / - 1 day.

[0217] In some embodiments of the methods, the one or more HLO is co-cultured with the immune cells in a droplet or microcavity array culture platform. In some embodiments, the composition and / or culture platform do not include a basement membrane matrix.

[0218] One skilled in the art will appreciate that various times of droplet or microcavity array culture platform can be used in accordance with various embodiments of the disclosure. These include, for example, Gri3D® plates; AggreWell™ plates; Elplasia® plates; ultra-low attachment (ULA), or ultra-low adhesion, plates; micro-patterned hydrogel plates; SmartSphero plates; Acura plates; Sphericalplates 5D; microfluidic culture devices; hanging drop plates; and the like. One skilled in the art can select an appropriate platform in order to achieve the desired outcome. Certain platforms, such as Gri3D® plates, lend themselves to automation more easily than others.

[0219] In some embodiments of the methods, the HLOs and the immune cells self- assemble into a three-dimensional form. In some embodiments, the immune cells spontaneously migrate toward the HLO. In some embodiments, the immune cells infiltrate the HLO.

[0220] In some embodiments of the methods, the first period of time is between about 12 hours to about 10 days, or longer; and / or the second period of time is between about 0 days to about 10 days, or longer; and / or the third period of time is between about 12 hours to about 10 days, or longer. In some embodiments, the immune cells and HLOs are co-cultured in a ratio of about 1:1, 5:1, 10:1, 50:1, 100:1, 200:1, 300:1, 400:1, 500:1, 600:1, 700:1, 800:1, 900:1, 1000:1, 1500:1, 2000:1, 5000:1, 10,000:1, or greater, or any value between these ratios, immune cells to HLOs; optionally about 50-5000:1 immune cells to HLOs. In some embodiments, the immune cells and HLOs are co-cultured in a ratio of about 1:10, 1:5, 1:4,1:3, 1:2, 1:1, 2:1, 3:1, 4:1, 5:1, 10:1, 20:1, 30:1, 40:1, 50:1, 100:1, or any value between these ratios, immune cells to liver cells; optionally about 1-50:1 immune cells to liver cells. In some embodiments, posterior foregut cells for forming the HLOs are seeded at a density of greater than about 1×104cells / well, greater than about 0.5×105cells / well, greater than about 1×105cells / well, greater than about 2×105cells / well, greater than about 3×105cells / well, greater than about 4×105cells / well, greater than about 5×105cells / well, or higher. In some embodiments, the HLOs for co-culturing are present in a well density of about 1-500 organoids per well; optionally about 5-200 organoids per well. In some embodiments, the HLOs for co-culturing are in a microcavity array culture platform in a well density of about 5-200 organoids per well; optionally about 30-100 organoids per well. In some embodiments, the HLOs for co-culturing are in a droplet culture platform in a well density of about 5-200 organoids per well; optionally about 10-70 organoids per well.

[0221] In some embodiments of the methods, the co-culture media composition includes a first culture media comprising hepatocyte basal medium (HBM) comprising transferrin, ascorbic acid, insulin, and bovine serum albumin (BSA), and a second culture media comprising X-VIVO15 or RPMI, and optionally further includes further includes Penicillin / Streptomycin (Pen / Strep), human serum, IL-2, IL-7, IL-15, and / or IL-21. In some embodiments of the methods, the co-culture media composition includes a first culture media comprising hepatocyte basal medium (HBM) comprising transferrin, ascorbic acid, insulin, andbovine serum albumin (BSA), and a second culture media comprising X-VIVO15 or RPMI, and further includes Penicillin / Streptomycin (Pen / Strep), human serum, IL-2, IL-7, IL-15, and IL-21.

[0222] In some embodiments of the methods, the HLO includes epithelial cells and mesenchymal cells. In some embodiments, the epithelial cells can include hepatocytes, and the mesenchymal cells can include hepatic stellate cells. In some embodiments, the HLO can include one or more additional cell type selected from hepatoblasts, cholangiocytes, endothelial cells, Kupffer cells, stellate cells. In some embodiments, the HLO includes a luminal structure. In some embodiments, the luminal structure includes internalized microvilli. In some embodiments, the HLO includes a structure with a single lumen. In some embodiments, the HLO is an artificial liver organoid and / or is generated in vitro. In some embodiments, the HLO is three-dimensional. In some embodiments, the HLO is a mature liver organoid.

[0223] In some embodiments, compositions provided herein are in vitro compositions, created outside of a multicellular living organism. In some embodiments, compositions provided herein may be introduced into a multicellular living organism. In some embodiments, compositions provided herein comprise exogenously provided components, reagents, and / or conditions. In some embodiments, compositions provided herein comprise exogenously provided components, reagents, and / or conditions that mimic in vivo characteristics desirable for inducing specific cellular differentiation and / or organoid organization.

[0224] In some embodiments, provided herein are compositions comprising a tissue culture surface that is coated with a basement membrane matrix or component thereof. In some embodiments, a basement membrane matrix or component thereof does not comprise non-human animal components. In some embodiments, a basement membrane matrix or component thereof does not comprise non-human animal components such that the basement membrane matrix or component thereof is xenogeneic to humans. In some embodiments, a basement membrane matrix or component thereof is not isolated from murine Engelbreth-Holm-Swarm (EHS) sarcoma cells, is not Matrigel®, is not Cultrex®, and / or is not Geltrex®. In some embodiments, a basement membrane matrix or component thereof comprises human laminin, collagen IV, entactin, perlecan, fibrin, and / or hydrogel.

[0225] In some embodiments, the tissue culture surface includes a droplet or microcavity array culture platform. In some embodiments, provided herein are compositionscomprising a tissue culture surface, such as a droplet or microcavity array culture platform, that is not coated with a basement membrane matrix or component thereof.

[0226] One skilled in the art will appreciate that various times of droplet or microcavity array culture platform can be used in accordance with various embodiments of the disclosure. These include, for example, Gri3D® plates; AggreWell™ plates; Elplasia® plates; ultra-low attachment (ULA), or ultra-low adhesion, plates; micro-patterned hydrogel plates; SmartSphero plates; Acura plates; Sphericalplates 5D; microfluidic culture devices; hanging drop plates; and the like. One skilled in the art can select an appropriate platform in order to achieve the desired outcome. Certain platforms, such as Gri3D® plates, lend themselves to automation more easily than others.

[0227] In some embodiments, provided herein are compositions that include an exogenous TGF-b pathway inhibitor. In some embodiments, an exogenous TGF-b pathway inhibitor comprises, consists essentially of, or consists of A83-01, RepSox, LY365947, and / or SB431542. In some embodiments, an exogenous TGF-b pathway inhibitor comprises, consists essentially of, or consists of TGF-b pathway inhibitor A83-01. In some embodiments, a composition comprises a TGF-b pathway inhibitor at a concentration of, or of about, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000 nM, or any concentration within a range defined by any two of the aforementioned concentrations. In some embodiments, a composition comprises a TGF-b pathway inhibitor at a concentration of, or of about, 500 nM.

[0228] In some embodiments, provided herein are compositions that include an exogenous FGF pathway activator. In some embodiments, a composition comprises an exogenous FGF pathway activator that comprises, consists essentially of, or consists of FGF1, FGF2, FGF3, FGF4, FGF4, FGF5, FGF6, FGF7, FGF8, FGF8, FGF9, FGF10, FGF11, FGF12, FGF13, FGF14, FGF15, FGF16, FGF17, FGF18, FGF19, FGF20, FGF21, FGF22, and / or FGF23. In some embodiments, an exogenous FGF pathway activator comprises, consists essentially of, or consists of FGF2. In some embodiments, a composition comprises a FGF pathway activator at a concentration of, or of about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 ng / mL, or any concentration within a range defined by any two of the aforementioned concentrations. In some embodiments, a composition comprises a FGF pathway activator at a concentration of, or of about 5 ng / mL.

[0229] In some embodiments, provided herein are compositions that include an exogenous Wnt pathway activator. In some embodiments, a composition comprises an exogenous Wnt pathway activator that comprises, consists essentially of, or consists of Wnt1, Wnt2, Wnt2b, Wnt3, Wnt3a, Wnt4, Wnt5a, Wnt5b, Wnt6, Wnt7a, Wnt7b, Wnt8a, Wnt8b, Wnt9a, Wnt9b, Wnt10a, Wnt10b, Wnt11, Wnt16, BML 284, IQ-1, WAY 262611, CHIR99021, CHIR 98014, AZD2858, BIO, AR-A014418, SB 216763, SB 415286, aloisine, indirubin, alsterpaullone, kenpaullone, lithium cHLOride, TDZD 8, and / or TWS119. In some embodiments, a composition comprises an exogenous Wnt pathway activator that comprises, consists essentially of, or consists of CHIR99021. In some embodiments, a composition comprises a Wnt pathway activator at a concentration of, or of about, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, or 8 µM, or any concentration within a range defined by any two of the aforementioned concentrations. In some embodiments, In some embodiments, a composition comprises a Wnt pathway activator at a concentration of, or of about, 3 µM.

[0230] In some embodiments, provided herein are compositions that include an exogenous VEGF pathway activator. In some embodiments, a composition comprises an exogenous VEGF pathway activator that comprises, consists essentially of, or consists of VEGF and / or GS4012. In some embodiments, a composition comprises an exogenous VEGF pathway activator that comprises, consists essentially of, or consists of VEGF. In some embodiments, a composition comprises a VEGF pathway activator at a concentration of, or of about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 ng / mL, or any concentration within a range defined by any two of the aforementioned concentrations. In some embodiments, a composition comprises a VEGF pathway activator at a concentration of, or of about 10 ng / mL.

[0231] In some embodiments, provided herein are compositions that include an exogenous EGF. In some embodiments, provided herein are compositions that do not include an exogenous EGF. In some embodiments, provided herein are compositions comprising EGF at a concentration of, or of about, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 ng / mL, or any concentration within a range defined by any two of the aforementioned concentrations. In some embodiments, provided herein are compositions comprising EGF at a concentration of, or of about, 20 ng / mL.

[0232] In some embodiments, provided herein are compositions that include exogenous and / or transgenically produced ascorbic acid. In some embodiments, provided herein are compositions that do not include exogenous and / or transgenically produced ascorbic acid. In some embodiments, provided herein are compositions comprising ascorbic acid at a concentration of, or of about, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 µg / mL or any concentration within a range defined by any two of the aforementioned concentrations. In some embodiments, provided herein are compositions comprising ascorbic acid at a concentration of, or of about, 50 µg / mL.

[0233] In some embodiments, provided herein are compositions that include a ROCK inhibitor. In some embodiments, provided herein are compositions that do not include a ROCK inhibitor. In some embodiments, a ROCK inhibitor comprises, consists essentially of, or consists of Y-27632. In some embodiments, provided herein are compositions comprising a ROCK inhibitor at a concentration of, or of about, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 µM, or any concentration within a range defined by any two of the aforementioned concentrations. In some embodiments, provided herein are compositions comprising a ROCK inhibitor at a concentration of, or of about, 10 µM.

[0234] In some embodiments, provided herein are compositions comprising liver organoids that have and / or that are being differentiated from stem cells. In some embodiments, provided herein are compositions comprising liver organoids that have and / or that are being differentiated from induced pluripotent stem cells. In some embodiments, provided herein are compositions comprising liver organoids comprising cells that have been passaged 1 time, 2 times, or 3 times. In some embodiments, provided herein are compositions comprising liver organoids comprising cells that have been passaged less than 4 times.

[0235] In some embodiments, provided herein are compositions comprising A83-01, FGF2, CHIR99021, VEGF, and / or Y-27632, optionally further comprising iPSCs, PSCs, and / or posterior foregut cells and / or posterior foregut endoderm cells.

[0236] In some embodiments, provided herein are compositions comprising: a) posterior foregut cells and / or posterior foregut endoderm cells, liver organoids and / or mature liver organoids, and b) a medium, wherein the medium optionally comprises hepatocyte culture medium and is optionally supplemented with a cMET tyrosine kinase receptor agonist, an IL-6family cytokine, and a corticosteroid, and wherein the composition optionally additionally comprises c) a retinoic acid pathway activator. In some embodiments, compositions provided herein comprise a cMET tyrosine kinase receptor agonist. In some embodiments, compositions provided herein comprise a cMET tyrosine kinase receptor agonist that comprises, consists essentially of, or consists of hepatocyte growth factor (HGF), PG-001, fosgonimeton, terevalefim, recombinant InlB321 protein, and / or an agonist c-Met antibody (e.g., LMH85).

[0237] In some embodiments, provided herein are compositions comprising an IL-6 family cytokine. In some embodiments, an IL-6 family cytokine comprises, consists essentially of, or consists of IL-6, Oncostatin M (OSM), leukemia inhibitory factor (LIF), cardiotrophin-1, ciliary neurotrophic factor (CTNF), and / or cardiotrophin-like cytokine (CLC).

[0238] In some embodiments, provided herein are compositions comprising a corticosteroid. In some embodiments, a corticosteroid comprises, consists essentially of, or consists of dexamethasone, beclometasone, betamethasone, fluocortolone, halometasone, and / or mometasone.

[0239] In some embodiments, provided herein are compositions comprising a hepatocyte culture media supplemented with HGF, OSM, and / or dexamethasone. In some embodiments, provided herein are compositions comprising a hepatocyte culture media supplemented with dexamethasone. In some embodiments, provided herein are compositions comprising a hepatocyte culture media supplemented with HGF. In some embodiments, provided herein are compositions comprising a hepatocyte culture media supplemented with OSM.

[0240] In some embodiments, provided herein are compositions comprising a retinoic acid pathway activator. In some embodiments, a retinoic acid pathway activator comprises, consists essentially of, or consists of retinoic acid, all-trans retinoic acid, 9-cis retinoic acid, CD437, EC23, BS 493, TTNPB, and / or AM580. In some embodiments, a retinoic acid pathway activator comprises, consists essentially of, or consists of retinoic acid. In some embodiments, compositions comprise a retinoic acid pathway activator at a concentration of, or of about, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, or 3.0 µM, or any concentration within a range defined by any two of the aforementioned concentrations. In some embodiments, compositions comprise a retinoic acid pathway activator at a concentration of, or of about, 2.0 µM.

[0241] In some embodiments, compositions comprise HGF. In some embodiments, compositions comprise HGF at a concentration of, or of about, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 ng / mL, or any concentration within a range defined by any two of the aforementioned concentrations. In some embodiments, compositions comprise HGF at a concentration of, or of about 10 ng / mL.

[0242] In some embodiments, compositions comprise OSM. In some embodiments, compositions comprise OSM at a concentration of, or of about, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 ng / mL, or any concentration within a range defined by any two of the aforementioned concentrations. In some embodiments, compositions comprise OSM at a concentration of, or of about 20 ng / mL.

[0243] In some embodiments, compositions comprise dexamethasone. In some embodiments, compositions comprise dexamethasone at concentration of, or of about, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or 200 nM, or any concentration within a range defined by any two of the aforementioned concentrations. In some embodiments, compositions comprise dexamethasone at a concentration of, or of about 100 nM.

[0244] In some embodiments, provided herein are compositions comprising mature liver organoids. In some embodiments, provided herein are compositions comprising mature liver organoids that exhibit luminal projections that resemble bile canaliculi, and / or a structure having a single lumen and generally a spherical shape. In some embodiments, provided herein are compositions comprising mature liver organoids that were produced through contact with a exposure to exogenous bilirubin.

[0245] Also provided herein, in some embodiments, are compositions comprising posterior foregut cells and / or posterior foregut endoderm cells, liver organoids and / or mature liver organoids that have been engineered to comprise a functional L-gulonolactone oxidase (GULO) protein and / or a gene or mRNA, or both, that encodes for the functional GULO protein, wherein the posterior foregut cells and / or posterior foregut endoderm cells, liver organoids and / or mature liver organoids are able to synthesize ascorbate. In some embodiments, provided herein are compositions comprising posterior foregut cells and / or posterior foregut endoderm cells, liver organoids and / or mature liver organoids engineered to express functional GULO protein, wherein the functional GULO protein is murine GULO (mGULO). In someembodiments, a gene that encodes for a functional GULO protein is conditionally expressed. In some embodiments, a gene that encodes for a functional GULO protein is constitutively expressed. In some embodiments, a gene that encodes for a functional GULO protein is conditionally expressed using a tetracycline inducible system.

[0246] In some embodiments, provided herein are compositions comprising posterior foregut cells and / or posterior foregut endoderm cells, liver organoids and / or mature liver organoids that are engineered to comprise a gene that encodes for a functional GULO protein using CRISPR mediated knock-in. In some embodiments, provided herein are compositions comprising posterior foregut cells and / or posterior foregut endoderm cells, liver organoids and / or mature liver organoids comprising a functional GULO encoding gene or mRNA, or both, that encodes for a functional GULO protein, wherein the functional gene was introduced to the posterior foregut cells and / or posterior foregut endoderm cells, liver organoids, mature liver organoids, and / or precursor cells by transfection. In some embodiments, provided herein are compositions comprising posterior foregut cells and / or posterior foregut endoderm cells, liver organoids and / or mature liver organoids that are engineered to comprise a gene that encodes for a functional GULO protein using adenovirus mediated gene transfection. In some embodiments, provided herein are compositions comprising posterior foregut cells and / or posterior foregut endoderm cells, liver organoids and / or mature liver organoids that are engineered to comprise a gene that encodes for a functional GULO protein using adeno-associated virus mediated gene transfection.

[0247] In some embodiments, compositions provided herein comprise liver organoids and / or mature liver organoids comprising a functional GULO protein, wherein said liver organoids and / or mature liver organoids express increased levels of NRF2 relative to liver organoids and / or mature liver organoids that do not comprise a functional GULO protein. In some embodiments, compositions provided herein comprise liver organoids and / or mature liver organoids comprising a functional GULO protein, wherein the liver organoids and / or mature liver organoids express reduced levels of IL1B, IL6, or TNFa, or any combination thereof, relative to liver organoids and / or mature liver organoids that do not comprise a functional GULO protein. In some embodiments, liver organoids and / or mature liver organoids comprising a functional GULO protein exhibit reduced caspase-3 activity relative to liver organoids and / ormature liver organoids that do not comprise a functional GULO protein. In some embodiments, liver organoids and / or mature liver organoids comprising a functional GULO protein express increased levels of ALB relative to liver organoids and / or mature liver organoids that do not comprise the functional GULO protein. In some embodiments, liver organoids and / or mature liver organoids comprising a functional GULO protein resemble periportal liver tissue and / or express periportal liver markers. In some embodiments, periportal liver markers comprise or consist of FAH, ALB, PAH, CPS1, HGD, or any combination thereof. In some embodiments, liver organoids and / or mature liver organoids comprising a functional GULO protein exhibit increased CYP3A4 and / or CYP1A2 protein levels and / or enzymatic activity relative to liver organoids and / or mature liver organoids that do not comprise a functional GULO protein. In some embodiments, liver organoids and / or mature liver organoids comprising a functional GULO protein exhibit increased bilirubin conjugation activity relative to liver organoids and / or mature liver organoids that do not comprise a functional GULO protein. In some embodiments, liver organoids and / or mature liver organoids comprising a functional GULO protein exhibit increased viability in culture relative to liver organoids and / or mature liver organoids that do not comprise a functional GULO protein. In some embodiments, liver organoids and / or mature liver organoids have been differentiated from pluripotent stem cells comprising a functional GULO protein and / or a gene or mRNA, or both, that encodes for the functional GULO protein, whereby the pluripotent stem cells are able to synthesize ascorbate. Immune Cell Priming and Compositions and Uses Thereof

[0248] Various types of immune cells can be co-cultured with HLOs, as described herein. The immune cells of compositions disclosed herein can include, for example, peripheral blood mononuclear cells (PBMCs). The immune cells of compositions disclosed herein can also, or alternatively, include, for example, one or more specific cell type, such as, CD8 T cells, CD4 T cells, NK cells, monocytes, macrophages, and / or dendritic cells.

[0249] The immune cells can be derived from pluripotent stem cells, such as embryonic stem cells or induced pluripotent stem cells. The immune cells can also, or alternatively, be derived from primary cells. In various embodiments, the immune cells can include T cells, such as CD4 and / or CD8 T cells, and / or monocyte-derived dendritic cells (mDCs). In some embodiments, the immune cells can include CD8 T lymphocytes, includingeffector CD8 cells, proliferating effector CD8 cells, antigen-activated CD8 cells, cytotoxic CD8 cells, effector memory CD8 cells, and / or regulatory CD8 cells. In accordance with various embodiments, the immune cells are CD8 T cells.

[0250] Exemplary methods of priming immune cells, and exemplary uses of the primed immune cells are also disclosed herein. For example, primed immune cells can be used in a reactivity assay. In addition, co-cultures of HLOs with primed immune cells can be used in immune-mediated damage assays. One skilled in the art will appreciate various assays that can be performed using primed immune cells, which are contemplated in accordance with the disclosure. Immune cell priming

[0251] An exemplary protocol for immune cell, e.g. CD8 T cell, priming was also determined, using culture conditions required to observe immune-driven toxicity to the liver, based on autoimmunity as well as drug-driven toxicity. Immune cell priming refers to the initial antigen encounter of a naïve T cell with its cognate antigen and is required for screening of new drugs. Priming and repetitive stimulation are commonly used to make conclusions about drug- dependent CD8 T cell responses.

[0252] In some embodiments, the immune cells are primed with one or more exogenous agent prior to co-culturing with the one or more HLO. The HLO can additionally be pre-treated with one or more exogenous agent. In some embodiments, the methods further include analyzing the co-culture to assess liver cell viability and / or function, and / or to assess immune cell maturation, proliferation, and / or activation, following treatment of the immune cells and / or HLO with the one or more exogenous agent. In some embodiments of the methods, the immune cells primed with one or more exogenous agent can include CD8 T cells.

[0253] In some embodiments, priming the immune cells with one or more exogenous agent prior to co-culturing includes: differentiating monocyte-derived dendritic cells (mDCs) and / or autologous antigen presenting cells (APCs), in the presence of the one or more exogenous agent, to provide pre-stimulated mDCs and / or pre-stimulated APCs; culturing naïve immune cells with the pre-stimulated mDCs and / or pre-stimulated APCs; and stimulating the naïve immune cells and pre-stimulated mDCs and / or pre-stimulated APCs with the one or more exogenous agent, to provide stimulated immune cells.

[0254] In some embodiments of the methods, the naïve immune cells include naïve CD8 T cells. In some embodiments, the mDCs and / or naïve immune cells are derived from peripheral blood mononuclear cells (PBMCs). In some embodiments, the APCs include a B cell lymphoblastoid line, and / or Kupffer cells; optionally wherein said APCs are primary or derived from hPSCs. Alternatively, the APCs may not necessarily need to be added externally, as they are already present at low percentage inside HLOs. In some embodiments, the mDCs and / or APCs are differentiated via EBV transformation.

[0255] In some embodiments of the methods, culturing naïve immune cells with the pre-stimulated mDCs and / or pre-stimulated APCs can be via an antigen presentation assay, wherein: sub-populations of the co-cultured DCs and CD8 T cells are re-stimulated with the first exogenous agent for one or more additional period of time, at one or more different concentrations; and / or sub-populations of the co-cultured DCs and CD8 T cells are stimulated with a control exogenous agent for one or more additional period of time, at the same or different concentrations.

[0256] In some embodiments, the methods can further include one, two, three, four, five, or more additional steps of re-stimulating the naïve immune cells and pre-stimulated mDCs and / or pre-stimulated APCs with the one or more exogenous agent. In some embodiments, the one or more exogenous agent is provided in different concentrations in two or more stimulation / re-stimulation steps. In some embodiments, the method further includes culturing the stimulated immune cells with a fresh population of pre-stimulated mDCs and / or pre-stimulated APCs. In some embodiments, the step of culturing naïve immune cells with the pre-stimulated mDCs and / or pre-stimulated APCs is in the presence of IL-21 and / or b-mercaptoethanol. In some embodiments, the stimulation and / or re-stimulation steps are in the presence of IL-7 and / or IL- 15.

[0257] In some embodiments, the methods can further include analyzing the co- culture to profile immune cells, and / or to assess viability following treatment with the one or more exogenous agent. In some embodiments, profiling immune cells includes assessing CD8 cell maturation, proliferation, and / or antigen-specific activation, and / or assessing viability includes detecting potential liver damage profile. In some embodiments, pre-treating the one or more HLO with one or more exogenous agent prior to co-culturing with the immune cellsincludes stimulating the one or more HLO with the one or more exogenous agent, to provide a stimulated HLO.

[0258] Additional embodiments of the disclosure include methods of priming immune cells, the methods including: differentiating monocyte-derived dendritic cells (mDCs) and / or autologous antigen presenting cells (APC) (e.g. a B cell lymphoblastoid line, and / or Kupffer cells; optionally wherein said APCs are primary or derived from hPSCs, or wherein said APCs are derived from the HLO) via EBV transformation, in the presence of the one or more exogenous agent, to provide pre-stimulated mDCs and / or pre-stimulated APCs; culturing naïve immune cells with the pre-stimulated mDCs and / or pre-stimulated APCs; and stimulating the naïve immune cells and pre-stimulated mDCs and / or pre-stimulated APCs with the one or more exogenous agent, to provide primed immune cells.

[0259] In some embodiments of the methods, the naïve immune cells include naïve CD8 T cells. In some embodiments, the mDCs and / or naïve immune cells are derived from peripheral blood mononuclear cells (PBMCs). In some embodiments, the APCs include a B cell lymphoblastoid line, and / or Kupffer cells; optionally wherein said APCs are primary or derived from hPSCs, or wherein said APCs are derived from the HLO. In some embodiments, the mDCs and / or APCs can be differentiated via EBV transformation.

[0260] In some embodiments of the methods, culturing naïve immune cells with the pre-stimulated mDCs and / or pre-stimulated APCs is via an antigen presentation assay, wherein: sub-populations of the co-cultured DCs and CD8 T cells are re-stimulated with the first exogenous agent for one or more additional period of time, at one or more different concentrations; and / or sub-populations of the co-cultured DCs and CD8 T cells are stimulated with a control exogenous agent for one or more additional period of time, at the same or different concentrations.

[0261] In some embodiments, the methods can further include one, two, three, four, five, or more additional steps of re-stimulating the naïve immune cells and pre-stimulated mDCs and / or pre-stimulated APCs with the one or more exogenous agent.

[0262] In some embodiments of the methods, the one or more exogenous agent is provided in different concentrations in two or more of the stimulation and re-stimulation steps.

[0263] In some embodiments, the methods further include culturing the stimulated immune cells with a fresh population of pre-stimulated mDCs and / or pre-stimulated APCs. In some embodiments, the step of culturing naïve immune cells with the pre-stimulated mDCs and / or pre-stimulated APCs is in the presence of GM-CSF, IFNγ, IL-4, IL-12, and / or IL-21. In some embodiments, the stimulation and / or re-stimulation steps are in the presence of IL-7 and / or IL-15.

[0264] In some embodiments, the methods further include analyzing the co-culture to profile immune cells, and / or to assess viability, following treatment with the one or more exogenous agent. In some embodiments, profiling immune cells includes assessing CD8 cell maturation, proliferation, and / or antigen-specific activation, and / or assessing viability includes detecting potential liver damage profile.

[0265] In some embodiments of the methods, the first exogenous agent can be a therapeutic or a therapeutic candidate. In some embodiments, the primed immune cell population is enriched with CD8 T cells which are reactive to the therapeutic or therapeutic candidate.

[0266] Additional embodiments of the disclosure include primed immune cell populations, prepared by the methods as described herein. In some embodiments, the compositions described herein include primed immune cells and / or pre-treated HLOs. Reactivity assay using primed immune cells

[0267] Antigen-specific priming of human naïve CD8 T cells and its role in immune- mediated ADR has heretofore been difficult to assess. Due the low initial frequency of the naïve specific CD8 T cell precursors, analysis of drug-mediated immune responses has been complicated by the requirement for repeated stimulations and prolonged culture time. This exemplary T cell priming and reactivity protocol (Fig. 6B) describes how to evaluate antigen- specific priming of CD8 T cells after a single specific stimulation. The assay provides reference conditions, which result in the expansion of antigen specific CD8 T cells from the naïve repertoire. This protocol is particularly relevant for drug development, allowing for the identification of underlying causes of conditions such as, for example, drug induced liver tissue injury (DILI), and the like. One skilled in the art will appreciate various other conditions which can be assayed using primed immune cells, in an HLO:immune cell co-culture media composition and composition as described herein.

[0268] An exemplary step-by-step protocol is shown in Fig. 8A, depicting a process used as described herein to generate CD8 T cells that recognize drug / drug-protein adducts which inflict specific damage to the autologous liver organoids (e.g. via adverse drug reaction (ADR)). In the first part of the procedure (shown in the top section of the flowchart of Fig. 8A), priming of naïve immune cells, e.g. CD8 T cells, is performed in the presence of drug-loaded antigen presenting dendritic cells (DC). The protocol can optionally include methods for the quantitative assessment of T cell maturation, proliferation, and activation at the end of the procedure. In the second part of the exemplary procedure, the HLO culture can optionally be established (shown in the bottom section of the flowchart of Fig. 8A), allowing for the creation of the co-culture of primed T cells:HLOs (as shown on the right-hand side of the flowchart of Fig. 8A). This co- culture system can be used, e.g., to test whether the obtained reactive T-cell populations from the first part of the protocol can inflict immune-mediated damage or kill the autologous HLO in the co-culture process.

[0269] This exemplary protocol employed PBMC monocyte-derived dendritic cells (mDCs). In the exemplary process described herein, mDCs were differentiated in the presence of low doses of IL-4 / GM-CSF and subsequentially underwent rapid maturation and activation induced with LPS / IFN-γ in the presence of the desired experimental drug. The mDCs were then used in co-culture with naïve CD8 T cells (priming) in the presence of IL-21, then IL-7 / IL-15. After initial priming, CD8 T cells were labeled with CFSE (1st time), and re-challenged with fresh mDCs. CD8 T cell priming efficacy was measured in a multi-color flow cytometry assay, determining maturation, proliferation, and activation capacity. HLO:immune cell co-culture and immune-mediated damage assay

[0270] CD8 T cells were labeled with CFSE (2nd time) and allowed to co-culture with the HLO for over 72 hours. An exemplary ratio for Gri3D® system co-culture was about 50k CD8 T cells per well with about 70 HLOs / single 96 well. Next, phenotypic screening and multivariate image information extraction were performed with ImageXpress Micro confocal and MetaXpress analysis systems, respectively (Molecular Devices). HLO masking, live-dead % of dead cells as based off 0.5% Triton X control (set to normalize for ~80-90% dead liver cells in HLO rate)), and morphological assessment were based on Hoechst (total liver cell counts; blue channel), DRAQ7 (dead liver cell counts; red channel), and morphology (white channel). HLOmarkers: CK18 (M65), albumin release and expression, and CYP3A4 expression were used to assess liver tissue damage and functionality respectively. CD8 T cell counts (SFSE; green channel) staining of the immune cells respectively can be used at the end of the co-culture process to allow for the precise measurement of immune cells infiltration. Additional immune cells markers: IFNg, TNFa, GrB (immune cells) can be used to assess immune cell functionality. A drug-induced “danger signal” can be assessed by chemokine (e.g. CXCL9) production, NKG2D ligand expression (e.g. ULBP1), and associated CD8 T cell HLO infiltration and activation correspondingly. T cells isolated from the blood of carriers and non-carriers of genetic risk factor for development of ADR (e.g., HLA-B∗57:01) can be compared in this assay, assessing the impact of patient’s genotype on CD8 T cells reactivity to drug (e.g., Flux) and efficiency of killing of autologous HLO. One skilled in the art will appreciate further assays that can be used in order to assess toxicity and / or determine a drug-induced “danger signal”.

[0271] Next, an autologous co-culture model of HLOs with PBMCs was established by comparing autologous (wherein the HLO and immune cells are derived from the blood of the same patient) and allogenic (isolated from the blood of a different patient from the one from which the HLOs were established) PBMCs. This allows for the evaluation of the physiological relevance of the immune responses observed in vitro. There were no major differences during 7 day of culture, based on a lack of apparent cell death. However, comparison of the cyto / chemokine profiles between autologous and allogenic co-cultures revealed a significant increase in the release of T cell effectors such as IFNg, Graz B or chemokines CXL9 / 10, which are well known to promote hepatic inflammation and recruitment of leukocytes to the liver parenchyma in chronic or acute liver injury, in allogeneic conditions.

[0272] A comparison was then performed between droplet (embedding in Matrigel) and Gri3D® (gel-free aggregation) cultures to evaluate direct organoid:immune cell interactions (not obstructed by the presence of gel). No major differences were observed between the two methods.

[0273] Given the complication of potential ADRs, such as flucloxacillin (Flux)- associated DILI, it was determined whether the HLO:immune cell co-culture system could be used as a model predictive system. To this end, the toxicity profile of flucloxacillin in the exemplary autologous HLO:immune cell co-culture system was evaluated to model immune-driven drug induced liver injury. Flux was found to exhibit direct toxicity to HLOs and immune cells at 10mM and above, whereas Flux-mediated effect in whole unprimed PBMCs was not detectable. Co-culture of HLO with unprimed PBMCs failed to model Flux-mediated drug induced liver injury in vitro.

[0274] The use of the HLO:immune cell co-culture system to identify danger signals was also evaluated. Flux was found to induce strong ULBP1, but not MICA / B or RAET1G expression. High concentrations of Flux did not induce IL-6 or TNFa expression nor affect albumin expression, indicating low or no liver cytotoxicity. However, Flux was found to induce increased expression of chemokines (e.g. CXCL9) and CYP3A4 in HLOs.

[0275] An HLO co-culture was then established with drug-primed CD8 T cells and T cell priming. An antigen presentation assay was performed using various concentrations of Flux and control peptide (pp65) in naïve CD8+ T cell or PBMC co-cultures with mDCs or autologous lymphoblastoid lines. Flux-loaded DC mediated priming of naïve CD8 T cells with 1 mM, but not 0.1 mM Flux induced significant CD8 cell maturation, proliferation and antigen-specific activation. Additional stimulation of Flux primed CD8 T cells did not further CD8 cell maturation, proliferation and antigen-specific activation, thus Flux-mediated disruption of antigen presentation (self vs non-self-recognition) to CD8 T cells, but not CD8 activation itself, was implicated in the development of DILI. This priming protocol was found to be effective in quantitatively assessing immune-mediated ADR to Flux in vitro.

[0276] An HLO co-culture with drug-primed CD8 T cells and proof of concept application with flucloxacillin was then studied. Naïve CD8 T cells obtained from carriers or HLA-B*57:01 are activated with flucloxacillin when dendritic cells present the drug antigen, as observed by increased proliferation, maturation and antigen-specific activation of T cells. Naive CD8 T cells obtained from a non-carrier donor exhibited only a slight increase in the overall maturation, but no increase in the proliferation or other activation markers, further supporting involvement of HLA-B*57:01 vs non-HLA-B*57:01 CD8 T cells in immune-mediated ADR to Flux. Increased cytotoxicity of Flux primed CD8 T cells toward autologous HLOs was observed, confirming the predictive capacity of autologous T cell:HLO co-culture in modelling immune- driven drug induced injury.

[0277] The ability to use an exemplary drug-primed T cell co-culture with HLOs in a microcavity array, e.g. Gri3D®, in modelling of immune-mediated drug induced liver injury was then validated across multiple donors. The T cell:HLO co-culture system was able to accurately predict and model potential adverse drug reactions leading to drug-induced liver injury, as evidenced by the activation of CD8 T cells followed by enhanced cytotoxicity of drug-primed T cells towards autologous HLO in carriers of HLA-B*57:01 but no toxicity in non-carriers or carriers which showed no reactivity to flucloxacillin. Human Liver Organoids

[0278] Human liver organoids (HLOs) can be derived from progenitor cells, such as, for example, patient-derived induced pluripotent stem cells (iPSCs), where the patient can be healthy or having a diseased condition, and are identical in genetic content to the respective patient. They express most liver markers that are expressed in the pre-natal stages of development. Furthermore, they are clonal and therefore reacts similarly to external stimuli and biochemical perturbations. These HLOs are highly scalable and tractable, allowing screening approaches to test a vast array of drugs and small molecules.

[0279] HLOs are easy to work with as model systems and have very low variation across batches. Large batches of HLOs can be generated within a couple of weeks. Leveraging these qualities, several drugs can be tested within a short span of time to identify pathways involved in liver diseases and disorders. In contrast, breeding model organisms such as mice and rats takes months of work and planning, and the chance of getting the desired genotype is relatively low. Furthermore, model organisms show high variations in responses to biochemical perturbations over generations. These rodents also run the risk of losing the desired genotype when bred over long periods of time, and also require complex training and procedures to model diseases and evaluate the efficacy of treatments. Compared to model organisms, genetic modifications are much easier in iPSC cell lines and they can be maintained easily over longer periods before differentiation into organoids.

[0280] The enzyme L-gulonolactone oxidase (GULO) catalyzes L-gulonolactone to produce L-xylo-hex-3-gulonolactone and hydrogen peroxide. The L- xylo-hex-3-gulonolactone then spontaneously converts to ascorbate (vitamin C). Accordingly, this enzyme is involved in the biosynthesis of vitamin C, which is an essential nutrient that is involved in many biologicalfunctions such as use as a cofactor for several important enzymes and as an antioxidant. Notably, humans, as well as other haplorrhine primates, certain species of bats, and Guinea pigs have evolved to harbor a non-functional GULO gene. Therefore, these organisms are unable to synthesize ascorbate and require vitamin C intake from diet or supplementation, where a deficiency of vitamin C can lead to scurvy. As applied to the disclosure herein, a “functional GULO protein” is a GULO protein that has L-gulonolactone catalytic activity to result in the production of ascorbate. Conversely, an “inactive” GULO protein or “non-functional” GULO protein is one that does not have the catalytic activity to produce ascorbate. Humans and cells that are derived from humans comprise a non-functional GULO protein and do not have the ability to synthesize ascorbate. However, as disclosed herein, human cells may be engineered to express a functional GULO protein to enable ascorbate synthesis ability. These functional GULO proteins may be expressed in human cells (or other cells that are unable to normally synthesize ascorbate) through conventional methods of cloning, such as genetically engineering cells to have genetic sequences that encode for a functional GULO protein.

[0281] Taking advantage of this, iPSC-derived organoids expressing a functional L- gulonolactone oxidase (GULO), such as murine GULO (mGULO), have been generated. When the iPSCs and organoids are human in origin, the expression of the functional L-gulonolactone allows for ascorbate synthesis, which is normally inactive in humans. These mGULO organoids exhibit increased efficiency in conjugating bilirubin and exhibited improved viability when treated with bilirubin. The production of ascorbate in mGULO organoids reduces oxidative stress in the organoids and drives expression of NRF2, which is a master regulator of cellular detoxification pathways and in turn promotes expression of UGT1A1, which catalyzes bilirubin conjugation. These mGULO organoids are otherwise genetically identical to the patients from which they are derived, and encompass the aspects of human bilirubin metabolism. Accordingly, these organoids can be used as model systems for elucidating the mechanistic development of liver-related diseases and disorders and developing therapeutic treatments thereto. Methods of Producing Liver Organoids

[0282] Methods of producing liver organoids have been explored previously in, for example, Ouchi et al. “Modeling Steatobepatitis in Humans with Pluripotent Stem Cell-Derived Organoids” Cell Metabolism (2019) 30(2):374~384; Shinozawa et al. “High-Fidelity Drug-Induced Liver Injury Screen Using Human Pluripotent Stem Cell Derived Organoids” Gastroenterology (2021) 160(3) 831-846; PCX Publications WO 2018 / 085615, WO 2018 / 191673, WO 2018 / 226267, WO 2019 / 126626, WO 2020 / 023245, WO 2020 / 069285, WO 2020 / 243613, WO 2021 / 030373, and WO 2021 / 262676, each of which is hereby expressly- incorporated by references in its entirety. Disclosure of liver organoid compositions and methods of making thereof are applicable to the human liver organoids (PILOs) described herein.

[0283] Embodiments of methods for producing liver organoids are provided herein. In some embodiments, the methods include a) contacting definitive endoderm cells (DE) with an FGF signaling pathway activator and a Wnt signaling pathway activator for a first period of tune; b) contacting the cells of step a) with the FGF signaling pathway activator, the Wnt signaling pathway activator, and a retinoic acid (RA) signaling pathway activator for a second period of time, thereby differentiating the DE to posterior foregut cells; and c) embedding the posterior foregut cells in a basement membrane matrix and culturing the posterior foregut spheroids for a third period of time to differentiate the posterior foregut cells to the liver organoid. Optionally, frozen posterior foregut cells can be used in accordance with various methods, rather than freshly generating posterior foregut cells each time, to render the process more scalable. In some embodiments, the DE has been derived from pluripotent stem cells. In some embodiments, the pluripotent stem cells are embryonic stem cells and / or induced pluripotent stem cells. In some embodiments, the first period of time is, is about, is at least, is at least about, is not more than, or is not more than about, 0.5, 1, 2, 3, or 4 days, or a range defined by any two of the preceding values, for example 0.5-4, 1-4, 0.5-2, or 3-4 days. In some embodiments, the second period of time is, is about, is at least, is at least about, is not more than, or is not more than about 0.5, 1, or 2 days. In some embodiments, the third period of time is, is about, is at least, is at least about, is not more than, or is not more than about, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, or 30 days, or a range defined by any two of the preceding values, for example 4-30, 10-30, 20-30, 4-17, 4-12, or 10-25 days. In some embodiments, the basement membrane matrix is Matrigel. In some embodiments, the liver organoid, DE, and / or pluripotent stem cells are derived from a patient.

[0284] In some embodiments of the methods of making liver organoids, the FGF signaling pathway activator is selected from the group consisting of FGF1, FGF2, FGF3, FGF4,FGF4, FGF 5, FGF6, FGF7, FGF8, FGF8, FGF9, FGF 10, FGF 11, FGF 12, FGF13, FGF 14, FGF 15, FGF 16, FGF 17, FGF 18, FGF 19, FGF20, FGF21 , FGF22, and FGF23. in some embodiments, the FGF signaling pathway activator is FGF4. In some embodiments, the FGF signaling pathway activator is contacted at a concentration that is, is about, is at least, is at least about, is not more than, or is not more than about, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, or 1000 ng / mL, or any concentration within a range defined by any two of the aforementioned concentrations, including 100-1000 ng / mL, 100-500 ng / mL, 500-1000 ng / mL, 250-750 ng / mL, or 400-600 ng / mL, In some embodiments, the FGF signaling pathway activator is contacted at a concentration of 500 ng / mL or about 500 ng / mL.

[0285] In some embodiments of the methods of making liver organoids, the Wnt signaling pathway activator is selected from the group consisting of Wnt1, Wnt2, Wnt2b, Wnt3, Wnt3a, Wnt4, Wnt5a, Wnt5b, Wnt6, Wnt7a, Wnt7b, Wnt8a, Wnt8b, Wnt9a, Wnt9b, Wnt10a, Wnt10b, Wnt11, Wntl6, BML 284, IQ-1, WAY 262611, CHIR99021, CHIR98014, AZD2858, BIO, AR-A014418, SB 216763, SB 415286, aloisine, indirubin, alsterpaullone, kenpaullone, lithium cHLOride, TDZD 8, and TWS119. In some embodiments, the Wnt signaling pathway activator is CHIR99021. In some embodiments, the Wnt signaling pathway activator is contacted at a concentration that is, is about, is at least, is at least about, is not more than, or is not more than about, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, or 3.5 mM, or any concentration within a range defined by any two of the aforementioned concentrations, including 0.5-3.5 mM, 0.5-2 mM, 2- 3.5 mM, 1-3 mM, or 1.5-2.5 mM. In some embodiments, the Wnt signaling pathway activator is contacted at a concentration of 2 mM or about 2 mM.

[0286] In some embodiments of the methods of making liver organoids, the RA signaling pathway activator is selected from the group consisting of retinoic acid, all-trans retinoic acid, 9-eis retinoic acid, CD437, EC23, BS 493, TTNPB, and AMS 80. In some embodiments, the RA signaling pathway activator is RA. In some embodiments, the RA signaling pathway activator is contacted at a concentration that is, is about, is at least, is at least about, is not more than, or is not more than about, 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.9, or 3 mM, or any concentration within a range defined by any two of the aforementioned concentrations, including 1-3 mM, 1-2 mM, 2-3 mM, or 1.5-2.5 mM.In some embodiments, the RA signaling pathway activator is contacted at a concentration of 2 mM or about 2 mM.

[0287] In some embodiments, one or more HLO used to produce the liver organoid can be engineered to express a functional GULO protein, which improves organoid viability and function as disclosed herein. In some embodiments, the liver organoid can include a functional GULO protein and / or a gene or mRNA, or both, that encodes for the functional GULO protein, whereby the liver organoid is able to synthesize ascorbate. In some embodiments, the functional GULO protein is murine GULO (mGULO). However, the functional GULO may alternatively be derived from any other animal species that includes a functional GULO protein. In some embodiments, the gene that encodes for the functional GULO protein is conditionally expressed. In some embodiments, the gene is conditionally expressed using a tetracycline inducible system or any other system for conditional expression generally known in the art. In some embodiments, the liver organoid can be engineered to include the gene that encodes for the functional GULO protein using CRISPR or any other method of genetic engineering generally known in the art. In some embodiments, the gene or mRNA, or both, that encodes for the functional GULO protein is introduced to the HLO by transfection. In some embodiments, the liver organoid includes the functional GULO protein expresses increased levels of NRF2 relative to a liver organoid that does not include the functional GULO protein. In some embodiments, the liver organoid including the functional GULO protein expresses reduced levels of IL1B, IL6, or TNFa, or any combination thereof, relative to a liver organoid that does not include the functional GULO protein, optionally when cultured in ascorbate-depleted medium. In some embodiments, the liver organoid including the functional GULO protein exhibits reduced caspase-3 activity relative to a liver organoid that does not include the functional GULO protein, optionally when cultured in ascorbate-depleted medium. In some embodiments, the liver organoid including the functional GULO protein expresses increased levels of ALB relative to a liver organoid that does not include the functional GULO protein. In some embodiments, the liver organoid including the functional GULO protein resembles periportal liver tissue and expresses periportal liver markers. In some embodiments, the periportal markers can include FAH, ALB, PAH, CPS1, HGD, or any combination thereof. In some embodiments, the liver organoid including the functional GULO protein exhibits increased CYP3A4 and CYP1A2 activity relative to a liver organoid that doesnot include the functional GULO protein. In some embodiments, the liver organoid including the functional GULO protein exhibits increased bilirubin conjugation activity relative to a liver organoid that does not include the functional GULO protein, in some embodiments, the liver organoid including the functional GULO protein exhibits increased viability in culture relative to a liver organoid that does not include the functional GULO protein.

[0288] In some embodiments, a HLO or co-culture of HLOs is contacted with a concentration of an exogenous agent in a hepatocyte culture medium, which can include, for example, hepatocyte basal medium (HBM). Representative compositions of these hepatocyte culture media (i.e. growth media that is designed for supporting hepatic tissues) are generally known in the art. In some embodiments, the hepatocyte culture medium includes transferrin, ascorbic acid, insulin, and bovine serum albumin (BSA). In some embodiments, the hepatocyte culture medium can additionally include hepatocyte growth factor and / or oncostatin M. In some embodiments, the hepatocyte culture medium can additionally include hepatocyte growth factor and oncostatin M. In some embodiments, the hepatocyte culture medium can additionally include dexamethasone.

[0289] In some embodiments, the liver organoid is human. In some embodiments, the liver organoid includes one or more HLO that has been differentiated from pluripotent stem cells. In some embodiments, the pluripotent stem cells are embryonic stem cells or induced pluripotent stem cells. In some embodiments, the liver organoid includes one or more HLO that has been differentiated from primary cells. In some embodiments, the pluripotent stem cells include a functional GULO protein and / or a gene or mRNA, or both, that encodes for the functional GULO protein, whereby the pluripotent stem cells are able to synthesize ascorbate.

[0290] Exemplary methods for producing liver organoids from pluripotent stem cells have been disclosed herein and are otherwise generally known in the art. In some embodiments, the HLOs co-cultured into a liver organoid have been made according to a method comprising: a) contacting definitive endoderm ceils (DE) with an FGF signaling pathway activator and a Wnt signaling pathway activator for a first period of time; b) contacting the cells of step a) with the FGF signaling pathway activator, the Wnt signaling pathway activator, and a retinoic acid (RA) signaling pathway activator for a second period of time, thereby differentiating the DE to posterior foregut cells; and c) embedding the posterior foregut cells in a basement membranematrix and culturing the posterior foregut spheroids for a third period of time to differentiate the posterior foregut cells to an HLO. Optionally, frozen posterior foregut cells can be used in accordance with various methods, rather than freshly generating posterior foregut cells each time, to render the process more scalable.

[0291] Also disclosed herein are the liver organoid-containing compositions provided through any of the methods described herein.

[0292] In some embodiments, provided herein are compositions comprising artificial liver organoids. In some embodiments, compositions provided herein include hepatocytes that have self-assembled into artificial liver organoids. In some embodiments, provided herein are artificial liver organoids including a structure that includes a single lumen. In some embodiments, provided herein are liver organoids including at least one distinctly observable (e.g., spatially, genetically, and / or phenotypically) immune cell population, such as a T cell population. In some embodiments, artificial liver organoids do not include hematopoietic tissue and / or acquired immune cells. In some embodiments, artificial liver organoids may develop and / or be colonized by hematopoietic tissue and / or acquired immune cells following introduction of the artificial liver organoid to a subject. Screening Assays Using Compositions

[0293] The compositions and co-culture media compositions, as described herein, can be used in various methods for screening a compound or composition. For example, the compound or composition to be screened can include the one or more exogenous agent used to prime the immune cells and / or pre-treat the HLO. In various embodiments, immune cells primed with the one or more compound to be screened can be co-cultured with one or more HLO in the co-culture media composition as described herein. The compound or composition to be screened can then be added to the co-culture of one or more HLO and primed immune cells. The HLO and immune cells can then be co-cultured with the compound or composition, after which time one or more effects of the compound or composition on the HLO and / or immune cells can be assessed, thereby screening the compound or composition.

[0294] Alternatively, naïve immune cells can be co-cultured with one or more HLO in the co-culture media composition as described herein. The compound or composition to be screened can then be added to the co-culture of one or more HLO and primed immune cells. TheHLO and immune cells can then be co-cultured with the compound or composition, after which time one or more effects of the compound or composition on the HLO and / or immune cells can be assessed, thereby screening the compound or composition.

[0295] In some embodiments of the methods, the screening of the compound or composition includes conducting one or more translational studies, predicting risk of immune- mediated adverse drug reaction (ADR), assessing toxicity, and / or modeling immune-driven drug- induced liver injury (DILI), following co-culturing with the compound or composition to be screened. In some embodiments, the screening includes determining one or more genetic risk factors for a subject from whom the HLO and / or immune cells are derived. In some embodiments, the screening includes evaluating an HLA type for a subject from whom the HLO and / or immune cells are derived; optionally wherein evaluating an HLA type includes determining HLA type contribution to one or more effect of the compound or composition on the HLO and / or immune cells; optionally wherein the effect of the compound or composition on the HLO and / or immune cells includes an adverse drug reaction and / or drug-induced liver injury.

[0296] In some embodiments of the methods, the screening can include providing a prognosis for a subject from whom the HLO and / or immune cells are derived. In some embodiments, the screening includes providing a prognosis based on an HLA type for a subject from whom the HLO and / or immune cells are derived. This method enables not only evaluation but potentially also discovery of the genetic susceptibility markers to immune-driven drug induced liver injury that may not be HLA-related. In some embodiments, providing a prognosis includes predicting risk of immune-mediated adverse drug reaction (ADR), toxicity, and / or immune-driven drug-induced liver injury (DILI).

[0297] In some embodiments, assessing toxicity includes assessing liver toxicity. In some embodiments, assessing toxicity includes assessing cell viability (live / dead), morphology, HLO functionality, immune cell functionality, albumin release and expression, CYP3A4 expression, and / or immune cell infiltration. In some embodiments, assessing HLO functionality includes determining levels of one or more HLO markers (e.g. CK18 (M65), albumin, and / or AST / ALT), and / or wherein assessing immune cell functionality includes determining levels of one or more immune cell markers (e.g. IFNg, TNFa, and / or Granzyme B). In some embodiments, toxicity includes increasing expression of one or more chemokines and / orNKG2D ligands, inducing chemotaxis, promoting differentiation and / or multiplication of leukocytes, causing tissue extravasation, and / or contributing to CD8 T cell immune-mediated liver injury. In some embodiments, assessing one or more effects of the compound or composition on the HLO and immune cells includes studying hepatocyte function and developmental divergence; studying liver-related disease; identifying therapeutic targets; and / or identifying therapeutic compounds and / or compositions effective in treating a liver-related disease or disorder, optionally wherein the therapeutic compound or composition comprises an immunotherapy.

[0298] In some embodiments of the methods, one or more effect of the compound or composition to be screened can be compared to a corresponding effect of a compound or composition associated with immune-driven drug-induced liver injury (DILI). In some embodiments, the compound or composition associated with DILI includes abacavir, carbamazepine, allopurinol, dapsone, phenytoin, lamotrigine, nevirapine, sulphamethoxazole, methazolamide, amoxicillin-clavulanate, flucloxacillin, lumiracoxib, ticlopidine, terbinafine, fenofibrate, trimethoprim-sulfamethoxazole, Polygonum multiflorum (green tea), minocycline, infliximab, pazopanib, methimazole, ximelagatran, nitrofurantoin, lumiracoxib, flupirtine, and / or one or more antithyroid, anti-HIV, and / or anti-TB therapeutic. In particular embodiments, the compound or composition includes flucloxacillin. One skilled in the art will appreciate that other compounds or compositions can be associated with ADR and / or immune-driven DILI, and screening of such compounds or compositions is contemplated in accordance with the disclosure.

[0299] In some embodiments of the methods, the HLO and immune cells are derived from a single subject. In some embodiments, the screening is to determine an effect of the compound or composition in a subject from whose cells the HLO and immune cells are derived.

[0300] In some embodiments of the methods, the subject can be a carrier of one or more genetic, acquired, or other risk factors to develop an ADR and / or immune-driven DILI. In some embodiments, ADR risk is determined by scanning confocal microscopy-based HLO morphological and killing profile assessment; CK18 and albumin secretion; CYP3A4 expression; and / or assaying and / or quantifying chemokine production (e.g. CXCL9), NKG2D ligand expression (e.g. ULBP1), and / or associated CD8 T cell HLO infiltration and activation. In someembodiments, the screening provides a differential response between a carrier and a non-carrier of one or more risk factors to develop an ADR and / or immune-driven DILI.

[0301] In some embodiments of the methods, the screening can be used for one or more translational studies. In some embodiments, the screening can be used for patient or treatment selection in a clinical trial. In some embodiments, the screening can be used for predicting risk of developing an ADR and / or immune-driven DILI. In some embodiments, the ADR includes drug-induced activation of T cells and / or immune-mediated damage of liver cells.

[0302] Additional embodiments of the disclosure include uses of the compositions as described herein, as an in vitro human model system for predicting risk for develop an ADR and / or immune-driven DILI; studying hepatocyte function and developmental divergence; studying liver-related disease; identifying therapeutic targets; identifying therapeutic compounds and / or compositions with a favorable safety profile and / or which are effective in treating a liver- related disease or disorder, optionally wherein the therapeutic compound or composition comprises an immunotherapy; identifying and / or validating mechanisms of immune-mediated drug toxicity in a physiologically relevant setting; identifying and / or validating drug mechanism of action (MOA); and / or correlating patient genotype with one or more phenotypic drug response. Idiosyncratic drug-induced liver injury (iDILI)

[0303] Idiosyncratic drug-induced liver injury (iDILI) remains a significant challenge in drug development and clinical practice due to its unpredictable, immune-mediated mechanisms, which are not effectively captured by conventional hepatotoxicity models. Indeed, iDILI is a leading cause of drug withdrawals and regulatory warnings, and accounts for a significant portion of acute liver failure cases unrelated to overdose. These outcomes often occur despite favorable safety profiles in standard preclinical models, highlighting a persistent translational gap between existing in vitro platforms, animal studies, and the human immune responses that ultimately drive patient outcomes. Unlike dose-dependent DILI, also referred to as intrinsic DILI, which can be predicted using standard preclinical hepatotoxicity models, iDILI is driven by immune-mediated mechanisms that are highly patient-specific and often go undetected during drug development.

[0304] The development of advanced in vitro models that account for both drug- and patient-specific factors is crucial for advancing precision medicine in drug safety and toxicity assessment. Such systems are particularly needed to improve the prediction and understanding of immune-mediated iDILI, a complex, multifactorial condition that remains difficult to foresee. While conventional liver models have enhanced the understanding of intrinsic DILI, they fail to recapitulate the adaptive and antigen-specific immune-mediated mechanisms underlying iDILI. The challenge in predicting in iDILI arises from the intricate interplay of multiple factors, including drug properties, genetic predisposition, patient comorbidities, immune activation, and hepatocyte susceptibility, which standard hepatotoxicity assays cannot adequately assess.

[0305] While genetic associations, particularly human leukocyte antigen (HLA) variants, have been linked to iDILI susceptibility, existing in vitro systems fail to model immune-specific hepatotoxic responses in a patient-specific manner. Genetic predisposition, particularly variations in HLA genes, has been associated with individual susceptibility to drug hypersensitivity reactions. A well-documented example is Flucloxacillin, an antibiotic linked to iDILI in individuals carrying the HLA-B*57:01 allele. However, despite this strong genetic association, only a subset of HLA-B*57:01 carriers develop liver injury upon exposure to Flucloxacillin, highlighting the multifactorial nature of iDILI. This low positive predictive value limits the clinical utility of preemptive genetic screening, reinforcing the need for functional, patient-specific approaches to better assess individual risk and improve precision medicine strategies.

[0306] Advances in the understanding of the immune mechanisms underlying iDILI have fueled efforts to develop more predictive laboratory models. However, existing approaches face critical limitations. Traditional animal models fail to replicate human immune responses, prompting a shift toward in vitro systems. Early models relied on hepatic cell lines such as HepG2 or Huh7, co-cultured with macrophage cell lines (e.g., THP-1) to study cytokine-driven inflammation, but these systems lack essential metabolic functions and fail to recreate the liver’s microenvironment. More recent approaches have incorporated primary human hepatocytes and microfluidic liver-on-a-chip platforms improving modeling of hepatic functions. However, they still lack adaptive immune components, limiting their ability to fully capture immune-mediated iDILI mechanisms. Additionally, the limited availability of genetically diverse hepatocytesources constrains patient-specific modeling, while the absence of key adaptive immune players, such as T cells, prevents accurate assessment of immune-driven hepatoxicity.

[0307] The high-throughput human liver organoid (HLO) microarray culture system that integrates Induced Pluripotent Stem Cells (iPSC)-derived liver organoids with autologous CD8+ T cells, developed as described herein, can be used to model immune-mediated liver injury in a patient-specific manner. When compared to primary cells or immortalized cell lines, iPSCs offer a distinct advantage by enabling the generation of genetically diverse, patient- specific liver microtissues containing functional hepatocytes and non-parenchymal cells. This approach overcomes donor availability constraints while allowing for controlled and reproducible studies of genetic risk factors.

[0308] To address this gap, a high-throughput autologous liver organoid–T cell co- culture system designed to study of immune-mediated hepatotoxicity in a patient-specific manner was developed as described herein. This fully autologous in vitro system integrates iPSC-derived liver organoids with antigen-specific CD8⁺ T cells, enabling physiologically relevant modelling of immune-driven hepatotoxicity.

[0309] As a proof-of-concept, we applied this platform to investigate Flucloxacillin- induced injury in the context of HLA-B*57:01, a genetic risk factor associated with heightened patient susceptibility, by modeling flucloxacillin-induced hepatotoxicity in HLA-B57:01 carriers. CD8⁺ T cells from two out of four HLA-B*57:01 carriers exhibited robust activation upon flucloxacillin priming, evidenced by a twofold increase in effector markers (HLA-DR, CD137, CD69) and cytotoxic degranulation marker CD107a. When co-cultured with autologous liver organoids, these primed CD8+ T cells triggered significant hepatocyte injury, as shown by a fourfold increase in DRAQ7⁺ cell death, elevated CK-18 release (a clinically validated biomarker of hepatocyte apoptosis). This cytotoxic response was further confirmed by the increased secretion of Granzyme B and TNF-α, underscoring the immune-driven nature of hepatoxicity. In contrast, CD8⁺ T cells from weak responders from HLA-B*57:01 carrier group (stratified based on the mDC priming assay), as well as non-carriers, failed to induce cytotoxic responses or hepatocyte damage.

[0310] Thus, using Flucloxacillin as a model drug, HLA-B*57:01-dependent immune activation and CD8+ T cell-mediated hepatocyte killing were successfully recapitulated. Thisestablishes a genetically defined platform to study idiosyncratic drug hypersensitivity. These findings demonstrate that T cell activation and subsequent T-cell-mediated hepatocyte injury - observed in a subset of HLA-B*57:01 carriers in clinical settings - can be faithfully reproduced in vitro. These findings are consistent with clinical variability observed in iDILI and reinforce the need for functional, patient-specific modeling tools.

[0311] This system effectively models the activation of naïve CD8+ T cells from healthy donors carrying risk alleles in response to Flucloxacillin-loaded autologous mDCs, while also capturing the liver injury induced by primed CD8+ T cells on autologous HLOs. This dual capability makes it a powerful tool for linking effector cell activation and function with clinically relevant liver injury outcome. Additionally, these results confirm donor variability in the magnitude of the CD8⁺ T cell response and subsequent T cell-driven cytotoxicity among HLA*B57:01 carriers, showing that HLA predisposition alone is insufficient to predict the variable risk of adverse drug reactions. The observed inter-individual variability highlights the importance of functional immunotoxicology assays to complement genetic screening in drug safety assessment and positions this platform as a valuable tool for investigating patient-specific and environmental factors contributing to iDILI susceptibility.

[0312] Previous efforts to establish a link between CD8⁺ T cells and liver damage in Flucloxacillin-induced iDILI in vitro have primarily relied on conditioned media transfer between drug-stimulated immune and hepatic cells. While these approaches have provided valuable insights, they mainly captured indirect effects mediated through cell released inflammatory or stress signaling, rather than direct T cell-mediated hepatotoxicity. This system overcomes these limitations by enabling direct, antigen-specific interactions between T cells and hepatocytes, providing a physiologically and mechanistically relevant model for studying immune-mediated liver toxicity.

[0313] By integrating both genetic diversity and adaptive immune components, the high-throughput HLO–T cell co-culture system described herein provides a physiologically relevant platform for dissecting immune-mediated iDILI mechanisms. Beyond Flucloxacillin, this platform can be adapted to study a broad range of immune-mediated drug toxicities, including those triggered by checkpoint inhibitors and biologics with known HLA associations. The ability to generate genetically defined, patient-specific liver models holds immense potentialfor preclinical drug safety assessments, functional validation of genetic risk factors, and personalized toxicity screening. By bridging the gap between genetic associations and functional immune responses, this approach could transform the prediction and mitigation of immune- driven hepatotoxicity, ultimately advancing precision medicine in drug development and clinical practice.

[0314] Beyond Flucloxacillin, this model is adaptable for studying a broader range of immune-mediated drug toxicities, including those linked to checkpoint inhibitors, biologics, and small-molecule drugs with known HLA associations. Additionally, it can be leveraged to explore immune modulation strategies aimed at mitigating T cell-driven hepatotoxicity. Given the increasing use of immune-targeted therapies, understanding how to prevent off-target immune effects while maintaining therapeutic efficacy is of high clinical relevance. Future studies could investigate strategies such as immune checkpoint modulation, cytokine blockade, or targeted inhibition of cytotoxic T cell pathways to prevent or reverse immune-mediated liver injury. Other Liver-Related Diseases and Disorders

[0315] The compositions of the disclosure can be used in treatment and / or studying or modeling liver-related diseases and disorders, for which their functionality and inclusion of immune cells is particularly advantageous and renders them applicable to a wide range of conditions. In some embodiments, the methods include administering any of the containing compositions disclosed herein. Also disclosed herein are the compositions disclosed herein for use in the manufacture of a medicament for the treatment of a liver-related disease or disorder. Also disclosed herein are the compositions disclosed herein for use in the treatment of a liver- related disease or disorder in a subject in need thereof.

[0316] For example, the compositions as described herein can be used an in vitro human model system for studying hepatocyte function and developmental divergence, studying liver-related disease, identifying and / or screening for therapeutic targets, and / or identifying therapeutic compounds and / or compositions effective in treating a liver-related disease or disorder. Accordingly, the compositions of the disclosure can allow for new developments in liver disease treatment and study.

[0317] Liver-related diseases and disorders relevant to the disclosure can include conditions such as liver dysfunction and / or failure (e.g. hyperammonemia and / orhyperbilirubinemia, and the like), hepatitis (e.g. hepatitis A, hepatitis B, hepatitis C, hepatitis D, hepatitis E, hepatitis G, hepatitis TT, and / or autoimmune hepatitis, and the like), viral hepatitis, hepatitis triggered by one or more checkpoint inhibitor, cholangitis, fibrosis, hepatic encephalopathy, hepatic porphyria, cirrhosis, cancer, drug-induced cholestasis, metabolic disease (e.g. metabolic dysfunction–associated liver disease (MASLD), MetALD, nonalcoholic fatty liver disease (NAFLD), metabolic dysfunction-associated steatohepatitis (MASH), and the like), autoimmune liver disease, biologic drug immunogenicity, Wilson’s disease, metabolic- associated fatty liver disease, hyperammonemia, hyperbilirubinemia, Crigler-Najjar Syndrome, urea cycle disorders, Wolman disease, hepatic cancer, hepatoblastoma, drug-induced liver injury (DILI), glycogen storage disease, hemorrhagic disease, hepatic cyst, and / or alcohol-associated liver disease. One skilled in the art will appreciate other liver-related diseases and conditions for which the liver organoids disclosed herein could have relevance.

[0318] Additional embodiments of the disclosure include uses of compositions as described herein, for treating a liver-related disease or disorder. Additional embodiments of the disclosure include compositions as described herein, for use in the manufacture of a medicament for the treatment of a liver-related disease or disorder. Stem Cells

[0319] The term “totipotent stem cells” (also known as omnipotent stem cells) as used herein has its plain and ordinary meaning as understood in light of the specification and are stem cells that can differentiate into embryonic and extra-embryonic cell types. Such cells can construct a complete, viable organism. These cells are produced from the fusion of an egg and sperm cell. Cells produced by the first few divisions of the fertilized egg are also totipotent.

[0320] The term “embryonic stem cells (ESCs),” also commonly abbreviated as ES cells, as used herein has its plain and ordinary meaning as understood in light of the specification and refers to cells that are pluripotent and derived from the inner cell mass of the blastocyst, an early- stage embryo. For purpose of the present disclosure, the term "ESCs" is used broadly sometimes to encompass the embryonic germ cells as well.

[0321] The term “pluripotent stem cells (PSCs)” as used herein has its plain and ordinary' meaning as understood in light of the specification and encompasses any cells that can differentiate into nearly all cell types of the body, i.e., cells derived from any of the three germlayers (germinal epithelium), including endoderm (interior stomach lining, gastrointestinal tract, the lungs), mesoderm (muscle, bone, blood, urogenital), and ectoderm (epidermal tissues and nervous system), PSCs can be the descendants of inner cell mass cells of the preimplantation blastocyst or obtained through induction of a non-pluripotent cell, such as an adult somatic cell, by forcing the expression of certain genes. Pluripotent stem cells can be derived from any suitable source. Examples of sources of pluripotent stem cells include mammalian sources, including human, rodent, porcine, and bovine.

[0322] The term “induced pluripotent stem cells (iPSCs),” also commonly abbreviated as iPS cells, as used herein has its plain and ordinary meaning as understood in light of the specification and refers to a type of pluripotent stem cells artificially derived from a normally non-pluripotent cell, such as an adult somatic cell, by inducing a "forced" expression of certain genes. hiPSC refers to human iPSCs. In some methods known in the art, iPSCs may be derived by transfection of certain stem cell-associated genes into non-pluripotent cells, such as adult fibroblasts. Transfection may be achieved through viral transduction using viruses such as retroviruses or lentiviruses. Transfected genes may include the master transcriptional regulators Oct-3 / 4 (PUU5F1) and Sox2, although other genes may enhance the efficiency of induction. After 3-4 weeks, small numbers of transfected cells begin to become morphologically and biochemically similar to pluripotent stem cells, and are typically isolated through morphological selection, doubling time, or through a reporter gene and antibiotic selection. As used herein, iPSCs include first generation iPSCs, second generation iPSCs in mice, and human induced pluripotent stem cells. In some methods, a retroviral system is used to transform human fibroblasts into pluripotent stem cells using four pivotal genes: Oct3 / 4, Sox2, Klf4, and c-Myc. In other methods, a lentiviral system is used to transform somatic cells with GCT4, SOX2, NANOG, and LIN28. Genes whose expression are induced in iPSCs include but are not limited to Oct-3 / 4 (POU5F1); certain members of the Sox gene family (e.g., Soxl, Sox2, Sox3, and Soxl5); certain members of the Klf family (e.g., Klfl, Klf2, Klf4, and Klf5), certain members of the Mye family (e.g., C-myc, L-myc, and N- myc), Nanog, LIN28, Tert, Fbxl5, ERas, EC ATI 5- 1, ECAT15-2, Tell, b-Catenm, EC ATI, Esgi, Dnmt3L, EC ATS, Gdf3, Fthll7, Sall4, Rexl, UTF1, Stella, Stat3, Grb2, Prdml4, Nr5al, Nr5a2, or E-cadherin, or any combination thereof.

[0323] The term “precursor cell” as used herein has its plain and ordinary meaning as understood in light of the specification and encompasses any cells that can be used in methods described herein, through which one or more precursor cells acquire the ability to renew itself or differentiate into one or more specialized cell types. In some embodiments, a precursor cell is pluripotent or has the capacity to becoming pluripotent. In some embodiments, the precursor cells are subjected to the treatment of external factors (e.g., growth factors) to acquire pluripotency. In some embodiments, a precursor cell can be a totipotent (or omnipotent) stem cell; a pluripotent stem cell (induced or non-induced); a multipotent stem cell; an oligopotent stem cells and a unipotent stem cell. In some embodiments, a precursor cell can be from an embryo, an infant, a child, or an adult. In some embodiments, a precursor cell can be a somatic cell subject to treatment such that pluripotency is conferred via genetic manipulation or protein / peptide treatment. Precursor cells include embryonic stem cells (ESC), embryonic carcinoma cells (ECs), and epiblast stem cells (EpiSC).

[0324] In some embodiments, one step can include obtaining stem cells that are pluripotent or can be induced to become pluripotent. In some embodiments, pluripotent stem cells are derived from embryonic stem cells, which are in turn derived from totipotent cells of the early mammalian embryo and are capable of unlimited, undifferentiated proliferation in vitro. Embryonic stem cells are pluripotent stem cells derived from the inner cell mass of the blastocyst, an early-stage embryo. Methods for deriving embryonic stem cells from blastocytes are well known in the art. It would be understood by one of skill in the art that the methods and systems described herein are applicable to any stem cells.

[0325] Additional stem cells that can be used in embodiments in accordance with the present disclosure include but are not limited to those provided by or described in the database hosted by the National Stem Cell Bank (NSCB), Human Embryonic Stem Cell Research Center at the University of California, San Francisco (UCSF); WISC cell Bank at the Wi Cell Research Institute; the University of Wisconsin Stem Cell and Regenerative Medicine Center (IJW- SCRMC); Novocell, Inc. (San Diego, Calif.); Cellartis AB (Goteborg, Sweden); ES Cell International Pte Ltd (Singapore); Techmon at the Israel Institute of Technology (Haifa, Israel); and the Stem Cell Database hosted by Princeton University and the University of Pennsylvania. Exemplary embryonic stem cells that can be used in embodiments in accordance with the presentdisclosure include but are not limited to SA01 (SA001); SA02 (SA002); ESDI (HES-1); ES02 (HES-2); ES03 (HES-3); ES04 (HES-4); ES05 (HES-5); ES06 (HES-6); BG01 (BGN-01); BG02 (BGN-02); BG03 (BGN-03); TE03 (13); TE04 (14); TE06 (16); UCOl (HSF1); UC06 (HSF6); WA01 (HI); WA07 (H7); WA09 (H9); WA13 (HI 3); WA14 (HI 4). Exemplary human pluripotent cell lines include but are not limited to TkDA3-4, 1231 A3, 317-D6, 317-A4, CDH1, 5-T-3, 3-34- 1, NAFLD27, NAFLD77, NAFLD150, WD90, WD91, WD92, 1.20012. C213, 1383D6, FF, or 317-12 cells.

[0326] In developmental biology, cellular differentiation is the process by which a less specialized cell becomes a more specialized cell type. As used herein, the term “directed differentiation” describes a process through which a less specialized cell becomes a particular specialized target cell type. The particularity of the specialized target cell type can be determined by any applicable methods that can be used to define or alter the destiny of the initial cell Exemplary methods include but are not limited to genetic manipulation, chemical treatment, protein treatment, and nucleic acid treatment.

[0327] In some embodiments, an adenovirus can be used to transport the requisite four genes, resulting in iPSCs substantially identical to embryonic stem cells. Since the adenovirus does not combine any of its own genes with the targeted host, the danger of creating tumors is eliminated, in some embodiments, non-viral based technologies are employed to generate iPSCs. In some embodiments, reprogramming can be accomplished via plasmid without any virus transfection system at all, although at very low efficiencies. In other embodiments, direct deliver}' of proteins is used to generate iPSCs, thus eliminating the need for viruses or genetic modification. In some embodiment, generation of mouse iPSCs is possible using a similar methodology: a repeated treatment of the cells with certain proteins channeled into the cells via poly-arginine anchors was sufficient to induce pluripotency. In some embodiments, the expression of pluripotency induction genes can also be increased by treating somatic cells with FGF2 under low oxygen conditions.

[0328] The term “feeder cell” as used herein has its plain and ordinary meaning as understood in light of the specification and refers to cells that support the growth of pluripotent stem cells, such as by secreting growth factors into the medium or displaying on the cell surface. Feeder cells are generally adherent cells and may be growth arrested. For example, feeder cellsare growth-arrested by irradiation (e.g. gamma rays), mitomycin-C treatment, electric pulses, or mild chemical fixation (e.g. with formaldehyde or glutaraldehyde). However, feeder cells do not necessarily have to be growth arrested. Feeder cells may serve purposes such as secreting growth factors, displaying growth factors on the cell surface, detoxifying the culture medium, or synthesizing extracellular matrix proteins. In some embodiments, the feeder cells are allogeneic or xenogeneic to the supported target stem cell, which may have implications m downstream applications. In some embodiments, the feeder cells are mouse cells. In some embodiments, the feeder cells are human cells. In some embodiments, the feeder cells are mouse fibroblasts, mouse embryonic fibroblasts, mouse STO cells, mouse 3T3 cells, mouse SNL 76 / 7 cells, human fibroblasts, human foreskin fibroblasts, human dermal fibroblasts, human adipose mesenchymal cells, human bone marrow mesenchymal cells, human amniotic mesenchymal cells, human amniotic epithelial cells, human umbilical cord mesenchymal cells, human fetal muscle cells, human fetal fibroblasts, or human adult fallopian tube epithelial cells. In some embodiments, conditioned medium prepared from feeder cells is used in lieu of feeder cell co-culture or in combination with feeder cell co-culture. In some embodiments, feeder cells are not used during the proliferation of the target stem cells. Differentiation of PSCs

[0329] Known methods for producing definitive endoderm from pluripotent cells (e.g., iPSCs or ESCs) are applicable to the methods described herein. In some embodiments, pluripotent cells are derived from a morula. In some embodiments, pluripotent stem cells are stem cells. Stem cells used in these methods can include, but are not limited to, embryonic stem cells or induced pluripotent stem cells. Embryonic stem cells can be derived from the embryonic inner cell mass or from the embryonic gonadal ridges. Embryonic stem cells or germ cells can originate from a variety of animal species including, but not limited to, various mammalian species including humans. In some embodiments, human embryonic stem cells are used to produce definitive endoderm. In some embodiments, human embryonic germ cells are used to produce definitive endoderm. In some embodiments, iPSCs are used to produce definitive endoderm. in some embodiments, human iPSCs (hiPSCs) are used to produce definitive endoderm.

[0330] In some embodiments, PSCs, such as ESCs and iPSCs, undergo directed differentiation into embryonic germ layer cells, organ tissue progenitor cells, and then into tissue such as liver tissue or any other biological tissue. In some embodiments, the directed differentiation is done in a stepwise manner to obtain each of the differentiated cell types where molecules (e.g. growth factors, ligands, agonists, antagonists) are added sequentially as differentiation progresses. In some embodiments, the directed differentiation is done in a non- stepwise manner where molecules (e.g. growth factors, ligands, agonists, antagonists) are added at the same time. In some embodiments, directed differentiation is achieved by selectively activating certain signaling pathways in the PSCs or any downstream cells.

[0331] In some embodiments, the embryonic stem cells or germ cells or iPSCs are treated with one or more small molecule compounds, activators, inhibitors, or growth factors for a time that is, is about, is at least, is at least about, is not more than, or is not more than about, 6 hours, 12 hours, 18 hours, 24 hours, 36 hours, 48 hours, 60 hours, 72 hours, 84 hours, 96 hours, 120 hours, 150 hours, 180 hours, 240 hours, 300 hours or any time within a range defined by any two of the aforementioned times, for example 6 hours to 300 hours, 24 hours to 120 hours, 48 hours to 96 hours, 6 hours to 72 hours, or 24 hours to 300 hours, in some embodiments, more than one small molecule compounds, activators, inhibitors, or growth factors are added. In these cases, the more than one small molecule compounds, activators, inhibitors, or growth factors can be added simultaneously or separately.

[0332] In some embodiments, the embryonic stem cells or germ cells or iPSCs are treated with one or more small molecule compounds, activators, inhibitors, or growth factors at a concentration that is, is about, is at least, is at least about, is not more than, or is not more than about, 10 ng / mL, 20 ng / mL, 50 ng / mL, 75 ng / mL, 100 ng / mL, 120 ng / mL, 150 ng / mL, 200 ng / mL, 500 ng / mL, 1000 ng / mL, 1200 ng / mL, 1500 ng / mL, 2000 ng / mL, 5000 ng / mL, 7000 ng / niL, 10000 ng / mL, or 15000 ng / mL, or any concentration that is within a range defined by any two of the aforementioned concentrations, for example, 10 ng / mL to 15000 ng / mL, 100 ng / mL to 5000 ng / mL, 500 ng / mL to 2000 ng / mL, 10 ng / mL to 2000 ng / mL, or 1000 ng / mL to 15000 ng / mL. In some embodiments, concentration of the one or more small molecule compounds, activators, inhibitors, or growth factors is maintained at a constant level throughout the treatment. In some embodiments, concentration of the one or more small moleculecompounds, activators, inhibitors, or growth factors is varied during the course of the treatment. In some embodiments, more than one small molecule compounds, activators, inhibitors, or growth factors are added. In these cases, the more than one small molecule compounds, activators, inhibitors, or growth factors can differ in concentrations.

[0333] In some embodiments, the ESCs or iPSCs, or the ESCs, germ cells, or iPSCs are cultured in growth media that supports the growth of stem cells. In some embodiments, the ESCs or iPSCs, or the ESCs, germ cells, or iPSCs, are cultured in stem cell growth media. In some embodiments, the stem cell growth media is RPMI 1640, DMEM, DMEM / F12, or Advanced DMEM / F12. In some embodiments, the stem cell growth media comprises fetal bovine serum (FBS). In some embodiments, the stem cell growth media comprises FBS at a concentration that is, is about, is at least, is at least about, is not more than, or is not more than about, 0%, 0.1%, 0.2%, 0.3%, 0.4%, 0.5%, 0,6%, 0.7%, 0.8%, 0,9%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, or 20%, or any percentage within a range defined by any two of the aforementioned concentrations, for example 0% to 20%, 0.2% to 10%, 2% to 5%, 0% to 5%, or 2% to 20%. In some embodiments, the stem cell growth media does not contain xenogeneic components. In some embodiments, the growth media comprises one or more small molecule compounds, activators, inhibitors, or growth factors.

[0334] In some embodiments, populations of cells enriched in definitive endoderm cells are used. In some embodiments, the definitive endoderm cells are isolated or substantially purified. In some embodiments, the isolated or substantially purified definitive endoderm cells express one or more (e.g. at least 1, 3) of SOX17, FOXA2, or CXRC4 markers to a greater extent than one or more (e.g. at least 1, 3, 5) of GCT4, AFP, I'M, SPARC, or SGX7 markers.

[0335] In some embodiments, pluripotent stem cells are prepared from somatic cells. In some embodiments, pluripotent stem cells are prepared from biological tissue obtained from a biopsy. In some embodiments, the pluripotent stem cells are cryopreserved. In some embodiments, the somatic cells are cryopreserved. In some embodiments, pluripotent stem cells are prepared from PBMCs. In some embodiments, human PSCs are prepared from human PBMCs. In some embodiments, pluripotent stem cells are prepared from cryopreserved PBMCs. In some embodiments, PBMCs are grown on a feeder cell substrate. In some embodiments,PBMCs are grown on a mouse embryonic fibroblast (MEF) feeder cell substrate. In some embodiments, PBMCs are grown on an irradiated MEF feeder cell substrate.

[0336] In some embodiments, stem cells are treated with one or more growth factors to differentiate to definitive endoderm cells. Such growth factors can include growth factors from the TGF-beta superfamily. In some embodiments, the one or more growth factors comprise the Nodal / Activin and / or the BMP subgroups of the TGF-beta superfamily of growth factors. In some embodiments, the one or more growth factors are selected from the group consisting of Nodal, Activin A, Activin B, BMP4, Wnt3a or combinations of any of these growth factors. In some embodiments, the stem cells are contacted with Activin A. In some embodiments, the stem cells are contacted with Activin A and BMP4.

[0337] In some embodiments, activin-induced definitive endoderm (DE) can further undergo anterior endoderm pattering, foregut specification and morphogenesis, dependent on FGF, Wnt, or retinoic acid, or any combination thereof, or on FGF, Wnt, BMP, or retinoic acid, or any combination thereof, and a liver culture system that promotes liver growth, morphogenesis and cytodifferentiation. In some embodiments, human PSCs are efficiently directed to differentiate in vitro into liver epithelium and mesenchyme, it will be understood that molecules such as growth factors can be added to any stage of the development to promote a particular type of hepatic tissue formation.

[0338] It will be understood by one of skill in the art that altering the concentration, expression or function of one or more Wnt signaling proteins in combination with altering the concentration, expression, or function of one or more FGF proteins can give rise to directed differentiation in accordance with the present disclosure. In some embodiments, cellular constituents associated with the FGF, Wnt, or retinoic acid (RA) signaling pathways, or with the FGF, Wnt, BMP, or retinoic acid (RA) signaling pathways, for example, natural inhibitors, antagonists, activators, or agonists of the pathways can be used to result in inhibition or activation of the FGF, Wnt, or retinoic acid signaling pathways, or of the FGF, Wnt, BMP, or retinoic acid signaling pathways. In some embodiments, siRNA and / or shRNA targeting cellular constituents associated with the FGF, Wnt, or retinoic acid signaling pathways, or the FGF, Wnt, BMP, or retinoic acid signaling pathways, are used to inhibit or activate these pathways.

[0339] In some embodiments, pluripotent stem cells, definitive endoderm, posterior foregut spheroids, or downstream liver cell types are contacted with a Wnt signaling pathway activator or Wnt signaling pathway inhibitor. In some embodiments, the Wnt signaling pathway activator comprises a Wnt protein, in some embodiments, the Wnt protein comprises a recombinant Wnt protein. In some embodiments, the Wnt signaling pathway activator comprises Wntl, Wnt2, Wnt2b, Wnt3, Wnt3a, Wnt4, WntSa, WntSb, Wnt6, Wnt7a, Wnt7b, Wnt8a, WntSb, Wnt9a, Wnt9b, WntlOa, WntlOb, Wnt11 Wnt16, BML 284, IQ-1, WAY 262611, or any combination thereof. In some embodiments, the Wnt signaling pathway activator comprises a GSK3 signaling pathway inhibitor. In some embodiments, the Wnt signaling pathway activator comprises CHIR99Q21, CfflR 98014, AZD2858, BIO, AR-A014418, SB 216763, SB 415286, aloisine, indirubin, alsterpaullone, kenpauilone, lithium cHLOride, TDZD 8, or TWS119, or any combination thereof. In some embodiments, the Wnt signaling pathway inhibitor comprises C59, PNU 74654, KY-02111, PRI-724, FH-535, DIF-1, or XAV939, or any combination thereof. In some embodiments, the cells are not treated with a Wnt signaling pathway activator or Wnt signaling pathway inhibitor. The Wnt signaling pathway activator or Wnt signaling pathway inhibitor provided herein may be used in combination with any of the other growth factors, signaling pathway activators, or signaling pathway inhibitors provided herein.

[0340] In some embodiments, pluripotent stem cells, definitive endoderm, posterior foregut spheroids, or downstream liver cell types are contacted with an FGF signaling pathway activator. In some embodiments, the FGF signaling pathway activator comprises an FGF protein. In some embodiments, the FGF protein comprises a recombinant FGF protein. In some embodiments, the FGF signaling pathway activator comprises one or more of FGF1 , FGF2, FGF3, FGF4, FGF4, FGF 5, FGF6, FGF7, FGF 8, FGF8, FGF9, FGF 10, FGF11, FGF 12, FGF 13, FGF 14, FGF 15 (FGF 19, FGF15 / FGF19), FGF 16, FGF 17, FGF 18, FGF20, FGF21, FGF22, or FGF23. In some embodiments, the cells are not treated with an FGF signaling pathway activator. The FGF signaling pathway activator provided herein may be used in combination with any of the other growth factors, signaling pathway activators, or signaling pathway inhibitors provided herein.

[0341] In some embodiments, pluripotent stem cells, definitive endoderm, posterior foregut spheroids, or downstream liver cell types are contacted with a retinoic acid signalingpathway activator or retinoic acid signaling pathway inhibitor. In some embodiments, the retinoic acid signaling pathway activator comprises retinoic acid, all-trans retinoic acid, 9-cis retinoic acid, CD437, EC23, BS 493, TTNPB, or AM580, or any combination thereof, in some embodiments, the retinoic acid signaling pathway inhibitor comprises guggulsterone. In some embodiments, the cells are not treated with a retinoic acid signaling pathway activator or retinoic acid signaling pathway inhibitor. The retinoic acid signaling pathway activator or retinoic acid signaling pathway inhibitor provided herein may be used in combination with any of the other growth factors, signaling pathway activators, or signaling pathway inhibitors provided herein.

[0342] In some embodiments, pluripotent stem cells are converted into liver cell types via a “one step” process. For example, one or more molecules that can differentiate pluripotent stem cells into DE culture (e.g., Activin A) are combined with additional molecules that can promote directed differentiation of DE culture (e.g., FGF4, CHIR99021, RA; or e.g., FGF4, Wnt, Noggin, RA) to directly treat pluripotent stem cells.

[0343] In some embodiments, iPSCs are expanded in cell culture. In some embodiments, pluripotent stem cells are expanded in a basement membrane matrix. In some embodiments, iPSCs are expanded in Matrigel, In some embodiments, the iPSCs are expanded in cell culture comprising a ROCK inhibitor (e.g. Y-27632). In some embodiments, the iPSCs are differentiated into definitive endoderm cells. In the iPSCs are differentiated into definitive endoderm cells by- contacting the iPSCs with Activin A, BMP4, or both. In some embodiments, the iPSCs are contacted with a concentration of Activin A that is, is about, is at least, is at least about, is not more than, or is not more than about, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or 200 ng / mL, or any concentration of Activin A within a range defined by any two of the aforementioned concentrations, for example, 10 to 200 ng / mL, 10 to 100 ng / mL, 100 to 200 ng / mL, or 50 to 150 ng / mL. In some embodiments, the pluripotent stem cells are contacted with Activin A at a concentration of 100 ng / mL or about 100 ng / mL. In some embodiments, the iPSCs are contacted with a concentration of BMP4 that is, is about, is at least, is at least about, is not more than, or is not more than about, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or 200 ng / mL, or any concentration of BMP4 within a range defined by any two of the aforementioned concentrations, for example, 1 to 200 ng / mL, 1 to 100 ng / mL, 25 to 200 ng / mL, 1 to 80 ng / mL,or 25 to 100 ng / mL, In some embodiments, the pluripotent stem cells are contacted with BMP4 at a concentration of 50 ng / mL or about 50 ng / mL.

[0344] In some embodiments, the PSCs are differentiated into definitive endoderm cells. In some embodiments, the PSCs are differentiated into posterior foregut cells, in some embodiments, the PSCs are differentiated into a liver organoid.

[0345] In some embodiments, any of the cells disclosed herein may be cryopreserved for later use. The cells can be cryopreserved according to methods generally known in the art, optionally including one or more cryoprotectants.

[0346] Cryoprotectants are cell composition additives to improve efficiency and yield of low temperature cryopreservation by preventing formation of large ice crystals. Cryoprotectants include but are not limited to DMSO, ethylene glycol, glycerol, propylene glycol, trehalose, formamide, methyl-formamide, dimethyl-formamide, glycerol 3 -phosphate, proline, sorbitol, diethyl glycol, sucrose, triethylene glycol, polyvinyl alcohol, polyethylene glycol, or hydroxy ethyl starch. Cryoprotectants can be used as part of a cryopreservation medium, which include other components such as nutrients (e.g. albumin, serum, bovine serum, fetal calf serum (FCS)) to enhance post-thawing survivability of the cells, in these cryopreservation media, at least one cryoprotectant may be found at a concentration that is, is about, is at least, is at least about, is not more than, or is not more than about, 0.01%, 0.05%, 0.1%, 0.5%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90%, or any percentage within a range defined by any two of the aforementioned numbers. Gene Editing

[0347] Embodiments of the disclosure can include PSCs, iPSCs, definitive endoderm cells, posterior foregut spheroids, or organoids which have been or which can be genetically modified or edited according to methods known in the art. For example, gene editing using CRISPR nucleases such as Cas9 are explored in PCT Publications WO 2013 / 176772, WO 2014 / 093595, WO 2014 / 093622, WO 2014 / 093655, WO 2014 / 093712, WO 2014 / 093661, WO 2014 / 204728, WO 2014 / 204729, WO 2015 / 071474, WO 2016 / 115326, WO 2016 / 141224, WO 2017 / 023803, and WO 2017 / 070633, each of which is hereby expressly incorporated by reference in its entirety.Pharmaceutical Compositions

[0348] Embodiments of the disclosure can include pharmaceutical compositions. Such pharmaceutical compositions can include one or more additional pharmaceutically acceptable components, which can include carriers, excipients, and / or stabilizers that are nontoxic to the cell or mammal being exposed thereto at the dosages and concentrations employed or that have an acceptable level of toxicity. A “pharmaceutically acceptable” “diluent,” “excipient,” and / or “carrier” as used herein have their plain and ordinary meaning as understood in light of the specification and are intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with administration to humans, cats, dogs, or other vertebrate hosts. Typically, a pharmaceutically acceptable diluent, excipient, and / or carrier is a diluent, excipient, and / or earner approved by a regulatory agency of a Federal, a state government, or other regulatory agency, or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, including humans as well as non-human mammals, such as cats and dogs. The term diluent, excipient, and / or “carrier” can refer to a diluent, adjuvant, excipient, or vehicle with which the pharmaceutical composition is administered. Such pharmaceutical diluent, excipient, and / or earners can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin. Water, saline solutions and aqueous dextrose and glycerol solutions can be employed as liquid diluents, excipients, and / or carriers, particularly for injectable solutions. Suitable pharmaceutical diluents and / or excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium cHLOride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like. A non-limiting example of a physiologically acceptable carrier is an aqueous pH buffered solution. The physiologically acceptable carrier may also comprise one or more of the following: antioxidants, such as ascorbic acid, low molecular weight (less than about 10 residues) polypeptides, proteins, such as serum albumin, gelatin, immunoglobulins, hydrophilic polymers such as polyvinylpyrrolidone, ammo acids, carbohydrates such as glucose, mannose, or dextrins, chelating agents such as EDTA, sugar alcohols such as mannitol or sorbitol, salt-forming counterions such as sodium, and nonionic surfactants such as TWEEN®, polyethylene glycol (PEG), and PLURONICS®. The composition, if desired, can also containminor amounts of wetting, bulking, emulsifying agents, or pH buffering agents. These compositions can take the form of solutions, suspensions, emulsion, sustained release formulations and the like. The formulation should suit the mode of administration.

[0349] Additional excipients with desirable properties include but are not limited to preservatives, adjuvants, stabilizers, solvents, buffers, diluents, solubilizing agents, detergents, surfactants, chelating agents, antioxidants, alcohols, ketones, aldehydes, ethylenediaminetetraacetic acid (EDTA), citric acid, salts, sodium cHLOride, sodium bicarbonate, sodium phosphate, sodium borate, sodium citrate, potassium cHLOride, potassium phosphate, magnesium sulfate sugars, dextrose, fructose, mannose, lactose, galactose, sucrose, sorbitol, cellulose, serum, amino acids, polysorbate 20, polysorbate 80, sodium deoxycholate, sodium taurodeoxycholate, magnesium stearate, octylphenol ethoxylate, benzethonium cHLOride, thimerosal, gelatin, esters, ethers, 2-phenoxyethanol, urea, or vitamins, or any combination thereof. Some excipients may be in residual amounts or contaminants from the process of manufacturing, including but not limited to serum, albumin, ovalbumin, antibiotics, inactivating agents, formaldehyde, glutaraldehyde, b-propiolactone, gelatin, cell debris, nucleic acids, peptides, ammo acids, or growth medium components or any combination thereof. The amount of the excipient may be found in composition at a percentage that is, is about, is at least, is at least about, is not more than, or is not more than about, 0%, 0.1%, 0.2%, 0.3%, 0.4%, 0.5%, 0.6%, 0.7%, 0.8%, 0.9%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 100% w / w or any percentage by weight in a range defined by any two of the aforementioned numbers.

[0350] Pharmaceutical compositions can include one or more “pharmaceutically acceptable salts”, which can include relatively non-toxic, inorganic and organic acid, or base addition salts of compositions or excipients, including without limitation, analgesic agents, therapeutic agents, other materials, and the like. Examples of pharmaceutically acceptable salts include those derived from mineral acids, such as hydrocHLOric acid and sulfuric acid, and those derived from organic acids, such as ethanesulfonic acid, benzenesulfonic acid, p- toluenesulfonic acid, and the like. Examples of suitable inorganic bases for the formation of salts include the hydroxides, carbonates, and bicarbonates of ammonia, sodium, lithium, potassium, calcium, magnesium, aluminum, zinc, and the like. Salts may also be formed with suitableorganic bases, including those that are non-toxic and strong enough to form such salts. For example, the class of such organic bases may include but are not limited to mono-, di-, and trialkylamines, including methylamine, dimethylamine, and triethylamine; mono-, di-, or trihydroxyalkylamines including mono-, di-, and triethanolamine; ammo acids, including glycine, arginine and lysine; guanidine; N-methylglucosamine; N-methylglucamine; L- glutamine; N-methylpiperazine; morpholine; ethylenediamine; N-benzylphenethylamine; trihydroxymethyl ammoethane.

[0351] Proper formulation is dependent upon the route of administration chosen. Techniques for formulation and administration of the compounds described herein are known to those skilled in the art. Multiple techniques of administering a compound exist in the art including, but not limited to, enteral, oral, rectal, topical, sublingual, buccal, intraaural, epidural, epicutaneous, aerosol, parenteral delivery, including intramuscular, subcutaneous, intra-arterial, intravenous, intraportal, intra-articular, intradermal, peritoneal, intramedullary injections, intrathecal, direct intraventricular, intraperitoneal, intranasal or intraocular injections. Pharmaceutical compositions will generally be tailored to the specific intended route of administration.

[0352] As used herein, a “carrier” has its plain and ordinary meaning as understood in light of the specification and can refer to a compound, particle, solid, semi-solid, liquid, or diluent that facilitates the passage, delivery and / or incorporation of a compound to cells, tissues and / or bodily organs.

[0353] As used herein, a “diluent” has its plain and ordinary meaning as understood in light of the specification and can refer to an ingredient in a pharmaceutical composition that lacks pharmacological activity but may be pharmaceutically necessary or desirable. For example, a diluent may be used to increase the bulk of a potent drug whose mass is too small for manufacture and / or administration. It may also be a liquid for the dissolution of a drug to be administered by injection, ingestion or inhalation. A common form of diluent in the art is a buffered aqueous solution such as, without limitation, phosphate buffered saline that mimics the composition of human blood. Dosage and Administration Routes

[0354] Embodiments of the disclosure can include methods of administering or treating an animal, which can involve administering an amount of at least one treatment, that is effective to treat the disease, condition, or disorder that the organism has, or is suspected of having, or is susceptible to, or to bring about a desired physiological effect. In some embodiments, the disease, condition, or disorder can be a liver-related disease or disorder.

[0355] In some embodiments, at least one treatment can include a composition or pharmaceutical composition, which can be administered to an animal (e.g., mammals, primates, monkeys, or humans) in an amount of about 0.005 to about 50 mg / kg body weight, about 0.01 to about 15 mg / kg body weight, about 0.1 to about 10 mg / kg body weight, about 0.5 to about 7 mg / kg body weight, about 0.005 mg / kg, about 0.01 mg / kg, about 0.05 mg / kg, about 0.1 mg / kg, about 0.5 mg / kg, about 1 mg / kg, about 3 mg / kg, about 5 mg / kg, about 5.5 mg / kg, about 6 mg / kg, about 6.5 mg / kg, about 7 mg / kg, about 7.5 mg / kg, about 8 mg / kg, about 10 mg / kg, about 12 mg / kg, or about 15 mg / kg. In regard to some conditions, the dosage can be about 0.5 mg / kg human body weight or about 6.5 mg / kg human body weight. In some instances, some subjects (e.g., mammals, mice, rabbits, feline, porcine, or canine) can be administered a dosage of about 0.005 to about 50 mg / kg body weight, about 0.01 to about 15 mg / kg body weight, about 0.1 to about 10 mg / kg body weight, about 0.5 to about 7 mg / kg body weight, about 0.005 mg / kg, about 0.01 mg / kg, about 0.05 mg / kg, about 0.1 mg / kg, about 1 mg / kg, about 5 mg / kg, about 10 mg / kg, about 20 mg / kg, about 30 mg / kg, about 40 mg / kg, about 50 mg / kg, about 80 mg / kg, about 100 mg / kg, or about 150 mg / kg. Of course, those skilled in the art will appreciate that it is possible to employ many concentrations in the methods of the present disclosure, and using, in part, the guidance provided herein, will be able to adjust and test any number of concentrations in order to find one that achieves the desired result in a given circumstance. In some embodiments, a dose or a therapeutically effective dose of a compound disclosed herein will be that which is sufficient to achieve a plasma concentration of the compound or its active metabolite(s) within a range set forth herein, e.g., about 1-10 nM, 10-100 nM, 0.1-1 µM, 1-10 µM, 10-100 µM, 100-200 µM, 200-500 µM, or even 500-1000 µM, preferably about 1-10 nM, 10-100 nM, or 0.1-1 µM.

[0356] In other embodiments, a treatment can be administered in combination with one or more other therapeutic agents for a given disease, condition, or disorder.

[0357] The compounds and pharmaceutical compositions are preferably prepared and administered in dose units. Solid dose units are tablets, capsules and suppositories. For treatment of a subject, depending on activity of the compound, manner of administration, nature and severity of the disease or disorder, age and body weight of the subject, different daily doses can be used.

[0358] Under certain circumstances, however, higher or lower daily doses can be appropriate. The administration of the daily dose can be carried out both by single administration in the form of an individual dose unit or else several smaller dose units and also by multiple administrations of subdivided doses at specific intervals.

[0359] A treatment can be administered locally or systemically in a therapeutically effective dose. Amounts effective for this use will, of course, depend on the severity of the disease or disorder and the weight and general state of the subject. Typically, dosages used in vitro can provide useful guidance in the amounts useful for in situ administration of the pharmaceutical composition, and animal models can be used to determine effective dosages for treatment of particular disorders.

[0360] Various considerations are described, e. g. , in Langer, 1990, Science, 249: 1527; Goodman and Gilman's (eds.), 1990, Id., each of which is herein incorporated by reference and for all purposes. Dosages for parenteral administration of active pharmaceutical agents can be converted into corresponding dosages for oral administration by multiplying parenteral dosages by appropriate conversion factors. As to general applications, the parenteral dosage in mg / mL times 1.8 = the corresponding oral dosage in milligrams (“mg”). As to oncology applications, the parenteral dosage in mg / mL times 1.6 = the corresponding oral dosage in mg. An average adult weighs about 70 kg. See e.g., Miller-Keane, 1992, Encyclopedia & Dictionary of Medicine, Nursing & Allied Health, 5th Ed., (W. B. Saunders Co.), pp.1708 and 1651.

[0361] It will be understood, however, that the specific dose level for any particular patient will depend upon a variety of factors including the activity of the specific compound employed, the age, body weight, general health, sex, diet, time of administration, route of administration, rate of excretion, drug combination and the severity of the particular disease undergoing therapy.

[0362] In some embodiments, the administration can include a unit dose of one or more treatments in combination with a pharmaceutically acceptable carrier and, in addition, can include other medicinal agents, pharmaceutical agents, carriers, adjuvants, diluents, and excipients. In certain embodiments, the carrier, vehicle or excipient can facilitate administration, delivery and / or improve preservation of the composition. In other embodiments, the one or more carriers, include but are not limited to, saline solutions such as normal saline, Ringer's solution, PBS (phosphate-buffered saline), and generally mixtures of various salts including potassium and phosphate salts with or without sugar additives such as glucose. Carriers can include aqueous and non-aqueous sterile injection solutions that can contain antioxidants, buffers, bacteriostats, bactericidal antibiotics, and solutes that render the formulation isotonic with the bodily fluids of the intended recipient; and aqueous and non-aqueous sterile suspensions, which can include suspending agents and thickening agents. In other embodiments, the one or more excipients can include, but are not limited to water, saline, dextrose, glycerol, ethanol, or the like, and combinations thereof. Nontoxic auxiliary substances, such as wetting agents, buffers, or emulsifiers may also be added to the composition. Oral formulations can include such normally employed excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, and magnesium carbonate.

[0363] The quantity of active component in a unit dose preparation can be varied or adjusted from 0.1 mg to 10000 mg, more typically 1.0 mg to 1000 mg, most typically 10 mg to 500 mg, according to the particular application and the potency of the active component. The composition can, if desired, also contain other compatible therapeutic agents.

[0364] A treatment can be administered to subjects by any number of suitable administration routes or formulations. The treatment, such as an immunotherapy, can also be used to treat subjects for a variety of diseases. Subjects include but are not limited to mammals, primates, monkeys (e.g., macaque, rhesus macaque, or pig tail macaque), humans, canine, feline, bovine, porcine, avian (e.g., chicken), mice, rabbits, and rats. In particular embodiments described herein, the subject is a human.

[0365] The route of administration of the compounds of the treatments described herein can be of any suitable route. Administration routes can be, but are not limited to the oral route, the parenteral route, the cutaneous route, the nasal route, the rectal route, the vaginal route,and the ocular route. In other embodiments, administration routes can be parenteral administration, a mucosal administration, intravenous administration, subcutaneous administration, topical administration, intradermal administration, oral administration, sublingual administration, intranasal administration, or intramuscular administration. The choice of administration route can depend on the compound identity (e.g., the physical and chemical properties of the compound) as well as the age and weight of the animal, the particular disease (e.g., type of cancer), and the severity of the disease (e.g., stage or severity of cancer). Of course, combinations of administration routes can be administered, as desired.

[0366] Some embodiments of the disclosure include a method for providing a subject with a treatment which comprises one or more administrations of one or more compositions; the compositions may be the same or different if there is more than one administration. Toxicity

[0367] The ratio between toxicity and therapeutic effect for a particular treatment is its therapeutic index and can be expressed as the ratio between LD50 (the amount of compound lethal in 50% of the population) and ED50 (the amount of compound effective in 50% of the population). Compounds that exhibit high therapeutic indices are preferred. Therapeutic index data obtained from in vitro assays, cell culture assays and / or animal studies can be used in formulating a range of dosages for use in humans. The dosage of such compounds preferably lies within a range of plasma concentrations that include the ED50 with little or no toxicity. The dosage can vary within this range depending upon the dosage form employed and the route of administration utilized. See, e.g. Fingl et al., In: THE PHARMACOLOGICAL BASIS OF THERAPEUTICS, Ch.1, p.l, 1975. The exact formulation, route of administration, and dosage can be chosen by the individual practitioner in view of the patient’s condition and the particular method in which the compound is used. For in vitro formulations, the exact formulation and dosage can be chosen by the individual practitioner in view of the patient’s condition and the particular method in which the compound is used. Kits

[0368] In some embodiments, also disclosed herein are kits providing means for performing any of the methods described herein. In some embodiments, also disclosed herein arekits comprising any of the compositions or means of producing the compositions described herein.

[0369] For example, kits can be prepared including means for preparing any of the compositions, performing any of the methods, or for any of the uses, as described herein. Various kits prepared according to the disclosure can include a co-culture media composition and / or composition as described herein.

[0370] In some embodiments, one or more of the co-culture media components or composition components can be provided in separate vials. In some embodiments, one or more of the co-culture media components or composition components can be pre-loaded onto one or more assay platform. In some embodiments, the one or more assay platform can include a droplet or microcavity array culture platform, optionally without a basement membrane matrix. In some embodiments, the one or more assay platform is Matrigel-free. In some embodiments, one or more of the co-culture media components, composition components, and / or assay platform can be pre-frozen.

[0371] One skilled in the art will appreciate that various times of droplet or microcavity array culture plate can be used in accordance with various embodiments of the disclosure. These include, for example, Gri3D® plates; AggreWell™ plates; Elplasia® plates; ultra-low attachment (ULA), or ultra-low adhesion, plates; micro-patterned hydrogel plates; SmartSphero plates; Acura plates; Sphericalplates 5D; microfluidic culture devices; hanging drop plates; and the like. One skilled in the art can select an appropriate platform in order to achieve the desired outcome. Certain platforms, such as Gri3D® plates, lend themselves to automation more easily than others.

[0372] In some embodiments, a kit can be prepared from readily available components and reagents. For example, such kits can comprise any one or more of the following components and / or reagents: enzymes, reaction tubes, buffers, detergent, primers, probes, antibodies, cell culture media, differentiation induction reagents, amino acid mixtures / supplements, engineered constructs and / or polynucleotides, transcription induction agents, bilirubin, ascorbic acid, ascorbate, retinoic acid pathway activators, corticosteroids, cMET tyrosine kinase receptor agonists, IL-6 family cytokines, TGF-b pathway inhibitors, FGF pathway activators, Wnt pathway activators, VEGF pathway activators, ROCK inhibitors,organoids, and / or cells. In some embodiments, components and reagents may be packaged together in any combination, and / or may be packaged individually. In some embodiments, kits may include components and reagents concentrated above the working concentrations disclosed herein, or at the working concentrations provided herein. In some embodiments, individual components may also be provided in a kit in concentrated amounts; in some aspects, a component is provided individually in the same concentration as it would be in a solution with other components. In some embodiments, concentrations of components may be provided as 1x, 2x, 5x, 10x, or 20x or more. In some embodiments, a kit may comprise components, which may be individually packaged or placed in a container, such as a tube, bottle, vial, syringe, or other suitable container means.

[0373] In some embodiments, a kit is housed in a container. Kits may further comprise instructions for using the kit for assessing expression and / or differentiation of cells. Agents in a kit for measuring expression and / or determining differentiation may comprise a plurality of PCR probes and / or primers for qRT-PCR and / or a plurality of antibody or fragments thereof for assessing expression of biomarkers appropriate for classifying cell states.

[0374] In some embodiments, kits are created using and comply with good manufacturing practice (GMP).

[0375] Having described various embodiments in detail, it will be apparent that modifications, variations, and equivalent embodiments are possible without departing from the scope of the disclosure as defined in the appended claims. Furthermore, it should be appreciated that all examples in the present disclosure are provided as non-limiting examples. EXAMPLES

[0376] The following non-limiting examples are provided to further illustrate embodiments of the disclosure herein. It should be appreciated by those of skill in the art that the techniques disclosed in the examples that follow represent approaches that have been found to function well in the practice of the disclosure, and thus can be considered to constitute examples of modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments thatare disclosed and still obtain a like or similar result without departing from the spirit and scope of the disclosure. EXAMPLE 1 Materials and methods

[0377] The materials and methods used in the experimentation described herein are detailed below for reference. Materials / Reagents

[0378] The reagents used for the HLOs in the experiments described herein include: Laminin iMatrix-511 Silk, stock 0.5 mg / ml (892021, Nacalai USA); Sterile Dulbecco's phosphate-buffered saline, no calcium, no magnesium (DPBS- / -) (14190, Gibco); mTeSR1 (85850, Stem Cell Technologies) optionally supplemented with 1X Penicillin / Streptomycin (Pen / Strep) (15140, Thermo-fisher); 10 μM Y27632, Rock inhibitor (1254, Tocris). Y27632 is used to increase cell viability during single cell passaging; Accutase, (AT104, Innovative Cell Technologies). This is a gentle enzyme mixture used for single cell passaging; Wash media: DMEM / F12 (11330, Gibco); RPMI base: RPMI 1640, (11875, Gibco) supplemented with 25 mM Hepes, (15630, Gibco). Glutamax (35050, Thermo), 1X Gentamycin / Amphotericin solution (R01510, Gibco); Day 0 media: RPMI Base supplemented with 50 ng / ml recombinant human bone morphogenetic protein-4 (314-BP, R&D Technologies), and 100 ng / ml recombinant human Activin A (338-AC, R&D Technologies); Day 1 media: RPMI Base supplemented with 100 ng / ml Activin A and 0.2% Knockout serum replacement (KSR) (A3181502, Gibco); Day 2 media: RPMI Base supplemented with 100 ng / ml Activin A and 2% KSR; Day 3-5 Media: Advanced DMEM Base supplemented with 500 ng / ml recombinant human fibroblast growth factor-4 (FGF-4), (100-31, Peprotech), and 3 μM CHIR99021, (4423, R&D Technologies); Enrichment (EP) medium: Advanced DMEM Base supplemented with 3 uM CHIR99021, 5 ng / ml FGF2, (233-FB, R&D Technologies), 10 ng / ml vascular endothelial growth factor (VEGF), (PHC9391, Life Technologies), 20 ng / ml epidermal growth factor (EGF), (236-EG, R&D Technologies), 0.5 uM A83-01, (2939, Tocris), 50 ug / ml Ascorbic Acid, (A4544, Sigma); Retinoic acid (RA) media: Advanced DMEM Base supplemented with 2 μM RA (R2625, Sigma); Matrigel, (356237, Corning); Complete hepatocyte culture media (HCM): Lonza HCMbullet kit (CC-3198, Lonza), prepared as per manufacturer’s instructions, except no EGF, supplemented with 100 nM Dexamethasone (D4902, Sigma), 20 ng / ml recombinant human oncostatin M (300-10, Peprotech), and 10 ng / ml recombinant human hepatocyte growth factor (HGF) (100-39, Peprotech); M8 co-culture media (M8 is Complete RPMI media mixed with equal volumes of modified hepatocyte culture media (mHCM: Lonza HCM bullet kit (CC-3198, Lonza), prepared with no EGF / HGF and no Dexamethasone, supplemented 1:1 with complete RPMI. Final concentrations of + 10 IU / ml IL-7 + 10 IU / ml IL-15).

[0379] The reagents for the immune cells (CD8 T cells, DCs) in the experiments described herein include: X-vivo15 medium (LONZA) cat# BEBP04-744Q; DC medium (Xvivo15 supplemented with 1% pen / strep, 2% human serum); DC diff medium (DC + 800 IU / ml GM-CSF + 100 IU / ml IL-4); DC activation medium (DC + 1600 IU / ml GM-CSF + 100 IU IL-4 + 100 IU / ml IFNγ + 50 ng / ml LPS); T cell purification medium (Xvivo15 + 1% P / S + 50 IU / ml IL-7); T cell rest medium (DC + 200 IU / ml IL-7); T cell priming medium (DC + 50 IU / ml IL-21 + 25 IU / ml IL-12); T cell growth medium (DC + 50 IU / ml IL-7 + 50 IU / ml IL-15); T cell assay medium (DC + 10 IU / ml IL-7 + 10 IU / ml IL-15); M8 co-culture media (M8 is Complete RPMI media mixed with equal volumes of modified hepatocyte culture media (mHCM: Lonza HCM bullet kit (CC-3198, Lonza), prepared with no EGF / HGF and no Dexamethasone, supplemented 1:1 with complete RPMI. Final concentrations of + 10 IU / ml IL-7 + 10 IU / ml IL- 15)

[0380] Recombinant human cytokines information (Peprotech): Cytokine aliquots (1 million IU / mL) in xVivo15 in PCR tubes / strips; Human IL-2, Cat# 200-02500 ug; lot# 022212 C2922; Activity 10k IU / ug; Human GM-CSF, Cat# 300-031 250 ug; lot# 111930 D2822; Activity 10k IU / ug; Human IFN-γ, Cat# 300-02100 ug; lot# 091927 C2422; Activity 20k IU / ug; Human IL-4, Cat# 200-04 100 ug; lot# 051914 K2221; Activity 5k IU / ug; Human IL-7, Cat# 200-07100 ug; lot# 052217 F0622; Activity 2k IU / ug; Human IL-15, Cat# 200-15100 ug; lot# 032224 D0622; Activity 2k IU / ug; Human IL-21, Cat# 200-21100 ug; lot# 0721226-1 A1722; Activity 2k IU / ug; Human IL-12, Cat# 200-12250 ug; lot# 0617S96-1; Activity 1k IU / ug; IL-7 0.2mL (1x10^6 IU / mL); GM-CSF 2.5mL (1x10^6 IU / mL) - aliquoted 50uL; IFN-γ 2mL (1x10^6 IU / mL); IL-4 500ul (1x10^6 IU / mL); IL-15 500ul (1x10^6 IU / mL); IL-21 200uL (1x10^6 IU / mL); IL-22.5mL (1x10^6 IU / mL); IL-12250uL (1x10^6 IU / mL).

[0381] Various supplies and consumables used for the experiments described herein include: EasySep Human Naïve CD8 T cells isolation kit II (STEMCELL) cat# 17968; MV (pp65) Peptide Pool (STEMCELL) cat# 100-0668; p65 MW is ~943.18 Da = 943.18g / mol; stock 50mg / mL - ~50mM; Normal Human Serum (Sigma; heat inactivated) cat# H3667 or autologous serum; enzonase Nuclease (Millipore-Sigma) cat# E1014; Pen-Strep (x100; Gibco) cat# 15140122; Ficoll Paque Plus (Cytiva) cat# 17-1440-03 or Lymphoprep (StemCell) cat# 07801; PBS Ca-Mg- (Gibco) cat# 14190144; StemCell SepMate™-50 CATALOG #15450; Cell culture dishes. BD Multi-well Flat-Bottom Dishes (353046, Corning); 500um 96-well Gri3D® (SUN bioscience) plates. iPSC Cell Lines and Cell Culture

[0382] The human iPSC lines used in this study are summarized in Table 1. Patient- derived cells were obtained with informed consent in compliance with institutional ethics guidelines (Institutional Review Board, Cincinnati Children’s Hospital Medical Center) and reprogrammed into iPSCs by the CCHMC Pluripotent Stem Cell Facility. Upon establishment, all human iPSC lines underwent comprehensive quality control following ISCCR and were routinely authenticated every 10 passages. Routine quality control assessments included karyotype analysis, short tandem repeat (STR) profiling, pluripotency marker expression, and mycoplasma contamination testing. iPSC expansion and maintenance were performed as known in the art. Briefly, undifferentiated iPSCs were cultured on Laminin-iMatrix-511 silk coated dishes (Nacalai) in mTSER complete medium (STEMCELL Technologies) supplemented with 10 uM Rock inhibitor Y27632 (Tocris). Cells were maintained at 37°C in 5% CO₂ and 95% air.

[0383] Induction of posterior foregut cells. Human iPSCs were differentiated into foregut cells using previously described methods. In brief, iPSCs were detached by Accutase (Thermo Fisher Scientific) and were seeded on laminin coated tissue culture plate with 100,000 cells / cm2. Medium was changed to RPMI 1640 medium (Life Technologies) containing 100 ng / mL Activin A (Irvine Scientific) and 50 ng / mL bone morphogenetic protein 4 (BMP4; R&D Systems) at day 1, 100 ng / mL Activin A and 0.2% Knockout serum replacement (KOSR; Gibco) at day 2, and 100 ng / mL Activin A and 2% KOSR at day 3. On days 4 to 6, cells were cultured in Advanced DMEM / F12 (Thermo Fisher Scientific) with B27 (Gibco) and N2 (Gibco)containing 500 ng / ml fibroblast growth factor (FGF4, Peprotech) and 3 μM CHIR99021 (R&D Technologies). Cells were maintained at 37 °C in 5% CO2 with 95% air and the medium was replaced every day. The foregut cells were detached by Accutase and seeded into Gri3D plates or used to generate standard HLO cultures in Matrigel dome.Table 1. Human iPSC lines used in this study. No Line ID Age†Sex†Race†HLA Haplotype Class I15 680 39 Female White A*01:01 / A*02:01-B*15:01 / B*57:01- C*03:03 / C*06:02Generation of HLO Microarray Culture

[0384] Foregut cells were dissociated using Accutase, centrifuged at 500g rpm for 5 minutes at 4°C, and resuspended in organoid enrichment medium. This medium consisted of Advanced DMEM / F12 supplemented with 3 uM CHIR99021, 5 ng / ml FGF2, (R&D Technologies), 10 ng / ml vascular endothelial growth factor (VEGF), (Life Technologies), 20 ng / ml epidermal growth factor (EGF), (R&D Technologies), 0.5 uM A83-01, (Tocris), 50 ug / ml Ascorbic Acid, (Sigma), and 2% Matrigel (Corning). The resulting cell suspension was seeded into Gri3D plates (500 μm microcavities, Sun Biosciences, Switzerland) at a density of 250 cells / 50uL per microcavity. After allowing cells to settle, 130 μL of organoid enrichment medium without Matrigel was added through the media exchange port. Cultures were incubated at 37°C. After four days, the medium was replaced with liver specification medium consisting of Advanced DMEM / F12 supplemented with 2 μM retinoic acid (RA, Sigma) and maintained for an additional four days. This was followed by nine-day culture in liver maturation medium. The liver maturation medium was based on HCM media (Lonza), prepared according to the manufacturer’s instructions, but without EGF, and supplemented with 100 nM Dexamethasone (Sigma), 20 ng / ml recombinant human oncostatin M (Peprotech), and 10 ng / ml recombinant human hepatocyte growth factor (HGF) (Peprotech). HLO microarray cultures were maintained at 37°C till they are fully matured. Media changes were performed every two days during the organoid formation and specification phases and daily during the liver maturation stage. Generation of Conventional HLO Culture

[0385] Foregut cells released using Accutase were centrifuged at 500g for 5 minutes, resuspended in Matrigel (Corning) and cultured using modified methods. Briefly, a total of 100,000 cells were embedded in 50μl Matrigel drop on the dishes in organoid formation media with 5 factors for 4 days. After organoid formation, the media was switched to liver specification media for 4 days. After the liver specification step, organoids were harvested from Matrigel by scratching and pipetting. Then organoids were re-embedded in Matrigel and grown in liver maturation media for an additional 9 days till they reached full maturation state. Immunostaining

[0386] HLOs were fixed in 4% paraformaldehyde (Wako) in phosphate-buffered saline overnight at 4°C. Samples were permeabilized with 0.5% Triton X-100 in 1×PBS, blocked with donkey serum (Millipore) and probed with primary antibodies against albumin (Bethyl) and Vimentin (Abcam) at 4 °C for 48h. Samples were probed with secondary antibodies conjugated with Alexa Fluor (Life Technologies) and DAPI (Sigma-Aldrich) for nuclear staining. Images were acquired using ImageXpress Micro Confocal High-Content Imaging System (Molecular Devices). Immunohistochemistry

[0387] Paraffin-embedded tissue sections were deparaffinized, rehydrated and boiled to retrieve antigens (10mM citrate buffer, pH=6) under heat-induced conditions, followed by two washes in PBS. Sections were blocked with 10% Normal Donkey Serum (NDS) in PBS-T (PBS / 0.1% Triton X-100) for 1h at RT. Primary antibodies were hand-applied and incubated for 32 minutes. After incubation, slides were treated with Multimer HRP, followed by the application of one drop of OmMap anti-Mouse HRP for 20 minutes. Detection was visualized using DAB chromogen, and sections were counterstained with Hematoxylin II for 8 minutes, followed by application of a bluing reagent for 4 minutes. Finally, slides were washed in PBS, dehydrated, and mounted with ProLong™ Gold Antifade Mountant (Invitrogen) For imaging, slides were analyzed using a Leica DM18. Antibodies used are listed in the key resources table. Gene Expression Analysis

[0388] RNA was extracted and purified by Quick-RNA miniprep kit (Zymo Research, cat. R1051) following manufacturer protocol. Briefly Matrigel embedded and Gri3D grown organoids were washed twice in PBS. Organoids were submerged in RNA lysis buffer, and debris was removed by centrifugation prior to purification. RNA concentration and purity was assessed by Nanodrop (Thermofisher). CDNA was synthesized using 200 ng total RNA using a Superscript IV VILO synthesis kit (Thermofisher). PCR was performed using TaqMan gene expression master mix (Applied Biosystems) on a QuantStudio 6 Flex Real-Time PCR System (Thermo, Applied biosystems). All primers and probes used are listed in the key resource table,Biochemical Assays

[0389] Culture supernatants were analyzed to quantify albumin and CK18 levels using sandwich ELISA kits (Albumin, Abcam and M65 EpiDeath® CK18Diapharma) according to manufacturer’s protocols. TNFα and Granzyme B secretion were measured using the Luminex Discovery Assay kit (R&D Systems / Biotechne) according to the manufacturer’s protocol. HLO Viability Assay

[0390] Cell viability was assessed using the CellTiter-Glo® 3D Cell Viability Assay (Promega, Cat. G9682) on Gri3D-grown human liver organoids (HLOs). Test compounds were added to experimental wells, and plates were incubated according to the culture protocol, ensuring lack of well-to-well contamination. Following a 7–day treatment, Gri3D plates were equilibrated to room temperature (22–25°C) for 30 minutes before adding an equal volume of CellTiter-Glo® 3D Reagent to the culture medium. The contents were mixed vigorously for 30 minutes to induce cell lysis, allowing ATP extraction from the 3D microtissues. Lysates were moved to opaque-walled 96-well plates for luminescence reading. Plates were then incubated at room temperature for an additional 25 minutes to stabilize the luminescent signal before recording luminescence using a Spectra Max iD3 microplate reader. Instrument settings were adjusted according to the manufacturer’s recommendations, with an integration time of 0.25–1 second per well. Image Analysis and Quantification

[0391] Acquired brightfield images were processed using INCarta® high-content image analysis software (Molecular Devices) and a deep learning-based model, SINAP, pretrained with thousands of images of stem cells and organoids. SINAP allows the user to define on-demand objects of interest specific for the use case and learns from the parameters captured in the training dataset (e.g., morphology, texture, intensity, etc.) to further finetune the hyperparameters of the pretrained model enabling accurate and fast image segmentation. A SINAP module was trained by encircling the boundaries of HLOs grown in Gri3D and Matrigel plates as signal while the background was defined by marking regions not covered by HLOs. Toensure the inclusiveness of different morphologies, HLO images were utilized from different donors, batches, and morphologies in training the SINAP model. SINAP-generated masks were visually compared to raw images and demonstrated high accuracy in segmenting HLOs. The number and size of the organoids were then analyzed using in-house written python scripts. PBMC Isolation and DC Differentiation

[0392] Peripheral blood mononuclear cells (PBMCs) were isolated from blood samples using density gradient centrifugation (SepMate™-50, STEMCELL Technologies). The whole blood was diluted with an equal volume of DPBS (Gibco) and layered over density gradient medium (Ficoll Paque Plus, Cytiva). The PBMCs were collected, washed with DPBS, and resuspended in X-Vivo15 medium (Lonza). Monocytes were isolated by adherence from PBMCs cultured for 3 hours in DC medium (X-Vivo supplemented with 1% penicillin / streptomycin and 2% human serum (ThermoFisher) and differentiated into dendritic cells (DCs) using a cocktail of 100 IU / ml IL-4 and 800 IU / ml GM-CSF (Peprotech) for 4 days. Naïve CD8+ T Cell Isolation and Priming

[0393] Naïve CD8⁺ T cells were isolated from PBMCs using the EasySep Human Naïve CD8 T Cell Isolation Kit II (STEMCELL Technologies) according to the manufacturer protocol. Isolated CD8+ T cells were resuspended in X-Vivo15 media supplemented with 1% penicillin / streptomycin (ThermoFisher) and 50 IU / ml IL-7 (Peprotech) and incubated at 37°C for 4 hours. For the initial priming, immature DCs were matured and activated with 1600 IU / ml GM-CSF, 100 IU / ml IL-4, 100 IU / ml IFN-γ (Peprotech), and 50 ng / ml LPS (InvivoGen). DCs were pulsed with Flucloxacillin at 1000 μM (Flux loading) or media alone as a mock condition. Naïve CD8+ T cells were added to Mock / Flux-loaded DCs in T cell priming medium consisting of DC medium supplemented with 50 IU / ml IL-21, 25 IU / ml IL-12 (Peprotech) at a 3:1 T cell- to-DC ratio. After three days, the medium was replaced with T cell growth medium containing DC medium with 50 IU / ml IL-7, 50 IU / ml IL-15 (Peprotech), and cells were cultured for an additional nine days, bringing the total culture time to 12 days. For the second priming, fresh DCs were prepared and loaded as described above. T cells were collected and co-cultured with the freshly prepared DCs at a 5:1 T cell-to-DC ratio for two days in DC medium supplementedwith 10 IU / ml IL-7, 10 IU / ml IL-15. T cell antigen-specific activation efficacy was evaluated using multi-color flow cytometry with Diva and FlowJo (BD software). T cell proliferation and activation were assessed using CFSE (1 µM, ThermoFisher) for proliferation, Human TruStain FcX for Fc receptor blocking, and a panel of antibodies including CD3 (clone UCHT1), CD8 (clone 3B5), CD4 (clone RPA-T4), CD45RO (clone UCHL1), CD107a (clone H4A3), HLA-DR (clone TU36), CD137 (clone 4B4), and CD69 (clone FN50). All reagents were used according to manufacturer’s recommendations and are detailed in the key resource table. The strength of the response was graded according to the stimulation index (SI). The stimulation index is defined as a fold-change increase in the CFSElow (divided) or T cell activation marker-positive cell population after priming with the Flucloxacillin relative to the CFSEhigh (undivided) marker- positive cells in non-primed population (medium alone). HLO and T Cell Co-Culture

[0394] Following initial 12 day priming as described above, CD8+ T cells were stained with CFSE (5 µM, Fisher Scientific, Catalog No. 11-0699-42) and resuspended in an optimized co-culture media. This media consisted of a 1:1 mixture of complete RPMI (RPMI + 1% penicillin / streptomycin and 150 IU / ml IL-2) and modified liver maturation media (excluding HGF, dexamethasone and hydrocortisone) supplemented with 10 IU / ml IL-7 and 10 IU / ml IL- 15. Labeled CD8+ T cells were added to mature (day 23) HLO microarray cultures at the specified effector-to-target ratios. Prior to co-culture, HLO were pretreated with 100 μM Flucloxacillin for 72 hours. The co-culture was maintained for 72 hours with media exchanges performed every 24 hours. When indicated, T cell activation was induced using anti-CD3 (1 μg ml–1, BioLegend) and anti-CD28 (1 μg ml–1, BioLegend) antibodies. Quantification and Statistical Analysis

[0395] Statistical analyses were carried out using GraphPad Prism 10.0 (GraphPad Software,Inc., CA, USA). Group sizes, definition of error bars and statistical analysis performed are indicated in figure legends.EXAMPLE 2 Methods of generating HLO:immune cell co-cultures

[0396] An exemplary process for generating HLOs, and subsequent HLO:immune cell co-cultures, is provided below. All incubation steps were at 37C unless stated otherwise. Differentiation of iPSCs to Posterior Foregut

[0397] Laminin dilution was used to coat the dish, as laminin provides a basement membrane for iPSCs to be grown and used for differentiation, and the dish was incubated.

[0398] Day -1: mTeSR1 was aspirated from existing iPSCs, and 1 mL Accutase / well was added to a multi-w...

Claims

CLAIMS What is claimed is:

1. A co-culture media composition for co-culturing human liver organoids (HLOs) with immune cells, wherein the co-culture media composition comprises a first culture media comprising hepatocyte basal medium (HBM) comprising transferrin, ascorbic acid, insulin, and bovine serum albumin (BSA), and a second culture media comprising X-VIVO15 or RPMI.

2. The co-culture media composition of claim 1, wherein: wherein the co-culture media composition further comprises oncostatin M (OSM) and hepatocyte growth factor (HGF).

3. The co-culture media composition of claim 1 or claim 2, wherein the co-culture media composition further comprises Penicillin / Streptomycin (Pen / Strep), human serum, IL-2, IL-7, IL-15, and / or IL-21, and wherein the co-culture media composition does not comprise epidermal growth factor (EGF).

4. The co-culture media composition of any of claims 1-3, wherein the co-culture media composition comprises IL-15 and IL-21 and does not comprise EGF.

5. The co-culture media composition of any of claims 1-4, wherein the first culture media and / or the second culture media is prepared without immunomodulators.

6. The co-culture media composition of any of claims 2-5, wherein immunomodulators comprise hydrocortisone, hEGF, HGF, and / or dexamethasone.

7. The co-culture media composition of any of claims 2-6, wherein the second culture media further comprises glutamine.

8. The co-culture media composition of any of claims 1-7, wherein the co-culture media composition comprises, by volume, about 10%-90%, 30%-70%, 40%-60%, or any intermediate or intervening ratio between these ratios, of the first culture media; and wherein the co-culture media composition further comprises about 10%-90%, 30%-70%, 40%-60%, or any intermediate or intervening ratio between these ratios, of the second culture media.

9. The co-culture media composition of any of claims 1-8, wherein the co-culture media composition comprises, by volume, about 30%-70%, or any intermediate or intervening ratio between these ratios, of the first culture media; and wherein the co-culture media composition further comprises about 30%-70%, or any intermediate or intervening ratio between these ratios, of the second culture media.

10. The co-culture media composition of any of claims 1-9, wherein the co-culture media composition comprises, by volume, about 45%-55% of the first culture media; and wherein the co-culture media composition further comprises about 45%-55% or any intermediate or intervening ratio between these ratios, of the second culture media; optionally wherein the co- culture media composition comprises, by volume, about 50% of the first culture media; and wherein the co-culture media composition further comprises about 50% of the second culture media.

11. The co-culture media composition of any of claims 1-10, wherein the co-culture media composition comprises the first culture media and the second culture media in a ratio, by volume, of about 1 / 99, 10 / 90, 20 / 80, 30 / 70, 40 / 60, 50 / 50, 60 / 40, 70 / 30, 80 / 20, 90 / 10, or 99 / 1, or any intermediate or intervening ratio between these ratios.

12. The co-culture media composition of any of claims 1-11, wherein the co-culture media composition comprises the first culture media and the second culture media in about a 40 / 60, 50 / 50, or 60 / 40 ratio, or any intermediate or intervening ratio between these ratios.

13. The co-culture media composition of any of claims 1-12, wherein the co-culture media composition comprises the first culture media and the second culture media in a ratio, by volume, of about 1 / 99, 10 / 90, 20 / 80, 30 / 70, 40 / 60, 50 / 50, 60 / 40, 70 / 30, 80 / 20, 90 / 10, or 99 / 1, or any intermediate or intervening ratio between these ratios, and further comprises about 0.01- 1000 ng / ml OSM, about 0.01-1000 ng / ml HGF, about 0.1-1000 IU / ml IL-2, about 0.1-1000 IU / ml IL-7, about 0.1-1000 IU / ml IL-15, and / or about 0.1-1000 IU / ml IL-21, or any intermediate or intervening ratio between these ratios.

14. The co-culture media composition of any of claims 1-13, wherein the co-culture media composition comprises the first culture media and the second culture media in about a 40 / 60, 50 / 50, or 60 / 40 ratio, or any intermediate or intervening ratio between these ratios, and further comprises about 0.1-50 ng / ml OSM, about 0.1-50 ng / ml HGF, about 1-100 IU / ml IL-2, about 1- 100 IU / ml IL-7, about 1-100 IU / ml IL-15, and / or about 1-100 IU / ml IL-21, or any intermediate or intervening ratio between these ratios.

15. The co-culture media composition of any of claims 1-14, wherein the co-culture media composition comprises about 10-1000 IU / mL, 50-500 IU / mL, or 80-300 IU / mL IL-2, and / or about 0.01%-10%, 0.1%-5%, or 0.5%-2% Pen / Strep.

16. The co-culture media composition of any of claims 1-15, wherein the co-culture media composition comprises about 100-250 IU / mL IL-2, and / or about 0.5-2% Pen / Strep.

17. The co-culture media composition of any of claims 1-16, wherein the co-culture media composition comprises about 45-55% the first culture media, about 45-55% the second culture media, and further comprises about 1-40 ng / ml OSM, about 1-40 ng / ml HGF, about 1-50 IU / ml IL-2, about 1-50 IU / ml IL-7, about 1-50 IU / ml IL-15, and / or about 1-50 IU / ml IL-21; optionally wherein the co-culture media further comprises about 0.5-2% Pen / Strep.

18. The co-culture media composition of any of claims 1-17, wherein the immune cells comprise CD8 T cells.

19. A composition, comprising the co-culture media composition of any of claims 1-18, and further comprising: one or more human liver organoid (HLO), and immune cells, thereby providing a HLO:immune cell composition in culture media.

20. A HLO:immune cell composition, comprising one or more human liver organoid (HLO), and immune cells, thereby providing a HLO:immune cell composition.

21. The composition of claim 19 or claim 20, wherein the immune cells comprise peripheral blood mononuclear cells (PBMCs).

22. The composition of any of claims 19-21, wherein the immune cells comprise CD8 T cells, CD4 T cells, NK cells, monocytes, macrophages, and / or dendritic cells.

23. The composition of any of claims 19-22, wherein the HLO and immune cells are co- cultured in the culture media.

24. The composition of any of claims 19-23, wherein the HLO and / or immune cells are derived from pluripotent stem cells; optionally wherein the pluripotent stem cells comprise embryonic stem cells or induced pluripotent stem cells.

25. The composition of any of claims 19-23, wherein the HLO and / or immune cells are derived from primary cells.

26. The composition of any of claims 19-25, wherein the immune cells comprise T cells and / or monocyte-derived dendritic cells (mDCs).

27. The composition of any of claims 19-26, wherein the immune cells comprise CD4 and / or CD8 T cells.

28. The composition of any of claims 19-27, wherein the immune cells comprise CD8 T lymphocytes, comprising effector CD8 cells, proliferating effector CD8 cells, antigen-activated CD8 cells, cytotoxic CD8 cells, effector memory CD8 cells, and / or regulatory CD8 cells.

29. The composition of any of claims 19-28, wherein the one or more HLO and the immune cells are derived from a single subject.

30. The composition of any of claims 19-29, wherein the one or more HLO and the immune cells are derived from different subjects; optionally wherein the HLO and / or immune cells are derived from a universal donor and / or from hypoimmune stem cells.

31. The composition of any of claims 19-30, wherein the immune cells have been primed with one or more exogenous agent prior to co-culturing with the HLO.

32. The composition of any of claims 19-31, wherein the HLO has been pre-treated with one or more exogenous agent prior to co-culturing with the immune cells.

33. The composition of any of claims 19-32, wherein the immune cells and HLOs are co- cultured in a ratio of about 1:1, 5:1, 10:1, 50:1, 100:1, 200:1, 300:1, 400:1, 500:1, 600:1, 700:1, 800:1, 900:1, 1000:1, 1500:1, 2000:1, 5000:1, 10,000:1, or greater, or any value between these ratios, immune cells to HLOs; optionally about 50-5000:1 immune cells to HLOs.

34. The composition of any of claims 19-33, wherein the immune cells and HLOs are co- cultured in a ratio of about 1:10, 1:5, 1:4,1:3, 1:2, 1:1, 2:1, 3:1, 4:1, 5:1, 10:1, 20:1, 30:1, 40:1, 50:1, 100:1, or any value between these ratios, immune cells to liver cells; optionally about 1- 50:1 immune cells to liver cells.

35. The composition of any of claims 19-34, wherein the HLOs and immune cells have been co-cultured in the culture media for a time period selected from about 12 hours to about 10 days, or longer.

36. The composition of any of claims 19-35, wherein the HLOs and immune cells have been co-cultured in the culture media for about 3 days, + / - 1 day, to about 7 days, + / - 1 day.

37. The composition of claims 19-36, wherein the composition is co-cultured via a droplet, multi-well plate, microcavity array culture platform, and / or organ-on-chip device.

38. The composition of claim 37, wherein the microcavity array culture platform comprises one or more Gri3D® plate; AggreWell™ plate; Elplasia® plate; ultra-low attachment (ULA), or ultra-low adhesion, plate; micro-patterned hydrogel plate; SmartSphero plate; Acura plate; Sphericalplate 5D; microfluidic culture device; and / or hanging drop plate.

39. The composition of claims 19-38, wherein the composition and / or culture platform do not comprise a basement membrane matrix.

40. The composition of any of claims 19-39, wherein the HLOs and the immune cells self- assemble.

41. The composition of any of claims 19-40, wherein the HLOs and the immune cells self- assemble into a three-dimensional form.

42. The composition of any of claims 19-41, wherein the immune cells spontaneously migrate toward the HLO.

43. The composition of any of claims 19-42, wherein the immune cells infiltrate the HLO.

44. The composition of any of claims 19-43, wherein the HLO comprises endothelial cells, mesenchymal cells, and cholangiocytes.

45. The composition of any of claims 19-44, wherein the HLO comprises one or more additional cell type selected from hepatoblasts, epithelial cells, Kupffer cells, stellate cells.

46. The composition of any of claims 19-45, wherein the HLO comprises epithelial cells comprising hepatocytes, and mesenchymal cells comprising hepatic stellate cells 47. The composition of any of claims 19-46, wherein the HLO comprises a luminal structure.

48. The composition of claim 47, wherein the luminal structure comprises internalized microvilli.

49. The composition of any of claims 19-48, wherein the HLO comprises a structure with a single lumen.

50. The composition of any of claims 19-49, wherein the HLO is an artificial liver organoid, and / or is generated in vitro.

51. The composition of any of claims 19-50, wherein the HLO is three-dimensional.

52. The composition of any of claims 19-51, wherein the HLO is a mature liver organoid.

53. An in vitro method for co-culturing one or more human liver organoid (HLO) with immune cells, the method comprising: differentiating and / or culturing the one or more HLO in a co-culture media composition according to any of claims 1-18 for a first period of time; suspending the immune cells in a co-culture media composition according to any of claims 1-18 for a second period of time; andco-culturing the one or more HLO with the immune cells in a co-culture media composition of any of claims 1-18 for a third period of time, to provide an HLO:immune cell co- culture system; and wherein the HLO and / or immune cells are derived from pluripotent stem cells and / or primary cells; optionally wherein the pluripotent stem cells are embryonic stem cells or induced pluripotent stem cells.

54. The method of claim 53, wherein the immune cells comprise peripheral blood mononuclear cells (PBMCs).

55. The method of any of claims 53-54, wherein the immune cells comprise CD8 T cells, CD4 T cells, NK cells, monocytes, macrophages, and / or dendritic cells.

56. The method of any of claims 53-55, wherein the immune cells comprise T cells and / or monocyte-derived dendritic cells (mDCs).

57. The method of claim 56, wherein the T cells comprise CD8 T lymphocytes, comprising effector CD8 cells, proliferating effector CD8 cells, antigen-activated CD8 cells, cytotoxic CD8 cells, effector memory CD8 cells, and / or regulatory CD8 cells.

58. The method of any of claims 53-57, wherein the one or more HLO and the immune cells are derived from a single subject.

59. The method of any of claims 53-57, wherein the one or more HLO and the immune cells are derived from different subjects; optionally wherein the HLO and / or immune cells are derived from a universal donor and / or from hypoimmune stem cells.

60. The method of any of claims 53-59, wherein the HLOs and immune cells have been co- cultured in the culture media for a time period selected from about 12 hours to about 10 days, or longer.

61. The method of any of claims 53-60, wherein the HLOs and immune cells have been co- cultured in the culture media for about 3 days, + / - 1 day, to about 7 days, + / - 1 day.

62. The method of any of claims 53-61, wherein the one or more HLO is co-cultured with the immune cells in a droplet or microcavity array culture platform.

63. The method of claim 62, wherein the droplet or microcavity array culture platform comprises one or more Gri3D® plate; AggreWell™ plate; Elplasia® plate; ultra-low attachment (ULA), or ultra-low adhesion, plate; micro-patterned hydrogel plate; SmartSphero plate; Acura plate; Sphericalplate 5D; microfluidic culture device; and / or hanging drop plate.

64. The method of any of claims 53-63, wherein the composition and / or culture platform do not comprise a basement membrane matrix.

65. The method of any of claims 53-64, wherein the HLOs and the immune cells self- assemble into a three-dimensional form.

66. The composition of any of claims 53-65, wherein the immune cells spontaneously migrate toward the HLO.

67. The composition of any of claims 53-66, wherein the immune cells infiltrate the HLO.

68. The method of any of claims 53-67, wherein the first period of time is between about 12 hours to about 10 days, or longer; and / or wherein the second period of time is between about 0 days to about 10 days, or longer; and / or wherein the third period of time is between about 12 hours to about 10 days, or longer.

69. The method of any of claims 53-68, wherein the immune cells and HLOs are co-cultured in a ratio of about 1:1, 5:1, 10:1, 50:1, 100:1, 200:1, 300:1, 400:1, 500:1, 600:1, 700:1, 800:1,900:1, 1000:1, 1500:1, 2000:1, 5000:1, 10,000:1, or greater, or any value between these ratios, immune cells to HLOs; optionally about 50-5000:1 immune cells to HLOs.

70. The method of any of claims 53-69, wherein the immune cells and HLOs are co-cultured in a ratio of about 1:10, 1:5, 1:4,1:3, 1:2, 1:1, 2:1, 3:1, 4:1, 5:1, 10:1, 20:1, 30:1, 40:1, 50:1, 100:1, or any value between these ratios, immune cells to liver cells; optionally about 1-50:1 immune cells to liver cells.

71. The method of any of claims 53-70, wherein posterior foregut cells for forming the HLOs are seeded at a density of greater than about 1×104cells / well, greater than about 0.5×105cells / well, greater than about 1×105cells / well, greater than about 2×105cells / well, greater than about 3×105cells / well, greater than about 4×105cells / well, greater than about 5×105cells / well, or higher.

72. The method of any of claims 53-71, wherein the HLOs for co-culturing are present in a well density of about 1-500 organoids per well; optionally about 5-200 organoids per well.

73. The method of any of claims 53-72, wherein the HLOs for co-culturing are in a microcavity array culture platform in a well density of about 5-200 organoids per well; optionally about 30-100 organoids per well.

74. The method of any of claims 53-73, wherein the HLOs for co-culturing are in a droplet culture platform in a well density of about 5-200 organoids per well; optionally about 10-70 organoids per well.

75. The method of any of claims 53-74, wherein the co-culture media composition comprises a first culture media comprising hepatocyte basal medium (HBM) comprising transferrin, ascorbic acid, insulin, and bovine serum albumin (BSA), and a second culture media comprising X-VIVO15 or RPMI, and optionally further comprises Penicillin / Streptomycin (Pen / Strep), human serum, IL-2, IL-7, IL-15, and / or IL-21.

76. The method of any of claims 53-75, wherein the HLO comprises endothelial cells, mesenchymal cells, and cholangiocytes.

77. The method of any of claims 53-76, wherein the HLO comprises one or more additional cell type selected from hepatoblasts, epithelial cells, Kupffer cells, stellate cells.

78. The method of any of claims 53-77, wherein the HLO comprises epithelial cells comprising hepatocytes, and mesenchymal cells comprising hepatic stellate cells.

79. The method of any of claims 53-78, wherein the HLO comprises a luminal structure.

80. The method of claim 79, wherein the luminal structure comprises internalized microvilli.

81. The method of any of claims 53-80, wherein the HLO comprises a structure with a single lumen.

82. The method of any of claims 53-81, wherein the HLO is an artificial liver organoid and / or is generated in vitro.

83. The method of any of claims 53-82, wherein the HLO is three-dimensional.

84. The method of any of claims 53-83, wherein the HLO is a mature liver organoid.

85. The method of any of claims 53-84, the method further comprising priming the immune cells with one or more exogenous agent, and / or pre-treating the HLO with one or more exogenous agent, prior to co-culturing with the one or more HLO; and optionally further comprising analyzing the composition to assess liver cell viability and / or function, and / or to assess immune cell maturation, proliferation, and / or activation, following treatment with the one or more exogenous agent.

86. The method of claim 85, wherein the immune cells primed with one or more exogenous agent comprise CD8 T cells.

87. The method of any of claims 85-86, wherein priming the immune cells with one or more exogenous agent prior to co-culturing comprises: differentiating monocyte-derived dendritic cells (mDCs) and / or autologous antigen presenting cells (APCs), in the presence of the one or more exogenous agent, to provide pre- stimulated mDCs and / or pre-stimulated APCs; culturing naïve immune cells with the pre-stimulated mDCs and / or pre-stimulated APCs; and stimulating the naïve immune cells and pre-stimulated mDCs and / or pre-stimulated APCs with the one or more exogenous agent, to provide stimulated immune cells.

88. The method of claim 87, wherein the naïve immune cells comprise naïve CD8 T cells.

89. The method of any of claims 87-88, wherein the mDCs and / or naïve immune cells are derived from peripheral blood mononuclear cells (PBMCs).

90. The method of any of claims 87-89, wherein the APCs comprise a B cell lymphoblastoid line, and / or Kupffer cells; optionally wherein said APCs are primary or derived from hPSCs, or wherein said APCs are derived from the HLO.

91. The method of any of claims 87-89, wherein the mDCs and / or APCs are differentiated via EBV transformation.

92. The method of any of claims 87-91, wherein culturing naïve immune cells with the pre- stimulated mDCs and / or pre-stimulated APCs is via an antigen presentation assay, wherein: sub-populations of the DCs and CD8 T cells are re-stimulated with the first exogenous agent for one or more additional period of time, at one or more different concentrations; and / orsub-populations of the DCs and CD8 T cells are stimulated with a control exogenous agent for one or more additional period of time, at the same or different concentrations.

93. The method of any of claims 87-92, wherein the method further comprises one, two, three, four, five, or more additional steps of re-stimulating the naïve immune cells and pre- stimulated mDCs and / or pre-stimulated APCs with the one or more exogenous agent.

94. The method of any of claims 87-93, wherein the one or more exogenous agent is provided in different concentrations in two or more of the stimulation and re-stimulation steps.

95. The method of any of claims 87-94, wherein the method further comprises culturing the stimulated immune cells with a fresh population of pre-stimulated mDCs and / or pre-stimulated APCs.

96. The method of any of claims 87-95, wherein the step of culturing naïve immune cells with the pre-stimulated mDCs and / or pre-stimulated APCs is in the presence of IL-21 and / or b- mercaptoethanol.

97. The method of any of claims 87-96, wherein the stimulation and / or re-stimulation steps are in the presence of IL-7 and / or IL-15.

98. The method of any of claims 87-97, further comprising analyzing the composition to profile immune cells, and / or to assess viability, following treatment with the one or more exogenous agent.

99. The method of claim 98, wherein profiling immune cells comprises assessing CD8 cell maturation, proliferation, and / or antigen-specific activation, and / or wherein assessing viability comprises detecting potential liver damage.

100. The method of any of claims 87-99, wherein pre-treating the one or more HLO with one or more exogenous agent prior to co-culturing with the immune cells comprises stimulating the one or more HLO with the one or more exogenous agent, to provide a stimulated HLO.

101. A method of priming immune cells, the method comprising: differentiating monocyte-derived dendritic cells (mDCs) and / or autologous antigen presenting cells (APC) (e.g. a B cell lymphoblastoid line, and / or Kupffer cells; optionally wherein said APCs are primary or derived from hPSCs, or wherein said APCs are derived from the HLO) via EBV transformation, in the presence of the one or more exogenous agent, to provide pre-stimulated mDCs and / or pre-stimulated APCs; culturing naïve immune cells with the pre-stimulated mDCs and / or pre-stimulated APCs; and stimulating the naïve immune cells and pre-stimulated mDCs and / or pre-stimulated APCs with the one or more exogenous agent, to provide primed immune cells.

102. The method of claim 101, wherein the naïve immune cells comprise naïve CD8 T cells.

103. The method of any of claims 101-102, wherein the mDCs and / or naïve immune cells are derived from peripheral blood mononuclear cells (PBMCs).

104. The method of any of claims 101-103, wherein the APCs comprise a B cell lymphoblastoid line, and / or Kupffer cells; optionally wherein said APCs are primary or derived from hPSCs, or wherein said APCs are derived from the HLO.

105. The method of any of claims 101-104, wherein the mDCs and / or APCs are differentiated via EBV transformation.

106. The method of any of claims 101-105, wherein culturing naïve immune cells with the pre-stimulated mDCs and / or pre-stimulated APCs is via an antigen presentation assay, wherein:sub-populations of DCs and CD8 T cells are re-stimulated with the first exogenous agent for one or more additional period of time, at one or more different concentrations; and / or sub-populations of DCs and CD8 T cells are stimulated with a control exogenous agent for one or more additional period of time, at the same or different concentrations.

107. The method of any of claims 101-106, wherein the method further comprises one, two, three, four, five, or more additional steps of re-stimulating the naïve immune cells and pre- stimulated mDCs and / or pre-stimulated APCs with the one or more exogenous agent.

108. The method of any of claims 101-107, the one or more exogenous agent is provided in different concentrations in two or more of the stimulation and re-stimulation steps.

109. The method of any of claims 101-108, wherein the method further comprises culturing the stimulated immune cells with a fresh population of pre-stimulated mDCs and / or pre- stimulated APCs.

110. The method of any of claims 101-109, wherein the step of culturing naïve immune cells with the pre-stimulated mDCs and / or pre-stimulated APCs is in the presence of GM-CSF, IFNγ, IL-4, IL-12, and / or IL-21.

111. The method of any of claims 101-110, wherein the stimulation and / or re-stimulation steps are in the presence of IL-7 and / or IL-15.

112. The method of any of claims 101-111, further comprising analyzing the composition to profile immune cells, and / or to assess viability, following treatment with the one or more exogenous agent.

113. The method of claim 112, wherein profiling immune cells comprises assessing CD8 cell maturation, proliferation, and / or antigen-specific activation, and / or wherein assessing viability comprises detecting potential liver damage.

114. The method of any of claims 101-113, wherein the first exogenous agent is a therapeutic or a therapeutic candidate.

115. The method of any of claims 101-114, wherein the primed immune cell population is enriched with CD8 T cells which are reactive to the therapeutic or therapeutic candidate.

116. A primed immune cell population, prepared by the method of any of claims 101-115.

117. A method for screening a compound or composition, wherein the compound or composition to be screened comprises one or more exogenous agent, the method comprising: culturing immune cells primed with the compound or composition, with one or more human liver organoid (HLO) in the co-culture media composition of any of claims 1-17; adding the compound or composition to the co-culture of one or more HLO and primed immune cells; culturing the HLO and immune cells with the compound or composition; and assessing one or more effects of the compound or composition on the HLO and / or immune cells, thereby screening the compound or composition.

118. The method of claim 117, wherein the screening of the compound or composition comprises conducting one or more translational studies, predicting risk of immune-mediated adverse drug reaction (ADR), assessing toxicity, and / or modeling immune-driven drug-induced liver injury (DILI), following culturing with the compound or composition to be screened.

119. The method of any of claims 117-118, wherein the screening comprises determining one or more genetic risk factors for a subject from whom the HLO and / or immune cells are derived.

120. The method of any of claims 117-119, wherein the screening comprises evaluating an HLA type for a subject from whom the HLO and / or immune cells are derived; optionally wherein evaluating an HLA type comprises determining HLA type contribution to one or moreeffect of the compound or composition on the HLO and / or immune cells; optionally wherein the effect of the compound or composition on the HLO and / or immune cells comprises an adverse drug reaction and / or drug-induced liver injury.

121. The method of any of claims 117-120, wherein the screening comprises providing a prognosis for a subject from whom the HLO and / or immune cells are derived.

122. The method of any of claims 117-121, wherein the screening comprises providing a prognosis based on an HLA type, or based on one or more biomarker indicating genetic susceptibility to immune-driven drug-induced liver injury (DILI), for a subject from whom the HLO and / or immune cells are derived.

123. The method of any of claims 121-122, wherein providing a prognosis comprises predicting risk of immune-mediated adverse drug reaction (ADR), toxicity, and / or immune- driven drug-induced liver injury (DILI).

124. The method of any of claims 118-123, wherein assessing toxicity comprises assessing liver toxicity.

125. The method of any of claims 118-124, wherein assessing toxicity comprises assessing cell viability (live / dead), morphology, HLO functionality, immune cell functionality, albumin release and expression, CYP3A4 expression, and / or immune cell infiltration.

126. The method of claim 125, wherein assessing HLO functionality comprises determining levels of one or more HLO markers (e.g. CK18 (M65), albumin, and / or AST / ALT), and / or wherein assessing immune cell functionality comprises determining levels of one or more immune cell markers (e.g. IFNg, TNFa, and / or Granzyme B).

127. The method of any of claims 118-126, wherein toxicity comprises increasing expression of one or more chemokines and / or NKG2D ligands, inducing chemotaxis, promotingdifferentiation and / or multiplication of leukocytes, causing tissue extravasation, and / or contributing to CD8 T cell immune-mediated liver injury.

128. The method of any of claims 117-127, wherein assessing one or more effects of the compound or composition on the HLO and immune cells comprises detecting toxicity of the compound or composition; studying hepatocyte function and developmental divergence; studying liver-related disease; identifying therapeutic targets; identifying compounds and / or compositions which induce immune-driven liver toxicity, and / or identifying therapeutic compounds and / or compositions effective in treating a liver-related disease or disorder, optionally wherein the therapeutic compound or composition comprises an immunotherapy.

129. The method of any of claims 117-128, wherein one or more effect of the compound or composition to be screened is compared to a corresponding effect of a compound or composition associated with immune-driven drug-induced liver injury (DILI); optionally wherein the compound or composition associated with DILI comprises abacavir, carbamazepine, allopurinol, dapsone, phenytoin, lamotrigine, nevirapine, sulphamethoxazole, methazolamide, amoxicillin- clavulanate, flucloxacillin, lumiracoxib, ticlopidine, terbinafine, fenofibrate, trimethoprim- sulfamethoxazole, Polygonum multiflorum (green tea), minocycline, infliximab, pazopanib, methimazole, ximelagatran, nitrofurantoin, lumiracoxib, flupirtine, and / or one or more antithyroid, anti-HIV, and / or anti-TB therapeutic; optionally wherein the compound or composition comprises flucloxacillin.

130. The method of any of claims 117-129, wherein the HLO and immune cells are derived from a single subject.

131. The method of any of claims 117-130, wherein the screening is to determine an effect of the compound or composition in a subject from whose cells the HLO and immune cells are derived.

132. The method of any of claims 117-131, wherein the subject is a carrier of one or more genetic, acquired, or other risk factors to develop an adverse drug reaction (ADR) and / or immune-driven drug-induced liver injury (DILI).

133. The method of any of claims 118-132, wherein ADR risk is determined by scanning confocal microscopy-based HLO morphological and killing profile assessment; CK18 and albumin secretion; CYP3A4 expression; and / or assaying and / or quantifying chemokine production (e.g. CXCL9), NKG2D ligand expression (e.g. ULBP1), and / or associated CD8 T cell HLO infiltration and activation.

134. The method of any of claims 117-133, wherein the screening provides a differential response between a carrier and a non-carrier of one or more risk factors to develop an ADR and / or immune-driven DILI.

135. The method of any of claims 117-134, wherein the screening is used for one or more translational studies.

136. The method of any of claims 117-135, wherein the screening is used for patient or treatment selection in a clinical trial.

137. The method of any of claims 117-136, wherein the screening is used for predicting risk of developing an adverse drug reaction (ADR) and / or immune-driven drug-induced liver injury (DILI).

138. The method of claim 137, wherein the ADR comprises drug-induced activation of T cells and / or immune-mediated damage of liver cells.

139. Use of the composition of any of claims 19-52, as an in vitro human model system for predicting risk for develop an adverse drug reaction (ADR) and / or immune-driven drug-induced liver injury (DILI); studying hepatocyte function and developmental divergence; studying liver-related disease; detecting toxicity of a compound or composition; identifying therapeutic targets; identifying therapeutic compounds and / or compositions with a favorable safety profile and / or which are effective in treating a liver-related disease or disorder, optionally wherein the therapeutic compound or composition comprises an immunotherapy; identifying compounds and / or compositions which induce immune-driven liver toxicity; identifying and / or validating mechanisms of immune-mediated drug toxicity in a physiologically relevant setting; identifying and / or validating drug mechanism of action (MOA); and / or correlating patient genotype with one or more phenotypic drug response.

140. The method of any of claims 53-100, or the composition of any of claims 19-52, wherein the HLO is made according to a method comprising: a) activating an FGF signaling pathway and a Wnt signaling pathway in definitive endoderm cells (DE) for a first period of time; b) activating an FGF signaling pathway, a Wnt signaling pathway, and a RA signaling pathway in the cells of step a) for a second period of time, thereby differentiating the DE to posterior foregut cells; and c) culturing the posterior foregut spheroids for a third period of time to differentiate the posterior foregut cells to the HLO.

141. The method of any of claims 53-100, or the composition of any of claims 19-52, wherein the culturing the posterior foregut cells under conditions to induce expression from the heterologous expression system occurs on or about day 17 of culture of the progenitor cell population.

142. The method of any of claims 53-100 or 151-152, or the composition of any of claims 19- 52, wherein the posterior foregut spheroids are seeded for culturing on a droplet or microcavity array culture platform.

143. The method of any of claims 53-100 or 151-153, or the composition of any of claims 19- 52, wherein the posterior foregut spheroids are cultured in the absence of a basement membrane matrix.

144. Use of the composition of any of claims 19-53, for treating a liver-related disease or disorder.

145. The composition of any of claims 19-53, for use in the manufacture of a medicament for the treatment of a liver-related disease or disorder.

146. A kit comprising means for preparing a co-culture media composition according to any one of claims 1-18, for preparing a composition according to any one of claims 19-53, or for performing the method according to any one of claims 53-115, 117-138, or 140-143.

147. A kit comprising the co-culture media composition according to any one of claims 1-18.

148. A kit comprising the composition according to any one of claims 19-53.

149. The kit of any of claims 146-148, wherein one or more of the co-culture media components or composition components are provided in separate vials.

150. The kit of any of claims 146-149, wherein one or more of the co-culture media components or composition components are pre-loaded onto one or more assay platform.

151. The kit of claim 150, wherein the one or more assay platform comprises a droplet or microcavity array culture platform.

152. The kit of claim 151, wherein the droplet or microcavity array culture platform comprises one or more one or more Gri3D® plate; AggreWell™ plate; Elplasia® plate; ultra-lowattachment (ULA), or ultra-low adhesion, plate; micro-patterned hydrogel plate; SmartSphero plate; Acura plate; Sphericalplate 5D; microfluidic culture device; and / or hanging drop plate.

153. The kit of any of claims 146-152, wherein one or more of the co-culture media components, composition components, and / or assay platform are pre-frozen.

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