Composition and methods of safety testing
Early extraembryonic cells are used to assess drug safety and toxicity by monitoring differentiation and marker expression, addressing the inefficiencies of animal testing and ethical constraints in clinical trials, providing a rapid and accurate evaluation of placental development.
Patent Information
- Application Number
- PCT/CN2025/126441
- Authority / Receiving Office
- WO · WO
- Patent Type
- Applications
- Current Assignee / Owner
- Priority Date
- 2025-05-13
- Filing Date
- 2025-10-09
- Publication Date
- 2026-04-16
AI Technical Summary
Current methods for evaluating drug safety for pregnant women and extraembryonic development are inadequate due to ethical constraints in clinical trials, inefficiencies in animal testing, and inaccuracies in extrapolating animal data to human physiology, particularly for placental development and embryonic toxicity.
Utilizing early extraembryonic cells, such as trophoblast stem cells, to assess the safety of candidate agents by monitoring changes in cell features like viability, morphology, and marker expression under controlled conditions, allowing differentiation into placental cells.
Provides a rapid and accurate method to evaluate the safety and toxicity of agents for extraembryonic development, including placental development, through monitoring cell differentiation and marker expression, overcoming limitations of animal testing.
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Figure CN2025126441_16042026_PF_FP_ABST
Abstract
Description
COMPOSITION AND METHODS OF SAFETY TESTINGCROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of priority to US Application No. 63 / 705,239, filed October 9, 2024, and US Application No. 63 / 805,153, filed May 13, 2025, the content of each of which is hereby expressly incorporated by reference in its entirety. REFERENCE TO AN ELECTRONIC SEQUENCE LISTING
[0002] The content of the electronic sequence listing (275162000840seqlist. xml; Size: 39,785 bytes; and Date of Creation: September 23, 2025) is herein incorporated by reference in its entirety.FIELD
[0003] The present invention relates to the field of assessing the safety of agents such as drugs or naturally occurring substances using cultured cells.BACKGROUND OF THE INVENTION
[0004] Reproductive disorders and birth defects are major public health issues. The safety evaluation of various foods, health products and drugs are of great significance for improving reproductive health and reducing reproductive disorders and birth defects. Due to ethical issues, the safety of mother and fetus is of paramount importance, so pregnant women rarely participate in clinical trials.
[0005] The International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use (ICH) testing guidelines provide testing methods and indicators for male reproductive capability and toxicity, but there is a lack of guiding principles and methods for drug toxicity evaluation for female reproduction. Common methods used are still based on animal testing, including rodents such as mice, rats and rabbits. Not only these methods have a long production cycle and high costs, but also the data obtained are quite different from those of the human body and cannot replicate many physiological conditions of the human body as the test animals are different from humans in terms of physiology and pharmacokinetics. For these reasons, it is especially difficult to evaluate the effects and toxicity of drugs on extraembryonic development (such as placental development) during early pregnancy. Some studies use cell models of zebrafish to detect the reproductive toxicity of drugs, but it is difficult to extrapolate these to human body. There are also some studies that use mathematical models to evaluate the safety of substances for pregnant women; however, the source of these data is based on experimental data from existing animal models, which has the various disadvantages as discussed.
[0006] Additionally, methods for evaluating safety for embryonic development and / or for organs heavily depend on animal testing. However, testing in animals are often conducted at exposures higher than those used in humans, and may not accurately inform safety for human patients.
[0007] Accordingly, there exists a need for methods and compositions suitable for evaluating the safe of an agent for pregnant women and extraembryonic development. There also exists a need for methods and compositions suitable for evaluating the safe of an agent for embryonic development and for organs.
[0008] Stem cells and differentiated cells therefrom have extremely important prospects in areas such as drug screening, regenerative medicine, disease mechanism research, and therapeutic decision making. Traditionally, embryonic stem cells are derived from early embryos at about 100 cells, and generally do not have the ability to develop extraembryonic tissues. In recent years, expanded potential stem cells (EPSC) , naive embryonic stem cells (naive ESC) , and 8-cell-like totipotent stem cells (8CLC) have been reported to be able to differentiate into various types of tissues / cells, including three embryonic germ layers and trophoblasts that is extraembryonic. Because of their ability to differentiate into the extraembryonic lineage, these cells can be induced to produce various early extraembryonic cells, such as trophoblast stem cells (TSC) and trophoblast progenitor cells. Trophoblast stem cells and trophoblast progenitor cells have also been isolated from placental tissues.
[0009] Other cells such as syncytiotrophoblast (STB) and extravillous trophoblast (EVT) also serve important roles for the health and development of extraembryonic tissues. STBs are a continuous, specialized layer of epithelial cells. They cover the entire surface of villous trees and are in direct contact with maternal blood to establish nutrient circulation between the embryo and the mother. STBs also secrete several hormones that are important for supporting early pregnancy, including human chorionic gonadotropin (hCG) , progesterone, leptin, and human placental lactogen. EVTs are another form of differentiated trophoblast cells of the placenta. They are invasive mesenchymal cells which function to establish critical tissue connection in the developing placental-uterine interface.
[0010] The disclosures of all publications, patents, patent applications and published patent applications referred to herein are hereby incorporated herein by reference in their entirety. BRIEF SUMMARY OF THE INVENTION
[0011] The present application in one aspect provides a method of evaluating a candidate agent for its safety for extraembryonic development, comprising: (i) contacting an early extraembryonic cell and / or a cell differentiated therefrom with a test sample comprising the candidate agent and / or a metabolic product thereof; and (ii) assessing change of one or more cell features of the early extraembryonic cell and / or the cell differentiated therefrom relative to a reference early extraembryonic cell and / or a cell differentiated therefrom without contacting with the test sample. In some embodiments, the extraembryonic development comprises placenta development and / or amniotic tissue development.
[0012] In another aspect, the present application provides a method of evaluating a candidate agent for its safety for embryonic development, comprising: (i) contacting an early extraembryonic cell and / or a cell differentiated therefrom with a test sample comprising the candidate agent and / or a metabolic product thereof; and (ii) assessing change of one or more cell features of the early extraembryonic cell and / or the cell differentiated therefrom relative to a reference early extraembryonic cell and / or a cell differentiated therefrom without contacting with the test sample. In some embodiments, embryonic development comprises liver, kidney, intestine, skin, and / or heart development.
[0013] In some embodiments according to any of the methods described above, the method further comprises subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation. In some embodiments, the early extraembryonic cell and / or the cell differentiated therefrom is contacted with the test sample simultaneously with being subjected to the condition that allows differentiation. In some embodiments, the early extraembryonic cell and / or the cell differentiated therefrom is contacted with the test sample prior to being subjected to the condition that allows differentiation. In some embodiments, the early extraembryonic cell and / or the cell differentiated therefrom is contacted with the test sample after being subjected to the condition that allows differentiation.
[0014] In some embodiments according to any of the methods described above, the condition that allows differentiation comprises a cell culture medium comprising DMEM / F12, β-mercaptoethanol, Penicillin-Streptomycin-Glutamine, BSA, ITS-X, Y27632, Forskolin, and / or KnockOut Serum Replacement.
[0015] In some embodiments according to any of the methods described above, the contacting comprises contacting the early extraembryonic cell and / or the cell differentiated therefrom with the test sample at different concentrations. In some embodiments, the candidate agent and / or the metabolic product of the candidate is at from about 10 nM to about 1000 mM in the test sample.
[0016] In some embodiments according to any of the methods described above, the one or more cell features comprises cell morphology, cell viability, cell proliferation and / or differentiation, molecular characteristics, characteristics of an organoid, and / or functional characteristics. In some embodiments, (1) cell proliferation and / or differentiation comprises rate of proliferation and / or rate of change to a differentiated state; (2) functional characteristics comprise property of a cellular organelle; (3) molecular characteristics comprise: (i) presence or absence of a biomarker; (ii) level of a biomarker; (iii) secretion of a biomarker; and / or (iv) the presence or absence of a reporter molecule; and / or (4) characteristics of an organoid comprises organoid morphology and / or structures.
[0017] In some embodiments, the biomarker is selected from the group consisting of a marker of cell cycle, cell death, genomic instability, epigenetic alternations (such as DNA, RNA and protein modifications) , loss of proteostasis, telomere attrition, organelle dysfunction, disabled macroautophagy, deregulated nutrient-sensing, altered intercellular communication, cellular senescence, chronic inflammation, differentiation, endogenous transposon elements, and stem cell exhaustion. In some embodiments, the biomarker is selected from the group consisting of: β-hCG, ISL1, ITGA5, VTCN1, GABRP, NANOG, OCT4, SSEA-4, SOX2, CD29, CD44, CD46, CD58, CD73, CD90, CD105, CD117, CD166, CD106, TFAP2C, TP63, CK18, GATA2, GATA3, ELF5, KRT7, TEAD4, CBG, GCM, HLA-A, HLA-B, HLA-C, HLA-G, ITGA1, MMP2, CGB, ERVW1, SDC1, ITGB6, MUC16, CGA, CGB3, CGB5, CSH1 / 2, OVOL, cleaved Caspase-3, cleaved, active N-terminal fragment of Gasdermin D, a Cyclin-Dependent Kinase (CDK) , and combinations thereof. In some embodiments, the biomarker is a marker of cell death comprising a marker of apoptosis, pyroptosis, and / or necrosis. In some embodiments, the biomarker is a caspase.
[0018] In some embodiments, the biomarker is an RNA molecule or a protein molecule.
[0019] In some embodiments, the cellular organelle is selected from the group consisting of: nucleus, mitochondria, proteosome, endoplasmic reticulum, and Golgi apparatus, and / or wherein the property of the cellular organelle comprises number, morphology, and function of the cellular organelle.
[0020] In some embodiments according to any of the methods described above, the change in one or more cell features are evaluated about 1 day to about 8 weeks after subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation.
[0021] In some embodiments according to any of the methods described above, the candidate agent is graded on its safety.
[0022] In some embodiments according to any of the methods described above, the methods comprise grading the candidate agent on its safety at different concentrations.
[0023] In some embodiments according to any of the methods described above, the candidate agent is a drug, a food product, a nutraceutical, a cosmetic product, a component thereof, or raw material therefor.
[0024] In some embodiments according to any of the methods described above, the candidate agent is selected from the group consisting of: an antibody, a virus, a virus-like, a small molecule, a peptide, a polypeptide, a DNA, an mRNA, a guide RNA, a microRNA, an RNAi, a lncRNA, an siRNA molecule, and an antisense RNA.
[0025] In some embodiments according to any of the methods described above, the candidate agent is a naturally occurring substance.
[0026] In some embodiments according to any of the methods described above, the test sample is selected from the group consisting of: a food sample, an environmental sample, and a body fluid sample. In some embodiments, the test sample is selected from the group consisting of: a blood sample, a urine sample, and a saliva sample.
[0027] The present application in another aspect provides a composition for evaluating extraembryonic development safety, comprising an early extraembryonic cell and / or a cell differentiated therefrom, wherein the early extraembryonic cell and / or the cell differentiated therefrom optionally comprises a reporter molecule or a heterologous nucleic acid encoding a reporter molecule that is indicative of viability or differentiation of the early extraembryonic cell and / or the cell differentiated therefrom. In some embodiments, extraembryonic development comprises placenta development and / or amniotic tissue development.
[0028] The present application in another aspect provides a composition for evaluating embryonic development safety, comprising an early extraembryonic cell and / or a cell differentiated therefrom, wherein the early extraembryonic cell and / or the cell differentiated therefrom optionally comprises a reporter molecule or a heterologous nucleic acid encoding a reporter molecule that is indicative of viability or differentiation of the early extraembryonic cell and / or the cell differentiated therefrom. In some embodiments, embryonic development comprises liver, kidney, intestine, skin, and / or heart development.
[0029] In some embodiments according to any of the methods or any of the compositions described above, the early extraembryonic cell is derived from an embryonic tissue, or an extraembryonic tissue.
[0030] In some embodiments according to any of the methods or any of the compositions described above, the early extraembryonic cell is derived from a totipotent stem cell or a pluripotent stem cell selected from the group consisting of: an embryonic stem cell, an extraembryonic stem cell, an expanded potential stem cell (EPSC) , a naive pluripotent stem cell, a primed pluripotent stem cell, an induced pluripotent stem cell (iPSC) , a2-cell like cell, a4-cell like cell, an 8-cell-like cell, and an extraembryonic progenitor cell. In some embodiments, the early extraembryonic cell is derived from a pre-implantation embryonic stem cell in the 2-to 8-cell stage or the morula stage. In some embodiments, the pre-implantation embryonic stem cell in the 2-to 8-cell stage or the morula stage cell is derived from an EPSC, a ESC, or an iPSC. In some embodiments, the iPSC is derived from a somatic cell. In some embodiments, the extraembryonic progenitor cell is a placental cell. In some embodiments, the placental cell is a placental stem cell, or a placental cell that can be reprogrammed to a placental stem cell. In some embodiments, the placental stem cell is a trophoblast stem cell (TSC) , or a placental cell that can be reprogrammed to a TSC. In some embodiments, the TSC expresses one or more markers selected from the group consisting of: TFAP2C, TP63, CK18, GATA2, GATA3, ELF5, TEAD4, and KRT7. In some embodiments, placental cell that can be reprogrammed to a TSC is a syncytiotrophoblast ( “STB” ) or an extravillous trophoblast ( “EVT” ) .
[0031] In some embodiments according to any of the methods or any of the compositions described above, the early extraembryonic cell is a trophoblast stem cell ( “TSC” ) or a trophoblast progenitor cell ( “TPC” ) . In some embodiments, the early extraembryonic cell is a trophoblast stem cell ( “TSC” ) .
[0032] In some embodiments according to any of the methods or any of the compositions described above, the cell differentiated from the early extraembryonic cell is a placental cell. In some embodiments, the cell differentiated from the early extraembryonic cell is a syncytiotrophoblast ( “STB” ) , or an extravillous trophoblast ( “EVT” ) . In some embodiments, the STB has one or more characteristics selected from the group consisting of: i) is multinucleated; ii) expresses SSEA4, GCM1, CD46, CGA, ERVW-1, GATA3, OVOL, SDC1, CGB3, CGB5, and / or GCM1; iii) secretes β-hCG. In some embodiments, the EVT has one or more characteristics selected from the group consisting of: i) has a spindle shape; ii) is invasive; iii) expresses KRT7, HLA-G, ITGA1, IGTA5 and / or MMP2; and iv) does not express or expresses in low levels GATA3, HLA-A, or HLA-B.
[0033] In some embodiments according to any of the methods or any of the compositions described above, the cell differentiated from the early extraembryonic cell is a cell in an organoid. In some embodiments, the organoid is a placental organoid and / or the organoid is an organ-on-chip.
[0034] In some embodiments according to any of the methods or any of the compositions described above, the early extraembryonic cell and / or the cell differentiated therefrom is derived from a human, a non-human primate, a pig, a cow, a mouse, a rat, a bat, a rabbit, a dog, a cat, and a sheep.
[0035] In some embodiments according to any of the methods or any of the compositions described above, the early extraembryonic cell and / or the cell differentiated therefrom is genetically modified.
[0036] The present application in another aspect provides a method of evaluating a candidate agent for its safety for extraembryonic development, comprising: i) contacting an expanded potential stem cell (EPSC) and / or a cell differentiated therefrom with a test sample comprising the candidate agent and / or a metabolic product thereof; and ii) assessing change of one or more cell features of the EPSC and / or the cell differentiated therefrom relative to an EPSC and / or a cell differentiated therefrom without contacting with the test sample.BRIEF DESCRIPTION OF THE DRAWINGS
[0037] FIG. 1 is a schematic drawing of early embryonic development and the derivation of expanded potential stem cells (EPSCs) and embryonic stem cells (ESCs) .
[0038] FIG. 2 is a schematic drawing of an exemplary workflow of evaluating a drug using EPSCs and extraembryonic cells such as trophoblast stem cells (TSCs) , syncytiotrophoblasts (STBs) and extravillous trophoblasts (EVTs) .
[0039] FIG. 3 shows images of cell morphology of M1 EPSC derived TSC at different concentrations of Remdesivir ( “Remd” ) and different time points.
[0040] FIGs. 4A-4B show the effects of Remdesivir ( “Remd” ) on TSC cell viability at different concentrations. FIG. 4A shows the effects of Remdesivir ( “Remd” ) on TSC cell viability at concentrations from 0 to 2000 nM at 48 hrs after drug administration. FIG. 4B shows the effects of Remdesivir ( “Remd” ) on TSC cell viability at concentrations from 0 to 8μM.
[0041] FIGs. 5A-5B show cytotoxicity test of Remdesivir to TSC cells. FIG. 5A shows the proportion of apoptotic cells in TSC cells in the control group and those treated with Remdesivir ( “Remd” ) at 2μM for 48 hours or at 5μM for 48 hours detected by flow cytometry. FIG. 5B shows representative bright-field images of TSC cells in the control (vehicle) group and those treated with Remdesivir at 0.5μM for 48h.
[0042] FIGs. 6A-6B show the expression of TSC markers in cells treated with Remdesivir compared to control. FIG. 6A shows the expression of TSC marker genes in cells treated with Remdesivir compared to a vehicle. FIG. 6B shows the relative expression levels of trophoblast-specific miRNAs in EPSC-TSC treated with vehicle control (triangles pointing upwards) or Remdesivir (triangles pointing downwards) . Data are mean±s.d., n=3.
[0043] FIG. 7 shows immunofluorescence images of differentiation of TSC to STB as the cells become multinucleated. The cells were stained by DAPI, GCAM1, and h-CG.
[0044] FIGs. 8A-8C show the effect of Remdesivir on STBs compared to control. FIG. 8A shows the morphology of Day 6 STBs treated with Remdesivir (500 nM) during differentiation from TSC compared to a vehicle. FIG. 8B shows the number of cells that are mature STB (multinucleated; day 6) in the group treated with Remdesivir at 500 nM for 6 days compared to a vehicle. FIG. 8C shows the percentage of cells that are CGB positive in the group treated with Remdesivir at 500 nM for 6 days compared to a vehicle.
[0045] FIG. 9 shows representative immunofluorescent images of CGB in eSTB treated with vehicle control or Remdesivir at 500 nM for 2 days.
[0046] FIG. 10 shows representative immunofluorescent images of CGB and GATA2 staining in eSTB (day 2) treated with vehicle control or Remdesivir at 500 nM for 2 days. The arrow indicates fused multi-nucleated STB in the control group.
[0047] FIG. 11 shows the expression of STB markers of EPSC-TSC differentiated STB at day 6 in the group treated with Remdesivir at 500 nM compared to a vehicle.
[0048] FIG. 12 shows the secretion of hCG by STBs treated with Remdesivir at 500 nM compared to a vehicle.
[0049] FIG. 13 shows the cell morphology of EVTs on Day 8 of differentiation in the group treated with Remdesivir at 500 nM compared to a vehicle.
[0050] FIG. 14 shows the expression of EVT markers on Day 8 of differentiation from TSC in the group treated with Remdesivir at 500 nM compared to a vehicle.
[0051] FIG. 15 shows the expression of EVT markers at different time points of differentiation from TSC (TSC, Day 4, Day 6, Day 8) in the group treated with Remdesivir at 500 nM.
[0052] FIG. 16 shows representative immunofluorescent images of EVT marker HLA-G on Day 8 of differentiation in the group treated with Remdesivir (5μM, 72h) compared to a vehicle.
[0053] FIG. 17 shows the expression of EVT marker HLA-G on Day 8 of differentiation using flow cytometry in cells treated with Remdesivir at 500 nM or a vehicle.
[0054] FIG. 18 shows the invasion ability of cells treated with Remdesivir (5μM, 72h) compared to control cells.
[0055] FIG. 19 shows ELISA (pg / mL) detection of MMP2 in supernatant from different EPSC-TSC and EVTs on differentiation day 8 treated with vehicle control or Remdesivir at 500 nM for 8 days.
[0056] FIG. 20 shows representative scanning electron microscopic images of STB treated with vehicle control or Remdesivir at 500 nM.
[0057] FIG. 21 shows pseudotime analysis depicting PI-TB to PI-STB development trajectory. The black dashed arrow indicates the imputed direction of differentiation. PI-TB to PI-STB subpopulations colored by machine learning predicted pseudotime. The x-axis indicates the predicted pseudotime, and the y-axis indicates the diffusion pseudotime computed using SCANPY. The grey dashed arrow describes the linear regression relationship between the predicted pseudotime and the diffusion pseudotime. Remdesivir treated at 500 nM (48 h) vs. vehicle control STB-D4 mapped against the PI-TB to PI-STB pseudotime trajectory.DETAILED DESCRIPTION OF THE INVENTION
[0058] Mature STB and EVT can be produced in vitro by inducing TSCs to differentiate for about 6-8 days, and TSCs can be derived from trophoblasts of pre-implantation embryos or placental tissue, or very early stem cells, such as human ESCs, primed ESCs or expanded potential stem cells (EPSCs) . Human TSCs derived from these very early stem cells are very similar in transcriptome and epigenetics to trophoblast precursor cells (CTBs) derived from placental tissues and can be considered in vitro counterpart of CTBs.
[0059] The present application leverages the unique properties of early extraembryonic cells and / or cells differentiated therefrom for testing safety of substances for extraembryonic development. The present application in one aspect provides a method of evaluating a candidate agent for its safety for extraembryonic development, comprising: i) contacting an early extraembryonic cell and / or a cell differentiated therefrom with a test sample comprising the candidate agent and / or a metabolic product of the candidate agent; and ii) assessing change of one or more cell features of the early extraembryonic cell and / or the cell differentiated therefrom relative to an early extraembryonic cell and / or a cell differentiated therefrom without contacting with the test sample. The method disclosed herein provides a solution for accurate and rapid evaluation of agents for effects and toxicity for extraembryonic development such as placenta development.
[0060] Another aspect of the invention relates to a composition for evaluating extraembryonic development safety, comprising an early extraembryonic cell and / or a cell differentiated therefrom, wherein the early extraembryonic cell and / or the cell differentiated therefrom optionally comprises a reporter molecule or a heterologous nucleic acid encoding a reporter molecule that is indicative of viability or differentiation of the early extraembryonic cell and / or the cell differentiated therefrom.
[0061] In some embodiments, the invention described herein comprises culturing early extraembryonic cells in a condition that allows differentiation of the early extraembryonic cells towards differentiated cells such as STBs and EVTs. By monitoring changes in features such as cell viability, cell morphology and expression of cell markers, the present invention can be used to evaluate the effects and potential toxicity of a candidate agent and / or its metabolic product on extraembryonic development.
[0062] All publications, including patent documents, scientific articles and databases, referred to in this application are incorporated by reference in their entirety for all purposes to the same extent as if each individual publication were individually incorporated by reference. If a definition set forth herein is contrary to or otherwise inconsistent with a definition set forth in the patents, applications, published applications and other publications that are herein incorporated by reference, the definition set forth herein prevails over the definition that is incorporated herein by reference.
[0063] The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described. I. Definitions
[0064] A number of terms and concepts are discussed below. They are intended to facilitate the understanding of various embodiments of the invention in conjunction with the rest of the present disclosure and the accompanying figures. These terms and concepts may be further clarified and understood based on the accepted conventions in the fields of the present invention and the description provided throughout the present disclosure and / or the accompanying figures. Some other terms can be explicitly or implicitly defined in other sections of this disclosure and in the accompanying figures and may be used and understood based on the accepted conventions in the fields of the present invention, the description provided throughout the present disclosure and / or the accompanying figures. The terms not explicitly defined can also be defined and understood based on the accepted conventions in the fields of the present invention and interpreted in the context of the present disclosure and / or the accompanying figures.
[0065] As used herein, the terms “a, ” “an, ” and “the” can refer to “one, ” “one or more” or “at least one, ” unless specifically noted otherwise.
[0066] The terms “about” or “approximately” are used herein to indicate that a value includes the inherent variation of error for the device, the method being employed to determine the value, or simply error-tolerance of a value. For example, the terms “about” or “approximately” may mean±1%, ±5%, ±10%, ±15%or±20%variation from a predetermined value.
[0067] As used herein, the terms “isolate, ” “separate” or “purify” and the related terms are not used necessarily to refer to the removal of all materials other than the components of interest from a sample. Instead, in some embodiments, the terms are used to refer to a procedure that enriches the amount of one or more components of interest relative to one or more other components present in the sample. In some embodiments, “isolation, ” “separation” or “purification” may be used to remove or decrease the amount of one or more components from a sample. For example, the expression “an isolated cell” can refer to a cell that has been substantially separated or purified away from other cells of a cell culture or an organism.
[0068] The term “derived” and the related expressions referring to cells or a biological sample indicate that the cell or sample was obtained from the stated source at some point in time. For example, a cell derived from an organism can represent a primary cell obtained directly from the individual (that is, unmodified) , or it can be modified, for example, by introduction of a recombinant vector, by exposure to or culturing under particular conditions, or immortalization. In some cases, a cell derived from a given source will undergo cell division and / or differentiation such that the original cell no longer exists, but the continuing cells will be understood to derive from the same source. The term “derive, ” “derivation” and the related terms and expressions can also be used in this disclosure to refer to creation of a cell population, cell, or culture from a different starting or preceding cell population, cell, or culture. For example, a trophoblast stem cell (TSC) described in the present disclosure can be described as being derived from Expanded Potential Stem Cells (EPSCs) .
[0069] The term “comprising” and the related terms ( “comprise, ” “comprises, ” etc. ) , when used in this disclosure to describe various embodiments of the invention, are open-ended, meaning that they do not exclude additional elements and synonymous with terms “including, ” “containing” or “having. ” When an embodiment of the invention is described using the term “comprising, ” it is intended to include the embodiments, in which the term comprising is replaced with the terms “consisting of” or “consisting essentially of” In other words, the description of the embodiments of the invention described in this disclosure using the term “comprising” and the related terms also provides the description of the related embodiments that use “consisting of” or “consisting essentially of” instead of “comprising” . The term “consisting of” excludes any elements (steps, ingredient etc. ) not specified in the description. The term “consisting essentially of” is intended to exclude only those elements not specified in the description that do not materially affect the basic and novel characteristics of the embodiment.
[0070] The term “lineage, ” when used in reference to cells, encompasses all of the stages of the development of a cell type, from the earliest precursor cell to a completely mature cell (aspecialized cell) .
[0071] In the context of cell culture, the term “dissociating” can refer to a process of isolating cells from other cells or from a surface, such as a culture plate surface. For example, cells can be dissociated from an organ or a tissue by mechanical or enzymatic methods. In another example, cells that aggregate in vitro can be dissociated from each other. In yet another example, adherent cells are dissociated from a culture plate or other surface. Dissociation can involve breaking cell interactions with extracellular matrix (ECM) and substrates (for example, culture surfaces) or breaking the ECM between cells.
[0072] The expression “induced pluripotent stem cell” (iPSC) refers to a pluripotent stem cell artificially derived from a non-pluripotent cell. For example, human iPSCs are artificially derived from a human non-pluripotent cell. iPSCs can be derived by introducing products of specific sets of pluripotency-associated genes, or “reprogramming factors, ” into a given cell type and / or exposing non-pluripotent cells to particular conditions. The reprogramming factors are usually active only transiently until the cells acquire pluripotent characteristics.
[0073] An “adult stem cell, ” which can also be termed “somatic stem cell, ” is a stem cell found, in an organism, among differentiated cells in a tissue or organ and can differentiate to yield some or all of the specialized cell times in the tissue or organ. Somatic stem cells can be grown in culture. When differentiating into specialized cells, they typically generate intermediate cells called “precursor” or “progenitor” cells. Somatic stem cells and progenitor cells can be described as “multipotent” or “oligopotent, ” depending on their degree of potency. Some examples of somatic stem cells are: hematopoietic stem cells that give rise to all the types of blood cells (red blood cells, B lymphocytes, T lymphocytes, natural killer cells, neutrophils, basophils, eosinophils, monocytes and macrophages) ; mesenchymal stem cells that include bone marrow stromal stem cells and skeletal stem cells and can give rise to bone cells (osteoblasts and osteocytes) , cartilage cells (chondrocytes) , fat cells (adipocytes) , and stromal cells that support blood formation; neural stem cells that can give rise to nerve cells (neurons) , astrocytes and oligodendrocytes; epithelial stem cells in the lining of the digestive tract that can give rise to absorptive cells, goblet cells, Paneth cells, and enteroendocrine cells; skin stem cells that occur in the basal layer of the epidermis (and can give rise to keratinocytes) and at the base of hair follicles (and can give rise to both the hair follicle and to the epidermis) . A tissue-specific progenitor cell is a cell devoid of self-renewal potential that is committed to differentiate into cells of a specific organ or tissue. Certain somatic stem cell types can differentiate into cell types seen in organs or tissues other than those expected from the somatic stem cell's origin. This phenomenon is called “transdifferentiation. ”
[0074] The terms “progenitor cell” or “precursor cell, ” as used herein, refers to the cells that can typically differentiate to form one or more kinds of cells. A “precursor cell” or “progenitor cell” can be any cell in a cell differentiation pathway that is capable of differentiating into a more mature cell. Progenitor cells can be primary cells obtained from an organism, cells proliferated in culture or cells derived from stem cells.
[0075] The term “placenta” and related terms refer to a temporary vascular organ in mammals, which connects the umbilical cord of the developing fetus to the wall of maternal uterus and mediates its metabolic exchange between the fetus and the maternal blood supply through association of placental tissues with uterine mucosa.
[0076] The term “trophoblast” and related terms refer to all the cells of the trophoblast lineage, which includes a group of the extraembryonic lineages (cytotrophoblast, syncytiotrophoblast, intermediate trophoblast) , and hence does not contribute directly to the cells of the fetal body. The extraembryonic lineages consist of chorion (the combination of trophoblast plus underlying extraembryonic mesoderm) , amnion, yolk sac, and allantois. In some contexts, the term “trophoblast” is also used to encompass trophectoderm.
[0077] The term “trophoblast stem cell” and related terms refer to a cell of a subpopulation of trophoblast cells with stem cell properties and the ability to differentiate into either syncytiotrophoblast cells by fusion or extravillous trophoblast cells.
[0078] The term “syncytiotrophoblast” and related terms refer to multi-nucleated cells (which can also be described as multinucleated structures) covering the surface of placental villi. Syncytiotrophoblasts are created by fusion of the underlying cytotrophoblast cells and represent the fetal side of the maternal-fetal interface. A distinct, early form of syncytiotrophoblast forms by fusion of trophectodermal cells in the blastocyst and facilitates implantation of the embryo into the maternal endometrium.
[0079] The term “extravillous trophoblast” and related terms refer to terminally differentiated trophoblast cells that invade into and restructure the uterine compartment. Extravillous trophoblast invasion serves to attach the pre-implantation embryo to the uterus and to enable access to nutrients for the embryo throughout pregnancy–secretions of the uterine glands in the first trimester, maternal blood in the second and third trimester. Their main function is remodeling the uterine spiral arteries, to achieve an increase in the spiral artery diameter of from four to six times. This changes them from high-resistance low-flow vessels into large, dilated vessels that provide good perfusion, and oxygenation to the developing placenta.
[0080] “Differentiation” is the process by which a less specialized cell becomes a more specialized cell type. For example, early development of a multicellular animal is characterized by the rapid proliferation of embryonic cells, which then differentiate to produce the many specialized types of cells that make up the tissues and organs of the multicellular animal. As cells differentiate, their rate of proliferation usually decreases. Some types of differentiated cells never divide again, but many differentiated cells are able to resume proliferation as required to replace cells that have been lost as a result of injury or cell death. Some cells divide continuously throughout life to replace cells that have a high rate of turnover in adult multicellular animals. Examples of differentiated cells are fibroblasts, hepatocytes, cardiomyocytes, myoblasts, neurons, osteoclasts, and lymphocytes.
[0081] The expression “modified cells” and the related terms and expressions encompass all cells that have been or are derived from the cells that have been artificially modified, by any methods, as compared to the original or cells from which they are derived. Modified cells can be produced from primary cells, secondary cells, stem cells, cultured cells and / or other modified cells. Modifications include, but are not limited to, genetic modification or engineering, in which case modified cells can be referred to as “genetically modified” or “genetically engineered. ” Genetic modification can be accomplished by various methods that result in incorporation of foreign or heterologous nucleic acids into the cells being modified. Some examples of such methods are transduction by a virus or a viral vector, or transfection of isolated nucleic acids into cells through transient pores in the cell membrane. Other modifications include exposing the source cells to biological and non-biological molecules or factors or culture conditions. Some examples of modified cells are iPSCs, genetically modified cells, including those used for gene therapies, one example being gene-edited cells, such as those modified using CRISPR / Cas9, TALENs or ZFNs.
[0082] The term “passage, ” “passaging” and the related terms and expressions used in the context of cell culture refer to subculturing, which typically involves transfer of cells from a previous culture into a fresh growth medium. Passaging is performed to ensure propagation of cells in culture. Cell proliferation in culture reduced or ceases when the cells reduce the capacity of the culture vessels and / or media to support further cell growth. For example, cells in adherent cultures may occupy all the available substrate and have no room left for expansion, while cells in suspension cultures exceed the capacity of the medium to support further growth. To keep cells in a culture at an optimal density for continued growth and to stimulate further proliferation, the culture must be expanded and fresh medium supplied. To divide the culture of adherent cells, for example, a monolayer culture of cells, such as cultures of differentiating EPSCs described on the present disclosure, the cells are first dissociated, for example, by enzymatic dissociation. Enzymatic dissociation can be performed by removing the incubation medium from the plates, adding to the plates a buffer, such as PBS and an enzymatic dissociation reagent, such as Accutase, TrypLE or Trypsin (available, for example, from Thermo Fisher Scientific) , incubating the cells with the buffer and dissociation reagent under appropriate conditions, and harvesting the resulting dissociated cells by centrifugation, sedimentation, filtering or other appropriate methods. The dissociated cells are transferred into similar or equivalent reaction vessels, such as flasks, with fresh media, to result in a lower cell density.
[0083] As used herein, “marker” refers to any molecule that can be observed or detected. For example, a marker can include, but is not limited to, a nucleic acid, such as a transcript of a specific gene, a polypeptide product of a gene, a non-gene product polypeptide, a glycoprotein, a carbohydrate, a glycolipid, a lipid, a lipoprotein or a small molecule (for example, molecules having a molecular weight of less than 10,000 AMU) . When a presence, absence of amount of a marker can be experimentally observed or detected, such a marker or its amount can be described as “observable” or “detectable. ” The presence or absence of the markers, as applied to the embodiments of the preset invention, means detectable presence or absence of the markers as detected by applicable methods for detecting such markers, and may mean certain detectable or undetectable levels of such markers. In other words, the presence may mean the presence above a certain detectable level, while the absence may mean the absence below a certain detectable level and not necessarily zero detectable level. For most markers described herein, the symbols provided are those developed and / or recognized by HUGO Gene Nomenclature Committee of European Bioinformatics Institute.
[0084] In the context of observable or detectable markers, such as markers of cell development or differentiation, “expression” refers to the production of a gene product (which can be a nucleic acid, such as RNA, or a protein) as well as the level or amount of production of a gene product. Thus, determining the expression of a specific marker refers to detecting either the relative or absolute amount of the marker (which can mean detecting expression of RNA or protein) that is expressed or simply detecting (which can mean detecting expression of RNA or protein) the presence or absence of the marker. If expression of RNA or protein corresponding to the marker is detected, the marker can be said to be “detectably expressed. ” Expression of certain markers can be determined by detecting the presence or absence of the marker in cells, cell culture or cell population. Expression of certain markers can also be determined by measuring the level at which the marker is present in cells, cell culture or cell population. Quantitative, qualitative or semi-quantitative techniques can be used to measure marker expression. For example, marker expression can be detected and / or quantitated through the use of techniques detecting nucleic acids, such as PCR-based detection or RNA (for example, real-time reverse-transcriptase PCR) , RNA sequencing (RNA-seq) , or RNA detection by nucleic acid array-based techniques. In another example, immunochemistry can be used to detect and / or quantitate marker proteins. For example, the expression of a marker gene product can be detected by using antibodies specific for the marker gene product of interest using Western blotting, immunofluorescence, flow cytometry analysis, etc. Various techniques of marker detection can be used in in conjunction to effectively and accurately characterize and identify cell types and determine both the amount and relative proportions of such markers in a subject cell type. The expression of certain markers can be determined by measuring the level at which the marker is present in the cells of the cell culture or cell population as compared to a standardized or normalized control marker. Identification and characterization of cells, cell cultures or cell population can be based on expression of a certain marker or different expression levels and patterns of more than one marker (including the presence or absence, the high or low expression, of one or more the markers) . Also, certain markers can have transient expression, when the marker exhibits higher expression during one or more stages of the processes described in this disclosure and lower expression during other stage or stages. II. Method of Evaluating Safety for Extraembryonic Development and Embryonic Development
[0085] In one aspect, the present application provides a method of evaluating a candidate agent for its safety for extraembryonic development, comprising: i) contacting an early extraembryonic cell and / or a cell differentiated therefrom with a test sample comprising the candidate agent and / or a metabolic product of the candidate agent; and ii) assessing change of one or more cell features of the early extraembryonic cell and / or the cell differentiated therefrom relative to a reference early extraembryonic cell and / or a cell differentiated therefrom without contacting with the test sample. In some embodiments, extraembryonic development comprises placenta development. In some embodiments, extraembryonic development comprises amniotic tissue development.
[0086] In another aspect, the present application provides a method of evaluating a candidate agent for its safety for embryonic development, comprising: i) contacting an early extraembryonic cell and / or a cell differentiated therefrom with a test sample comprising the candidate agent and / or a metabolic product of the candidate agent; and ii) assessing change of one or more cell features of the early extraembryonic cell and / or the cell differentiated therefrom relative to a reference early extraembryonic cell and / or a cell differentiated therefrom without contacting with the test sample. In some embodiments, embryonic development comprises liver, kidney, intestine, skin, and / or heart development.
[0087] In some embodiments, the method disclosed herein further comprises subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation. The early extraembryonic cell and / or the cell differentiated therefrom can be contacted with the test sample at any time. In some embodiments, the early extraembryonic cell and / or the cell differentiated therefrom is contacted with the test sample simultaneously with being subjected to the condition that allows differentiation. In some embodiments, the early extraembryonic cell and / or the cell differentiated therefrom is contacted with the test sample prior to being subjected to the condition that allows differentiation. In some embodiments, the early extraembryonic cell and / or the cell differentiated therefrom is contacted with the test sample after being subjected to the condition that allows differentiation.
[0088] In some embodiments, there is provided a method of evaluating a candidate agent for its safety for extraembryonic development (such as placenta development) or embryonic development, comprising: i) contacting an early extraembryonic cell (such as TSC) with a test sample comprising the candidate agent and / or a metabolic product of the candidate agent; and ii) assessing change of one or more cell features of the early extraembryonic cell relative to a reference early extraembryonic cell not contacted with the test sample. In some embodiments, the early extraembryonic cell is derived from an EPSC. In some embodiments, the method further comprises obtaining the early extraembryonic cell from an EPSC. In some embodiments, the one or more cell features is selected from the group consisting of: 1) cell morphology, 2) cell viability / cell death (e.g., apoptosis) , 3) rate of proliferation, 4) expression of cell markers including but not limited to: TFAP2C, TP63, CK18, GATA2, GATA3, ELF5, TEAD4 and / or KRT7, and 5) expression of CGA, CGB, HLA-A and / or HLA-B. In some embodiments, the test sample is a food sample, a body fluid sample, or an environmental sample. In some embodiments, the body fluid sample is a blood sample, a urine sample, or a saliva sample, and the metabolic product of the candidate agent is analyzed. In some embodiments, the test sample is a processed sample. In some embodiments, the changes are assessed within any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the early extraembryonic cell is contacted with the test sample. In some embodiments, the changes are assessed after any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the early extraembryonic cell is contacted with the test sample. In some embodiments, the one or more cell features are assessed at two or more (e.g., 3, 4, 5, 6, 7, or more) different time points.
[0089] In some embodiments, there is provided a method of evaluating a candidate agent for its safety for extraembryonic development (such as placenta development) or embryonic development, comprising: i) contacting an early extraembryonic cell (such as TSC) with a test sample comprising the candidate agent and / or a metabolic product of the candidate agent; and ii) subjecting the early extraembryonic cells to a condition that allows differentiation to a differentiated cell (such as a STB) , and 3) assessing one or more cell features of the early extraembryonic cell relative to a reference early extraembryonic cell not contacted with the test sample. In some embodiments, the early extraembryonic stem cell is derived from an EPSC. In some embodiments, the method further comprises obtaining the extraembryonic stem cell from an EPSC. In some embodiments, the one or more cell features is selected from the group consisting of: 1) cell morphology, 2) rate of differentiation, 3) cell viability / cell death (e.g., apoptosis) , 4) rate of proliferation, 5) expression of cell markers including but not limited to: TFAP2C, TP63, CK18, GATA2, GATA3, ELF5, TEAD4 and / or KRT7, 6) expression of CGA, CGB, HLA-A, HLA-B, HLA-C, and / or HLA-G, 7) number of nuclei, 8) expression of cell markers including but not limited to: SSEA4, CD46, CGA, CGB, and / or GCM 1, and 9) secretion of β-hCG. In some embodiments, the test sample is a food sample, a body fluid sample, or an environmental sample. In some embodiments, the body fluid sample is a blood sample, a urine sample, or a saliva sample, and the metabolic product of the candidate agent is analyzed. In some embodiments, the sample is a processed sample. In some embodiments, the early extraembryonic cells are subject to a condition that allows differentiation to a differentiated cell within any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the early extraembryonic cell is contacted with the test sample. In some embodiments, the early extraembryonic cells are subject to a condition that allows differentiation to a differentiated cell after any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the early extraembryonic cell is contacted with the test sample. In some embodiments, the changes are assessed within any of 1, 2, 3, 4, 5, 6, 7, or 8 days after subjecting the early extraembryonic cell to a condition that allows differentiation to a differentiated cell. In some embodiments, the changes are assessed after any of 1, 2, 3, 4, 5, 6, 7, or 8 days after subjecting the early extraembryonic cell to a condition that allows differentiation to a differentiated cell. In some embodiments, the one or more cell features are assessed at two or more (e.g., 3, 4, 5, 6, 7, or more) different time points.
[0090] In some embodiments, there is provided a method of evaluating a candidate agent for its safety for extraembryonic development (such as placenta development) or embryonic development, comprising: i) contacting an early extraembryonic cell (such as TSC) with a test sample comprising the candidate agent and / or a metabolic product of the candidate agent; and ii) subjecting the early extraembryonic cells to a condition that allows differentiation to a differentiated cell (such as an EVT) , and 3) assessing one or more cell features of the early extraembryonic cell relative to a reference early extraembryonic cell not contacted with the test sample. In some embodiments, the early extraembryonic stem cell is derived from an EPSC. In some embodiments, the method further comprises obtaining the extraembryonic stem cell from an EPSC. In some embodiments, the one or more cell features is selected from the group consisting of: 1) cell morphology, 2) rate of differentiation, 3) cell viability / cell death (e.g., apoptosis) , 4) rate of proliferation, 5) expression of cell markers including but not limited to: TFAP2C, TP63, CK18, GATA2, GATA3, ELF5, TEAD4 and / or KRT7, 6) expression of CGA, CGB, HLA-A, HLA-B, and / or HLA-C, 7) expression of cell markers including but not limited to: KRT7, HLA-G, ITGA1, IGTA5 and / or MMP2, and 8) ability to invade. In some embodiments, the test sample is a food sample, a body fluid sample, or an environmental sample. In some embodiments, the body fluid sample is a blood sample, a urine sample, or a saliva sample, and the metabolic product of the candidate agent is analyzed. In some embodiments, the sample is a processed sample. In some embodiments, the early extraembryonic cells are subject to a condition that allows differentiation to a differentiated cell within any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the early extraembryonic cell is contacted with the test sample. In some embodiments, the early extraembryonic cells are subject to a condition that allows differentiation to a differentiated cell after any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the early extraembryonic cell is contacted with the test sample. In some embodiments, the changes are assessed within any of 1, 2, 3, 4, 5, 6, 7, or 8 days after subjecting the early extraembryonic cell to a condition that allows differentiation to a differentiated cell. In some embodiments, the changes are assessed after any of 1, 2, 3, 4, 5, 6, 7, or 8 days after subjecting the early extraembryonic cell to a condition that allows differentiation to a differentiated cell. In some embodiments, the one or more cell features are assessed at two or more (e.g., 3, 4, 5, 6, 7, or more) different time points.
[0091] In some embodiments, there is provided a method of evaluating a candidate agent for its safety for extraembryonic development (such as placenta development) or embryonic development, comprising: i) contacting an expanded potential stem cell (EPSC) with a test sample comprising the candidate agent and / or a metabolic product of the candidate agent; and ii) subjecting the EPSC to a condition that allows differentiation to a differentiated cell (such as a TSC) , and 3) assessing one or more cell features of the EPSC relative to a reference EPSC not contacted with the test sample. In some embodiments, the EPSC is derived from an iPSC. In some embodiments, the method further comprises obtaining the EPSC from an iPSC. In some embodiments, the one or more cell features is selected from the group consisting of: 1) cell morphology, 2) rate of differentiation, 3) cell viability / cell death (e.g., apoptosis) , 4) rate of proliferation, 5) expression of cell markers including but not limited to: TFAP2C, TP63, CK18, GATA2, GATA3, ELF5, TEAD4 and / or KRT7, and 6) expression of CGA, CGB, HLA-Aand / or HLA-B, and / or HLA-G. In some embodiments, the test sample is a food sample, a body fluid sample, or an environmental sample. In some embodiments, the body fluid sample is a blood sample, a urine sample, or a saliva sample, and the metabolic product of the candidate agent is analyzed. In some embodiments, the sample is a processed sample. In some embodiments, the EPSC is subject to a condition that allows differentiation to a differentiated cell within any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the EPSC is contacted with the test sample. In some embodiments, the EPSC is subject to a condition that allows differentiation to a differentiated cell after any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the EPSC is contacted with the test sample. In some embodiments, the changes are assessed within any of 1, 2, 3, 4, 5, 6, 7, or 8 days after subjecting the EPSC to a condition that allows differentiation to a differentiated cell. In some embodiments, the changes are assessed after any of 1, 2, 3, 4, 5, 6, 7, or 8 days after subjecting the EPSC to a condition that allows differentiation to a differentiated cell. In some embodiments, the one or more cell features are assessed at two or more (e.g., 3, 4, 5, 6, 7, or more) different time points.
[0092] In some embodiments, there is provided a method of evaluating a candidate agent for its safety for extraembryonic development (such as placenta development) or embryonic development, comprising: i) subjecting an early extraembryonic cell (such as a TSC) to a condition that allows differentiation to a differentiated cell (such as a STB) ; ii) contacting the cell differentiated from the early extraembryonic cell with a test sample comprising the candidate agent and / or a metabolic product of the candidate agent; and 3) assessing change of one or more cell features of the differentiated cell relative to a reference cell differentiated from an early extraembryonic cell not contacted with the test sample. In some embodiments, the early extraembryonic cell is derived from an EPSC. In some embodiments, the method further comprises obtaining the early extraembryonic cell from an EPSC. In some embodiments, the one or more cell features is selected from the group consisting of: 1) cell morphology, 2) rate of differentiation, 3) cell viability / cell death (e.g., apoptosis) , 4) rate of proliferation, 5) expression of cell markers including but not limited to: TFAP2C, TP63, CK18, GATA2, GATA3, ELF5, TEAD4 and / or KRT7, 6) expression of CGA, CGB, HLA-A and / or HLA-B, HLA-C, and / or HLA-G, 7) number of nuclei, 8) expression of cell markers including but not limited to: SSEA4, CD46, CGA, CGB, and / or GCM 1, and 9) secretion ofβ-hCG. In some embodiments, the test sample is a food sample, a body fluid sample, or an environmental sample. In some embodiments, the body fluid sample is a blood sample, a urine sample, or a saliva sample, and the metabolic product of the candidate agent is analyzed. In some embodiments, the test sample is a processed sample. In some embodiments, the differentiated cells are contacted with the test sample within any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the early extraembryonic cells are subject to a condition that allows differentiation to a differentiated cell. In some embodiments, the early extraembryonic cell is contacted with the test sample after any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the early extraembryonic cells are subject to a condition that allows differentiation to a differentiated cell. In some embodiments, the changes are assessed within any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the differentiated cell is contacted with the test sample. In some embodiments, the changes are assessed after any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the differentiated cell is contacted with the test sample. In some embodiments, the one or more cell features are assessed at two or more (e.g., 3, 4, 5, 6, 7, or more) different time points.
[0093] In some embodiments, there is provided a method of evaluating a candidate agent for its safety for extraembryonic development (such as placenta development) or embryonic development, comprising: i) subjecting an early extraembryonic cell (such as a TSC) to a condition that allows differentiation to a differentiated cell (such as an EVT) ; ii) contacting the cell differentiated from the early extraembryonic cell with a test sample comprising the candidate agent and / or a metabolic product of the candidate agent; and 3) assessing change of one or more cell features of the differentiated cell relative to a reference cell differentiated from an early extraembryonic cell not contacted with the test sample. In some embodiments, the early extraembryonic cell is derived from an EPSC. In some embodiments, the method further comprises obtaining the early extraembryonic cell from an EPSC. In some embodiments, the one or more cell features is selected from the group consisting of: 1) cell morphology, 2) rate of differentiation, 3) cell viability / cell death (e.g., apoptosis) , 4) rate of proliferation, 5) expression of cell markers including but not limited to: TFAP2C, TP63, CK18, GATA2, GATA3, ELF5, TEAD4 and / or KRT7, 6) expression of HLA-A, HLA-B, and / or HLA-C, 7) expression of cell markers including but not limited to: KRT7, HLA-G, ITGA1, IGTA5 and / or MMP2, and 8) ability to invade. In some embodiments, the test sample is a food sample, a body fluid sample, or an environmental sample. In some embodiments, the body fluid sample is a blood sample, a urine sample, or a saliva sample, and the metabolic product of the candidate agent is analyzed. In some embodiments, the test sample is a processed sample. In some embodiments, the differentiated cell is contacted with the test sample within any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the early extraembryonic cell is subjected to a condition that allows differentiation to a differentiated cell. In some embodiments, the differentiated cell is contacted with the test sample after any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the early extraembryonic cell is subjected to a condition that allows differentiation to a differentiated cell. In some embodiments, the changes are assessed within any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the differentiated cell is contacted with the test sample. In some embodiments, the changes are assessed after any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the differentiated cell is contacted with the test sample. In some embodiments, the one or more cell features are assessed at two or more (e.g., 3, 4, 5, 6, 7, or more) different time points.
[0094] In some embodiments, there is provided a method of evaluating a candidate agent for its safety for extraembryonic development (such as placenta development) or embryonic development, comprising: i) subjecting the EPSC to a condition that allows differentiation to a differentiated cell (such as a TSC) ; and ii) contacting the cell differentiated from the EPSC with a test sample comprising the candidate agent and / or a metabolic product of the candidate agent; and 3) assessing one or more cell features of the differentiated cell relative to a reference cell differentiated from an EPSC not contacted with the test sample. In some embodiments, the EPSC is derived from an iPSC. In some embodiments, the method further comprises obtaining the EPSC from an iPSC. In some embodiments, the one or more cell features is selected from the group consisting of: 1) cell morphology, 2) rate of differentiation, 3) cell viability / cell death (e.g., apoptosis) , 4) rate of proliferation, 5) expression of cell markers including but not limited to: TFAP2C, TP63, CK18, GATA2, GATA3, ELF5, TEAD4 and / or KRT7, and 6) expression of CGA, CGB, HLA-A, HLA-B, HLA-C and / or HLA-G. In some embodiments, the test sample is a food sample, a body fluid sample, or an environmental sample. In some embodiments, the body fluid sample is a blood sample, a urine sample, or a saliva sample, and the metabolic product of the candidate agent is analyzed. In some embodiments, the sample is a processed sample. In some embodiments, the differentiated cells are contacted with the test sample within any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the EPSC is subjected to a condition that allows differentiation to a differentiated cell. In some embodiments, the differentiated cells are contacted with the test sample after any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the EPSC is subjected to a condition that allows differentiation to a differentiated cell. In some embodiments, the changes are assessed within any of 1, 2, 3, 4, 5, 6, 7, or 8 days after subjecting the EPSC to a condition that allows differentiation to a differentiated cell. In some embodiments, the changes are assessed after any of 1, 2, 3, 4, 5, 6, 7, or 8 days after subjecting the EPSC to a condition that allows differentiation to a differentiated cell. In some embodiments, the one or more cell features are assessed at two or more (e.g., 3, 4, 5, 6, 7, or more) different time points.
[0095] In some embodiments, there is provided a method of evaluating a candidate agent for its safety for extraembryonic development (such as placenta development) or embryonic development, comprising: i) contacting a cell differentiated from an early extraembryonic cell (such as STB or EVT) with a test sample comprising the candidate agent and / or a metabolic product of the candidate agent; and ii) assessing change of one or more cell features of the differentiated cell relative to a reference differentiated cell not contacted with the test sample. In some embodiments, the early extraembryonic stem cells are differentiated from EPSCs. In some embodiments, the method further comprises obtaining the differentiated cell from the early extraembryonic cell. In some embodiments, the method further comprises obtaining the extraembryonic stem cell from EPSC. In some embodiments, the one or more cell features is selected from the group consisting of: 1) cell morphology, 2) cell viability / cell death (e.g., apoptosis) , 3) rate of proliferation, 4) number of nuclei, 5) expression of cell markers including but not limited to: SSEA4, CD46, CGA, CGB, and / or GCM 1, 6) secretion ofβ-hCG, 7) expression of GATA3, HLA-A and / or HLA-B, and / or HLA-C 8) expression of KRT7, HLA-G, ITGA1, IGTA5 and / or MMP2, and 9) ability to invade. In some embodiments, the test sample is a food sample, a body fluid sample, or an environmental sample. In some embodiments, the test sample is a processed sample. In some embodiments, the body fluid sample is a blood sample, a urine sample, or a saliva sample, and the metabolic product of the candidate agent is analyzed. In some embodiments, the changes are assessed within any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the differentiated cell is contacted with the test sample. In some embodiments, the changes are assessed after any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the differentiated cell is contacted with the test sample. In some embodiments, the one or more cell features are assessed at two or more (e.g., 3, 4, 5, 6, 7, or more) different time points.
[0096] In some embodiments, there is provided a method of evaluating a candidate agent for its safety for extraembryonic development (such as placenta development) or embryonic development, comprising: i) contacting an STB with a test sample comprising the candidate agent and / or a metabolic product of the candidate agent; and ii) assessing change of one or more cell features of the STB relative to a reference STB not contacted with the test sample. In some embodiments, the STB is differentiated from an EPSC. In some embodiments, the method further comprises obtaining the STB from an EPSC. In some embodiments, the one or more cell features is selected from the group consisting of: 1) cell morphology, 2) cell viability / cell death (e.g., apoptosis) , 3) rate of proliferation, 4) number of nuclei, 5) expression of cell markers including but not limited to: SSEA4, CD46, CGA, CGB, and / or GCM 1, and 6) secretion ofβ-hCG. In some embodiments, the test sample is a food sample, a body fluid sample, or an environmental sample. In some embodiments, the test sample is a processed sample. In some embodiments, the body fluid sample is a blood sample, a urine sample, or a saliva sample, and the metabolic product of the candidate agent is analyzed. In some embodiments, the changes are assessed within any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the STB is contacted with the test sample. In some embodiments, the changes are assessed after any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the STB is contacted with the test sample. In some embodiments, the one or more cell features are assessed at two or more (e.g., 3, 4, 5, 6, 7, or more) different time points.
[0097] In some embodiments, there is provided a method of evaluating a candidate agent for its safety for extraembryonic development (such as placenta development) or embryonic development, comprising: i) contacting an EVT with a test sample comprising the candidate agent and / or a metabolic product of the candidate agent; and ii) assessing change of one or more cell features of the EVT relative to a reference EVT not contacted with the test sample. In some embodiments, the EVT is differentiated from an EPSC. In some embodiments, the method further comprises obtaining the EVT from EPSC. In some embodiments, the one or more cell features is selected from the group consisting of: 1) cell morphology, 2) cell viability / cell death (e.g., apoptosis) , 3) rate of proliferation, 4) expression of cell markers including but not limited to: GATA3, HLA-A and / or HLA-B, 5) expression of cell markers including but not limited to: KRT7, HLA-G, ITGA1, IGTA5 and / or MMP2, and 6) ability to invade. In some embodiments, the test sample is a food sample, a body fluid sample, or an environmental sample. In some embodiments, the body fluid sample is a blood sample, a urine sample, or a saliva sample, and the metabolic product of the candidate agent is analyzed. In some embodiments, the test sample is a processed sample. In some embodiments, the changes are assessed within any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the EVT is contacted with the test sample. In some embodiments, the changes are assessed after any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the EVT is contacted with the test sample. In some embodiments, the one or more cell features are assessed at two or more (e.g., 3, 4, 5, 6, 7, or more) different time points.
[0098] In some embodiments, there is provided a method of evaluating a candidate agent for its safety for extraembryonic development (such as placenta development) , comprising: i) contacting a placental organoid with a test sample comprising the candidate agent and / or a metabolic product of the candidate agent; and ii) assessing change of one or more features of the placental organoid relative to a reference placental organoid not contacted with the test sample. In some embodiments, the placental organoid is differentiated from a TSC. In some embodiments, the method further comprises obtaining the placental organoid from TSC. In some embodiments, the one or more features is selected from the group consisting of: 1) morphology of the placental organoid, 2) cell viability / cell death (e.g., apoptosis) , 3) expression of markers including but not limited to: GATA3, ITGA6, TEAD4, ERVW-1 and CGB, 4) secretion ofβ-hCG, 5) expression of miRNAs including but not limited to: has-miR-517a and 525-3p, 6) cell morphology, and 7) ability to invade. In some embodiments, the test sample is a food sample, a body fluid sample, or an environmental sample. In some embodiments, the test sample is a processed sample. In some embodiments, the body fluid sample is a blood sample, a urine sample, or a saliva sample, and the metabolic product of the candidate agent is analyzed. In some embodiments, the changes are assessed within any of 1, 2, 3, 4, 5, 6, 7, or 8 weeks after the placental organoid is contacted with the test sample. In some embodiments, the changes are assessed after any of 1, 2, 3, 4, 5, 6, 7, or 8 weeks after the placental organoid is contacted with the test sample. In some embodiments, the one or more features are assessed at two or more (e.g., 3, 4, 5, 6, 7, or more) different time points.
[0099] In some embodiments, there is provided a method of evaluating a candidate agent for its safety for embryonic development (such as liver development) , comprising: i) contacting an organoid (such as a liver organoid) with a test sample comprising the candidate agent and / or a metabolic product of the candidate agent; and ii) assessing change of one or more features of the organoid relative to a reference organoid not contacted with the test sample. In some embodiments, the organoid is differentiated from an EPSC. In some embodiments, the method further comprises obtaining the organoid from EPSC. In some embodiments, the one or more features is selected from the group consisting of: 1) morphology and / or structure of the organoid, 2) cell viability / cell death (e.g., apoptosis) , 3) expression of markers including but not limited to: GATA3, ITGA6, TEAD4, ERVW-1 and CGB, 4) secretion ofβ-hCG, 5) expression of miRNAs including but not limited to: has-miR-517a and 525-3p, 6) cell morphology, and 7) ability to invade. In some embodiments, the test sample is a food sample, a body fluid sample, or an environmental sample. In some embodiments, the test sample is a processed sample. In some embodiments, the body fluid sample is a blood sample, a urine sample, or a saliva sample, and the metabolic product of the candidate agent is analyzed. In some embodiments, the changes are assessed within any of 1, 2, 3, 4, 5, 6, 7, or 8 weeks after the placental organoid is contacted with the test sample. In some embodiments, the changes are assessed after any of 1, 2, 3, 4, 5, 6, 7, or 8 weeks after the placental organoid is contacted with the test sample. In some embodiments, the one or more features are assessed at two or more (e.g., 3, 4, 5, 6, 7, or more) different time points.
[0100] In some embodiments, there is provided a method of evaluating a candidate agent for its safety for extraembryonic development, comprising: i) contacting an expanded potential stem cell (EPSC) and / or a cell differentiated therefrom with a test sample comprising the candidate agent and / or a metabolic product thereof; and ii) assessing change of one or more cell features of the EPSC and / or the cell differentiated therefrom relative to an EPSC and / or a cell differentiated therefrom without contacting with the test sample. In some embodiments, the method further comprises obtaining the EPSC from a totipotent cell, a pluripotent cell, or a somatic cell. In some embodiments, the one or more cell features is selected from the group consisting of: 1) cell morphology, 2) cell viability / cell death (e.g., apoptosis) , 3) rate of proliferation, 4) expression of cell markers including but not limited to: GATA4, SOX2, NANOG, ESRRB, KLF2, KLF4, EOMES, PEG10, ASCL2 (MASH2) , ESX1, and / or GATA3. In some embodiments, the test sample is a food sample, a body fluid sample, or an environmental sample. In some embodiments, the body fluid sample is a blood sample, a urine sample, or a saliva sample, and the metabolic product of the candidate agent is analyzed. In some embodiments, the test sample is a processed sample. In some embodiments, the changes are assessed within any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the EPSC and / or the cell differentiated therefrom is contacted with the test sample. In some embodiments, the changes are assessed after any of 1, 2, 3, 4, 5, 6, 7, or 8 days after the EPSC and / or the cell differentiated therefrom is contacted with the test sample. In some embodiments, the one or more cell features are assessed at two or more (e.g., 3, 4, 5, 6, 7, or more) different time points. 1. Assessment of Cell Features
[0101] In some embodiments, the one or more cell features comprises cell morphology, proliferation and / or differentiation, one or more molecular characteristics, characteristics of an organoid, and / or one or more functional characteristics. In some embodiments, the early extraembryonic cell is a trophoblast stem cell ( “TSC” ) or a trophoblast progenitor cell ( “TPC” ) . In some embodiments, the cell differentiated therefrom is STB or EVT. In some embodiments, the cell differentiated therefrom is a cell in an organoid, such as liver, kidney, heart, intestine, or skin organoid.
[0102] In some embodiments, the one or more cell features comprise cell morphology. Cell morphological properties such as cell volume, area, and thickness can be determined using microscopy. TSC cells are characterized as mononucleated epithelial cells with well-demarcated cell borders and large nuclei. STB cells are featured with villous multinucleated entities. EVTs are characterized as spindle-shaped cells.
[0103] In some embodiments, the one or more cell features comprise rate of proliferation and / or rate of change to a differentiated state. In one particular embodiment, TSCs that are not contacted with a candidate agent or a metabolic product thereof become early STBs around day 2-3, and mature STBs around day 6. In another embodiment, TSCs that are not contacted with an agent or a metabolic product thereof become EVTs around day 8. The rate of change to a differentiated state can be determined as the amount of time it takes for the cells to become STBs and / or EVTs in comparison to a reference cell that is not contacted with an agent or a metabolic product thereof.
[0104] In some embodiments, the one or more cell features comprises cell viability. Methods for assaying cell viability are known in the art, including MTT assay, tetrazolium reduction, resazurin reduction, protease markers, and ATP detection. Cell viability can also be assessed through intensity / cell count quantification with confocal microscope imaging of Hoechst-stained live cells or fixed attached cells. In some embodiments, cell viability is assessed by methods such as CCK8 assay. Cell death (apoptosis) can be assessed by methods such as annexin V staining of cell suspensions and detection of cleaved caspase-3 and the nuclear enzyme poly (ADP-ribose) polymerase (PARP) . Cell viability can be determined as the percentage of cells that are viable and compared to a reference group that is not contacted with an agent or a metabolic product thereof. Cell death can be determined as the percentage of cells that are undergoing apoptosis and compared to a reference group that is not contacted with an agent or a metabolic product thereof.
[0105] In some embodiments, the one or more cell features comprises cell death, such as apoptosis, pyroptosis, and necrosis. Apoptosis is a highly programmed and regulated process, often referred to as "cell suicide. " Its primary purpose is to remove unwanted or damaged cells without causing a disturbance. Pyroptosis is also a programmed form of cell death, but it is explicitly designed to be an alarm system, typically in response to infections or danger signals. Necrosis is an unregulated and accidental form of cell death caused by severe external stress, such as physical trauma, toxins, or energy deprivation. Key characteristics of apoptosis include: 1) presence of cleaved Caspase-3; 2) the cell membrane undergoes blebbing (forming outward bulges) and exposes "eat-me" signals like phosphatidylserine (PS) to attract phagocytes; 3) the membrane remains largely intact until the very end; and 4) the nucleus undergoes orderly and characteristic fragmentation of DNA, which can be detected by a TUNEL assay. Key characteristics of pyroptosis include: 1) presence of cleaved, active N-terminal fragment of Gasdermin D; 2) pore formation by GSDMD, leading to cell swelling and eventual rupture; 3) the nucleus undergoes condensation, but it is distinct from the orderly fragmentation seen in apoptosis. Key characteristics of necrosis include: 1) the membrane ruptures completely and uncontrollably; 2) the nucleus undergoes disorganized lysis (dissolution) rather than programmed fragmentation; and 3) release of intracellular proteins like HMGB1 (from the nucleus) or LDH (from the cytoplasm) into the extracellular space. In some embodiments, markers for apoptosis and / or pyroptosis include the presence or level of one or more caspase family members, such as Caspase-1, Caspase-2, Caspase-3, Caspase-4, Caspase-5, Caspase-6, Caspase-7, Caspase-8, Caspase-9, or Caspase-10.
[0106] In some embodiments, the one or more molecular characteristics comprise i) presence or absence of a biomarker; ii) level of a biomarker; iii) secretion of a biomarker; and / or iv) the presence or absence of a reporter molecule. In some embodiments, the cell marker is selected from the group consisting of a marker of genomic instability, epigenetic alternations (such as DNA, RNA and protein modifications) , loss of proteostasis, telomere attrition, organelle dysfunction, disabled macroautophagy, deregulated nutrient-sensing, altered intercellular communication, cellular senescence, chronic inflammation, differentiation, endogenous transposon elements, cell cycle, cell death, and stem cell exhaustion. For example, in some embodiments, the cell marker is selected from the group consisting of: β-hCG, ISL1, ITGA5, VTCN1, GABRP, NANOG, OCT4, SSEA-4, SOX2, CD29, CD44, CD46, CD58, CD73, CD90, CD105, CD117, CD166, CD106, TFAP2C, TP63, CK18, GATA2, GATA3, ELF5, KRT7, TEAD4, CBG, GCM, HLA-A, HLA-B, HLA-C, HLA-G, ITGA1, MMP2, CGB, ERVW1, SDC1, ITGB6, MUC16, CGA, CGB3, CGB5, CSH1 / 2, OVOL, cleaved Caspase-3, cleaved, active N-terminal fragment of Gasdermin D, a Cyclin-Dependent Kinase (CDK) , and combinations thereof. In some embodiments, the cell marker is an miRNA such as has-miR-517-5p, has-miR-525-3p, has-miR-526b-3p, has-miR-519d-5p, has-miR-520c-3p, has-miR-517c-3p. In some embodiments, the Cyclin-Dependent Kinase is CDK1, CDK2, CDK3, CDK4 / 6, CDK5, CDK7, CDK8, CDK19, CDK9, CDK10, CDK11, CDK12, CDK13,
[0107] The biomarkers can be detected or measured at the mRNA level or the protein level. Various methods are available for mRNA level detection / measurement, including RNA sequencing, RT-qPCR, and in situ hybridization. Methods for protein level detection / measurement include western blot, ELISA, proteomics, and immunofluorescence. In some embodiments, the expression level of the biomarker is normalized to ensure comparable and consistent data for exploratory or differential expression analysis while limiting false positive or negative results. In some embodiments, the expression level of the biomarker is represented as a relative expression level to a reference gene, such as GAPDH.
[0108] In some embodiments, the functional characteristics comprise a number of nuclei in the early extraembryonic cell and / or the cell differentiated therefrom. STBs are multinucleated, and the number of nuclei is not consistent in all the STB cells. The number of nuclei can be determined by DAPI or Hoechst staining and quantified with confocal microscope.
[0109] In some embodiments, the functional characteristics comprise property of a cellular organelle. In some embodiments, the cellular organelle is selected from the group consisting of: nucleus, mitochondria, proteosome, endoplasmic reticulum, Golgi apparatus. In some embodiments, the property of the cellular organelle comprises number, morphology, and function of the organelle. As early extraembryonic cells differentiate towards STBs, properties (including the number, morphology, and function) of mitochondria are expected to change. Mitophagy is expected to increase. The properties can be studied using methods such as mitochondrial labeling and / or electric microscopy imaging. As the early extraembryonic cell differentiate towards STB, the cell will become multinucleated. Thus, in some embodiments, the number of nuclei is assessed. In some embodiments, the property of the nucleus comprises properties of the nucleus envelope, including the number, morphology, and function of the nucleus envelope. Accumulated damaged and misfolded proteins in senescence cells result from a functional decline in the proteosomes, which can be marked by E3 ubiquitin ligases and chaperone family heat shock proteins (HSP) dysfunction. The endoplasmic reticulum (ER) and Golgi apparatus are both part of the membranous tubular network that plays a major role in ions homeostasis, lipid, and protein biosynthesis. Together with proteosomes, they maintain the protein homeostasis (also called proteostasis) . Due to different kinds of stress such as nutrient deprivation, viral infection and hypoxia, unfolded or misfolded proteins can accumulate and aggregate in these organelles, and hence become detrimental to cell survival. ER stress activates ER transmembrane proteins PKR-like ER kinase (PERK) , IRE1α, and ATF6α. Golgi apparatus is important for the bidirectional vesicular trafficking among the ER, proteosomes and mitochondria. Molecules related to Golgi apparatus include Nir2, CERT, and oxysterol-binding protein (OSBP) .
[0110] In some embodiments, the function characteristics comprise the invasive ability of the cells (e.g., EVTs) , which can be measured by cell invasion assay.
[0111] In some embodiments, the one or more cell features comprise characteristics of an organoid. In some embodiments, the organoid is a placental organoid. In some embodiments, the organoid is a liver organoid. In some embodiments, the organoid is a kidney organoid. In some embodiments, the organoid is a intestine organoid. In some embodiments, the organoid is a skin organoid. In some embodiments, the organoid is a heart organoid. In some embodiments, the characteristics of an organoid include 1) the morphology and / or structure of the organoid, 2) cell viability / cell death, 3) expression of markers including but not limited to: GATA3, ITGA6, TEAD4, ERVW-1 and CGB, 4) secretion ofβ-hCG, 5) expression of miRNAs including but not limited to: has-miR-517a and 525-3p, 6) cell morphology, and 7) ability to invade.
[0112] In some embodiments, the change in one or more cell features are evaluated about 1 day to about 8 weeks after subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation. In some embodiments, the change in one or more cell features are evaluated on day 1 after subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation. In some embodiments, the change in one or more cell features is evaluated on day 2 after subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation. In some embodiments, the change in one or more cell features are evaluated on day 3 after subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation. In some embodiments, the change in one or more cell features are evaluated on day 4 after subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation. In some embodiments, the change in one or more cell features are evaluated on day 5 after subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation. In some embodiments, the change in one or more cell features are evaluated on day 6 after subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation. In some embodiments, the change in one or more cell features are evaluated on day 7 after subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation. In some embodiments, the change in one or more cell features are evaluated on day 8 after subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation. In some embodiments, the change in one or more cell features are evaluated at week 2 after subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation. In some embodiments, the change in one or more cell features are evaluated at week 3 after subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation. In some embodiments, the change in one or more cell features are evaluated at week 4 after subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation. In some embodiments, the change in one or more cell features are evaluated at week 5 after subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation. In some embodiments, the change in one or more cell features are evaluated at week 6 after subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation. In some embodiments, the change in one or more cell features is evaluated at week 7 after subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation. In some embodiments, the change in one or more cell features are evaluated at week 8 after subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation.
[0113] In some embodiments, the change in one or more cell features is quantified by comparing to a reference early extraembryonic cell and / or a cell differentiated therefrom without contacting with the test sample. For instance, in some embodiments, the change in one or more cell features (e.g., expression level of a marker) is normalized by the corresponding cell feature (e.g., expression level of a marker) in a reference early extraembryonic cell and / or a cell differentiated therefrom without contacting with the test sample.
[0114] In some embodiments, the methods disclosed herein comprise grading the candidate agent on its safety for extraembryonic development. In some embodiments, the candidate agent is Grade 1 if the change of one or more cell features of the early extraembryonic cell and / or the cell differentiated therefrom relative to a reference early extraembryonic cell and / or a cell differentiated therefrom without contacting with the test sample is<10%. In some embodiments, the candidate agent is Grade 2 if the change of one or more cell features of the early extraembryonic cell and / or the cell differentiated therefrom relative to a reference early extraembryonic cell and / or a cell differentiated therefrom without contacting with the test sample is±10%-25%. In some embodiments, the candidate agent is Grade 3 if the change of one or more cell features of the early extraembryonic cell and / or the cell differentiated therefrom relative to a reference early extraembryonic cell and / or a cell differentiated therefrom without contacting with the test sample is±25%-50%. In some embodiments, the candidate agent is Grade 4 ifthe change of one or more cell features of the early extraembryonic cell and / or the cell differentiated therefrom relative to a reference early extraembryonic cell and / or a cell differentiated therefrom without contacting with the test sample is±50%-75%. In some embodiments, the candidate agent is Grade 5 if the change of one or more cell features of the early extraembryonic cell and / or the cell differentiated therefrom relative to a reference early extraembryonic cell and / or a cell differentiated therefrom without contacting with the test sample is more than±75%. A reference early extraembryonic cell and / or a cell differentiated could be a cell of the same type as the cell that contacted the test sample.
[0115] In some embodiments, the method disclosed herein comprises contacting the early extraembryonic cell and / or the cell differentiated therefrom with the test sample at different concentrations. In some embodiments, the candidate agent and / or the metabolic product of the candidate is at from about 10 nM to about 1000 mM in the test sample. In some embodiments, the candidate agent and / or the metabolic product of the candidate is at from about 10 nM, about 20 nM, about 30 nM, about 40 nM, about 50 nM, about 60 nM, about 70 nM, about 80 nM, about 90 nM, about 100 nM, about 200 nM, about 300 nM, about 400 nM, about 500 nM, about 600 nM, about 700 nM, about 800 nM, about 900 nM, about 1μM, about 2μM, about 3μM, about 4μM, about 5μM, about 6μM, about 7μM, about 8μM, about 9μM, about 10μM, about 100μM, about 1 mM, about 10 mM, about 100 mM, about 500 mM, or about 1000 mM, in the test sample.
[0116] In some embodiments, the method disclosed herein comprises grading the candidate agent on its safety for extraembryonic development at different concentrations. In some embodiments, the candidate agent is graded on its safety for extraembryonic development at about 10 nM, about 20 nM, about 30 nM, about 40 nM, about 50 nM, about 60 nM, about 70 nM, about 80 nM, about 90 nM, about 100 nM, about 200 nM, about 300 nM, about 400 nM, about 500 nM, about 600 nM, about 700 nM, about 800 nM, about 900 nM, about 1μM, about 2μM, about 3μM, about 4μM, about 5μM, about 6μM, about 7μM, about 8μM, about 9μM, about 10μM, about 100μM, about 1 mM, about 10 mM, about 100 mM, about 500 mM, or about 1000 mM in the test sample.
[0117] In some embodiments, the method disclosed herein further comprises calculating the half-maximal inhibitory concentration (IC50) of the candidate agent and / or a metabolic product thereof. IC50 is a measure of the concentration of a drug or compound required to inhibit a particular biological or biochemical process by 50%. For instance, in some embodiments, the IC50 of the candidate agent and / or a metabolic product thereof is calculated as the concentration at which the viability of the early extraembryonic cell and / or the cell differentiated therefrom is inhibited by 50%. The IC50 of an agent can be determined by constructing a dose-response curve and examining the effect of different concentrations of the agent.
[0118] In some embodiments, the method disclosed herein further comprises calculating the cytotoxic concentration 50% (CC50) of the candidate agent and / or a metabolic product thereof. The CC50 value is a measure of the concentration of a drug or compound that is cytotoxic to 50%of a population of cells. For instance, in some embodiments, the CC50 of the candidate agent and / or a metabolic product thereof is calculated as the concentration at which 50%of the early extraembryonic cell and / or the cell differentiated therefrom undergo apoptosis.
[0119] In some embodiments, the method disclosed herein further comprises calculating the maximum safety concentration of the candidate agent and / or a metabolic product thereof. In some embodiments, the maximum safety concentration is the concentration at which the candidate agent and / or a metabolic product thereof does not cause any change to the one or more cell features. In some embodiments, the maximum safety concentration is the concentration at which the candidate agent and / or a metabolic product thereof causes change that is less than 10%to the one or more cell features relative to a reference early extraembryonic cell and / or a cell differentiated therefrom without contacting with the test sample.
[0120] In some embodiments, the method disclosed herein further comprises producing a report of the evaluation results. In some embodiments, the report comprises the grading of the candidate agent and / or a metabolic product thereof. In some embodiments, the report comprises the IC50 of the candidate agent and / or a metabolic product thereof. In some embodiments, the report comprises the CC50 of the candidate agent and / or a metabolic product thereof. In some embodiments, the report comprises the maximum safety concentration of the candidate agent and / or a metabolic product thereof. 2. Candidate Agents
[0121] In some embodiments, the candidate agent is a drug, a food product, a nutraceutical, a cosmetic product, a component thereof, or raw materials therefor. In some embodiments, the candidate agent is selected from the group consisting of: an antibody, a virus, a virus-like, a small molecule, a peptide, a polypeptide, a DNA, an mRNA, a guide RNA, a microRNA, an RNAi, an lncRNA, an siRNA molecule, and an antisense RNA. In some embodiments, the candidate agent is a naturally occurring substance.
[0122] In some embodiments, the test sample is selected from the group consisting of: a food sample, an environmental sample, and a body fluid sample. In some embodiments, the test sample is selected from the group consisting of: a blood sample, a urine sample, and a saliva sample. The test sample could comprise the candidate agent and / or a metabolic product of the candidate agent. For instance, in some embodiments, the test sample is a body fluid sample, and the safety of the metabolic product of the candidate agent is assessed.
[0123] In some embodiments, the test sample is a processed sample. The processing can involve dissolving, homogenizing, filtering, sterilizing, diluting, concentrating, crystalizing, etc. 3. Culturing Conditions
[0124] In some embodiments, the condition that allows differentiation comprises a cell culture medium that allows for differentiation from the early extraembryonic cell (e.g., TSC or a trophoblast progenitor cell (TPC) ) into STB. Methods for inducing TSCs to differentiate towards STBs are known in the art (See, e.g., US20230220334A1) . In some embodiments, the condition for STB differentiation comprises a cell culture medium comprising DMEM / F12, β-mercaptoethanol, Penicillin-Streptomycin-Glutamine, BSA, ITS-X, Y27632, Forskolin, and KnockOut Serum Replacement. In some embodiments, TSCs are cultured in syncytiotrophoblasts medium (STBM) for around 6 days. The STBM comprises: DMEM / F12 supplemented with 50μMβ-mercaptoethanol, 0.5%Penicillin-Streptomycin-Glutamine, 0.3%BSA, 1.0%ITS-X, 2.5μM Y-27632, 2μM Forskolin (Sigma-Aldrich, Cat. F3917) , and 4%KnockOut Serum Replacement (Thermo. Cat. 10828028) . The cells that are not contacted with the test sample typically become early syncytiotrophoblasts on day 2-3, and mature syncytiotrophoblasts around day 6.
[0125] In some embodiments, the condition that allows differentiation comprises a cell culture medium that allows for differentiation from the early extraembryonic cell (e.g., TSC or TPC) into EVT. In some embodiments, the condition for EVT differentiation comprises a cell culture medium comprising DMEM / F12, β-mercaptoethanol, Penicillin-Streptomycin-Glutamine, BSA, ITS-X, Y27632, and A83-01. In some embodiments, the cell culture medium for EVT differentiation comprises: DMEM / F12 supplemented with 50μMβ-mercaptoethanol, 0.5%Penicillin-Streptomycin-Glutamine, 0.3%BSA, 1.0%ITS-X, 2.5μM Y-27632, and 7.5μM A83-01. In some embodiments, KnockOut Serum Replacement, NRG1, and Basement Membrane Matrix are later added to the cell culture medium for EVT differentiation. For instance, in some embodiments, in the first two days, 4%KnockOut Serum Replacement, 100 ng / mL NRG1 and 2% Basement Membrane Matrix were added. In some embodiments, on day 3, the medium is switched to 2 mL of EVT medium, with 4%KnockOut Serum Replacement and 0.5% Basement Membrane Matrix. In some embodiments, on day 6, the medium is switched to 2 mL of EVT medium with 0.5% Basement Membrane Matrix. The cells that are not contacted with the test sample typically become EVTs on day 8.
[0126] In some embodiments, the condition that allows differentiation comprises a cell culture medium that allows differentiation from the early extraembryonic cell (e.g., TSC or TPC) into an extraembryonic organoid. In some embodiments, the extraembryonic organoid is a placental organoid. Methods for culturing extraembryonic organoids such as placental organoids are known in the art (see, e.g., Ruan et al., “Human early syncytiotrophoblasts are highly susceptible to SARS-CoV-2 infection” , Cell Reports Medicine 3, 100849, December 20, 2022) . In some embodiments, the condition for placental organoid differentiation comprises a cell culture medium comprising N2B27 basic medium with recombinant human epidermal growth factor, CHIR99021, recombinant human R-spondin-1 protein, recombinant human fibroblast growth factors, recombinant human hepatocyte growth factor, A83-01, prostaglandin E2, and Y-27632. In some embodiments, the medium for placental organoid differentiation comprises N2B27 basic medium with 50ng / mL recombinant human epidermal growth factor, 1.5μM CHIR99021, 80 ng / mL recombinant human R-spondin-1 protein, 100 ng / mL recombinant human fibroblast growth factors, 50 ng / mL recombinant human hepatocyte growth factor, 500 nM A83-01, 2.5μM prostaglandin E2, and 2μM Y-27632.
[0127] In another aspect, there is provided a method of evaluating a candidate agent for its safety for extraembryonic development, comprising: i) contacting the EPSC with a test sample comprising the candidate agent and / or a metabolic product of the candidate agent; and ii) assessing change of one or more cell features of the EPSC relative to an EPSC without contacting with the test sample. In some embodiments, the method further comprises inducing the EPSC to differentiate into TSC. Methods for inducing EPSCs to differentiate into TSCs are known in the art. An exemplary protocol is described in Okae et al., 2018, Cell stem cell, 22 (1) , 50-63, the content of which is incorporated herein in its entirety. In some embodiments, methods for inducing EPSCs to differentiate into TSCs comprises culturing the cells in a cell culture medium comprising DMEM / F12, β-mercaptoethanol, FBS, Penicillin-Streptomycin, bovine albumin fraction V (BSA) , Insulin-Transferrin-Selenium-Ethanolamine (ITS-X) supplement, 2-phospho-L-ascorbic-acid (Vc) , EGF, CHIR99021, A83-01, SB431542, Valproic acid (VPA) , and Y27632. In some embodiments, the cell culture medium comprises DMEM / F12 supplemented with 110μMβ-mercaptoethanol, 0.2%FBS, 0.5%Penicillin-Streptomycin, 0.3%BSA, 1x ITS-X supplement, 50.0μg / mL Vc, 50.0 ng / mL EGF, 2.0μM CHIR99021, 0.5μM A83-01, 1.0μM SB431542, 0.8μM VPA, and 5.0μM Y27632. 4. Exemplary Evaluation Workflow
[0128] An exemplary evaluation workflow is illustrated in FIG. 2. In one particular embodiment, EPSCs are induced to differentiate into TSCs. TSCs are subjected to a condition that allows for differentiation into STB or EVT and are contacted with the candidate agent simultaneously. In another embodiment, TSCs are subjected to a condition that allows for differentiation into STB, and the cells are contacted with the candidate agent once they have differentiated into early STB, and the cells continue to culture in the condition that allows for further differentiation. In yet another embodiment, TSCs are subjected to a condition that allows for differentiation into EVT, and the cells are contacted with the candidate agent once they have differentiated into early EVT, and the cells continue to culture in the condition that allows for further differentiation. III. Composition for Evaluating Safety for Extraembryonic Development
[0129] The present application in one aspect provides a composition for evaluating extraembryonic development safety, comprising an early extraembryonic cell and / or a cell differentiated therefrom, wherein the early extraembryonic cell and / or the cell differentiated therefrom optionally comprises a reporter molecule or a heterologous nucleic acid encoding a reporter molecule that is indicative of viability or differentiation of the early extraembryonic cell and / or the cell differentiated therefrom. The present application in another aspect provides a composition for evaluating extraembryonic development safety, comprising an expanded potential stem cell (EPSC) and / or a cell differentiated therefrom, wherein the EPSC and / or the cell differentiated therefrom optionally comprises a reporter molecule or a heterologous nucleic acid encoding a reporter molecule that is indicative of viability or differentiation of the EPSC and / or the cell differentiated therefrom. 1. Cellsfor Evaluating Safety
[0130] In some embodiments, the early extraembryonic cell of the methods or the compositions disclosed herein is derived from an embryonic tissue or an extraembryonic tissue. In some embodiments, the early extraembryonic cell of the methods or the compositions disclosed herein is derived from a placental tissue. In some embodiments, the early extraembryonic cell of the methods or the compositions disclosed herein is derived from a totipotent stem cell or a pluripotent stem cell selected from the group consisting of: an embryonic stem cell, an extraembryonic stem cell, an expanded potential stem cell (EPSC) , a naive pluripotent stem cell, a primed pluripotent stem cell, an induced pluripotent stem cell (iPSC) , a2-cell like cell, a4-cell like cell, an 8-cell-like cell, and an extraembryonic progenitor cell.
[0131] Totipotent stem cells are cells that have the capacity to self-renew by dividing and to develop into the three primary germ cell layers of the early embryo and into extraembryonic tissues such as the placenta. Totipotency exists transiently in zygote and 2-cell embryo stages during early development, which subsequently commit to two distinct lineages, i.e., the embryonic cell lineage (inner cell mass, ICM) that forms embryo proper and the extraembryonic cell lineage (trophectoderm, TE) that forms the placental tissue. Pluripotent stem cells including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) have the potential to differentiate into all somatic cell types. Recent studies have shown that pluripotent stem cells could be programmed to produce extraembryonic cells such as trophoblast stem cells (Dong et al., 2020, eLife 9: e52504) .
[0132] Methods for obtaining totipotent stem cells and induced pluripotent stem cells are known in the art. Totipotent stem cells could be obtained by methods such as transferring a somatic nucleus into an enucleated oocyte, which is also known as the somatic cell nuclear transfer (SCNT) technique. The SCNT procedure involves three major steps: enucleation, injection / fusion, and activation. After removing the oocyte nucleus, the donor cell nucleus is injected or fused with the enucleated oocytes before the reconstructed embryos are activated. Successful cloning of more than 20 mammalian species using SCNT has been reported (Matoba et al., Cell Stem Cell. 2018 Oct 4; 23 (4) : 471-485) . In addition to animal cloning, SCNT technology holds great potential for stem cell biology and human therapeutics. Similar to the derivation of embryonic stem cells (ESCs) from blastocysts of fertilized eggs, SCNT-generated blastocysts could be used to derive pluripotent stem cells.
[0133] Induced pluripotent stem cells (iPSCs) are typically derived by introducing a specific set of pluripotency-associated genes, or “reprogramming factors, ” into an adult cell type. The original set of reprogramming factors (also called Yamanaka factors) are the genes Oct4 (Pou5f1) , Sox2, cMyc, and Klf4. There are multiple methods to generate iPSCs, including retrovirus or lentivirus-mediated gene transduction and chemical induction. To generate the iPSCs, each of the pluripotency factors can be also replaced by related transcription factors, miRNAs or small molecules (Ghaedi et al., Methods Mol Biol. 2019; 1576: 55-92) . In some embodiments, the iPSC is derived by genetic engineering, tissue engineering, or induction by small molecule (s) .
[0134] In some embodiments, the iPSC is derived from a somatic cell. In some embodiments, the somatic cell is selected from the group consisting of: an epithelial cell, a muscle cell, a neural cell, a glial cell, a blood cell, an adipose cell, a fibroblast, an endothelial cell, a liver cell, an islet cell, a bone cell, a chondrocyte, a retinal cell, and a somatic stem cell.
[0135] In some embodiments, the embryonic stem cell is a pre-implantation embryonic stem cell in the 2-to 8-cell stage or the morula stage. In some embodiments, the pre-implantation embryonic stem cell in the 2-to 8-cell stage or the morula stage cell is derived from an EPSC, a ESC, or an iPSC.
[0136] In some embodiments, the early extraembryonic cell is a TSC. In one particular embodiment, the TSC is derived from an expanded potential stem cell (EPSC) . EPSCs derived from cleavage-stage preimplantation embryos retain developmental potential for both extraembryonic and embryonic cell lineages (Yang et al., 2017, Cell 169, 243–257. e25; Yang et al., 2017, Nature 550, 393–397; Ruan et al., 2022, Cell Reports Medicine 3, 100849; Gao et al., 2019, Nat. Cell Biol. 21, 687–699., each of which is incorporated herein in its entirety) . Methods for inducing EPSCs to differentiate into TSCs are known in the art and described in Section II. 3.
[0137] In some embodiments, the TSC is derived from a naive pluripotent stem cell (e.g., a embryonic stem cell) . Naive pluripotent stem cells differ from primed pluripotent stem cells in that primed pluripotent stem cells are poised for lineage commitment. One type of naive pluripotent stem cells, embryonic stem cells (ESCs) readily differentiate to somatic or germ lineages but have impaired ability to form extra-embryonic lineages such as placenta or yolk sac. Recent studies have shown that human ESCs can be transdifferentiated to cells that exhibit the cellular and molecular phenotypes of human trophoblast stem cells (hTSCs) derived from human placenta or blastocyst. An exemplary protocol is described in Cinkornpumin et al., 2020, Stem Cell Rep, 15, 198–213, the content of which is incorporated herein in its entirety.
[0138] In some embodiments, the cell differentiated from the early extraembryonic cell is a STB. The STB can have one or more characteristics selected from the group consisting of: i) multinucleated; ii) secretion ofβ-hCG; and iii) expression of SSEA4, GCM1, CD46, CGA, CGB3, CGB5, CSH1 / 2, ERVW-1, GATA3, OVOL, and SDC1.
[0139] In some embodiments, the cell differentiated from the early extraembryonic cell is an EVT. The EVT can have one or more characteristics selected from the group consisting of: i) has a spindle shape; ii) expresses KRT7, HLA-G, ITGA1, IGTA5 and / or MMP2; iii) does not express or expresses in low levels GATA2, GATA3, HLA-A, or HLA-B; and iv) is highly invasive.
[0140] In some embodiments, the early extraembryonic cell and / or the cell differentiated therefrom is derived from a human, a non-human primate (such as a monkey) , a pig, a cow, a mouse, a rat, a bat, a rabbit, a dog, a cat, and a sheep.
[0141] In some embodiments, the early extraembryonic cell and / or the cell differentiated therefrom is naturally occurring. For instance, in some embodiments, the early extraembryonic cell and / or the cell differentiated therefrom is derived from an embryonic tissue or an extraembryonic tissue, such as a placental tissue.
[0142] Methods of obtaining EPSCs is known in the art. For example, US11913018B2 discloses in vitro conversion of cells from mouse or human, or pluripotent cells into expanded potential stem cells (EPSCs) , the content of which is incorporated herein in its entirety. In some embodiments, the method disclosed herein comprises reprogramming a somatic cell into an induced pluripotent stem cell (iPSC) and then culturing the iPSC in an EPSC medium (EPSCM) . 2. Modification of the Cells
[0143] In some embodiments, the early extraembryonic cell and / or the cell differentiated therefrom is genetically modified. For instance, in some embodiments, the early extraembryonic cell and / or the cell differentiated therefrom comprises a heterologous nucleic acid and the heterologous nucleic acid is introduced into the early extraembryonic cell and / or the cell differentiated therefrom by a gene editing tool. Examples of gene editing tools include but are not limited to (1) clustered regularly interspaced short palindromic repeats (CRISPR) -CRISPR-associated protein (Cas) , (2) transcription activator-like effector nucleases (TALENs) , (3) zinc-finger nucleases (ZFNs) , and (4) homing endonucleases or mega nucleases.
[0144] In some embodiments, the early extraembryonic cell and / or the cell differentiated therefrom comprises a reporter molecule. Examples of reporter molecules include physically activated molecules and chemically activated molecules. The reporter molecule could be fluorescent or non-fluorescent. Examples of physically activated molecules include but are not limited to light activated sensing molecules, such as GFP, RFP, mCherry, photoconvertible fluorescent proteins, etc. Examples of chemically activated molecules include but are not limited to: 1) enzyme-activated sensing molecules, such as bioluminescence (e.g., luciferase) and enzyme assays (e.g., β-galactosidase, β-glucuronidase, andβ-lactamase) ; 2) antibody-based assays, such as IF antibody assays; 3) chloramphenicol acetyltransferase; and 4) biosensors (e.g., probes) .
[0145] In some embodiments, the early extraembryonic cell and / or the cell differentiated therefrom comprises a heterologous nucleic acid encoding a reporter molecule. The heterologous nucleic acid may be integrated into the genome of the stem cell or early extraembryonic cell by techniques such as gene editing as described below. In some embodiments, the heterologous nucleic acid is under the control of a promoter of an endogenous biomarker gene encoding a biomarker indicative of viability of the early extraembryonic cell or its differentiation towards a differentiated cell (such as a STB or EVT) . As a result, if the promoter is being actively expressed within the cell, the reporter gene will also be expressed, which can be detected / measured. Reporter genes can produce a protein that has little obvious or immediate effect on the cell culture or organism. They are ideally not present in the native genome to be able to isolate reporter gene expression as a result of the gene of interest's expression. Reporter genes can be incorporated genetically into the host DNA of individual cells.
[0146] Reporter genes may replace the stop codon of the gene of interest to create a gene fusion, so that they can be expressed with the gene of interest. Also, in building the reporter gene system, a segment of DNA coding for a flexible polypeptide linker region such as T2A and IRES is usually inserted right in front of the reporter genes. This method is an example of using cis-acting elements where the two genes are under the same promoter elements and are transcribed into a single messenger RNA molecule. The mRNA is then translated into protein, and linker region like T2A or IRES mediates co-translational cleavage. In this way, both proteins are able to properly fold into their active conformations instead of becoming a fusion protein. The reporter and the product of the gene of interest will only minimally interfere with one another.
[0147] Reporter genes can also be under the control of a transcriptional regulatory complex (e.g. a promoter) that is inducible, with the transcriptional regulatory elements responding to endogenous cell signals (e.g., transcription factors and transcription-regulating complexes) or exogenous chemical or physical conditions that can initiate and regulate reporter gene expression.
[0148] A reporter system typically includes 2 components: a specific gene and regulatory complex, and a specific substrate that interacts with the gene product. The reporter gene product is a protein-either an enzyme that catalyzes a chemical reaction or a protein that fluoresces on exposure to light. Examples of commonly used reporter system pairs include radionuclide-based pairs (e.g., HSV1-tk [herpes simplex virus type 1 thymidine kinase] and 124 / 131I-FIAU [5-iodo-2′-fluoro-2′deoxy-1-β-d-arabinofuranosyluracil] or 18F-FEAU [2′-deoxy-2′-18F-fluoro-5-ethyl-1-β-d-arabinofuranosyluracil] ) , bioluminescent pairs (e.g., firefly luciferase [FLuc] and d-luciferin) , and fluorescent pairs (e.g., green fluorescent protein [GFP] and activating blue light) , plus sensors exploiting fluorescence resonance energy transfer between 2 mutant GFP molecules.
[0149] In some embodiments, the reporter molecule is selected from the group consisting of Green Fluorescent Protein (GFP) , Red Fluorescent Protein (RFP) , Yellow Fluorescent Protein (YFP) , mCherry, tdTomato and photoconvertible fluorescent proteins. When expressed, the reporter molecule can be detected using methods such as fluorescent microscopy and flow cytometry (See, e.g., Kremers et al., J Cell Sci. 2011, 124 (2) : 157–160; Chudakov et al., Physiol Rev. 2010, 90 (3) : 1103-63. )
[0150] In some embodiments of the system disclosed herein, the early extraembryonic cell and / or the cell differentiated therefrom may comprise more than one reporter molecule or more than one heterologous nucleic acid encoding a reporter molecule, or a combination thereof. For example, an early extraembryonic cell used in the system disclosed herein may comprise a first heterologous nucleic acid encoding a Green Fluorescent Protein under the control of a promoter of gene A and a second heterologous nucleic acid encoding a Red Fluorescent Protein under the control of a promoter of gene B. The differentiation of the cell can be assessed by the intensity of the Green Fluorescent Protein and the Red Fluorescent Protein, indicating the expression level of gene A and gene B, respectively.
[0151] Suitable methods for genetically modifying the stem cell or early extraembryonic cell are known in the art, including clustered regularly interspaced short palindromic repeats (CRISPR) -CRISPR-associated protein (Cas) , transcription activator-like effector nucleases (TALENs) , zinc-finger nucleases (ZFNs) , homing endonucleases or mega nucleases, and base editing. The outcomes of the genetic modification might be gene knock-out / knock-in, gene mutations, or gene inversion.
[0152] CRISPR is a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria and archaea. These sequences are derived from DNA fragments of bacteriophages that had previously infected the prokaryote. They are used to detect and destroy DNA from similar bacteriophages during subsequent infections. CRISPR-Cas systems are composed of CRISPR repeat-spacer arrays, which can be further transcribed into CRISPR RNA (crRNA) and trans-activating CRISPR RNA (tracrRNA) , and a set of CRISPR-associated (cas) genes which encode Cas proteins with endonuclease activity. CRISPR-Cas systems can be classified into 2 classes (Class 1 and Class 2) , 6 types (I to VI) and several subtypes, with multi-Cas protein effector complexes in Class 1 systems (Type I, III, and IV) and a single effector protein in Class 2 systems (Type II, V, and VI) . Type II CRISPR-Cas9 system derived from Streptococcus pyogenes (SpCas9) is one of the best characterized and most commonly used categories in numerous CRISPR-Cas systems. The main components of CRISPR-Cas9 system are RNA-guided Cas9 endonuclease and a single-guide RNA (sgRNA) . The Cas9 protein possesses two nuclease domains, named HNH and RuvC, and each cleaves one strand of the target double-stranded DNA. A single-guide RNA (sgRNA) is a simplified combination of crRNA and tracrRNA. The Cas9 nuclease and sgRNA form a Cas9 ribonucleoprotein (RNP) , which can bind and cleave the specific DNA target. Furthermore, a protospacer adjacent motif (PAM) sequence is required for Cas9 protein’s binding to the target DNA.
[0153] ZFNs are fusions between a custom-designed Cys2-His2 zinc-finger protein and the cleavage domain of the FokI restriction endonuclease. ZFNs function as dimers, with each monomer recognizing a specific “half site” sequence-typically nine to 18 base pairs (bps) of DNA-via the zinc-finger DNA-binding domain.
[0154] TALENs are structurally similar to ZFNs. Both methods use the Fokl nuclease to cut DNA and require dimerization to function, however, the DNA binding domains differ. TALENs use transcription activator-like effectors (TALEs) , tandem arrays of 33-35 amino acid repeats. The amino acid repeats possess single-nucleotide recognition, thereby increasing targeting capabilities and specificity compared to ZFNs.
[0155] Homing endonucleases, also known as meganucleases are a collection of naturally occurring enzymes that recognize and cleave long DNA sequences (14 to 40 bps) . These enzymes make extensive sequence-specific contacts with their DNA substrate and thus typically show exquisite specificity.
[0156] Base editing is a relatively new method of genome editing derived from CRISPR-Cas9. Unlike traditional CRISPR systems, base editors (BEs) do not induce double-stranded breaks in the genome. Base editing systems use a ‘catalytically dead’ Cas9 (dCas9) , which cannot cleave DNA, fused to bacterial enzymes called DNA deaminases. Cytidine deaminases, which induce C to T substitutions, are naturally occurring in bacteria, while adenine deaminases, which induce A to G substitutions, were engineered from bacterial enzymes specifically for base editing purposes. Fusing dCas9 to either a cytidine deaminase (CBEs) or an adenine deaminase (ABEs) and providing a sgRNA to direct it to the target sequence, allows researchers to introduce substitutions in DNA. EXEMPLARY EMBODIMENTS
[0157] Embodiment 1. A method of evaluating a candidate agent for its safety for extraembryonic development, comprising: i) contacting an early extraembryonic cell and / or a cell differentiated therefrom with a test sample comprising the candidate agent and / or a metabolic product thereof; and ii) assessing change of one or more cell features of the early extraembryonic cell and / or the cell differentiated therefrom relative to a reference early extraembryonic cell and / or a cell differentiated therefrom without contacting with the test sample.
[0158] Embodiment 2. The method of Embodiment 1, wherein extraembryonic development comprises placenta development.
[0159] Embodiment 3. The method of Embodiment 1 or 2, further comprising subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation.
[0160] Embodiment 4. The method of Embodiment 3, wherein the early extraembryonic cell and / or the cell differentiated therefrom is contacted with the test sample simultaneously with being subjected to the condition that allows differentiation.
[0161] Embodiment 5. The method of Embodiment 3, wherein the early extraembryonic cell and / or the cell differentiated therefrom is contacted with the test sample prior to being subjected to the condition that allows differentiation.
[0162] Embodiment 6. The method of Embodiment 3, wherein the early extraembryonic cell and / or the cell differentiated therefrom is contacted with the test sample after being subjected to the condition that allows differentiation.
[0163] Embodiment 7. The method of any one of Embodiments 3-6, wherein the condition that allows differentiation comprises a cell culture medium comprising DMEM / F12, β-mercaptoethanol, Penicillin-Streptomycin-Glutamine, BSA, ITS-X, Y27632, Forskolin, and / or KnockOut Serum Replacement.
[0164] Embodiment 8. The method of any one of Embodiments 1-7, wherein the contacting comprises contacting the early extraembryonic cell and / or the cell differentiated therefrom with the test sample at different concentrations.
[0165] Embodiment 9. The method of any one of Embodiments 1-8, wherein the candidate agent and / or the metabolic product of the candidate is at from about 10 nM to about 10μM in the test sample.
[0166] Embodiment 10. The method of any one of Embodiments 1-9, wherein the one or more cell features comprises cell viability, cell morphology, proliferation and / or differentiation, molecular characteristics, characteristics of an organoid, and / or functional characteristics.
[0167] Embodiment 11. The method of Embodiment 10, wherein proliferation and / or differentiation comprises rate of proliferation and / or rate of change to a differentiated state.
[0168] Embodiment 12. The method of Embodiment 10, wherein functional characteristics comprise property of a cellular organelle.
[0169] Embodiment 13. The method of Embodiment 10, wherein the molecular characteristics comprise: i) presence or absence of a biomarker; ii) level of a biomarker; iii) secretion of a biomarker; and / or iv) the presence or absence of a reporter molecule.
[0170] Embodiment 14. The method of Embodiment 13, wherein the biomarker is selected from the group consisting of a marker of genomic instability, epigenetic alternations (such as DNA, RNA and protein modifications) , loss of proteostasis, telomere attrition, organelle dysfunction, disabled macroautophagy, deregulated nutrient-sensing, altered intercellular communication, cellular senescence, chronic inflammation, differentiation, endogenous transposon elements, cell cycle, cell death, and stem cell exhaustion.
[0171] Embodiment 15. The method of Embodiment 14, wherein the biomarker is selected from the group consisting of: β-hCG, ISL1, ITGA5, VTCN1, GABRP, NANOG, OCT4, SSEA-4, SOX2, CD29, CD44, CD46, CD58, CD73, CD90, CD105, CD117, CD166, CD106, TFAP2C, TP63, CK18, GATA2, GATA3, ELF5, KRT7, TEAD4, CBG, GCM, HLA-A, HLA-B, HLA-C, HLA-G, ITGA1, MMP2, CGB, ERVW1, SDC1, ITGB6, MUC16, CGA, CGB3, CGB5, CSH1 / 2, OVOL, and combinations thereof.
[0172] Embodiment 16. The method of any one of Embodiments 13-15, wherein the biomarker is an RNA molecule.
[0173] Embodiment 17. The method of Embodiments 16, wherein assessing change of one or more cell features comprises RT-qPCR, RNA sequencing, and / or in situ hybridization.
[0174] Embodiment 18. The method of Embodiment 16 or 17, wherein assessing change of one or more cell features comprises single-cell RNA sequencing.
[0175] Embodiment 19. The method of any one of Embodiments 13-15, wherein the biomarker is a protein molecule.
[0176] Embodiment 20. The method of Embodiment 19, wherein assessing change of one or more cell features comprises Western blot, ELISA, proteomics, flowcytometry, immunochemistry, and / or immunofluorescence.
[0177] Embodiment 21. The method of Embodiment 12, wherein the cellular organelle is selected from the group consisting of: nucleus, mitochondria, proteosome, endoplasmic reticulum, and Golgi apparatus.
[0178] Embodiment 22. The method of Embodiment 21, wherein the property of the cellular organelle comprises number, morphology, and function of the cellular organelle.
[0179] Embodiment 23. The method of any one of Embodiments 3-22, wherein the change in one or more cell features are evaluated about 1 day to about 8 weeks after subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation.
[0180] Embodiment 24. The method of any one of Embodiments 1-23, wherein the candidate agent is graded on its safety for extraembryonic development.
[0181] Embodiment 25. The method of Embodiment 24, wherein the candidate agent is Grade 1 if the change of one or more cell features of the early extraembryonic cell and / or the cell differentiated therefrom relative to a reference early extraembryonic cell and / or a cell differentiated therefrom without contacting with the test sample is<10%.
[0182] Embodiment 26. The method of Embodiment 24, wherein the candidate agent is Grade 2 if the change of one or more cell features of the early extraembryonic cell and / or the cell differentiated therefrom relative to a reference early extraembryonic cell and / or a cell differentiated therefrom without contacting with the test sample is±10%-25%.
[0183] Embodiment 27. The method of Embodiment 24, wherein the candidate agent is Grade 3 if the change of one or more cell features of the early extraembryonic cell and / or the cell differentiated therefrom relative to a reference early extraembryonic cell and / or a cell differentiated therefrom without contacting with the test sample is±25%-50%.
[0184] Embodiment 28. The method of Embodiment 24, wherein the candidate agent is Grade 4 if the change of one or more cell features of the early extraembryonic cell and / or the cell differentiated therefrom relative to a reference early extraembryonic cell and / or a cell differentiated therefrom without contacting with the test sample is±50%-75%.
[0185] Embodiment 29. The method of Embodiment 24, wherein the candidate agent is Grade 5 if the change of one or more cell features of the early extraembryonic cell and / or the cell differentiated therefrom relative to a reference early extraembryonic cell and / or a cell differentiated therefrom without contacting with the test sample is more than±75%.
[0186] Embodiment 30. The method of any one of Embodiments 8-29, comprising grading the candidate agent on its safety for extraembryonic development at different concentrations.
[0187] Embodiment 31. The method of any one of Embodiments 1-30, wherein the candidate agent is a drug, a food product, a nutraceutical, a cosmetic product, a component thereof, or raw material therefor.
[0188] Embodiment 32. The method of any one of Embodiments 1-31, wherein the candidate agent is selected from the group consisting of: an antibody, a virus, a virus-like, a small molecule, a peptide, a polypeptide, a DNA, an mRNA, a guide RNA, a microRNA, an RNAi, a lncRNA, an siRNA molecule, and an antisense RNA.
[0189] Embodiment 33. The method of any one of Embodiments 1-32, wherein the candidate agent is a naturally occurring substance.
[0190] Embodiment 34. The method of any one of Embodiments 1-33, wherein the test sample is selected from the group consisting of: a food sample, an environmental sample, and a body fluid sample.
[0191] Embodiment 35. The method of any one of Embodiments 1-34, wherein the test sample is selected from the group consisting of: a blood sample, a urine sample, and a saliva sample.
[0192] Embodiment 36. A composition for evaluating extraembryonic development safety, comprising an early extraembryonic cell and / or a cell differentiated therefrom, wherein the early extraembryonic cell and / or the cell differentiated therefrom optionally comprises a reporter molecule or a heterologous nucleic acid encoding a reporter molecule that is indicative of viability or differentiation of the early extraembryonic cell and / or the cell differentiated therefrom.
[0193] Embodiment 37. The method of any one of Embodiments 1-35 or the composition of Embodiment 36, wherein the early extraembryonic cell is derived from an embryonic tissue, or an extraembryonic tissue.
[0194] Embodiment 38. The method or the composition of any one of Embodiments 1-37, wherein the early extraembryonic cell is derived from a totipotent stem cell or a pluripotent stem cell selected from the group consisting of: an embryonic stem cell, an extraembryonic stem cell, an expanded potential stem cell (EPSC) , a naive pluripotent stem cell, a primed pluripotent stem cell, an induced pluripotent stem cell (iPSC) , a2-cell like cell, a4-cell like cell, an 8-cell-like cell, and an extraembryonic progenitor cell.
[0195] Embodiment 39. The method or the composition of Embodiment 38, wherein the early extraembryonic cell is derived from a pre-implantation embryonic stem cell in the 2-to 8-cell stage or the morula stage.
[0196] Embodiment 40. The method or the composition of Embodiment 39, wherein the pre-implantation embryonic stem cell in the 2-to 8-cell stage or the morula stage cell is derived from an EPSC, a ESC, or an iPSC.
[0197] Embodiment 41. The method or the composition of Embodiment 40, wherein the iPSC is derived from a somatic cell.
[0198] Embodiment 42. The method or the composition of Embodiment 41, wherein the iPSC is derived by genetic engineering, tissue engineering, or induction by small molecule (s) .
[0199] Embodiment 43. The method or the composition of Embodiment 41, wherein the somatic cell is selected from the group consisting of: an epithelial cell, a muscle cell, a neural cell, a glial cell, a blood cell, an adipose cell, a fibroblast, an endothelial cell, a liver cell, an islet cell, a bone cell, a chondrocyte, a retinal cell, and a somatic stem cell.
[0200] Embodiment 44. The method or the composition of Embodiment 38, wherein the extraembryonic progenitor cell is a placental cell.
[0201] Embodiment 45. The method or the composition of Embodiment 44, wherein the placental cell is a placental stem cell, or a placental cell that can be reprogrammed to a placental stem cell.
[0202] 46. The method or the composition of Embodiment 45, wherein the placental stem cell is a trophoblast stem cell (TSC) , or a placental cell that can be reprogrammed to a TSC.
[0203] Embodiment 47. The method or the composition of Embodiment 46, wherein the TSC expresses one or more markers selected from the group consisting of: TFAP2C, TP63, CK18, GATA2, GATA3, ELF5, TEAD4, and KRT7.
[0204] Embodiment 48. The method or the composition of Embodiment 46, wherein placental cell that can be reprogrammed to a TSC is a syncytiotrophoblast ( “STB” ) or an extravillous trophoblast ( “EVT” ) .
[0205] Embodiment 49. The method or the composition of any one of Embodiments 1-48, wherein the early extraembryonic cell is a trophoblast stem cell ( “TSC” ) or a trophoblast progenitor cell ( “TPC” ) .
[0206] Embodiment 50. The method or the composition of any one of Embodiments 1-49, wherein the early extraembryonic cell is a trophoblast stem cell ( “TSC” ) .
[0207] Embodiment 51. The method or the composition of any one of Embodiments 1-50, wherein the cell differentiated from the early extraembryonic cell is a placental cell.
[0208] Embodiment 52. The method or the composition of any one of Embodiments 1-51, wherein the cell differentiated from the early extraembryonic cell is a syncytiotrophoblast ( “STB” ) , or an extravillous trophoblast ( “EVT” ) .
[0209] Embodiment 53. The method or the composition of any one of Embodiments 1-51, wherein the cell differentiated from the early extraembryonic cell is a cell in an organoid.
[0210] Embodiment 54. The method or the composition of Embodiment 53, wherein the organoid is a placental organoid.
[0211] Embodiment 55. The method or the composition of Embodiment 52, wherein the STB has one or more characteristics selected from the group consisting of: i) is multinucleated; ii) expresses SSEA4, GCM1, CD46, CGA, ERVW-1, GATA3, OVOL, SDC1, CGB3, CGB5, and / or GCM1; iii) secretesβ-hCG.
[0212] Embodiment 56. The method or the composition of Embodiment 52, wherein the EVT has one or more characteristics selected from the group consisting of: i) has a spindle shape; ii) is invasive; iii) expresses KRT7, HLA-G, ITGA1, IGTA5 and / or MMP2; and iv) does not express or expresses in low levels GATA3, HLA-A, or HLA-B.
[0213] Embodiment 57. The method or the composition of any one of Embodiments 1-56, wherein the early extraembryonic cell and / or the cell differentiated therefrom is derived from a human, a pig, a cow, a mouse, a rat, a bat, a rabbit, a dog, a cat, and a sheep.
[0214] Embodiment 58. The method or the composition of any one of Embodiments 1-57, wherein the early extraembryonic cell and / or the cell differentiated therefrom is naturally occurring.
[0215] Embodiment 59. The method or the composition of any one of Embodiments 1-57, wherein the early extraembryonic cell and / or the cell differentiated therefrom is genetically modified.
[0216] Embodiment 60. A method of evaluating a candidate agent for its safety for extraembryonic development, comprising: i) contacting an expanded potential stem cell (EPSC) and / or a cell differentiated therefrom with a test sample comprising the candidate agent and / or a metabolic product thereof; and ii) assessing change of one or more cell features of the EPSC and / or the cell differentiated therefrom relative to an EPSC and / or a cell differentiated therefrom without contacting with the test sample. EXAMPLES Example 1: Methods 1.1 Cell Lines
[0217] The radiation-treated STO cells were prepared 3-4 days in advance on a culture plate with 0.1%gelatin at a density of~3.125×104 cells / cm2 and were routinely cultured in M10 medium (knockout DMEM+10%fetal bovine serum, 1×glutamine penicillin-streptomycin+1×(MEM) vitamin solution) . Human embryonic stem cells (hESCs) Man-1 / M1, human Em1, and Em4 cell lines were transformed into human expanded potential stem cells (hEPSCs) and cultured on STO feeder cells.
[0218] All cells were cultured at 37℃ in a 5%CO2 incubator, and Mycoplasma was routinely checked using PlasmoTest (InvivoGen) . 1.2 Cell culture
[0219] Human EPSC cells were maintained on STO feeder layers and passaged at a ratio of 1: 10 every 3-5 days. When the cells grew to a density of 80%, after washing with DPBS once, the cells were digested using the cell digestion enzyme TrypLETM Express enzyme (1x) for 5 minutes and neutralized with M10 culture medium (M10: enzyme=1: 1) and blew into single cells. After centrifugation at 300g for 3 minutes, the supernatant was removed, and the cells were resuspended in hEPSC medium supplemented with 5.0μM Y27632 (Tocris. Cat. 1254) . The hEPSCM is a N2B27-based media (1: 1 DMEM / F12 (Thermo, Cat. 21331020) , Neurobasal Medium (Thermo, Cat. 21103049) , 200× N2, 100× B27, 100x ITS-X, 50.0 μM β-mercaptoethanol, 1%Penicillin-Streptomycin-Glutamine, 100x Non-essential amino acid solution, 50μg / mL Vitamin C) supplemented with 4 small molecules: 5μM XAV939, 1μM CHIR99021 and 0.1μM A419259 as previously published (Gao, X., et al, (2019) . Establishment of porcine and human expanded potential stem cells. Nat. Cell Biol. 21, 687–699, the content of which is incorporated herein in its entirety) .
[0220] stem cells were maintained on inactivated MEF (mouse embryonic fibroblasts) feeder layers in PXGL medium. The PXGL medium is prepared by supplementing N2B27 basal medium with PD0325901 (1μM) , XAV-939 (2μM) , 6983 (2μM) , 0.45%BSA and human leukemia inhibitory factor (hLIF, 10 ng / mL) as previously reported (Guo et al., (2021) . Human epiblast cells possess unrestricted lineage potential. Cell Stem Cell 28, 1040–1056. e6., the content of each of which is incorporated herein in its entirety) . 1.3 Differentiation to the trophoblast lineage by inhibiting TGF-βsignaling of hEPSC
[0221] hEPSCs were digested and separated into single cells by the cell separation reagent TrypLE and then seeded into a 6-well plate coated with GELTREXTM LDEV-Free Reduced Growth Factor Basement Membrane Matrix. The seeding density was 100,000 per well. The seeded cells were cultured for one day in basal medium containing 20% serum replacement (KSR) and 10μM ROCK signaling inhibitor Y27632. Starting the second day, cells were then cultured in medium containing 20% serum replacement (KSR) and 10μM TGF-βsignaling pathway inhibitor SB431542. At different time points, cells were harvested for further analysis. 1.4 Human trophoblast stem cell line (hTSCs) establishment
[0222] To generate the hTSC cell lines, the single cell suspension of hEPSCs were plated on a 6-well plate (2x103 cells / well) pre-coated with GELTREXTM LDEV-Free Reduced Growth Factor Basement Membrane Matrix (diluted 100x) and cultured in human trophoblast stem cell medium (hTSCM) for 12-14 days. Then single colonies of the differentiated cells on the 6-well plate that show the typical TSC morphologies were picked and expanded. The established TSC cell lines were passaged 7-9 times before being collected for further differentiation into STB or EVT. The hTSCM is DMEM / F12 based medium supported with: 50.0μMβ-mercaptoethanol, 0.2%FBS, 0.5%Penicillin-Streptomycin-Glutamine, 0.3%BSA, 1.0%ITS-X supplement, 50.0 μg / mL Vc, 50.0 ng / mL EGF, 2.0μM CHIR99021, 0.5μM A83-01, 1.0μM SB431542, 10.0μM VPA, and 5.0μM Y27632. 1.5 Differentiation of STB
[0223] Established TSC cells were seeded at 1.0x105 cells / well in a six-well plate pre-coated with Matrigel (100X) and were induced to differentiate into STBs after culturing in 2 mL of syncytiotrophoblasts medium (STBM) . The STBM comprises: DMEM / F12 supplemented with 50μMβ-mercaptoethanol, 0.5%Penicillin-Streptomycin-Glutamine, 0.3%BSA, 1.0%ITS-X, 2.5μM Y-27632, 2μM Forskolin (Sigma-Aldrich, Cat. F3917) , and 4%KnockOut Serum Replacement (Thermo. Cat. 10828028) . 1.6 Differentiation of EVT
[0224] Established TSC cells were seeded at 1.0x105 cells / well in a six-well plate pre-coated with Matrigel (100X) and were induced to differentiate into STBs after culturing in 3 mL of EVT medium. The EVT medium comprises: DMEM / F12 supplemented with 50 μM β-mercaptoethanol, 0.5%Penicillin-Streptomycin-Glutamine, 0.3%BSA, 1.0%ITS-X, 2.5μM Y-27632, and 7.5μM A83-01. In the first two days, 4%KnockOut Serum Replacement, 100 ng / mL NRG1 and 2% Basement Membrane Matrix were added. On day 3, the medium was switched to 2 mL of EVT medium, with 4%KnockOut Serum Replacement and 0.5% Basement Membrane Matrix. On day 6, the medium was switched to 2 mL of EVT medium with 0.5% Basement Membrane Matrix. The cells were cultured for two more days and were collected on day 8 for downstream analyses. 1.7 Differentiation of Placental Organoids
[0225] Human EPSCs were treated with the digestion isolation reagent TrypLE to be separated into single cells, which were then centrifuged and collected for later use. Each 40μl placental organoid droplet was prepared to contain 60%cytokine-reduced Matrigel and 40%placental organoid culture medium. 1x105 collected cells were mixed into each placental organoid droplet and seeded onto a plate. The droplets were placed in a 37℃ carbon dioxide cell incubator for 3 minutes to pre-coagulate. After 3 minutes, the plates were taken out and shaken to ensure that the cells were evenly distributed in the droplets. The plates were incubated in the incubator for another 15 minutes completely solidify and form a dome shape. 500μl of placental organoid medium was gently added to each well. Placental organoids usually form after 4-6 days of culturing. The placental organoid culture medium comprises N2B27 basic medium with 50ng / mL recombinant human epidermal growth factor, 1.5μM CHIR99021, 80 ng / mL recombinant human R-spondin-1 protein, 100 ng / mL recombinant human fibroblast growth factors, 50 ng / mL recombinant human hepatocyte growth factor, 500 nM A83-01, 2.5μM prostaglandin E2, and 2μM Y-27632. The placental organoid culture medium can be kept at 4℃for 2 weeks. 1.8 Other Evaluation Methods
[0226] RT-qPCR: Total RNA was extracted using RNeasy Mini Kit (Qiagen) per manufacturer specification. Extracted RNA was then reverse transcribed to cDNA using Fastking gDNA diselling RT SuperMix (Tiangen) . Gene expression was measured using PowerUpTM SYBRTM Green Master Mix (Applied Biosystems) and StepOnePlusTM Real-Time PCR(Applied Biosystems) with the primers listed in Table E1A. Raw gene expression data was normalized to GAPDH by using theΔCt method. Statistical analysis was carried out using either one / two-tailed student’s t-test in Prism 8 (GraphPad) . Table E1A. Primers used in RT-qPCR (5’ to 3’)
[0227] Immunofluorescence staining (IF) : Samples were fixed in 4%paraformaldehyde (Sigma Cat. P6148) at room temperature for 15 min and blocked for 0.5-1h with 5%donkey serum (Sigma. Cat. D9663) and 1%BSA (Sigma. Cat. A2153) in PBS. This was followed by incubation with primary antibodies in a 4℃cold room overnight. The cells were incubated with fluorophore-conjugated secondary antibodies at room temperature for 1 h. The cells were counterstained with 10μg / mL DAPI (Thermo Fisher Scientific. Cat. 62248) for 10 min to mark nuclei and were imaged under a confocal microscope.
[0228] Immunoblotting: Proteins were separated on a 7.5%polyacrylamide gel (Bio-Rad. Cat. 1610180) and transferred to a Bio-Rad transblot PVDF membrane according to the manufacturer's instructions. The following primary antibodies were used: rabbit ACE2 (1: 500, Abclonal. Cat. A4612) and rabbitβ-actin (1: 5000, Abmart. Cat. P30002M) . Goat anti-rabbit IgG H&L (HRP. Cat. Ab205718) was used as secondary antibody. Images were taken and analyzed using the ChemiDoc imaging system.
[0229] Flow cytometry: Cells were digested with 0.25%trypsin / EDTA for 2–3 min at 37℃and dissociated to single cells by pipetting. The dissociated cells were filtered through a 40μm nylon mesh (Kangning cat. 352235) to remove cell clumps. After centrifugation, the cells were fixed using Fixation Medium (BD Cytofix, Cat. 554655) according to the manufacturer’s protocol and the washed cells were stored at 4℃in PBS supplemented with 0.1%NaN3 (Sigma. Cat. 199931) and 5%FBS (Gibco. Cat. 10270) before analysis with flow cytometry. All the samples were assayed by ACEA NovoCyte Quanteon. 488nm (530 / 30 bandpass filter) and 561nm (610 / 20 bandpass filter) channels were used to detect FITC and exclude autofluorescence. 405nm (445 / 45 bandpass filter) channel was used to detect DAPI positive cells. FACS data was analyzed by the Flowjo software.
[0230] RNA sequencing: Adapter sequences and low-quality 3’ end sequences were removed using Cutadapt. Processed reads were mapped to the human hg38 genome assembly by hisat2. Genes with mean count number<5 were filtered out. Transposable element annotations were obtained from UCSC Genome Browser (RepeatMasker) . SQuIRE with “total” mode was used to quantify TE expressions. DESeq2 was used to analyze differentially expressed genes and TEs. Genes and TEs with>1.5-fold change (p<0.05) were considered to be significantly differentially expressed. R package clusterprofiler was used for gene ontology (GO) and KEGG analysis. GSEA (Gene Set Enrichment Analysis) was performed by GSEApy, and the gene sets were downloaded directly from https: / / www. gsea-msigdb. org. Bigwig files for RNA-seq signal were generated by bamCoverage from Deeptools and IGV was used for visualization. For data deposited in E-MTAB-10429, the processed count table was used directly. Example 2: Safety Evaluation
[0231] 1. Cell viability:
[0232] Cell viability can be measured using CCK-8 proliferation test. WST-8 in CCK-8 is reduced by intracellular dehydrogenase during the metabolism of living cells to generate an orange methazole dye. The dye is soluble so it will pass into the culture medium. The metabolic activity of cells is related to the number of cells and the health of the cells, so the higher the cell activity, the higher the concentration of orange dye produced. The optical density (OD value) of the dye solution can be measured at a wavelength of 450 nm using a microplate reader. Changes in OD value can reflect cell viability and proliferation.
[0233] Approximately 5,000 TSC cells were seeded in Matrigel-coated 96-well plates and placed in an incubator overnight. After the cells adhered to the wall, corresponding concentrations of the test agent and the positive control were added, and the cells were treated for 24-72 hours. The cells were then incubated in CCK8 for 1-4 hours, absorbance was measured at 450nm to calculate the relative cell viability value.
[0234] Within a certain drug treatment range (such as 10 nM~10μM) , the experimental results of the agents to be tested were compared to the positive control group to calculate the percent change in viability.
[0235] The results show that cell morphology was affected by Remdesivir, affected by both the drug concentration and incubation time (FIG. 3) . And as the drug concentration increases, the number of cells decreases significantly after incubation for 48 hours (FIGs. 4A-4B) .
[0236] 2. Cell death
[0237] When cells undergo apoptosis, the permeability of cell membranes also increases, but the degree is between that of normal cells and necrotic cells. Taking advantage of this feature, cells can be stained with fluorescein or related reagents, and the fluorescence intensity or reagent spectrum in the cell suspension can be measured using a flow cytometer to distinguish normal cells, necrotic cells and apoptotic cells.
[0238] Approximately 50,000 TSC cells were seeded in Matrigel-coated 6-well plates and placed in an incubator overnight. After the cells adhered to the wall, corresponding concentrations of the test agent and the positive control were added, and the cells were treated for 24-72 hours. Cells were imaged under a light microscope and digested using trypsin. The cell suspension of each group was collected and stained with a commercial apoptosis kit (Biolegend) , and then quantitatively analyzed using a flow cytometer.
[0239] Within a certain drug treatment range (such as 10 nM–10μM) , the experimental results of the test sample were compared with the control group to calculate the proportion of apoptotic cells to evaluate the effect of the drug / test substance on cell apoptosis.
[0240] As shown in FIG. 5A, after adding 2μM and 5μM drug (Remdesivir) for 48 hours, the apoptosis rate was 3.78%, 5.23%, and 30.86%in the control group, 2μM group, and 5μM group, respectively. The proportion of cell apoptosis significantly increased as the drug concentration increased. The reduction of cell numbers in the Remdesivir-treated group can also be seen in FIG. 5B.
[0241] 4. TSC Cell Markers and miRNA expression
[0242] Trophoblast stem cells (TSCs) normally express markers, such as TFAP2C, TP63, CK18, GATA3, ELF5, TEAD4 and KRT7, etc., and have low or no expression of HLA class I molecules HLA-A and HLA-B.
[0243] Approximately 50,000 TSC cells were seeded in Matrigel-coated 6-well plates and placed in an incubator overnight. After the cells adhered to the wall, corresponding concentrations of the test agent and the positive control were added, and the cells were treated for 24-72 hours. The cells were imaged under a light microscope and digested using trypsin. Trizol was used to extract RNA and perform reverse transcription, and then cell marker expression was quantified use qPCR.
[0244] Expression of the markers can be normalized against GAPHD and measured as percent or fold increase as compared to the control. As shown in FIG. 6A, after incubating with 500 nM drug (Remdesivir) for 48 hours, a series of marker genes such as ITGA6, GATA3, TFAP2A, TEAD4, TFAP2C and TP63 in the treatment group were significantly lower than those in the control group.
[0245] Additionally, as shown in FIG. 6B, miRNA expression decreased after incubation with Remdesivir.
[0246] 5. TSC-STB differentiation
[0247] EPSC derived TSCs were induced to differentiate into syncytiotrophoblasts (STBs) . During differentiation, the expression of trophoblast precursor cell transcription factor gene TP63 decreases while STB genes such as GCM1, beta-chorionic gonadotropin 3 (CGB3) and CGB5 increase rapidly. Immunofluorescence staining showed that syncytiotrophoblast cells on the sixth day of differentiation (STB-D6) should be GCM1-positive, CGB-positive and multinucleated STBs. Untreated STB also secretesβ-hCG that can be detected by ELISA by Day 6 of differentiation.
[0248] During differentiation, cell morphology was regularly monitored and recorded (e.g., on Day 3, Day 4, Day 5, Day 6) under a light microscope, and percentage of cells that are multinucleated was calculated and recorded. The cells were stained using anti-CGB antibody. Trizol was used to extract RNA and perform reverse transcription and then cell marker expression was quantified use qPCR. Cell supernatant was collected on Day 3-Day 6 of differentiation andβ-hCG was detected using commercially availableβ-hCG ELISA kits (e.g., RayBiotech) .
[0249] The following measurements in the treatment groups were compared to the control:
[0250] 1) percentage of cells that are multinucleated;
[0251] 2) percentage cells that are CGB positive;
[0252] 3) precent decrease of markers for STB maturation, including CD46, CGA, CGB3, CGB5, CSH1 / 2, ERVW-1, GATA3, OVOL, SDC1; and
[0253] 4) percent decrease ofβ-hCG secretion.
[0254] Cell morphology of a normal TSC-STB differentiation process is shown in FIG. 7. Remdesivir (500 nM) treatment group showed less cell fusion (FIGs. 8A and 10) , less cells that are multinucleated (FIG. 8B) , less cells that are CGB positive (FIGs. 8C and 9) , reduced expression of STB markers (CD46, CGA, CGB3, CGB5, CSH1 / 2, ERVW-1, GATA3, OVOL, and SDC1) (FIG. 11) , and reduced secretion ofβ-hCG (FIG. 12) . Remdesivir also severely distorted the microvilli morphologies of eSTB (FIG. 20) shown by TEM. Furthermore, the bulk transcriptome of Remdesivir-treated STB appeared to revert to a developmentally earlier state of post-implantation trophoblast and away from the vehicle-treated control (FIG. 21) . These observations suggested that Remdesivir-induced cytotoxicity may hinder the hTSC-to-eSTB-to-STB maturation.
[0255] 6. TSC-EVT differentiation
[0256] By inhibiting the TGFβsignaling pathway, TSCs can be efficiently induced to differentiate into extravillous trophoblast cells (EVTs) , which show a typical spindle-shaped EVT cell morphology. During TSC-EVT differentiation, the expression levels of EVT marker genes ITGA1, MMP2 and HLA-G increase rapidly while the expression level of GATA3 decreases (FIG. 15) . Mature EVTs are KRT7, HLA-G, ITGA1 and IGTA5 positive. Some mature EVTs are HLA-G positive and GATA3 negative. Specifically, on the 8th day after induction of TSC differentiation into EVT, 80%of the cells are HLA-G positive, >80%of the cells are ITGA1 positive, and>95%are ITGA5 positive. Additionally, TSC-differentiated EVTs have strong invasive ability, which can be measured by cell invasion assay.
[0257] Approximately 25,00 to 5,000 TSC cells were seeded in Matrigel-coated 12-well plates or glass-bottomedμbidi dishes and placed in an incubator overnight. After the cells adhered to the wall, corresponding concentrations of the test agent and the positive control were added, and the cells were treated for 24-72 hours. The cells were imaged under a light microscope.
[0258] Cells in Matrigel-coated 12-well plates continued to culture in the EVT medium for another 4-8 days, after which they were digested using trypsin. Trizol was used to extract RNA and perform reverse transcription and then cell marker expression was quantified using qPCR.
[0259] Cells in glass-bottomedμbidi dishes continued to culture in the EVT medium for another 4-8 day, and then fixed in paraformaldehyde, immunofluorescent stained for the classic EVT marker HLA-G, and then photographed using a fluorescence microscope.
[0260] The invasion chamber was incubated with warm DMEM basal medium at 37℃ for 1 hour, and the medium was removed after rehydration. TSC derived EVTs (1×105 cells / well) were prepared in DMEM basal medium. The mixture was added to the invasion chamber, placed in a 24-well culture plate, and the lower chamber was filled with DMEM containing 10%fetal calf serum. The cells were allowed to pass through the chamber and attach to the lower bottom of the polycarbonate membrane. After 22 hours, the culture medium from the top insert and wipe the upper surface of non-invading / migrating cells was wiped off with a cotton bud. The infiltrated / migrated cells on the lower surface were stained with crystal violet for 15 min, and the cell membrane was observed under a light microscope and photographed.
[0261] For evaluating the safety of an agent, cell markers as described above in the treatment group are compared to the control group, and the agent is scored for its safety based on the increase of decrease of the measurements, including: expression of EVT markers such as KRT7, HLA-G, ITGA1 and IGTA5 and lack of expression of genes such as HLA-A and HLA-B, and percentage of cells that are invasive.
[0262] The results show that cells in the Remdesivir (500 nM) treatment group showed altered cell morphology compared to the control group; for example, the cells in the treatment group did not show the typical spindle morphology (FIG. 13) . Cells in the Remdesivir (500 nM) treatment group also showed decreased expression of markers such as HLA-G, ITGA1, ITGA5, MMP2 (normalized against GAPDH) (FIGs. 14-17, and 19) , and were less invasive (FIG. 18) .
[0263] The toxicity of Remdesivir to other organs have been evidenced in animal studies and clinical studies. In animal studies, elevated alanine aminotransferase (ALT) and aspartate aminotransferase (AST) indicated liver cell injury. Microscopic examination of liver tissue showed evidence of inflammation (hepatocellular degeneration and necrosis) . Increased Blood Urea Nitrogen (BUN) and creatinine indicated reduced kidney function. Studies also showed that Remdesivir lead to renal tubular degeneration (U.S. Food and Drug Administration (FDA) . (2020, October 22) . Review of Regulatory Information -NDA 214787 / Original 1 (Veklury / Remdesivir) . In the large, randomized Adaptive COVID-19 Treatment Trial (ACTT-1) , Grade 3 or 4 elevations in ALT (>5 times the upper limit of normal) occurred in a higher proportion of Remdesivir recipients compared to the placebo group (Beigel, J. H., et al. (2020) . Remdesivir for the Treatment of Covid-19-Final Report. The New England Journal of Medicine (NEJM) , 383, 1813-1826) . Numerous observational studies have confirmed that a significant minority of patients (estimates vary from~10%to over 20%) experience elevations in liver enzymes during treatment. Post-marketing data and larger observational studies have reported cases of acute kidney injury (AKI) in patients receiving Remdesivir (Wong, G. L., et al. (2021) . Adverse effects of remdesivir in hospitalized patients with COVID-19: a population-based study. Alimentary Pharmacology&Therapeutics, 54 (2) , 175-177. ) . The incidence is lower than liver toxicity but is a recognized risk.
[0264] It will be appreciated that while the cells in the above examples were human cells, mammal cells could also be used.
[0265] It will also be appreciated while the cells in the above examples were in a 2D culture, the cells could also be in a 3D culture.
Claims
1.A method of evaluating a candidate agent for its safety for extraembryonic development, comprising:(i) contacting an early extraembryonic cell and / or a cell differentiated therefrom with a test sample comprising the candidate agent and / or a metabolic product thereof; and(ii) assessing change of one or more cell features of the early extraembryonic cell and / or the cell differentiated therefrom relative to a reference early extraembryonic cell and / or a cell differentiated therefrom without contacting with the test sample.2.The method of claim 1, wherein extraembryonic development comprises placenta development and / or amniotic tissue development.3.A method of evaluating a candidate agent for its safety for embryonic development, comprising:(i) contacting an early extraembryonic cell and / or a cell differentiated therefrom with a test sample comprising the candidate agent and / or a metabolic product thereof; and(ii) assessing change of one or more features of the early extraembryonic cell and / or the cell differentiated therefrom relative to a reference early extraembryonic cell and / or a cell differentiated therefrom without contacting with the test sample.4.The method of claim 3, wherein embryonic development comprises liver, kidney, intestine, skin, and / or heart development.5.The method of any one of claims 1-4, further comprising subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation.6.The method of claim 5, wherein the early extraembryonic cell and / or the cell differentiated therefrom is contacted with the test sample simultaneously with, prior to, or after being subjected to the condition that allows differentiation.7.The method of any one of claims 1-6, wherein the contacting comprises contacting the early extraembryonic cell and / or the cell differentiated therefrom with the test sample at different concentrations.8.The method of any one of claims 1-7, wherein the candidate agent and / or the metabolic product of the candidate is at from about 10 nM to about 1000 mM in the test sample.9.The method of any one of claims 1-9, wherein the one or more features comprises cell viability, cell morphology, cell proliferation and / or differentiation, molecular characteristics, characteristics of an organoid, and / or functional characteristics.10.The method of claim 9, wherein:(1) cell proliferation and / or differentiation comprises rate of proliferation and / or rate of change to a differentiated state;(2) functional characteristics comprise property of a cellular organelle;(3) molecular characteristics comprise:(i) presence or absence of a biomarker;(ii) level of a biomarker;(iii) secretion of a biomarker; and / or(iv) the presence or absence of a reporter molecule; and / or(4) characteristics of an organoid comprises organoid morphology and / or structure.11.The method of claim 10, wherein the biomarker is selected from the group consisting of a marker of cell cycle, cell death, genomic instability, epigenetic alternations (such as DNA, RNA and protein modifications) , loss ofproteostasis, telomere attrition, organelle dysfunction, disabled macroautophagy, deregulated nutrient-sensing, altered intercellular communication, cellular senescence, chronic inflammation, differentiation, endogenous transposon elements, and stem cell exhaustion.12.The method of claim 11, wherein the biomarker is selected from the group consisting of: β-hCG, ISL1, ITGA5, VTCN1, GABRP, NANOG, OCT4, SSEA-4, SOX2, CD29, CD44, CD46, CD58, CD73, CD90, CD105, CD117, CD166, CD106, TFAP2C, TP63, CK18, GATA2, GATA3, ELF5, KRT7, TEAD4, CBG, GCM, HLA-A, HLA-B, HLA-C, HLA-G, ITGA1, MMP2, CGB, ERVW1, SDC1, ITGB6, MUC16, CGA, CGB3, CGB5, CSH1 / 2, OVOL, cleaved Caspase-3, cleaved, active N-terminal fragment of Gasdermin D, a Cyclin-Dependent Kinase (CDK) , and combinations thereof.13.The method of claim 11, wherein the biomarker is a marker of cell death comprising a marker of apoptosis, pyroptosis, and / or necrosis.14.The method of claim 13, wherein the biomarker is a caspase.15.The method of any one of claims 10-14, wherein the biomarker is an RNA molecule or a protein molecule.16.The method of claim 10, wherein the cellular organelle is selected from the group consisting of: nucleus, mitochondria, proteosome, endoplasmic reticulum, and Golgi apparatus, and / or wherein the property of the cellular organelle comprises number, morphology, and function of the cellular organelle.17.The method of any one of claims 5-16, wherein the change in one or more cell features are evaluated about 1 day to about 8 weeks after subjecting the early extraembryonic cell and / or the cell differentiated therefrom to a condition that allows differentiation.18.The method of any one of claims 1-17, wherein the candidate agent is graded on its safety.19.The method of any one of claims 7-18, comprising grading the candidate agent on its safety at different concentrations.20.The method of any one of claims 1-19, wherein:(1) the candidate agent is a drug, a food product, a nutraceutical, a cosmetic product, a component thereof, or raw material therefor;(2) the candidate agent is selected from the group consisting of: an antibody, a virus, a virus-like, a small molecule, a peptide, a polypeptide, a DNA, an mRNA, a guide RNA, a microRNA, an RNAi, a lncRNA, an siRNA molecule, and an antisense RNA;(3) the candidate agent is a naturally occurring substance; and / or(4) the test sample is selected from the group consisting of: a food sample, an environmental sample, and a body fluid sample, optionally wherein the body fluid sample is a blood sample, a urine sample, or a saliva sample.21.A composition for evaluating safety for extraembryonic development of a candidate agent, comprising an early extraembryonic cell and / or a cell differentiated therefrom, wherein the early extraembryonic cell and / or the cell differentiated therefrom optionally comprises a reporter molecule or a heterologous nucleic acid encoding a reporter molecule that is indicative of viability or differentiation of the early extraembryonic cell and / or the cell differentiated therefrom.22.The composition of claim 21, wherein extraembryonic development comprises placenta development and / or amniotic tissue development.23.A composition for evaluating safety for embryonic development of a candidate agent, comprising an early extraembryonic cell and / or a cell differentiated therefrom, wherein the early extraembryonic cell and / or the cell differentiated therefrom optionally comprises a reporter molecule or a heterologous nucleic acid encoding a reporter molecule that is indicative of viability or differentiation of the early extraembryonic cell and / or the cell differentiated therefrom.24.The composition of claim 23, wherein embryonic development comprises liver, kidney, intestine, skin, and / or heart development.25.The method of any one of claims 1-20 or the composition ofclaim any one of claims 21-24, wherein the early extraembryonic cell is derived from an embryonic tissue, or an extraembryonic tissue.26.The method or the composition ofany one of claims 1-25, wherein the early extraembryonic cell is derived from a totipotent stem cell or a pluripotent stem cell selected from the group consisting of: an embryonic stem cell, an extraembryonic stem cell, an expanded potential stem cell (EPSC) , a naive pluripotent stem cell, a primed pluripotent stem cell, an induced pluripotent stem cell (iPSC) , a 2-cell like cell, a 4-cell like cell, an 8-cell-like cell, and an extraembryonic progenitor cell.27.The method or the composition of claim 26, wherein the early extraembryonic cell is derived from a pre-implantation embryonic stem cell in the 2-to 8-cell stage or the morula stage.28.The method or the composition of claim 27, wherein the pre-implantation embryonic stem cell in the 2-to 8-cell stage or the morula stage cell is derived from an EPSC, a ESC, or an iPSC, optionally where the iPSC is derived from a somatic cell.29.The method or the composition of claim 26, wherein the extraembryonic progenitor cell is a placental cell, optionally wherein the placental cell is a placental stem cell, or a placental cell that can be reprogrammed to a placental stem cell.30.The method or the composition of claim 29, wherein the placental stem cell is a trophoblast stem cell (TSC) , or a placental cell that can be reprogrammed to a TSC.31.The method or the composition of claim 30, wherein the TSC expresses one or more markers selected from the group consisting of: TFAP2C, TP63, CK18, GATA2, GATA3, ELF5, TEAD4, and KRT7.32.The method or the composition of claim 30, wherein placental cell that can be reprogrammed to a TSC is a syncytiotrophoblast ( “STB” ) or an extravillous trophoblast ( “EVT” ) .33.The method or the composition of any one of claims 1-32, wherein the early extraembryonic cell is a trophoblast stem cell ( “TSC” ) or a trophoblast progenitor cell ( “TPC” ) .34.The method or the composition of any one of claims 1-33, wherein the early extraembryonic cell is a trophoblast stem cell ( “TSC” ) .35.The method or the composition of any one of claims 1-34, wherein the cell differentiated from the early extraembryonic cell is a placental cell.36.The method or the composition of any one of claims 1-35, wherein the cell differentiated from the early extraembryonic cell is a syncytiotrophoblast ( “STB” ) , or an extravillous trophoblast ( “EVT” ) .37.The method or the composition of any one of claims 1-35, wherein the cell differentiated from the early extraembryonic cell is a cell in an organoid.38.The method or the composition of claim 37, wherein the organoid is a placental organoid, and / or the organoid is an organ-on-chip.39.The method or the composition of claim 36, wherein the STB has one or more characteristics selected from the group consisting of:(i) is multinucleated;(ii) expresses SSEA4, GCM1, CD46, CGA, ERVW-1, GATA3, OVOL, SDC1, CGB3, CGB5, and / or GCM1; and(iii) secretesβ-hCG.40.The method or the composition ofclaim 36, wherein the EVT has one or more characteristics selected from the group consisting of:(i) has a spindle shape;(ii) is invasive;(iii) expresses KRT7, HLA-G, ITGA1, IGTA5 and / or MMP2; and(iv) does not express or expresses in low levels GATA3, HLA-A, or HLA-B.41.The method or the composition of any one of claims 1-40, wherein:(1) the early extraembryonic cell and / or the cell differentiated therefrom is derived from a human, a non-human primate, a pig, a cow, a mouse, a rat, a bat, a rabbit, a dog, a cat, and a sheep; and / or(2) the early extraembryonic cell and / or the cell differentiated therefrom is naturally occurring or genetically modified.42.A method of evaluating a candidate agent for its safety for extraembryonic development, comprising:(i) contacting an expanded potential stem cell (EPSC) and / or a cell differentiated therefrom with a test sample comprising the candidate agent and / or a metabolic product thereof; and(ii) assessing change of one or more cell features of the EPSC and / or the cell differentiated therefrom relative to an EPSC and / or a cell differentiated therefrom without contacting with the test sample.
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