HDAC inhibitors for treating cancers with altered STK11 activity or expression

Abstract

The present disclosure relates to methods of treating cancers, including cancers having altered STK11 activity or expression, by administering an effective amount of a histone deacetylase (HDAC) inhibitor.

Description

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS

[0002] This application claims priority to and the benefit of U.S. Provisional Patent Application No. 63 / 395,503 filed on August 5, 2022, U.S. Provisional Patent Application No. 63 / 422,723 filed on November 4, 2022, U.S. Provisional Patent Application No. 63 / 490,217 filed on March 14, 2023, and U.S. Provisional Patent Application No. 63 / 496,290 filed on April 14, 2023, the entire contents of which are incorporated herein by reference for all purposes. Background Art

[0003] STK11 is a tumor suppressor gene that drives immune evasion when deleted or inactivated and is frequently mutated in lung adenocarcinomas such as non-small cell lung cancer (NSCLC). Identifying drug targets that can disable immune evasion caused by STK11 loss-of-function mutations could reverse cancer cell immune evasion and enable immune cells to eliminate cancer cells containing STK11 mutations.

[0004] The current standard of care for treating patients with lung adenocarcinoma generally includes the administration of anti-PD-1 therapy or anti-PD-L1 therapy. However, patients with lung adenocarcinoma with STK11 loss-of-function mutations respond poorly to such anti-PD-1 and anti-PD-L1 therapies. Skoulidis, F. et al. Cancer Discovery 8(7):822-835(2018)(DOI:10.1158 / 2159-8290.CD-18-0099) and Skoulidis, F. et al. Journal of Clinical Oncology 37(15):Suppl. 102(2019)(DOI:10.1200 / JCO.2019.37.15_suppl.102), each of which is hereby incorporated by reference in its entirety.

[0005] Attempts to improve outcomes for patients with lung adenocarcinoma include the development of a class of compounds called Kristen rat sarcoma 2 viral oncogene homolog (KRAS) inhibitors, which have been developed to treat patients with certain KRAS-positive lung cancers (e.g., KRAS G12C ) mutations in patients with cancer (e.g., NSCLC). However, such compounds have certain limitations, and there remains a need to improve outcomes for patients for whom current standard of care is inadequate.

[0006] Therefore, there is a need to identify methods for treating cancer patients harboring STK11 mutations. Summary of the invention

[0007] Provided herein are methods of treating a subject having or at risk of developing cancer, the methods comprising administering to the subject an effective amount of a histone deacetylase inhibitor, wherein the cancer is identified as having altered STK11 activity or expression.

[0008] Also provided herein are methods for selecting a subject for treatment with an HDAC inhibitor, the method comprising: identifying a subject having a cancer characterized by the presence of cells having altered STK11 activity or expression; and selecting the subject thus identified for treatment with the HDAC inhibitor.

[0009] Also provided is a method for ascertaining the sensitivity of a subject to treatment with an HDAC inhibitor, the method comprising: determining: i) the presence or absence of a STK11 mutation in the subject or a sample derived from the subject; and / or ii) the level of STK11 activity or expression; wherein the presence of a STK11 mutation and / or altered level of STK11 activity or expression indicates sensitivity to treatment with an HDAC inhibitor. BRIEF DESCRIPTION OF THE DRAWINGS

[0010] Figure 1A Depicted are tumor growth curves of mice bearing MC38_sgSTK11 tumors treated with a control antibody anti-IgG2a (10 mg / kg ip BIW), a combination of Compound I (3, 10, 30, 75 and 150 / 100 mg / kg po, QD) + a control antibody anti-IgG2a (10 mg / kg ip BIW), an anti-PD1 inhibitor (10 mg / kg i.p., BIW), and a combination of Compound I (3, 10, 30, 75 and 150 / 100 mg / kg po, QD) + an anti-PD1 inhibitor (10 mg / kg i.p., BIW). Data were plotted according to the groups described in Example 1.

[0011] Figure 1B Tumor growth curves in the MC38 STK11 knockout mouse model treated with anti-IgG2a (10 mg / kg ip, BIW), anti-PD1 (10 mg / kg i.p., BIW), Compound I (30 mg / kg po, QD) or anti-PD1 (10 mg / kg ip, BIW) + Compound I (30 mg / kg p.o., QD) were monitored during treatment and plotted for individual animals.

[0012] Figure 2ADepicted are the survival curves of mice bearing MC38_sgSTK11 tumors treated with control antibody anti-IgG2a (10 mg / kg ip, BIW), a combination of Compound I (3, 10, 30, 75 and 150 / 100 mg / kg po, QD) + control antibody anti-IgG2a (10 mg / kg ip BIW) or an anti-PD1 inhibitor (10 mg / kg ip, BIW). The data were plotted according to the groups described in Example 1.

[0013] Figure 2B Survival curves of mice bearing MC38_sgSTK11 tumors treated with control antibody anti-IgG2a (10 mg / kg ip, BIW), Compound I (3, 10, 30, 75 and 150 / 100 mg / kg poQD) + anti-PD1 inhibitor (10 mg / kg ip, BIW) or anti-PD1 inhibitor (10 mg / kg ip, BIW) are depicted. Data were plotted according to the groups described in Example 1.

[0014] Figure 2C Shown are survival graphs of mice bearing STK11-deficient MC38 tumors treated with anti-IgG2a (10 mg / kg, ip, BIW), anti-IgG2a (10 mg / kg, ip, BIW) + Compound I (30 mg / kg, po, QD), anti-PD1 (10 mg / kg, ip, BIW), or anti-PD1 (10 mg / kg, ip, BIW) + Compound I (30 mg / kg, po, QD) as indicated.

[0015] Figure 3A Depicted are tumor growth curves of untreated control mice and mice that had survived treatment with a combination of Compound I (75 mg / kg, po, QD) + control antibody anti-IgG2a (10 mg / kg, ip, BIW) or an exemplary HDAC inhibitor (3, 10, 30, 75 and 150 / 100 mg / kg) + anti-PD1 inhibitor (10 mg / kg, ip, BIW) and re-challenged with MC38_sgSTK11 implants as described in Example 2.

[0016] Figure 3B Graph showing tumor volume in mice re-challenged with STK11 -deficient MC38 tumors in parallel with a control group of previously untreated mice (combined in a single group) as described in Example 2. All animals remained off treatment and tumor size over time after re-challenge is plotted.

[0017] Figure 4Depicted are tumor growth curves of MC38_sgSTK11 tumor-bearing mice treated with control antibody anti-IgG2a (10 mg / kg ip BIW), Compound I (30 mg / kg, po QD), anti-PD1 inhibitor (10 mg / kg ip, BIW) and a combination of Compound I (30 mg / kg po, QD) + anti-PD1 inhibitor (10 mg / kg i.p., BIW). Mice with complete tumor regression in the initial experiment were re-challenged with MC38_sgSTK11 implants on day 69.

[0018] Figure 5A Volcano plot showing an unbiased in vivo CRISPR screen identifying HDAC1 knockout as a sensitizing factor to anti-PD1 in STK11-deficient MC38 tumors.

[0019] Figure 5B A waterfall plot of Project Achilles CRISPR scores for HDAC1, HDAC2, and HDAC3 in a cell line repertoire is shown. Negative scores indicate depletion of cells with knockout of the indicated gene.

[0020] Fig. 6A Shown is a graph showing dose-dependent binding of Compound I to HDAC1 by cellular NanoBRET target engagement assay.

[0021] Figure 6B Shown is a graph of dose-dependent binding of Compound 1 to HDAC2 by cellular NanoBRET target engagement assay.

[0022] Figure 6C Shown is a graph of dose-dependent binding of Compound I inhibitor to HDAC3 by cellular NanoBRET target engagement assay.

[0023] Fig. 7A Tumor growth curves in the CT26 STK11 knockout mouse model treated with control antibody anti-IgG2a (10 mg / kg, ip, BIW), anti-IgG2a (10 mg / kg, ip, BIW) + Compound I (75 mg / kg, po, QD), anti-PD1 (10 mg / kg, ip, BIW) or (anti-PD1 10 mg / kg, ip, BIW) + Compound I (75 mg / kg, po, QD) are depicted. Tumor volume was monitored during treatment and plotted per individual animal. STK11 knockout renders CT26 tumors resistant to anti-PD1 treatment.

[0024] Figure 7BShown are survival graphs of mice bearing STK11-deficient CT26 tumors treated with the indicated control antibodies anti-IgG2a (10 mg / kg, ip, BIW), anti-IgG2a (10 mg / kg, ip, BIW) + Compound I (75 mg / kg, po, QD), anti-PD1 (10 mg / kg, ip, BIW) or anti-PD1 (10 mg / kg, ip, BIW) + Compound I (75 mg / kg, po, QD).

[0025] Fig. 8A Depicted are tumor growth curves of STK11-deficient MC38 tumor cells in C57BL / 6 animals and athymic BALB / c nude mice treated with anti-IgG2a (10 mg / kg, ip, BIW), anti-IgG2a (10 mg / kg, ip, BIW) + Compound I (30 mg / kg, po, QD), anti-PD1 (10 mg / kg, ip, BIW), or anti-PD1 (10 mg / kg, ip, BIW) + Compound I (30 mg / kg, po, QD) as indicated.

[0026] Figure 8B Depicted are tumor growth curves of STK11-deficient MC38 tumor cells in C57BL / 6 animals and athymic BALB / c nude mice treated with anti-IgG2a (10 mg / kg, ip, BIW), anti-IgG2a (10 mg / kg, ip, BIW) + Compound I (75 mg / kg, po, QD), anti-PD1 (10 mg / kg, ip, BIW), or anti-PD1 (10 mg / kg, ip, BIW) + Compound I (75 mg / kg, po, QD) as indicated.

[0027] Fig.9A Shown is a graph depicting changes in gene expression of CXCL9, 10 and 11 measured by Nanostring PanCancer IO 360 in STK11- / - MC38 tumors treated with 30 mg / kg Compound I or anti-PD1 alone or in combination for 7 days.

[0028] Fig. 9B Shown are graphs depicting changes in gene expression of CCL1 and CCL22 measured by Nanostring PanCancer IO 360 in STK11- / - MC38 tumors treated with 30 mg / kg Compound I or anti-PD1 alone or in combination for 7 days.

[0029] Fig. 9CShown is a graph depicting changes in gene expression of HLA genes measured by Nanostring PanCancer IO 360 in STK11- / - MC38 tumors treated for 4 days with 0.2 uM Compound I or solvent control.

[0030] Figure 10A-10B A graph showing TIL profiling by flow cytometry of STK11 -deficient MC38 tumors treated with 10 mg / kg Compound I alone or in combination with anti-PD1 for 7 days.

[0031] Figure 10C-10D Tumors treated with Compound I alone or in combination with anti-PD1 for 72 hours are shown ( Fig. 10C ) or co-culture of human NSCLC cells with PBMC and fibroblasts ( Fig. 10D ) is a graph of IFNγ expression in .

[0032] Fig.10E Shown is a graph profiling the relative abundance of all T cells and T regulatory cells from STK11 -deficient MC38 tumors of mice treated for 7 days with vehicle, 10 mg / kg Compound I alone or in combination with anti-PD1.

[0033] Figure 11A-11C Shown are graphs of gene expression changes in A549 cells treated with vorinostat, domatinostat, and compound I as determined using the PanCancer IO360 repertoire, and the top three gene ontology groups for each compound as determined from Nanostring data using nSolver software.

[0034] Fig. 12A Shown are graphs of erythrocyte and bone marrow cell viability following treatment with various concentrations of Compound I as indicated. The effective dose range of Compound I is also plotted (shaded area, 3 mg / kg to 75 mg / kg).

[0035] Figure 12B-Figure 12C Describes the use of clinically relevant doses of vorinostat ( Fig. 12B ) or compound I ( Fig. 12C ) Tumor growth curves of STK11-deficient MC38 tumors in a mouse model treated alone or in combination with anti-PD1 antibodies.

[0036] Fig.12D Shown are graphs comparing Compound I concentrations with HDAC1 or HDAC3 inhibition in vivo. The shaded boxes indicate the tolerated and effective dose ranges for Compound I.

[0037] Fig.13Shown is a graph of predicted plasma concentrations (ng / mL) over time following administration to humans and the predicted window between the effective dose and the non-selective dose.

[0038] Fig.14A Shown is a Western blot of acetylated histone 3 lysine 9 (H3K9Ac) from mouse MC38 tumor tissues after 7 days of treatment with Compound I at the indicated doses.

[0039] Fig. 14B Quantification of H3K9Ac western blots in (E) is shown and normalized to total histone H3.

[0040] Fig. 14C Shown are plasma concentrations of Compound I administered QD for two days at 30 mg / kg, 100 mg / kg, and 300 mg / kg starting at 1 hour after the last dose.

[0041] Fig.14D Shown is the quantification of the levels of acetyl-histone H2B in PBMC samples by flow cytometry at the indicated time points after two days of administration of Compound I at 30 mg / kg, 100 mg / kg and 300 mg / kg QD to MC38 tumor-bearing mice

[0042] Fig.14E Shown is the quantification of acetyl-histone H3B levels by Western blot in tumor samples collected at the indicated time points after two days of administration of Compound I at 30 mg / kg, 100 mg / kg and 300 mg / kg QD to MC38 tumor-bearing mice

[0043] Fig.15A Tumor growth curves in the STK11-null CT26 (KRAS G12D mutant colon cancer) syngeneic mouse model are depicted. Mice were treated with anti-IgG2, anti-PD1 (10 mg / kg), Compound I (75 mg / kg), or anti-PD1 (10 mg / kg) + Compound I (75 mg / kg). Tumor volume was monitored during treatment and plotted per individual animal.

[0044] Fig. 15B Tumor growth curves in the STK11 null CT26 (KRAS G12D mutant colon cancer) model are depicted. Animals were treated with anti-IgG2, Compound I (75 mg / kg), anti-PD1 (10 mg / kg), or anti-PD1 (10 mg / kg) + Compound I (75 mg / kg). Tumor volume was monitored during treatment and plotted by treatment group.

[0045] Fig. 15CSurvival curves of the KRAS G12D mutant CT26-STK11 knockout syngeneic mouse model treated with anti-IgG2, anti-PD1 (10 mg / kg), Compound I (75 mg / kg), or anti-PD1 (10 mg / kg) + Compound I (75 mg / kg) are depicted.

[0046] Fig.15D Tumor growth curves in the wild-type / parental CT26 (KRAS G12D mutant colon cancer) model are depicted. Animals were treated with anti-IgG2, Compound I (75 mg / kg), anti-PD1 (10 mg / kg), or anti-PD1 (10 mg / kg) + Compound I (75 mg / kg). Tumor volume was monitored during treatment and plotted by treatment group

[0047] Fig.15E Tumor growth curves in the wild-type / parental CT26 (KRAS G12D mutant colon cancer) model are depicted. Animals were treated with anti-IgG2, Compound I (75 mg / kg), anti-PD1 (10 mg / kg), or anti-PD1 (10 mg / kg) + Compound I (75 mg / kg). Tumor volume was monitored during treatment for Groups 1 and 4 and plotted per individual animal.

[0048] Fig.16A Tumor growth curves in the wild-type / parental CT26 (KRAS G12D mutant colon cancer) model are depicted. Animals were treated with anti-IgG2, Compound I (75 mg / kg), anti-CTL4A (10 mg / kg), or anti-CTL4A (10 mg / kg) + Compound I (75 mg / kg). Tumor volume was monitored during treatment and plotted by treatment group

[0049] Fig. 16B Tumor growth curves in the wild-type / parental CT26 (KRAS G12D mutant colon cancer) model are depicted. Animals were treated with anti-IgG2, Compound I (75 mg / kg), anti-CTL4A (10 mg / kg), or anti-CTL4A (10 mg / kg) + Compound I (75 mg / kg). Tumor volume was monitored during treatment for Groups 1 and 4 and plotted per individual animal.

[0050] Fig. 16C Depicted are tumor growth curves in the STK11-null CT26 (KRAS G12D mutant colon cancer) model treated with anti-IgG2, Compound I (75 mg / kg), anti-CTL4A (10 mg / kg), or anti-CTL4A (10 mg / kg) + Compound I (75 mg / kg). Tumor volume was monitored during treatment and plotted by treatment group.

[0051] Fig.16D Depicted are tumor growth curves in the STK11-null CT26 (KRAS G12D mutant colon cancer) model treated with anti-IgG2, Compound I (75 mg / kg), anti-CTL4A (10 mg / kg), or anti-CTL4A (10 mg / kg) + Compound I (75 mg / kg). Tumor volume was monitored during treatment for Groups 1 and 4 and plotted per individual animal.

[0052] Fig.17A Tumor growth curves in the STK11 null 3LL model treated with anti-IgG2, anti-PD1 (10 mg / kg), Compound I (75 mg / kg), or anti-PD1 (10 mg / kg) + Compound I (75 mg / kg) are depicted, and tumor volume was monitored for the depicted durations and plotted by treatment group.

[0053] Fig. 17B Survival curves of the STK11 -null 3LL model treated with anti-IgG2, anti-PD1 (10 mg / kg), Compound I (75 mg / kg), or anti-PD1 (10 mg / kg) + Compound I (75 mg / kg) are depicted, and survival is plotted by treatment group. DETAILED DESCRIPTION

[0054] As generally described herein, provided are methods of treating a subject having or at risk of developing cancer, the methods comprising administering to the subject an effective amount of a histone deacetylase inhibitor, wherein the cancer is identified as having altered STK11 activity or expression.

[0055] The disclosure herein sets forth exemplary methods, parameters, etc. However, it should be appreciated that such descriptions are not intended as limitations on the scope of the present disclosure, but are provided as descriptions of exemplary embodiments to appropriately assist the reader.

[0056] As used in this disclosure, certain words and phrases (and grammatical equivalents such as verb conjugations, inflections, etc.) are generally intended to have the meanings defined herein, unless expressly stated otherwise or the context in which they are used indicates otherwise.

[0057] STK11

[0058] Serine / threonine kinase 11 protein, abbreviated as STK11 and also known as PJS, liver kinase B1 (LKB1), renal cancer antigen NY-REN-19 and hLKB1 protein, is a protein kinase encoded by the STK11 gene (HGNC symbol STK11, Ensembl ID ENSG00000118046.16) in humans. Research (2021) 81(16): 4194–4204 (doi: 10.1158 / 0008-5472) (which is hereby incorporated by reference in its entirety): "The serine / threonine kinase LKB1 belongs to the calmodulin family that is ubiquitously expressed in several tissues and highly conserved in eukaryotes. Over the past 15 years, LKB1 has been implicated in many fundamental biological processes such as cell cycle control, cellular energy metabolism, angiogenesis, cell polarity, and DNA damage response. The subcellular localization and activity of LKB1 are determined by its association with STRAD and armadillo repeat-containing proteins. "LKB1 regulates the activity of at least 14 downstream kinases related to the AMPK family and phosphorylates other substrates, including STRAD, PTEN, and p21CDKN1A. LKB1 is phosphorylated on at least eight residues, and evidence suggests that LKB1 itself is autophosphorylated on at least four of these residues, while the other four are phosphorylated by upstream kinases. Although these post-translational modifications do not appear to alter its kinase activity, they are implicated in different biological responses associated with LKB1 and may involve its interactions with other partners."

[0059] The STK11 gene is located on human chromosome 19p 13. The gene includes nine coding exons and one non-coding exon and encodes a 433-amino acid serine / threonine protein kinase STK11 protein that is widely expressed in all tissues (Hemminki A et al. Nature, 1998, 18, 184-187; Alessi, DR et al. Annu. Rev. Biochem. 2006, 75, 137-163; Sanchez-Cespedes M. Oncogene 2007, 26, 7825-7832). Somatic mutations or deletions of the STK11 gene are present in many cancers, including but not limited to lung adenocarcinoma (~15%), non-melanoma skin cancer (~5%), bile duct cancer (~3%), ovarian cancer (approximately 3%), and pancreatic adenocarcinoma (~2%) (Sanchez-Cespedes M et al. Cancer Res 2002, 62, 3659-62; Sanchez-Vega F et al. Cell 2018, 173, 321-337.e10; Gurumurthy S et al. Nature 2010, 468, 659-63; Ji H et al. Nature 2007, 448, 807-10; Gill RK et al. Oncogene 2011, 30, 3784-3791; Gao J et al. Sci Signal 2013, 6(269), pl1; Cerami E et al. Cancer Discov 2012, 2, 401-404; Zehir A et al. Nat Med. 2017, 23(6), 703-713; Robinson DR et al. Nature. 2017, 548, 297-303).

[0060] STK11 mutations found in cancer include point mutations (e.g., nonsense mutations or frameshift mutations) (Chakravarty D et al. JCO Precis Oncol. 2017, 2017) or small insertions and deletions (indels) predicted to be harmful and carcinogenic. Mutations in the STK11 gene often occur together with other STK11 genomic changes such as copy number changes or gene deletions. These mutations and changes lead to the loss of STK11 protein expression or the loss of wild-type STK11 protein activity. Non-mutation mechanisms that alter expression (e.g., loss of expression) or alter activity (e.g., loss of wild-type activity) include genomic loss or promoter methylation.

[0061] As further described in Koenig, M. et al. Cancer Research (2021) 81(16):4194–4204 (doi:10.1158 / 0008-5472), which is hereby incorporated by reference in its entirety: "To date, more than 400 unique mutations of the STK11 gene have been described, of which ~70% of these mutations promote protein truncation, while the other 30% represent missense mutations (COSMIC and TCGA-Bioportal). As a tumor suppressor, many studies have demonstrated the contribution of genetic loss of LKB1 to tumorigenesis. LKB1 has been shown to control the cell cycle through transcriptional regulation of cyclin D1 and p21CDKN1A5, where re-expression of LKB1 leads to G1 cell cycle arrest. The role of LKB1 in controlling cellular metabolism through AMPK signaling has been extensively documented. It is known that the LKB1-AMPK axis controls lipid and glucose metabolism and acts as a negative regulator of the Warburg effect that inhibits tumor growth. LKB1 is also important in the following aspects: : Regulation of catabolic pathways leading to increased glucose uptake and modulation of glycolysis or mobilization of lipid reserves by stimulating lipases such as adipose triglyceride lipase to release fatty acids from triglyceride reserves. Pathways stimulated by LKB1-AMPK also include increased turnover of macromolecules through autophagy, allowing turnover of old and damaged molecules, or replenishing nutrient reserves under starvation. In addition, several investigations have demonstrated a role for LKB1 in regulating physiological and pathological angiogenesis through regulation of VEGF, MMP-2, MMP-9, bFGF, and NOX1 expression and its involvement in neuropilin-1 degradation. Loss-of-function studies of LKB1 have also revealed its role in cell polarity and motility through regulation of PAK115 and modulation of the phosphorylation state of FAK and CDC42 activation. Collectively, these functions contribute to the induction of epithelial-mesenchymal transition (EMT) and metastasis. In addition to this, in vivo experiments have demonstrated evidence for the contribution of LKB1 to the genotoxic DNA damage response and DNA damage repair. ”

[0062] It has been reported that patients with lung adenocarcinoma with cancer cells carrying STK11 loss-of-function mutations respond poorly to standard-of-care anti-PD-1 and anti-PD-L1 therapies. Skoulidis, F. et al. Cancer Discovery 8(7):822-835(2018)(DOI:10.1158 / 2159-8290.CD-18-0099) and Skoulidis, F. et al. Journal of Clinical Oncology 37(15):Suppl. 102(2019)(DOI:10.1200 / JCO.2019.37.15_suppl.102), each of which is hereby incorporated by reference in its entirety. A combined CRISPR-Cas9-based in vivo screen was performed and STK11 was identified as an immune escape context, where depletion of STK11 drives resistance to immune stress in immune-competent mice. Min, C. et al. Cancer Research 81(Supp. 13): 1905(2021) (DOI: 10.1158 / 1538-7445.AM2021-1905), which is hereby incorporated by reference in its entirety.

[0063] STK11 mutations have been associated with low levels of T cell inflammation and tumor PD-L1 expression. Biton J et al. Clin Cancer Res 2018;24:5710–23, which is hereby incorporated by reference in its entirety.

[0064] Similarly, STK11 mutations in NSCLC have been associated with poor responses to other treatment modalities, including anti-VEGF therapy, platinum chemotherapy, and additional single-agent chemotherapy. Papillon-Cavanagh S. et al. ESMO Open, 2020, 5, E000706, which is hereby incorporated by reference in its entirety.

[0065] As used herein, "altered expression" (e.g., altered expression of STK11) refers to a change in the expression level of a protein in a cell (e.g., a cancer cell) compared to a reference cell (e.g., a healthy cell) (i.e., a decrease or increase in the expression level). In some embodiments, the increased or decreased expression level of a protein (e.g., STK11 protein) can be assessed by measuring the number of copies of a gene encoding the protein (e.g., the number of copies of the STK11 gene) in a patient sample (e.g., a tumor sample) and comparing these levels with those present in a control sample (e.g., a healthy tissue sample). In some embodiments, the increased or decreased expression level of a protein (e.g., STK11 protein) can be assessed by measuring the level of the protein (e.g., STK11 protein) or mRNA in a patient sample (e.g., a tumor sample) and comparing these levels with those present in a control sample (e.g., a healthy tissue sample).

[0066] As used herein, "altered activity" (e.g., altered activity of STK11) refers to a change in the level of biological activity (e.g., enzymatic activity) of a protein in a cell (e.g., a cancer cell) compared to a reference cell (e.g., a healthy cell) (i.e., a decrease or increase in the level of serine / threonine kinase activity of STK11). Mutations in a gene encoding a protein (e.g., a STK11 mutation) can result in the expression of a protein (e.g., a mutant STK11 protein) having an enzymatic activity level that is different from that of the wild-type protein.

[0067] As used herein, a "STK11 mutation" is a mutation selected from the group consisting of:

[0068] (i) mutations in the nucleotide sequence encoding STK11;

[0069] (ii) mutations in regulatory sequences that control the expression of the nucleotide sequence encoding STK11;

[0070] (iii) mutations in nucleotides encoding proteins that interact with the transcript of the STK11 gene;

[0071] (iv) a mutation in the translation product of the STK11 gene; and

[0072] (v) Mutations in the transcripts of the STK11 gene.

[0073] In some embodiments, the STK11 mutation is a mutation selected from the group consisting of:

[0074] (i) mutations in the nucleotide sequence encoding STK11;

[0075] (ii) mutations in regulatory sequences that control the expression of the nucleotide sequence encoding STK11;

[0076] as well as

[0077] (iii) A mutation in a nucleotide encoding a protein that interacts with the transcription product of the STK11 gene.

[0078] In some embodiments, the STK11 mutation is a mutation in a nucleotide sequence encoding STK11. In some embodiments, the STK11 mutation is a mutation in a regulatory sequence that controls the expression of a nucleotide sequence encoding STK11. In some embodiments, the STK11 mutation is a mutation in a nucleotide encoding a protein that interacts with a transcription product of the STK11 gene. In some embodiments, the STK11 mutation is a mutation in a translation product of the STK11 gene. In some embodiments, the STK11 mutation is a mutation in a transcription product of the STK11 gene.

[0079] In some embodiments, the STK11 mutation is an inactivating mutation or a loss-of-function mutation.

[0080] As used herein, "loss-of-function mutation", also referred to as "inactivation mutation", refers to a mutation that results in the expression of a mutant protein that exhibits reduced or absent biological or enzymatic activity compared to the wild-type protein. Loss-of-function mutations in a gene (e.g., the STK11 gene) may also result in the non-expression of the wild-type protein, or only the expression of a protein fragment that exhibits reduced or absent biological or enzymatic activity compared to the wild-type protein. The mutation may be in a DNA nucleotide sequence, an mRNA sequence, or a protein sequence. In some embodiments, the mutation is a DNA mutation (e.g., a substitution, deletion, insertion, truncation, splice site, translation start site, fusion, or frameshift mutation).

[0081] In some embodiments, the loss-of-function mutation (e.g., a loss-of-function STK11 mutation) is one of the following:

[0082] 1) Nonsense mutation (a genetic change that causes premature termination of protein production). The altered protein can be partially or completely inactivated, leading to changes or loss of protein function;

[0083] 2) Frameshift mutations (involving the insertion or deletion of many base pairs that are not a multiple of three, which thus disrupt the triplet reading frame of the DNA sequence). Frameshift mutations usually result in the generation of premature stop (stop) codons and produce truncated protein products;

[0084] 3) Splice site mutations (genetic changes that occur in the DNA sequence at the boundaries of exons and introns (splice sites)). Such changes can disrupt RNA splicing, leading to the loss of exons or the inclusion of introns and altered protein coding sequences;

[0085] 4) Translation start site mutation (mutation that destroys the translation start sequence, eliminates translation initiation at the normal start site, causes loss of mRNA translation or abnormal messenger RNA (mRNA) translation). Translation start site mutation leads to loss of protein expression or leads to the synthesis of proteins with abnormal amino acid sequences;

[0086] 5) recurrent somatic mutations (at least 5 instances recorded in the Catalogue of Somatic Mutations in Cancer (COSMIC) database) (Tate JG et al. Nucleic Acids Res (2019) 47(D1), D941-D947);

[0087] 6) DNA fusion (a gene created by joining parts of two different genes; can occur when a portion of DNA from a chromosome moves to another chromosome);

[0088] 7) Any other mutation predicted by the OncoKB algorithm (Chakravarty D et al. JCO Precis Oncol. 2017, 2017) or MutationAssessor (Reva B, Antipin Y, Sander C. Nucleic acids research. 2011; 39(17): el 18) to reduce the function of the encoded protein;

[0089] In certain embodiments, the mutation is not a variant of unknown significance (a mutation whose association with disease risk is unclear, also known as an unclassified variant, a variant of uncertain significance, or a VUS (Richards S et al. Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015 May; 17(5): 405-424.).

[0090] In some embodiments, the mutation is not a germline mutation (a genetic change in a reproductive cell (egg or sperm) that is incorporated into the DNA of every cell in the body of offspring) identified in dbSNP (Sherry, ST et al. Nucleic Acids Res, 2001, 29:308-311).

[0091] Loss-of-function mutations in the STK11 gene (e.g., in cancer cells) can result in loss of STK11 protein expression, expression of only STK11 protein fragments, or expression of STK11 protein with reduced or absent enzymatic activity (e.g., no serine / threonine kinase enzymatic activity).

[0092] Non-limiting examples of STK11 mutations that are loss-of-function mutations as defined herein are listed in Table 1 (adapted from WO2022087270). The mutations included in Table 1 are predicted to have deleterious functions by OncoKB or appear at least 5 times in COSMIC, and exclude mutations of unknown significance and copy number changes (ie, VUS) and germline mutations.

[0093] Those skilled in the art will recognize that many STK11 mutations are known, or are otherwise identifiable.

[0094] Table 1 - Exemplary STK11 loss-of-function mutations

[0095]

[0096]

[0097]

[0098]

[0099]

[0100]

[0101] Those skilled in the art will also recognize that STK11 mutations can occur with other mutations. Mutations in STK11 often occur with KRAS mutations. (Koivunen, J. et al. Br J Cancer 2008, 99, 245–252). STK11 somatic mutations also often occur with KEAP1 mutations (see Papillon-Cavanagh S. et al. ESMO Open, 2020, 5, E000706). Some authors report that the presence of STK11 and KEAP1 mutations has a greater effect on immunotherapy resistance in patients with KRAS mutations than in patients with wild-type KRAS (see Ricciuti B. et al. Journal of Thoracic Oncology 2021, 17, 400-410).

[0102] In some embodiments provided herein, the cancer is identified as having altered STK11 activity or expression and having altered KRAS activity or expression. In some embodiments, the altered KRAS activity or expression is the presence of a mutant KRAS. In some embodiments, the mutant KRAS is selected from KRAS G12C 、KRAS G12D 、KRAS G12V 、KRAS G12A 、KRAS G12S 、KRAS G12R 、KRAS G13C 、KRAS G13D 、KRAS G13S 、KRAS Q61H and KRAS Q61K In some embodiments, the mutant KRAS is selected from KRAS G12C 、KRAS G12D and KRAS G12V In some embodiments provided herein, a cancer is identified as having altered STK11 activity or expression and having wild-type KRAS activity or expression. In some embodiments provided herein, a cancer is identified as having altered STK11 activity or expression and having altered KRAS (e.g., KRAS G12C 、KRAS G12D 、KRAS G12V ) activity or expression or wild-type KRAS activity or expression. In some embodiments, the cancer is further identified as having altered KEAP1 activity or expression (e.g., a KEAP1 mutation).

[0103] Those skilled in the art will also recognize that STK11 mutations may frequently occur in certain diseases (eg, cancer).

[0104] Histone deacetylase inhibitors

[0105] In some embodiments, the method for treating a subject suffering from cancer or being at risk of developing cancer as described herein includes administering a histone deacetylase (HDAC) inhibitor to the subject. Unless otherwise indicated, mentioning HDAC inhibitors in the methods and uses described herein refers to any HDAC inhibitor class and HDAC inhibitor compound described herein (e.g., in this section).

[0106] Histone deacetylase (HDAC) inhibitors are generally a class of therapeutic drugs that inhibit histone deacetylase. 18 isoforms of histone deacetylase have been identified and divided into four categories: Class I, Class II, Class III and Class IV. Class II HDAC is further grouped into Class IIa and Class IIb. These four categories distinguish the 18 identified isoforms of HDAC into two main families: HDAC 1-11 and SIRT 1-7, which are zinc-dependent metalloenzymes. Class I HDAC includes HDAC1, HDAC2, HDAC3 and HDAC8. Class II HDAC includes Class IIa and Class IIb. Class IIa HDAC includes HDAC4, HDAC 5, HDAC7 and HDAC9. Class IIb HDAC includes HDAC6 and HDAC10. Class III HDAC, also known as longevity protein (sirtuin, SIRT), includes SIRT1, SIRT2, SIRT3, SIRT4, SIRT5, SIRT6 and SIRT7. And Class IV HDAC includes HDAC11. A review of HDACs, including composition and sequence characteristics, is described in Li, G. et al. Frontiers in Cell and Developmental Biology (2020) 8:576946 (doi: 10.3389 / fcell.2020.576946), which is hereby incorporated by reference in its entirety.

[0107] The HDAC inhibitor may be a pan-HDAC inhibitor, which generally inhibits most or all HDAC isoforms, or a selective HDAC inhibitor, which generally selectively inhibits one or more HDAC isoforms and not other HDAC isoforms.Many HDAC inhibitors have been described in the art.

[0108] For example, a review of HDAC inhibitors in more than 30 years of development is described in Ho, TCS et al. Journal of Medicinal Chemistry (2020) 63 (21): 12460-12484 (doi: 10.1021 / acs.jmedchem.0c00830), which is hereby incorporated by reference in its entirety. A review of the development of HDAC inhibitors is described in Bondarev, A. et al. British Journal of Clinical Pharmacology (2021) 87: 4577–4597 (doi: 10.1111 / bcp.14889), which is hereby incorporated by reference in its entirety. A review of hybrid multi-targeted HDAC inhibitors is described in Bass, AKA et al. European Journal of Medicinal Chemistry (2021) 209: 112904 (doi: 10.1016 / j.ejmech.2020.112904), which is hereby incorporated by reference in its entirety. Those skilled in the art will recognize that many HDAC inhibitors have been described in the art via patent disclosures, posters, conferences, and journals. Some of these HDAC inhibitors are described as pan-HDAC inhibitors. Some of these HDAC inhibitors are described as selective HDAC inhibitors, inhibiting a particular class of HDACs (e.g., class I, class IIa, class IIb, class III, or class IV) or inhibiting a particular isoform of HDAC (e.g., HDAC1, HDAC2, HDAC3, HDAC4, HDAC5, HDAC6, HDAC7, HDAC8, HDAC9, HDAC10, HDAC11, SIRT1, SIRT2, SIRT3, SIRT4, SIRT5, SIRT6, and / or SIRT7).

[0109] Examples of selective HDAC inhibitors have been described in the art. For example, HDAC inhibitors are described in International Patent Publications WO / 2010 / 014611 and WO / 2010 / 144371, each of which is hereby incorporated by reference in its entirety.

[0110] As used herein and with respect to HDAC inhibitors, "selectivity" refers to the HDAC inhibition properties of a compound that preferentially inhibits one or more HDAC isoforms, including preferential inhibition of one or more HDAC isoforms in a specific biological complex. Selective HDAC inhibitors inhibit target HDACs (including, for example, HDAC isoforms that are part of a specific complex such as CoREST) ​​at a concentration lower than that at which they inhibit non-target HDACs (including, for example, the same HDAC isoforms that are part of a different complex). Therefore, selective HDAC inhibitors are more effective (have lower IC ) for target HDACs than for non-target HDACs. 50 In one embodiment, the selective HDAC inhibitor has a potency against the target HDAC of at least 3 times greater than that against the non-target HDAC (i.e., an IC 50 The IC of non-target HDAC 50 In one embodiment, the selective HDAC inhibitor has a potency against the target HDAC of at least 5 times greater than that against the non-target HDAC (i.e., an IC 50 The IC of non-target HDAC 50 In one embodiment, the selective HDAC inhibitor has a potency against the target HDAC of at least 10 times greater than that against the non-target HDAC (i.e., an IC 50 The IC of non-target HDAC 50 In one embodiment, the selective HDAC inhibitor has a potency against the target HDAC of at least 30 times greater than that against the non-target HDAC (i.e., an IC against the target HDAC). 50 The IC of non-target HDAC 50 In one embodiment, the selective HDAC inhibitor is at least 50 times more potent against the target HDAC than against the non-target HDAC (i.e., the IC 50 The IC of non-target HDAC 50 In one embodiment, the selective HDAC inhibitor is at least 100 times more potent against the target HDAC than against the non-target HDAC (i.e., the IC 50 The IC of non-target HDAC 50 In one embodiment, the selective HDAC inhibitor is at least 500 times more potent against the target HDAC than against the non-target HDAC (i.e., the IC 50 The IC of non-target HDAC 50In one embodiment, the selective HDAC inhibitor is at least 1000 times more potent against the target HDAC than against the non-target HDAC (i.e., the IC 50 The IC of non-target HDAC 50 at most 1 / 1000 of the original value).

[0111] For example, HDAC1,2 selective inhibitors are described in International Patent Publications WO / 2016 / 094824, WO / 2016 / 109549, WO / 2018 / 098296, WO / 2019 / 012172, WO / 2020 / 068950, and WO / 2020 / 076951, each of which is hereby incorporated by reference in its entirety.

[0112] Some biological complexes include some classes or isoforms of HDAC. For example, at least four biological complexes include various class I HDAC isoforms and other subunits. The HDAC co-repressor of the repressor element-1 silencing transcription factor (CoREST) ​​complex includes HDAC1 and HDAC2, and other subunits such as LSD1 and RCOR1. The nucleosome remodeling and deacetylase (NuRD) complex also includes HDAC1 and HDAC2, and other subunits such as MTA3 and RBBP7. The Sin3-HDAC (Sin3) complex has also been described as including HDAC1 and HDAC2 and other subunits Sin3 and RBBP7. The NCoR complex has been described as including HDAC3 and other subunits NCoR, HSPA and TBL1.

[0113] HDAC inhibitors can selectively inhibit certain isoforms of certain biological complexes relative to the same isoforms in different complexes. For example, CoREST complex selective HDAC inhibitors are described in Fuller, NO et al. (2019) CS Chem. Neurosci. 10 (3): 1729–1743 (10.1021 / acschemneuro.8b00620), which is hereby incorporated by reference as a whole. Fuller et al. describe certain efforts, in which HDACs (CI-994 and BML-210) in the benzamide chemical class show selectivity for CoREST, NuRD and NCoR, but not for Sin3 complexes. Fuller et al. further describe compounds that selectively target HDACs (e.g., HDAC1 and HDAC2) in the CoREST complex.

[0114] The structure of the CoREST complex selective HDAC inhibitor described by Fuller is shown below:

[0115]

[0116] Reports describing other compounds that selectively target HDACs (eg, HDAC 1 and HDAC2) in the CoREST complex have also been published. The compound "RDN-929" has been identified.

[0117] In some embodiments, the histone deacetylase inhibitor is an HDAC inhibitor that selectively inhibits HDAC1 relative to HDAC3. In some embodiments, the histone deacetylase inhibitor is an HDAC inhibitor that selectively inhibits HDAC1 and HDAC2 relative to HDAC3. In some embodiments, the histone deacetylase inhibitor is an HDAC inhibitor that selectively inhibits HDAC1 relative to HDAC8. In some embodiments, the histone deacetylase inhibitor is an HDAC inhibitor that selectively inhibits HDAC1 and HDAC2 relative to HDAC8. In some embodiments, the histone deacetylase inhibitor is an HDAC inhibitor that selectively inhibits HDAC1 relative to HDAC3 and HDAC8. In some embodiments, the histone deacetylase inhibitor is an HDAC inhibitor that selectively inhibits HDAC1 relative to HDAC3 and HDAC8. In some embodiments, the histone deacetylase inhibitor is an HDAC inhibitor that selectively inhibits HDAC1 and HDAC2 relative to HDAC3 and HDAC8.

[0118] In some embodiments, the histone deacetylase inhibitor is an HDAC class I selective inhibitor. In some embodiments, the histone deacetylase inhibitor is an HDAC class I inhibitor that selectively inhibits HDAC1 relative to HDAC3. In some embodiments, the histone deacetylase inhibitor is an HDAC class I inhibitor that selectively inhibits HDAC1 and HDAC2 relative to HDAC3. In some embodiments, the histone deacetylase inhibitor is an HDAC class I inhibitor that selectively inhibits HDAC1 relative to HDAC8. In some embodiments, the histone deacetylase inhibitor is an HDAC class I inhibitor that selectively inhibits HDAC1 and HDAC2 relative to HDAC8. In some embodiments, the histone deacetylase inhibitor is an HDAC class I inhibitor that selectively inhibits HDAC1 relative to HDAC3 and HDAC8. In some embodiments, the histone deacetylase inhibitor is an HDAC class I inhibitor that selectively inhibits HDAC1 relative to HDAC3 and HDAC8. In some embodiments, the histone deacetylase inhibitor is an HDAC class I inhibitor that selectively inhibits HDAC1 and HDAC2 relative to HDAC3 and HDAC8. In some embodiments, the histone deacetylase inhibitor is an HDAC class I inhibitor that selectively inhibits HDAC1 and HDAC2 relative to all other HDAC isoforms.

[0119] In some embodiments, a method of treating a subject having or at risk of developing cancer comprises administering to the subject a selective HDAC1 inhibitor.

[0120] In some embodiments, the histone deacetylase inhibitor is an HDAC1 selective inhibitor. In some embodiments, the histone deacetylase inhibitor is an HDAC1,2 selective inhibitor. In some embodiments, the histone deacetylase inhibitor is an HDAC1 selective inhibitor that selectively inhibits HDAC 1 relative to HDAC3. In some embodiments, the histone deacetylase inhibitor is an HDAC1,2 selective inhibitor that selectively inhibits HDAC1,2 relative to HDAC3. In some embodiments, the histone deacetylase inhibitor is an HDAC1 selective inhibitor that selectively inhibits HDAC 1 relative to HDAC8. In some embodiments, the histone deacetylase inhibitor is an HDAC1,2 selective inhibitor that selectively inhibits HDAC1,2 relative to HDAC8. In some embodiments, the histone deacetylase inhibitor is an HDAC1 selective inhibitor that selectively inhibits HDAC 1 relative to HDAC3 and HDAC8. In some embodiments, the histone deacetylase inhibitor is an HDAC1,2 selective inhibitor that selectively inhibits HDAC1,2 relative to HDAC3 and HDAC8.

[0121] In some embodiments, a method of treating a subject having or at risk of developing cancer comprises administering to the subject a CoREST selective deacetylase inhibitor.

[0122] In some embodiments, the histone deacetylase inhibitor is a CoREST selective deacetylase inhibitor. In some embodiments, the histone deacetylase inhibitor is a CoREST selective deacetylase inhibitor that inhibits HDAC1. In some embodiments, the histone deacetylase inhibitor is a CoREST selective deacetylase inhibitor that inhibits HDAC1 and HDAC2.

[0123] In some embodiments, the selective HDAC1,2 inhibitors have reduced cytotoxicity and improved therapeutic index relative to less selective HDAC inhibitors. In some embodiments, the selective HDAC1,2 inhibitors have reduced cytotoxicity to erythroid and / or myeloid cells.

[0124] In some embodiments of any of the methods and uses described herein, the histone deacetylase (HDAC) inhibitor is (R)-N-(4-amino-4'-fluoro-[1,1'-biphenyl]-3-yl)-4-(S-methylsulfonylimide)benzamide, which has formula (I) (Compound I), also known as TNG260.

[0125]

[0126] or a pharmaceutically acceptable salt thereof.

[0127] Pharmaceutical compositions and administration

[0128] Typically, histone deacetylase (HDAC) inhibitors are administered in an effective amount (e.g., a therapeutically effective amount). The amount of the compound described herein (e.g., HDAC inhibitor) actually administered will typically be determined by a physician based on relevant circumstances, including the condition to be treated, the selected route of administration, the HDAC inhibitor actually administered, the age, body weight and response of individual patients, the severity of patient symptoms, etc.

[0129] When used as a medicament, the compounds described herein (eg, HDAC inhibitors) are generally administered in the form of a pharmaceutical composition. Such compositions can be prepared in a manner well known in the pharmaceutical art and contain at least one active compound.

[0130] In some embodiments, the compounds described herein (e.g., HDAC inhibitors) are administered as pharmaceutical compositions comprising an effective amount of an HDAC inhibitor as described herein and a pharmaceutically acceptable carrier. In some embodiments, regarding pharmaceutical compositions, the carrier is a parenteral carrier, an oral or topical carrier. The term "pharmaceutically acceptable carrier" refers to a carrier, adjuvant or vehicle that can be administered to a patient together with the compound provided therewith, and when administered in a dose sufficient to deliver a therapeutic amount of the compound, does not destroy its pharmacological activity and is nontoxic. Pharmaceutically acceptable carriers that can be used in the pharmaceutical compositions provided herein include, but are not limited to, ion exchangers, alumina, aluminum stearate, lecithin, self-emulsifying drug delivery systems (SEDDS) such as d-α-tocopheryl polyethylene glycol 1000 succinate, surfactants used in pharmaceutical dosage forms such as Tween or other similar polymer delivery matrices, serum proteins such as human serum albumin, buffer substances such as phosphates, glycine, sorbic acid, potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, water, salts or electrolytes such as protamine sulfate, disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts, colloidal silicon dioxide, magnesium trisilicate, polyvinyl pyrrolidone, cellulose-based materials, polyethylene glycol, sodium carboxymethyl cellulose, polyacrylates, waxes, polyethylene-polyoxypropylene block polymers, polyethylene glycol, and lanolin. Cyclodextrins such as α-cyclodextrin, β-cyclodextrin, and γ-cyclodextrin, or chemically modified derivatives such as hydroxyalkylcyclodextrins, including 2- and 3-hydroxypropyl-β-cyclodextrin, or other solubilized derivatives may also be advantageously used to enhance the delivery of the compounds described herein (e.g., HDAC inhibitors).

[0131] The pharmaceutical composition provided therewith can be administered orally, parenterally, by inhalation spray, topically, rectally, nasally, buccally, vaginally or via an implanted reservoir, preferably by oral administration or by injection. The pharmaceutical composition provided therewith can contain any conventional nontoxic pharmaceutically acceptable carrier, adjuvant or vehicle. In some cases, the pH of the formulation can be adjusted with a pharmaceutically acceptable acid, base or buffer to enhance the stability of the compound or its delivery form of the formulation. The term parenteral as used herein includes subcutaneous, intradermal, intravenous, intramuscular, intraarticular, intraarterial, intrasynovial, intrasternal, intrathecal, intralesional and intracranial injection or infusion techniques.

[0132] Compositions for oral administration can take the form of bulk liquid solutions or suspensions or bulk powders. However, more commonly, compositions are presented in unit dosage forms for accurate administration. The term "unit dosage form" refers to physically discrete units suitable as unit doses for human subjects and other mammals, each unit containing a predetermined amount of active materials associated with a suitable pharmaceutical excipient that is calculated to produce a desired therapeutic effect. Typical unit dosage forms include pre-loaded, pre-measured ampoules or syringes of liquid compositions, or in the case of solid compositions, pills, tablets, capsules, etc. In such compositions, the compound is usually a minor component (about 0.1 to about 50% by weight or preferably about 1 to about 40% by weight), and the rest are various vehicles or carriers and processing aids that help form the desired dosage form.

[0133] Liquid forms suitable for oral administration may include suitable aqueous or non-aqueous vehicles with buffers, suspending and dispersing agents, colorants, flavoring agents, etc. Solid forms may include, for example, any of the following ingredients or compounds of a similar nature: binders such as microcrystalline cellulose, tragacanth, or gelatin; excipients such as starch or lactose; disintegrants such as alginic acid, Primogel, or corn starch; lubricants such as magnesium stearate; glidants such as colloidal silicon dioxide; sweeteners such as sucrose or saccharin; or flavoring agents such as peppermint, methyl salicylate, or orange flavor.

[0134] Injectable compositions are usually based on injectable sterile saline or phosphate buffered saline or other injectable carriers known in the art. As previously mentioned, the active compound in such compositions is usually a minor component, often about 0.05 to 10% by weight, and the rest is an injectable carrier, etc. The pharmaceutical composition can be in the form of a sterile injectable preparation, for example, as a sterile injectable aqueous or oily suspension. The suspension can be prepared using a suitable dispersant or wetting agent (e.g., Tween 80) and a suspending agent according to techniques known in the art. Sterile injectable preparations can also be sterile injectable solutions or suspensions in non-toxic, parenterally acceptable diluents or solvents, for example, as solutions in 1,3-butanediol. Acceptable vehicles and solvents that can be used are mannitol, water, Ringer's solution, and isotonic sodium chloride solution. In addition, sterile, non-volatile oils are routinely used as solvents or suspension media. For this purpose, any mild non-volatile oil can be used, including synthetic monoglycerides or diglycerides. Fatty acids, such as oleic acid and its glyceride derivatives can be used to prepare injections, such as natural pharmaceutically acceptable oils, such as olive oil or castor oil, especially in their polyoxyethylated forms. These oil solutions or suspensions can also contain long-chain alcohol diluents or dispersants, or carboxymethyl cellulose or similar dispersants, which are generally used to prepare pharmaceutically acceptable dosage forms, such as emulsions and / or suspensions. For the purpose of preparation, other conventional surfactants, such as Tweens or Spans and / or other similar emulsifiers or bioavailability enhancers, which are generally used to make pharmaceutically acceptable solids, liquids or other dosage forms, can also be used.

[0135] Transdermal compositions are usually formulated into topical ointments or creams containing active ingredients, and the amount of active ingredients usually ranges from about 0.01 to about 20 weight %, preferably from about 0.1 to about 20 weight %, preferably from about 0.1 to about 10 weight %, and more preferably from about 0.5 to about 15 weight %. When formulated into an ointment, the active ingredient will usually be combined with paraffin or a water miscible ointment base. Alternatively, the active ingredient can be formulated into an emulsion together with, for example, an oil-in-water cream base. Such transdermal formulations are well known in the art, and typically include additional ingredients to enhance the stability skin penetration of the active ingredient or formulation. All such known transdermal formulations and ingredients are included in the scope provided herein.

[0136] The HDAC inhibitors provided herein can also be administered via transdermal devices. Thus, transdermal administration can be achieved using patches of the reservoir or porous membrane type or of the solid matrix variety.

[0137] The pharmaceutical compositions provided herewith can be administered in the form of suppositories for rectal administration. These compositions can be prepared by mixing the compounds provided herewith with suitable non-irritating excipients that are solid at room temperature but liquid at rectal temperature and will therefore melt in the rectum to release the active ingredient. Such materials include, but are not limited to, cocoa butter, beeswax, and polyethylene glycols.

[0138] The pharmaceutical compositions provided herewith can be administered by nasal aerosol or inhalation. Such compositions are prepared according to techniques well known in the art of pharmaceutical formulations and can be prepared as saline solutions using benzyl alcohol or other suitable preservatives, absorption promoters to enhance bioavailability, fluorocarbons and / or other solubilizing or dispersing agents known in the art.

[0139] The above components for oral, injectable or topical, rectal and nasal compositions are representative only. Other materials and processing techniques are described in Part 8 of Remington's Pharmaceutical Sciences, 17th edition, 1985, Mack Publishing Company, Easton, Pennsylvania, which is hereby incorporated in its entirety.

[0140] The compounds described herein (eg, HDAC inhibitors) can also be administered in a sustained release form or from a sustained release drug delivery system. Descriptions of representative sustained release materials can be found in Remington's Pharmaceutical Sciences.

[0141] When the composition provided therewith comprises a compound as described herein (e.g., an HDAC inhibitor) and a combination of one or more additional therapeutic agents or preventive agents, the compound and the additional agent should be present at a dosage level between about 1% and 100% of the dosage normally administered in a monotherapy regimen, and more preferably between about 5% and 95%. The additional agent can be administered separately from the compound provided therewith as part of a multiple dose regimen. Alternatively, those agents can be part of a single dosage form, mixed in a single composition with the compound provided therewith.

[0142] The compounds described herein (e.g., HDAC inhibitors) can be administered, for example, by injection, intravenous, intraarterial, subcutaneous, intraperitoneal, intramuscular or subcutaneous; or orally, buccal, nasal, transmucosal, topical, in the form of ophthalmic preparations or by inhalation every 4 to 120 hours, or according to the requirements of a particular drug, with a dosage range of about 0.5 to about 100 mg / kg body weight, alternatively a dosage of 1 mg to 1000 mg / agent. The methods herein contemplate the administration of an effective amount of a compound or composition to achieve the desired or stated effect. Typically, the pharmaceutical composition provided therewith will be administered about 1 to about 6 times a day, or alternatively in the form of a continuous infusion. Such administration can be used as a chronic or acute therapy. The amount of active ingredient that can be combined with a carrier material to produce a single dosage form will vary depending on the host being treated and the specific mode of administration. A typical preparation will contain about 5% to about 95% of the active compound (w / w). Alternatively, such preparations contain about 20% to about 80% of the active compound.

[0143] Lower or higher doses than those recited above may be required. The specific dosage and treatment regimen for any particular patient will depend on a variety of factors, including the activity of the specific compound employed, age, weight, general health, sex, diet, time of administration, rate of excretion, drug combination, severity and course of the disease, condition or symptom, the patient's predisposition to the disease, condition or symptom, and the judgment of the treating physician.

[0144] After improving the patient's condition, if necessary, a maintenance dose of the compound (e.g., HDAC inhibitor), composition or combination provided therewith can be used. Subsequently, the dosage or frequency of use or both can be reduced to the level of maintaining the improved condition when the symptoms have been alleviated to the desired level according to the symptoms. However, in any recurrence of disease symptoms, the patient may need long-term intermittent treatment.

[0145] "Effective amount"

[0146] In general, the "effective amount" of a compound (e.g., an HDAC inhibitor) refers to an amount sufficient to induce a desired biological response (e.g., to treat a disease or condition described herein). As will be appreciated by those of ordinary skill in the art, the effective amount of the disclosed compounds can vary according to factors such as the desired biological endpoint, the pharmacokinetics of the compound, the disease being treated, the mode of administration, and the age, health, and condition of the subject. The effective amount encompasses therapeutic and preventive treatments (i.e., encompasses "therapeutically effective amounts" and "preventive effective amounts").

[0147] As used herein, and unless otherwise indicated, a "therapeutically effective amount" of a compound is an amount sufficient to provide a therapeutic benefit in the therapeutic treatment of a disease, disorder, or condition, or to delay or minimize one or more symptoms associated with the disease, disorder, or condition. A therapeutically effective amount of a compound means an amount of a therapeutic agent, alone or in combination with other therapies, that provides a therapeutic benefit in the therapeutic treatment of a disease, disorder, or condition. The term "therapeutically effective amount" can encompass an amount that improves overall therapy, reduces or avoids symptoms or causes of a disease or condition, or enhances the therapeutic efficacy of another therapeutic agent.

[0148] As used herein, and unless otherwise indicated, a "prophylactically effective amount" of a compound is an amount sufficient to prevent a disease, disorder, or condition, or one or more symptoms associated with a disease, disorder, or condition, or to prevent its recurrence. A prophylactically effective amount of a compound means an amount of a therapeutic agent, alone or in combination with other agents, that provides a prophylactic benefit in the prevention of a disease, disorder, or condition. The term "prophylactically effective amount" may encompass an amount that improves overall prevention or enhances the prophylactic efficacy of another prophylactic agent.

[0149] Treatment

[0150] Provided herein are methods of treating a subject having a disease or disorder or at risk of developing a disease or disorder, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor.

[0151] In some embodiments, a method of treating a subject having or at risk of developing a disease or condition is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor, wherein the cancer is identified as having altered STK11 activity or expression.

[0152] In some embodiments, a method of treating a subject having or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor, wherein the cancer is identified as having altered STK11 activity or expression.

[0153] In some embodiments, the method comprises selecting a patient for treatment using one of the patient selection methods described herein prior to administering the histone deacetylase inhibitor and optionally one or more additional therapeutic agents to the patient.

[0154] In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the cancer is identified as having altered STK11 activity or expression and the cancer is identified as having wild-type KRAS activity or expression. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the cancer is identified as having altered STK11 activity or expression and the cancer is identified as having altered KRAS (e.g., KRAS G12C 、KRAS G12D 、KRAS G12V ) activity or expression. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the cancer is identified as having altered STK11 activity or expression and the cancer is identified as having altered KRAS (e.g., KRAS G12C 、KRAS G12D 、KRAS G12V ) activity or expression or wild-type KRAS activity or expression.

[0155] In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with an immune checkpoint modulator, wherein the cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the cancer is identified as having altered STK11 activity or expression, wherein the anti-PD1 agent or the anti-PD-L1 agent is selected from nivolumab; CT-011; AMP-224; pembrolizumab; pidilizumab; cemiplimab; dostarlimab; prolgolimab; spartalizumab; camrelizumab izumab; sasanlimab, sintilimab; tislelizumab; toripalimab; retifanlimab; MEDI0680; budigalimab; geptanolimab; BMS936559; durvalumab; avelumab; envafolimab; cosibelimab; sugemalimab; AUNP-12; atezolizumab, and CA-170. In some embodiments, a method of treating a subject having or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with an anti-PD1 therapy or an anti-PD-L1 therapy, wherein the cancer is identified as having altered STK11 activity or expression.

[0156] In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of a selective histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of a selective histone deacetylase inhibitor in combination with an immune checkpoint regulator, wherein the cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of a selective histone deacetylase inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of a selective histone deacetylase inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the cancer is identified as having altered STK11 activity or expression, wherein the anti-PD1 agent or the anti-PD-L1 agent is selected from nivolumab; CT-011; AMP-224; pembrolizumab; pipristina Delizumab; Cimiprilimab; Dostalimab; Palolizumab; Spartalizumab; Camrelizumab; Sasanlizumab, Sintilimab; Tislelizumab; Toripalimab; Rivulimab; MEDI0680; Bugelimab; Gelolimab, BMS936559; Durvalumab; Avelumab; Envolizumab; Coxilimab; Sugelimab, AUNP-12; Atezolizumab and CA-170. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of a selective histone deacetylase inhibitor in combination with an anti-PD1 therapy or an anti-PD-L1 therapy, wherein the cancer is identified as having altered STK11 activity or expression.

[0157] In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of an HDAC class I selective histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of an HDAC class I selective histone deacetylase inhibitor in combination with an immune checkpoint regulator, wherein the cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of an HDAC class I selective histone deacetylase inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of an HDAC class I selective histone deacetylase inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent. Class I selective histone deacetylase inhibitor, wherein the cancer is identified as having altered STK11 activity or expression, wherein the anti-PD1 agent or anti-PD-L1 agent is selected from nivolumab; CT-011; AMP-224; pembrolizumab; pidilizumab; cemiplizumab; dostalimab; palolizumab; spartalizumab; carrelizumab; sazanlimab, sintilimab; tislelizumab; toripalimab; rivalizumab; MEDI0680; bruglimab; gelotrimazole, BMS936559; durvalumab; avelumab; envolimab; coxilimab; sugemalimab, AUNP-12; atezolizumab and CA-170. In some embodiments, a method of treating a subject having or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of an HDAC class I selective histone deacetylase inhibitor in combination with an anti-PD1 therapy or an anti-PD-L1 therapy, wherein the cancer is identified as having altered STK11 activity or expression.

[0158] In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of an HDAC1 selective histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of an HDAC1 selective histone deacetylase inhibitor in combination with an immune checkpoint regulator, wherein the cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of an HDAC1 selective inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of an HDAC1 selective histone deacetylase inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the cancer is identified as having altered STK11 activity or expression, wherein the anti-PD1 agent or the anti-PD-L1 agent is selected from nivolumab; CT-011; AMP-224; pembrolizumab ; Pidilimab; Cimiprilimab; Dostalimab; Palolizumab; Spartalizumab; Camrelizumab; Sasanlizumab, Sintilimab; Tislelizumab; Teplizumab; Rivulimab; MEDI0680; Bugelimab; Gelolimab, BMS936559; Durvalumab; Avelumab; Envolizumab; Coxilimab; Sugelimab, AUNP-12; Atezolizumab and CA-170. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of an HDAC1 selective inhibitor in combination with an anti-PD1 therapy or an anti-PD-L1 therapy, wherein the cancer is identified as having altered STK11 activity or expression.

[0159] In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of an HDAC1,2 selective histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of an HDAC1,2 selective inhibitor in combination with an immune checkpoint regulator, wherein the cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of an HDAC1,2 selective inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of an HDAC1,2 selective inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the cancer is identified as having altered STK11 activity or expression, wherein the anti-PD1 agent or the anti-PD-L1 agent is selected from nivolumab; CT-011; AMP-224; pembrolizumab; picolide; Delizumab; Cimiprilimab; Dostalimab; Palolizumab; Spartalizumab; Camrelizumab; Sasanlizumab, Sintilimab; Tislelizumab; Toripalimab; Rivulimab; MEDI0680; Bugelimab; Gelolimab, BMS936559; Durvalumab; Avelumab; Envolizumab; Coxilimab; Sugelimab, AUNP-12; Atezolizumab and CA-170. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of an HDAC1,2 selective inhibitor in combination with an anti-PD1 therapy or an anti-PD-L1 therapy, wherein the cancer is identified as having altered STK11 activity or expression.

[0160] In some embodiments, a method for treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of a CoREST selective deacetylase inhibitor in combination with a second therapeutic agent, wherein the cancer is identified as having altered STK11 activity or expression. In some embodiments, a method for treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of a CoREST selective deacetylase inhibitor in combination with an immune checkpoint regulator, wherein the cancer is identified as having altered STK11 activity or expression. In some embodiments, a method for treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of a CoREST selective deacetylase inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of a CoREST selective deacetylase inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the cancer is identified as having altered STK11 activity or expression, wherein the anti-PD1 agent or the anti-PD-L1 agent is selected from nivolumab; CT-011; AMP-224; pembrolizumab; Pidilimab; Cimiprilimab; Dostalimab; Palolizumab; Spartalizumab; Camrelizumab; Sasanlizumab, Sintilimab; Tislelizumab; Teplizumab; Rivulimab; MEDI0680; Bugelimab; Gelolimab, BMS936559; Durvalumab; Avelumab; Envolizumab; Coxilimab; Sugelimab, AUNP-12; Atezolizumab and CA-170. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of a CoREST selective deacetylase inhibitor in combination with an anti-PD1 therapy or an anti-PD-L1 therapy, wherein the cancer is identified as having altered STK11 activity or expression.

[0161] In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor, wherein the cancer is identified as having altered STK11 activity or expression and the cancer is identified as resistant to anti-PD1 therapy or anti-PD-L1 therapy. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor, wherein the cancer is identified as having altered STK11 activity or expression and the cancer is identified as having inherent resistance to anti-PD1 therapy or anti-PD-L1 therapy. In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor, wherein the cancer is identified as having altered STK11 activity or expression and the cancer is identified as having acquired resistance to anti-PD1 therapy or anti-PD-L1 therapy.

[0162] In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the lung cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the lung cancer is identified as having altered STK11 activity or expression and the lung cancer is identified as having wild-type KRAS activity or expression. In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the lung cancer is identified as having altered STK11 activity or expression and the lung cancer is identified as having altered KRAS (e.g., KRAS G12C 、KRAS G12D 、KRAS G12V ) activity or expression. In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the lung cancer is identified as having altered STK11 activity or expression and the lung cancer is identified as having altered KRAS (e.g., KRAS G12C 、KRAS G12D 、KRAS G12V) activity or expression or wild-type KRAS activity or expression. In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with an immune checkpoint regulator, wherein the lung cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the lung cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the lung cancer is identified as having altered STK11 activity or expression, wherein the anti-PD1 agent or anti-PD-L1 agent is selected from nivolumab; CT-011; AMP-224; pembrolizumab; pitilizumab In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with an anti-PD1 therapy or an anti-PD-L1 therapy, wherein the lung cancer is identified as having altered STK11 activity or expression.

[0163] In some embodiments, a method for treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor, wherein the lung cancer is identified as having altered STK11 activity or expression and the lung cancer is identified as resistant to anti-PD1 therapy or anti-PD-L1 therapy. In some embodiments, a method for treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor, wherein the lung cancer is identified as having altered STK11 activity or expression and the lung cancer is identified as having inherent resistance to anti-PD1 therapy or anti-PD-L1 therapy. In some embodiments, a method for treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor, wherein the lung cancer is identified as having altered STK11 activity or expression and the lung cancer is identified as having acquired resistance to anti-PD1 therapy or anti-PD-L1 therapy.

[0164] In some embodiments, a method for treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of a selective histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the lung cancer is identified as having altered STK11 activity or expression. In some embodiments, a method for treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of a selective histone deacetylase inhibitor in combination with an immune checkpoint regulator, wherein the lung cancer is identified as having altered STK11 activity or expression. In some embodiments, a method for treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of a selective histone deacetylase inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the lung cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of a selective histone deacetylase inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the lung cancer is identified as having altered STK11 activity or expression, wherein the anti-PD1 agent or the anti-PD-L1 agent is selected from nivolumab; CT-011; AMP-224; pembrolizumab; pipristina Delizumab; Cimiprilimab; Dostalimab; Palolizumab; Spartalizumab; Camrelizumab; Sasanlizumab, Sintilimab; Tislelizumab; Toripalimab; Refulimab; MEDI0680; Bugelimab; Gelolimab, BMS936559; Durvalumab; Avelumab; Envolizumab; Coxilimab; Sugelimab, AUNP-12; Atezolizumab and CA-170. In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of a selective histone deacetylase inhibitor in combination with an anti-PD1 therapy or an anti-PD-L1 therapy, wherein the lung cancer is identified as having altered STK11 activity or expression.

[0165] In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of an HDAC class I selective histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the lung cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of an HDAC class I selective histone deacetylase inhibitor in combination with an immune checkpoint regulator, wherein the lung cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of an HDAC class I selective histone deacetylase inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the lung cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of an HDAC class I selective histone deacetylase inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent. A class I selective histone deacetylase inhibitor, wherein the lung cancer is identified as having altered STK11 activity or expression, wherein the anti-PD1 agent or anti-PD-L1 agent is selected from nivolumab; CT-011; AMP-224; pembrolizumab; pidilizumab; cemiplizumab; dostalimab; palolizumab; spartalizumab; carrelizumab; santolizumab, sintilimab; tislelizumab; toripalimab; rivulimab; MEDI0680; bruglimab; gelotrimazole, BMS936559; durvalumab; avelumab; envolimab; coxilimab; sugemalimab, AUNP-12; atezolizumab and CA-170. In some embodiments, a method of treating a subject having or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of an HDAC class I selective histone deacetylase inhibitor in combination with an anti-PD1 therapy or an anti-PD-L1 therapy, wherein the lung cancer is identified as having altered STK11 activity or expression.

[0166] In some embodiments, a method for treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of an HDAC1 selective histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the lung cancer is identified as having altered STK11 activity or expression. In some embodiments, a method for treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of an HDAC1 selective histone deacetylase inhibitor in combination with an immune checkpoint regulator, wherein the lung cancer is identified as having altered STK11 activity or expression. In some embodiments, a method for treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of an HDAC1 selective inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the lung cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of an HDAC1 selective histone deacetylase inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the lung cancer is identified as having altered STK11 activity or expression, wherein the anti-PD1 agent or the anti-PD-L1 agent is selected from nivolumab; CT-011; AMP-224; pembrolizumab ; Pidilimab; Cimiprilimab; Dostalimab; Palolizumab; Spartalizumab; Camrelizumab; Sasanlizumab, Sintilimab; Tislelizumab; Toripalimab; Rivulimab; MEDI0680; Bugelimab; Gelolimab, BMS936559; Durvalumab; Avelumab; Envolizumab; Coxilimab; Sugelimab, AUNP-12; Atezolizumab and CA-170. In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of an HDAC1 selective inhibitor in combination with an anti-PD1 therapy or an anti-PD-L1 therapy, wherein the lung cancer is identified as having altered STK11 activity or expression.

[0167] In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of an HDAC1,2 selective histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the lung cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of an HDAC1,2 selective inhibitor in combination with an immune checkpoint regulator, wherein the lung cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of an HDAC1,2 selective inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the lung cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of an HDAC1,2 selective histone deacetylase inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the lung cancer is identified as having altered STK11 activity or expression, wherein the anti-PD1 agent or the anti-PD-L1 agent is selected from nivolumab; CT-011; AMP-224; pembrolizumab Anti-; pidilizumab; cemiprilimab; dostalimab; palolizumab; spartalizumab; carrelizumab; santolizumab, sintilimab; tislelizumab; toripalimab; rivalimab; MEDI0680; brugalimab; gelolimab, BMS936559; durvalumab; avelumab; envolizumab; coxilimab; sugemalimab, AUNP-12; atezolizumab and CA-170. In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of an HDAC1,2 selective inhibitor in combination with an anti-PD1 therapy or an anti-PD-L1 therapy, wherein the lung cancer is identified as having altered STK11 activity or expression.

[0168] In some embodiments, a method for treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of a CoREST selective deacetylase inhibitor in combination with a second therapeutic agent, wherein the lung cancer is identified as having altered STK11 activity or expression. In some embodiments, a method for treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of a CoREST selective deacetylase inhibitor in combination with an immune checkpoint regulator, wherein the lung cancer is identified as having altered STK11 activity or expression. In some embodiments, a method for treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of a CoREST selective deacetylase inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the lung cancer is identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of a CoREST selective deacetylase inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the lung cancer is identified as having altered STK11 activity or expression, wherein the anti-PD1 agent or the anti-PD-L1 agent is selected from nivolumab; CT-011; AMP-224; pembrolizumab; Pidilimab; Cimiprilimab; Dostalimab; Palolizumab; Spartalizumab; Camrelizumab; Sasanlizumab, Sintilimab; Tislelizumab; Teplizumab; Rivulimab; MEDI0680; Bugelimab; Gelolimab, BMS936559; Durvalumab; Avelumab; Envolizumab; Coxilimab; Sugelimab, AUNP-12; Atezolizumab and CA-170. In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, the method comprising administering to the subject an effective amount of a CoREST selective deacetylase inhibitor in combination with an anti-PD1 therapy or an anti-PD-L1 therapy, wherein the lung cancer is identified as having altered STK11 activity or expression.

[0169] In some embodiments described herein, the combination of an HDAC inhibitor (e.g., a selective HDAC inhibitor, an HDAC1 selective inhibitor, an HDAC1,2 selective inhibitor, a class I selective HDAC inhibitor, a CoREST complex selective HDAC inhibitor) and an immune checkpoint modulator is synergistic.

[0170] In some embodiments described herein, the method comprises identifying the subject as having one or more cancer cells with altered STK11 activity or expression. In some embodiments described herein, the method comprises identifying the subject as having one or more cancer cells with altered STK11 activity or expression and resistant to anti-PD1 therapy or anti-PD-L1 therapy.

[0171] In some embodiments described herein, the method comprises administering an immune checkpoint modulator and an HDAC inhibitor to a subject, wherein the treatment modulates and / or improves the ratio of Teff cells to Treg cells in a tumor or tumor microenvironment.

[0172] In some embodiments described herein, the method comprises administering an immune checkpoint modulator and an HDAC inhibitor to a subject, wherein the treatment reduces or depletes Treg cells in the tumor or tumor microenvironment.

[0173] In some embodiments described herein, the method comprises administering to the subject an immune checkpoint regulator and an HDAC inhibitor, wherein the treatment induces or increases the expression of a cytokine that promotes anti-tumor activity. In some embodiments, the method further comprises a cytokine selected from the group consisting of CXCL9, CXCL10, and CXCL11.

[0174] In some embodiments described herein, the method comprises administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment reduces the expression of a cytokine that promotes Treg recruitment. In some embodiments, the cytokine is CCL1 or CCL22.

[0175] In some embodiments described herein, the method comprises administering an immune checkpoint modulator and an HDAC inhibitor to a subject, wherein administration of the HDAC inhibitor does not substantially reduce red blood cell or myeloid cell viability (e.g., reduces cell viability by less than 10%, less than 20%, less than 30%, less than 40%, or less than 50%).

[0176] In some embodiments described herein, the cancer presents an immune escape phenotype characterized by expression of a STK11 mutant, comprising: administering an HDAC1,2 selective inhibitor, wherein the HDAC1,2 selective inhibitor is capable of attenuating or reversing the immune escape phenotype. In some embodiments, the method further comprises administering an immune checkpoint regulator.

[0177] In some embodiments described herein, the method comprises administering an immune checkpoint modulator and an HDAC inhibitor to a subject, wherein the treatment results in increased IFNγ expression in the tumor or tumor microenvironment.

[0178] In some embodiments, a method for treating a subject having an immune evasion cancer or being at risk of developing an immune evasion cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor, wherein the immune evasion cancer is identified as having altered STK11 activity or expression. In some embodiments, a method for treating a subject having an immune evasion cancer or being at risk of developing an immune evasion cancer is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the immune evasion cancer is identified as having altered STK11 activity or expression. In some embodiments, the second therapeutic agent is an immune checkpoint regulator as described herein.

[0179] In some embodiments, there is provided a method of reversing immune escape of a subject having cancer or at risk of developing cancer, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor, wherein the cancer is identified as having altered STK11 activity or expression. In some embodiments, there is provided a method of reversing immune escape of a subject having cancer or at risk of developing cancer, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the cancer is identified as having altered STK11 activity or expression. In some embodiments, there is provided a method of reversing immune escape of a subject having cancer or at risk of developing cancer, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the cancer is identified as having altered STK11 activity or expression and immune escape is caused by anti-PD1 therapy or anti-PD-L1 therapy. In some embodiments, the second therapeutic agent is an immune checkpoint regulator as described herein.

[0180] In some embodiments described herein, the subject has cancer. In some embodiments, the subject is at risk of developing cancer.

[0181] In some embodiments described herein, the cancer is lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC), squamous cell lung cancer), colorectal cancer (e.g., colon adenocarcinoma, rectal adenocarcinoma), breast cancer (e.g., invasive ductal carcinoma), pancreatic cancer (e.g., pancreatic adenocarcinoma), endometrial cancer (e.g., endometrioid carcinoma), neuroendocrine cancer (e.g., large cell neuroendocrine carcinoma), melanoma, non-melanoma skin cancer (e.g., squamous cell carcinoma of the skin), bile duct cancer, gallbladder cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), bladder cancer (e.g., bladder urothelial carcinoma), prostate cancer (e.g., prostate adenocarcinoma), cervical cancer, endocervical cancer, or cancer of unknown primary (e.g., adenocarcinoma of unknown primary).

[0182] In some embodiments described herein, the cancer is lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC)), colorectal cancer (e.g., colon adenocarcinoma), pancreatic cancer (e.g., pancreatic adenocarcinoma), endometrial cancer (e.g., endometrioid carcinoma), melanoma, non-melanoma skin cancer (e.g., squamous cell carcinoma of the skin), bile duct cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), cervical cancer, endocervical cancer, or cancer of unknown primary (e.g., adenocarcinoma of unknown primary).

[0183] In some embodiments described herein, the cancer is lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC)), colorectal cancer (e.g., colon adenocarcinoma), pancreatic cancer (e.g., pancreatic adenocarcinoma), endometrial cancer (e.g., endometrioid carcinoma), melanoma, non-melanoma skin cancer (e.g., cutaneous squamous cell carcinoma), bile duct cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), or cancer of unknown primary (e.g., adenocarcinoma of unknown primary).

[0184] In some embodiments described herein, the cancer is lung cancer. In some embodiments described herein, the cancer is lung adenocarcinoma. In some embodiments described herein, the cancer is non-small cell lung cancer (NSCLC).

[0185] In some embodiments described herein, the cancer is colon cancer. In some embodiments described herein, the cancer is colon adenocarcinoma. In some embodiments described herein, the cancer is colorectal cancer.

[0186] In some embodiments described herein, the cancer is breast cancer (e.g., invasive ductal carcinoma). In some embodiments described herein, the cancer is pancreatic cancer (e.g., pancreatic adenocarcinoma). In some embodiments described herein, the cancer is endometrial cancer (e.g., endometrioid carcinoma). In some embodiments described herein, the cancer is neuroendocrine cancer (e.g., large cell neuroendocrine carcinoma). In some embodiments described herein, the cancer is melanoma. In some embodiments described herein, the cancer is non-melanoma skin cancer (e.g., squamous cell carcinoma of the skin). In some embodiments described herein, the cancer is bile duct cancer. In some embodiments described herein, the cancer is gallbladder cancer. In some embodiments described herein, the cancer is ovarian cancer (e.g., ovarian serous adenocarcinoma). In some embodiments described herein, the cancer is bladder cancer (e.g., bladder urothelial carcinoma). In some embodiments described herein, the cancer is prostate cancer (e.g., prostate adenocarcinoma). In some embodiments described herein, the cancer is cervical cancer. In some embodiments described herein, the cancer is endocervical cancer. In some embodiments described herein, the cancer is a cancer of unknown primary (eg, an adenocarcinoma of unknown primary).

[0187] In some embodiments described herein (e.g., in this section), the cancer has increased or decreased STK11 expression. In one embodiment, increased or decreased STK expression is assessed by determining the number of copies of the gene encoding STK11 relative to a control sample, wherein an increase in the number of copies indicates an increased expression level, and a decrease in the number of copies indicates a decreased expression level. In one embodiment, increased or decreased STK expression is assessed by determining the level of STK11 protein or mRNA relative to a control sample. In one embodiment, the cancer has decreased STK11 expression.

[0188] In some embodiments described herein (e.g., in this section), the cancer has a STK11 mutation. In one embodiment, the STK11 mutation is a mutation selected from the following: selected from the following mutations: (i) a mutation in a nucleotide sequence encoding STK11; (ii) a mutation in a regulatory sequence that controls the expression of a nucleotide sequence encoding STK11; (iii) a mutation in a nucleotide encoding a protein that interacts with a transcription product of the STK11 gene; (iv) a mutation in a translation product of the STK11 gene; and (v) a mutation in a transcription product of the STK11 gene.

[0189] In one embodiment, the STK11 mutation is a mutation selected from the following: (i) a mutation in a nucleotide sequence encoding STK11; (ii) a mutation in a regulatory sequence that controls the expression of a nucleotide sequence encoding STK11; and (iii) a mutation in a nucleotide encoding a protein that interacts with a transcription product of the STK11 gene.

[0190] In one embodiment, the STK11 mutation is a mutation in the nucleotide sequence encoding STK11. In one embodiment, the STK11 mutation is a mutation in the translation product of the STK11 gene. In one embodiment, the STK11 mutation is a mutation in the transcription product of the STK11 gene. In one embodiment, the STK11 mutation is an inactivating (loss-of-function) mutation.

[0191] In some embodiments described herein (e.g., in this section), the cancer is resistant to anti-PD1 therapy or anti-PD-L1 therapy. In one embodiment, the cancer is intrinsically resistant to anti-PD1 therapy or anti-PD-L1 therapy. In one embodiment, the cancer is acquired resistance to anti-PD1 therapy or anti-PD-L1 therapy.

[0192] In some embodiments described herein (e.g., in this section), the cancer is resistant to chemotherapy (e.g., platinum-containing chemotherapy). In one embodiment, the cancer is intrinsically resistant to chemotherapy (e.g., platinum-containing chemotherapy). In one embodiment, the cancer is acquired resistance to chemotherapy (e.g., platinum-containing chemotherapy).

[0193] In some embodiments described herein (e.g., in this section), the cancer does not respond to or benefit from treatment with an immune checkpoint modulator when administered alone or as part of a treatment regimen that does not include an HDAC inhibitor.

[0194] "Subject"

[0195] "Subjects" contemplated for administration include, but are not limited to, humans (i.e., males or females of any age group, e.g., pediatric subjects (e.g., infants, children, adolescents) or adult subjects (e.g., young adults, middle-aged adults, or elderly adults)) and / or non-human animals, e.g., mammals such as primates (e.g., cynomolgus monkeys, rhesus monkeys), cattle, pigs, horses, sheep, goats, rodents, cats, and / or dogs. In some embodiments, the subject is a human. In certain embodiments, the subject is a non-human animal. The terms "human," "patient," and "subject" are used interchangeably herein where the context permits.

[0196] "treat"

[0197] As used herein, and unless otherwise indicated, the terms "treat," "treating," and "treatment" contemplate an effect that occurs when a subject suffers from a specified disease, disorder, or condition (e.g., cancer) to reduce the severity of the disease, disorder, or condition, or to delay or slow the progression of the disease, disorder, or condition ("therapeutic treatment"), and also contemplates an effect that occurs before a subject begins to suffer from a specified disease, disorder, or condition ("prophylactic treatment"). In some embodiments, provided herein are intended methods of therapeutic treatment, wherein the effect occurs when a subject suffers from a specified disease, disorder, or condition (e.g., cancer), and causes a reduction in the severity of the disease, disorder, or condition, or a delay or slowing of the progression of the disease, disorder, or condition. In an alternative embodiment, provided herein are methods of prophylactic treatment, wherein the effect occurs before a subject begins to suffer from a specified disease, disorder, or condition (e.g., cancer), and causes the prevention of a disease, disorder, or condition, or one or more symptoms associated with the disease, disorder, or condition, or the prevention of the recurrence of the disease, disorder, or condition.

[0198] Combination therapy

[0199] Provided herein are methods of treating a disease or disorder (eg, a cancer with altered STK11 activity or expression) using a HDAC inhibitor in combination with one or more additional therapeutic agents.

[0200] The term "combination" refers to a fixed combination in the form of a dosage unit, or to a combined administration, in which the compound described herein (e.g., HDAC inhibitor) and the combination partner (e.g., another drug as explained below, also referred to as "additional therapeutic agent" or "adjuvant agent") can be administered independently at the same time or separately at time intervals, especially when these time intervals allow the combination partner to show a cooperative effect, such as a synergistic effect. The single components can be packaged in a kit or packaged separately. One or two of these components (e.g., powder or liquid) can be reconstituted or diluted to the desired amount before administration. The terms "co-administration" or "combined administration" and the like as used herein are intended to cover the administration of the selected combination partner to a single subject (e.g., patient) in need, and are intended to include treatment regimens in which the agents are not necessarily administered by the same route of administration or at the same time. The term "drug combination" as used herein means a product obtained by mixing or combining more than one therapeutic agent, and includes fixed and non-fixed combinations of therapeutic agents. The term "fixed combination" means that both therapeutic agents, such as compounds described herein (e.g., HDAC inhibitors) and combination partners are administered to patients simultaneously in the form of a single entity or single dose. The term "non-fixed combination" means that a therapeutic agent, such as a compound described herein (e.g., an HDAC inhibitor) and a combination partner are administered to a patient simultaneously, concurrently or sequentially as separate entities, without specific time limits, wherein such administration provides therapeutically effective levels of the two compounds in the patient. The latter also applies to mixed therapies, such as the administration of three or more therapeutic agents.

[0201] The term "combination therapy" refers to the administration of two or more therapeutic agents to treat the treatment condition or illness described in the present disclosure. Such administration encompasses the co-administration of these therapeutic agents in a substantially simultaneous manner, such as co-administration in a single capsule with a fixed ratio of active ingredients. Alternatively, such administration encompasses co-administration in multiple containers or separate containers (e.g., tablets, capsules, powders, and liquids) for each active ingredient. Powders and / or liquids can be reconstituted or diluted to a desired amount before administration. In addition, such administration also encompasses the use of each type of therapeutic agent in a sequential manner at approximately the same time or at different times.

[0202] In certain embodiments, the compounds described herein (e.g., HDAC inhibitors) are combined with other therapeutic agents, including but not limited to immune checkpoint modulators and other immunotherapies, other anti-cancer agents (e.g., chemotherapeutic agents, targeted agents), anti-allergic agents, anti-nausea agents (or antiemetics), analgesics, cytoprotective agents, radiation therapy, and combinations thereof.

[0203] In some embodiments, the combination therapy regulates the ratio of TEM to Treg cells. In some embodiments, the combination therapy increases the ratio of TEM to Treg cells in a tumor or tumor microenvironment. Effector memory T cells (TEM) express CD45RO but lack the expression of CCR7 and CD62L. They also have moderate to high expression of CD44. CD62L acts as a "homing receptor" for lymphocytes to enter secondary lymphoid tissues. Therefore, TEM cells are usually found in peripheral circulation and tissues, rather than in lymph nodes, and exhibit immediate effector functions. In response to antigen stimulation, TEM cells proliferate and differentiate into CD62L - Effector T cells. Effector T cells (Teff) are fully differentiated T cells. Effector T cells are short-lived cells, in contrast to memory cells, which have the potential for long-term survival but have strong cytotoxic activity.

[0204] Regulatory T cells (Tregs) are specialized subsets of T cells that function to suppress immune responses, thereby maintaining homeostasis and self-tolerance. Tregs can inhibit T cell proliferation and cytokine production and play a key role in preventing autoimmunity.

[0205] In some embodiments, the combination therapy modulates cytokine secretion in a tumor or tumor microenvironment. In some embodiments, the cytokine is selected from the group of CXCL9, CXCL10, and CXCL11. In some embodiments, the expression of CXCL9, CXCL10, and / or CXCL11 is increased. In some embodiments, the cytokine is selected from the group of CCL1 and CCL22. In some embodiments, the expression of CCL1 and / or CCL22 is reduced.

[0206] In some embodiments, the combination therapy modulates IFNy expression and / or secretion in a tumor or tumor microenvironment. In some embodiments, IFNy expression and / or secretion is increased.

[0207] Immunotherapy

[0208] In some embodiments, at least one of the other therapeutic agents is an immunotherapeutic agent. In some embodiments, a method of treating a disease or condition (e.g., a cancer with altered STK11 activity or expression) is provided, the method comprising administering or co-administering a compound described herein (e.g., an HDAC inhibitor) and one or more immunotherapeutic agents to a patient in need thereof in any order.

[0209] In some embodiments, immunotherapeutic agents are cell-based therapies. In some embodiments, a method for treating a disease or condition (e.g., a cancer with altered STK11 activity or expression) is provided, the method comprising administering or co-administering a compound described herein (e.g., an HDAC inhibitor) and an adoptive cell-based therapy to a patient in need in any order. In some embodiments, the adoptive cell-based therapy is CAR-T therapy or TIL therapy. In some embodiments, the adoptive cell-based therapy is CAR-T therapy. In some embodiments, the adoptive cell-based therapy is TIL therapy.

[0210] In some embodiments, the immunotherapeutic agent is a cancer vaccine, such as a neoantigen. These vaccines can be developed using peptides or RNA, and in some embodiments, the immunotherapeutic agent is an oncolytic virus. In some embodiments, the immunotherapeutic agent is a STING pathway agonist. Exemplary STING agonists include MK-1454 and ADU-S100.

[0211] In some embodiments, the immunotherapeutic agent is an immune checkpoint modulator as described herein.

[0212] Immune checkpoint modulators

[0213] As used herein, "immune checkpoint regulator" is an agent that regulates immune checkpoint pathways by blocking any inhibitory immune checkpoint protein or by activating any stimulatory immune checkpoint protein. Unless otherwise indicated, reference to immune checkpoint regulators in the methods and uses described herein refers to any immune checkpoint regulator described herein (e.g., in this section).

[0214] In one embodiment, the immune checkpoint regulator is a T cell co-stimulatory receptor agonist or a dendritic cell co-stimulatory receptor agonist. In one embodiment, the immune checkpoint regulator is a T cell co-stimulatory receptor agonist. In one embodiment, the immune checkpoint regulator is a dendritic cell co-stimulatory receptor agonist.

[0215] In some embodiments, the immune checkpoint modulator is an immune checkpoint inhibitor. In some embodiments, the immune checkpoint inhibitor is an antibody.

[0216] In one embodiment, the immune checkpoint regulator is a co-stimulatory antibody (e.g., anti-4-1BB antibody, anti-OX40 antibody, anti-GITR antibody, anti-CD28 antibody, anti-CD27 antibody, anti-ICOS antibody, anti-CD40 antibody). In one embodiment, the immune checkpoint regulator is an anti-4-1BB antibody. In one embodiment, the immune checkpoint regulator is an anti-OX40 antibody. In one embodiment, the immune checkpoint regulator is an anti-GITR antibody. In one embodiment, the immune checkpoint regulator is an anti-CD28 antibody. In one embodiment, the immune checkpoint regulator is an anti-CD27 antibody. In one embodiment, the immune checkpoint regulator is an anti-ICOS antibody. In one embodiment, the immune checkpoint regulator is an anti-CD40 antibody.

[0217] In one embodiment, the immune checkpoint regulator is an anti-CTLA agent. In one embodiment, the immune checkpoint regulator is an anti-CTLA-4 antibody (e.g., ipilimumab, tremelimumab). In one embodiment, the immune checkpoint regulator is ipilimumab. In one embodiment, the immune checkpoint regulator is tremelimumab.

[0218] Anti-PD-1 / PD-L1 therapy is designed to block the activity of the PD-1 and PDL1 immune checkpoint proteins, preventing the "off" signal from being transmitted to T cells, thereby allowing T cells to infiltrate and destroy tumors. Anti-PD-1 / PD-L1 agents prevent the association of programmed death ligand 1 (PD-L1) with its receptor, programmed cell death protein 1 (PD-1). Anti-PD-1 agents bind to the PD-1 protein, while anti-PD-L1 agents bind to the PD-L1 ligand.

[0219] In one embodiment, the immune checkpoint modulator is a PD-1 ligand (ie, PD-LI, B7-HI, or CD274) or a PD-2 ligand (ie, PD-L2, B7-DC, or CD273)).

[0220] In one embodiment, the immune checkpoint regulator is an anti-PD-1 agent (PD-1 inhibitor). In one embodiment, the immune checkpoint regulator is an anti-PD-1 antibody (e.g., nivolumab (ie, MDX-1106, BMS-936558, ONO-4538); AMP-224; pembrolizumab (MK-3475); pidilizumab (CT-011), cemiprilimab; dostalimab; palolizumab; spartalizumab; carrelizumab; sazanlizumab, sintilimab; tislelizumab; toripalizumab; rivulimab; MEDI0680; buglizumab; gelolimab). In one embodiment, the immune checkpoint regulator is nivolumab. In one embodiment, the immune checkpoint regulator is pembrolizumab. In one embodiment, the immune checkpoint regulator is pidilizumab. In one embodiment, the immune checkpoint inhibitor is cemiplizumab. In one embodiment, the immune checkpoint inhibitor is dostalimumab. In one embodiment, the immune checkpoint inhibitor is palolizumab. In one embodiment, the immune checkpoint inhibitor is spartalizumab. In one embodiment, the immune checkpoint inhibitor is carrelizumab. In one embodiment, the immune checkpoint inhibitor is santolizumab, sindilimab. In one embodiment, the immune checkpoint inhibitor is tislelizumab. In one embodiment, the immune checkpoint inhibitor is toripalizumab. In one embodiment, the immune checkpoint inhibitor is rivulizumab. In one embodiment, the immune checkpoint inhibitor is MEDI0680. In one embodiment, the immune checkpoint inhibitor is buglizumab. In one embodiment, the immune checkpoint inhibitor is gelotrimazole.

[0221] In one embodiment, the immune checkpoint modulator is an anti-PD-L1 agent (PD-L1 inhibitor). In one embodiment, the immune checkpoint modulator is an anti-PD-L1 antibody (e.g., BMS936559 (i.e., MDX-1105); durvalumab (MEDI4736); avelumab (MSB0010718C); envoralizumab; cocilimab; sugemalizumab, AUNP-12; or atezolizumab (MPDL-3280A). In one embodiment, the immune checkpoint modulator is durvalumab. In one embodiment, the immune checkpoint modulator is atezolizumab. In one embodiment, the immune checkpoint modulator is avelumab. In one embodiment, the immune checkpoint modulator is envoralizumab. In one embodiment, the immune checkpoint modulator is cocilimab. In one embodiment, the immune checkpoint modulator is sugemalizumab. In one embodiment, the immune checkpoint modulator is AUNP-12. In one embodiment, the immune checkpoint inhibitor is an anti-PD-L1 small molecule (e.g., CA-170).

[0222] In one embodiment, the immune checkpoint modulator is a checkpoint co-inhibitory antibody (e.g., anti-TIM3, anti-LAG3, Eftilagimod alpha (IMP321), anti-TIGIT, anti-B7-H3 (e.g., enoblituzumab (MGA271)).

[0223] In one embodiment, the immune checkpoint regulator is an anti-TWEAKR antibody, an anti-HVEM antibody, an anti-TIM-1 antibody, or an anti-VISTA antibody.

[0224] In one embodiment, a method of treating a subject having cancer or at risk of developing cancer is provided, wherein the cancer is identified as having altered STK11 activity or expression, the method comprising administering to the subject an effective amount of a histone deacetylase (HDAC) inhibitor and one or more immune checkpoint regulators, the immune checkpoint regulators independently selected from anti-CTLA-4 antibodies, anti-PD-1 antibodies, anti-PD-L1 antibodies, anti-4-1BB antibodies, anti-OX-40 antibodies, anti-GITR antibodies, anti-CD27 antibodies, anti-CD28 antibodies, anti-CD40 antibodies, anti-LAG3 antibodies, anti-ICOS antibodies, anti-TWEAKR antibodies, anti-HVEM antibodies, anti-TIM-1 antibodies, anti-TIM-3 antibodies, anti-VISTA antibodies, and anti-TIGIT antibodies.

[0225] Chemotherapy

[0226] In one embodiment, at least one of the additional therapeutic agents is a chemotherapeutic agent.

[0227] Chemotherapeutic agents considered for combination therapy include anastrozole Bicalutamide Bleomycin sulfate Busulfan Busulfan Injection Capecitabine N4-pentyloxycarbonyl-5-deoxy-5-fluorocytidine, carboplatin Carmustine Chlorambucil (Leu ), Cisplatin Cladribine Cyclophosphamide ( or ), cytarabine, cytosine arabinoside (Cytosar- ), Cytarabine Liposome Injection Dacarbazine (DTIC- ), dactinomycin (Actinomycin D, Cosmegan), daunorubicin hydrochloride (Cerubid ), daunorubicin citrate liposome injection Dexamethasone, docetaxel Doxorubicin Hydrochloride Etoposide Fludarabine phosphate 5-Fluorouracil Flutamide Tezacitibine, gemcitabine (difluorodeoxycytidine), hydroxyurea Idabi Ifosfamide Irinotecan L-Asparaginase Calcium leucovorin, melphalan 6-Mercaptopurine Methotrexate Mitoxantrone Mylotarg, Taxol ), nab-paclitaxel Pemetrexed Phoenix (yttrium 90 / MX-DTPA), pentostatin, polyphenylpropanone 20 implant with carmustine Tamoxifen citrate Teniposide 6-thioguanine, thiotepa, tirapazamine Topotecan hydrochloride for injection ), Vinblastine Vincristine and Navelb ).

[0228] In some embodiments, each chemotherapeutic agent is independently selected from cisplatin Carboplatin Paclitaxel nab-paclitaxel Docetaxel Gemcitabine (difluorodeoxycytidine), vinorelbine Etoposide Ipemetrexed

[0229] In one embodiment, at least one chemotherapeutic agent is a platinum-containing therapeutic agent (e.g., cisplatin or carboplatin). In one embodiment, at least one chemotherapeutic agent is cisplatin. In one embodiment, one chemotherapeutic agent is a platinum-containing chemotherapeutic agent and the second chemotherapeutic agent is pemetrexed.

[0230] Targeted therapy

[0231] In one embodiment, at least one of the additional therapeutic agents is a targeting agent.

[0232] In one embodiment, each targeting agent is independently selected from an anti-angiogenic agent (eg, an anti-VEGF agent), a KRAS inhibitor, an ALK inhibitor, a ROS1 inhibitor, a BRAF inhibitor, a RET inhibitor, a MEK inhibitor, a MET inhibitor, and a TRK inhibitor.

[0233] In one embodiment, each targeting agent is independently selected from bevacizumab, ramucirumab, sotoracib, crizotinib, ceritinib, alectinib, brigatinib, lorlatinib, entrectinib, dabrafenib, trametinib, capmatinib, tepotinib, and larotrectinib

[0234] In some embodiments, a method of treating a disease or condition (e.g., a cancer with altered STK11 activity or expression) is provided, the method comprising administering or co-administering a compound described herein (e.g., an HDAC inhibitor) and a KRAS inhibitor to a patient in need thereof in any order. In some embodiments, the KRAS inhibitor is KRAS G12CInhibitors (e.g., sotorasib, adagrasib, ARS-3248, LY3499446, LY3537982, GDC-6036, D3s-001, D-1553, JDQ443, BI 1823911, RMC-6291, GFH925, JAB-21822, BPI-421286, HBI-2438). In some embodiments, KRAS G12C The inhibitor is sotolacib. In some embodiments, the KRAS inhibitor is KRAS G12D Inhibitors (e.g., MRTX1133, RMC-9805). In some embodiments, the KRAS inhibitor is KRAS Q61H Inhibitors (e.g., RMC-0708). In some embodiments, the KRAS inhibitor is KRAS G13C Inhibitors (eg, RMC-8839). In some embodiments, the KRAS inhibitor is a pan-KRAS inhibitor (eg, RMC-6236, BI 1701963).

[0235] In some embodiments, a method of treating a disease or condition (e.g., a cancer with altered STK11 activity or expression) is provided, the method comprising administering or co-administering a compound described herein (e.g., an HDAC inhibitor) and a HDM2 inhibitor and / or with 5-FU, in any order, to a patient in need thereof.

[0236] In some embodiments, a method of treating a disease or condition (e.g., a cancer with altered STK11 activity or expression) is provided, the method comprising administering or co-administering a compound described herein (e.g., an HDAC inhibitor) and a CDK4 inhibitor, including but not limited to LEE011 or a CDK 4 / 6 inhibitor (e.g., palbociclib) to a patient in need thereof, in any order. Ribociclib and abemaciclib

[0237] In some embodiments, a method of treating a disease or condition (e.g., a cancer with altered STK11 activity or expression) is provided, the method comprising administering or co-administering a compound described herein (e.g., an HDAC inhibitor) and a targeted therapy to a patient in need thereof, in any order, wherein the targeted therapy depends on the dependence of the individual target tumor on the relevant pathway, as determined by appropriate predictive markers, including but not limited to inhibitors of HDM2i, PI3K / mTOR-I, MAPKi, RTKi (FGFRi, METi, IGFiRi, JAKi, and WNTi).

[0238] In some embodiments, a method of treating a disease or condition (e.g., a cancer with altered STK11 activity or expression) is provided, the method comprising administering or co-administering a compound described herein (e.g., an HDAC inhibitor) and a disease-specific huMAB (e.g., an anti-HER3 huMAB) in any order to a patient in need thereof.

[0239] In some embodiments, a method of treating a disease or condition (e.g., a cancer with altered STK11 activity or expression) is provided, the method comprising administering or co-administering, in any order, a compound described herein (e.g., an HDAC inhibitor) and an ADC / ADCC that depends on the expression of a relevant surface target on a target tumor of interest to a patient in need thereof.

[0240] In some embodiments, a method of treating a disease or condition (e.g., a cancer with altered STK11 activity or expression) is provided, the method comprising administering or co-administering a compound described herein (e.g., an HDAC inhibitor) and a CAAP1 inhibitor, in any order, to a patient in need thereof.

[0241] In some embodiments, a method of treating a disease or condition (e.g., a cancer with altered STK11 activity or expression) is provided, the method comprising administering or co-administering a compound described herein (e.g., an HDAC inhibitor) and an AKAP17A inhibitor, in any order, to a patient in need thereof.

[0242] In some embodiments, a method of treating a disease or condition (e.g., a cancer with altered STK11 activity or expression) is provided, the method comprising administering or co-administering a compound described herein (e.g., an HDAC inhibitor) and a BCL2L1 inhibitor to a patient in need thereof in any order. In some embodiments, the BCL2L1 inhibitor is AT-101.

[0243] In some embodiments, a method of treating a disease or condition (e.g., a cancer with altered STK11 activity or expression) is provided, the method comprising administering or co-administering a compound described herein (e.g., an HDAC inhibitor) and a TSC1 / 2 inhibitor in any order to a patient in need thereof.

[0244] In some embodiments, a method of treating a disease or condition (e.g., a cancer with altered STK11 activity or expression) is provided, the method comprising administering or co-administering a compound described herein (e.g., an HDAC inhibitor) and a UBE2H inhibitor in any order to a patient in need thereof.

[0245] In some embodiments, a method of treating a disease or condition (e.g., a cancer with altered STK11 activity or expression) is provided, the method comprising administering or co-administering a compound described herein (e.g., an HDAC inhibitor) and a NF2 inhibitor in any order to a patient in need thereof.

[0246] In some embodiments, a method of treating a disease or condition (e.g., a cancer with altered STK11 activity or expression) is provided, the method comprising administering or co-administering a compound described herein (e.g., an HDAC inhibitor) and a ZC3HC1 inhibitor, in any order, to a patient in need thereof.

[0247] In some embodiments, a method of treating a disease or condition (e.g., a cancer with altered STK11 activity or expression) is provided, the method comprising administering or co-administering a compound described herein (e.g., an HDAC inhibitor) and an MGEA5 inhibitor, in any order, to a patient in need thereof.

[0248] In some embodiments, a method of treating a disease or condition (e.g., a cancer with altered STK11 activity or expression) is provided, the method comprising administering or co-administering a compound described herein (e.g., an HDAC inhibitor) and a CNOT4 inhibitor in any order to a patient in need thereof.

[0249] In some embodiments, a method of treating a disease or condition (e.g., a cancer with altered STK11 activity or expression) is provided, the method comprising administering or co-administering a compound described herein (e.g., an HDAC inhibitor) and an API5 inhibitor in any order to a patient in need thereof.

[0250] In some embodiments, a method of treating a disease or condition (e.g., a cancer with altered STK11 activity or expression) is provided, the method comprising administering or co-administering a compound described herein (e.g., an HDAC inhibitor) and a HEXIM1 inhibitor in any order to a patient in need thereof.

[0251] In some embodiments, a method of treating a disease or condition (e.g., a cancer with altered STK11 activity or expression) is provided, the method comprising administering or co-administering a compound described herein (e.g., an HDAC inhibitor) and a PTEN inhibitor in any order to a patient in need thereof.

[0252] In some embodiments, a method of treating a disease or condition (e.g., a cancer with altered STK11 activity or expression) is provided, the method comprising administering or co-administering a compound described herein (e.g., an HDAC inhibitor) and a DNA damage pathway inhibitor to a patient in need thereof in any order. In some embodiments, the DNA damage pathway inhibitor is selected from bleomycin, an ATM inhibitor (e.g., AZD1390), a USP1 inhibitor, a WEE1 inhibitor (e.g., AZD1775), and a Chk1 inhibitor (e.g., AZD7762).

[0253] Other therapeutic agents

[0254] Some patients may experience allergic reactions to the compounds described herein (e.g., HDAC inhibitors) and / or other anticancer agents during or after administration; therefore, antiallergic agents are often administered to minimize the risk of allergic reactions. Suitable antiallergic agents include corticosteroids, including but not limited to dexamethasone (e.g., ), beclomethasone (e.g. ), hydrocortisone (also known as cortisone, hydrocortisone sodium succinate, hydrocortisone sodium phosphate, and under the trade name Ala- Hydrocortisone phosphate, Solu- 、Hydrocort and (sold under the trade name Delta- and Sold under the trade name 、Liquid , and Methylprednisolone (also known as 6-methylprednisolone, methylprednisolone acetate, methylprednisolone sodium succinate, and sold under the trade name 、M- and Solu- antihistamines, such as diphenhydramine (e.g. ), hydroxyzine, and cyproheptadine; and bronchodilators, such as beta-adrenergic receptor agonists, albuterol (e.g., ) and terbutaline

[0255] Some patients may experience nausea during and after administration of the compounds described herein (e.g., HDAC inhibitors) and / or other anticancer agents; therefore, antiemetics are used to prevent nausea (epigastric) and vomiting. Suitable antiemetics include aprepitant Ondansetron Granisetron HCl Lorazepam ( Dexamethasone Prochlorperazine Cassopitant and ) and their combinations.

[0256] Medications to relieve pain experienced during treatment are often prescribed to make the patient more comfortable. Common over-the-counter pain relievers such as However, opioid analgesics include, but are not limited to, hydrocodone / acetaminophen or hydrocodone / acetaminophen (e.g., ), morphine (e.g. or ), oxycodone (e.g., or ), Oxymorphone Hydrochloride and fentanyl (e.g., ) can also be used for moderate or severe pain.

[0257] To protect normal cells from treatment toxicity and limit organ toxicity, cytoprotectants (such as neuroprotectants, free radical scavengers, cardioprotectants, anthracycline extravasation neutralizers, nutrients, etc.) can be used as adjunctive therapy. Suitable cytoprotectants include amifostine Glutamine, Dimethoate Mesna Right rezoxan or ), Zali Roden and folinic acid (also known as calcium folinate, aurantium factor, and folinic acid).

[0258] The structures of the active compounds identified by code numbers, generic names or trade names can be taken from the actual version of the standard compendium "The Merck Index" or from databases such as the Patents International (eg IMS World Publications).

[0259] The above compounds that can be used in combination with the compounds described herein (eg, HDAC inhibitors) can be prepared and administered as described in the art, including but not limited to in the references cited herein.

[0260] In some embodiments, a pharmaceutical composition is provided, comprising at least one compound described herein (e.g., an HDAC inhibitor) and a pharmaceutically acceptable carrier suitable for administration to a human or animal subject alone or with other anticancer agents. Specifically, the composition will be formulated together or administered separately as a combination therapeutic agent.

[0261] In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, the method comprising administering to the subject a combination of an HDAC inhibitor as described herein (e.g., a selective HDAC inhibitor, an HDAC1 selective inhibitor, an HDAC1,2 selective inhibitor, a class I selective HDAC inhibitor, a CoREST complex selective HDAC inhibitor), an immune checkpoint modulator as described herein (e.g., an anti-CTLA-4 antibody, an anti-PD-1 antibody, an anti-PD-L1 antibody, or a combination thereof), and an additional therapeutic agent as described herein (e.g., a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof).

[0262] In combination therapy, the compounds described herein (eg, HDAC inhibitors) and other anticancer agents can be administered simultaneously, concurrently or sequentially without specific time limits, wherein such administration provides therapeutically effective levels of both compounds in the patient.

[0263] In one embodiment, the HDAC inhibitor is administered concurrently with the additional therapeutic agent.

[0264] In one embodiment, the HDAC inhibitor and the additional therapeutic agent are administered sequentially.

[0265] In one embodiment, the HDAC inhibitor is administered prior to the additional therapeutic agent.

[0266] In one embodiment, the HDAC inhibitor is administered after the additional therapeutic agent.

[0267] In one embodiment, the method comprises administering an immune checkpoint modulator to the subject, followed by administering an HDAC inhibitor to the subject.

[0268] In one embodiment, the method comprises administering to the subject an HDAC inhibitor, followed by administering to the subject an immune checkpoint modulator.

[0269] In one embodiment, the method comprises administering an immune checkpoint modulator to the subject, followed by administering a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof to the subject, followed by administering an HDAC inhibitor to the subject.

[0270] In one embodiment, the method comprises administering an immune checkpoint modulator to the subject, followed by administering an HDAC inhibitor to the subject, followed by administering a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof to the subject.

[0271] In one embodiment, the method comprises administering to the subject an HDAC inhibitor, followed by administering to the subject a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof, followed by administering to the subject an immune checkpoint modulator.

[0272] In one embodiment, the method comprises administering to the subject an HDAC inhibitor, followed by administering to the subject an immune checkpoint modulator, followed by administering to the subject a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof.

[0273] In one embodiment, the method comprises administering to the subject a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof, followed by administering to the subject an immune checkpoint modulator, followed by administering to the subject an HDAC inhibitor.

[0274] In one embodiment, the method comprises administering to the subject a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof, followed by administering to the subject an HDAC inhibitor, followed by administering to the subject an immune checkpoint modulator.

[0275] In some embodiments, compounds described herein (e.g., HDAC inhibitors) and other anticancer agents are usually administered sequentially in any order by infusion or oral administration. Dosage regimens can vary according to the staging of the disease, the patient's physical health, the safety of individual drugs and the tolerance of individual drugs, and other standards known to the attending physician and practitioner of the combination. Compounds described herein (e.g., HDAC inhibitors) and other anticancer agents can be administered within a few minutes, hours, days or even weeks apart from each other, depending on the specific cycle used for treatment. In addition, the cycle can include a drug more often administered than another drug during the treatment cycle, and each drug is administered with different doses.

[0276] In some embodiments, kits are provided, which include one or more compounds described herein (e.g., HDAC inhibitors) and a second therapeutic agent as disclosed herein. Representative kits include (a) a compound described herein (e.g., HDAC inhibitors) and (b) at least one other therapeutic agent, such as described above, whereby such kits may include a package insert or other label, including instructions for administration.

[0277] The compounds described herein (eg, HDAC inhibitors) can also be used in combination with known treatment methods, such as administration of hormones or, in particular, radiation.

[0278] Patient selection and monitoring

[0279] Selecting patients for treatment

[0280] In one embodiment, a method of selecting a subject for treatment with an HDAC inhibitor is provided, the method comprising: identifying a subject having a cancer characterized by the presence of cells with altered STK11 activity or expression; and selecting the subject thus identified for treatment with one of the treatment methods described herein.

[0281] In one embodiment, a method of selecting a subject for treatment with an HDAC inhibitor is provided, the method comprising: identifying a subject having a cancer characterized by the presence of cells having altered STK11 activity or expression; and selecting the subject thus identified for treatment with the HDAC inhibitor.

[0282] In one embodiment, a method of selecting a subject for treatment with a combination of an HDAC inhibitor and one or more additional therapeutic agents is provided, the method comprising: identifying a subject having a cancer characterized by the presence of cells having altered STK11 activity or expression; and selecting the subject thus identified for treatment with the HDAC inhibitor and the one or more additional therapeutic agents.

[0283] In one embodiment, a method of selecting a subject for treatment with a combination of an HDAC inhibitor and one or more additional therapeutic agents is provided, the method comprising: identifying a subject having a cancer characterized by the presence of cells with altered STK11 activity or expression; and selecting the subject thus identified for treatment with an HDAC inhibitor and one or more immune checkpoint modulators.

[0284] In one embodiment, a method of selecting a subject for treatment with a combination of an HDAC inhibitor and two or more additional therapeutic agents is provided, the method comprising: identifying a subject having a cancer characterized by the presence of cells with altered STK11 activity or expression; and selecting the subject thus identified for treatment with an HDAC inhibitor and two or more additional therapeutic agents, wherein at least two of the additional therapeutic agents are immune checkpoint modulators.

[0285] In one embodiment, a method for selecting a subject for treatment with a combination of an HDAC inhibitor, an immune checkpoint modulator, and one or more additional therapeutic agents selected from chemotherapeutic agents, targeted agents, and radiation therapy is provided, the method comprising: identifying a subject who has previously been treated with a combination of an immune checkpoint modulator and one or more additional therapeutic agents selected from chemotherapeutic agents, targeted agents, and radiation therapy, wherein treatment with the combination of the immune checkpoint modulator and the additional therapeutic agent did not provide any additional benefit compared to treatment with the additional therapeutic agent alone; and selecting the subject thus identified for treatment.

[0286] In one embodiment, the method further comprises: identifying a subject having a cancer characterized by the presence of cells having reduced STK11 activity or expression; and selecting the subject thus identified for treatment.

[0287] In some embodiments described herein, the cancer is lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC), squamous cell lung cancer), colorectal cancer (e.g., colon adenocarcinoma, rectal adenocarcinoma), breast cancer (e.g., invasive ductal carcinoma), pancreatic cancer (e.g., pancreatic adenocarcinoma), endometrial cancer (e.g., endometrioid carcinoma), neuroendocrine cancer (e.g., large cell neuroendocrine carcinoma), melanoma, non-melanoma skin cancer (e.g., squamous cell carcinoma of the skin), bile duct cancer, gallbladder cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), bladder cancer (e.g., bladder urothelial carcinoma), prostate cancer (e.g., prostate adenocarcinoma), cervical cancer, endocervical cancer, or cancer of unknown primary (e.g., adenocarcinoma of unknown primary).

[0288] In some embodiments described herein, the cancer is lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC)), colorectal cancer (e.g., colon adenocarcinoma), pancreatic cancer (e.g., pancreatic adenocarcinoma), endometrial cancer (e.g., endometrioid carcinoma), melanoma, non-melanoma skin cancer (e.g., squamous cell carcinoma of the skin), bile duct cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), cervical cancer, endocervical cancer, or cancer of unknown primary (e.g., adenocarcinoma of unknown primary).

[0289] In some embodiments described herein, the cancer is lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC)), colorectal cancer (e.g., colon adenocarcinoma), pancreatic cancer (e.g., pancreatic adenocarcinoma), endometrial cancer (e.g., endometrioid carcinoma), melanoma, non-melanoma skin cancer (e.g., cutaneous squamous cell carcinoma), bile duct cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), or cancer of unknown primary (e.g., adenocarcinoma of unknown primary).

[0290] In some embodiments described herein, the cancer is lung cancer. In some embodiments described herein, the cancer is lung adenocarcinoma. In some embodiments described herein, the cancer is non-small cell lung cancer (NSCLC).

[0291] In some embodiments described herein, the cancer is colon cancer. In some embodiments described herein, the cancer is colon adenocarcinoma. In some embodiments described herein, the cancer is colorectal cancer.

[0292] In some embodiments described herein (e.g., in this section), the cancer has increased or decreased STK11 expression. In one embodiment, increased or decreased STK expression is assessed by determining the number of copies of the gene encoding STK11 relative to a control sample, wherein an increase in the number of copies indicates an increased expression level, and a decrease in the number of copies indicates a decreased expression level. In one embodiment, increased or decreased STK expression is assessed by determining the level of STK11 protein or mRNA relative to a control sample. In one embodiment, the cancer has decreased STK11 expression.

[0293] In some embodiments described herein (e.g., in this section), the cancer has a STK11 mutation. In one embodiment, the STK11 mutation is a mutation selected from the following: selected from the following mutations: (i) a mutation in a nucleotide sequence encoding STK11; (ii) a mutation in a regulatory sequence that controls the expression of a nucleotide sequence encoding STK11; (iii) a mutation in a nucleotide encoding a protein that interacts with a transcription product of the STK11 gene; (iv) a mutation in a translation product of the STK11 gene; and (v) a mutation in a transcription product of the STK11 gene.

[0294] In one embodiment, the STK11 mutation is a mutation selected from the following: (i) a mutation in a nucleotide sequence encoding STK11; (ii) a mutation in a regulatory sequence that controls the expression of a nucleotide sequence encoding STK11; and (iii) a mutation in a nucleotide encoding a protein that interacts with a transcription product of the STK11 gene.

[0295] In one embodiment, the STK11 mutation is a mutation in the nucleotide sequence encoding STK11. In one embodiment, the STK11 mutation is a mutation in the translation product of the STK11 gene. In one embodiment, the STK11 mutation is a mutation in the transcription product of the STK11 gene. In one embodiment, the STK11 mutation is an inactivating (loss-of-function) mutation.

[0296] In one embodiment, the cancer is also characterized by one or more additional mutations. In one embodiment, additional mutations are selected from KRAS mutations and KEAP1 mutations. In one embodiment, additional mutations are KRAS mutations. In one embodiment, KRAS mutations are selected from G12C, G12D, G12V, G12A, G12S, G12R, G13C, G13D, G13S, Q61H and Q61K mutations. In one embodiment, KRAS mutations are mutations at position G12, optionally wherein KRAS mutations are selected from G12D mutations, G12C mutations, G12V mutations or combinations thereof. In one embodiment, KRAS mutations are activating mutations. In one embodiment, additional mutations are KEAP1 mutations. In one embodiment, KEAP1 mutations are inactivating mutations. In one embodiment, additional mutations are KRAS mutations and KEAP1 mutations. In one embodiment, the cancer is characterized by a lack of EGFR mutations.

[0297] In one embodiment, the cancer is resistant to anti-PD1 therapy or anti-PD-L1 therapy. In one embodiment, the cancer is intrinsically resistant to anti-PD1 therapy or anti-PD-L1 therapy. In one embodiment, the cancer is acquired resistance to anti-PD1 therapy or anti-PD-L1 therapy.

[0298] In one embodiment, the cancer is resistant to chemotherapy (e.g., platinum-containing chemotherapy). In one embodiment, the cancer is intrinsically resistant to chemotherapy (e.g., platinum-containing chemotherapy). In one embodiment, the cancer is acquired resistance to chemotherapy (e.g., platinum-containing chemotherapy).

[0299] In one embodiment, the cancer is not responsive to or does not benefit from treatment with an immune checkpoint modulator when administered alone or as part of a treatment regimen that does not include an HDAC inhibitor.

[0300] In some embodiments, the patient is immunocompetent. In some embodiments, the patient has received adoptive cell therapy. In some embodiments, the adoptive cell therapy is TIL-T therapy or CAR-T therapy.

[0301] Determine whether a subject will respond to treatment with an HDAC inhibitor

[0302] In one embodiment, a method for ascertaining the sensitivity of a subject having or diagnosed with cancer to treatment with an HDAC inhibitor is provided, the method comprising: determining: i) the presence or absence of a STK11 mutation in the subject or a sample derived from the subject; and / or ii) the level of STK11 activity or expression; wherein the presence of a STK11 mutation (e.g., a STK loss-of-function mutation) and / or altered (e.g., decreased) level of STK11 activity or expression indicates sensitivity to treatment with an HDAC inhibitor.

[0303] In one embodiment, a method for ascertaining the sensitivity of a subject having or diagnosed with cancer to combined treatment with an HDAC inhibitor as described herein and an immune checkpoint regulator as described herein is provided, the method comprising: determining: i) the presence or absence of an STK11 mutation in the subject or a sample derived from the subject; and / or ii) the level of STK11 activity or expression; wherein the presence of an STK11 mutation (e.g., an STK loss-of-function mutation) and / or altered (e.g., decreased) level of STK11 activity or expression indicates sensitivity to combined treatment with an HDAC inhibitor and an immune checkpoint regulator.

[0304] In one embodiment, the expression level of STK11 is assessed by determining the number of copies of the gene encoding STK11 relative to a control sample, wherein an increase in the number of copies indicates an increase in the expression level and a decrease in the number of copies indicates a decrease in the expression level. In one embodiment, the expression level of STK11 is assessed by determining the level of STK11 protein or mRNA relative to a control sample.

[0305] In one embodiment, a method for determining whether a subject having or diagnosed with cancer will respond to treatment with an HDAC inhibitor as described herein is provided, the method comprising: determining the presence or absence of a STK11 mutation in the subject or a sample derived from the subject, wherein the presence of a STK11 mutation (e.g., a STK loss-of-function mutation) indicates that the subject will respond to treatment with an HDAC inhibitor.

[0306] In one embodiment, a method for determining whether a subject having or diagnosed with cancer will respond to treatment with an HDAC inhibitor as described herein and an immune checkpoint regulator as described herein is provided, the method comprising: determining the presence or absence of an STK11 mutation in the subject or a sample derived from the subject, wherein the presence of an STK11 mutation (e.g., an STK loss-of-function mutation) indicates that the subject will respond to combined treatment with an HDAC inhibitor and an immune checkpoint regulator.

[0307] In one embodiment, a method for determining whether a subject having or diagnosed with cancer will respond to treatment with an HDAC inhibitor as described herein is provided, the method comprising:

[0308] a) detecting the level of STK11 (e.g., STK11 protein and / or STK11 mRNA) in a cancer test sample (e.g., a cancer sample obtained from a subject);

[0309] b) comparing the cancer test sample to a reference (eg, a reference sample taken from a non-cancerous subject or a normal control subject), wherein an altered (eg, decreased) STK11 level in the test sample indicates that the subject will respond to treatment with an HDAC inhibitor.

[0310] In one embodiment, a method for determining whether a subject having or diagnosed with cancer will respond to treatment with an HDAC inhibitor as described herein and an immune checkpoint modulator as described herein is provided, the method comprising:

[0311] a) detecting the level of STK11 (e.g., STK11 protein and / or STK11 mRNA) in a cancer test sample (e.g., a cancer sample obtained from a subject);

[0312] b) comparing the cancer test sample to a reference (e.g., a reference sample taken from a non-cancerous subject or a normal control subject), wherein an altered (e.g., decreased) STK11 level in the test sample indicates that the subject will respond to a combination treatment with an HDAC inhibitor and an immune checkpoint modulator.

[0313] In one embodiment, a method for determining whether a subject having or diagnosed with cancer will respond to treatment with an HDAC inhibitor as described herein is provided, the method comprising:

[0314] a) determining the copy number of a gene encoding STK11 in a cancer test sample (e.g., a cancer sample obtained from a subject);

[0315] b) comparing the cancer test sample to a reference (eg, a reference sample taken from a non-cancerous subject or a normal control subject), wherein a decrease in copy number indicates that the subject will respond to treatment with an HDAC inhibitor.

[0316] In one embodiment, a method for determining whether a subject having or diagnosed with cancer will respond to treatment with an HDAC inhibitor as described herein and an immune checkpoint modulator as described herein is provided, the method comprising:

[0317] a) determining the copy number of a gene encoding STK11 in a cancer test sample (e.g., a cancer sample obtained from a subject);

[0318] b) comparing the cancer test sample to a reference (e.g., a reference sample taken from a non-cancerous subject or a normal control subject), wherein a decrease in copy number indicates that the subject will respond to treatment with a combination of an HDAC inhibitor and an immune checkpoint modulator.

[0319] In one embodiment, the STK11 mutation is a loss-of-function mutation. In one embodiment, the changed STK11 activity or expression level is determined by comparing the activity or expression level in a subject or a sample derived from the subject (e.g., a tumor sample) and comparing it with a control (e.g., a healthy subject or a sample derived from a healthy subject). In one embodiment, the changed STK11 activity level is a reduced STK11 activity level.

[0320] In one embodiment, the cancer is lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC), squamous cell lung cancer), colorectal cancer (e.g., colon adenocarcinoma, rectal adenocarcinoma), breast cancer (e.g., invasive ductal carcinoma), pancreatic cancer (e.g., pancreatic adenocarcinoma), endometrial cancer (e.g., endometrioid carcinoma), neuroendocrine cancer (e.g., large cell neuroendocrine carcinoma), melanoma, non-melanoma skin cancer (e.g., squamous cell carcinoma of the skin), bile duct cancer, gallbladder cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), bladder cancer (e.g., bladder urothelial carcinoma), prostate cancer (e.g., prostate adenocarcinoma), cervical cancer, endocervical cancer, or cancer of unknown primary (e.g., adenocarcinoma of unknown primary).

[0321] In one embodiment, the cancer is lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC)), colorectal cancer (e.g., colon adenocarcinoma), pancreatic cancer (e.g., pancreatic adenocarcinoma), endometrial cancer (e.g., endometrioid carcinoma), melanoma, non-melanoma skin cancer (e.g., squamous cell carcinoma of the skin), bile duct cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), cervical cancer, endocervical cancer, or cancer of unknown primary (e.g., adenocarcinoma of unknown primary).

[0322] In one embodiment, the cancer is lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC)), colorectal cancer (e.g., colon adenocarcinoma), pancreatic cancer (e.g., pancreatic adenocarcinoma), endometrial cancer (e.g., endometrioid carcinoma), melanoma, non-melanoma skin cancer (e.g., cutaneous squamous cell carcinoma), bile duct cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), or cancer of unknown primary (e.g., adenocarcinoma of unknown primary).

[0323] In one embodiment, the cancer is lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC)). In one embodiment, the cancer is lung adenocarcinoma. In one embodiment, the cancer is non-small cell lung cancer (NSCLC).

[0324] In some embodiments described herein, the cancer is colon cancer. In some embodiments described herein, the cancer is colon adenocarcinoma. In some embodiments described herein, the cancer is colorectal cancer.

[0325] Determining whether a cancer will respond to treatment with an HDAC inhibitor

[0326] In one embodiment, a method for ascertaining the sensitivity of cancer to treatment with an HDAC inhibitor as described herein is provided, the method comprising: determining: i) the presence or absence of an STK11 mutation in a cancer test sample (e.g., a sample derived from a subject); and / or ii) the level of STK11 activity or expression; wherein the presence of an STK11 mutation (e.g., an STK loss-of-function mutation) and / or an altered (e.g., decreased) level of STK11 activity or expression indicates sensitivity to treatment with an HDAC inhibitor.

[0327] In one embodiment, a method for exploring the sensitivity of cancer to combined treatment with an HDAC inhibitor as described herein and an immune checkpoint regulator as described herein is provided, the method comprising: determining: i) the presence or absence of an STK11 mutation in a cancer test sample (e.g., a sample derived from a subject); and / or ii) the level of STK11 activity or expression; wherein the presence of an STK11 mutation (e.g., an STK loss-of-function mutation) and / or altered (e.g., decreased) level of STK11 activity or expression indicates sensitivity to combined treatment with an HDAC inhibitor and an immune checkpoint regulator.

[0328] In one embodiment, the expression level of STK11 is assessed by determining the number of copies of the gene encoding STK11 relative to a control sample, wherein an increase in the number of copies indicates an increase in the expression level and a decrease in the number of copies indicates a decrease in the expression level. In one embodiment, the expression level of STK11 is assessed by determining the level of STK11 protein or mRNA relative to a control sample.

[0329] In one embodiment, a method for determining whether a cancer will respond to treatment with an HDAC inhibitor as described herein is provided, the method comprising: determining the presence or absence of a STK11 mutation in a cancer test sample (e.g., a sample derived from a subject), wherein the presence of a STK11 mutation (e.g., a STK loss-of-function mutation) indicates that the cancer will respond to treatment with an HDAC inhibitor.

[0330] In one embodiment, a method for determining whether a cancer will respond to treatment with an HDAC inhibitor as described herein and an immune checkpoint regulator as described herein is provided, the method comprising: determining the presence or absence of a STK11 mutation in a cancer test sample (e.g., a sample derived from a subject), wherein the presence of a STK11 mutation (e.g., a STK loss-of-function mutation) indicates that the cancer will respond to treatment with a combination of an HDAC inhibitor and an immune checkpoint regulator.

[0331] In one embodiment, a method for determining whether a cancer will respond to treatment with an HDAC inhibitor as described herein is provided, the method comprising:

[0332] a) detecting the level of STK11 (e.g., STK11 protein and / or STK11 mRNA) in a cancer test sample (e.g., a cancer sample obtained from a subject);

[0333] b) comparing the cancer test sample to a reference (eg, a reference sample taken from a non-cancerous subject or a normal control subject), wherein an altered (eg, decreased) level of STK11 in the test sample indicates that the cancer will respond to treatment with an HDAC inhibitor.

[0334] In one embodiment, a method for determining whether a cancer will respond to treatment with an HDAC inhibitor as described herein and an immune checkpoint modulator as described herein is provided, the method comprising:

[0335] a) detecting the level of STK11 (e.g., STK11 protein and / or STK11 mRNA) in a cancer test sample (e.g., a cancer sample obtained from a subject);

[0336] b) comparing the cancer test sample to a reference (e.g., a reference sample taken from a non-cancerous subject or a normal control subject), wherein an altered (e.g., decreased) level of STK11 in the test sample indicates that the cancer will respond to treatment with a combination of an HDAC inhibitor and an immune checkpoint modulator.

[0337] In one embodiment, a method for determining whether a cancer will respond to treatment with an HDAC inhibitor as described herein is provided, the method comprising:

[0338] a) determining the copy number of a gene encoding STK11 in a cancer test sample (e.g., a cancer sample obtained from a subject);

[0339] b) comparing the cancer test sample to a reference (eg, a reference sample taken from a non-cancerous subject or a normal control subject), wherein a decrease in copy number indicates that the cancer will respond to treatment with an HDAC inhibitor.

[0340] In one embodiment, a method for determining whether a cancer will respond to treatment with an HDAC inhibitor as described herein and an immune checkpoint modulator as described herein is provided, the method comprising:

[0341] a) determining the copy number of a gene encoding STK11 in a cancer test sample (e.g., a cancer sample obtained from a subject);

[0342] b) comparing the cancer test sample to a reference (e.g., a reference sample taken from a non-cancerous subject or a normal control subject), wherein a decrease in copy number indicates that the cancer will respond to treatment with a combination of an HDAC inhibitor and an immune checkpoint modulator.

[0343] In one embodiment, the STK11 mutation is a loss-of-function mutation. In one embodiment, the changed STK11 activity or expression level is determined by comparing the activity or expression level in a cancer test sample (e.g., a sample derived from a subject) and comparing it with a control (e.g., a sample derived from a healthy subject). In one embodiment, the changed STK11 activity level is a reduced STK11 activity level.

[0344] In one embodiment, the cancer is lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC), squamous cell lung cancer), colorectal cancer (e.g., colon adenocarcinoma, rectal adenocarcinoma), breast cancer (e.g., invasive ductal carcinoma), pancreatic cancer (e.g., pancreatic adenocarcinoma), endometrial cancer (e.g., endometrioid carcinoma), neuroendocrine cancer (e.g., large cell neuroendocrine carcinoma), melanoma, non-melanoma skin cancer (e.g., squamous cell carcinoma of the skin), bile duct cancer, gallbladder cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), bladder cancer (e.g., bladder urothelial carcinoma), prostate cancer (e.g., prostate adenocarcinoma), cervical cancer, endocervical cancer, or cancer of unknown primary (e.g., adenocarcinoma of unknown primary).

[0345] In one embodiment, the cancer is lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC)), colorectal cancer (e.g., colon adenocarcinoma), pancreatic cancer (e.g., pancreatic adenocarcinoma), endometrial cancer (e.g., endometrioid carcinoma), melanoma, non-melanoma skin cancer (e.g., squamous cell carcinoma of the skin), bile duct cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), cervical cancer, endocervical cancer, or cancer of unknown primary (e.g., adenocarcinoma of unknown primary).

[0346] In one embodiment, the cancer is lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC)), colorectal cancer (e.g., colon adenocarcinoma), pancreatic cancer (e.g., pancreatic adenocarcinoma), endometrial cancer (e.g., endometrioid carcinoma), melanoma, non-melanoma skin cancer (e.g., cutaneous squamous cell carcinoma), bile duct cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), or cancer of unknown primary (e.g., adenocarcinoma of unknown primary).

[0347] In one embodiment, the cancer is lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC)). In one embodiment, the cancer is lung adenocarcinoma. In one embodiment, the cancer is non-small cell lung cancer (NSCLC).

[0348] In some embodiments described herein, the cancer is colon cancer. In some embodiments described herein, the cancer is colon adenocarcinoma. In some embodiments described herein, the cancer is colorectal cancer.

[0349] Sample preparation

[0350] The method may include detecting somatic mutations, loss of heterozygosity, whole gene deletion, decreased expression, or DNA methylation in the promoter region of STK11. In some embodiments, mutations in STK11 may occur at multiple sites in cancer.

[0351] The present disclosure also provides an assay for detecting STK11 (e.g., STK11 protein and / or STK11 mRNA) levels. In one embodiment, the present disclosure provides an assay for detecting loss of STK11 protein expression (e.g., as measured by immunohistochemistry). The present disclosure also provides an assay for detecting STK11 mutations (e.g., STK11 loss-of-function mutations).

[0352] Gene mutation or expression can be analyzed from patient samples.Patient samples can be any body tissue or fluid including nucleic acid from cancer (e.g., lung cancer) in a subject.In some embodiments, sample is body fluid, such as blood (e.g., serum or plasma) bone marrow, cerebrospinal fluid, peritoneal / pleural fluid, lymph, ascites, serous fluid, sputum, tears, feces and urine.In certain embodiments, sample is a blood sample comprising circulating tumor cells or cell-free DNA.In some embodiments, sample is not a blood sample.In other embodiments, sample can be tissue, including normal tissue or tumor tissue (e.g., lung tissue).Tissue can be fresh frozen or formalin fixed, paraffin embedded (FFPE).In certain embodiments, tumor FFPE (e.g., lung tumor FFPE) sample is obtained.

[0353] Methods and reagents for obtaining, processing, and analyzing samples are known in the art.

[0354] Cells can be harvested from biological samples using standard techniques known in the art. Methods for extracting cellular DNA from fluid or tissue samples are known in the art. For example, cells can be harvested by centrifuging a cell sample and resuspending the pelleted cells. The cells can be resuspended in a buffer solution such as phosphate buffered saline (PBS). After the cell suspension is centrifuged to obtain a cell pellet, the cells can be lysed (e.g., with a detergent) to extract the DNA. After cell lysis, various proteases are used to remove proteins from the DNA. The DNA is then extracted with phenol, precipitated in alcohol, and dissolved in an aqueous solution. Alternatively, a kit such as Tissue kit (Qiagen, Chatsworth, Calif.) and Genomic DNA was extracted using a Genomic DNA purification kit (Promega).

[0355] Measurement of gene expression

[0356] In some embodiments, the altered (e.g., decreased) STK11 level is an altered (e.g., decreased) STK11 gene expression level. In some embodiments, the altered (e.g., decreased) STK11 level is an altered (e.g., decreased) STK11 mRNA level. The measurement of gene expression can be performed using any method or reagent known in the art.

[0357] Gene expression can be detected by any appropriate method, including, for example, detecting the amount of mRNA transcribed from the gene or the amount of cDNA produced by reverse transcription of mRNA transcribed from the gene, or the amount of polypeptide or protein encoded by the gene. These methods can be performed or modified on a sample-by-sample basis for high-throughput analysis. For example, using Affymetrix TM U133 microarray chip.

[0358] In some embodiments, gene expression is detected and quantified by hybridization to a probe that specifically hybridizes to an appropriate probe for that biomarker.Probes can also be attached to a solid support for use in high throughput screening assays using methods known in the art.

[0359] In some embodiments, the expression level of the gene is determined by exposing the nucleic acid sample to a probe-modified chip. The extracted nucleic acid is labeled, for example, with a fluorescent tag, preferably during the amplification step.

[0360] Hybridization of the labeled samples is performed at an appropriate level of stringency. The extent of probe-nucleic acid hybridization is quantitatively measured using a detection device.

[0361] Alternatively, any one of gene copy number, transcription or translation can be determined using known techniques. For example, amplification methods such as PCR may be useful. The general procedure of PCR is taught in MacPherson et al., PCR: A Practical Approach, (IRL Press at Oxford University Press (1991)). However, the PCR conditions for each application reaction are determined empirically. Many parameters can affect the success of the reaction. Among them are annealing temperature and time, extension time, Mg 2+ and / or ATP concentration, pH and the relative concentrations of primers, templates and deoxyribonucleotides. After amplification, the resulting DNA fragments can be detected by agarose gel electrophoresis, followed by visualization with ethidium bromide staining and ultraviolet irradiation. In some embodiments, hybridized nucleic acids are detected by detecting one or more labels attached to the sample nucleic acid. The label can be incorporated by any of a variety of methods well known to those skilled in the art. However, in some embodiments, labels are incorporated simultaneously during the amplification step in the sample nucleic acid preparation. Therefore, for example, a polymerase chain reaction (PCR) using labeled primers or labeled nucleotides will provide labeled amplification products. In a separate embodiment, as described above, a label is incorporated into the transcribed nucleic acid using transcriptional amplification of labeled nucleotides (eg, fluorescein-labeled UTP and / or CTP).

[0362] Alternatively, the label can be added directly to the original nucleic acid sample (e.g., mRNA, polyA, mRNA, cDNA, etc.) or added to the amplification product after amplification is completed. Means for attaching labels to nucleic acids are well known to those skilled in the art and include, for example, nick translation or end labeling (e.g., with labeled RNA) by the action of nucleic acid kinases and subsequent attachment of nucleic acid linkers that connect the sample nucleic acid to the label (e.g., fluorophore).

[0363] In one example, gene expression can be measured by in situ hybridization protocols that can detect RNA molecules on slides containing tissue sections or cells (e.g., by ).

[0364] Detectable labels suitable for use in the methods disclosed herein include any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means. Useful labels include biotin for staining with labeled streptavidin conjugates, magnetic beads (e.g., Dynabeads TM ), fluorescent dyes (e.g., fluorescein, Texas Red, rhodamine, green fluorescent protein, etc.), radioactive labels (e.g., 3 H. 125 I. 35 S.14 C or 32 P), enzymes (e.g., horseradish peroxidase, alkaline phosphatase, and other enzymes commonly used in ELISA), and calorimetric labels such as colloidal gold or colored glass or plastic (e.g., polystyrene, polypropylene, latex, etc.) beads.

[0365] The detection of labeling is well known to those skilled in the art. Therefore, for example, radioactive labels can be detected using photographic film or scintillation counters, and fluorescent markers can be detected using photodetectors to detect emitted light. Enzyme labels are usually detected by providing a substrate to the enzyme and detecting the reaction product produced by the action of the enzyme on the substrate, and calorimetric labels are detected by simply visualizing colored labels. Detectable labels can be added to the target (sample) nucleic acid before or after hybridization, such as described in WO 97 / 10365. These detectable labels are directly attached or incorporated into the target (sample) nucleic acid before hybridization. On the contrary, "indirect labeling" is connected with a hybrid duplex after hybridization. Generally, indirect labeling is attached to a binding portion that has been attached to the target nucleic acid before hybridization. For example, the target nucleic acid can be biotinylated before hybridization. After hybridization, the fluorophore conjugated with avidin will be combined with the hybrid duplex with biotin, thereby providing a label that is easy to detect. For a detailed review of methods for labeling nucleic acids and detecting labeled hybrid nucleic acids, see Laboratory Techniques in Biochemistry and Molecular Biology, Vol. 24: Hybridization with Nucleic Acid Probes, ed. P. Tijssen, Elsevier, NY (1993).

[0366] In some embodiments, detecting altered (eg, decreased) STK11 levels is performed by quantitative reverse transcriptase (RT)-polymerase chain reaction (PCR), RNA-Seq, or microarray.

[0367] Detection of peptides

[0368] STK11 protein levels can be determined by examining protein expression or protein product. Determining protein levels involves measuring the amount of any immunospecific binding that occurs between antibodies that selectively recognize and bind to a polypeptide of a biomarker in a sample obtained from a subject and comparing it to the amount of immunospecific binding of at least one biomarker in a control sample.

[0369] There are many techniques in the art that can be used for protein analysis. They include, but are not limited to, radioimmunoassay, ELISA (enzyme-linked immunosorbent assay), "sandwich" immunoassay, immunoradiometric assay, in situ immunoassay (using, for example, colloidal gold, enzyme or radioisotope labeling), Western blot analysis, immunoprecipitation assay, immunofluorescence assay, flow cytometry, immunohistochemistry, HPLC, mass spectrometry, confocal microscopy, enzymatic assay, surface plasmon resonance and PAGE-SDS.

[0370] In some embodiments, the detection of altered (e.g., reduced) STK11 protein levels is performed by Western blotting. In some embodiments, the detection of altered (e.g., reduced) STK11 protein levels is performed by fluorescence activated cell sorting (FACS). In some embodiments, the detection of altered (e.g., reduced) STK11 protein levels is performed by immunohistochemistry.

[0371] Other detection methods

[0372] Mutations in a target of interest (eg, STK11 mutations) can be detected by methods known to those skilled in the art.

[0373] In order to detect somatic mutations, DNA extracted from tissues such as tumor tissues can be sequenced. Tumor tissues can be fresh tissues or preserved tissues (e.g., formalin-fixed tissues, such as paraffin-embedded tissues). Cell-free DNA can also be used for sequencing. Next generation sequencing (NGS) or Sanger sequencing are used to sequence the coding region of the gene of interest and sometimes adjacent regions (e.g., introns, promoters). Secondary methods such as qPCR, PCR, immunohistochemistry, Sanger sequencing, comparative genomic hybridization or PacBio systems can be used to detect or verify loss-of-function mutations or gene rearrangements.

[0374] Selected implementation

[0375] Embodiment 1. A method of treating a subject having or at risk of developing cancer, the method comprising administering to the subject an effective amount of a histone deacetylase (HDAC) inhibitor, wherein the cancer is identified as having altered STK11 activity or expression.

[0376] Embodiment 2. The method of embodiment 1, wherein the histone deacetylase inhibitor is administered in combination with one or more additional therapeutic agents.

[0377] Embodiment 3. A method as described in Embodiment 2, wherein at least one of the additional therapeutic agents is an immune checkpoint regulator.

[0378] Embodiment 4. A method for treating cancer in a subject, the method comprising administering an immune checkpoint modulator and an HDAC inhibitor to the subject, wherein the treatment modulates and / or improves the ratio of Teff cells to Treg cells in a tumor or tumor microenvironment, wherein the cancer is identified as having altered STK11 activity or expression.

[0379] Embodiment 5. A method of treating cancer in a subject, the method comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment reduces or depletes Treg cells in a tumor or tumor microenvironment, wherein the cancer is identified as having altered STK11 activity or expression.

[0380] Embodiment 6. A method of treating cancer in a subject, the method comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment induces or increases expression of cytokines that promote anti-tumor activity, wherein the cancer is identified as having altered STK11 activity or expression.

[0381] Embodiment 7. The method of embodiment 6, wherein the cytokine is selected from the group consisting of CXCL9, CXCL10 and CXCL11.

[0382] Embodiment 8. A method of treating cancer in a subject, the method comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment reduces expression of cytokines that promote Treg cell recruitment, wherein the cancer is identified as having altered STK11 activity or expression.

[0383] Embodiment 9. The method of embodiment 8, wherein the cytokine is CCL1 or CCL22.

[0384] Embodiment 10. A method of treating cancer in a subject, the method comprising administering to the subject an HDAC inhibitor, wherein the administration of the HDAC inhibitor does not reduce red blood cell or myeloid cell viability, wherein the cancer is identified as having altered STK11 activity or expression.

[0385] Embodiment 11. A method of treating cancer in a subject, wherein the cancer presents an immune escape phenotype characterized by expression of a STK11 mutant, the method comprising: administering an HDAC1,2 selective inhibitor, wherein the HDAC1,2 selective inhibitor is capable of attenuating or reversing the immune escape phenotype.

[0386] Embodiment 12. The method of embodiment 10 or 11, further comprising administering an immune checkpoint regulator.

[0387] Embodiment 13. A method of treating cancer in a subject, the method comprising administering an HDAC inhibitor to the subject, wherein an immune checkpoint modulator has been, is being, or will be administered to the subject, wherein the cancer is identified as having altered STK11 activity or expression.

[0388] Embodiment 14. A method of treating cancer in a subject, the method comprising administering to the subject an immune checkpoint modulator, wherein an HDAC inhibitor has been, is being, or will be administered to the subject, wherein the cancer is identified as having altered STK11 activity or expression.

[0389] Embodiment 15. The method of Embodiment 2, wherein the HDAC inhibitor is administered in combination with two or more additional therapeutic agents, wherein at least two of the additional therapeutic agents are immune checkpoint modulators.

[0390] Embodiment 16. A method as described in any of Embodiments 3-15, wherein each immune checkpoint modulator is independently a checkpoint inhibitor, a T cell co-stimulatory receptor agonist, or a dendritic cell co-stimulatory receptor agonist.

[0391] Embodiment 17. A method as described in any of Embodiments 3-16, wherein at least one immune checkpoint regulator is independently a T cell co-stimulatory receptor agonist or a dendritic cell co-stimulatory receptor agonist.

[0392] Embodiment 18. The method of any one of Embodiments 3-16, wherein at least one immune checkpoint modulator is a checkpoint inhibitor.

[0393] Embodiment 19. A method as described in Embodiment 18, wherein each check point inhibitor is independently selected from anti-CTLA-4 agents, anti-PD-1 agents, anti-PD-L1 agents, anti-4-1BB agents, anti-OX-40 agents, anti-GITR agents, anti-CD27 agents, anti-CD28 agents, anti-CD40 agents, anti-LAG3 agents, anti-ICOS agents, anti-TWEAKR agents, anti-HVEM agents, anti-TIM-1 agents, anti-TIM-3 agents, anti-VISTA agents and anti-TIGIT agents.

[0394] Embodiment 20. The method of embodiment 18, wherein each checkpoint inhibitor is independently selected from an anti-CTLA-4 agent, an anti-PD-1 agent, and an anti-PD-L1 agent.

[0395] Embodiment 21. A method as described in Embodiment 18, wherein each check point inhibitor is independently selected from an anti-PD1 agent and an anti-PD-L1 agent.

[0396] Embodiment 22. A method as described in Embodiment 18, wherein the checkpoint inhibitor is an anti-PD1 agent.

[0397] Embodiment 23. A method as described in Embodiment 18, wherein the checkpoint inhibitor is an anti-PD-L1 agent.

[0398] Embodiment 24. The method of embodiment 2, wherein the HDAC inhibitor is administered in combination with an anti-CTLA-4 agent and an anti-PD-1 agent or an anti-PD-L1 agent.

[0399] Embodiment 25. The method of any one of Embodiments 18-22, wherein each immune checkpoint inhibitor is independently an antibody.

[0400] Embodiment 26. A method as described in Embodiment 25, wherein each of the check point inhibitors is independently selected from anti-CTLA-4 antibodies, anti-PD-1 antibodies, anti-PD-L1 antibodies, anti-4-1BB antibodies, anti-OX-40 antibodies, anti-GITR antibodies, anti-CD27 antibodies, anti-CD28 antibodies, anti-CD40 antibodies, anti-LAG3 antibodies, anti-ICOS antibodies, anti-TWEAKR antibodies, anti-HVEM antibodies, anti-TIM-1 antibodies, anti-TIM-3 antibodies, anti-VISTA antibodies and anti-TIGIT antibodies.

[0401] Embodiment 27. The method of embodiment 25, wherein each checkpoint inhibitor is independently selected from an anti-CTLA-4 antibody, an anti-PD-1 antibody, and an anti-PD-L1 antibody.

[0402] Embodiment 28. The method of embodiment 25, wherein each immune checkpoint inhibitor is independently selected from nivolumab; CT-011; AMP-224; pembrolizumab; pidilizumab; cemiplizumab; dostalimumab; palolizumab; spartalizumab; carrelizumab; santolizumab, sintilimab; tislelizumab; toripalimab; rivalimab; MEDI0680; bruglimab; gelolimab, BMS936559; durvalumab; avelumab; envolimab; coxilimab; sugemalimab; AUNP-12; atezolizumab and CA-170.

[0403] Embodiment 29. A method as described in Embodiment 25, wherein each checkpoint inhibitor is independently selected from an anti-PD1 antibody and an anti-PD-L1 antibody.

[0404] Embodiment 30. A method as described in Embodiment 25, wherein the checkpoint inhibitor is an anti-PD1 antibody.

[0405] Embodiment 31. A method as described in Embodiment 25, wherein the checkpoint inhibitor is an anti-PD1-L1 antibody.

[0406] Embodiment 32. The method of embodiment 26 or 27, wherein the anti-CTLA-4 antibody is ipilimumab.

[0407] Embodiment 33. The method of any one of Embodiments 26, 27, 29, and 30, wherein the anti-PD-1 antibody is pembrolizumab or nivolumab.

[0408] Embodiment 34. The method of any one of Embodiments 26, 27, 29, and 30, wherein the anti-PD-1 antibody is pembrolizumab.

[0409] Embodiment 35. The method of any one of Embodiments 26, 27, 29, and 30, wherein the anti-PD-1 antibody is nivolumab.

[0410] Embodiment 36. The method of any one of embodiments 26, 27, 29 and 31, wherein the anti-PD-L1 antibody is atezolizumab (CAS No. 1380723-44-3), avelumab (CAS No. 1537032-82-8) or durvalumab (CAS No. 1428935-60-7).

[0411] Embodiment 37. A method as described in any of Embodiments 3-15, wherein the immune checkpoint regulator is a T cell co-stimulatory receptor agonist or a dendritic cell co-stimulatory receptor agonist.

[0412] Embodiment 38. The method of any one of Embodiments 2-37, wherein at least one additional therapeutic agent is a targeting agent.

[0413] Embodiment 39. A method as described in Embodiment 38, wherein each targeting agent is independently selected from anti-angiogenic agents (e.g., anti-VEGF agents), KRAS inhibitors, ALK inhibitors, ROS1 inhibitors, BRAF inhibitors, RET inhibitors, MEK inhibitors, MET inhibitors and TRK inhibitors.

[0414] Embodiment 40. The method of embodiment 38, wherein each targeting agent is independently selected from bevacizumab, ramucirumab, sotolacib, crizotinib, ceritinib, alectinib, brigatinib, lorlatinib, entrectinib, dabrafenib, trametinib, capmatinib, tepotinib and larotrectinib.

[0415] Embodiment 41. The method of any one of Embodiments 2-40, wherein at least one additional therapeutic agent is a chemotherapeutic agent.

[0416] Embodiment 42. The method of embodiment 41, wherein each chemotherapeutic agent is independently selected from cisplatin, carboplatin, paclitaxel, nab-paclitaxel (nab-paclitaxel), docetaxel, gemcitabine, vinorelbine, etoposide and pemetrexed.

[0417] Embodiment 43. The method of embodiment 41, wherein at least one chemotherapeutic agent is a platinum-containing therapeutic agent.

[0418] Embodiment 44. The method of embodiment 41, wherein one chemotherapeutic agent is a platinum-containing chemotherapeutic agent (eg, cisplatin) and the second chemotherapeutic agent is pemetrexed.

[0419] Embodiment 45. The method of any one of Embodiments 2-44, wherein at least one additional therapeutic agent is radiation.

[0420] Embodiment 46. The method of any one of Embodiments 1-45, wherein the cancer is resistant to anti-PD1 therapy or anti-PD-L1 therapy.

[0421] Embodiment 47. A method as described in Embodiment 46, wherein the cancer is intrinsically resistant to anti-PD1 therapy or anti-PD-L1 therapy.

[0422] Embodiment 48. A method as described in Embodiment 46, wherein the cancer has acquired resistance to anti-PD1 therapy or anti-PD-L1 therapy.

[0423] Embodiment 49. The method of any one of Embodiments 1-48, wherein the cancer is resistant to chemotherapy (e.g., platinum-containing chemotherapy).

[0424] Embodiment 50. The method of Embodiment 49, wherein the cancer is intrinsically resistant to chemotherapy (e.g., platinum-containing chemotherapy).

[0425] Embodiment 51. The method of Embodiment 49, wherein the cancer has acquired resistance to chemotherapy (e.g., platinum-containing chemotherapy).

[0426] Embodiment 52. The method of any one of Embodiments 1-51, wherein the cancer is unresponsive to or does not benefit from treatment with an immune checkpoint modulator when administered alone or as part of a treatment regimen that does not include an HDAC inhibitor.

[0427] Embodiment 53. A method as described in any of embodiments 1-51, wherein the cancer is selected from: lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC), squamous cell lung cancer), colorectal cancer (e.g., colon adenocarcinoma, rectal adenocarcinoma), breast cancer (e.g., invasive ductal carcinoma), pancreatic cancer (e.g., pancreatic adenocarcinoma), endometrial cancer (e.g., endometrioid carcinoma), neuroendocrine cancer (e.g., large cell neuroendocrine carcinoma), melanoma, non-melanoma skin cancer (e.g., squamous cell carcinoma of the skin), bile duct cancer, gallbladder cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), bladder cancer (e.g., bladder urothelial carcinoma), prostate cancer (e.g., prostate adenocarcinoma), cervical cancer, endocervical cancer, or cancer of unknown primary (e.g., adenocarcinoma of unknown primary).

[0428] Embodiment 54. The method of embodiment 52, wherein the cancer is lung cancer.

[0429] Embodiment 55. The method of embodiment 54, wherein the cancer is lung adenocarcinoma.

[0430] Embodiment 56. The method of Embodiment 54, wherein the cancer is non-small cell lung cancer (NSCLC).

[0431] Embodiment 57. The method of Embodiment 56, wherein the cancer is non-squamous non-small cell lung cancer (NSCLC).

[0432] Embodiment 58. The method of embodiment 52, wherein the cancer is colorectal cancer or colon adenocarcinoma.

[0433] Embodiment 59. The method of any one of Embodiments 1-58, wherein the cancer is identified as having a STK11 mutation and one or more additional mutations.

[0434] Embodiment 60. The method of embodiment 59, wherein the additional mutation is selected from a KRAS mutation and a KEAP1 mutation.

[0435] Embodiment 61. The method of Embodiment 59, wherein the additional mutation is a KRAS mutation.

[0436] Embodiment 62. A method as described in Embodiment 61, wherein the KRAS mutation is a mutation at position G12, optionally wherein the KRAS mutation is selected from a G12D mutation, a G12C mutation, a G12V mutation, or a combination thereof.

[0437] Embodiment 63. The method of embodiment 59, wherein the additional mutation is a KEAP1 mutation.

[0438] Embodiment 64. The method of embodiment 59, wherein the additional mutations are KRAS mutations and KEAP1 mutations.

[0439] Embodiment 65. The method of any one of Embodiments 1-64, wherein the cancer is free of EGFR mutations.

[0440] Embodiment 66. The method of any one of Embodiments 1-65, wherein the cancer has increased or decreased expression of STK11.

[0441] Embodiment 67. A method as described in Embodiment 66, wherein the increased or decreased STK expression is assessed by determining the copy number of the gene encoding STK11 relative to a control sample, wherein an increase in the copy number indicates an increased expression level and a decrease in the copy number indicates a decreased expression level.

[0442] Embodiment 68. The method of embodiment 66, wherein the increased or decreased STK expression is assessed by determining the level of STK11 protein or mRNA relative to a control sample.

[0443] Embodiment 69. The method of Embodiment 67 or 68, wherein the cancer has reduced expression of STK11.

[0444] Embodiment 70. The method of any one of Embodiments 1-65, wherein the cancer has a STK11 mutation.

[0445] Embodiment 71. The method of embodiment 70, wherein the STK11 mutation is a mutation selected from the group consisting of:

[0446] (i) mutations in the nucleotide sequence encoding STK11;

[0447] (ii) mutations in regulatory sequences that control the expression of the nucleotide sequence encoding STK11;

[0448] (iii) A mutation in a nucleotide encoding a protein that interacts with the transcription product of the STK11 gene.

[0449] Embodiment 72. The method of embodiment 70, wherein the STK11 mutation is a mutation in the translation product of the STK11 gene.

[0450] Embodiment 73. The method of embodiment 70, wherein the STK11 mutation is a mutation in the transcription product of the STK11 gene.

[0451] Embodiment 74. The method of any one of Embodiments 70-73, wherein the STK11 mutation is an inactivating (loss-of-function) mutation.

[0452] Embodiment 75. The method of any one of Embodiments 66-69, wherein the increased or decreased STK11 expression is determined in a sample derived from the subject.

[0453] Embodiment 76. The method of embodiment 75, wherein the increased or decreased STK11 expression is determined relative to a control.

[0454] Embodiment 77. A method as described in Embodiment 76, wherein the control is healthy tissue, preferably the same tissue type as the cancerous tissue.

[0455] Embodiment 78. The method of any one of Embodiments 70-74, wherein the STK11 mutation is identified in a sample derived from the subject.

[0456] Embodiment 79. The method of Embodiment 78, wherein the STK11 mutation is identified in a tumor sample derived from the subject.

[0457] Embodiment 80. The method of Embodiment 78, wherein the STK11 mutation is not identified in a healthy tissue sample derived from the subject.

[0458] Embodiment 81. The method of any one of Embodiments 1-80, wherein the STK11 mutation is not a germline mutation.

[0459] Embodiment 82. The method of any one of Embodiments 2-81, wherein the HDAC inhibitor is administered concurrently with the additional therapeutic agent.

[0460] Embodiment 83. The method of any one of Embodiments 2-81, wherein the HDAC inhibitor and the additional therapeutic agent are administered separately.

[0461] Embodiment 84. The method of any one of Embodiments 2-81, wherein the HDAC inhibitor and the additional therapeutic agent are administered sequentially.

[0462] Embodiment 85. The method of any one of Embodiments 2-81, wherein the HDAC inhibitor is administered prior to the additional therapeutic agent.

[0463] Embodiment 86. The method of any one of Embodiments 2-81, wherein the HDAC inhibitor is administered after the additional therapeutic agent.

[0464] Embodiment 87. The method of any one of Embodiments 2-81, comprising administering an immune checkpoint modulator to the subject followed by administering an HDAC inhibitor to the subject.

[0465] Embodiment 88. The method of any one of Embodiments 2-81, comprising administering to the subject an HDAC inhibitor followed by administering to the subject an immune checkpoint modulator.

[0466] Embodiment 89. The method of any one of Embodiments 2-81, comprising administering an immune checkpoint modulator to the subject, followed by administering a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof to the subject, followed by administering an HDAC inhibitor to the subject.

[0467] Embodiment 90. The method of any one of Embodiments 2-81, comprising administering to the subject an immune checkpoint modulator, followed by administering to the subject an HDAC inhibitor, followed by administering to the subject a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof.

[0468] Embodiment 91. The method of any one of Embodiments 2-81, comprising administering an HDAC inhibitor to the subject, followed by administering a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof to the subject, followed by administering an immune checkpoint modulator to the subject.

[0469] Embodiment 92. The method of any one of Embodiments 2-81, comprising administering to the subject an HDAC inhibitor, followed by administering to the subject an immune checkpoint modulator, followed by administering to the subject a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof.

[0470] Embodiment 93. The method of any one of Embodiments 2-81, comprising administering to the subject a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof, followed by administering to the subject an immune checkpoint modulator, followed by administering to the subject an HDAC inhibitor.

[0471] Embodiment 94. The method of any one of Embodiments 2-81, comprising administering to the subject a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof, followed by administering to the subject an HDAC inhibitor, followed by administering to the subject an immune checkpoint modulator.

[0472] Embodiment 95. The method of any one of Embodiments 1-94, wherein the subject has a cancer identified as having altered STK11 activity or expression.

[0473] Embodiment 96. The method of any one of embodiments 1-95, wherein the histone deacetylase inhibitor is a selective inhibitor of histone deacetylase 1 (HDAC1 selective inhibitor).

[0474] Embodiment 97. The method of any one of embodiments 1-95, wherein the histone deacetylase inhibitor is a selective inhibitor of histone deacetylase 1 and histone deacetylase 2 (HDAC1,2 selective inhibitor).

[0475] Embodiment 98. The method of any one of embodiments 1-95, wherein the histone deacetylase inhibitor is a selective HDAC class I inhibitor.

[0476] Embodiment 99. The method of any one of Embodiments 1-95, wherein the histone deacetylase inhibitor is a CoREST selective deacetylase inhibitor.

[0477] Embodiment 100. A method of selecting a subject for treatment with an HDAC inhibitor, the method comprising: identifying a subject having a cancer characterized by the presence of cells having altered STK11 activity or expression; and selecting the subject thus identified for treatment with the HDAC inhibitor.

[0478] Embodiment 101. A method of selecting a subject for treatment with a combination of an HDAC inhibitor and one or more additional therapeutic agents, the method comprising: identifying a subject having a cancer characterized by the presence of cells with altered STK11 activity or expression; and selecting the subject thus identified for treatment with the HDAC inhibitor and the one or more additional therapeutic agents.

[0479] Embodiment 102. The method of Embodiment 101, wherein at least one of the additional therapeutic agents is an immune checkpoint modulator.

[0480] Embodiment 103. A method of selecting a subject for treatment with a combination of an HDAC inhibitor and two or more additional therapeutic agents, the method comprising: identifying a subject having a cancer characterized by the presence of cells with altered STK11 activity or expression; and selecting the subject thus identified for treatment with an HDAC inhibitor and two or more additional therapeutic agents, wherein at least two of the additional therapeutic agents are immune checkpoint modulators.

[0481] Embodiment 104. A method for selecting a subject for treatment with a combination of an HDAC inhibitor, an immune checkpoint modulator, and one or more additional therapeutic agents selected from chemotherapeutic agents, targeted agents, and radiation therapy, the method comprising: identifying a subject who has previously been treated with a combination of an immune checkpoint modulator and one or more additional therapeutic agents selected from chemotherapeutic agents, targeted agents, and radiation therapy, wherein treatment with the combination of the immune checkpoint modulator and the additional therapeutic agent did not provide any additional benefit compared to treatment with the additional therapeutic agent alone; and selecting the subject thus identified for treatment.

[0482] Embodiment 105. The method of embodiment 104, wherein the method further comprises: identifying a subject having a cancer characterized by the presence of cells having reduced STK11 activity or expression; and selecting the subject thus identified for treatment.

[0483] Embodiment 106. A method as described in embodiments 102-105, wherein each immune checkpoint regulator is independently a checkpoint inhibitor, a T cell co-stimulatory receptor agonist, or a dendritic cell co-stimulatory receptor agonist.

[0484] Embodiment 107. The method of any one of Embodiments 102-106, wherein at least one immune checkpoint regulator is independently a T cell co-stimulatory receptor agonist or a dendritic cell co-stimulatory receptor agonist.

[0485] Embodiment 108. The method of any one of Embodiments 102-107, wherein at least one immune checkpoint modulator is a checkpoint inhibitor.

[0486] Embodiment 109. A method as described in Embodiment 108, wherein each check point inhibitor is independently selected from an anti-CTLA-4 agent, an anti-PD-1 agent, an anti-PD-L1 agent, an anti-4-1BB agent, an anti-OX-40 agent, an anti-GITR agent, an anti-CD27 agent, an anti-CD28 agent, an anti-CD40 agent, an anti-LAG3 agent, an anti-ICOS agent, an anti-TWEAKR agent, an anti-HVEM agent, an anti-TIM-1 agent, an anti-TIM-3 agent, an anti-VISTA agent, and an anti-TIGIT agent.

[0487] Embodiment 110. The method of embodiment 108, wherein each check point inhibitor is independently selected from an anti-CTLA-4 agent, an anti-PD-1 agent, and an anti-PD-L1 agent.

[0488] Embodiment 111. The method of Embodiment 108, wherein each check point inhibitor is independently selected from an anti-PD1 agent and an anti-PD-L1 agent.

[0489] Embodiment 112. A method as described in Embodiment 108, wherein the checkpoint inhibitor is an anti-PD1 agent.

[0490] Embodiment 113. A method as described in Embodiment 108, wherein the check point inhibitor is an anti-PD-L1 agent.

[0491] Embodiment 114. The method of Embodiment 103, wherein the HDAC inhibitor is administered in combination with an anti-CTLA-4 agent and an anti-PD-1 agent or an anti-PD-L1 agent.

[0492] Embodiment 115. The method of any one of Embodiments 108-114, wherein each immune checkpoint inhibitor is independently an antibody.

[0493] Embodiment 116. A method as described in Embodiment 115, wherein each of the check point inhibitors is independently selected from anti-CTLA-4 antibodies, anti-PD-1 antibodies, anti-PD-L1 antibodies, anti-4-1BB antibodies, anti-OX-40 antibodies, anti-GITR antibodies, anti-CD27 antibodies, anti-CD28 antibodies, anti-CD40 antibodies, anti-LAG3 antibodies, anti-ICOS antibodies, anti-TWEAKR antibodies, anti-HVEM antibodies, anti-TIM-1 antibodies, anti-TIM-3 antibodies, anti-VISTA antibodies and anti-TIGIT antibodies.

[0494] Embodiment 117. The method of embodiment 115, wherein each checkpoint inhibitor is independently selected from an anti-CTLA-4 antibody, an anti-PD-1 antibody, and an anti-PD-L1 antibody.

[0495] Embodiment 118. The method of embodiment 115, wherein each immune checkpoint inhibitor is independently selected from nivolumab; CT-011; AMP-224; pembrolizumab; pidilizumab; cemiplizumab; dostalimumab; palolizumab; spartalizumab; carrelizumab; sazanalizumab, sintilimab; tislelizumab; toripalizumab; rivalizumab; MEDI0680; bruglimumab and gelotrimazole.

[0496] Embodiment 119. The method of embodiment 115, wherein each check point inhibitor is independently selected from an anti-PD1 antibody and an anti-PD-L1 antibody.

[0497] Embodiment 120. A method as described in Embodiment 115, wherein the checkpoint inhibitor is an anti-PD1 antibody.

[0498] Embodiment 121. A method as described in Embodiment 115, wherein the checkpoint inhibitor is an anti-PD1-L1 antibody.

[0499] Embodiment 122. The method of embodiment 116 or 117, wherein the anti-CTLA-4 antibody is ipilimumab.

[0500] Embodiment 123. The method of any one of Embodiments 116, 117, 119, and 120, wherein the anti-PD-1 antibody is pembrolizumab or nivolumab.

[0501] Embodiment 124. The method of any one of Embodiments 116, 117, 119, and 120, wherein the anti-PD-1 antibody is pembrolizumab.

[0502] Embodiment 125. The method of any one of Embodiments 116, 117, 119, and 120, wherein the anti-PD-1 antibody is nivolumab.

[0503] Embodiment 126. The method of any one of Embodiments 116, 117, 119 and 121, wherein the anti-PD-L1 antibody is atezolizumab (CAS No. 1380723-44-3), avelumab (CAS No. 1537032-82-8) or durvalumab (CAS No. 1428935-60-7).

[0504] Embodiment 127. A method as described in Embodiment 102, wherein the immune checkpoint regulator is a T cell co-stimulatory receptor agonist or a dendritic cell co-stimulatory receptor agonist.

[0505] Embodiment 128. The method of any one of Embodiments 101-127, wherein at least one additional therapeutic agent is a targeting agent.

[0506] Embodiment 129. A method as described in Embodiment 128, wherein each targeting agent is independently selected from anti-angiogenic agents (e.g., anti-VEGF agents), KRAS inhibitors, ALK inhibitors, ROS1 inhibitors, BRAF inhibitors, RET inhibitors, MEK inhibitors, MET inhibitors and TRK inhibitors.

[0507] Embodiment 130. The method of embodiment 128, wherein each targeting agent is independently selected from bevacizumab, ramucirumab, sotoracib, crizotinib, ceritinib, alectinib, brigatinib, lorlatinib, entrectinib, dabrafenib, trametinib, capmatinib, tepotinib and larotrectinib.

[0508] Embodiment 131. The method of any one of Embodiments 101-130, wherein at least one additional therapeutic agent is a chemotherapeutic agent.

[0509] Embodiment 132. The method of embodiment 131, wherein each chemotherapeutic agent is independently selected from cisplatin, carboplatin, paclitaxel, nab-paclitaxel (nab-paclitaxel), docetaxel, gemcitabine, vinorelbine, etoposide, and pemetrexed.

[0510] Embodiment 133. The method of embodiment 131, wherein at least one chemotherapeutic agent is a platinum-containing therapeutic agent.

[0511] Embodiment 134. The method of embodiment 131, wherein one chemotherapeutic agent is a platinum-containing chemotherapeutic agent (eg, cisplatin) and the second chemotherapeutic agent is pemetrexed.

[0512] Embodiment 135. The method of any one of Embodiments 101-134, wherein at least one additional therapeutic agent is radiation.

[0513] Embodiment 136. The method of any one of Embodiments 100-135, wherein the cancer is resistant to anti-PD1 therapy or anti-PD-L1 therapy.

[0514] Embodiment 137. A method as described in Embodiment 136, wherein the cancer is intrinsically resistant to anti-PD1 therapy or anti-PD-L1 therapy.

[0515] Embodiment 138. The method of Embodiment 136, wherein the cancer has acquired resistance to anti-PD1 therapy or anti-PD-L1 therapy.

[0516] Embodiment 139. The method of any one of Embodiments 100-138, wherein the cancer is resistant to chemotherapy (e.g., platinum-containing chemotherapy).

[0517] Embodiment 140. The method of Embodiment 139, wherein the cancer is intrinsically resistant to chemotherapy (e.g., platinum-containing chemotherapy).

[0518] Embodiment 141. The method of Embodiment 140, wherein the cancer has acquired resistance to chemotherapy (e.g., platinum-containing chemotherapy).

[0519] Embodiment 142. The method of any one of Embodiments 100-141, wherein the cancer is unresponsive to or does not benefit from treatment with an immune checkpoint modulator when administered alone or as part of a treatment regimen that does not include an HDAC inhibitor.

[0520] Embodiment 143. A method as described in any of Embodiments 100-142, wherein the cancer is selected from: lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC), squamous cell lung cancer), colorectal cancer (e.g., colon adenocarcinoma, rectal adenocarcinoma), breast cancer (e.g., invasive ductal carcinoma), pancreatic cancer (e.g., pancreatic adenocarcinoma), endometrial cancer (e.g., endometrioid carcinoma), neuroendocrine cancer (e.g., large cell neuroendocrine carcinoma), melanoma, non-melanoma skin cancer (e.g., squamous cell carcinoma of the skin), bile duct cancer, gallbladder cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), bladder cancer (e.g., bladder urothelial carcinoma), prostate cancer (e.g., prostate adenocarcinoma), cervical cancer, endocervical cancer, or cancer of unknown primary (e.g., adenocarcinoma of unknown primary).

[0521] Embodiment 144. The method of embodiment 142, wherein the cancer is lung cancer.

[0522] Embodiment 145. The method of embodiment 144, wherein the cancer is lung adenocarcinoma.

[0523] Embodiment 146. The method of Embodiment 144, wherein the cancer is non-small cell lung cancer (NSCLC).

[0524] Embodiment 147. The method of Embodiment 146, wherein the cancer is non-squamous non-small cell lung cancer (NSCLC).

[0525] Embodiment 148. The method of any one of Embodiments 100-147, wherein the cancer is identified as having a STK11 mutation and one or more additional mutations.

[0526] Embodiment 149. The method of embodiment 148, wherein the additional mutation is selected from a KRAS mutation and a KEAP1 mutation.

[0527] Embodiment 150. The method of Embodiment 148, wherein the additional mutation is a KRAS mutation.

[0528] Embodiment 151. A method as described in Embodiment 150, wherein the KRAS mutation is a mutation at position G12, optionally wherein the KRAS mutation is selected from a G12D mutation, a G12C mutation, a G12V mutation, or a combination thereof.

[0529] Embodiment 152. The method of Embodiment 148, wherein the additional mutation is a KEAP1 mutation.

[0530] Embodiment 153. The method of Embodiment 148, wherein the additional mutations are KRAS mutations and KEAP1 mutations.

[0531] Embodiment 154. The method of any one of Embodiments 100-153, wherein the cancer is free of EGFR mutations.

[0532] Embodiment 155. The method of any one of Embodiments 100-154, wherein the cancer has increased or decreased expression of STK11.

[0533] Embodiment 156. A method as described in Embodiment 155, wherein the increased or decreased STK expression is assessed by determining the copy number of the gene encoding STK11 relative to a control sample, wherein an increase in the copy number indicates an increased expression level and a decrease in the copy number indicates a decreased expression level.

[0534] Embodiment 157. The method of embodiment 155, wherein the increased or decreased STK expression is assessed by determining the level of STK11 protein or mRNA relative to a control sample.

[0535] Embodiment 158. The method of Embodiments 155 to 157, wherein the cancer has reduced expression of STK11.

[0536] Embodiment 159. The method of any one of Embodiments 100-154, wherein the cancer has a STK11 mutation.

[0537] Embodiment 160. The method of embodiment 159, wherein the STK11 mutation is a mutation selected from the group consisting of:

[0538] (i) mutations in the nucleotide sequence encoding STK11;

[0539] (ii) mutations in regulatory sequences that control the expression of the nucleotide sequence encoding STK11;

[0540] (iii) A mutation in a nucleotide encoding a protein that interacts with the transcription product of the STK11 gene.

[0541] Embodiment 161. The method of embodiment 159, wherein the STK11 mutation is a mutation in the translation product of the STK11 gene.

[0542] Embodiment 162. The method of embodiment 159, wherein the STK11 mutation is a mutation in the transcription product of the STK11 gene.

[0543] Embodiment 163. The method of any one of Embodiments 159-161, wherein the STK11 mutation is an inactivating (loss-of-function) mutation.

[0544] Embodiment 164. The method of any one of Embodiments 155-158, wherein the increased or decreased STK11 expression is determined in a sample derived from the subject.

[0545] Embodiment 165. The method of Embodiment 164, wherein the increased or decreased STK11 expression is determined relative to a control.

[0546] Embodiment 166. A method as described in Embodiment 165, wherein the control is healthy tissue, preferably the same tissue type as the cancerous tissue.

[0547] Embodiment 167. The method of any one of Embodiments 159-163, wherein the STK11 mutation is identified in a sample derived from the subject.

[0548] Embodiment 168. The method of Embodiment 167, wherein the STK11 mutation is identified in a tumor sample derived from the subject.

[0549] Embodiment 169. The method of Embodiment 167, wherein the STK11 mutation is not identified in a healthy tissue sample derived from the subject.

[0550] Embodiment 170. The method of any one of Embodiments 100-169, wherein the STK11 mutation is not a germline mutation.

[0551] Embodiment 171. A method of treating cancer in a subject, the method comprising administering to the subject a combination of an HDAC inhibitor and an immune checkpoint modulator, wherein the subject has been selected for treatment using a method according to any one of Embodiments 100-170.

[0552] Embodiment 172. A method of treating cancer in a subject, the method comprising administering an HDAC inhibitor to the subject, wherein an immune checkpoint modulator has been, is being, or will be administered to the subject, wherein the subject has been selected for treatment using a method according to any one of Embodiments 100-170.

[0553] Embodiment 173. A method of treating cancer in a subject, the method comprising administering an immune checkpoint modulator to the subject, wherein an HDAC inhibitor has been, is being, or will be administered to the subject, wherein the subject has been selected for treatment using a method according to any one of Embodiments 100-170.

[0554] Embodiment 174. The method of any one of embodiments 100-173, wherein the histone deacetylase inhibitor is a selective inhibitor of histone deacetylase 1 (HDAC1 selective inhibitor).

[0555] Embodiment 175. The method of any one of embodiments 100-173, wherein the histone deacetylase inhibitor is a selective inhibitor of histone deacetylase 1 and histone deacetylase 2 (HDAC1,2 selective inhibitor).

[0556] Embodiment 176. The method of any one of Embodiments 100-173, wherein the histone deacetylase inhibitor is a selective HDAC class I inhibitor.

[0557] Embodiment 177. The method of any one of Embodiments 100-173, wherein the histone deacetylase inhibitor is a CoREST selective deacetylase inhibitor.

[0558] Embodiment 178. An HDAC inhibitor for use in a method of treating a subject having or at risk of developing cancer, the method comprising administering to the subject an effective amount of a histone deacetylase (HDAC) inhibitor, wherein the cancer is identified as having altered STK11 activity or expression.

[0559] Embodiment 179. An HDAC inhibitor for use as described in embodiment 178, wherein the histone deacetylase inhibitor is administered in combination with one or more additional therapeutic agents.

[0560] Embodiment 180. An HDAC inhibitor for use as described in Embodiment 179, wherein at least one of the additional therapeutic agents is an immune checkpoint modulator.

[0561] Embodiment 181. An HDAC inhibitor for use in a method of treating cancer in a subject, the method comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment modulates and / or improves the ratio of Teff cells to Treg cells in a tumor or tumor microenvironment, wherein the cancer is identified as having altered STK11 activity or expression.

[0562] Embodiment 182. An HDAC inhibitor for use in a method of treating cancer in a subject, the method comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment reduces or depletes Treg cells in a tumor or tumor microenvironment, wherein the cancer is identified as having altered STK11 activity or expression.

[0563] Embodiment 183. An HDAC inhibitor for use in a method of treating cancer in a subject, the method comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment induces or increases expression of cytokines that promote anti-tumor activity, wherein the cancer is identified as having altered STK11 activity or expression.

[0564] Embodiment 184. An HDAC inhibitor for use in a method as described in embodiment 183, wherein the cytokine is selected from the group consisting of CXCL9, CXCL10 and CXCL11.

[0565] Embodiment 185. An HDAC inhibitor for use in a method of treating cancer in a subject, the method comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment reduces expression of cytokines that promote Treg cell recruitment, wherein the cancer is identified as having altered STK11 activity or expression.

[0566] Embodiment 186. An HDAC inhibitor for use in a method as described in Embodiment 185, wherein the cytokine is CCL1 or CCL22.

[0567] Embodiment 187. An HDAC inhibitor for use in a method of treating cancer in a subject, the method comprising administering an HDAC inhibitor to the subject, wherein the administration of the HDAC inhibitor does not reduce red blood cell or myeloid cell viability, wherein the cancer is identified as having altered STK11 activity or expression.

[0568] Embodiment 188. An HDAC inhibitor for use in a method of treating cancer in a subject, wherein the cancer presents an immune escape phenotype characterized by expression of a STK11 mutant, the method comprising: administering an HDAC1,2 selective inhibitor, wherein the HDAC1,2 selective inhibitor is capable of attenuating or reversing the immune escape phenotype.

[0569] Embodiment 189. An HDAC inhibitor for use in a method as described in Embodiment 187 or 188, the method further comprising administering an immune checkpoint modulator.

[0570] Embodiment 190. An HDAC inhibitor for use in a method of treating cancer in a subject, the method comprising administering the HDAC inhibitor to the subject, wherein an immune checkpoint modulator has been, is being, or will be administered to the subject, wherein the cancer is identified as having altered STK11 activity or expression.

[0571] Embodiment 191. An HDAC inhibitor for use in a method of treating cancer in a subject, the method comprising administering an immune checkpoint modulator to the subject, wherein the HDAC inhibitor has been, is being, or will be administered to the subject, wherein the cancer is identified as having altered STK11 activity or expression.

[0572] Embodiment 192. An HDAC inhibitor for use as described in Embodiment 179, wherein the HDAC inhibitor is administered in combination with two or more additional therapeutic agents, wherein at least two of the additional therapeutic agents are immune checkpoint modulators.

[0573] Embodiment 193. An HDAC inhibitor for use as described in any one of Embodiments 180-192, wherein each immune checkpoint modulator is independently a checkpoint inhibitor, a T cell co-stimulatory receptor agonist, or a dendritic cell co-stimulatory receptor agonist.

[0574] Embodiment 194. An HDAC inhibitor for use as described in any one of Embodiments 180-193, wherein at least one immune checkpoint regulator is independently a T cell co-stimulatory receptor agonist or a dendritic cell co-stimulatory receptor agonist.

[0575] Embodiment 195. An HDAC inhibitor for use as described in any one of Embodiments 180-193, wherein at least one immune checkpoint modulator is a checkpoint inhibitor.

[0576] Embodiment 196. An HDAC inhibitor for use as described in Embodiment 195, wherein each checkpoint inhibitor is independently selected from an anti-CTLA-4 agent, an anti-PD-1 agent, an anti-PD-L1 agent, an anti-4-1BB agent, an anti-OX-40 agent, an anti-GITR agent, an anti-CD27 agent, an anti-CD28 agent, an anti-CD40 agent, an anti-LAG3 agent, an anti-ICOS agent, an anti-TWEAKR agent, an anti-HVEM agent, an anti-TIM-1 agent, an anti-TIM-3 agent, an anti-VISTA agent, and an anti-TIGIT agent.

[0577] Embodiment 197. An HDAC inhibitor for use as described in Embodiment 195, wherein each checkpoint inhibitor is independently selected from an anti-CTLA-4 agent, an anti-PD-1 agent, and an anti-PD-L1 agent.

[0578] Embodiment 198. An HDAC inhibitor for use as described in Embodiment 195, wherein each checkpoint inhibitor is independently selected from an anti-PD1 agent and an anti-PD-L1 agent.

[0579] Embodiment 199. An HDAC inhibitor for use as described in Embodiment 195, wherein the checkpoint inhibitor is an anti-PD1 agent.

[0580] Embodiment 200. An HDAC inhibitor for use as described in Embodiment 195, wherein the checkpoint inhibitor is an anti-PD-L1 agent.

[0581] Embodiment 201. An HDAC inhibitor for use as described in Embodiment 179, wherein the HDAC inhibitor is administered in combination with an anti-CTLA-4 agent and an anti-PD-1 agent or an anti-PD-L1 agent.

[0582] Embodiment 202. An HDAC inhibitor for use as described in any one of embodiments 195-200, wherein each immune checkpoint inhibitor is independently an antibody.

[0583] Embodiment 203. An HDAC inhibitor for use as described in Embodiment 202, wherein each of the checkpoint inhibitors is independently selected from anti-CTLA-4 antibodies, anti-PD-1 antibodies, anti-PD-L1 antibodies, anti-4-1BB antibodies, anti-OX-40 antibodies, anti-GITR antibodies, anti-CD27 antibodies, anti-CD28 antibodies, anti-CD40 antibodies, anti-LAG3 antibodies, anti-ICOS antibodies, anti-TWEAKR antibodies, anti-HVEM antibodies, anti-TIM-1 antibodies, anti-TIM-3 antibodies, anti-VISTA antibodies, and anti-TIGIT antibodies.

[0584] Embodiment 204. An HDAC inhibitor for use as described in Embodiment 202, wherein each checkpoint inhibitor is independently selected from an anti-CTLA-4 antibody, an anti-PD-1 antibody, and an anti-PD-L1 antibody.

[0585] Embodiment 205. An HDAC inhibitor for use as described in embodiment 202, wherein each immune checkpoint inhibitor is independently selected from nivolumab; CT-011; AMP-224; pembrolizumab; pidilizumab; cemiplizumab; dostalimumab; palolizumab; spartalizumab; carrelizumab; sazanalizumab, sintilimab; tislelizumab; toripalizumab; rivalizumab; MEDI0680; bruglimumab and gelotrimazole.

[0586] Embodiment 206. An HDAC inhibitor for use as described in Embodiment 202, wherein each checkpoint inhibitor is independently selected from an anti-PD1 antibody and an anti-PD-L1 antibody.

[0587] Embodiment 207. An HDAC inhibitor for use as described in Embodiment 202, wherein the checkpoint inhibitor is an anti-PD1 antibody.

[0588] Embodiment 208. An HDAC inhibitor for use as described in Embodiment 202, wherein the checkpoint inhibitor is an anti-PD1-L1 antibody.

[0589] Embodiment 209. An HDAC inhibitor for use as described in embodiment 203 or 204, wherein the anti-CTLA-4 antibody is ipilimumab.

[0590] Embodiment 210. An HDAC inhibitor for use as described in any one of Embodiments 203, 204, 206 and 207, wherein the anti-PD-1 antibody is pembrolizumab or nivolumab.

[0591] Embodiment 211. An HDAC inhibitor for use as described in any one of Embodiments 203, 204, 206 and 207, wherein the anti-PD-1 antibody is pembrolizumab.

[0592] Embodiment 212. An HDAC inhibitor for use as described in any one of Embodiments 203, 204, 206 and 207, wherein the anti-PD-1 antibody is nivolumab.

[0593] Embodiment 213. An HDAC inhibitor for use as described in any one of Embodiments 203, 204, 206 and 208, wherein the anti-PD-L1 antibody is atezolizumab (CAS No. 1380723-44-3), avelumab (CAS No. 1537032-82-8) or durvalumab (CAS No. 1428935-60-7).

[0594] Embodiment 214. An HDAC inhibitor for use as described in any one of Embodiments 180-193, wherein the immune checkpoint regulator is a T cell co-stimulatory receptor agonist or a dendritic cell co-stimulatory receptor agonist.

[0595] Embodiment 215. An HDAC inhibitor for use as described in any one of embodiments 179-214, wherein at least one additional therapeutic agent is a targeting agent.

[0596] Embodiment 216. An HDAC inhibitor for use as described in Embodiment 215, wherein each targeting agent is independently selected from anti-angiogenic agents (e.g., anti-VEGF agents), KRAS inhibitors, ALK inhibitors, ROS1 inhibitors, BRAF inhibitors, RET inhibitors, MEK inhibitors, MET inhibitors, and TRK inhibitors.

[0597] Embodiment 217. An HDAC inhibitor for use as described in Embodiment 215, wherein each targeting agent is independently selected from bevacizumab, ramucirumab, sotolacib, crizotinib, ceritinib, alectinib, brigatinib, lorlatinib, entrectinib, dabrafenib, trametinib, capmatinib, tepotinib and larotrectinib.

[0598] Embodiment 218. An HDAC inhibitor for use as described in any one of embodiments 179-217, wherein at least one additional therapeutic agent is a chemotherapeutic agent.

[0599] Embodiment 219. An HDAC inhibitor for use as described in Embodiment 218, wherein each chemotherapeutic agent is independently selected from cisplatin, carboplatin, paclitaxel, nab-paclitaxel (nab-paclitaxel), docetaxel, gemcitabine, vinorelbine, etoposide and pemetrexed.

[0600] Embodiment 220. An HDAC inhibitor for use as described in embodiment 218, wherein at least one chemotherapeutic agent is a platinum-containing therapeutic agent.

[0601] Embodiment 221. An HDAC inhibitor for use as described in Embodiment 218, wherein one chemotherapeutic agent is a platinum-containing chemotherapeutic agent (eg, cisplatin) and the second chemotherapeutic agent is pemetrexed.

[0602] Embodiment 222. An HDAC inhibitor for use as described in any one of embodiments 179-221, wherein at least one additional therapeutic agent is radiation.

[0603] Embodiment 223. An HDAC inhibitor for use as described in any one of Embodiments 178-222, wherein the cancer is resistant to anti-PD1 therapy or anti-PD-L1 therapy.

[0604] Embodiment 224. An HDAC inhibitor for use as described in Embodiment 223, wherein the cancer is intrinsically resistant to anti-PD1 therapy or anti-PD-L1 therapy.

[0605] Embodiment 225. An HDAC inhibitor for use as described in Embodiment 223, wherein the cancer has acquired resistance to anti-PD1 therapy or anti-PD-L1 therapy.

[0606] Embodiment 226. An HDAC inhibitor for use as described in any one of Embodiments 178-225, wherein the cancer is resistant to chemotherapy (eg, platinum-containing chemotherapy).

[0607] Embodiment 227. An HDAC inhibitor for use as described in Embodiment 226, wherein the cancer is intrinsically resistant to chemotherapy (eg, platinum-containing chemotherapy).

[0608] Embodiment 228. An HDAC inhibitor for use as described in Embodiment 226, wherein the cancer has acquired resistance to chemotherapy (eg, platinum-containing chemotherapy).

[0609] Embodiment 229. An HDAC inhibitor for use as described in any one of Embodiments 178-228, wherein the cancer is unresponsive to or does not benefit from treatment with an immune checkpoint modulator when administered alone or as part of a treatment regimen that does not include an HDAC inhibitor.

[0610] Embodiment 230. An HDAC inhibitor for use as described in any one of embodiments 178-229, wherein the cancer is selected from: lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC), squamous cell lung cancer), colorectal cancer (e.g., colon adenocarcinoma, rectal adenocarcinoma), breast cancer (e.g., invasive ductal carcinoma), pancreatic cancer (e.g., pancreatic adenocarcinoma), endometrial cancer (e.g., endometrioid carcinoma), neuroendocrine cancer (e.g., large cell neuroendocrine carcinoma), melanoma, non-melanoma skin cancer (e.g., squamous cell carcinoma of the skin), bile duct cancer, gallbladder cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), bladder cancer (e.g., bladder urothelial carcinoma), prostate cancer (e.g., prostate adenocarcinoma), cervical cancer, endocervical cancer, or cancer of unknown primary (e.g., adenocarcinoma of unknown primary).

[0611] Embodiment 231. An HDAC inhibitor for use as described in Embodiment 230, wherein the cancer is lung cancer.

[0612] Embodiment 232. An HDAC inhibitor for use as described in embodiment 231, wherein the cancer is lung adenocarcinoma.

[0613] Embodiment 233. An HDAC inhibitor for use as described in Embodiment 231, wherein the cancer is non-small cell lung cancer (NSCLC).

[0614] Embodiment 234. An HDAC inhibitor for use as described in Embodiment 233, wherein the cancer is non-squamous non-small cell lung cancer (NSCLC).

[0615] Embodiment 235. An HDAC inhibitor for use as described in Embodiment 230, wherein the cancer is colorectal cancer or colon adenocarcinoma.

[0616] Embodiment 236. An HDAC inhibitor for use as described in any one of embodiments 178-235, wherein the cancer is identified as having a STK11 mutation and one or more additional mutations.

[0617] Embodiment 237. An HDAC inhibitor for use as described in embodiment 236, wherein the additional mutation is selected from the group consisting of a KRAS mutation and a KEAP1 mutation.

[0618] Embodiment 238. An HDAC inhibitor for use as described in embodiment 236, wherein the additional mutation is a KRAS mutation.

[0619] Embodiment 239. An HDAC inhibitor for use as described in Embodiment 238, wherein the KRAS mutation is a mutation at position G12, optionally wherein the KRAS mutation is selected from a G12D mutation, a G12C mutation, a G12V mutation, or a combination thereof.

[0620] Embodiment 240. An HDAC inhibitor for use as described in embodiment 236, wherein the additional mutation is a KEAP1 mutation.

[0621] Embodiment 241. An HDAC inhibitor for use as described in embodiment 236, wherein the additional mutations are KRAS mutations and KEAP1 mutations.

[0622] Embodiment 242. An HDAC inhibitor for use as described in any one of embodiments 178-241, wherein the cancer does not have an EGFR mutation.

[0623] Embodiment 243. An HDAC inhibitor for use as described in any one of embodiments 178-242, wherein the cancer has increased or decreased STK11 expression.

[0624] Embodiment 244. An HDAC inhibitor for use as described in Embodiment 243, wherein the increased or decreased STK expression is assessed by determining the copy number of the gene encoding STK11 relative to a control sample, wherein an increase in the copy number indicates an increased expression level and a decrease in the copy number indicates a decreased expression level.

[0625] Embodiment 245. An HDAC inhibitor for use as described in embodiment 243, wherein the increased or decreased STK expression is assessed by determining the level of STK11 protein or mRNA relative to a control sample.

[0626] Embodiment 246. An HDAC inhibitor for use as described in any one of Embodiments 244 or 245, wherein the cancer has reduced STK11 expression.

[0627] Embodiment 247. An HDAC inhibitor for use as described in any one of embodiments 178-242, wherein the cancer has a STK11 mutation.

[0628] Embodiment 248. An HDAC inhibitor for use as described in embodiment 247, wherein the STK11 mutation is a mutation selected from the group consisting of:

[0629] (i) mutations in the nucleotide sequence encoding STK11;

[0630] (ii) mutations in regulatory sequences that control the expression of the nucleotide sequence encoding STK11;

[0631] (iii) A mutation in a nucleotide encoding a protein that interacts with the transcription product of the STK11 gene.

[0632] Embodiment 249. An HDAC inhibitor for use as described in embodiment 247, wherein the STK11 mutation is a mutation in the translation product of the STK11 gene.

[0633] Embodiment 250. An HDAC inhibitor for use as described in embodiment 247, wherein the STK11 mutation is a mutation in the transcription product of the STK11 gene.

[0634] Embodiment 251. An HDAC inhibitor for use as described in any one of embodiments 247-250, wherein the STK11 mutation is an inactivating (loss-of-function) mutation.

[0635] Embodiment 252. An HDAC inhibitor for use as described in any one of embodiments 243-246, wherein said increased or decreased STK11 expression is determined in a sample derived from said subject.

[0636] Embodiment 253. An HDAC inhibitor for use as described in embodiment 252, wherein the increased or decreased STK11 expression is determined relative to a control.

[0637] Embodiment 254. An HDAC inhibitor for use as described in embodiment 253, wherein the control is a healthy tissue, preferably the same tissue type as the cancer tissue.

[0638] Embodiment 255. An HDAC inhibitor for use as described in any one of embodiments 247-250, wherein the STK11 mutation is identified in a sample derived from the subject.

[0639] Embodiment 256. An HDAC inhibitor for use as described in Embodiment 255, wherein the STK11 mutation is identified in a tumor sample derived from the subject.

[0640] Embodiment 257. An HDAC inhibitor for use as described in embodiment 255, wherein the STK11 mutation is not identified in a healthy tissue sample derived from the subject.

[0641] Embodiment 258. An HDAC inhibitor for use as described in any one of embodiments 178-257, wherein the STK11 mutation is not a germline mutation.

[0642] Embodiment 259. An HDAC inhibitor for use as described in any one of embodiments 179-258, wherein the HDAC inhibitor is administered concurrently with the additional therapeutic agent.

[0643] Embodiment 260. An HDAC inhibitor for use as described in any one of embodiments 179-258, wherein the HDAC inhibitor and the additional therapeutic agent are administered separately.

[0644] Embodiment 261. An HDAC inhibitor for use as described in any one of embodiments 179-258, wherein the HDAC inhibitor and the additional therapeutic agent are administered sequentially.

[0645] Embodiment 262. An HDAC inhibitor for use as described in any one of embodiments 179-258, wherein the HDAC inhibitor is administered before the additional therapeutic agent.

[0646] Embodiment 263. An HDAC inhibitor for use as described in any one of embodiments 179-258, wherein the HDAC inhibitor is administered after the additional therapeutic agent.

[0647] Embodiment 264. An HDAC inhibitor for use as described in any one of Embodiments 179-258, wherein the method comprises administering an immune checkpoint modulator to the subject followed by administering the HDAC inhibitor to the subject.

[0648] Embodiment 265. An HDAC inhibitor for use as described in any one of Embodiments 179-258, wherein the method comprises administering an HDAC inhibitor to the subject followed by administering an immune checkpoint modulator to the subject.

[0649] Embodiment 266. An HDAC inhibitor for use as described in any one of Embodiments 179-258, wherein the method comprises administering an immune checkpoint modulator to the subject, followed by administering a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof to the subject, followed by administering the HDAC inhibitor to the subject.

[0650] Embodiment 267. An HDAC inhibitor for use as described in any one of Embodiments 179-258, wherein the method comprises administering an immune checkpoint modulator to the subject, followed by administering an HDAC inhibitor to the subject, followed by administering a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof to the subject.

[0651] Embodiment 268. An HDAC inhibitor for use as described in any one of Embodiments 179-258, wherein the method comprises administering an HDAC inhibitor to the subject, followed by administering a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof to the subject, followed by administering an immune checkpoint modulator to the subject.

[0652] Embodiment 269. An HDAC inhibitor for use as described in any one of Embodiments 179-258, wherein the method comprises administering an HDAC inhibitor to the subject, followed by administering an immune checkpoint modulator to the subject, followed by administering a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof to the subject.

[0653] Embodiment 270. An HDAC inhibitor for use as described in any one of Embodiments 179-258, wherein the method comprises administering to the subject a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof, followed by administering to the subject an immune checkpoint modulator, followed by administering to the subject an HDAC inhibitor.

[0654] Embodiment 271. An HDAC inhibitor for use as described in any one of Embodiments 179-258, wherein the method comprises administering to the subject a targeting agent, a chemotherapeutic agent, radiation, or a combination thereof, followed by administering to the subject an HDAC inhibitor, followed by administering to the subject an immune checkpoint modulator.

[0655] Embodiment 272. An HDAC inhibitor for use as described in any one of Embodiments 178-271, wherein the subject has a cancer identified as having altered STK11 activity or expression.

[0656] Embodiment 273. An HDAC inhibitor for use as described in any one of embodiments 178-272, wherein the histone deacetylase inhibitor is a selective inhibitor of histone deacetylase 1 (HDAC1 selective inhibitor).

[0657] Embodiment 274. An HDAC inhibitor for use as described in any one of embodiments 178-272, wherein the histone deacetylase inhibitor is a selective inhibitor of histone deacetylase 1 and histone deacetylase 2 (HDAC1,2 selective inhibitor).

[0658] Embodiment 275. An HDAC inhibitor for use as described in any one of embodiments 178-272, wherein the histone deacetylase inhibitor is a selective HDAC class I inhibitor.

[0659] Embodiment 276. An HDAC inhibitor for use as described in any one of embodiments 178-272, wherein the histone deacetylase inhibitor is a CoREST selective deacetylase inhibitor.

[0660] Embodiment 277. Use of an HDAC inhibitor in the manufacture of a medicament for treating a subject having or at risk of developing cancer, wherein the treatment comprises administering to the subject an effective amount of the histone deacetylase (HDAC) inhibitor, wherein the cancer is identified as having altered STK11 activity or expression.

[0661] Embodiment 278. The use according to Embodiment 277, wherein the histone deacetylase inhibitor is administered in combination with one or more additional therapeutic agents.

[0662] Embodiment 279. The use of Embodiment 278, wherein at least one of the additional therapeutic agents is an immune checkpoint modulator.

[0663] Embodiment 280. Use of an HDAC inhibitor in the manufacture of a medicament for treating cancer in a subject, wherein the treatment comprises administering an immune checkpoint modulator and an HDAC inhibitor to the subject, wherein the treatment modulates and / or improves the ratio of Teff cells to Treg cells in a tumor or tumor microenvironment, wherein the cancer is identified as having altered STK11 activity or expression.

[0664] Embodiment 281. Use of an HDAC inhibitor in the manufacture of a medicament for treating cancer in a subject, wherein the treatment comprises administering an immune checkpoint modulator and an HDAC inhibitor to the subject, wherein the treatment reduces or depletes Treg cells in a tumor or tumor microenvironment, wherein the cancer is identified as having altered STK11 activity or expression.

[0665] Embodiment 282. Use of an HDAC inhibitor in the manufacture of a medicament for treating cancer in a subject, wherein the treatment comprises administering an immune checkpoint modulator and an HDAC inhibitor to the subject, wherein the treatment induces or increases expression of cytokines that promote anti-tumor activity, wherein the cancer is identified as having altered STK11 activity or expression.

[0666] Embodiment 283. The use according to embodiment 282, wherein the cytokine is selected from the group consisting of CXCL9, CXCL10 and CXCL11.

[0667] Embodiment 284. Use of an HDAC inhibitor in the manufacture of a medicament for treating cancer in a subject, wherein the treatment comprises administering an immune checkpoint modulator and an HDAC inhibitor to the subject, wherein the treatment reduces expression of cytokines that promote Treg cell recruitment, wherein the cancer is identified as having altered STK11 activity or expression.

[0668] Embodiment 285. The use according to embodiment 284, wherein the cytokine is CCL1 or CCL22.

[0669] Embodiment 286. Use of an HDAC inhibitor in the manufacture of a medicament for treating cancer in a subject, wherein the treatment comprises administering an HDAC inhibitor to the subject, wherein the administration of the HDAC inhibitor does not reduce red blood cell or myeloid cell viability, wherein the cancer is identified as having altered STK11 activity or expression.

[0670] Embodiment 287. Use of an HDAC inhibitor in the manufacture of a medicament for treating cancer in a subject, wherein the cancer presents an immune escape phenotype characterized by expression of a STK11 mutant, the method comprising: administering an HDAC1,2 selective inhibitor, wherein the HDAC1,2 selective inhibitor is capable of attenuating or reversing the immune escape phenotype.

[0671] Embodiment 288. The use of Embodiment 286 or 287, further comprising administering an immune checkpoint regulator.

[0672] Embodiment 289. Use of an HDAC inhibitor in the manufacture of a medicament for treating cancer in a subject, wherein the treatment comprises administering an HDAC inhibitor to the subject, wherein an immune checkpoint modulator has been, is being, or will be administered to the subject, wherein the cancer is identified as having altered STK11 activity or expression.

[0673] Embodiment 290. Use of an HDAC inhibitor in the manufacture of a medicament for treating cancer in a subject, wherein the treatment comprises administering an immune checkpoint modulator to the subject, wherein the HDAC inhibitor has been, is being, or will be administered to the subject, wherein the cancer is identified as having altered STK11 activity or expression.

[0674] Embodiment 291. The use of Embodiment 277, wherein the HDAC inhibitor is administered in combination with two or more additional therapeutic agents, wherein at least two of the additional therapeutic agents are immune checkpoint modulators.

[0675] Embodiment 292. The use of any one of embodiments 279-290, wherein each immune checkpoint modulator is independently a checkpoint inhibitor, a T cell co-stimulatory receptor agonist, or a dendritic cell co-stimulatory receptor agonist.

[0676] Embodiment 293. The use of any one of Embodiments 279-292, wherein at least one immune checkpoint regulator is independently a T cell co-stimulatory receptor agonist or a dendritic cell co-stimulatory receptor agonist.

[0677] Embodiment 294. The use of any one of Embodiments 279-292, wherein at least one immune checkpoint modulator is a checkpoint inhibitor.

[0678] Embodiment 295. The use as described in Embodiment 294, wherein each check point inhibitor is independently selected from anti-CTLA-4 agents, anti-PD-1 agents, anti-PD-L1 agents, anti-4-1BB agents, anti-OX-40 agents, anti-GITR agents, anti-CD27 agents, anti-CD28 agents, anti-CD40 agents, anti-LAG3 agents, anti-ICOS agents, anti-TWEAKR agents, anti-HVEM agents, anti-TIM-1 agents, anti-TIM-3 agents, anti-VISTA agents and anti-TIGIT agents.

[0679] Embodiment 296. The use of embodiment 294, wherein each check point inhibitor is independently selected from an anti-CTLA-4 agent, an anti-PD-1 agent, and an anti-PD-L1 agent.

[0680] Embodiment 297. The use of Embodiment 294, wherein each check point inhibitor is independently selected from an anti-PD1 agent and an anti-PD-L1 agent.

[0681] Embodiment 298. The use as described in Embodiment 294, wherein the checkpoint inhibitor is an anti-PD1 agent.

[0682] Embodiment 299. The use according to Embodiment 294, wherein the checkpoint inhibitor is an anti-PD-L1 agent.

[0683] Embodiment 300. The use according to Embodiment 277, wherein the HDAC inhibitor is administered in combination with an anti-CTLA-4 agent and an anti-PD-1 agent or an anti-PD-L1 agent.

[0684] Embodiment 301. The use of any one of Embodiments 294-299, wherein each immune checkpoint inhibitor is independently an antibody.

[0685] Embodiment 302. The use as described in Embodiment 301, wherein each check point inhibitor is independently selected from anti-CTLA-4 antibody, anti-PD-1 antibody, anti-PD-L1 antibody, anti-4-1BB antibody, anti-OX-40 antibody, anti-GITR antibody, anti-CD27 antibody, anti-CD28 antibody, anti-CD40 antibody, anti-LAG3 antibody, anti-ICOS antibody, anti-TWEAKR antibody, anti-HVEM antibody, anti-TIM-1 antibody, anti-TIM-3 antibody, anti-VISTA antibody and anti-TIGIT antibody.

[0686] Embodiment 303. The use according to embodiment 301, wherein each checkpoint inhibitor is independently selected from an anti-CTLA-4 antibody, an anti-PD-1 antibody, and an anti-PD-L1 antibody.

[0687] Embodiment 304. The use as described in embodiment 301, wherein each immune checkpoint inhibitor is independently selected from nivolumab; CT-011; AMP-224; pembrolizumab; pidilizumab; cemiplizumab; dostalimumab; palolizumab; spartalizumab; carrelizumab; sazanalizumab, sintilimab; tislelizumab; toripalizumab; rivalizumab; MEDI0680; bruglimumab and gelotrimazole.

[0688] Embodiment 305. The use according to embodiment 301, wherein each check point inhibitor is independently selected from an anti-PD1 antibody and an anti-PD-L1 antibody.

[0689] Embodiment 306. The use as described in Embodiment 301, wherein the checkpoint inhibitor is an anti-PD1 antibody.

[0690] Embodiment 307. The use according to Embodiment 301, wherein the checkpoint inhibitor is an anti-PD1-L1 antibody.

[0691] Embodiment 308. The use of embodiment 302 or 303, wherein the anti-CTLA-4 antibody is ipilimumab.

[0692] Embodiment 309. The use of any one of Embodiments 302, 303, 305 and 306, wherein the anti-PD-1 antibody is pembrolizumab or nivolumab.

[0693] Embodiment 310. The use of any one of Embodiments 302, 303, 305 and 306, wherein the anti-PD-1 antibody is pembrolizumab.

[0694] Embodiment 311. The use of any one of Embodiments 302, 303, 305 and 306, wherein the anti-PD-1 antibody is nivolumab.

[0695] Embodiment 312. The use of any one of Embodiments 302, 303, 305 and 307, wherein the anti-PD-L1 antibody is atezolizumab (CAS No. 1380723-44-3), avelumab (CAS No. 1537032-82-8) or durvalumab (CAS No. 1428935-60-7).

[0696] Embodiment 313. The use of any one of Embodiments 279-291, wherein the immune checkpoint regulator is a T cell co-stimulatory receptor agonist or a dendritic cell co-stimulatory receptor agonist.

[0697] Embodiment 314. The use of any one of embodiments 278-313, wherein at least one additional therapeutic agent is a targeting agent.

[0698] Embodiment 315. The use as described in Embodiment 314, wherein each targeting agent is independently selected from anti-angiogenic agents (e.g., anti-VEGF agents), KRAS inhibitors, ALK inhibitors, ROS1 inhibitors, BRAF inhibitors, RET inhibitors, MEK inhibitors, MET inhibitors and TRK inhibitors.

[0699] Embodiment 316. The use according to embodiment 314, wherein each targeting agent is independently selected from bevacizumab, ramucirumab, sotolacib, crizotinib, ceritinib, alectinib, brigatinib, lorlatinib, entrectinib, dabrafenib, trametinib, capmatinib, tepotinib and larotrectinib.

[0700] Embodiment 317. The use of any one of embodiments 278-316, wherein at least one additional therapeutic agent is a chemotherapeutic agent.

[0701] Embodiment 318. The use according to embodiment 317, wherein each chemotherapeutic agent is independently selected from cisplatin, carboplatin, paclitaxel, nab-paclitaxel (nab-paclitaxel), docetaxel, gemcitabine, vinorelbine, etoposide and pemetrexed.

[0702] Embodiment 319. The use according to embodiment 317, wherein at least one chemotherapeutic agent is a platinum-containing therapeutic agent.

[0703] Embodiment 320. The use according to embodiment 317, wherein one chemotherapeutic agent is a platinum-containing chemotherapeutic agent (eg, cisplatin) and the second chemotherapeutic agent is pemetrexed.

[0704] Embodiment 321. The use of any one of Embodiments 278-320, wherein at least one additional therapeutic agent is radiation.

[0705] Embodiment 322. The use of any one of Embodiments 278-321, wherein the cancer is resistant to anti-PD1 therapy or anti-PD-L1 therapy.

[0706] Embodiment 323. The use according to Embodiment 322, wherein the cancer is intrinsically resistant to anti-PD1 therapy or anti-PD-L1 therapy.

[0707] Embodiment 324. The use according to Embodiment 322, wherein the cancer has acquired resistance to anti-PD1 therapy or anti-PD-L1 therapy.

[0708] Embodiment 325. The use of any one of Embodiments 277-324, wherein the cancer is resistant to chemotherapy (eg, platinum-containing chemotherapy).

[0709] Embodiment 326. The use as described in Embodiment 325, wherein the cancer is intrinsically resistant to chemotherapy (e.g., platinum-containing chemotherapy).

[0710] Embodiment 327. The use of Embodiment 325, wherein the cancer has acquired resistance to chemotherapy (eg, platinum-containing chemotherapy).

[0711] Embodiment 328. The use of any one of Embodiments 277-327, wherein the cancer is unresponsive to or does not benefit from treatment with an immune checkpoint modulator when administered alone or as part of a treatment regimen that does not include an HDAC inhibitor.

[0712] Embodiment 329. The use of any one of embodiments 277-328, wherein the cancer is selected from: lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC), squamous cell lung cancer), colorectal cancer (e.g., colon adenocarcinoma, rectal adenocarcinoma), breast cancer (e.g., invasive ductal carcinoma), pancreatic cancer (e.g., pancreatic adenocarcinoma), endometrial cancer (e.g., endometrioid carcinoma), neuroendocrine cancer (e.g., large cell neuroendocrine carcinoma), melanoma, non-melanoma skin cancer (e.g., squamous cell carcinoma of the skin), bile duct cancer, gallbladder cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), bladder cancer (e.g., bladder urothelial carcinoma), prostate cancer (e.g., prostate adenocarcinoma), cervical cancer, endocervical cancer, or cancer of unknown primary (e.g., adenocarcinoma of unknown primary).

[0713] Embodiment 330. The use according to embodiment 329, wherein the cancer is lung cancer.

[0714] Embodiment 331. The use according to embodiment 330, wherein the cancer is lung adenocarcinoma.

[0715] Embodiment 332. The use according to embodiment 330, wherein the cancer is non-small cell lung cancer (NSCLC).

[0716] Embodiment 333. The use according to embodiment 332, wherein the cancer is non-squamous non-small cell lung cancer (NSCLC).

[0717] Embodiment 334. The use according to embodiment 329, wherein the cancer is colorectal cancer or colon adenocarcinoma.

[0718] Embodiment 335. The use of any one of Embodiments 277-334, wherein the cancer is identified as having a STK11 mutation and one or more additional mutations.

[0719] Embodiment 336. The use according to embodiment 335, wherein the additional mutation is selected from a KRAS mutation and a KEAP1 mutation.

[0720] Embodiment 337. The use according to Embodiment 335, wherein the additional mutation is a KRAS mutation.

[0721] Embodiment 338. The use as described in Embodiment 337, wherein the KRAS mutation is a mutation at position G12, optionally wherein the KRAS mutation is selected from a G12D mutation, a G12C mutation, a G12V mutation, or a combination thereof.

[0722] Embodiment 339. The use according to embodiment 335, wherein the additional mutation is a KEAP1 mutation.

[0723] Embodiment 340. The use according to embodiment 335, wherein the additional mutations are KRAS mutations and KEAP1 mutations.

[0724] Embodiment 341. The use of any one of Embodiments 277-340, wherein the cancer does not have an EGFR mutation.

[0725] Embodiment 342. The use of any one of Embodiments 277-341, wherein the cancer has increased or decreased expression of STK11.

[0726] Embodiment 343. The use as described in embodiment 342, wherein the increased or decreased STK expression is assessed by determining the copy number of the gene encoding STK11 relative to a control sample, wherein an increase in the copy number indicates an increased expression level and a decrease in the copy number indicates a decreased expression level.

[0727] Embodiment 344. The use according to embodiment 342, wherein the increased or decreased STK expression is assessed by determining the level of STK11 protein or mRNA relative to a control sample.

[0728] Embodiment 345. The use of Embodiment 343 or 344, wherein the cancer has reduced expression of STK11.

[0729] Embodiment 346. The use of any one of Embodiments 277-311, wherein the cancer has a STK11 mutation.

[0730] Embodiment 347. The use according to embodiment 346, wherein the STK11 mutation is a mutation selected from the group consisting of:

[0731] (i) mutations in the nucleotide sequence encoding STK11;

[0732] (ii) mutations in regulatory sequences that control the expression of the nucleotide sequence encoding STK11;

[0733] (iii) A mutation in a nucleotide encoding a protein that interacts with the transcription product of the STK11 gene.

[0734] Embodiment 348. The use according to embodiment 346, wherein the STK11 mutation is a mutation in the translation product of the STK11 gene.

[0735] Embodiment 349. The use according to embodiment 346, wherein the STK11 mutation is a mutation in the transcription product of the STK11 gene.

[0736] Embodiment 350. The use of any one of embodiments 346-349, wherein the STK11 mutation is an inactivating (loss-of-function) mutation.

[0737] Embodiment 351. The use of any one of Embodiments 342-345, wherein the increased or decreased STK11 expression is determined in a sample derived from the subject.

[0738] Embodiment 352. The use according to embodiment 351, wherein the increased or decreased STK11 expression is determined relative to a control.

[0739] Embodiment 353. The use according to embodiment 352, wherein the control is healthy tissue, preferably the same tissue type as the cancerous tissue.

[0740] Embodiment 354. The use of any one of Embodiments 346-350, wherein the STK11 mutation is identified in a sample derived from the subject.

[0741] Embodiment 355. The use according to Embodiment 354, wherein the STK11 mutation is identified in a tumor sample derived from the subject.

[0742] Embodiment 356. The use according to Embodiment 354, wherein the STK11 mutation is not identified in a healthy tissue sample derived from the subject.

[0743] Embodiment 357. The use of any one of Embodiments 277-356, wherein the STK11 mutation is not a germline mutation.

[0744] Embodiment 358. The use of any one of Embodiments 277-357, wherein the HDAC inhibitor is administered concurrently with the additional therapeutic agent.

[0745] Embodiment 359. The use of any one of Embodiments 277-357, wherein the HDAC inhibitor and the additional therapeutic agent are administered separately.

[0746] Embodiment 360. The use of any one of Embodiments 277-357, wherein the HDAC inhibitor and the additional therapeutic agent are administered sequentially.

[0747] Embodiment 361. The use of any one of Embodiments 277-357, wherein the HDAC inhibitor is administered prior to the additional therapeutic agent.

[0748] Embodiment 362. The use of any one of Embodiments 277-357, wherein the HDAC inhibitor is administered after the additional therapeutic agent.

[0749] Embodiment 363. The use of any one of Embodiments 277-357, wherein the method comprises administering an immune checkpoint modulator to the subject followed by administering an HDAC inhibitor to the subject.

[0750] Embodiment 364. The use of any one of Embodiments 277-357, wherein the method comprises administering an HDAC inhibitor to the subject followed by administering an immune checkpoint modulator to the subject.

[0751] Embodiment 365. The use of any one of Embodiments 277-357, wherein the method comprises administering an immune checkpoint modulator to the subject, followed by administering a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof to the subject, followed by administering an HDAC inhibitor to the subject.

[0752] Embodiment 366. The use of any one of Embodiments 277-357, wherein the method comprises administering an immune checkpoint modulator to the subject, followed by administering an HDAC inhibitor to the subject, followed by administering a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof to the subject.

[0753] Embodiment 367. The use of any one of Embodiments 277-357, wherein the method comprises administering an HDAC inhibitor to the subject, followed by administering a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof to the subject, followed by administering an immune checkpoint modulator to the subject.

[0754] Embodiment 368. The use of any one of Embodiments 277-357, wherein the method comprises administering an HDAC inhibitor to the subject, followed by administering an immune checkpoint modulator to the subject, followed by administering a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof to the subject.

[0755] Embodiment 369. The use of any one of Embodiments 277-357, wherein the method comprises administering to the subject a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof, followed by administering to the subject an immune checkpoint modulator, followed by administering to the subject an HDAC inhibitor.

[0756] Embodiment 370. The use of any one of Embodiments 277-357, wherein the method comprises administering to the subject a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof, followed by administering to the subject an HDAC inhibitor, followed by administering to the subject an immune checkpoint modulator.

[0757] Embodiment 371. The use of any one of Embodiments 277-370, wherein the subject has a cancer identified as having altered STK11 activity or expression.

[0758] Embodiment 372. The use of any one of embodiments 277-371, wherein the histone deacetylase inhibitor is a selective inhibitor of histone deacetylase 1 (HDAC1 selective inhibitor).

[0759] Embodiment 373. The use of any one of embodiments 277-371, wherein the histone deacetylase inhibitor is a selective inhibitor of histone deacetylase 1 and histone deacetylase 2 (HDAC1,2 selective inhibitor).

[0760] Embodiment 374. The use of any one of embodiments 277-371, wherein the histone deacetylase inhibitor is a selective HDAC class I inhibitor.

[0761] Embodiment 375. The use of any one of embodiments 277-371, wherein the histone deacetylase inhibitor is a CoREST selective deacetylase inhibitor.

[0762] Embodiment 376. A method for determining the sensitivity of a subject having or diagnosed with cancer to treatment with an HDAC inhibitor, the method comprising: determining: i) the presence or absence of a STK11 mutation in the subject or in a sample derived from the subject; and / or ii) the level of STK11 activity or expression; wherein the presence of a STK11 mutation and / or the level of altered STK11 activity or expression indicates sensitivity to treatment with an HDAC inhibitor.

[0763] Embodiment 377. A method for determining the sensitivity of a subject having or diagnosed with cancer to a combination treatment with an HDAC inhibitor and an immune checkpoint regulator, the method comprising: determining: i) the presence or absence of an STK11 mutation in the subject or in a sample derived from the subject; and / or ii) the level of STK11 activity or expression; wherein the presence of an STK11 mutation and / or the level of altered STK11 activity or expression indicates sensitivity to a combination treatment with an HDAC inhibitor and an immune checkpoint regulator.

[0764] Embodiment 378. A method for determining the sensitivity of a subject having or diagnosed with cancer to treatment with a method as described in any one of Embodiments 1-99, the method for determining comprising: determining: i) the presence or absence of a STK11 mutation in the subject or in a sample derived from the subject; and / or ii) the level of STK11 activity or expression; wherein the presence of a STK11 mutation and / or the level of altered STK11 activity or expression indicates sensitivity to treatment with a method as described in any one of Embodiments 1-99.

[0765] Embodiment 379. The method of any one of embodiments 1-177, the compound for use of any one of embodiments 187-276, or the use of any one of embodiments 277-371, wherein the histone deacetylase inhibitor is a compound of formula (I)

[0766] or a pharmaceutically acceptable salt thereof.

[0767] Example

[0768] The following examples are given for the purpose of illustrating various embodiments of the present invention and are not intended to limit the present invention in any way. The present examples and the methods described herein currently represent preferred embodiments, are exemplary, and are not intended to be used as limitations on the scope of the present invention. Those skilled in the art will recognize changes therein and other uses within the spirit of the present invention as defined by the scope of the claims.

[0769] Example 1: Anti-tumor activity of the combination of anti-PD1 and compound I in the subcutaneous MC38_sgStk11 tumor model in mice

[0770] summary : In vivo antitumor efficacy study of dual combination therapy of anti-PD1 and HDAC1,2 selective inhibitors in the subcutaneous MC38_sgStk11 tumor model in C57BL / 6 mice.

[0771] Experimental design : A table summarizing the experimental design is provided in Table 1-1.

[0772] Table 1-1: Experimental design summary

[0773]

[0774] a The administration volume for each dose was 10 μL / g.

[0775] Material :

[0776] animal

[0777] 96 mice plus 39 spare mice of the following species: House mouse (mus musculus); strain: C57BL / 6; age: 8-10 weeks; sex: female; and weight: 16.9-20.0 g

[0778] Animal supplier: Shanghai SLAC Laboratory Animal Co., Ltd.

[0779] Mice were kept in individually ventilated cages at constant temperature (approximately 20-26°C) and constant humidity (approximately 40-70%), with 4 animals in each cage. The size of each cage was approximately 300mm x 200mm x 180mm. The bedding in each cage was corn cobs, which were changed twice a week. The identification label of each cage contained the following information: number of animals, sex, strain, receipt date, treatment, study number, group number, and treatment start date.

[0780] During the entire study period, animals had free access to irradiated sterilized dry pelleted food. Animals had free access to sterile drinking water. Animals were identified with ear tags.

[0781] Compound

[0782] Anti-PD1 (solution) was supplied by BioXcell and stored at about 4°C. Anti-IgG2a (solution) was supplied by BioXcell and stored at about 4°C. Compound I (solid) was supplied by Tango Therapeutics and stored at about room temperature. Compound I used in Example 1 exhibited >10-fold selectivity for HDAC1 compared to HDAC3 in intact cells. Compound I used in Example 1 exhibited significant selectivity for CoREST deacetylase compared to NCoR, NuRD, and Sin3 as described herein.

[0783] method

[0784] Cell culture

[0785] MC38_sgStk11 tumor cells were maintained in vitro as monolayer cultures in DMEM + 2 mM glutamine supplemented with about 10% heat-inactivated fetal bovine serum, about 100 U / ml penicillin and 100 μg / ml streptomycin at about 37° C. in an atmosphere of about 5% CO 2 in air. Tumor cells were routinely subcultured twice a week by trypsin-EDTA treatment. Cells growing in the exponential growth phase were harvested and counted for tumor inoculation.

[0786] Tumor inoculation and animal grouping

[0787] Each mouse was subcutaneously inoculated with MC38_sgStk11 tumor cells (0.5x106 cells) in 0.1 ml PBS in the right upper flank for tumor development. On day 4 after tumor inoculation, when the average tumor size reached 52 mm 3 Treatment was started at 1:00 p.m. Animals were divided into groups according to the standard operating procedure based on their tumor volume. Each group consisted of 8 tumor-bearing mice. The test articles were administered to mice according to the predetermined scheme shown in the experimental design table (Table 1-1).

[0788] Observations

[0789] All procedures related to animal handling, care and treatment in the study were performed according to the guidelines approved by the Institutional Animal Care and Use Committee (IACUC) of the supplier, in accordance with the guidance of the Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC). During routine monitoring, animals were checked daily for any effects of tumor growth and treatment on normal behavior, such as activity, food and water consumption, weight gain / loss (weight was measured three times a week), eyes / hair tangles, and any other abnormal effects stated in the protocol. Deaths and observed clinical signs were recorded based on the number of animals in each subset.

[0790] Tumor Measurements and End Points

[0791] The primary endpoint is to observe whether tumor growth can be delayed or whether mice can be cured. Tumor size was measured in two dimensions using a caliper three times a week, and the volume was expressed in mm3 using the following formula: V = 0.5ax b2, where a and b are the long and short diameters of the tumor, respectively. The T / C value (in percentage) is an indication of antitumor effectiveness; T and C are the average volumes of the treatment group and the control group on a given day, respectively. The TGI of each group was calculated using the following formula: TGI (%) = [1-(Ti-T0) / (Vi-V0)] × 100; Ti is the average tumor volume of the treatment group on a given day, T0 is the average tumor volume of the treatment group on the day the treatment started, Vi is the average tumor volume of the vehicle control group on the same day as Ti, and V0 is the average tumor volume of the vehicle group on the day the treatment started.

[0792] Statistical analysis

[0793] Data obtained at the optimal treatment time point of day 11 after the start of treatment were statistically analyzed for differences in tumor volume between groups. One-way ANOVA was performed for comparison between groups. Intergroup survival analysis was performed using the Kaplan-Meier test. p<0.05 was considered statistically significant.

[0794] result

[0795] The mean tumor volumes over time in C57BL / 6 mice bearing MC38_sgStk11 tumors dosed with the combination treatment are shown in Table 1-2 (anti-IgG2a) and Table 1-3 (anti-PD1).

[0796] Table 1-2: Tumor volume (mm) of each anti-IgG2a group over time 3)(measurements of surviving animals only)

[0797]

[0798] a Mean ± SEM

[0799] b Days after treatment started

[0800] EU = mice with heavy tumor burden (>3,000 mm 3 ) Early euthanasia

[0801] Table 1-3: Tumor volume (mm) of each anti-PD1 group over time 3 )(measurements of surviving animals only)

[0802]

[0803] a Mean ± SEM

[0804] b Days after treatment started

[0805] EU = mice with heavy tumor burden (>3,000 mm 3 ) Early euthanasia

[0806] Table 1-4: Calculated tumor growth inhibition in the MC38_sgStk11 syngeneic model based on tumor volume measurements of PG-D11

[0807]

[0808]

[0809] a Mean ± SEM.

[0810] b Tumor growth inhibition (T / C) was calculated by dividing the mean tumor volume of the treatment group by the mean tumor volume of the control group.

[0811] c TGI (%) = [1-(T11-T0) / (V11-V0)] × 100; T11 is the average tumor volume of the treatment group on day 11, T0 is the average tumor volume of the treatment group on day 0 after treatment, V11 is the average tumor volume of the vehicle control group on the same day as T11, and V0 is the average tumor volume of the vehicle group on day 0 after treatment.

[0812] dAll data were analyzed using SPSS 17.0. One-way ANOVA was used for comparisons between groups, followed by Games-Howell (assuming unequal variances) or Dunnett's (assuming equal variances) tests. *p≤0.05; **p≤0.01; ***p≤0.001; p≤0.0001.

[0813] Table 1-5: Analysis of tumor regression responses in the MC38_sgStk11 syngeneic model based on tumor volume measurements

[0814]

[0815]

[0816] a PR (partial regression) is a tumor volume that is 50% or less of its day 1 volume for three consecutive measurements during the course of the study and equal to or greater than 13.5 mm3 for one or more of these three measurements.

[0817] b CR (complete regression) was defined as a tumor volume less than 13.5 mm3 for three consecutive measurements during the course of the study.

[0818] c ORR = CR (complete response) + PR (partial response).

[0819] The combination treatment of Compound I with anti-PD1 produced significant antitumor activity against the MC38_sgStk11 tumor model. The mean tumor size of vehicle-treated animals reached 2,132 mm on day 11 after the start of treatment. 3 The combination treatment of anti-PD1 and compound I at different dose levels (3 mg / kg, 10 mg / kg, 30 mg / kg and 75 mg / kg) produced significant anti-tumor activity, while their average tumor size was about 708 mm 3 、884mm 3 、399mm 3 and 542mm 3 (T / C values ​​= 33.2%, 41.5%, 18.7% and 25.4%; TGI = 68.5%, 60.0%, 83.3% and 76.4%; p < 0.001, < 0.001, < 0.001 and < 0.001, respectively, compared to the vehicle group).

[0820] Tumor volume and survival were monitored during treatment. Figure 1A ) and by individual animal ( Figure 1B ) Tumor volume was plotted.

[0821] Survival rates were plotted by tumor group ( Figure 2A , showing groups 1, 7, 2, 3, 4, 5, and 6; Figure 2B , showing groups 1, 7, 8, 9, 10, 11, and 12; Figure 2C , showing groups 1, 4, 7, and 10).

[0822] Example 2: Rechallenge study of Example 1

[0823] summary : Rechallenge studies of Example 1 were performed to evaluate whether surviving animals from Example 1 had acquired T memory against the same tumor.

[0824] Experimental design and materials : Surviving animals of the efficacy portion were re-challenged with MC38_sgStk11 cells on the opposite side of the primary tumor.

[0825] A table summarizing the surviving animals from Example 1 is provided in Table 2-1.

[0826] Table 2-1: Summary of Animals in the Rechallenge Study

[0827]

[0828]

[0829] method

[0830] Cell culture

[0831] MC38_sgStk11 tumor cells were maintained in vitro as monolayer cultures in DMEM + 2 mM glutamine supplemented with about 10% heat-inactivated fetal bovine serum, 100 U / ml penicillin and 100 μg / ml streptomycin at about 37° C. in an atmosphere of about 5% CO 2 in air. Tumor cells were routinely subcultured twice a week by trypsin-EDTA treatment. Cells growing in the exponential growth phase were harvested and counted for tumor inoculation.

[0832] Tumor inoculation and animal grouping

[0833] Mice were inoculated subcutaneously in the left lower flank with MC38_sgStk11 tumor cells (0.5 x 106) in 0.1 ml PBS for tumor development. The number of animals and cells per group are shown in the experimental design (Table 2-1). Surviving animals from Example 1 were monitored post-treatment for 21 days before rechallenge.

[0834] Observations

[0835] All procedures related to animal handling, care and treatment in the study were performed according to the guidelines approved by the Institutional Animal Care and Use Committee (IACUC) of the supplier and in accordance with the guidance of the Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC). During routine monitoring, animals were checked daily for any effects of tumor growth and treatment on normal behavior, such as activity, food and water consumption, weight gain / loss (weight measured twice a week), eyes / hair tangles, and any other abnormal effects stated in the protocol. Deaths and observed clinical signs were recorded based on the number of animals in each subset.

[0836] Tumor Measurements and End Points

[0837] Tumor size was measured in three dimensions using calipers three times a week, and volume was expressed in mm3 using the following formula: V = 0.5 a x b2, where a and b are the major and minor diameters of the tumor, respectively.

[0838] result

[0839] The mean tumor volume over time in C57BL / 6 mice re-challenged with MC38_sgStk11 is shown in Table 2-2.

[0840] Table 2-2: Tumor volume (mm) of each MC38_sgStk11 re-stimulation group over time 3 )

[0841]

[0842] a Mean ± SEM

[0843] b Days after cell seeding

[0844] There was no tumor growth in the surviving animals re-challenged with MC38_sgStk11 cells. The results may indicate that the surviving animals have acquired T memory against the MC38_sgStk11 tumor.

[0845] All animals remained off treatment and tumor size over time after rechallenge was plotted: Figure 3A Tumor size is shown by group; all previously treated groups overlapped with no tumor growth; Figure 3B Shown are tumor sizes for the combined group of previously treated mice and an untreated control group). Figure 4The complete timeline for Experiments 1 and 2 and the tumor sizes at the indicated time points are shown.

[0846] Example 3: Identification of anti-PD1 antibody sensitive genes in STK-11 deficient tumors

[0847] In this example, genes whose inhibition reverses anti-PD1 resistance driven by STK11 loss were identified. Briefly, genes encoding HDAC1, HDAC2, or HDAC3 were deleted or disabled using CRISPR in an in vivo knockout screen in STK-11-deficient MC38 tumor cells grown in C57Bl / 6 mice treated with anti-PD1 antibodies. The results showed that HDAC1 is a sensitive factor to anti-PD1 in STK11-deficient cancers ( Figure 5A In addition, the toxicity of CRISPR-mediated deletion / disruption of HDAC1, HDAC2, or HDAC3 was tested in several cell lines. The results showed that cells depleted of HDAC1, HDAC2, or HDAC3 knockouts, with HDAC3 knockouts showing the highest toxicity in the cell line panel ( Figure 5B ).

[0848] Example 4: Identification of CoREST selective deacetylase inhibitors

[0849] In this example, the CoREST complex selective compound I was identified using the NanoBRET (bioluminescence resonance energy transfer) target engagement assay. Briefly, cells were treated with compound 1 for 4 hours before measuring the BRET signal. The dose-dependent binding of compound I to purified HDAC1, HDAC2, and HDAC3 was then measured at various concentrations of compound I, and the respective IC50 values ​​were determined. The results showed that the IC50 of compound I for HDAC1 was 0.01uM, for HDAC2 was 0.17uM, and for HDAC3 was 1.07uM ( Figures 6A-6C and Table 3-1).

[0850] Table 3-1 Evaluation of the inhibition of HDAC1, 2, 3, 6 and 10 by Compound I and other less selective HDAC inhibitors (TCA, Entinostat and Chidamide) in the cellular NanoBRET assay

[0851]

[0852]

[0853] Determine the HDAC inhibition of compound I to HDAC complex CoREST, NCoR, NuRD and Sin3 by fluorescence-based deacetylase assay.In brief, HDAC complex CoREST, NCoR, NuRD and Sin3 are co-immunoprecipitated with complex selective antibodies from A549 cells (lung adenocarcinoma model), and the complex is incubated with compound I or low-selectivity HDAC inhibitors vorinostat, tucidinostat and domatinostat. Suberoylanilide hydroxamic acid (a pan-HDAC inhibitor targeting all 4 complexes) is used as a positive control for complex activity, to prove that the separated complex retains functional deacetylase activity, and to establish background measurement fluorescence.HDAC inhibition is analyzed in fluorescence-based deacetylase assay.Exemplary IC is shown in Table 3-2 50 The results in Table 3-2 show that compound I is selective for the CoREST complex.

[0854] Table 3-2. IC50 of Compound I and other HDAC inhibitors (vorinostat, tolcinostat, domatinostat) in in vitro deacetylase assays of cell-derived intact HDAC complexes CoREST, NCoR, NuRD and Sin3

[0855] Compound CoREST NCoR NuRD Sin3 Vorinostat 0.061 0.525 0.133 0.160 Toxistat 0.120 0.2 1.4 >100 Domatinostat 0.087 0.193 30 >100 Compound 1 0.170 >100 >100 >100

[0856] Example 5: Anti-tumor effect of combination of anti-PD1 and compound I in subcutaneous CT26 STK11-deficient mouse tumor model active

[0857] In this example, the anti-tumor activity of the combination therapy of anti-PD1 antibody and Compound I was determined in vivo in a STK11-deficient syngeneic mouse model.

[0858] Briefly, mice were inoculated with a STK11-deficient CT26 (murine colorectal cancer cell line) tumor model in a manner similar to that described in Example 1. By knocking out STK11, the tumor model is resistant to murine anti-PD1 antibodies. Mice were treated orally with Compound I once daily and twice weekly with anti-PD1, anti-IgG2a control, or anti-PD1 control, as indicated. Tumor volume and survival were monitored during treatment, and tumor volume was plotted by individual animal ( Fig. 7A ) and plotting survival by group ( Figure 7B ).

[0859] The results of Example 1 and Example 5 show that Compound I reverses resistance to STK11 loss-driven immune checkpoint blockade in tumor models of colon adenocarcinoma and colorectal cancer.

[0860] Example 6: Efficacy of Compound I in combination with anti-PD1 antibody in mouse models with or without T cells

[0861] The efficacy of Compound I in combination with anti-PD1 antibody was determined in vivo in a mouse model with or without T cells.

[0862] Briefly, athymic BALB / c nude mice and C57BL / 6 animals bearing STK11-deficient MC38 tumors were orally dosed once daily with 30 mg / kg or 75 mg / kg of Compound I alone or in combination with anti-PD1 twice a week ( Fig. 8A and Figure 8B ). The results show that the efficacy of Compound I and anti-PD1 requires an intact T cell compartment.

[0863] Example 7: Cytokine Profiling of Tumors Treated with Compound I

[0864] Cytokine expression of tumors from mice treated with Compound I was determined by Nanostring PanCancer IO 360 analysis.

[0865] Briefly, STK11- / - MC38 tumors from mice treated with 30 mg / kg Compound I or anti-PD1 antibodies alone or in combination for 7 days were collected 8 hours after the last dose. The gene expression profiles of CXCL9, CXCL10, and CXCL11 of the tumors were determined by Nanostring PanCancer IO 360 ( Fig.9A In addition, the gene expression profiles of the tumor Treg recruitment chemokines CCL1 and CCL22 were determined by Nanostring PanCancer IO 360 ( Fig. 9B ).

[0866] Compared with the DMSO solvent control, the HLA gene expression profile of STK11-deficient MC38 cells was also analyzed in vitro by Nanostring IO360 repertoire after 4 days of treatment with 0.2uM of Compound I ( Fig. 9C ).

[0867] Results showed that HDAC1,2 selective inhibitor treatment drove the expression of cytokines that promoted antitumor activity. Additionally, Compound I treatment reversed immune evasion on tumor cells by altering the expression of cytokines and antigen presentation genes.

[0868] Example 8: T cell activity after treatment with compound I in combination with anti-PD1 antibody

[0869] In this example, the ability of Compound 1 to increase T cell activity in combination with an anti-PD1 antibody was determined.

[0870] Briefly, mice bearing STK11-deficient MC38 tumors were treated with 10 mg / kg of Compound I alone or in combination with anti-PD1 as described above for 7 days. Tumor tissues were collected 8 hours after the last dose and analyzed by flow cytometry for tumor infiltrating lymphocytes (TILs). T cell populations were analyzed for total CD45+ cells, CD4+ cells, CD8+ cells, and CD8+ T effector memory (TEM) cells and Treg cells ( Fig. 10A and Fig. 10B Flow cytometry of T regulatory (Treg) cells showed a significant decrease in the frequency of Treg cells in the combination arm ( Fig. 10B The ratio of CD8+ T effector cells to T regulatory cells in each treatment group showed a significantly increased ratio in the combination arm ( Fig. 10B ).

[0871] IFNγ levels were evaluated by Luminex analysis in tumors treated with 30 mg / kg Compound I or in combination with anti-PD1 ( Fig. 10C ).

[0872] Co-cultures of human NSCLC cells with PBMCs and fibroblasts were treated with a dose response of Compound I alone or in combination with a fixed dose of anti-PD1 for 72 hours. IFNγ levels were quantified from tissue culture supernatants by ELISA ( Fig. 10D ).

[0873] The results showed that the combination of Compound I and anti-PD1 antibody increased T cell activity and depleted Tregs in the tumor microenvironment.

[0874] To determine the immune relevance of the response to Compound I in combination with anti-PD-1 in the microenvironment of STK11 mutant tumors, MC38_sgStk11 tumor-bearing mice were treated with vehicle (5% DMA + 30% PEG 400 + 65% 30% HPβCD in water and 10 mg / kg anti-IgG2a), 30 mg / kg Compound I, 10 mg / kg anti-PD-1 or the combination for 7 days. Tumors were harvested after 7 days and snap-frozen for analysis using a gene expression panel of mouse tissues.

[0875] The total number of T cells was increased by anti-PD-1 alone or in combination with Compound I ( Fig.10E). Anti-PD-1 also increased the abundance of regulatory T cells (Tregs). However, anti-PD-1 + Compound I combination treatment prevented the increase in Tregs caused by anti-PD-1 treatment alone. STK11 loss-of-function mutations are known to be associated with primary resistance to anti-PD-1 treatment (Skoulidis et al. 2018). These data demonstrate that Compound I and anti-PD-1 combination therapy uncouples the recruitment of T effector cells and Tregs, resulting in an increased ratio of effector / regulatory T cells, which strongly favors immune cell-mediated tumor cell killing.

[0876] Example 9: Analysis of gene regulation by Compound I

[0877] In this example, changes in gene expression between CoreDAC and other HDAC inhibitors were determined by Nanostring analysis.

[0878] Briefly, A549 cells were treated in vitro for 96 hours with the HDAC inhibitors vorinostat, domatinostat, and compound I. To select equivalent doses for each compound, an H3K9Ac AlphaLISA was performed, and a dose that increased H3K9Ac by two-fold was selected for each inhibitor. Cells were harvested and Nanostring analysis was performed on the three treatment groups using the PanCancer IO360 repertoire ( Fig.11A -C). Use nSolver software to determine if ( Fig.11A -C) The top three gene ontology groups for each compound as determined by Nanostring data ( Fig.11A -C lower figure). The results showed that compound I regulated the expression of fewer genes than the less selective HDAC inhibitors vorinostat and domatinostat.

[0879] Example 10: Therapeutic Index and Cytotoxicity Analysis of Compound I

[0880] In this example, the toxicity and therapeutic index of Compound 1 were determined in vitro and in vivo.

[0881] In brief, colony forming unit assays were performed in vitro to evaluate the effects of HDAC inhibitors on erythrocyte and bone marrow cell viability. Cells were treated with each compound of the dose response for 14 days. Cell colonies were quantified at the end of the experiment and compared with solvent controls. The effective dose range of Compound I was also plotted (ranging between 3 mg / kg and 75 mg / kg) ( Fig. 12A ). The IC50 of each compound was calculated from the erythrocyte and bone marrow colony forming unit assays. These IC50s were normalized to the potency of the compound against HDAC1 in the cellular NanoBRET assay to allow head-to-head compound comparisons (Table 4-1).

[0882] IC50s were derived from erythroid and bone marrow colony forming unit assays, normalized to potency against HDAC1 (Table 4.1).

[0883]

[0884] The clinically relevant dose of vorinostat for mice was calculated using body surface area conversion. Mice bearing STK11-deficient MC38 tumors were treated in vivo with vorinostat or compound I alone or in combination with anti-PD1. Tumor volume ( Fig. 12B For Vorinostat, Fig. 12C is compound 1). Vorinostat or compound I in Fig. 12B and Fig. 12C The doses used in 平均 and HDAC1 IC50 at this dose 平均 The coverage is shown in Table 4-2.

[0885] Table 4-2: C of HDAC inhibitors 平均 and IC50

[0886] treat C average, u (uM) Multiples of HDAC1 IC50 Vorinostat (pan-dose) 0.132* 0.3 Compound I (CoreDAC) 0.192 3.5

[0887] Compound I concentration versus in vivo HDAC1 or HDAC3 inhibition was plotted in Fig.12D The shaded boxes indicate the tolerated and effective dose ranges of Compound I. Non-tolerable exposures exceeded 150 mg / kg.

[0888] The results show that Compound I has low cytotoxicity and an improved therapeutic index relative to less selective HDAC inhibitors such as vorinostat. CoreDAC Compound I has an improved therapeutic index compared to previously developed HDAC inhibitors.

[0889] Example 11: Pharmacological properties of Compound I

[0890] The pharmacokinetics (PK) of Compound I in rats was determined after a single IV bolus injection of 1 mg / kg of 20% weight / volume HPβCD in saline, 1% volume / volume DMSO, or a single PO 3 mg / kg dose of 0.5% methylcellulose (MC) in water (IV in the fed condition and PO in the fasted condition) to male Sprague Dawley rats. Plasma samples were collected from 3 animals / group at 0.05, 0.25, 0.5, 1, 2, 3, 4, 8, and 24 hours after dosing. Selected PK parameters for Compound I are presented in Table 5. The PO bioavailability was 95.4%.

[0891] The PK of Compound I in beagles was determined in plasma after a single IV bolus and PO administration to non-naive male and female beagles. The vehicle for IV was 20% weight / volume 2-hydroxypropyl β-cyclodextrin (HPβCD), 1% volume / volume DMSO in saline, and PO was in 5% DMA, 30% PEG400 and 65% (30% HPβCD in water) (solution) or 0.5% MC (suspension). Plasma samples were collected from 3 animals / group at 0.083, 0.25, 0.5, 1, 3, 6, 9, 12, 24 and 48 hours after dosing. The selected PK parameters of Compound I are presented in Table 5. When Compound I was administered as a solution at 3 mg / kg under fasting conditions, the PO bioavailability was 67.4%.

[0892] The PK of Compound I in male cynomolgus monkeys was determined in plasma after a single IV bolus and PO administration to non-naive male cynomolgus monkeys. The vehicle for IV was 20% weight / volume HPβCD, 1% volume / volume DMSO in saline, and the vehicle for PO was in 0.5% MC (suspension). Plasma samples were collected from 3 animals / group at 0.083, 0.25, 0.5, 1, 3, 6, 9, 12, 24 and 48 hours after dosing. The selected PK parameters of Compound I are presented in Table 5. When Compound I was given as a suspension at 3 mg / kg under fed conditions, the PO bioavailability was 83%.

[0893] The effect of compound I on cloned human ether-à-go-go related gene (hERG) potassium channels stably expressed in human embryonic kidney (HEK) 293 cells was measured using manual patch clamp technology. In brief, compound I was soluble at 100uM in 0.3% DMSO (pH 6.9). A dose range finding (DRF) assay was performed with compound I at 3, 30 and 100uM concentrations. Compound I inhibited hERG currents by 15.67%, 45.85% and 73.57% at 3, 30 and 100μM, respectively. The deterministic hERG assay was used to detect the IC50 of compound I. In the deterministic hERG assay, each concentration was repeated 3 times. The IC50 value of the inhibitory effect of compound I on hERG potassium currents was 71.07μM.

[0894] Drug metabolizing enzymes involved in the biotransformation of Compound I were investigated using human liver microsomes (HLM) and recombinant enzymes. Compound I was stable in HLM (>93% remaining after 240 min incubation with an HLM protein concentration of 0.6 mg / ml). CYP selective inhibitor experiments were not performed due to the lack of significant turnover of Compound I. Compound I was minimally metabolized by recombinant human CYPs (rhCYP; terminal half-life (T 1 / 2 )>60 minutes).

[0895] Table 5. Pharmacological properties of Compound I in rats, dogs and monkeys

[0896]

[0897] Abbreviations: PO, oral; PK, pharmacokinetics; T 1 / 2, terminal half-life; CL, systemic clearance; hERG, human ether-à-go-go related gene;

[0898] Example 12: Predicted Human PK of Compound I

[0899] Human PK parameters for predicted efficacious Compound I doses were calculated based on data from rodent and dog studies and are presented in Table 6.

[0900] Table 6.

[0901]

[0902]

[0903] Predicted human pharmacokinetics and therapeutic window Fig.13 Modeling in.

[0904] Example 13: Mouse PK / PD of Compound I

[0905] The formation and accumulation of acetylated histone 3 lysine 9 (H3K9Ac) in mouse MC38 tumor tissue after treatment with compound I was determined by Western blotting. Briefly, female C57BL / 6 mice with MC38 tumors were treated with compound I at the indicated doses (3 mg / kg, 10 mg / kg, and 30 mg / kg) for 7 days. Tissues were collected 8 hours after the last dose, and H3K9Ac accumulation was quantified by Western blotting ( Fig.14A ) and normalized to total histone H3 ( Fig. 14B ). The results showed that incubation with compound I resulted in a dose-dependent accumulation of H3K9Ac.

[0906] In a separate PK / PD study, female C57BL / 6 mice (12 / group) bearing MC38 tumors were assigned to mice with a 430 mm 3 The patients were treated with a similar mean tumor volume and treated with vehicle (5% N,N-dimethylacetamide [DMA] + 30% polyethylene glycol [PEG] 400 + 65% of 30% 2-hydroxypropyl-β-cyclodextrin [HP-β-CD] aqueous solution) or 30, 100 and 300 mg / kg of Compound I once a day (QD) for 2 days. Plasma samples were collected 1, 2, 8 and 24 hours after the last dose and analyzed for Compound I concentration. Peripheral blood mononuclear cells (PBMCs) and tumor samples were harvested 2, 8 and 24 hours after the last dose. PBMC samples were processed to determine the mean fluorescence level of acetyl histone H2B by flow cytometry. Tumor samples were processed to determine the protein level of acetyl histone H3 by Western blot. During this study, no significant weight loss or adverse clinical signs of more than 5% were observed from Compound I treatment.

[0907] Plasma concentrations of Compound I were dose proportional with the maximum concentration observed 1 hour after the last dose ( Fig. 14C ). Based on a 10.05% free fraction in C57BL / 6 mouse plasma, free unbound exposure in plasma was 5470, 17238, and 69665 h.ng / mL for 30, 100, and 300 mg / kg QD doses, respectively, indicating that dose proportionality was achieved within the dose range. Compound I treatment at 30, 100, and 300 mg / kg QD caused a dose-dependent increase in tumor acetyl histone levels starting 2 hours after the last dose. A maximum of 8-fold and 3.7-fold induction of histone acetylation was observed in PBMCs and tumors, respectively, 24 hours after the last dose of 300 mg / kg QD Compound I (2 days of treatment) compared to vehicle control. Fig.14D and Fig.14E ).

[0908] Overall, the PK / PD relationship was dose-dependent, and when Compound I plasma concentrations were maintained above the in vitro IC50 of HDAC1, induction of histone acetylation was sustainable throughout the 24-h treatment period.

[0909] Example 14: Combination of anti-PD-1 and compound I in patients with KRAS mutation and STK11KO (CT26_STK11KO) Antitumor activity in colon cancer models with and without STK11 alterations (parental CT26 or wild-type CT26)

[0910] The in vivo anti-tumor efficacy of the combination therapy of anti-PD1 and Compound I was evaluated in the CT26 mouse model. CT26 is a colon cancer cell line with an endogenous KRAS G12D mutation. Experiments were performed in the parental / wild-type line and in a line engineered with STK11 knockout (CT26_STK11KO), generating an anti-PD1 resistance model with lower CD8+ T cell infiltration.

[0911] In each experiment, animals (8 / group) were divided into four groups. Group 1 was treated with control antibody anti-IgG2, Group 2 was treated with Compound I 75 mg / kg, Group 3 was treated with anti-PD1 antibody, and Group 4 was treated with Compound I 75 mg / kg and anti-PD1 antibody. Tumor volume and survival were monitored during treatment. For the CT26_STK11KO model, the tumor volume was monitored by individual animals ( Fig.15A ) and by treatment group ( Fig. 15B ) Tumor volume was plotted. Survival was plotted by treatment group ( Fig. 15C ).

[0912] For the CT26 parental model, by treatment group ( Fig.15D ) and for groups 1 and 4, by individual animal ( Fig.15E ) Tumor volume was plotted.

[0913] The experiment showed that Compound I as a single agent had better efficacy in the parental model (84% TGI) than in the STK11KO model (39% TGI), while combination treatment showed similar efficacy: ORR% in the parental model and STK11KO model were 86% (6 / 7) and 88% (7 / 8), respectively.

[0914] Example 15: Anti-tumor activity of the combination of anti-CTLA4 and Compound I in a colon cancer model

[0915] The in vivo anti-tumor efficacy of the combination therapy of anti-CTLA4 and Compound I was evaluated in the CT26 mouse model. CT26 is a colon cancer cell line with an endogenous KRAS G12D mutation. Experiments were performed in the parental / wild-type line and in a line engineered with STK11 knockout (CT26_STK11KO), generating an anti-CTLA4 resistance model.

[0916] The in vivo anti-tumor efficacy of dual combination therapy of anti-CTLA4 and Compound I was studied in the CT26 syngeneic model. CT26 is a colon cancer cell line. Experiments were also performed with the STK11 null CT26 model, which is CTLA4 resistant.

[0917] There were 8 mice in each group. Group 1 was treated with control antibody anti-IgG2, Group 2 was treated with Compound I 75 mg / kg, Group 3 was treated with anti-CTLA4 antibody, and Group 4 was treated with Compound I 75 mg / kg and anti-CTLA4 antibody. Tumor volume was monitored during treatment. Tumor volume was plotted by treatment group ( Fig.16A ), and for the parental model, individual animals in groups 1 and 4 were plotted ( Fig. 16B ). Tumor volume was plotted by treatment group ( Fig. 16C ), and for the STK11 knockout model, individual animals in groups 1 and 4 were plotted ( Fig.16D ).

[0918] Compound I showed better efficacy in the parental model (84% TGI) than in the STK11KO model (39% TGI). 100% of mice responded to the combination treatment in the parental model, while 75% (6 / 8) mice showed a response in the STK11KO model.

[0919] Table 7 summarizes the results from the combination treatment of Example 14 and Example 15.

[0920] Table 7. Summary of efficacy of combination of Compound I and checkpoint inhibitors in the CT26 model

[0921]

[0922]

[0923] *Compound I 75 mg / kg QD administration

[0924] Example 16: Anti-tumor activity of the combination of anti-PD-1 and compound I in the Lewis lung cancer model

[0925] In vivo anti-tumor efficacy studies of dual combination treatment of anti-PD1 and Compound I in the PD-1 resistant STK11 null 3LL model were performed. The parental (non-STK11 KO) 3LL line is relatively resistant to anti-PD1 treatment.

[0926] Animals (8 / group) were divided into 4 groups: Group 1 was treated with control antibody anti-IgG2, Group 2 was treated with anti-PD1 antibody, Group 3 was treated with Compound I 75 mg / kg, and Group 4 was treated with Compound I 75 mg / kg and anti-PD1 antibody. Tumor volume and survival were monitored during treatment. Tumor volume and survival were plotted by treatment group (respectively Fig.17A and Fig. 17B). Combination treatment with Compound I reduced the PD-1 resistance of this model caused by SKT11 knockout to the baseline characteristics of the parental line compared to the other groups, as shown by reduced tumor volume and increased survival rate in Group 4 over time.

[0927] The median time to event (TTE) and P values ​​compared to Control Group 1 (Vehicle) are summarized in Table 8.

[0928] Table 8. Median TTE of PD-1 resistant STK11 null 3LL model groups for indicated treatments

[0929] vehicle Anti-PD1 TNG260 combination Median TTE (days) 10 19 18 26 P relative to vehicle -- 0.0007 0.003 <0.0001

Claims

1. An HDAC inhibitor for use in a method of treating a subject having or at risk of developing cancer, the method comprising administering to the subject an effective amount of a histone deacetylase (HDAC) inhibitor, wherein the cancer is identified as having altered STK11 activity or expression.

2. An HDAC inhibitor for use as claimed in claim 1, wherein the histone deacetylase inhibitor is administered in combination with one or more additional therapeutic agents.

3. An HDAC inhibitor for use as claimed in claim 2, wherein at least one of the additional therapeutic agents is an immune checkpoint modulator.

4. An HDAC inhibitor for use in a method of treating cancer in a subject, the method comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment modulates and / or improves the ratio of Teff cells to Treg cells in a tumor or tumor microenvironment, wherein the cancer is identified as having altered STK11 activity or expression.

5. An HDAC inhibitor for use in a method of treating cancer in a subject, the method comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment reduces or depletes Treg cells in a tumor or tumor microenvironment, wherein the cancer is identified as having altered STK11 activity or expression.

6. An HDAC inhibitor for use in a method of treating cancer in a subject, the method comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment induces or increases expression of cytokines that promote anti-tumor activity, wherein the cancer is identified as having altered STK11 activity or expression.

7. The HDAC inhibitor for use in the method of claim 6, wherein the cytokine is selected from the group consisting of CXCL9, CXCL10 and CXCL11.

8. An HDAC inhibitor for use in a method of treating cancer in a subject, the method comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment reduces expression of cytokines that promote Treg cell recruitment, wherein the cancer is identified as having altered STK11 activity or expression.

9. The HDAC inhibitor for use in the method of claim 8, wherein the cytokine is CCL1 or CCL22.

10. An HDAC inhibitor for use in a method of treating cancer in a subject, the method comprising administering an HDAC inhibitor to the subject, wherein the administration of the HDAC inhibitor does not reduce erythroid or myeloid cell viability, wherein the cancer is identified as having altered STK11 activity or expression.

11. An HDAC inhibitor for use in a method of treating cancer in a subject, wherein the cancer exhibits an immune escape phenotype characterized by expression of a STK11 mutant, the method comprising: Administering an HDAC1,2 selective inhibitor, wherein the HDAC1,2 selective inhibitor is capable of attenuating or reversing the immune escape phenotype.

12. The HDAC inhibitor for use in a method according to claim 10 or 11, further comprising administering an immune checkpoint regulator.

13. An HDAC inhibitor for use in a method of treating cancer in a subject, the method comprising administering the HDAC inhibitor to the subject, wherein an immune checkpoint modulator has been, is being or will be administered to the subject, wherein the cancer is identified as having altered STK11 activity or expression.

14. An HDAC inhibitor for use in a method of treating cancer in a subject, the method comprising administering to the subject an immune checkpoint modulator, wherein the HDAC inhibitor has been, is being or will be administered to the subject, wherein the cancer is identified as having altered STK11 activity or expression.

15. The HDAC inhibitor for use according to claim 1, wherein the HDAC inhibitor is administered in combination with two or more additional therapeutic agents, wherein at least two of the additional therapeutic agents are immune checkpoint modulators.

16. An HDAC inhibitor for use as claimed in any one of claims 3 to 9 and 12 to 15, wherein each immune checkpoint regulator is independently a checkpoint inhibitor, a T cell co-stimulatory receptor agonist or a dendritic cell co-stimulatory receptor agonist.

17. An HDAC inhibitor for use as claimed in any one of claims 3 to 9 and 12 to 15, wherein at least one immune checkpoint regulator is independently a T cell co-stimulatory receptor agonist or a dendritic cell co-stimulatory receptor agonist.

18. An HDAC inhibitor for use as claimed in any one of claims 3 to 9 and 12 to 15, wherein at least one immune checkpoint modulator is a checkpoint inhibitor.

19. An HDAC inhibitor for use as claimed in claim 18, wherein each checkpoint inhibitor is independently selected from anti-CTLA-4 agents, anti-PD-1 agents, anti-PD-L1 agents, anti-4-1BB agents, anti-OX-40 agents, anti-GITR agents, anti-CD27 agents, anti-CD28 agents, anti-CD40 agents, anti-LAG3 agents, anti-ICOS agents, anti-TWEAKR agents, anti-HVEM agents, anti-TIM-1 agents, anti-TIM-3 agents, anti-VISTA agents and anti-TIGIT agents.

20. The HDAC inhibitor for use as claimed in claim 18, wherein each checkpoint inhibitor is independently selected from an anti-CTLA-4 agent, an anti-PD-1 agent and an anti-PD-L1 agent.

21. The HDAC inhibitor for use according to claim 18, wherein the checkpoint inhibitor is an anti-CTLA-4 agent.

22. The HDAC inhibitor for use as claimed in claim 18, wherein the checkpoint inhibitor is an anti-PD1 agent.

23. The HDAC inhibitor for use according to claim 18, wherein the checkpoint inhibitor is an anti-PD-L1 agent.

24. The HDAC inhibitor for use according to claim 1, wherein the HDAC inhibitor is administered in combination with an anti-CTLA-4 agent and an anti-PD-1 agent or an anti-PD-L1 agent.

25. An HDAC inhibitor for use as claimed in any one of claims 3 to 9 and 12 to 24, wherein each immune checkpoint inhibitor is independently an antibody.

26. An HDAC inhibitor for use as claimed in claim 25, wherein each of the checkpoint inhibitors is independently selected from anti-CTLA-4 antibodies, anti-PD-1 antibodies, anti-PD-L1 antibodies, anti-4-1BB antibodies, anti-OX-40 antibodies, anti-GITR antibodies, anti-CD27 antibodies, anti-CD28 antibodies, anti-CD40 antibodies, anti-LAG3 antibodies, anti-ICOS antibodies, anti-TWEAKR antibodies, anti-HVEM antibodies, anti-TIM-1 antibodies, anti-TIM-3 antibodies, anti-VISTA antibodies and anti-TIGIT antibodies.

27. The HDAC inhibitor for use as claimed in claim 25, wherein each checkpoint inhibitor is independently selected from anti-CTLA-4 antibody, anti-PD-1 antibody and anti-PD-L1 antibody.

28. An HDAC inhibitor for use as claimed in claim 25, wherein each immune checkpoint inhibitor is independently selected from nivolumab; CT-011; AMP-224; pembrolizumab; pidilizumab; cemiplizumab; dostalimumab; palolizumab; spartalizumab; carrelizumab; sazanalizumab, sintilimab; tislelizumab; toripalizumab; rivalizumab; MEDI0680; bruglimumab and gelotrimazole.

29. The HDAC inhibitor for use as claimed in claim 25, wherein each checkpoint inhibitor is independently selected from an anti-PD1 antibody and an anti-PD-L1 antibody.

30. The HDAC inhibitor for use as claimed in claim 25, wherein the checkpoint inhibitor is an anti-CTLA-4 antibody.

31. The HDAC inhibitor for use as claimed in claim 25, wherein the checkpoint inhibitor is an anti-PD1 antibody.

32. The HDAC inhibitor for use as claimed in claim 25, wherein the checkpoint inhibitor is an anti-PD1-L1 antibody.

33. The HDAC inhibitor for use as claimed in claims 26, 27 and 30, wherein the anti-CTLA-4 antibody is ipilimumab.

34. The HDAC inhibitor for use according to any one of claims 26, 27, 29 and 31, wherein the anti-PD-1 antibody is pembrolizumab or nivolumab.

35. The HDAC inhibitor for use according to any one of claims 26, 27, 29 and 31, wherein the anti-PD-1 antibody is pembrolizumab.

36. The HDAC inhibitor for use according to any one of claims 26, 27, 29 and 31, wherein the anti-PD-1 antibody is nivolumab.

37. The HDAC inhibitor for use according to any one of claims 26, 27, 29 and 32, wherein the anti-PD-L1 antibody is atezolizumab (CAS No. 1380723-44-3), avelumab (CAS No. 1537032-82-8) or durvalumab (CAS No. 1428935-60-7).

38. An HDAC inhibitor for use as claimed in any one of claims 3 to 9 and 12 to 24, wherein the immune checkpoint regulator is a T cell co-stimulatory receptor agonist or a dendritic cell co-stimulatory receptor agonist.

39. An HDAC inhibitor for use as claimed in any one of claims 2 to 9 and 12 to 38, wherein at least one additional therapeutic agent is a targeting agent.

40. An HDAC inhibitor for use as claimed in claim 39, wherein each targeting agent is independently selected from anti-angiogenic agents (e.g., anti-VEGF agents), KRAS inhibitors, ALK inhibitors, ROS1 inhibitors, BRAF inhibitors, RET inhibitors, MEK inhibitors, MET inhibitors and TRK inhibitors.

41. An HDAC inhibitor for use as claimed in claim 39, wherein each targeting agent is independently selected from bevacizumab, ramucirumab, sotolacib, crizotinib, ceritinib, alectinib, brigatinib, lorlatinib, entrectinib, dabrafenib, trametinib, capmatinib, tepotinib and larotrectinib.

42. An HDAC inhibitor for use as claimed in any one of claims 3 to 9 and 12 to 41, wherein at least one additional therapeutic agent is a chemotherapeutic agent.

43. The HDAC inhibitor for use as claimed in claim 42, wherein each chemotherapeutic agent is independently selected from cisplatin, carboplatin, paclitaxel, nab-paclitaxel (nab-paclitaxel), docetaxel, gemcitabine, vinorelbine, etoposide and pemetrexed.

44. An HDAC inhibitor for use as claimed in claim 42, wherein at least one chemotherapeutic agent is a platinum-containing therapeutic agent.

45. An HDAC inhibitor for use as claimed in claim 42, wherein one chemotherapeutic agent is a platinum-containing chemotherapeutic agent (eg, cisplatin) and the second chemotherapeutic agent is pemetrexed.

46. ​​An HDAC inhibitor for use as claimed in any one of claims 3 to 9 and 12 to 45, wherein at least one additional therapeutic agent is radiation.

47. An HDAC inhibitor for use according to any one of claims 1 to 46, wherein the cancer is resistant to anti-PD1 therapy or anti-PD-L1 therapy.

48. An HDAC inhibitor for use as claimed in any one of claims 1 to 47, wherein the cancer is resistant to chemotherapy (eg, platinum-containing chemotherapy).

49. An HDAC inhibitor for use as claimed in any one of claims 1 to 48, wherein the cancer is unresponsive to or does not benefit from treatment with an immune checkpoint modulator when administered alone or as part of a treatment regimen that does not include an HDAC inhibitor.

50. An HDAC inhibitor for use as described in any one of claims 1 to 49, wherein the cancer is selected from: lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC), squamous cell lung cancer), colorectal cancer (e.g., colon adenocarcinoma, rectal adenocarcinoma), breast cancer (e.g., invasive ductal carcinoma), pancreatic cancer (e.g., pancreatic adenocarcinoma), endometrial cancer (e.g., endometrioid carcinoma), neuroendocrine cancer (e.g., large cell neuroendocrine carcinoma), melanoma, non-melanoma skin cancer (e.g., squamous cell carcinoma of the skin), bile duct cancer, gallbladder cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), bladder cancer (e.g., bladder urothelial carcinoma), prostate cancer (e.g., prostate adenocarcinoma), cervical cancer, endocervical cancer, or cancer of unknown primary (e.g., adenocarcinoma of unknown primary).

51. An HDAC inhibitor for use as claimed in claim 50, wherein the cancer is lung cancer.

52. An HDAC inhibitor for use as claimed in claim 51, wherein the cancer is lung adenocarcinoma.

53. The HDAC inhibitor for use according to claim 51, wherein the cancer is non-small cell lung cancer (NSCLC).

54. An HDAC inhibitor for use according to claim 53, wherein the cancer is non-squamous non-small cell lung cancer (NSCLC).

55. The HDAC inhibitor for use according to claim 50, wherein the cancer is colorectal cancer or colon adenocarcinoma.

56. An HDAC inhibitor for use according to any one of claims 1 to 55, wherein the cancer has reduced STK11 expression.

57. An HDAC inhibitor for use according to any one of claims 1 to 55, wherein the cancer has a STK11 mutation.

58. An HDAC inhibitor for use according to any one of claims 1 to 55, wherein the cancer is identified as having a STK11 mutation and one or more additional mutations.

59. An HDAC inhibitor for use as claimed in claim 58, wherein the additional mutation is selected from the group consisting of a KRAS mutation and a KEAP1 mutation.

60. An HDAC inhibitor for use as claimed in claim 58, wherein the additional mutation is a KRAS mutation.

61. The HDAC inhibitor for use as claimed in claim 59 or 60, wherein the KRAS mutation is a mutation at position G12, optionally wherein the KRAS mutation is selected from a G12D mutation, a G12C mutation, a G12V mutation or a combination thereof.

62. An HDAC inhibitor for use as claimed in claim 59, wherein the additional mutation is a KEAP1 mutation.

63. The HDAC inhibitor for use as claimed in claim 59, wherein the additional mutations are KRAS mutations and KEAP1 mutations.

64. The HDAC inhibitor for use according to any one of claims 57 to 63, wherein the STK11 mutation is an inactivating (loss-of-function) mutation.

65. An HDAC inhibitor for use according to any one of claims 1 to 64, wherein the histone deacetylase inhibitor is a selective inhibitor of histone deacetylase 1 (HDAC1 selective inhibitor).

66. An HDAC inhibitor for use according to any one of claims 1 to 64, wherein the histone deacetylase inhibitor is a selective inhibitor of histone deacetylase 1 and histone deacetylase 2 (HDAC1,2 selective inhibitor).

67. An HDAC inhibitor for use according to any one of claims 1 to 64, wherein the histone deacetylase inhibitor is a selective HDAC class I inhibitor.

68. An HDAC inhibitor for use according to any one of claims 1 to 67, wherein the histone deacetylase inhibitor is a CoREST selective deacetylase inhibitor.

69. A method for determining the sensitivity of a subject having or diagnosed with cancer to treatment with an HDAC inhibitor, the method comprising: Determining: i) the presence or absence of a STK11 mutation; and / or ii) the level of STK11 activity or expression in the subject or a sample derived from the subject; wherein the presence of a STK11 mutation and / or altered level of STK11 activity or expression indicates sensitivity to treatment with an HDAC inhibitor.

70. An HDAC inhibitor for use as claimed in any one of claims 1 to 68, wherein the HDAC inhibitor is a compound of formula (I) or a pharmaceutically acceptable salt thereof.

71. A method for determining the sensitivity of a subject having or diagnosed with cancer to treatment with a combination of an HDAC inhibitor and an immune checkpoint modulator, the method comprising: Determining: i) the presence or absence of a STK11 mutation in the subject or a sample derived from the subject; and / or ii) the level of STK11 activity or expression; wherein the presence of a STK11 mutation and / or the altered level of STK11 activity or expression indicates sensitivity to a combination treatment with an HDAC inhibitor and an immune checkpoint modulator.

72. A method for determining the sensitivity of a subject having or diagnosed with cancer to the use of an HDAC inhibitor in the treatment method of any one of claims 1 to 70, the method for determining comprising: Determining: i) the presence or absence of a STK11 mutation in the subject or a sample derived from the subject; and / or ii) the level of STK11 activity or expression; wherein the presence of a STK11 mutation and / or the altered level of STK11 activity or expression indicates sensitivity to the use of an HDAC inhibitor in the therapeutic method of any one of claims 1 to 70.

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