HDAC inhibitors for treating cancers in which STK11 activity or expression is altered

Abstract

The present disclosure relates to methods of treating cancer, including cancers in which STK11 activity or expression is altered, by administering an effective amount of a histone deacetylase (HDAC) inhibitor. The present invention provides, for example, an HDAC inhibitor for use in a method of treating a subject having cancer 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 has been identified as having altered STK11 activity or expression.

Description

[Technical Field]

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS This application claims priority to and the benefit of U.S. Provisional Patent Application No. 63 / 395,503, filed August 5, 2022, U.S. Provisional Patent Application No. 63 / 422,723, filed November 4, 2022, U.S. Provisional Patent Application No. 63 / 490,217, filed March 14, 2023, and U.S. Provisional Patent Application No. 63 / 496,290, filed April 14, 2023, the entire contents of which are incorporated by reference herein for all purposes. [Background technology]

[0002] STK11 is a tumor suppressor gene that, when deleted or inactivated, drives immune evasion and is frequently mutated in lung adenocarcinomas, such as non-small cell lung cancer (NSCLC). Identifying drug targets that can abolish immune evasion caused by STK11 loss-of-function mutations may reverse immune evasion in cancer cells, allowing immune cells to eliminate cancer cells harboring STK11 mutations.

[0003] The current standard of care for treating patients with lung adenocarcinoma typically involves the administration of anti-PD-1 or anti-PD-L1 therapy. However, lung adenocarcinoma patients with STK11 loss-of-function mutations respond poorly to such anti-PD-1 and anti-PD-L1 therapy. 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):supp 102(2019) (DOI:10.1200 / JCO.2019.37.15_suppl.102) (each of which is incorporated herein by reference in its entirety).

[0004] Attempts to improve outcomes for patients with lung adenocarcinoma include targeting specific KRAS (e.g., KRAS G12CThis includes the development of a class of compounds called Kirsten rat sarcoma 2 viral oncogene homolog (KRAS) inhibitors, which have been developed to treat cancers (e.g., NSCLC) in patients with KRAS mutations. However, such compounds have certain limitations, and there remains a need to improve outcomes for patients for whom current standard therapies are inadequate. Therefore, there is a need to identify methods to treat cancer patients with STK11 mutations. [Prior art documents] [Non-patent literature]

[0005] [Non-Patent Document 1] Skoulidis, F., et al Cancer Discovery 8(7):822-835(2018)(DOI:10.1158 / 2159-8290.CD-18-0099) [Non-patent document 2] Skoulidis,F.,et al Journal of Clinical Oncology 37(15):supp 102(2019)(DOI:10.1200 / JCO.2019.37.15_suppl.102) Summary of the Invention [Means for solving the problem]

[0006] Provided herein is 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 inhibitor, wherein the cancer has been identified as having altered STK11 activity or expression.

[0007] Provided herein is a method 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 in which STK11 activity or expression is altered, and selecting the thus identified subject for treatment with the HDAC inhibitor.

[0008] Also provided is a method for determining a subject's sensitivity to treatment with an HDAC inhibitor, the method comprising determining i) the presence or absence of an 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 the STK11 mutation and / or an altered level of STK11 activity or expression indicates sensitivity to treatment with an HDAC inhibitor. [Brief explanation of the drawings]

[0009] [Figure 1A]

[0033] Figure 1 shows tumor growth curves for MC38_sgSTK11 tumor-bearing mice treated with control antibody anti-IgG2a (10 mg / kg, intraperitoneally, twice weekly), a combination of Compound I (3, 10, 30, 75, and 150 / 100 mg / kg, orally, once daily) plus control antibody anti-IgG2a (10 mg / kg, intraperitoneally, twice weekly), an anti-PD1 inhibitor (10 mg / kg, intraperitoneally, twice weekly), and a combination of Compound I (3, 10, 30, 75, and 150 / 100 mg / kg, orally, once daily) plus an anti-PD1 inhibitor (10 mg / kg, intraperitoneally, twice weekly). Data are plotted according to the groups described in Example 1. [Figure 1B] Figure 1 shows tumor growth curves in the MC38 STK11 knockout mouse model treated with either anti-IgG2a (10 mg / kg i.p. bid), anti-PD1 (10 mg / kg i.p. bid), Compound I (30 mg / kg orally qd), or anti-PD1 (10 mg / kg i.p. bid) plus Compound I (30 mg / kg orally qd), monitored over the treatment period and plotted for individual animals. [Figure 2A]Figure 1 shows survival curves for mice bearing MC38_sgSTK11 tumors treated with control antibody anti-IgG2a (10 mg / kg, intraperitoneal, twice weekly), a combination of Compound I (3, 10, 30, 75, and 150 / 100 mg / kg, oral, once daily) plus control antibody anti-IgG2a (10 mg / kg, intraperitoneal, twice weekly), or an anti-PD1 inhibitor (10 mg / kg, intraperitoneal, twice weekly). Data are plotted according to the groups described in Example 1. [Figure 2B] Figure 1 shows survival curves for MC38_sgSTK11 tumor-bearing mice treated with control antibody anti-IgG2a (10 mg / kg, intraperitoneal, twice weekly), a combination of Compound I (3, 10, 30, 75, and 150 / 100 mg / kg, oral, once daily) plus an anti-PD1 inhibitor (10 mg / kg, intraperitoneal, twice weekly), or an anti-PD1 inhibitor (10 mg / kg, intraperitoneal, twice weekly). Data are plotted according to the groups described in Example 1. [Figure 2C] Figure 1 shows survival plots of mice bearing STK11-deficient MC38 tumors treated with anti-IgG2a 10 mg / kg (i.p., twice a week), anti-IgG2a 10 mg / kg (i.p., twice a week) plus compound I 30 mg / kg (p.o., once daily), anti-PD1 10 mg / kg (i.p., twice a week), or anti-PD1 10 mg / kg (i.p., twice a week) plus compound I 30 mg / kg (p.o., once daily), as indicated. [Figure 3A] Tumor growth curves are shown for untreated control mice and mice surviving treatment with either Compound I (75 mg / kg, orally, once daily) plus control antibody anti-IgG2a (10 mg / kg, intraperitoneally, twice weekly) or exemplary HDAC inhibitors (3, 10, 30, 75, and 150 / 100 mg / kg) plus anti-PD1 inhibitors (10 mg / kg, intraperitoneally, twice weekly) when re-challenged with MC38_sgSTK11 as described in Example 2. [Figure 3B]Plots of tumor volume in mice (combined into a single group) re-challenged with STK11-deficient MC38 tumors are shown alongside a control group of previously untreated mice, as described in Example 2. All animals remained off treatment, and tumor size was plotted over time after re-challenge. [Figure 4] Figure 1 shows tumor growth curves for mice bearing MC38_sgSTK11 tumors treated with control antibody anti-IgG2a (10 mg / kg, i.p., twice weekly), Compound I (30 mg / kg, orally, once daily), anti-PD1 inhibitor (10 mg / kg, i.p., twice weekly), and a combination of Compound I (30 mg / kg, orally, once daily) and anti-PD1 inhibitor (10 mg / kg, i.p., twice weekly). Mice that experienced complete tumor regression in the initial experiment were rechallenged with MC38_sgSTK11 on day 69. [Figure 5A] Volcano plot of an unbiased in vivo CRISPR screen identifying HDAC1 knockout as a sensitizer to anti-PD1 in STK11-deficient MC38 tumors. [Figure 5B] A waterfall plot of Project Achilles CRISPR scores for HDAC1, HDAC2, and HDAC3 in a panel of cell lines is shown. Negative scores indicate loss of cells due to knockout of the indicated gene. [Figure 6A] 1 shows a graph of dose-dependent binding of Compound I to HDAC1 by intracellular NanoBRET target binding assay. [Figure 6B] 1 shows a graph of dose-dependent binding of Compound I to HDAC2 by intracellular NanoBRET target binding assay. [Figure 6C] 1 shows a graph of dose-dependent binding of Compound I inhibitor to HDAC3 by an intracellular NanoBRET target binding assay. [Figure 7A]Figure 1 shows tumor growth curves in the CT26 STK11 knockout mouse model treated with either control antibody anti-IgG2a (10 mg / kg, intraperitoneal, twice weekly), anti-IgG2a (10 mg / kg, intraperitoneal, twice weekly) plus Compound I (75 mg / kg, oral, once daily), anti-PD1 (10 mg / kg, intraperitoneal, twice weekly), or (anti-PD1 10 mg / kg, intraperitoneal, twice weekly) plus Compound I (75 mg / kg, oral, once daily). Tumor volume was monitored over the treatment period and plotted for individual animals. STK11 knockout renders CT26 tumors resistant to anti-PD1 treatment. [Figure 7B] Figure 1 shows survival plots of mice bearing STK11-deficient CT26 tumors treated with control antibody anti-IgG2a (10 mg / kg, intraperitoneal, twice weekly), anti-IgG2a (10 mg / kg, intraperitoneal, twice weekly) plus Compound I (75 mg / kg, oral, once daily), anti-PD1 (10 mg / kg, intraperitoneal, twice weekly), or anti-PD1 (10 mg / kg, intraperitoneal, twice weekly) plus Compound I (75 mg / kg, oral, once daily), as indicated. [Figure 8A] 1 shows 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, intraperitoneal, twice a week), anti-IgG2a (10 mg / kg, intraperitoneal, twice a week) plus Compound I (30 mg / kg, oral, once daily), anti-PD1 (10 mg / kg, intraperitoneal, twice a week), or anti-PD1 (10 mg / kg, intraperitoneal, twice a week) plus Compound I (30 mg / kg, oral, once daily), as indicated. [Figure 8B] 1 shows 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, intraperitoneal, twice a week), anti-IgG2a (10 mg / kg, intraperitoneal, twice a week) plus Compound I (75 mg / kg, oral, once daily), anti-PD1 (10 mg / kg, intraperitoneal, twice a week), or anti-PD1 (10 mg / kg, intraperitoneal, twice a week) plus Compound I (75 mg / kg, oral, once daily), as indicated. [Figure 9A] 1 shows a graph depicting the changes in gene expression of CXCL9, 10, and 11 as measured by Nanostring PanCancer IO 360 in STK11− / − MC38 tumors treated with 30 mg / kg of Compound I or anti-PD1 alone or in combination for 7 days. [Figure 9B] 1 shows a graph depicting the changes in gene expression of CCL1 and CCL22 measured by Nanostring PanCancer IO 360 in STK11− / − MC38 tumors treated with 30 mg / kg of Compound I or anti-PD1 alone or in combination for 7 days. [Figure 9C] 1 shows a graph depicting changes in gene expression of HLA genes measured by Nanostring PanCancer IO 360 in STK11- / -MC38 tumors treated with 0.2 uM Compound I or vehicle control for 4 days. [Figure 10A] 1 shows a graph of TIL profiling by flow cytometry of STK11-deficient MC38 tumors treated with 10 mg / kg of Compound I alone or in combination with anti-PD1 for 7 days. [Figure 10B] 1 shows a graph of TIL profiling by flow cytometry of STK11-deficient MC38 tumors treated with 10 mg / kg of Compound I alone or in combination with anti-PD1 for 7 days. [Figure 10C] Graphs of IFNγ expression by tumors (C) or in co-cultures of human NSCLC cells with PBMCs and fibroblasts (D) treated with Compound I alone or in combination with anti-PD1 for 72 hours are shown. [Figure 10D] Graphs of IFNγ expression by tumors (C) or in co-cultures of human NSCLC cells with PBMCs and fibroblasts (D) treated with Compound I alone or in combination with anti-PD1 for 72 hours are shown. [Figure 10E]1 shows graphs profiling the relative abundance of total T cells and regulatory T cells in STK11-deficient MC38 tumors from mice treated with vehicle, 10 mg / kg of Compound I alone, or in combination with anti-PD1 for 7 days. [Figure 11A] Plot of gene expression changes in A549 cells treated with vorinostat, domatinostat, and Compound I using the PanCancer IO360 panel, along with the three highest ranked Gene Ontology groups for each compound as determined from NanoString data using nSolver software. [Figure 11B] Plot of gene expression changes in A549 cells treated with vorinostat, domatinostat, and Compound I using the PanCancer IO360 panel, along with the three highest ranked Gene Ontology groups for each compound as determined from NanoString data using nSolver software. [Figure 11C] Plot of gene expression changes in A549 cells treated with vorinostat, domatinostat, and Compound I using the PanCancer IO360 panel, along with the three highest ranked Gene Ontology groups for each compound as determined from NanoString data using nSolver software. [Figure 12A] 1 shows plots of erythroid and myeloid cell viability following treatment with Compound I at the different concentrations indicated. The effective dose range of Compound I is also plotted (shaded area, 3 mg / kg to 75 mg / kg). [Figure 12B] 1 shows tumor growth curves of STK11-deficient MC38 tumors in a mouse model treated with clinically relevant doses of vorinostat, alone or in combination with an anti-PD1 antibody. [Figure 12C] 1 shows tumor growth curves of STK11-deficient MC38 tumors in a mouse model treated with clinically relevant doses of Compound I, alone or in combination with an anti-PD1 antibody. [Figure 12D]1 shows plots comparing the concentration of Compound I with the inhibition of HDAC1 or HDAC3 in vivo. The shaded boxes indicate the tolerated dose and effective dose range of Compound I. [Figure 13] 1 shows plots of predicted plasma concentrations (ng / mL) over time after administration to humans and the prediction window between effective and non-selective doses. [Figure 14A] 1 shows a Western blot of acetylated histone 3 lysine 9 (H3K9Ac) from mouse MC38 tumor tissue after treatment with Compound I for 7 days at the doses indicated. [Figure 14B] Quantification of H3K9Ac Western blot in (E) is shown and normalized to total histone H3. [Figure 14C] Plasma concentrations of Compound I administered at 30 mg / kg, 100 mg / kg, and 300 mg / kg QD for 2 days are shown, starting 1 hour after the last dose. [Figure 14D] MC38 tumor-bearing mice were dosed with Compound I at 30 mg / kg, 100 mg / kg, and 300 mg / kg QD for 2 days, and the levels of acetyl histone H2B were quantified by flow cytometry in PBMC samples at the indicated time points. [Figure 14E] MC38 tumor-bearing mice were dosed with Compound I at 30 mg / kg, 100 mg / kg, and 300 mg / kg QD for 2 days, and acetyl histone H3B levels were quantified by Western blot in tumor samples collected at the indicated time points. [Figure 15A] Figure 1 shows tumor growth curves in a STK11-null CT26 (KRAS G12D mutant colon cancer) syngeneic mouse model. Mice were treated with either 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 over the treatment period and plotted for each individual animal. [Figure 15B]Figure 1 shows tumor growth curves in an STK11-null CT26 (KRAS G12D mutant colon cancer) model. Animals were treated with either 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 over the treatment period and plotted by treatment group. [Figure 15C] 1 shows survival curves for a KRAS G12D mutant CT26-STK11 knockout syngeneic mouse model treated with either anti-IgG2, anti-PD1 (10 mg / kg), Compound I (75 mg / kg), or anti-PD1 (10 mg / kg) + Compound I (75 mg / kg). [Figure 15D] Figure 1 shows tumor growth curves in a wild-type / parental CT26 (KRAS G12D mutant colon cancer) model. Animals were treated with either 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 over the treatment period and plotted by treatment group. [Figure 15E] Figure 1 shows tumor growth curves in a wild-type / parental CT26 (KRAS G12D mutant colon cancer) model. Animals were treated with either 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 over the treatment period and plotted for individual animals in Groups 1 and 4. [Figure 16A] Figure 1 shows tumor growth curves in wild-type / parental CT26 (KRAS G12D mutant colon cancer) models. Animals were treated with either 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 over the treatment period and plotted by treatment group. [Figure 16B]1 shows tumor growth curves in a wild-type / parental CT26 (KRAS G12D mutant colon cancer) model. Animals were treated with either 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 over the treatment period and plotted for individual animals in Groups 1 and 4. [Figure 16C] 1 shows tumor growth curves in an STK11-null CT26 (KRAS G12D mutant colon cancer) model treated with either 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 over the treatment period and plotted by treatment group. [Figure 16D] 1 shows tumor growth curves in an STK11-null CT26 (KRAS G12D mutant colon cancer) model treated with either anti-IgG2, Compound I (75 mg / kg), anti-CTL4A (10 mg / kg), or anti-CTL4A (10 mg / kg) + Compound I (75 mg / kg). Tumor volumes were monitored over the treatment period and plotted for individual animals in Groups 1 and 4. [Figure 17A] Figure 1 shows tumor growth curves in the STK11-null 3LL model treated with either anti-IgG2, anti-PD1 (10 mg / kg), Compound I (75 mg / kg), or anti-PD1 (10 mg / kg) + Compound I (75 mg / kg). Tumor volumes were monitored for the indicated time periods and plotted by treatment group. [Figure 17B] Figure 1 shows survival curves for STK11-null 3LL models treated with either anti-IgG2, anti-PD1 (10 mg / kg), Compound I (75 mg / kg), or anti-PD1 (10 mg / kg) + Compound I (75 mg / kg). Survival rates are plotted by treatment group. DETAILED DESCRIPTION OF THE INVENTION

[0010] 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 has been identified as having altered STK11 activity or expression.

[0011] The disclosure herein describes exemplary methods, parameters, etc. However, it should be recognized that such description is not intended as a limitation on the scope of the disclosure, but rather is provided as a description of exemplary embodiments to assist the reader accordingly.

[0012] As used in this disclosure, certain words and phrases (and grammatical equivalents, e.g., conjugations, inflections, etc.) are generally intended to have the meanings defined herein, unless expressly indicated otherwise or the context in which they are used dictates otherwise.

[0013] STK11 Serine / threonine kinase 11 protein, abbreviated as STK11, is also known as PJS, liver kinase B1 (LKB1), renal cancer antigen NY-EN-19, and hLKB1 protein, and is a protein kinase encoded by the STK11 gene (HGNC symbol STK11, Ensembl ID ENSG00000118046.16) in humans. Koenig, M. et al. Cancer Research (2021) 81 (16): 4194-4204 (doi: 10.1158 / 0008-5472) (the entire contents of which are incorporated herein by reference) is described as follows: "The serine / threonine kinase LKB1 belongs to the calcium-calmodulin family, which is ubiquitously expressed in several tissues and is highly conserved among eukaryotes. Over the past 15 years, LKB1 has been implicated in many essential biological processes, including cell cycle control, cellular energy metabolism, angiogenesis, cell polarity, and DNA damage response. The subcellular localization and activity of LKB1 are regulated through interactions with STRAD and armadillo repeat-containing mouse protein 25 (Mo25). 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 indicates that LKB1 autophosphorylates itself on at least four of these residues, while the remaining four are phosphorylated by upstream kinases. These post-translational modifications do not appear to alter its kinase activity but are involved in distinct biological responses associated with LKB1 and may allow LKB1 to interact with other partners."

[0014] The STK11 gene is located on human chromosome 19p13. This gene contains nine coding exons and one non-coding exon and encodes the 433-amino acid serine / threonine protein kinase STK11 protein, which 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 (approximately 15%), non-melanoma skin cancer (approximately 5%), cholangiocarcinoma (approximately 3%), ovarian cancer (approximately 3%), and pancreatic adenocarcinoma (approximately 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),pl 1;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).

[0015] STK11 mutations found in cancer include point mutations (e.g., nonsense or frameshift mutations) or small indels that are predicted to be deleterious and oncogenic (Chakravarty D, et al. JCO Precis Oncol. 2017, 2017). STK11 gene mutations often co-occur with other STK11 genomic alterations, such as copy number changes or gene deletions. These mutations and alterations result in loss of STK11 protein expression or loss of wild-type STK11 protein activity. Non-mutational mechanisms for altered expression (e.g., loss of expression) or activity (e.g., loss of wild-type activity) include genomic loss or promoter methylation.

[0016] Koenig, M. et al Cancer Research (2021) 81(16):4194-4204 (doi:10.1158 / 0008-5472) (incorporated herein by reference in its entirety) further states: "More than 400 unique mutations in the STK11 gene have been reported to date, with approximately 70% of these mutations promoting protein truncation and the remaining 30% being missense mutations (COSMIC and TCGA-Bioportal). As a tumor suppressor, numerous 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, and re-expression of LKB1 leads to G1 cell cycle arrest. The role of LKB1 in regulating cellular metabolism through AMPK signaling has been widely reported. The LKB1-AMPK axis is known to control lipid and glucose metabolism, act as a negative regulator of the Warburg effect, and suppress tumor growth. LKB1 is also important in regulating catabolic pathways, increasing glucose uptake and regulating glycolysis, or LKB1-AMPK stimulation results in the mobilization of stored lipids by stimulating lipases, such as adipocyte triglyceride lipase, to release fatty acids from stored triglycerides. The LKB1-AMPK stimulation pathway also includes increased macromolecular turnover through autophagy, which allows for the turnover of old and damaged molecules and the replenishment of nutrient stores during starvation. Furthermore, several studies suggest a role for LKB1 in regulating physiological and pathological angiogenesis through its involvement in the regulation of VEGF, MMP-2, MMP-9, bFGF, and NOX1 expression, as well as neuropilin-1 degradation. Loss-of-function studies of LKB1 have also revealed its role in cell polarity and motility through the regulation of PAK115 and the modulation of FAK phosphorylation status and CDC42 activation. Collectively, these functions contribute to the induction of epithelial-mesenchymal transition (EMT) and metastasis. Additionally, in vivo studies provide evidence that LKB1 contributes to genotoxic DNA damage response and DNA damage repair.

[0017] It has been reported that lung adenocarcinoma patients with cancer cells harboring STK11 loss-of-function mutations respond poorly to standard anti-PD-1 and anti-PD-L1 therapy. 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):supp 102(2019) (DOI:10.1200 / JCO.2019.37.15_suppl.102) (each of which is incorporated herein by reference in its entirety). A pooled CRISPR-Cas9-based in vivo screen identified STK11 as a potential immune evasion strategy. In this screen, reduction of STK11 in immunocompetent mice induced resistance to immune pressure. Min, C., et al Cancer Research 81(Supp.13):1905(2021)(DOI:10.1158 / 1538-7445.AM2021-1905) (incorporated by reference in its entirety).

[0018] STK11 mutations are associated with low levels of T cell inflammation and tumor PD-L1 expression. Biton J, et al. Clin Cancer Res 2018;24:5710-23 (incorporated herein by reference in its entirety).

[0019] Similarly, STK11 mutations in NSCLC are associated with poor response 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 (incorporated herein by reference in its entirety).

[0020] As used herein, "altered expression" (e.g., altered expression of STK11) refers to a change in the expression level of a protein (i.e., a decrease or increase in the expression level) in a cell (e.g., a cancer cell) compared to a reference cell (e.g., a healthy cell). In some embodiments, an increase or decrease in the expression level of a protein (e.g., STK11 protein) can be assessed by determining the copy number of the gene encoding the protein (e.g., the copy number of the STK11 gene) in a patient sample (e.g., a tumor sample) and comparing that level to that present in a control sample (e.g., a healthy tissue sample). In some embodiments, an increase or decrease in the expression level of a protein (e.g., STK11 protein) can be assessed by determining the level of the protein (e.g., STK11 protein) or mRNA in a patient sample (e.g., a tumor sample) and comparing that level to that present in a control sample (e.g., a healthy tissue sample).

[0021] 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 (i.e., a decrease or increase in the level of serine / threonine kinase activity of STK11) in a cell (e.g., a cancer cell) compared to a reference cell (e.g., a healthy cell). A mutation in the gene encoding the protein (e.g., an STK11 mutation) can result in expression of the protein (e.g., a mutant STK11 protein) at an enzymatic activity level that differs from the enzymatic activity of the wild-type protein.

[0022] As used herein, an "STK11 mutation" refers to a mutation selected from the following: (i) a mutation in the nucleotide sequence encoding STK11; (ii) a mutation in a regulatory sequence controlling expression of the nucleotide sequence encoding STK11; (iii) a mutation in a nucleotide encoding a protein that interacts with the transcript of the STK11 gene; (iv) mutations in the translation product of the STK11 gene, and (v) Mutations in the transcripts of the STK11 gene.

[0023] In some embodiments, the STK11 mutation is a mutation selected from the following: (i) a mutation in the nucleotide sequence encoding STK11; (ii) a mutation in a regulatory sequence controlling expression of the nucleotide sequence encoding STK11; (iii) a mutation in a nucleotide encoding a protein that interacts with the transcript of the STK11 gene.

[0024] In some embodiments, the STK11 mutation is a mutation in the nucleotide sequence encoding STK11. In some embodiments, the STK11 mutation is a mutation in a regulatory sequence that controls the expression of the nucleotide sequence encoding STK11. In some embodiments, the STK11 mutation is a mutation in a nucleotide that encodes a protein that interacts with the transcription product of the STK11 gene. In some embodiments, the STK11 mutation is a mutation in the translation product of the STK11 gene. In some embodiments, the STK11 mutation is a mutation in the transcription product of the STK11 gene.

[0025] In some embodiments, the STK11 mutation is an inactivating mutation or a loss-of-function mutation.

[0026] As used herein, a "loss-of-function mutation," also referred to as an "inactivating mutation," refers to a mutation that results in the expression of a mutant protein that exhibits reduced or no biological or enzymatic activity compared to the wild-type protein. A loss-of-function mutation in a gene (e.g., the STK11 gene) may not result in the expression of the wild-type protein, or may result in the expression of only a fragment of the protein that exhibits reduced or no biological or enzymatic activity compared to the wild-type protein. The mutation may be present 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).

[0027] In some embodiments, the loss-of-function mutation (e.g., a loss-of-function STK11 mutation) is one of the following: 1) Nonsense mutations (genetic changes that cause premature termination of a protein). The altered protein can be partially or completely inactivated, resulting in altered or lost protein function; 2) Frameshift mutations (insertion or deletion involving a number of base pairs that is not a multiple of three, resulting in a disruption of the triplet reading frame of a DNA sequence). Frameshift mutations generally result in the production of a premature termination (stop) codon, resulting in a truncated protein product; 3) splice site mutations (genetic changes in DNA sequence occurring at exon-intron boundaries (splice sites) that can interfere with RNA splicing, resulting in the loss of exons or inclusion of introns and alterations in the protein-coding sequence; 4) Translation start site mutations (mutations that disrupt the translation initiation sequence and prevent translation from initiating at the normal start site, resulting in loss of mRNA translation or translation of abnormal messenger RNA (mRNA)). Translation start site mutations result in loss of protein expression or synthesis of proteins with abnormal amino acid sequences; 5) Recurrent somatic mutations (at least five cases documented in the Catalogue of Somatic Mutations in Cancer (COSMIC) database) (Tate JG, et al. Nucleic acids Res (2019) 47 (D1), D941-D947); 6) DNA fusion (a gene created by joining parts of two different genes; it can also occur when part of a chromosomal DNA moves to another chromosome); 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. 201 l;39(17):el 18) to reduce the function of the encoded protein;

[0028] In certain embodiments, the variant is not a variant of unknown significance (also known as a variant with no clear association with disease risk, 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.).

[0029] In some embodiments, the mutation is not a germline mutation (a genetic change in a germ cell (egg or sperm) that is incorporated into the DNA of every cell in the body of an offspring) and was identified in dbSNP (Sherry, ST, et al., Nucleic Acids Res, 2001, 29:308-311).

[0030] Loss-of-function mutations in the STK11 gene (e.g., in cancer cells) can result in loss of expression of the STK11 protein, expression of only a fragment of the STK11 protein, or expression of an STK11 protein with reduced or absent enzymatic activity (e.g., no serine / threonine kinase enzymatic activity).

[0031] Non-limiting examples of STK11 mutations that are loss-of-function mutations as defined herein are listed in Table 1 (adapted from WO2022087270). Mutations included in Table 1 were predicted to have deleterious function by OncoKB or appeared at least five times in COSMIC, excluding mutations of unknown significance and copy number variations (i.e., VUS) and germline mutations.

[0032] Those skilled in the art will appreciate that many STK11 mutations are known or otherwise identifiable.

[0033] [Table 1-1] [Table 1-2] [Table 1-3] [Table 1-4] [Table 1-5] [Table 1-6]

[0034] Those skilled in the art will also understand that STK11 mutations may co-occur with other mutations. STK11 mutations frequently co-occur with KRAS mutations. (Koivunen, J. et al. Br J Cancer 2008, 99, 245-252) STK11 somatic mutations also frequently co-occur with KEAP1 mutations (see Papillon-Cavanagh S. et al. ESMO Open, 2020, 5, E000706). Some authors have reported that the presence of STK11 and KEAP1 mutations has a greater impact 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).

[0035] In some embodiments provided herein, the cancer is identified as having altered STK11 activity or expression and altered KRAS activity or expression. In some embodiments, the altered KRAS activity or expression is the presence of mutant KRAS. In some embodiments, the mutant KRAS is 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 G12VIn some embodiments provided herein, the cancer is identified as having altered STK11 activity or expression and wild-type KRAS activity or expression. In some embodiments provided herein, the cancer is identified as having altered STK11 activity or expression and wild-type KRAS (e.g., KRAS G12C , KRAS G12D , KRAS G12V In some embodiments, the cancer is further identified as having altered KEAP1 activity or expression (e.g., a KEAP1 mutation).

[0036] Those skilled in the art will also appreciate that STK11 mutations may occur with high frequency in certain diseases (eg, cancer).

[0037] Histone deacetylase inhibitors In some embodiments, the methods of treating a subject having or at risk of developing cancer described herein comprise administering to the subject a histone deacetylase (HDAC) inhibitor. Unless otherwise specified, references to HDAC inhibitors in the methods and uses described herein refer to any of the HDAC inhibitor classes and HDAC inhibitor compounds described herein (e.g., in this section).

[0038] Histone deacetylase (HDAC) inhibitors are a class of therapeutic agents that generally inhibit histone deacetylases. Eighteen isoforms of histone deacetylases have been identified and are divided into four classes: class I, class II, class III, and class IV. Class II HDACs are further grouped into class IIa and class IIb. These four classes separate the 18 identified isoforms of HDACs into two major families: zinc-dependent metalloenzymes (HDACs 1-11) and SIRTs 1-7. Class I HDACs include HDAC1, HDAC2, HDAC3, and HDAC8. Class II HDACs include class IIa and class IIb. Class IIa HDACs include HDAC4, HDAC5, HDAC7, and HDAC9. Class IIb HDACs include HDAC6 and HDAC10. Class III HDACs, also known as sirtuins (SIRTs), include SIRT1, SIRT2, SIRT3, SIRT4, SIRT5, SIRT6, and SIRT7. Class IV HDACs include HDAC11. A review of HDACs, including their composition and sequence characteristics, is provided in Li, G. et al. Frontiers in Cell and Developmental Biology (2020) 8:576946 (doi:10.3389 / fcell.2020.576946), which is incorporated herein by reference in its entirety.

[0039] HDAC inhibitors can be either pan-HDAC inhibitors, which generally inhibit most or all HDAC isoforms, or selective HDAC inhibitors, which generally selectively inhibit one or more HDAC isoforms over other HDAC isoforms. Many HDAC inhibitors have been described in the art.

[0040] For example, a review of HDAC inhibitors over 30 years of development is provided in Ho, TCS, et al. Journal of Medicinal Chemistry (2020) 63(21): 12460-12484 (doi: 10.1021 / acs.jmedchem.0c00830), which is incorporated herein by reference in its entirety. A review of the development of HDAC inhibitors is provided in Bondarev, A., et al. British Journal of Clinical Pharmacology (2021) 87: 4577-4597 (doi: 10.1111 / bcp.14889), which is incorporated herein by reference in its entirety. A review of hybrid multi-targeted HDAC inhibitors is provided in Bass, AKA, et al. European Journal of Medicinal Chemistry (2021) 209:112904 (doi:10.1016 / j.ejmech.2020.112904), which is incorporated herein by reference in its entirety. Those skilled in the art will appreciate that many HDAC inhibitors have been described in the art through patent publications, posters, conferences, and journals. Some of these HDAC inhibitors have been described as pan-HDAC inhibitors. Some of these HDAC inhibitors are described as selective HDAC inhibitors, which inhibit a particular class of HDAC (e.g., class I, class IIa, class IIb, class III, or class IV) or inhibit 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).

[0041] Examples of selective HDAC inhibitors are described in the art, for example, HDAC inhibitors are described in WO / 2010 / 014611 and WO / 2010 / 144371 (each of which is incorporated by reference in its entirety).

[0042] As used herein, "selective" in reference to HDAC inhibitors refers to the HDAC inhibitory properties of a compound that preferentially inhibits one or more HDAC isoforms, including preferentially inhibiting one or more HDAC isoforms within a particular biological complex. A selective HDAC inhibitor inhibits target HDACs (e.g., including HDAC isoforms that are part of a particular complex, such as CoREST) at concentrations lower than those that inhibit non-target HDACs (e.g., including the same HDAC isoforms that are part of a different complex). Thus, a selective HDAC inhibitor is more potent (has a lower IC) against target HDACs than against non-target HDACs. 50 In one embodiment, the selective HDAC inhibitor is at least three times more potent against the targeted HDAC than against a non-targeted HDAC (i.e., has an IC 50 IC against untargeted HDACs 50 In one embodiment, the selective HDAC inhibitor is at least 5-fold more potent against the targeted HDAC than against a non-targeted HDAC (i.e., the IC 50 IC against untargeted HDACs 50 In one embodiment, the selective HDAC inhibitor is at least 10 times more potent against the targeted HDAC than against a non-targeted HDAC (i.e., the IC 50 IC against untargeted HDACs 50 In one embodiment, the selective HDAC inhibitor is at least 30 times more potent against the targeted HDAC than against a non-targeted HDAC (i.e., the IC 50 IC against untargeted HDACs 50 In one embodiment, the selective HDAC inhibitor is at least 50 times more potent against the targeted HDAC than against a non-targeted HDAC (i.e., the IC 50 IC against untargeted HDACs 50In one embodiment, the selective HDAC inhibitor is at least 100 times more potent against the targeted HDAC than against a non-targeted HDAC (i.e., the IC 50 IC against untargeted HDACs 50 In one embodiment, the selective HDAC inhibitor is at least 500 times more potent against the targeted HDAC than against a non-targeted HDAC (i.e., the IC 50 IC against untargeted HDACs 50 In one embodiment, the selective HDAC inhibitor is at least 1000 times more potent against the targeted HDAC than against a non-targeted HDAC (i.e., the IC 50 IC against untargeted HDACs 50 (At least 1 / 1000th of the original value).

[0043] 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 incorporated by reference in its entirety.

[0044] Certain biological complexes contain certain classes or isoforms of HDAC. For example, at least four biological complexes contain various class I HDAC isoforms and other subunits. The corepressor of HDAC-repressor element 1 silencing transcription factor (CoREST) complex contains HDAC1 and HDAC2, as well as other subunits such as LSD1 and RCOR1. The nucleosome remodeling and deacetylase (NuRD) complex also contains HDAC1 and HDAC2, as well as other subunits such as MTA3 and RBBP7. The Sin3-HDAC (Sin3) complex has also been described as containing HDAC1 and HDAC2, as well as other subunits such as Sin3 and RBBP7. The NCoR complex has been described as containing HDAC3 and other subunits such as NCoR, HSPA, and TBL1.

[0045] HDAC inhibitors may selectively inhibit a particular isoform of a particular biological complex over the same isoform in a different complex. 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) (incorporated herein by reference in its entirety). Fuller et al. describe a particular approach in which HDACs of the benzamide chemical class (CI-994 and BML-210) showed selectivity for CoREST, NuRD, and NCoR, but not for the Sin3 complex. Fuller et al. further describe compounds that selectively target HDACs (e.g., HDAC1 and HDAC2) in the CoREST complex.

[0046] The structure of the CoREST complex-selective HDAC inhibitor described by Fuller is shown below: [ka]

[0047] In a report describing other compounds that selectively target HDACs (eg, HDAC1 and HDAC2) in the CoREST complex, a compound designated "RDN-929" was identified and also published.

[0048] In some embodiments, the histone deacetylase inhibitor is an HDAC inhibitor that selectively inhibits HDAC1 over HDAC3. In some embodiments, the histone deacetylase inhibitor is an HDAC inhibitor that selectively inhibits HDAC1 and HDAC2 over HDAC3. In some embodiments, the histone deacetylase inhibitor is an HDAC inhibitor that selectively inhibits HDAC1 over HDAC8. In some embodiments, the histone deacetylase inhibitor is an HDAC inhibitor that selectively inhibits HDAC1 and HDAC2 over HDAC8. In some embodiments, the histone deacetylase inhibitor is an HDAC inhibitor that selectively inhibits HDAC1 over HDAC3 and HDAC8. In some embodiments, the histone deacetylase inhibitor is an HDAC inhibitor that selectively inhibits HDAC1 and HDAC2 over HDAC3 and HDAC8.

[0049] 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 over HDAC3. In some embodiments, the histone deacetylase inhibitor is an HDAC class I inhibitor that selectively inhibits HDAC1 and HDAC2 over HDAC3. In some embodiments, the histone deacetylase inhibitor is an HDAC class I inhibitor that selectively inhibits HDAC1 over HDAC8. In some embodiments, the histone deacetylase inhibitor is an HDAC class I inhibitor that selectively inhibits HDAC1 and HDAC2 over HDAC8. In some embodiments, the histone deacetylase inhibitor is an HDAC class I inhibitor that selectively inhibits HDAC1 over HDAC3 and HDAC8. In some embodiments, the histone deacetylase inhibitor is an HDAC class I inhibitor that selectively inhibits HDAC1 and HDAC2 over HDAC3 and HDAC8. In some embodiments, the histone deacetylase inhibitor is an HDAC class I inhibitor that selectively inhibits HDAC1 and HDAC2 over all other HDAC isoforms.

[0050] 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.

[0051] 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 HDAC1 over HDAC3. In some embodiments, the histone deacetylase inhibitor is an HDAC1,2-selective inhibitor that selectively inhibits HDAC1,2 over HDAC3. In some embodiments, the histone deacetylase inhibitor is an HDAC1-selective inhibitor that selectively inhibits HDAC1 over HDAC8. In some embodiments, the histone deacetylase inhibitor is an HDAC1,2-selective inhibitor that selectively inhibits HDAC1,2 over HDAC8. In some embodiments, the histone deacetylase inhibitor is an HDAC1-selective inhibitor that selectively inhibits HDAC1 over HDAC3 and HDAC8. In some embodiments, the histone deacetylase inhibitor is a HDAC1,2 selective inhibitor that selectively inhibits HDAC1,2 over HDAC3 and HDAC8.

[0052] 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.

[0053] 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.

[0054] In some embodiments, selective HDAC1,2 inhibitors have reduced cytotoxicity and improved therapeutic index compared to less selective HDAC inhibitors, hi some embodiments, selective HDAC1,2 inhibitors have reduced cytotoxicity against erythroid and / or myeloid cells.

[0055] 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-methylsulfonimidoyl)benzamide, also known as TNG260, Formula (I) (Compound I): [ka] or a pharmaceutically acceptable salt thereof.

[0056] Pharmaceutical Compositions and Administration Generally, histone deacetylase (HDAC) inhibitors are administered in an effective amount (e.g., a therapeutically effective amount). The amount of a compound (e.g., HDAC inhibitor) described herein actually administered will typically be determined by a physician in light of the relevant circumstances, including the condition being treated, the selected route of administration, the HDAC inhibitor actually administered, the age, weight, and response of the individual patient, the severity of the patient's symptoms, etc.

[0057] When used as a pharmaceutical, the compounds described herein (e.g., HDAC inhibitors) are typically administered in the form of pharmaceutical compositions. Such compositions can be prepared by methods well known in the pharmaceutical arts and can contain at least one active compound.

[0058] In some embodiments, a compound described herein (e.g., an HDAC inhibitor) is administered as a pharmaceutical composition comprising an effective amount of an HDAC inhibitor described herein and a pharmaceutically acceptable carrier. In some embodiments, with respect to a pharmaceutical composition, the carrier is a parenteral carrier, an oral carrier, or a topical carrier. The term "pharmaceutically acceptable carrier" refers to a carrier, adjuvant, or vehicle that may be administered to a patient together with a compound provided herein, which does not impair the pharmacological activity of the compound, and which is non-toxic when administered in a dosage sufficient to deliver a therapeutic amount of the compound. Pharmaceutically acceptable carriers that may 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-tocopherol polyethylene glycol 1000 succinate, surfactants used in pharmaceutical dosage forms such as Tween® or other similar polymeric 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 silica, magnesium trisilicate, polyvinylpyrrolidone, cellulosic substances, polyethylene glycol, sodium carboxymethylcellulose, polyacrylates, waxes, polyethylene polyoxypropylene block polymers, polyethylene glycol, and wool fat. Cyclodextrins, such as α-, β-, and γ-cyclodextrin, or chemically modified derivatives, such as hydroxyalkyl cyclodextrins, including 2 and 3 hydroxypropyl-β-cyclodextrin, or other solubilizing derivatives, can also be advantageously used to enhance delivery of the compounds described herein (e.g., HDAC inhibitors).

[0059] The pharmaceutical compositions provided herein may be administered orally, parenterally, by inhalation spray, topically, rectally, nasally, bucally, vaginally, or via an implanted reservoir, preferably orally or by injection. The pharmaceutical compositions provided herein may contain any conventional non-toxic pharmaceutically acceptable carrier, adjuvant, or vehicle. In some cases, the pH of the formulation may be adjusted with a pharmaceutically acceptable acid, base, or buffer to improve the stability of the formulated compound or its delivery form. The term parenteral, as used herein, includes subcutaneous, intradermal, intravenous, intramuscular, intraarticular, intraarterial, intrasynovial, intrasternal, intrathecal, intralesional, and intracranial injection or infusion techniques.

[0060] Compositions for oral administration can take the form of bulk liquid solutions or suspensions, or bulk powders. However, more commonly, compositions are provided in unit dosage forms to facilitate accurate dosing. The term "unit dosage form" refers to physically discrete units suitable as unitary doses for human subjects and other mammals, each containing a predetermined amount of active agent calculated to produce a desired therapeutic effect in association with a suitable pharmaceutical excipient. Typical unit dosage forms include prefilled, premeasured ampoules or syringes for liquid compositions, and pills, tablets, capsules, and the like for solid compositions. In such compositions, the compound is usually present as an accessory ingredient (about 0.1 to about 50% by weight, or preferably about 1 to about 40% by weight), with the remainder being various excipients or carriers and processing aids that serve to form the desired dosage form.

[0061] Liquid forms suitable for oral administration may include a suitable aqueous or nonaqueous vehicle with buffers, suspending and dispensing agents, colorants, flavors, etc. Solid forms may include, for example, any of the following ingredients: a binder such as microcrystalline cellulose, gum tragacanth, or gelatin; an excipient such as starch or lactose; a disintegrating agent such as alginic acid, Primogel, or corn starch; a lubricant such as magnesium stearate; a glidant such as colloidal silicon dioxide; a sweetener such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring, or compounds of a similar nature.

[0062] Injectable compositions are typically based on injectable sterile saline or phosphate-buffered saline or other injectable carriers known in the art. As mentioned above, the active compound in such compositions is typically a minor component, often about 0.05 to 10% by weight, with the remainder being the injectable carrier and the like. Pharmaceutical compositions may be in the form of a sterile injectable preparation, such as a sterile injectable aqueous or oleaginous suspension. This suspension can be formulated according to techniques known in the art using suitable dispersing or wetting agents (e.g., Tween 80, etc.) and suspending agents. Sterile injectable preparations may also be sterile injectable solutions or suspensions in a non-toxic parenterally acceptable diluent or solvent, such as a solution in 1,3-butanediol. Acceptable vehicles and solvents that may be used include mannitol, water, Ringer's solution, and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally used as solvents or suspending media. For this purpose, any non-irritating, fixed oil, including synthetic monoglycerides or diglycerides, may be used. Fatty acids such as oleic acid and its glyceride derivatives are useful for preparing injectables, as are natural pharmaceutically acceptable oils, such as olive oil or castor oil, especially their polyoxyethylated versions. These oil solutions or suspensions may also contain long-chain alcohol diluents or dispersants, or carboxymethylcellulose or similar dispersants, which are commonly used in the preparation of pharmaceutically acceptable dosage forms such as emulsions and / or suspensions. Other commonly used surfactants, such as Tween or Span, and / or other similar emulsifiers or bioavailability enhancers commonly used in the manufacture of pharmaceutically acceptable solid, liquid, or other dosage forms may also be used for formulation purposes.

[0063] Transdermal compositions are typically formulated as topical ointments or creams containing the active ingredient(s) in an amount generally ranging from about 0.01 to about 20% by weight, preferably from about 0.1 to about 20% by weight, preferably from about 0.1 to about 10% by weight, and more preferably from about 0.5 to about 15% by weight. When formulated as an ointment, the active ingredient is typically combined with either a paraffinic or a water-miscible ointment base. Alternatively, the active ingredient may be formulated in a cream containing, for example, an oil-in-water cream base. Such transdermal formulations are well known in the art and generally include additional ingredients to enhance skin penetration or stability of the active ingredient or formulation. All such known transdermal formulations and ingredients are included within the scope provided herein.

[0064] The HDAC inhibitors provided herein can also be administered by a transdermal device. Accordingly, transdermal administration can be accomplished using a patch either of the reservoir or porous membrane type, or of a solid matrix variety.

[0065] The pharmaceutical compositions provided herein may be administered in the form of suppositories for rectal administration.These compositions can be prepared by mixing the compounds provided herein with suitable non-irritating excipients that are solid at room temperature but liquid at rectal temperature, and therefore melt in the rectum to release the active ingredient.Such materials include, but are not limited to, cocoa butter, beeswax, and polyethylene glycol.

[0066] The pharmaceutical compositions provided herein may be administered by nasal aerosol or inhalation. Such compositions are prepared according to techniques well known in the art of pharmaceutical formulation and may be prepared as a solution in saline using benzyl alcohol or other suitable preservatives, absorption enhancers to enhance bioavailability, fluorocarbons, and / or other solubilizing or dispersing agents known in the art.

[0067] The above components for orally administrable, injectable or topically administrable, rectally administrable, and nasally administrable compositions are merely representative. Other materials, processing techniques, and the like are described in Part 8 of Remington's Pharmaceutical Sciences, 17th edition, 1985, Mack Publishing Company, Easton, Pennsylvania, which is incorporated herein in its entirety.

[0068] The compounds described herein (e.g., HDAC inhibitors) can also be administered in sustained release forms or from sustained release drug delivery systems. A description of representative sustained release materials can be found in Remington's Pharmaceutical Sciences.

[0069] When the compositions provided herein include a combination of a compound described herein (e.g., an HDAC inhibitor) with one or more additional therapeutic or prophylactic agents, both the compound and the additional agents should be present at dosage levels that are about 1-100%, more preferably about 5-95%, of the dosage normally administered in a monotherapy regimen. The additional agents can be administered separately from the compounds provided herein as part of a multiple-dose regimen. Alternatively, the agents can be part of a single dosage form, mixed together with the compounds provided herein in a single composition.

[0070] The compounds (e.g., HDAC inhibitors) described herein can be administered, for example, by injection, intravenously, intraarterially, subdermally, intraperitoneally, intramuscularly, or subcutaneously, or in oral, buccal, nasal, transmucosal, topical, or ophthalmic formulations, or by inhalation, at dosages ranging from about 0.5 to about 100 mg / kg body weight, or at dosages of 1 mg to 1000 mg per dose, every 4 to 120 hours, or depending on the requirements of the particular drug. The methods herein contemplate administering an effective amount of the compound or composition to achieve the desired or specified effect. Typically, the pharmaceutical compositions provided herein are administered about once to about six times per day, or alternatively as a continuous infusion. Such administration can be used as a chronic or acute therapy. The amount of active ingredient that can be combined with the carrier materials to produce a single dosage form will vary depending on the host treated and the particular method of administration. Typical formulations contain from about 5% to about 95% active compound (w / w). Alternatively, such preparations contain from about 20% to about 80% active compound.

[0071] 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 used, age, body weight, general health, sex, diet, time of administration, rate of excretion, drug combination, severity and course of the disease, condition or symptom, predisposition of the patient to the disease, condition or symptom, and the judgment of the attending physician.

[0072] When patient's condition improves, if necessary, the maintenance dose of provided herein compound (for example, HDAC inhibitor), composition or combination can be administered.Then, depending on symptoms, dosage or administration frequency, or both, can be reduced to the level that maintains the improved condition when symptoms are alleviated to desired level.However, patient may need to be intermittently treated for a long period of time if any disease symptoms recur.

[0073] "Effective amount" Generally, the "effective amount" of a compound (e.g., an HDAC inhibitor) refers to an amount sufficient to induce a desired biological response, for example, to treat a disease or disorder described herein. As will be understood by those skilled in the art, the effective amount of a compound of the present disclosure may vary depending on factors such as the desired biological endpoint, the pharmacokinetics of the compound, the disease being treated, the method of administration, and the age, health, and condition of the subject. The effective amount encompasses therapeutic and prophylactic treatments (i.e., encompasses "therapeutically effective amount" and "prophylactically effective amount").

[0074] As used herein, and unless otherwise specified, 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 a disease, disorder, or condition. A therapeutically effective amount of a compound means an amount of a therapeutic agent, alone or in combination with other treatments, 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 treatment, reduces or avoids the symptoms or pathogenesis of a disease or condition, or enhances the therapeutic effectiveness of another therapeutic agent.

[0075] As used herein, and unless otherwise specified, a "prophylactically effective amount" of a compound is an amount sufficient to prevent or prevent the recurrence of a disease, disorder, or condition, or one or more symptoms associated with a disease, disorder, or condition. 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" can encompass an amount that improves overall prophylaxis or enhances the prophylactic effectiveness of another prophylactic agent.

[0076] Treatment method Provided herein are methods of treating a subject having or at risk of developing a disease or disorder, the methods comprising administering to the subject an effective amount of a histone deacetylase inhibitor.

[0077] In some embodiments, a method of treating a subject having or at risk of developing a disease or disorder is provided, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor, wherein the cancer has been identified as having altered STK11 activity or expression.

[0078] In some embodiments, methods are provided for 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 has been identified as having altered STK11 activity or expression.

[0079] In some embodiments, the methods include selecting a patient for treatment using one of the patient selection methods described herein prior to administering to the patient a histone deacetylase inhibitor and optionally one or more additional therapeutic agents.

[0080] In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the cancer has been 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, comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the cancer has been identified as having altered STK11 activity or expression, and the cancer has been 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, comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the cancer has been identified as having altered STK11 activity or expression, and the cancer has been identified as having wild-type KRAS activity or expression. G12C , KRAS G12D , KRAS G12VIn some embodiments, a method is provided for treating a subject having cancer or at risk of developing cancer, comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the cancer has been 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 has been identified as having wild-type KRAS activity or expression.

[0081] In some embodiments, methods are provided for treating a subject having cancer or at risk of developing cancer, the methods comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with an immune checkpoint modulator, wherein the cancer has been identified as having altered STK11 activity or expression. In some embodiments, methods are provided for treating a subject having cancer or at risk of developing cancer, the methods 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 has been identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having or at risk of developing cancer comprises 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 has been identified as having altered STK11 activity or expression, and the anti-PD1 agent or the anti-PD-L1 agent is selected from the group consisting of nivolumab, CT-011, AMP-224, pembrolizumab, pidilizumab, cefotaxime ... In some embodiments, methods are provided for treating a subject having or at risk of developing cancer, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with anti-PD1 therapy or anti-PD-L1 therapy, wherein the cancer has been identified as having altered STK11 activity or expression.

[0082] In some embodiments, methods are provided for treating a subject having cancer or at risk of developing cancer, comprising administering to the subject an effective amount of a selective histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the cancer has been identified as having altered STK11 activity or expression. In some embodiments, methods are provided for treating a subject having cancer or at risk of developing cancer, comprising administering to the subject an effective amount of a selective histone deacetylase inhibitor in combination with an immune checkpoint modulator, wherein the cancer has been identified as having altered STK11 activity or expression. In some embodiments, methods are provided for treating a subject having cancer or at risk of developing cancer, 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 has been identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having or at risk of developing cancer comprises 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 has been identified as having altered STK11 activity or expression, and the anti-PD1 agent or the anti-PD-L1 agent is selected from the group consisting of nivolumab, CT-011, AMP-224, pembrolizumab, pidilizumab, , cemiplimab, dostallimab, prorugolimab, spartalizumab, camrelizumab, sasanlimab, sintilimab, tislelizumab, toripalimab, retifanlimab, MEDI0680, budigalimab, geptanolimab, BMS936559, durvalumab, avelumab, embafolimab, cosibelimab, sugemalimab, AUNP-12, atezolizumab, and CA-170. In some embodiments, methods are provided for treating a subject having or at risk of developing cancer, comprising administering to the subject an effective amount of a selective histone deacetylase inhibitor in combination with anti-PD1 therapy or anti-PD-L1 therapy, wherein the cancer has been identified as having altered STK11 activity or expression.

[0083] In some embodiments, methods are provided for treating a subject having cancer or at risk of developing cancer, 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 has been identified as having altered STK11 activity or expression. In some embodiments, methods are provided for treating a subject having cancer or at risk of developing cancer, comprising administering to the subject an effective amount of an HDAC class I-selective inhibitor in combination with an immune checkpoint modulator, wherein the cancer has been identified as having altered STK11 activity or expression. In some embodiments, methods are provided for treating a subject having cancer or at risk of developing cancer, comprising administering to the subject an effective amount of an HDAC class I-selective inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the cancer has been identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having or at risk of developing cancer comprises administering to the subject an effective amount of an HDAC class I selective inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the cancer has been identified as having altered STK11 activity or expression, and the anti-PD1 agent or the anti-PD-L1 agent is selected from the group consisting of nivolumab, CT-011, AMP-224, pembrolizumab, pidilizumab, cefotaxime ... In some embodiments, methods are provided for treating a subject having or at risk of developing cancer, the method comprising administering to the subject an effective amount of an HDAC class I selective inhibitor in combination with anti-PD1 therapy or anti-PD-L1 therapy, wherein the cancer has been identified as having altered STK11 activity or expression.

[0084] In some embodiments, methods are provided for treating a subject having cancer or at risk of developing cancer, 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 has been identified as having altered STK11 activity or expression. In some embodiments, methods are provided for treating a subject having cancer or at risk of developing cancer, comprising administering to the subject an effective amount of an HDAC1-selective inhibitor in combination with an immune checkpoint modulator, wherein the cancer has been identified as having altered STK11 activity or expression. In some embodiments, methods are provided for treating a subject having cancer or at risk of developing cancer, 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 has been identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having or at risk of developing cancer comprises 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 has been identified as having altered STK11 activity or expression, and the anti-PD1 agent or the anti-PD-L1 agent is selected from the group consisting of nivolumab, CT-011, AMP-224, pembrolizumab, pidilizumab, semiprotamine, pembrolizumab ... In some embodiments, methods are provided for treating a subject having or at risk of developing cancer, the method comprising administering to the subject an effective amount of an HDAC1-selective inhibitor in combination with anti-PD1 therapy or anti-PD-L1 therapy, wherein the cancer has been identified as having altered STK11 activity or expression.

[0085] In some embodiments, methods are provided for treating a subject having cancer or at risk of developing cancer, 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 has been identified as having altered STK11 activity or expression. In some embodiments, methods are provided for treating a subject having cancer or at risk of developing cancer, comprising administering to the subject an effective amount of an HDAC1,2-selective inhibitor in combination with an immune checkpoint modulator, wherein the cancer has been identified as having altered STK11 activity or expression. In some embodiments, methods are provided for treating a subject having cancer or at risk of developing cancer, 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 has been identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having or at risk of developing cancer comprises 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 has been identified as having altered STK11 activity or expression, and the anti-PD1 agent or the anti-PD-L1 agent is selected from the group consisting of nivolumab, CT-011, AMP-224, pembrolizumab, pidilizumab, semi- In some embodiments, methods are provided for treating a subject having or at risk of developing cancer, the method comprising administering to the subject an effective amount of an HDAC1,2 selective inhibitor in combination with anti-PD1 therapy or anti-PD-L1 therapy, wherein the cancer has been identified as having altered STK11 activity or expression.

[0086] In some embodiments, methods are provided for treating a subject having cancer or at risk of developing cancer, comprising administering to the subject an effective amount of a CoREST selective deacetylase inhibitor in combination with a second therapeutic agent, wherein the cancer has been identified as having altered STK11 activity or expression. In some embodiments, methods are provided for treating a subject having cancer or at risk of developing cancer, comprising administering to the subject an effective amount of a CoREST selective deacetylase inhibitor in combination with an immune checkpoint modulator, wherein the cancer has been identified as having altered STK11 activity or expression. In some embodiments, methods are provided for treating a subject having cancer or at risk of developing cancer, 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 has been identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having or at risk of developing cancer comprises 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 has been identified as having altered STK11 activity or expression, and the anti-PD1 agent or the anti-PD-L1 agent is selected from the group consisting of nivolumab, CT-011, AMP-224, pembrolizumab, pidilisumab, and the like. In some embodiments, methods are provided for treating a subject having or at risk of developing cancer, 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 has been identified as having altered STK11 activity or expression.

[0087] In some embodiments, a method of treating a subject having cancer or at risk of developing cancer is provided, comprising administering to the subject an effective amount of a histone deacetylase inhibitor, wherein the cancer has been identified as having altered STK11 activity or expression, and the cancer has been identified as being 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, comprising administering to the subject an effective amount of a histone deacetylase inhibitor, wherein the cancer has been identified as having altered STK11 activity or expression, and the cancer has been identified as having natural 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, comprising administering to the subject an effective amount of a histone deacetylase inhibitor, wherein the cancer has been identified as having altered STK11 activity or expression, and the cancer has been identified as having acquired resistance to anti-PD1 therapy or anti-PD-L1 therapy.

[0088] In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the lung cancer has been 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, comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the lung cancer has been identified as having altered STK11 activity or expression, and the lung cancer has been 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, comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the lung cancer has been identified as having altered STK11 activity or expression, and the lung cancer has been identified as having wild-type KRAS activity or expression. G12C , KRAS G12D , KRAS G12V In some embodiments, a method is provided for treating a subject having or at risk of developing lung 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 lung cancer has been identified as having altered STK11 activity or expression, and the lung cancer has been identified as having altered KRAS (e.g., KRAS G12C , KRAS G12D , KRAS G12VIn some embodiments, a method is provided for treating a subject having lung cancer or at risk of developing lung cancer, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with an immune checkpoint modulator, wherein the lung cancer has been identified as having altered STK11 activity or expression. In some embodiments, a method is provided for treating a subject having lung cancer or at risk of developing lung cancer, 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 has been identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having or at risk of developing lung cancer comprises 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 has been identified as having altered STK11 activity or expression, and the anti-PD1 agent or the anti-PD-L1 agent is selected from the group consisting of nivolumab, CT-011, AMP-224, pembrolizumab, pidilizumab, cefotaxime ... In some embodiments, methods are provided for treating a subject having or at risk of developing lung cancer, the method comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with anti-PD1 therapy or anti-PD-L1 therapy, wherein the lung cancer has been identified as having altered STK11 activity or expression.

[0089] In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, comprising administering to the subject an effective amount of a histone deacetylase inhibitor, wherein the lung cancer has been identified as having altered STK11 activity or expression, and the lung cancer has been identified as being resistant to anti-PD1 or anti-PD-L1 therapy. In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, comprising administering to the subject an effective amount of a histone deacetylase inhibitor, wherein the lung cancer has been identified as having altered STK11 activity or expression, and the lung cancer has been identified as having natural resistance to anti-PD1 or anti-PD-L1 therapy. In some embodiments, a method of treating a subject having lung cancer or at risk of developing lung cancer is provided, comprising administering to the subject an effective amount of a histone deacetylase inhibitor, wherein the lung cancer has been identified as having altered STK11 activity or expression, and the lung cancer has been identified as having acquired resistance to anti-PD1 or anti-PD-L1 therapy.

[0090] In some embodiments, methods are provided for treating a subject having lung cancer or at risk of developing lung cancer, 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 has been identified as having altered STK11 activity or expression. In some embodiments, methods are provided for treating a subject having lung cancer or at risk of developing lung cancer, comprising administering to the subject an effective amount of a selective histone deacetylase inhibitor in combination with an immune checkpoint modulator, wherein the lung cancer has been identified as having altered STK11 activity or expression. In some embodiments, methods are provided for treating a subject having lung cancer or at risk of developing lung cancer, 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 has been identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having or at risk of developing lung cancer comprises 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 has been identified as having altered STK11 activity or expression, and the anti-PD1 agent or the anti-PD-L1 agent is selected from the group consisting of nivolumab, CT-011, AMP-224, pembrolizumab, pidilizumab, and the like. , cemiplimab, dostallimab, prorugolimab, spartalizumab, camrelizumab, sasanlimab, sintilimab, tislelizumab, toripalimab, retifanlimab, MEDI0680, budigalimab, geptanolimab, BMS936559, durvalumab, avelumab, embafolimab, cosibelimab, 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, comprising administering to the subject an effective amount of a selective histone deacetylase inhibitor in combination with anti-PD1 therapy or anti-PD-L1 therapy, wherein the lung cancer has been identified as having altered STK11 activity or expression.

[0091] In some embodiments, methods are provided for treating a subject having lung cancer or at risk of developing lung cancer, 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 has been identified as having altered STK11 activity or expression. In some embodiments, methods are provided for treating a subject having lung cancer or at risk of developing lung cancer, comprising administering to the subject an effective amount of an HDAC class I-selective inhibitor in combination with an immune checkpoint modulator, wherein the lung cancer has been identified as having altered STK11 activity or expression. In some embodiments, methods are provided for treating a subject having lung cancer or at risk of developing lung cancer, comprising administering to the subject an effective amount of an HDAC class I-selective inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the lung cancer has been identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having or at risk of developing lung cancer comprises administering to the subject an effective amount of an HDAC class I selective inhibitor in combination with an anti-PD1 agent or an anti-PD-L1 agent, wherein the lung cancer has been identified as having altered STK11 activity or expression, and the anti-PD1 agent or the anti-PD-L1 agent is selected from the group consisting of nivolumab, CT-011, AMP-224, pembrolizumab, pidilizumab, cefotaxime ... In some embodiments, methods are provided for treating a subject having or at risk of developing lung cancer, the method comprising administering to the subject an effective amount of an HDAC class I selective inhibitor in combination with anti-PD1 therapy or anti-PD-L1 therapy, wherein the lung cancer has been identified as having altered STK11 activity or expression.

[0092] In some embodiments, methods are provided for treating a subject having lung cancer or at risk of developing lung cancer, 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 has been identified as having altered STK11 activity or expression. In some embodiments, methods are provided for treating a subject having lung cancer or at risk of developing lung cancer, comprising administering to the subject an effective amount of an HDAC1-selective inhibitor in combination with an immune checkpoint modulator, wherein the lung cancer has been identified as having altered STK11 activity or expression. In some embodiments, methods are provided for treating a subject having lung cancer or at risk of developing lung cancer, 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 has been identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having or at risk of developing lung cancer comprises 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 has been identified as having altered STK11 activity or expression, and the anti-PD1 agent or the anti-PD-L1 agent is selected from the group consisting of nivolumab, CT-011, AMP-224, pembrolizumab, pidilizumab, semiprotamine, pembrolizumab ... In some embodiments, methods are provided for treating a subject having or at risk of developing lung cancer, the method comprising administering to the subject an effective amount of an HDAC1-selective inhibitor in combination with anti-PD1 therapy or anti-PD-L1 therapy, wherein the lung cancer has been identified as having altered STK11 activity or expression.

[0093] In some embodiments, methods are provided for treating a subject having or at risk of developing lung cancer, 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 has been identified as having altered STK11 activity or expression. In some embodiments, methods are provided for treating a subject having or at risk of developing lung cancer, comprising administering to the subject an effective amount of an HDAC1,2-selective inhibitor in combination with an immune checkpoint modulator, wherein the lung cancer has been identified as having altered STK11 activity or expression. In some embodiments, methods are provided for treating a subject having or at risk of developing lung cancer, 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 has been identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having or at risk of developing lung cancer comprises 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 has been identified as having altered STK11 activity or expression, and the anti-PD1 agent or the anti-PD-L1 agent is selected from the group consisting of nivolumab, CT-011, AMP-224, pembrolizumab, pidilizumab, semi- In some embodiments, methods are provided for treating a subject having or at risk of developing lung cancer, the method comprising administering to the subject an effective amount of an HDAC1,2 selective inhibitor in combination with anti-PD1 therapy or anti-PD-L1 therapy, wherein the lung cancer has been identified as having altered STK11 activity or expression.

[0094] In some embodiments, methods are provided for treating a subject having or at risk of developing lung cancer, 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 has been identified as having altered STK11 activity or expression. In some embodiments, methods are provided for treating a subject having or at risk of developing lung cancer, comprising administering to the subject an effective amount of a CoREST selective deacetylase inhibitor in combination with an immune checkpoint modulator, wherein the lung cancer has been identified as having altered STK11 activity or expression. In some embodiments, methods are provided for treating a subject having or at risk of developing lung cancer, 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 has been identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having or at risk of developing lung cancer comprises 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 has been identified as having altered STK11 activity or expression, and the anti-PD1 agent or the anti-PD-L1 agent is selected from the group consisting of nivolumab, CT-011, AMP-224, pembrolizumab, pidilisumab, and the like. In some embodiments, methods are provided for treating a subject having or at risk of developing lung cancer, the method comprising administering to the subject an effective amount of a CoREST selective deacetylase inhibitor in combination with anti-PD1 therapy or anti-PD-L1 therapy, wherein the lung cancer has been identified as having altered STK11 activity or expression.

[0095] In some of the 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) with an immune checkpoint modulator is synergistic.

[0096] In some embodiments described herein, the methods include identifying a subject as having one or more cancer cells with altered STK11 activity or expression. In some embodiments described herein, the methods include identifying a subject as having one or more cancer cells with altered STK11 activity or expression and that are resistant to anti-PD1 therapy or anti-PD-L1 therapy.

[0097] In some embodiments described herein, the methods comprise administering to a 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 the tumor or tumor microenvironment.

[0098] In some embodiments described herein, the methods comprise administering to a subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment reduces or depletes Treg cells in the tumor or tumor microenvironment.

[0099] In some embodiments described herein, the methods include administering to a subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment induces or increases expression of a cytokine that promotes anti-tumor activity. In some embodiments, the methods further include wherein the cytokine is selected from the group consisting of CXCL9, CXCL10, and CXCL11.

[0100] In some embodiments described herein, the methods include administering to a subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment reduces expression of a cytokine that promotes Treg cell recruitment. In some embodiments, the cytokine is CCL1 or CCL22.

[0101] In some embodiments described herein, the methods include administering to a subject an immune checkpoint modulator and an HDAC inhibitor, wherein administration of the HDAC inhibitor does not substantially reduce viability of erythroid or myeloid cells (e.g., reduces cell viability by less than 10%, less than 20%, less than 30%, less than 40%, or less than 50%).

[0102] In some embodiments described herein, the cancer exhibits an immune evasion phenotype characterized by STK11 mutant expression, which comprises administering an HDAC1,2-selective inhibitor, which can attenuate or reverse the immune evasion phenotype. In some embodiments, the method further comprises administering an immune checkpoint modulator.

[0103] In some embodiments described herein, the methods comprise administering to a subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment increases expression of IFNγ in the tumor or tumor microenvironment.

[0104] In some embodiments, a method of treating a subject having or at risk of developing an immune evasive cancer is provided, comprising administering to the subject an effective amount of a histone deacetylase inhibitor, wherein the immune evasive cancer has been identified as having altered STK11 activity or expression. In some embodiments, a method of treating a subject having or at risk of developing an immune evasive cancer is provided, comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the immune evasive cancer has been identified as having altered STK11 activity or expression. In some embodiments, the second therapeutic agent is an immune checkpoint modulator as described herein.

[0105] In some embodiments, a method for reversing immune evasion in a subject having cancer or at risk of developing cancer is provided, comprising administering to the subject an effective amount of a histone deacetylase inhibitor, wherein the cancer has been identified as having altered STK11 activity or expression. In some embodiments, a method for reversing immune evasion in a subject having cancer or at risk of developing cancer is provided, comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the cancer has been identified as having altered STK11 activity or expression. In some embodiments, a method for reversing immune evasion in a subject having cancer or at risk of developing cancer is provided, comprising administering to the subject an effective amount of a histone deacetylase inhibitor in combination with a second therapeutic agent, wherein the cancer has been identified as having altered STK11 activity or expression, and the immune evasion is caused by anti-PD1 therapy or anti-PD-L1 therapy. In some embodiments, the second therapeutic agent is an immune checkpoint modulator described herein.

[0106] In some embodiments described herein, the subject has cancer. In some embodiments, the subject is at risk of developing cancer.

[0107] In some embodiments described herein, the cancer is lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC), lung squamous cell carcinoma), 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 carcinoma (e.g., large cell neuroendocrine carcinoma), melanoma, non-melanoma skin cancer (e.g., cutaneous squamous cell carcinoma), bile duct carcinoma, gallbladder cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), bladder cancer (e.g., bladder urothelial carcinoma), prostate cancer (e.g., prostate adenocarcinoma), cervical cancer, cervical canal carcinoma, or cancer of unknown primary origin (e.g., adenocarcinoma of unknown primary origin).

[0108] 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), cholangiocarcinoma, ovarian cancer (e.g., ovarian serous adenocarcinoma), cervical cancer, cervical canal carcinoma, or cancer of unknown primary origin (e.g., adenocarcinoma of unknown primary origin).

[0109] 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), cholangiocarcinoma, ovarian cancer (e.g., ovarian serous adenocarcinoma), or cancer of unknown primary origin (e.g., adenocarcinoma of unknown primary origin).

[0110] 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).

[0111] 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.

[0112] 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 carcinoma (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., cutaneous squamous cell carcinoma). In some embodiments described herein, the cancer is cholangiocarcinoma. In some embodiments described herein, the cancer is gallbladder carcinoma. 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 cervical cancer. In some embodiments described herein, the cancer is cancer of unknown primary origin (e.g., adenocarcinoma of unknown primary origin).

[0113] In some embodiments described herein (e.g., this section), the cancer has increased or decreased STK11 expression. In one embodiment, increased or decreased STK expression is assessed by determining the copy number of the gene encoding STK11 compared to a control sample, where an increased copy number indicates an elevated expression level and a decreased copy number indicates a decreased expression level. In one embodiment, increased or decreased STK expression is assessed by determining the level of STK11 protein or mRNA compared to a control sample. In one embodiment, the cancer has decreased STK11 expression.

[0114] In some embodiments described herein (e.g., in this section), the cancer has an STK11 mutation. In one embodiment, the STK11 mutation is a mutation selected from (i) a mutation in a nucleotide sequence encoding STK11, (ii) a mutation in a regulatory sequence controlling expression of a nucleotide sequence encoding STK11, (iii) a mutation in a nucleotide encoding a protein that interacts with a transcript of the STK11 gene, (iv) a mutation in a translation product of the STK11 gene, and (v) a mutation in a transcript of the STK11 gene.

[0115] In one embodiment, the STK11 mutation is a mutation selected from (i) a mutation in the nucleotide sequence encoding STK11, (ii) a mutation in a regulatory sequence that controls the expression of the nucleotide sequence encoding STK11, and (iii) a mutation in a nucleotide that encodes a protein that interacts with the transcription product of the STK11 gene.

[0116] 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.

[0117] In some embodiments described herein (e.g., in this section), the cancer is resistant to anti-PD1 or anti-PD-L1 therapy. In one embodiment, the cancer has natural resistance to anti-PD1 or anti-PD-L1 therapy. In one embodiment, the cancer has acquired resistance to anti-PD1 or anti-PD-L1 therapy.

[0118] 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 has natural resistance to chemotherapy (e.g., platinum-containing chemotherapy). In one embodiment, the cancer has acquired resistance to chemotherapy (e.g., platinum-containing chemotherapy).

[0119] In some of the embodiments described herein (e.g., in this section), the cancer does not respond to or does not benefit from treatment with the immune checkpoint modulator when administered alone or as part of a treatment regimen that does not include an HDAC inhibitor.

[0120] "subject" "Subjects" to which administration is contemplated 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, e.g., primates (e.g., cynomolgus monkeys, rhesus monkeys), cows, 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" may be used interchangeably herein, where the context allows.

[0121] "treatment" As used herein, and unless otherwise specified, the terms "treat," "treating," and "treatment" contemplate effects that occur while a subject is afflicted with a specified disease, disorder, or condition (e.g., cancer) and that reduce the severity of the disease, disorder, or condition, or delay or slow the progression of the disease, disorder, or condition ("therapeutic treatment"), and also contemplate effects that occur before a subject begins to suffer from a specified disease, disorder, or condition ("prophylactic treatment"). In some embodiments, provided herein are contemplated methods of therapeutic treatment that occur while a subject is afflicted with a specified disease, disorder, or condition (e.g., cancer) and result in 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 alternative embodiments, provided herein are prophylactic treatment methods that occur before a subject begins to suffer from a specified disease, disorder, or condition (e.g., cancer) and result in the prevention of the 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.

[0122] Combination therapy Provided herein are methods of treating diseases or disorders (eg, cancers in which STK11 activity or expression is altered) with a combination of an HDAC inhibitor and one or more additional therapeutic agents.

[0123] The term "combination" refers to either a fixed combination in a single unit dosage form, or a combined administration in which a compound described herein (e.g., an HDAC inhibitor) and a combination partner (e.g., another drug as described below, also referred to as an "additional therapeutic agent" or "co-agent") can be administered independently, simultaneously, or separately at time intervals (e.g., such time intervals allow the combination partners to exhibit a coordinated, e.g., synergistic, effect). The individual components can be packaged in a kit or separately. One or both components (e.g., powder or liquid) can be reconstituted or diluted to the desired dose before administration. As used herein, terms such as "co-administration" or "co-administration" are intended to encompass the administration of selected combination partners to an individual subject (e.g., patient) in need of administration and are intended to include treatment regimens in which agents are not necessarily administered by the same route of administration or at the same time. As used herein, the term "pharmaceutical combination" refers to a product obtained by mixing or combining two or more therapeutic agents, and includes both 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 a patient simultaneously in the form of a single entity or dosage. The term "non-fixed combination" means that both therapeutic agents, such as compounds described herein (e.g., HDAC inhibitors), and combination partners are administered to a patient as separate entities simultaneously, in parallel, or sequentially, without any specific time limit, such that such administration results in therapeutically effective levels of the two compounds in the patient's body. The latter also applies to cocktail therapy, e.g., the administration of three or more therapeutic agents.

[0124] The term "combination therapy" refers to the administration of two or more therapeutic agents to treat a therapeutic condition or disorder described in this disclosure. Such administration includes co-administration of these therapeutic agents substantially simultaneously, for example, in a single capsule having a fixed ratio of active ingredients. Alternatively, such administration includes co-administration in multiple or separate containers (e.g., tablets, capsules, powders, and liquids) for each active ingredient. The powders and / or liquids can be reconstituted or diluted to the desired dose prior to administration. In addition, such administration also includes the sequential use of each type of therapeutic agent, either at approximately the same time or at different times.

[0125] In certain embodiments, the compounds described herein (e.g., HDAC inhibitors) are used in combination with other therapeutic agents, including, but not limited to, immune checkpoint modulators and other immunotherapeutic agents, other anti-cancer agents (e.g., chemotherapeutic agents, targeted agents), anti-allergy agents, anti-nausea agents (or antiemetic agents), analgesics, cytoprotective agents, radiation therapy, and combinations thereof.

[0126] In some embodiments, the combination therapy modulates the Tem to Treg cell ratio. In some embodiments, the combination therapy increases the Tem to Treg cell ratio in the tumor or tumor microenvironment. Effector memory T cells (Tem) express CD45RO but lack 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. Thus, Tem cells are typically found in the peripheral circulation and tissues, but not in lymph nodes, where they exert immediate effector functions. In response to antigenic stimulation, Tem cells proliferate and express CD62L. - They differentiate into effector T cells. Effector T cells (Teff) are fully differentiated T cells. Effector T cells are short-lived cells, in contrast to memory T cells, which have the potential for long-term survival but strong cytotoxic activity.

[0127] Regulatory T cells (Tregs) are a specialized subpopulation of T cells that act to suppress immune responses, thereby maintaining homeostasis and self-tolerance. Tregs can inhibit T cell proliferation and cytokine production, playing a crucial role in preventing autoimmunity.

[0128] In some embodiments, the combination therapy modulates cytokine secretion in the tumor or tumor microenvironment. In some embodiments, the cytokine is selected from the group of CXCL9, CXCL10, and CXCL11. In some embodiments, 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, expression of CCL1 and / or CCL22 is decreased.

[0129] In some embodiments, the combination therapy modulates the expression and / or secretion of IFNγ in the tumor or tumor microenvironment, hi some embodiments, the expression and / or secretion of IFNγ is increased.

[0130] immunotherapy In some embodiments, at least one of the other therapeutic agents is an immunotherapeutic agent. In some embodiments, provided are methods of treating a disease or disorder (e.g., a cancer in which STK11 activity or expression is altered), comprising administering or co-administering, in any order, a compound described herein (e.g., an HDAC inhibitor) and one or more immunotherapeutic agents to a patient in need thereof.

[0131] In some embodiments, the immunotherapeutic agent is a cell-based therapy. In some embodiments, provided are methods of treating a disease or disorder (e.g., a cancer in which STK11 activity or expression is altered), comprising administering or co-administering, in any order, a compound described herein (e.g., an HDAC inhibitor) and an adoptive cell-based therapy to a patient in need thereof. 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.

[0132] In some embodiments, the immunotherapeutic agent is a cancer vaccine, such as a neoantigen. These vaccines can be developed using peptides or RNA. 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.

[0133] In some embodiments, the immunotherapeutic agent is an immune checkpoint modulator described herein.

[0134] Immune checkpoint modulators As used herein, an "immune checkpoint modulator" is an agent that modulates an immune checkpoint pathway by blocking any inhibitory immune checkpoint protein or by activating any stimulatory immune checkpoint protein. Unless otherwise specified, reference to an immune checkpoint modulator in the methods and uses described herein refers to any of the immune checkpoint modulators described herein (e.g., in this section).

[0135] In one embodiment, the immune checkpoint modulator is a T cell costimulatory receptor agonist or a dendritic cell costimulatory receptor agonist. In one embodiment, the immune checkpoint modulator is a T cell costimulatory receptor agonist. In one embodiment, the immune checkpoint modulator is a dendritic cell costimulatory receptor agonist.

[0136] In some embodiments, the immune checkpoint modulator is an immune checkpoint inhibitor, hi some embodiments, the immune checkpoint inhibitor is an antibody.

[0137] In one embodiment, the immune checkpoint modulator is a costimulatory antibody (e.g., an anti-4-1BB antibody, an anti-OX40 antibody, an anti-GITR antibody, an anti-CD28 antibody, an anti-CD27 antibody, an anti-ICOS antibody, an anti-CD40 antibody). In one embodiment, the immune checkpoint modulator is an anti-4-1BB antibody. In one embodiment, the immune checkpoint modulator is an anti-OX40 antibody. In one embodiment, the immune checkpoint modulator is an anti-GITR antibody. In one embodiment, the immune checkpoint modulator is an anti-CD28 antibody. In one embodiment, the immune checkpoint modulator is an anti-CD27 antibody. In one embodiment, the immune checkpoint modulator is an anti-ICOS antibody. In one embodiment, the immune checkpoint modulator is an anti-CD40 antibody.

[0138] In one embodiment, the immune checkpoint modulating agent is an anti-CTLA agent. In one embodiment, the immune checkpoint modulating agent is an anti-CTLA-4 antibody (e.g., ipilimumab, tremelimumab). In one embodiment, the immune checkpoint modulating agent is ipilimumab. In one embodiment, the immune checkpoint modulating agent is tremelimumab.

[0139] Anti-PD-1 / PD-L1 therapy aims to block the activity of PD-1 and PDL1 immune checkpoint proteins, preventing them from transmitting "off" signals 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.

[0140] In one embodiment, the immune checkpoint modulator is a PD-1 ligand (i.e., PD-LI, B7-HI, or CD274) or a PD-2 ligand (i.e., PD-L2, B7-DC, or CD273).

[0141] In one embodiment, the immune checkpoint modulator is an anti-PD-1 agent (PD-1 inhibitor). In some embodiments, the immune checkpoint modulator is an anti-PD-1 antibody (e.g., nivolumab (i.e., MDX-1106, BMS-936558, ONO-4538), AMP-224, pembrolizumab (MK-3475), pidilizumab (CT-011), cemiplimab, dostallimab, prorugolimab, spartalizumab, camrelizumab, sasanlimab, sintilimab, tislelizumab, toripalimab, retifanlimab, MEDI0680, budigalimab, geptanolimab). In one embodiment, the immune checkpoint modulator is nivolumab. In one embodiment, the immune checkpoint modulator is pembrolizumab. In one embodiment, the immune checkpoint modulator is pidilizumab. In one embodiment, the immune checkpoint inhibitor is cemiplimab. In one embodiment, the immune checkpoint inhibitor is dostarlimab. In one embodiment, the immune checkpoint inhibitor is prorugolimab. In one embodiment, the immune checkpoint inhibitor is spartalizumab. In one embodiment, the immune checkpoint inhibitor is camrelizumab. In one embodiment, the immune checkpoint inhibitor is sasanlimab or sintilimab. In one embodiment, the immune checkpoint inhibitor is tislelizumab. In one embodiment, the immune checkpoint inhibitor is toripalimab. In one embodiment, the immune checkpoint inhibitor is retifanlimab. In one embodiment, the immune checkpoint inhibitor is MEDI0680. In one embodiment, the immune checkpoint inhibitor is budigalimab. In one embodiment, the immune checkpoint inhibitor is geptanolimab.

[0142] 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), embafolimab, cosibelimab, sugemalimab, 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 emvafolimab. In one embodiment, the immune checkpoint modulator is cosibelimab. In one embodiment, the immune checkpoint modulator is sugemalimab. 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).

[0143] In one embodiment, the immune checkpoint modulator is a checkpoint co-inhibitory antibody (e.g., anti-TIM3, anti-LAG3, eftiragimoda alfa (IMP321), anti-TIGIT, anti-B7-H3 (e.g., enoblituzumab (MGA271))).

[0144] In one embodiment, the immune checkpoint modulator is an anti-TWEAKR antibody, an anti-HVEM antibody, an anti-TIM-1 antibody, or an anti-VISTA antibody.

[0145] In one embodiment, a method of treating a subject having or at risk of developing cancer is provided, wherein the cancer has been 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 modulators independently selected from an anti-CTLA-4 antibody, an anti-PD-1 antibody, an anti-PD-L1 antibody, an anti-4-1BB antibody, an anti-OX-40 antibody, an anti-GITR antibody, an anti-CD27 antibody, an anti-CD28 antibody, an anti-CD40 antibody, an anti-LAG3 antibody, an anti-ICOS antibody, an anti-TWEAKR antibody, an anti-HVEM antibody, an anti-TIM-1 antibody, an anti-TIM-3 antibody, an anti-VISTA antibody, and an anti-TIGIT antibody.

[0146] chemotherapy In one embodiment, at least one of the other therapeutic agents is a chemotherapeutic agent.

[0147] Chemotherapeutic agents being considered for use in combination therapy include anastrozole (Arimidex®), bicalutamide (Casodex®), bleomycin sulfate (Blenoxane®), busulfan (Myleran®), busulfan for intravenous infusion (Busulfex®), capecitabine (Xeloda®), N4-pentoxycarbonyl-5-deoxy-5-fluorocytidine, carboplatin (Paraplatin®), carmustine (BiCNU®), and ribosomal steroids (RIs). ®), chlorambucil (Leukeran®), cisplatin (Platinol®), cladribine (Leustatin®), cyclophosphamide (Cytoxan® or Neosar®), cytarabine, cytosine arabinoside (Cytosar-U®), cytarabine liposome injection (DepoCyt®), dacarbazine (DTIC-Dome®), dactinomycin (actinomycin D, Cosmegan), daunorubicin hydrochloride (Ce rubidine (registered trademark), daunorubicin citrate liposomal injection (DaunoXome (registered trademark), dexamethasone, docetaxel (Taxotere (registered trademark), doxorubicin hydrochloride (Adriamycin (registered trademark), Rubex (registered trademark)), etoposide (Vepesid (registered trademark), fludarabine phosphate (Fludara (registered trademark), 5-fluorouracil (Adrucil (registered trademark), Efudex (registered trademark)), flutamide (Eulexin (registered trademark), tezacitibine, gemcitabine (di fluorodeoxycytidine), hydroxyurea (Hydrea®), idarubicin (Idamycin®), ifosfamide (IFEX®), irinotecan (Camptosar®), L-asparaginase (ELSPAR®), leucovorin calcium, melphalan (Alkeran®), 6-mercaptopurine (Purinethol®), methotrexate (Folex®), mitoxantrone (Novantrone®), Mylotarg,These include paclitaxel (Taxol®), nab-paclitaxel (Abraxane®), pemetrexed (Alimta®), phoenix (Yttrium 90 / MX-DTPA), pentostatin, carmustine-containing porifeprosan 20 intracerebral implant (Gliadel®), tamoxifen citrate (Nolvadex®), teniposide (Vumon®), 6-thioguanine, thiotepa, tirapazamine (Tirazone®), injectable topotecan hydrochloride (Hycamptin®), vinblastine (Velban®), vincristine (Oncovin®), and vinorelbine (Navelbine®).

[0148] In some embodiments, each chemotherapeutic agent is independently selected from cisplatin (Platinol®), carboplatin (Paraplatin®), paclitaxel (Taxol®), nab-paclitaxel (Abraxane®), docetaxel (Taxotere®), gemcitabine (difluorodeoxycytidine), vinorelbine (Navelbine®), etoposide (Vepesid®), and pemetrexed (Alimta®).

[0149] 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 a second chemotherapeutic agent is pemetrexed.

[0150] targeted therapy In one embodiment, at least one of the other therapeutic agents is a targeting agent.

[0151] In one embodiment, each targeting agent is independently selected from an anti-angiogenic agent (e.g., 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.

[0152] In one embodiment, each targeted agent is independently selected from bevacizumab, ramucirumab, sotorasib, crizotinib, ceritinib, alectinib, brigutinib, lorlatinib, entrectinib, dabrafenib, trametinib, capmatinib, tepotinib, and larotrectinib.

[0153] In some embodiments, provided are methods of treating a disease or disorder (e.g., cancer in which STK11 activity or expression is altered), comprising administering or co-administering, in any order, a compound described herein (e.g., an HDAC inhibitor) and a KRAS inhibitor to a patient in need thereof. In some embodiments, the KRAS inhibitor inhibits KRAS G12C In some embodiments, the KRAS inhibitor is a KRAS inhibitor (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). G12C In some embodiments, the KRAS inhibitor is sotorasib. G12D In some embodiments, the KRAS inhibitor is a KRAS inhibitor (e.g., MRTX1133, RMC-9805). Q61H In some embodiments, the KRAS inhibitor is a KRAS inhibitor (e.g., RMC-0708). G13C In some embodiments, the KRAS inhibitor is a pan-KRAS inhibitor (e.g., RMC-8839). In some embodiments, the KRAS inhibitor is a pan-KRAS inhibitor (e.g., RMC-6236, BI 1701963).

[0154] In some embodiments, methods are provided for treating a disease or disorder (e.g., a cancer in which STK11 activity or expression is altered), comprising administering or co-administering, in any order, a compound described herein (e.g., an HDAC inhibitor) and an HDM2 inhibitor and / or 5-FU to a patient in need thereof.

[0155] In some embodiments, methods are provided for treating a disease or disorder (e.g., a cancer in which STK11 activity or expression is altered), comprising administering or co-administering, in any order, to a patient in need thereof a compound described herein (e.g., an HDAC inhibitor) and a CDK4 inhibitor (LEE011 or a CDK4 / 6 inhibitor (e.g., including but not limited to palbociclib (Ibrance®), ribociclib (Kisqali®), and abemaciclib (Verzenio®)).

[0156] In some embodiments, methods are provided for treating a disease or disorder (e.g., a cancer in which STK11 activity or expression is altered), comprising administering or co-administering to a patient in need thereof a compound described herein (e.g., an HDAC inhibitor) and, depending on the dependency of the individual target tumor on the relevant pathway as determined by suitable predictive markers, a targeted treatment (including but not limited to inhibitors of HDM2i, PI3K / mTOR-I, MAPKi, RTKi (FGFRi, MEti, IGF1Ri, JAKi, and WNTi)), in any order.

[0157] In some embodiments, provided are methods for treating a disease or disorder (e.g., a cancer in which STK11 activity or expression is altered), comprising administering or co-administering, in any order, a compound described herein (e.g., an HDAC inhibitor) and a disease-specific huMAB (e.g., an anti-HER3 huMAB) to a patient in need thereof.

[0158] In some embodiments, provided are methods of treating a disease or disorder (e.g., a cancer in which STK11 activity or expression is altered) comprising administering or co-administering, in any order, to a patient in need thereof a compound described herein (e.g., an HDAC inhibitor) and ADC / ADCC in response to expression of relevant surface targets on a target tumor of interest.

[0159] In some embodiments, provided are methods for treating a disease or disorder (e.g., a cancer in which STK11 activity or expression is altered), comprising administering or co-administering, in any order, a compound described herein (e.g., an HDAC inhibitor) and a CAAP1 inhibitor to a patient in need thereof.

[0160] In some embodiments, a method is provided for treating a disease or disorder (e.g., a cancer in which STK11 activity or expression is altered), comprising administering or co-administering, in any order, a compound described herein (e.g., an HDAC inhibitor) and an AKAP17A inhibitor to a patient in need thereof.

[0161] In some embodiments, methods are provided for treating a disease or disorder (e.g., cancer in which STK11 activity or expression is altered), comprising administering or co-administering, in any order, a compound described herein (e.g., an HDAC inhibitor) and a BCL2L1 inhibitor to a patient in need thereof. In some embodiments, the BCL2L1 inhibitor is AT-101.

[0162] In some embodiments, methods are provided for treating a disease or disorder (e.g., a cancer in which STK11 activity or expression is altered), comprising administering or co-administering, in any order, a compound described herein (e.g., an HDAC inhibitor) and a TSC1 / 2 inhibitor to a patient in need thereof.

[0163] In some embodiments, provided are methods for treating a disease or disorder (e.g., a cancer in which STK11 activity or expression is altered), comprising administering or co-administering, in any order, a compound described herein (e.g., an HDAC inhibitor) and a UBE2H inhibitor to a patient in need thereof.

[0164] In some embodiments, provided are methods for treating a disease or disorder (e.g., a cancer in which STK11 activity or expression is altered), comprising administering or co-administering, in any order, a compound described herein (e.g., an HDAC inhibitor) and an NF2 inhibitor to a patient in need thereof.

[0165] In some embodiments, a method is provided for treating a disease or disorder (e.g., a cancer in which STK11 activity or expression is altered), comprising administering or co-administering, in any order, a compound described herein (e.g., an HDAC inhibitor) and a ZC3HC1 inhibitor to a patient in need thereof.

[0166] In some embodiments, provided are methods for treating a disease or disorder (e.g., a cancer in which STK11 activity or expression is altered), comprising administering or co-administering, in any order, a compound described herein (e.g., an HDAC inhibitor) and an MGEA5 inhibitor to a patient in need thereof.

[0167] In some embodiments, provided are methods for treating a disease or disorder (e.g., a cancer in which STK11 activity or expression is altered), comprising administering or co-administering, in any order, a compound described herein (e.g., an HDAC inhibitor) and a CNOT4 inhibitor to a patient in need thereof.

[0168] In some embodiments, provided are methods for treating a disease or disorder (e.g., cancer in which STK11 activity or expression is altered), comprising administering or co-administering, in any order, a compound described herein (e.g., an HDAC inhibitor) and an API5 inhibitor to a patient in need thereof.

[0169] In some embodiments, a method is provided for treating a disease or disorder (e.g., a cancer in which STK11 activity or expression is altered), comprising administering or co-administering, in any order, a compound described herein (e.g., an HDAC inhibitor) and a HEXIM1 inhibitor to a patient in need thereof.

[0170] In some embodiments, provided are methods for treating a disease or disorder (e.g., a cancer in which STK11 activity or expression is altered), comprising administering or co-administering, in any order, a compound described herein (e.g., an HDAC inhibitor) and a PTEN inhibitor to a patient in need thereof.

[0171] In some embodiments, provided are methods of treating a disease or disorder (e.g., cancer in which STK11 activity or expression is altered), comprising administering or co-administering, in any order, a compound described herein (e.g., an HDAC inhibitor) and a DNA damage pathway inhibitor to a patient in need thereof. In some embodiments, the DNA damage pathway inhibitor is selected from the group consisting of bleomycin, an ATM inhibitor (e.g., AZD1390), a USP1 inhibitor, a WEE1 inhibitor (e.g., AZD1775), and a Chk1 inhibitor (e.g., AZD7762).

[0172] Other therapeutic agents Because some patients may experience allergic reactions to the compounds described herein (e.g., HDAC inhibitors) and / or other anti-cancer agent(s) during or after administration, anti-allergic agents are often administered to minimize the risk of an allergic reaction. Suitable anti-allergic agents include corticosteroids, such as, but not limited to, dexamethasone (e.g., Decadron®), beclomethasone (e.g., Beclovent®), hydrocortisone (also known as cortisone, hydrocortisone sodium succinate, and hydrocortisone sodium phosphate, sold under the trade names Ala-Cort®, hydrocortisone phosphate, Solu-Cortef®, Hydrocort Acetate®, and Lanacort®), prednisolone (sold under the trade names Delta-Cortel®, Orapred®, Pediapred®, and Prelone®), prednisone (sold under the trade names Deltasone®, Liquid Red®, Meticorten®, and Orasone®), methylprednisolone (also known as 6-methylprednisolone, methylprednisolone acetate, methylprednisolone sodium succinate, and sold under the trade names Duralone®, Medralone®, Medrol®, M-Prednisol®, and Solu-Medrol®); antihistamines, such as diphenhydramine (e.g., Benadryl®), hydroxyzine, and cyproheptadine; and bronchodilators, such as the beta-adrenergic receptor agonists, albuterol (e.g., Proventil®), and terbutaline (Brethine®).

[0173] Some patients may experience nausea during and after administration of the compounds described herein (e.g., HDAC inhibitors) and / or other anticancer agent(s), and antiemetics are used to prevent nausea (upper abdominal) and vomiting. Suitable antiemetics include aprepitant (Emend®), ondansetron (Zofran®), granisetron HCl (Kytril®), lorazepam (Ativan®), dexamethasone (Decadron®), prochlorperazine (Compazine®), casopitant (Rezonic® and Zunrisa®), and combinations thereof.

[0174] To make patients more comfortable, medications are often prescribed to alleviate pain experienced during the procedure. Common over-the-counter painkillers, such as Tylenol®, are often used. However, opioid analgesics, including but not limited to hydrocodone / paracetamol or hydrocodone / acetaminophen (e.g., Vicodin®), morphine (e.g., Astramorph® or Avinza®), oxycodone (e.g., OxyContin® or Percocet®), oxymorphone hydrochloride (Opana®), and fentanyl (e.g., Duragesic®), are also useful for moderate or severe pain.

[0175] To protect normal cells from treatment toxicity and limit organ toxicity, cytoprotective agents (e.g., neuroprotective agents, free radical scavengers, cardioprotective agents, anthracycline extravasation neutralizers, nutritional supplements, etc.) may be used as adjunctive therapy. Suitable cytoprotective agents include amifostine (Ethyol®), glutamine, dimesna (Tavocept®), mesna (Mesnex®), dexrazoxane (Zinecard® or Totect®), xaliproden (Xaprila®), and leucovorin (also known as leucovorin calcium, citrovorum factor, and folinic acid).

[0176] The structures of active compounds identified by code number, generic name, or trade name can be obtained from the current edition of the standard compendium "The Merck Index" or from databases such as Patents International (e.g., IMS World Publications).

[0177] Compounds that may be used in combination with compounds described herein (e.g., HDAC inhibitors) can be prepared and administered as described in the art, including but not limited to the references cited herein.

[0178] In some embodiments, pharmaceutical compositions comprising at least one compound (e.g., HDAC inhibitor) described herein, together with a pharmaceutically acceptable carrier suitable for administration to a human or animal subject, are provided, either alone or with other anti-cancer agents. In particular, the compositions are formulated together as a combined therapeutic agent or are administered separately.

[0179] In some embodiments, provided are methods of treating a subject having or at risk of developing cancer, the method comprising administering to the subject a combination of an HDAC inhibitor 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 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 described herein (e.g., a targeted agent, a chemotherapeutic agent, radiation, or a combination thereof).

[0180] In combination therapy, the compounds described herein (e.g., HDAC inhibitors) and other anti-cancer agent(s) may be administered simultaneously, concurrently, or sequentially, without any specific time restrictions, such administration resulting in therapeutically effective levels of the two compounds in the patient's body.

[0181] In one embodiment, the HDAC inhibitor is administered simultaneously with the additional therapeutic agent.

[0182] In one embodiment, the HDAC inhibitor is administered sequentially with the additional therapeutic agent.

[0183] In one embodiment, the HDAC inhibitor is administered before the additional therapeutic agent.

[0184] In one embodiment, the HDAC inhibitor is administered after the additional therapeutic agent.

[0185] In one embodiment, the method comprises administering to the subject an immune checkpoint modulator, followed by administering to the subject an HDAC inhibitor.

[0186] In one embodiment, the method comprises administering to the subject an HDAC inhibitor, followed by administering to the subject an immune checkpoint modulator.

[0187] In one embodiment, the method comprises 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, followed by administering to the subject an HDAC inhibitor.

[0188] In one embodiment, the method comprises 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.

[0189] 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.

[0190] 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.

[0191] 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.

[0192] 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.

[0193] In some embodiments, the compounds described herein (e.g., HDAC inhibitors) and other anticancer drug(s) are generally administered sequentially in any order by injection or orally. Dosage regimens can vary depending on the stage of the disease, the patient's physical condition, the safety profile and tolerability of each individual drug, and other criteria known to the attending physician and doctor(s) administering the combination. The compounds described herein (e.g., HDAC inhibitors) and other anticancer drug(s) can be administered minutes apart, hours apart, days apart, or even weeks apart, depending on the particular cycle used for treatment. In addition, cycles can include administering some drugs more frequently than others during a treatment cycle and at different doses per administration of the drugs.

[0194] In some embodiments, kits are provided that include one or more compounds described herein (e.g., HDAC inhibitors) and a second therapeutic agent disclosed herein. Exemplary kits include (a) a compound described herein (e.g., an HDAC inhibitor) and (b) at least one other therapeutic agent (e.g., as described above), and such kits may include a package insert or other label containing instructions for administration.

[0195] The compounds described herein (eg, HDAC inhibitors) can also be used in combination with known therapeutic processes, such as the administration of hormones or, particularly, radiation.

[0196] Patient Selection and Monitoring Patient Selection for Treatment In one embodiment, a method is provided 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 in which STK11 activity or expression is altered, and selecting the subject thus identified for treatment with one of the treatment methods described herein.

[0197] In one embodiment, a method for 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 in which STK11 activity or expression is altered, and selecting the subject thus identified for treatment with the HDAC inhibitor.

[0198] In one embodiment, a method is provided for 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 thus identified subject for treatment with the HDAC inhibitor and one or more additional therapeutic agents.

[0199] In one embodiment, a method is provided for 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 so identified for treatment with the HDAC inhibitor and one or more immune checkpoint modulators.

[0200] In one embodiment, a method is provided for 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 so identified for treatment with the HDAC inhibitor and two or more additional therapeutic agents, wherein at least two of the additional therapeutic agents are immune checkpoint modulators.

[0201] In one embodiment, there is provided a method of 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 a chemotherapeutic agent, a targeted agent, 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 a chemotherapeutic agent, a targeted agent, and radiation therapy, and in which treatment with the combination of the immune checkpoint modulator and the additional therapeutic agent(s) did not provide any additional benefit compared to treatment with the additional therapeutic agent(s) alone, and selecting the subject so identified for treatment.

[0202] In one embodiment, the method further includes identifying a subject having a cancer characterized by the presence of cells with decreased STK11 activity or expression, and selecting the thus identified subject for treatment.

[0203] In some embodiments described herein, the cancer is lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC), lung squamous cell carcinoma), 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 carcinoma (e.g., large cell neuroendocrine carcinoma), melanoma, non-melanoma skin cancer (e.g., cutaneous squamous cell carcinoma), bile duct carcinoma, gallbladder cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), bladder cancer (e.g., bladder urothelial carcinoma), prostate cancer (e.g., prostate adenocarcinoma), cervical cancer, cervical canal carcinoma, or cancer of unknown primary origin (e.g., adenocarcinoma of unknown primary origin).

[0204] 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), cholangiocarcinoma, ovarian cancer (e.g., ovarian serous adenocarcinoma), cervical cancer, cervical canal carcinoma, or cancer of unknown primary origin (e.g., adenocarcinoma of unknown primary origin).

[0205] 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), cholangiocarcinoma, ovarian cancer (e.g., ovarian serous adenocarcinoma), or cancer of unknown primary origin (e.g., adenocarcinoma of unknown primary origin).

[0206] 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).

[0207] 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.

[0208] In some embodiments described herein (e.g., this section), the cancer has increased or decreased STK11 expression. In one embodiment, increased or decreased STK expression is assessed by determining the copy number of the gene encoding STK11 compared to a control sample, where an increased copy number indicates an elevated expression level and a decreased copy number indicates a decreased expression level. In one embodiment, increased or decreased STK expression is assessed by determining the level of STK11 protein or mRNA compared to a control sample. In one embodiment, the cancer has decreased STK11 expression.

[0209] In some embodiments described herein (e.g., in this section), the cancer has an STK11 mutation. In one embodiment, the STK11 mutation is a mutation selected from (i) a mutation in a nucleotide sequence encoding STK11, (ii) a mutation in a regulatory sequence controlling expression of a nucleotide sequence encoding STK11, (iii) a mutation in a nucleotide encoding a protein that interacts with a transcript of the STK11 gene, (iv) a mutation in a translation product of the STK11 gene, and (v) a mutation in a transcript of the STK11 gene.

[0210] In one embodiment, the STK11 mutation is a mutation selected from (i) a mutation in the nucleotide sequence encoding STK11, (ii) a mutation in a regulatory sequence that controls the expression of the nucleotide sequence encoding STK11, and (iii) a mutation in a nucleotide that encodes a protein that interacts with the transcription product of the STK11 gene.

[0211] 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.

[0212] In one embodiment, the cancer is further characterized by one or more additional mutations. In one embodiment, the additional mutation is selected from a KRAS mutation and a KEAP1 mutation. In one embodiment, the additional mutation is a KRAS mutation. In one embodiment, the KRAS mutation is selected from a G12C, G12D, G12V, G12A, G12S, G12R, G13C, G13D, G13S, Q61H, and Q61K mutation. In one embodiment, the KRAS mutation is a mutation at position G12, optionally the KRAS mutation is selected from a G12D mutation, a G12C mutation, a G12V mutation, or a combination thereof. In one embodiment, the KRAS mutation is an activating mutation. In one embodiment, the additional mutation is a KEAP1 mutation. In one embodiment, the KEAP1 mutation is an inactivating mutation. In one embodiment, the additional mutation is a KRAS mutation and a KEAP1 mutation. In one embodiment, the cancer is characterized by the absence of an EGFR mutation.

[0213] In one embodiment, the cancer is resistant to anti-PD1 or anti-PD-L1 therapy. In one embodiment, the cancer has natural resistance to anti-PD1 or anti-PD-L1 therapy. In one embodiment, the cancer has acquired resistance to anti-PD1 or anti-PD-L1 therapy.

[0214] In one embodiment, the cancer is resistant to chemotherapy (e.g., platinum-containing chemotherapy). In one embodiment, the cancer has innate resistance to chemotherapy (e.g., platinum-containing chemotherapy). In one embodiment, the cancer has acquired resistance to chemotherapy (e.g., platinum-containing chemotherapy).

[0215] In one embodiment, the cancer does not respond 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.

[0216] In some embodiments, the patient is immunocompetent. In some embodiments, the patient has undergone adoptive cell therapy. In some embodiments, the adoptive cell therapy is TIL therapy or CAR-T cell therapy.

[0217] Determining Whether a Subject Responds to Treatment with an HDAC Inhibitor In one embodiment, a method is provided for determining the sensitivity of a subject having or diagnosed with cancer to treatment with an HDAC inhibitor described herein, the method comprising determining i) the presence or absence of an 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 the STK11 mutation (e.g., a loss-of-function STK mutation) and / or altered (e.g., decreased) level of STK11 activity or expression indicates sensitivity to treatment with an HDAC inhibitor.

[0218] In one embodiment, there is provided a method for determining the susceptibility of a subject having or diagnosed with cancer to treatment with a combination of an HDAC inhibitor described herein and an immune checkpoint modulator described herein, the method comprising determining i) the presence or absence of an 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 the STK11 mutation (e.g., an STK loss-of-function mutation) and / or altered (e.g., decreased) level of STK11 activity or expression is indicative of susceptibility to treatment with a combination of an HDAC inhibitor and an immune checkpoint modulator.

[0219] In one embodiment, the STK11 expression level is assessed by determining the copy number of the gene encoding STK11 compared to a control sample, where an increased copy number indicates an increased expression level and a decreased copy number indicates a decreased expression level. In one embodiment, the STK11 expression level is assessed by determining the level of STK11 protein or mRNA compared to a control sample.

[0220] In one embodiment, a method is provided for determining whether a subject having or diagnosed with cancer will respond to treatment with an HDAC inhibitor described herein, 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 the STK11 mutation (e.g., an STK loss-of-function mutation) indicates that the subject will respond to treatment with an HDAC inhibitor.

[0221] In one embodiment, there is provided a method for determining whether a subject having or diagnosed with cancer will respond to treatment with an HDAC inhibitor described herein and an immune checkpoint modulator described herein, the method comprising determining the presence or absence of an STK11 mutation in the subject or in a sample derived from the subject, wherein the presence of the STK11 mutation (e.g., an STK loss-of-function mutation) indicates that the subject will respond to treatment with the HDAC inhibitor in combination with the immune checkpoint modulator.

[0222] In one embodiment, there is provided a method for determining whether a subject having or diagnosed with cancer will respond to treatment with an HDAC inhibitor as described herein, the method comprising: a) detecting the level of STK11 (e.g., STK11 protein and / or STK11 mRNA) in a cancer test sample (e.g., in a cancer sample obtained from a subject); b) comparing the cancer test sample with a reference (e.g., a reference sample taken from a non-cancerous or normal control subject), wherein an altered (e.g., decreased) level of STK11 in the test sample indicates that the subject will respond to treatment with an HDAC inhibitor; A method is provided that includes:

[0223] In one embodiment, there is provided a method for determining whether a subject having or diagnosed with cancer will respond to treatment with an HDAC inhibitor described herein and an immune checkpoint modulator described herein, the method comprising: a) detecting the level of STK11 (e.g., STK11 protein and / or STK11 mRNA) in a cancer test sample (e.g., in a cancer sample obtained from a subject); b) comparing the cancer test sample with a reference (e.g., a reference sample taken from a non-cancerous or normal control subject), wherein an altered (e.g., decreased) level of STK11 in the test sample indicates that the subject will respond to treatment with a combination of an HDAC inhibitor and an immune checkpoint modulator; A method is provided that includes:

[0224] In one embodiment, there is provided a method for determining whether a subject having or diagnosed with cancer will respond to treatment with an HDAC inhibitor as described herein, the method comprising: a) determining the copy number of the gene encoding STK11 in a cancer test sample (e.g., in a cancer sample obtained from a subject); b) comparing the cancer test sample with a reference (e.g., a reference sample taken from a non-cancerous or normal control subject), wherein a reduction in copy number indicates that the subject will respond to treatment with an HDAC inhibitor; A method is provided that includes:

[0225] In one embodiment, there is provided a method for determining whether a subject having or diagnosed with cancer will respond to treatment with an HDAC inhibitor described herein and an immune checkpoint modulator described herein, the method comprising: a) determining the copy number of the gene encoding STK11 in a cancer test sample (e.g., in a cancer sample obtained from a subject); b) comparing the cancer test sample with a reference (e.g., a reference sample taken from a non-cancerous or normal control subject), wherein a reduction in copy number indicates that the subject will respond to treatment with a combination HDAC inhibitor and immune checkpoint modulator; A method is provided that includes:

[0226] In some embodiments, the STK11 mutation is a loss-of-function mutation. In one embodiment, the altered level of STK11 activity or expression is determined by comparing the activity or expression level in a subject or a sample derived from a 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 altered level of STK11 activity is a reduced level of STK11 activity.

[0227] In one embodiment, the cancer is lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC), lung squamous cell carcinoma), 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 carcinoma (e.g., large cell neuroendocrine carcinoma), melanoma, non-melanoma skin cancer (e.g., cutaneous squamous cell carcinoma), bile duct carcinoma, gallbladder cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), bladder cancer (e.g., bladder urothelial carcinoma), prostate cancer (e.g., prostate adenocarcinoma), cervical cancer, cervical canal carcinoma, or cancer of unknown primary origin (e.g., adenocarcinoma of unknown primary origin).

[0228] 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), cholangiocarcinoma, ovarian cancer (e.g., ovarian serous adenocarcinoma), cervical cancer, cervical canal carcinoma, or cancer of unknown primary origin (e.g., adenocarcinoma of unknown primary origin).

[0229] 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), cholangiocarcinoma, ovarian cancer (e.g., ovarian serous adenocarcinoma), or cancer of unknown primary origin (e.g., adenocarcinoma of unknown primary origin).

[0230] In one embodiment, the cancer is lung cancer (e.g., lung adenocarcinoma or 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).

[0231] 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.

[0232] Determining whether the cancer will respond to treatment with an HDAC inhibitor In one embodiment, a method is provided for determining the sensitivity of a cancer to treatment with an HDAC inhibitor described herein, the method comprising determining i) the presence or absence of an STK11 mutation and / or ii) the level of STK11 activity or expression in a cancer test sample (e.g., a sample derived from a subject), wherein the presence of the STK11 mutation (e.g., an STK loss-of-function mutation) and / or altered (e.g., reduced) level of STK11 activity or expression indicates sensitivity to treatment with an HDAC inhibitor.

[0233] In one embodiment, there is provided a method for determining the susceptibility of a cancer to treatment with a combination of an HDAC inhibitor described herein and an immune checkpoint modulator described herein, the method comprising determining i) the presence or absence of an STK11 mutation and / or ii) the level of STK11 activity or expression in a cancer test sample (e.g., a sample from a subject), wherein the presence of the STK11 mutation (e.g., an STK loss-of-function mutation) and / or altered (e.g., decreased) level of STK11 activity or expression is indicative of susceptibility to treatment with a combination of an HDAC inhibitor and an immune checkpoint modulator.

[0234] In one embodiment, the STK11 expression level is assessed by determining the copy number of the gene encoding STK11 compared to a control sample, where an increased copy number indicates an increased expression level and a decreased copy number indicates a decreased expression level. In one embodiment, the STK11 expression level is assessed by determining the level of STK11 protein or mRNA compared to a control sample.

[0235] In one embodiment, a method is provided for determining whether a cancer will respond to treatment with an HDAC inhibitor described herein, the method comprising determining the presence or absence of an STK11 mutation in a cancer test sample (e.g., a sample derived from a subject), wherein the presence of the STK11 mutation (e.g., an STK loss-of-function mutation) indicates that the cancer will respond to treatment with an HDAC inhibitor.

[0236] In one embodiment, a method is provided for determining whether a cancer will respond to treatment with an HDAC inhibitor described herein and an immune checkpoint modulator described herein, the method comprising determining the presence or absence of an STK11 mutation in a cancer test sample (e.g., a sample from a subject), wherein the presence of the STK11 mutation (e.g., an STK loss-of-function mutation) indicates that the cancer will respond to treatment with the HDAC inhibitor and immune checkpoint modulator in combination.

[0237] In one embodiment, there is provided a method for determining whether a cancer will respond to treatment with an HDAC inhibitor as described herein, the method comprising: a) detecting the level of STK11 (e.g., STK11 protein and / or STK11 mRNA) in a cancer test sample (e.g., in a cancer sample obtained from a subject); b) comparing the cancer test sample with a reference (e.g., a reference sample taken from a non-cancerous or 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 an HDAC inhibitor; A method is provided which includes:

[0238] In one embodiment, there is provided a method for determining whether a cancer will respond to treatment with an HDAC inhibitor described herein and an immune checkpoint modulator described herein, the method comprising: a) detecting the level of STK11 (e.g., STK11 protein and / or STK11 mRNA) in a cancer test sample (e.g., in a cancer sample obtained from a subject); b) comparing the cancer test sample with a reference (e.g., a reference sample taken from a non-cancerous or 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; A method is provided that includes:

[0239] In one embodiment, there is provided a method for determining whether a cancer will respond to treatment with an HDAC inhibitor as described herein, the method comprising: a) determining the copy number of the gene encoding STK11 in a cancer test sample (e.g., in a cancer sample obtained from a subject); b) comparing the cancer test sample with a reference (e.g., a reference sample taken from a non-cancerous or normal control subject), wherein a decrease in copy number indicates that the cancer will respond to treatment with an HDAC inhibitor; A method is provided that includes:

[0240] In one embodiment, there is provided a method for determining whether a cancer will respond to treatment with an HDAC inhibitor described herein and an immune checkpoint modulator described herein, the method comprising: a) determining the copy number of the gene encoding STK11 in a cancer test sample (e.g., in a cancer sample obtained from a subject); b) comparing the cancer test sample with a reference (e.g., a reference sample taken from a non-cancerous or 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; A method is provided that includes:

[0241] In some embodiments, the STK11 mutation is a loss-of-function mutation. In one embodiment, the altered level of STK11 activity or expression 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 altered level of STK11 activity is a reduced level of STK11 activity.

[0242] In one embodiment, the cancer is lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC), lung squamous cell carcinoma), 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 carcinoma (e.g., large cell neuroendocrine carcinoma), melanoma, non-melanoma skin cancer (e.g., cutaneous squamous cell carcinoma), bile duct carcinoma, gallbladder cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), bladder cancer (e.g., bladder urothelial carcinoma), prostate cancer (e.g., prostate adenocarcinoma), cervical cancer, cervical canal carcinoma, or cancer of unknown primary origin (e.g., adenocarcinoma of unknown primary origin).

[0243] 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), cholangiocarcinoma, ovarian cancer (e.g., ovarian serous adenocarcinoma), cervical cancer, cervical canal carcinoma, or cancer of unknown primary origin (e.g., adenocarcinoma of unknown primary origin).

[0244] 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), cholangiocarcinoma, ovarian cancer (e.g., ovarian serous adenocarcinoma), or cancer of unknown primary origin (e.g., adenocarcinoma of unknown primary origin).

[0245] In one embodiment, the cancer is lung cancer (e.g., lung adenocarcinoma or 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).

[0246] 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.

[0247] Sample preparation The method may include detecting somatic mutations, loss of heterozygosity, whole gene deletion, reduced expression, or DNA methylation in the promoter region of STK11. In some embodiments, STK11 mutations may occur at various sites in cancer.

[0248] The present disclosure further provides assays for detecting levels of STK11 (e.g., STK11 protein and / or STK11 mRNA). In one embodiment, the present disclosure provides assays for detecting loss of STK11 protein expression (e.g., as measured by immunohistochemistry). The present disclosure further provides assays for detecting STK11 mutations (e.g., loss-of-function mutations of STK11).

[0249] Gene mutations or expression can be analyzed from patient samples. The patient sample can be any bodily tissue or fluid containing nucleic acids derived from cancer (e.g., lung cancer) in a subject. In some embodiments, the sample is a bodily fluid such as blood (e.g., serum or plasma), bone marrow, cerebrospinal fluid, peritoneal / pleural fluid, lymphatic fluid, ascites, serous fluid, sputum, tears, stool, and urine. In certain embodiments, the sample is a blood sample containing circulating tumor cells or cell-free DNA. In some embodiments, the sample is not a blood sample. In other embodiments, the sample can be tissue (e.g., lung tissue), including normal tissue or tumor tissue. The tissue can be fresh-frozen or formalin-fixed, paraffin-embedded (FFPE). In certain embodiments, a tumor FFPE (e.g., lung tumor FFPE) sample is obtained.

[0250] Methods and reagents for sample acquisition, processing, and analysis are known in the art.

[0251] Cells can be collected from biological samples using standard techniques known in the art. Methods for extracting cellular DNA from liquid or tissue samples are known in the art. For example, cells can be collected by centrifuging the cell sample and resuspending the precipitated cells. Cells can be resuspended in a buffer such as phosphate-buffered saline (PBS). After centrifuging the cell suspension to obtain a cell pellet, the cells can be lysed (e.g., with a detergent) and DNA can be extracted. After cell lysis, proteins are removed from DNA using various proteases. DNA is then extracted with phenol, precipitated in alcohol, and dissolved in aqueous solution. Alternatively, genomic DNA can be extracted using kits such as the QIAamp® Tissue Kit (Qiagen, Chatsworth, Calif.) and the Wizard® Genomic DNA Purification Kit (Promega).

[0252] Measurement of gene expression In some embodiments, the altered (e.g., reduced) level of STK11 is an altered (e.g., reduced) STK11 gene expression level. In some embodiments, the altered (e.g., reduced) level of STK11 is an altered (e.g., reduced) STK11 mRNA level. Measurement of gene expression can be performed using any method or reagent known in the art.

[0253] The detection of gene expression can be carried out by any suitable method, including, for example, detecting the amount of mRNA transcribed from gene, or the amount of cDNA produced from reverse transcription of mRNA transcribed from gene, or the amount of polypeptide or protein coded by gene.These methods can be carried out on a sample-by-sample basis, or can be modified for high-throughput analysis.For example, Affymetrix (TM) U133 microarray chip is used.

[0254] In some embodiments, gene expression is detected and quantified by hybridization to a probe that specifically hybridizes to an appropriate probe for that biomarker. The probes can also be attached to a solid support for use in high-throughput screening assays, using methods known in the art.

[0255] 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 preferably labeled, for example with a fluorescent tag, during the amplification step.

[0256] Hybridization of the labeled sample is carried out at an appropriate stringency level, and the degree of probe-nucleic acid hybridization is quantitatively measured using a detection device.

[0257] Alternatively, any one of gene copy number, transcription, or translation can be determined using known techniques. For example, amplification methods such as PCR can be useful. The general procedure for PCR is taught in MacPherson et al., PCR: A Practical Approach, (IRL Press at Oxford University Press (1991)). However, the PCR conditions used for each application reaction are determined empirically. Several parameters affect the success of the reaction, including annealing temperature and time, extension time, Mg2+ and / or ATP concentration, pH, and the relative concentrations of primers, template, and deoxyribonucleotides. After amplification, the resulting DNA fragments can be detected by agarose gel electrophoresis, followed by visualization with ethidium bromide staining and ultraviolet illumination. In some embodiments, the hybridized nucleic acid is detected by detecting one or more labels attached to the sample nucleic acid. Labels can be incorporated by any of a number of means well known to those skilled in the art. However, in some embodiments, labels are simultaneously incorporated during the amplification step in the preparation of the sample nucleic acid. Thus, for example, polymerase chain reaction (PCR) using labeled primers or labeled nucleotides provides labeled amplification products. In another embodiment, transcription amplification as described above using labeled nucleotides (e.g., fluorescein-labeled UTP and / or CTP) incorporates a label into the transcribed nucleic acid.

[0258] Alternatively, a label may be added directly to the original nucleic acid sample (e.g., mRNA, polyA, mRNA, cDNA, etc.) or to the amplification product after amplification is completed. Means for attaching labels to nucleic acids are well known to those of skill in the art and include, for example, nick translation, or end-labeling (e.g., with labeled RNA) where the sample nucleic acid is kinased and then attached to a label (e.g., a fluorophore) by ligation of a nucleic acid linker.

[0259] In one example, gene expression can be measured by in situ hybridization protocols (eg, by RNAscope®) that can detect RNA molecules on tissue sections or slides containing cells.

[0260] 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™), 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 ELISAs), and colorimetric labels such as colloidal gold or colored glass or plastic (e.g., polystyrene, polypropylene, latex, etc.) beads.

[0261] Detection of labels is well known to those skilled in the art. Thus, 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 typically detected by providing a substrate to the enzyme and detecting the reaction product produced by the action of the enzyme on the substrate, while colorimetric labels are detected by simply visualizing the colored label. Detectable labels can be added to the target (sample) nucleic acid(s) before or after hybridization, as described in WO97 / 10365, for example. These detectable labels are directly bound to or incorporated into the target (sample) nucleic acid before hybridization. In contrast, "indirect labels" are added to the hybrid duplex after hybridization. Generally, indirect labels are bound to a binding moiety that is bound to the target nucleic acid before hybridization. For example, the target nucleic acid can be biotinylated before hybridization. After hybridization, an avidin-conjugated fluorophore binds to the biotin-containing hybrid duplex, providing an easily detectable label. For a detailed review of methods for labeling nucleic acids and detecting labeled hybridized nucleic acids, see Laboratory Techniques in Biochemistry and Molecular Biology, Vol. 24: Hybridization with Nucleic Acid Probes, P. Tijssen, ed. Elsevier, NY (1993).

[0262] In some embodiments, detection of altered (eg, reduced) levels of STK11 is by quantitative reverse transcriptase (RT)-polymerase chain reaction (PCR), RNA-Seq, or microarray.

[0263] Polypeptide detection The protein level of STK11 can be determined by examining protein expression or protein products, which involves measuring the amount of any immunospecific binding that occurs between an antibody that selectively recognizes and binds to a biomarker polypeptide in a sample obtained from a subject, and comparing this with the amount of immunospecific binding of at least one biomarker in a control sample.

[0264] A variety of techniques are available in the art for protein analysis, including, but not limited to, radioimmunoassays, ELISA (enzyme-linked immunosorbent assays), "sandwich" immunoassays, immunoradiometric assays, in situ immunoassays (using, for example, colloidal gold, enzyme or radioisotope labels), Western blot analysis, immunoprecipitation assays, immunofluorescence assays, flow cytometry, immunohistochemistry, HPLC, mass spectrometry, confocal microscopy, enzyme assays, surface plasmon resonance, and PAGE-SDS.

[0265] In some embodiments, detection of altered (e.g., reduced) STK11 protein levels is by Western blot. In some embodiments, detection of altered (e.g., reduced) STK11 protein levels is by fluorescence-activated cell sorting (FACS). In some embodiments, detection of altered (e.g., reduced) STK11 protein levels is by immunohistochemistry.

[0266] Other detection methods Mutations in a target of interest (eg, STK11 mutations) can be detected by methods known to those of skill in the art.

[0267] To detect somatic mutations, sequencing can be performed on DNA extracted from tissues such as tumor tissue. The tumor tissue can be fresh or preserved (e.g., formalin-fixed or paraffin-embedded). Sequencing can also be performed using cell-free DNA. The coding region of the gene of interest and sometimes adjacent regions (e.g., introns, promoters) are sequenced using next-generation sequencing (NGS) or Sanger sequencing. Loss-of-function mutations or gene rearrangements can be detected or verified using secondary methods such as qPCR, PCR, immunohistochemistry, Sanger sequencing, comparative genomic hybridization, or the PacBio system.

[0268] Selected Embodiments Embodiment 1. A method for treating a subject having cancer or at risk of developing cancer, comprising administering to the subject an effective amount of a histone deacetylase (HDAC) inhibitor, wherein the cancer has been identified as having altered STK11 activity or expression.

[0269] Embodiment 2. 2. The method of embodiment 1, wherein the histone deacetylase inhibitor is administered in combination with one or more additional therapeutic agents.

[0270] Embodiment 3. 3. The method of embodiment 2, wherein at least one of the additional therapeutic agents is an immune checkpoint modulator.

[0271] Embodiment 4. 1. A method of treating cancer in a subject 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 the tumor or tumor microenvironment, and the cancer has been identified as having altered STK11 activity or expression.

[0272] Embodiment 5. 1. A method of treating cancer in a subject comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment reduces or depletes Treg cells in the tumor or tumor microenvironment, and the cancer has been identified as having altered STK11 activity or expression.

[0273] Embodiment 6. 1. A method of treating cancer in a subject comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment induces or increases expression of a cytokine that promotes anti-tumor activity, and the cancer has been identified as having altered STK11 activity or expression.

[0274] Embodiment 7. 7. The method of embodiment 6, wherein the cytokine is selected from the group of CXCL9, CXCL10, and CXCL11.

[0275] Embodiment 8. 1. A method of treating cancer in a subject comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment reduces expression of cytokines that promote the recruitment of Treg cells, and the cancer has been identified as having altered STK11 activity or expression.

[0276] Embodiment 9. 9. The method of embodiment 8, wherein the cytokine is CCL1 or CCL22.

[0277] Embodiment 10. A method for treating cancer in a subject, comprising administering an HDAC inhibitor to the subject, wherein administration of the HDAC inhibitor does not reduce the viability of erythroid or myeloid cells, and the cancer has been identified as having altered STK11 activity or expression.

[0278] Embodiment 11. A method for treating cancer in a subject, comprising administering an HDAC1,2 selective inhibitor, wherein the cancer exhibits an immune evasion phenotype characterized by STK11 mutant expression, and the HDAC1,2 selective inhibitor can attenuate or reverse the immune evasion phenotype.

[0279] Embodiment 12. 12. The method of embodiment 10 or 11, further comprising administering an immune checkpoint modulator.

[0280] Embodiment 13. A method of treating cancer in a subject comprising administering to the subject an HDAC inhibitor, wherein an immune checkpoint modulator has been administered, is being administered, or will be administered to the subject, and the cancer has been identified as having altered STK11 activity or expression.

[0281] Embodiment 14. A method of treating cancer in a subject comprising administering to the subject an immune checkpoint modulator, wherein an HDAC inhibitor has been administered, is being administered, or will be administered to the subject, and the cancer has been identified as having altered STK11 activity or expression.

[0282] Embodiment 15. 3. 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.

[0283] Embodiment 16. 16. The method of any one of embodiments 3-15, wherein each immune checkpoint modulator is independently a checkpoint inhibitor, a T cell costimulatory receptor agonist, or a dendritic cell costimulatory receptor agonist.

[0284] Embodiment 17. 17. The method of any one of embodiments 3-16, wherein at least one immune checkpoint modulator is independently a T cell costimulatory receptor agonist or a dendritic cell costimulatory receptor agonist.

[0285] Embodiment 18. 17. The method of any one of embodiments 3-16, wherein at least one immune checkpoint modulator is a checkpoint inhibitor.

[0286] Embodiment 19. 19. The method of embodiment 18, 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.

[0287] Embodiment 20. 19. 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.

[0288] Embodiment 21. 19. The method of embodiment 18, wherein each checkpoint inhibitor is independently selected from an anti-PD1 agent and an anti-PD-L1 agent.

[0289] Embodiment 22. 19. The method of embodiment 18, wherein the checkpoint inhibitor is an anti-PD1 agent.

[0290] Embodiment 23. 19. The method of embodiment 18, wherein the checkpoint inhibitor is an anti-PD-L1 agent.

[0291] Embodiment 24. 3. 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.

[0292] Embodiment 25. 23. The method of any one of embodiments 18-22, wherein each immune checkpoint inhibitor is independently an antibody.

[0293] Embodiment 26. 26. The method of embodiment 25, wherein each checkpoint inhibitor is independently selected from an anti-CTLA-4 antibody, an anti-PD-1 antibody, an anti-PD-L1 antibody, an anti-4-1BB antibody, an anti-OX-40 antibody, an anti-GITR antibody, an anti-CD27 antibody, an anti-CD28 antibody, an anti-CD40 antibody, an anti-LAG3 antibody, an anti-ICOS antibody, an anti-TWEAKR antibody, an anti-HVEM antibody, an anti-TIM-1 antibody, an anti-TIM-3 antibody, an anti-VISTA antibody, and an anti-TIGIT antibody.

[0294] Embodiment 27. 26. 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.

[0295] Embodiment 28. 26. The method of embodiment 25, wherein each immune checkpoint inhibitor is independently selected from nivolumab, CT-011, AMP-224, pembrolizumab, pidilizumab, cemiplimab, dostallimab, prorugolimab, spartalizumab, camrelizumab, sasanlimab, sintilimab, tislelizumab, toripalimab, retifanlimab, MEDI0680, budigalimab, geptanolimab, BMS936559, durvalumab, avelumab, embafolimab, cosibelimab, sugemalimab, AUNP-12, atezolizumab, and CA-170.

[0296] Embodiment 29. 26. The method of embodiment 25, wherein each checkpoint inhibitor is independently selected from an anti-PD1 antibody and an anti-PD-L1 antibody.

[0297] Embodiment 30. 26. The method of embodiment 25, wherein the checkpoint inhibitor is an anti-PD1 antibody.

[0298] Embodiment 31. 26. The method of embodiment 25, wherein the checkpoint inhibitor is an anti-PD1-L1 antibody.

[0299] Embodiment 32. 28. The method of embodiment 26 or 27, wherein the anti-CTLA-4 antibody is ipilimumab.

[0300] Embodiment 33. The method of any one of embodiments 26, 27, 29, and 30, wherein the anti-PD-1 antibody is pembrolizumab or nivolumab.

[0301] Embodiment 34. The method of any one of embodiments 26, 27, 29, and 30, wherein the anti-PD-1 antibody is pembrolizumab.

[0302] Embodiment 35. The method of any one of embodiments 26, 27, 29, and 30, wherein the anti-PD-1 antibody is nivolumab.

[0303] 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).

[0304] Embodiment 37. 16. The method of any one of embodiments 3-15, wherein the immune checkpoint modulator is a T cell costimulatory receptor agonist or a dendritic cell costimulatory receptor agonist.

[0305] Embodiment 38. 38. The method of any one of embodiments 2-37, wherein at least one additional therapeutic agent is a targeting agent.

[0306] Embodiment 39. 39. The method of embodiment 38, wherein each targeting agent is independently selected from an anti-angiogenic agent (e.g., 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.

[0307] Embodiment 40. 39. The method of embodiment 38, wherein each targeted agent is independently selected from bevacizumab, ramucirumab, sotorasib, crizotinib, ceritinib, alectinib, brigutinib, lorlatinib, entrectinib, dabrafenib, trametinib, capmatinib, tepotinib, and larotrectinib.

[0308] Embodiment 41. The method of any one of embodiments 2-40, wherein the at least one additional therapeutic agent is a chemotherapeutic agent.

[0309] Embodiment 42. 42. The method of embodiment 41, wherein each chemotherapeutic agent is independently selected from cisplatin, carboplatin, paclitaxel, albumin-bound paclitaxel (nab-paclitaxel), docetaxel, gemcitabine, vinorelbine, etoposide, and pemetrexed.

[0310] Embodiment 43. 42. The method of embodiment 41, wherein at least one chemotherapeutic agent is a platinum-containing therapeutic agent.

[0311] Embodiment 44. The method of embodiment 41, wherein one chemotherapeutic agent is a platinum-containing chemotherapeutic agent (e.g., cisplatin) and the second chemotherapeutic agent is pemetrexed.

[0312] Embodiment 45. 45. The method of any one of embodiments 2-44, wherein at least one additional therapeutic agent is radiation.

[0313] Embodiment 46. 46. The method of any one of embodiments 1-45, wherein the cancer is resistant to anti-PD1 therapy or anti-PD-L1 therapy.

[0314] Embodiment 47. 47. The method of embodiment 46, wherein the cancer has natural resistance to anti-PD1 therapy or anti-PD-L1 therapy.

[0315] Embodiment 48. 47. The method of embodiment 46, wherein the cancer has acquired resistance to anti-PD1 therapy or anti-PD-L1 therapy.

[0316] Embodiment 49. The method of any one of embodiments 1-48, wherein the cancer is resistant to chemotherapy (e.g., platinum-containing chemotherapy).

[0317] Embodiment 50. 50. The method of embodiment 49, wherein the cancer has natural resistance to chemotherapy (e.g., platinum-containing chemotherapy).

[0318] Embodiment 51. 50. The method of embodiment 49, wherein the cancer has acquired resistance to chemotherapy (e.g., platinum-containing chemotherapy).

[0319] Embodiment 52. 52. The method of any one of embodiments 1-51, wherein the cancer does not respond to or does not benefit from treatment with the immune checkpoint modulator when administered alone or as part of a treatment regimen that does not include an HDAC inhibitor.

[0320] Embodiment 53. 52. The method of any one of embodiments 1 to 51, wherein the cancer is selected from the group consisting of lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC), lung squamous cell carcinoma), 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 carcinoma (e.g., large cell neuroendocrine carcinoma), melanoma, non-melanoma skin cancer (e.g., cutaneous squamous cell carcinoma), bile duct carcinoma, gallbladder cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), bladder cancer (e.g., bladder urothelial carcinoma), prostate cancer (e.g., prostate adenocarcinoma), cervical cancer, cervical canal carcinoma, or cancer of unknown primary origin (e.g., adenocarcinoma of unknown primary origin).

[0321] Embodiment 54. 53. The method of embodiment 52, wherein the cancer is lung cancer.

[0322] Embodiment 55. 55. The method of embodiment 54, wherein the cancer is lung adenocarcinoma.

[0323] Embodiment 56. 55. The method of embodiment 54, wherein the cancer is non-small cell lung cancer (NSCLC).

[0324] Embodiment 57. 57. The method of embodiment 56, wherein the cancer is non-squamous non-small cell lung cancer (NSCLC).

[0325] Embodiment 58. 53. The method of embodiment 52, wherein the cancer is colorectal cancer or colon adenocarcinoma.

[0326] Embodiment 59. The method of any one of embodiments 1-58, wherein the cancer is identified as having an STK11 mutation and one or more additional mutations.

[0327] Embodiment 60. 60. The method of embodiment 59, wherein the additional mutation is selected from a KRAS mutation and a KEAP1 mutation.

[0328] Embodiment 61. 60. The method of embodiment 59, wherein the additional mutation is a KRAS mutation.

[0329] Embodiment 62. 62. The method of 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.

[0330] Embodiment 63. 60. The method of embodiment 59, wherein the additional mutation is a KEAP1 mutation.

[0331] Embodiment 64. 60. The method of embodiment 59, wherein the additional mutations are a KRAS mutation and a KEAP1 mutation.

[0332] Embodiment 65. 65. The method of any one of embodiments 1-64, wherein the cancer does not have an EGFR mutation.

[0333] Embodiment 66. 66. The method of any one of embodiments 1 to 65, wherein the cancer has increased or decreased STK11 expression.

[0334] Embodiment 67. The method of embodiment 66, wherein an increase or decrease in STK expression is assessed by determining the copy number of the gene encoding STK11 compared to a control sample, wherein an increase in copy number indicates an elevated expression level and a decrease in copy number indicates a decreased expression level.

[0335] Embodiment 68. 67. The method of embodiment 66, wherein the increase or decrease in STK expression is assessed by determining the level of STK11 protein or mRNA compared to a control sample.

[0336] Embodiment 69. The method of embodiment 67 or 68, wherein the cancer has decreased STK11 expression.

[0337] Embodiment 70. 66. The method of any one of embodiments 1-65, wherein the cancer has an STK11 mutation.

[0338] Embodiment 71. STK11 mutations include: (i) a mutation in the nucleotide sequence encoding STK11; (ii) a mutation in a regulatory sequence controlling expression of the nucleotide sequence encoding STK11; (iii) a mutation in a nucleotide encoding a protein that interacts with the transcript of the STK11 gene; 71. The method of embodiment 70, wherein the mutation is selected from:

[0339] Embodiment 72. 71. The method of embodiment 70, wherein the STK11 mutation is a mutation in the translation product of the STK11 gene.

[0340] Embodiment 73. 71. The method of embodiment 70, wherein the STK11 mutation is a mutation in the transcript of the STK11 gene.

[0341] Embodiment 74. The method of any one of embodiments 70 to 73, wherein the STK11 mutation is an inactivating (loss-of-function) mutation.

[0342] Embodiment 75. The method of any one of embodiments 66 to 69, wherein an increase or decrease in STK11 expression is measured in a sample derived from the subject.

[0343] Embodiment 76. 76. The method of embodiment 75, wherein an increase or decrease in STK11 expression is measured relative to a control.

[0344] Embodiment 77. 77. The method of embodiment 76, wherein the control is a healthy tissue, preferably of the same tissue type as the cancer tissue.

[0345] Embodiment 78. The method of any one of embodiments 70 to 74, wherein the STK11 mutation has been identified in a sample derived from the subject.

[0346] Embodiment 79. 79. The method of embodiment 78, wherein the STK11 mutation has been identified in a tumor sample from the subject.

[0347] Embodiment 80. 79. The method of embodiment 78, wherein the STK11 mutation is not identified in a healthy tissue sample derived from the subject.

[0348] Embodiment 81. 81. The method of any one of embodiments 1 to 80, wherein the STK11 mutation is not a germline mutation.

[0349] Embodiment 82. The method of any one of embodiments 2-81, wherein the HDAC inhibitor is administered simultaneously with the additional therapeutic agent.

[0350] Embodiment 83. The method of any one of embodiments 2-81, wherein the HDAC inhibitor is administered separately from the additional therapeutic agent.

[0351] Embodiment 84. The method of any one of embodiments 2-81, wherein the HDAC inhibitor is administered sequentially with the additional therapeutic agent.

[0352] Embodiment 85. The method of any one of embodiments 2-81, wherein the HDAC inhibitor is administered before the additional therapeutic agent.

[0353] Embodiment 86. The method of any one of embodiments 2-81, wherein the HDAC inhibitor is administered after the additional therapeutic agent.

[0354] Embodiment 87. 82. 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.

[0355] Embodiment 88. 82. The method of any one of embodiments 2-81, comprising administering to the subject an HDAC inhibitor, and subsequently administering to the subject an immune checkpoint modulator.

[0356] Embodiment 89. 82. The method of any one of embodiments 2-81, comprising 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, followed by administering to the subject an HDAC inhibitor.

[0357] Embodiment 90. 82. 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.

[0358] Embodiment 91. 82. The method of any one of embodiments 2-81, comprising 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.

[0359] Embodiment 92. 82. 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.

[0360] Embodiment 93. 82. 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.

[0361] 94. 82. 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.

[0362] 95. 95. The method of any one of embodiments 1-94, wherein the subject has a cancer identified as having altered STK11 activity or expression.

[0363] 96. 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).

[0364] 97. The method of any one of embodiments 1 to 95, wherein the histone deacetylase inhibitor is a selective inhibitor of histone deacetylase 1 and histone deacetylase 2 (HDAC1,2 selective inhibitor).

[0365] Embodiment 98. 96. The method of any one of embodiments 1-95, wherein the histone deacetylase inhibitor is a selective HDAC class I inhibitor.

[0366] Embodiment 99. 96. The method of any one of embodiments 1-95, wherein the histone deacetylase inhibitor is a CoREST selective deacetylase inhibitor.

[0367] Embodiment 100. A method 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 in which STK11 activity or expression is altered, and selecting the subject thus identified for treatment with the HDAC inhibitor.

[0368] Embodiment 101. A method for 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 in which STK11 activity or expression is altered, and selecting the subject thus identified for treatment with the HDAC inhibitor and one or more additional therapeutic agents.

[0369] Embodiment 102. 102. The method of embodiment 101, wherein at least one of the additional therapeutic agents is an immune checkpoint modulator.

[0370] Embodiment 103. 1. A method for selecting a subject for treatment with a combination of an HDAC inhibitor and two or more additional therapeutic agents, 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 two or more additional therapeutic agents, wherein at least two of the additional therapeutic agents are immune checkpoint modulators.

[0371] Embodiment 104. 1. A method of 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 a chemotherapeutic agent, a targeted agent, 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 a chemotherapeutic agent, a targeted agent, and radiation therapy, and in which treatment with the combination of the immune checkpoint modulator and the additional therapeutic agent(s) did not provide any additional benefit compared to treatment with the additional therapeutic agent(s) alone, and selecting the subject so identified for treatment.

[0372] Embodiment 105. The method of embodiment 104, further comprising identifying a subject having a cancer characterized by the presence of cells with decreased STK11 activity or expression, and selecting the thus identified subject for treatment.

[0373] Embodiment 106. 106. The method of embodiments 102-105, wherein each immune checkpoint modulator is independently a checkpoint inhibitor, a T cell costimulatory receptor agonist, or a dendritic cell costimulatory receptor agonist.

[0374] Embodiment 107. 107. The method of any one of embodiments 102-106, wherein at least one immune checkpoint modulator is independently a T cell costimulatory receptor agonist or a dendritic cell costimulatory receptor agonist.

[0375] Embodiment 108. 108. The method of any one of embodiments 102-107, wherein at least one immune checkpoint modulator is a checkpoint inhibitor.

[0376] Embodiment 109. 109. The method of embodiment 108, 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.

[0377] Embodiment 110. 109. The method of embodiment 108, wherein each checkpoint inhibitor is independently selected from an anti-CTLA-4 agent, an anti-PD-1 agent, and an anti-PD-L1 agent.

[0378] Embodiment 111. 109. The method of embodiment 108, wherein each checkpoint inhibitor is independently selected from an anti-PD1 agent and an anti-PD-L1 agent.

[0379] Embodiment 112. 109. The method of embodiment 108, wherein the checkpoint inhibitor is an anti-PD1 agent.

[0380] Embodiment 113. 109. The method of embodiment 108, wherein the checkpoint inhibitor is an anti-PD-L1 agent.

[0381] Embodiment 114. 104. 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.

[0382] Embodiment 115. 115. The method of any one of embodiments 108-114, wherein each immune checkpoint inhibitor is independently an antibody.

[0383] Embodiment 116. 116. The method of embodiment 115, wherein each checkpoint inhibitor is independently selected from an anti-CTLA-4 antibody, an anti-PD-1 antibody, an anti-PD-L1 antibody, an anti-4-1BB antibody, an anti-OX-40 antibody, an anti-GITR antibody, an anti-CD27 antibody, an anti-CD28 antibody, an anti-CD40 antibody, an anti-LAG3 antibody, an anti-ICOS antibody, an anti-TWEAKR antibody, an anti-HVEM antibody, an anti-TIM-1 antibody, an anti-TIM-3 antibody, an anti-VISTA antibody, and an anti-TIGIT antibody.

[0384] Embodiment 117. 116. 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.

[0385] Embodiment 118. 116. The method of embodiment 115, wherein each immune checkpoint inhibitor is independently selected from nivolumab, CT-011, AMP-224, pembrolizumab, pidilizumab, cemiplimab, dostallimab, prorugolimab, spartalizumab, camrelizumab, sasanlimab, sintilimab, tislelizumab, toripalimab, retifanlimab, MEDI0680, budigalimab, and geptanolimab.

[0386] Embodiment 119. 116. The method of embodiment 115, wherein each checkpoint inhibitor is independently selected from an anti-PD1 antibody and an anti-PD-L1 antibody.

[0387] Embodiment 120. 116. The method of embodiment 115, wherein the checkpoint inhibitor is an anti-PD1 antibody.

[0388] Embodiment 121. 116. The method of embodiment 115, wherein the checkpoint inhibitor is an anti-PD1-L1 antibody.

[0389] Embodiment 122. The method of embodiment 116 or 117, wherein the anti-CTLA-4 antibody is ipilimumab.

[0390] Embodiment 123. 121. The method of any one of embodiments 116, 117, 119, and 120, wherein the anti-PD-1 antibody is pembrolizumab or nivolumab.

[0391] Embodiment 124. 121. The method of any one of embodiments 116, 117, 119, and 120, wherein the anti-PD-1 antibody is pembrolizumab.

[0392] Embodiment 125. 121. The method of any one of embodiments 116, 117, 119, and 120, wherein the anti-PD-1 antibody is nivolumab.

[0393] Embodiment 126. 122. 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).

[0394] Embodiment 127. 103. The method of embodiment 102, wherein the immune checkpoint modulator is a T cell costimulatory receptor agonist or a dendritic cell costimulatory receptor agonist.

[0395] Embodiment 128. The method of any one of embodiments 101-127, wherein at least one additional therapeutic agent is a targeting agent.

[0396] Embodiment 129. 129. The method of embodiment 128, wherein each targeting agent is independently selected from an anti-angiogenic agent (e.g., 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.

[0397] Embodiment 130. 129. The method of embodiment 128, wherein each targeted agent is independently selected from bevacizumab, ramucirumab, sotorasib, crizotinib, ceritinib, alectinib, brigutinib, lorlatinib, entrectinib, dabrafenib, trametinib, capmatinib, tepotinib, and larotrectinib.

[0398] Embodiment 131. The method of any one of embodiments 101-130, wherein at least one additional therapeutic agent is a chemotherapeutic agent.

[0399] Embodiment 132. 132. The method of embodiment 131, wherein each chemotherapeutic agent is independently selected from cisplatin, carboplatin, paclitaxel, albumin-bound paclitaxel (nab-paclitaxel), docetaxel, gemcitabine, vinorelbine, etoposide, and pemetrexed.

[0400] Embodiment 133. 132. The method of embodiment 131, wherein at least one chemotherapeutic agent is a platinum-containing therapeutic agent.

[0401] Embodiment 134. The method of embodiment 131, wherein one chemotherapeutic agent is a platinum-containing chemotherapeutic agent (e.g., cisplatin) and the second chemotherapeutic agent is pemetrexed.

[0402] Embodiment 135. The method of any one of embodiments 101-134, wherein at least one additional therapeutic agent is radiation.

[0403] 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.

[0404] Embodiment 137. 137. The method of embodiment 136, wherein the cancer has natural resistance to anti-PD1 therapy or anti-PD-L1 therapy.

[0405] Embodiment 138. 137. The method of embodiment 136, wherein the cancer has acquired resistance to anti-PD1 therapy or anti-PD-L1 therapy.

[0406] Embodiment 139. The method of any one of embodiments 100-138, wherein the cancer is resistant to chemotherapy (e.g., platinum-containing chemotherapy).

[0407] Embodiment 140. 140. The method of embodiment 139, wherein the cancer has natural resistance to chemotherapy (e.g., platinum-containing chemotherapy).

[0408] Embodiment 141. The method of embodiment 140, wherein the cancer has acquired resistance to chemotherapy (e.g., platinum-containing chemotherapy).

[0409] Embodiment 142. 142. The method of any one of embodiments 100-141, wherein the cancer does not respond to or does not benefit from treatment with the immune checkpoint modulator when administered alone or as part of a treatment regimen that does not include an HDAC inhibitor.

[0410] Embodiment 143. The method of any one of embodiments 100 to 142, wherein the cancer is selected from the group consisting of lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC), lung squamous cell carcinoma), 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 carcinoma (e.g., large cell neuroendocrine carcinoma), melanoma, non-melanoma skin cancer (e.g., cutaneous squamous cell carcinoma), bile duct carcinoma, gallbladder cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), bladder cancer (e.g., bladder urothelial carcinoma), prostate cancer (e.g., prostate adenocarcinoma), cervical cancer, cervical canal carcinoma, or cancer of unknown primary origin (e.g., adenocarcinoma of unknown primary origin).

[0411] Embodiment 144. 143. The method of embodiment 142, wherein the cancer is lung cancer.

[0412] Embodiment 145. 145. The method of embodiment 144, wherein the cancer is lung adenocarcinoma.

[0413] Embodiment 146. 145. The method of embodiment 144, wherein the cancer is non-small cell lung cancer (NSCLC).

[0414] Embodiment 147. 147. The method of embodiment 146, wherein the cancer is non-squamous non-small cell lung cancer (NSCLC).

[0415] Embodiment 148. The method of any one of embodiments 100-147, wherein the cancer is identified as having an STK11 mutation and one or more additional mutations.

[0416] Embodiment 149. 149. The method of embodiment 148, wherein the additional mutation is selected from a KRAS mutation and a KEAP1 mutation.

[0417] 150. 149. The method of embodiment 148, wherein the additional mutation is a KRAS mutation.

[0418] Embodiment 151. 151. The method of 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.

[0419] Embodiment 152. 149. The method of embodiment 148, wherein the additional mutation is a KEAP1 mutation.

[0420] Embodiment 153. 149. The method of embodiment 148, wherein the additional mutations are a KRAS mutation and a KEAP1 mutation.

[0421] Embodiment 154. The method of any one of embodiments 100-153, wherein the cancer does not have an EGFR mutation.

[0422] Embodiment 155. The method of any one of embodiments 100 to 154, wherein the cancer has increased or decreased STK11 expression.

[0423] Embodiment 156. The method of embodiment 155, wherein an increase or decrease in STK expression is assessed by determining the copy number of the gene encoding STK11 compared to a control sample, wherein an increase in copy number indicates an elevated expression level and a decrease in copy number indicates a decreased expression level.

[0424] Embodiment 157. 156. The method of embodiment 155, wherein the increase or decrease in STK expression is assessed by determining the level of STK11 protein or mRNA compared to a control sample.

[0425] Embodiment 158. The method of embodiments 155-157, wherein the cancer has decreased STK11 expression.

[0426] Embodiment 159. The method of any one of embodiments 100 to 154, wherein the cancer has an STK11 mutation.

[0427] Embodiment 160. STK11 mutations include: (i) a mutation in the nucleotide sequence encoding STK11; (ii) a mutation in a regulatory sequence controlling expression of the nucleotide sequence encoding STK11; (iii) a mutation in a nucleotide encoding a protein that interacts with the transcript of the STK11 gene; 160. The method of embodiment 159, wherein the mutation is selected from:

[0428] Embodiment 161. 160. The method of embodiment 159, wherein the STK11 mutation is a mutation in the translation product of the STK11 gene.

[0429] Embodiment 162. 160. The method of embodiment 159, wherein the STK11 mutation is a mutation in the transcript of the STK11 gene.

[0430] Embodiment 163. The method of any one of embodiments 159 to 161, wherein the STK11 mutation is an inactivating (loss-of-function) mutation.

[0431] Embodiment 164. The method of any one of embodiments 155 to 158, wherein an increase or decrease in STK11 expression is measured in a sample derived from the subject.

[0432] 165. The method of embodiment 164, wherein an increase or decrease in STK11 expression is measured relative to a control.

[0433] Embodiment 166. 166. The method of embodiment 165, wherein the control is a healthy tissue, preferably of the same tissue type as the cancer tissue.

[0434] Embodiment 167. The method of any one of embodiments 159 to 163, wherein the STK11 mutation has been identified in a sample derived from the subject.

[0435] Embodiment 168. 168. The method of embodiment 167, wherein the STK11 mutation has been identified in a tumor sample derived from the subject.

[0436] Embodiment 169. 168. The method of embodiment 167, wherein the STK11 mutation is not identified in a healthy tissue sample derived from the subject.

[0437] Embodiment 170. 169. The method of any one of embodiments 100 to 169, wherein the STK11 mutation is not a germline mutation.

[0438] Embodiment 171. 171. A method of treating cancer in a subject, comprising administering to the subject a combination of an HDAC inhibitor and an immune checkpoint modulator, wherein the subject has been selected for treatment with the method of any one of embodiments 100-170.

[0439] Embodiment 172. 170. A method of treating cancer in a subject comprising administering to the subject an HDAC inhibitor, wherein an immune checkpoint modulator has been administered, is being administered, or will be administered to the subject, and the subject has been selected for treatment with the method of any one of embodiments 100-170.

[0440] Embodiment 173. A method of treating cancer in a subject comprising administering to the subject an immune checkpoint modulator, wherein an HDAC inhibitor has been administered, is being administered, or will be administered to the subject, and the subject has been selected for treatment with the method of any one of embodiments 100-170.

[0441] Embodiment 174. The method of any one of embodiments 100 to 173, wherein the histone deacetylase inhibitor is a selective inhibitor of histone deacetylase 1 (HDAC1 selective inhibitor).

[0442] Embodiment 175. The method of any one of embodiments 100 to 173, wherein the histone deacetylase inhibitor is a selective inhibitor of histone deacetylase 1 and histone deacetylase 2 (HDAC1,2 selective inhibitor).

[0443] Embodiment 176. The method of any one of embodiments 100-173, wherein the histone deacetylase inhibitor is a selective HDAC class I inhibitor.

[0444] Embodiment 177. The method of any one of embodiments 100-173, wherein the histone deacetylase inhibitor is a CoREST selective deacetylase inhibitor.

[0445] Embodiment 178. An HDAC inhibitor for use in a method of treating a subject having cancer 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 has been identified as having altered STK11 activity or expression.

[0446] Embodiment 179. The HDAC inhibitor for use according to embodiment 178, wherein the histone deacetylase inhibitor is administered in combination with one or more additional therapeutic agents.

[0447] Embodiment 180. The HDAC inhibitor for use according to embodiment 179, wherein at least one of the additional therapeutic agents is an immune checkpoint modulator.

[0448] Embodiment 181. 1. An HDAC inhibitor for use in a method of treating cancer in a subject 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 the tumor or tumor microenvironment, and the cancer has been identified as having altered STK11 activity or expression.

[0449] Embodiment 182. 1. An HDAC inhibitor for use in a method of treating cancer in a subject comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment reduces or depletes Treg cells in the tumor or tumor microenvironment, and the cancer has been identified as having altered STK11 activity or expression.

[0450] Embodiment 183. 1. An HDAC inhibitor for use in a method of treating cancer in a subject comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment induces or increases expression of a cytokine that promotes anti-tumor activity, and the cancer has been identified as having altered STK11 activity or expression.

[0451] Embodiment 184. 184. The HDAC inhibitor for use in the method of embodiment 183, wherein the cytokine is selected from the group of CXCL9, CXCL10, and CXCL11.

[0452] Embodiment 185. 1. An HDAC inhibitor for use in a method of treating cancer in a subject comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment reduces expression of cytokines that promote the recruitment of Treg cells, and the cancer has been identified as having altered STK11 activity or expression.

[0453] Embodiment 186. 186. The HDAC inhibitor for use in the method of embodiment 185, wherein the cytokine is CCL1 or CCL22.

[0454] Embodiment 187. An HDAC inhibitor for use in a method of treating cancer in a subject comprising administering the HDAC inhibitor to the subject, wherein said administration of the HDAC inhibitor does not reduce the viability of erythroid or myeloid cells, and the cancer has been identified as having altered STK11 activity or expression.

[0455] Embodiment 188. An HDAC inhibitor for use in a method of treating cancer in a subject, comprising administering an HDAC1,2 selective inhibitor, wherein the cancer exhibits an immune evasion phenotype characterized by STK11 mutant expression, and the HDAC1,2 selective inhibitor can attenuate or reverse the immune evasion phenotype.

[0456] Embodiment 189. 189. The HDAC inhibitor for use in the method of embodiment 187 or 188, further comprising administering an immune checkpoint modulator.

[0457] Embodiment 190. 1. An HDAC inhibitor for use in a method of treating cancer in a subject comprising administering the HDAC inhibitor to the subject, wherein an immune checkpoint modulator has been administered, is being administered, or will be administered to the subject, and the cancer has been identified as having altered STK11 activity or expression.

[0458] Embodiment 191. 1. An HDAC inhibitor for use in a method of treating cancer in a subject comprising administering to the subject an immune checkpoint modulator, wherein the HDAC inhibitor has been administered, is being administered, or will be administered to the subject, and the cancer has been identified as having altered STK11 activity or expression.

[0459] Embodiment 192. The HDAC inhibitor for use according to 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.

[0460] Embodiment 193. 193. The HDAC inhibitor for use according to any one of embodiments 180-192, wherein each immune checkpoint modulator is independently a checkpoint inhibitor, a T cell costimulatory receptor agonist, or a dendritic cell costimulatory receptor agonist.

[0461] Embodiment 194. 194. The HDAC inhibitor for use according to any one of embodiments 180 to 193, wherein at least one immune checkpoint modulator is independently a T cell costimulatory receptor agonist or a dendritic cell costimulatory receptor agonist.

[0462] Embodiment 195. The HDAC inhibitor for use according to any one of embodiments 180 to 193, wherein at least one immune checkpoint modulator is a checkpoint inhibitor.

[0463] Embodiment 196. 196. The HDAC inhibitor for use according to 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.

[0464] Embodiment 197. The HDAC inhibitor for use according to 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.

[0465] Embodiment 198. The HDAC inhibitor for use according to embodiment 195, wherein each checkpoint inhibitor is independently selected from an anti-PD1 agent and an anti-PD-L1 agent.

[0466] Embodiment 199. The HDAC inhibitor for use according to embodiment 195, wherein the checkpoint inhibitor is an anti-PD1 agent.

[0467] Embodiment 200. The HDAC inhibitor for use according to embodiment 195, wherein the checkpoint inhibitor is an anti-PD-L1 agent.

[0468] Embodiment 201. The HDAC inhibitor for use according to 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.

[0469] Embodiment 202. The HDAC inhibitor for use according to any one of embodiments 195 to 200, wherein each immune checkpoint inhibitor is independently an antibody.

[0470] Embodiment 203. 203. The HDAC inhibitor for use according to embodiment 202, wherein each checkpoint inhibitor is independently selected from an anti-CTLA-4 antibody, an anti-PD-1 antibody, an anti-PD-L1 antibody, an anti-4-1BB antibody, an anti-OX-40 antibody, an anti-GITR antibody, an anti-CD27 antibody, an anti-CD28 antibody, an anti-CD40 antibody, an anti-LAG3 antibody, an anti-ICOS antibody, an anti-TWEAKR antibody, an anti-HVEM antibody, an anti-TIM-1 antibody, an anti-TIM-3 antibody, an anti-VISTA antibody, and an anti-TIGIT antibody.

[0471] Embodiment 204. 203. The HDAC inhibitor for use according to 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.

[0472] Embodiment 205. 203. The HDAC inhibitor for use according to embodiment 202, wherein each immune checkpoint inhibitor is independently selected from nivolumab, CT-011, AMP-224, pembrolizumab, pidilizumab, cemiplimab, dostallimab, prorugolimab, spartalizumab, camrelizumab, sasanlimab, sintilimab, tislelizumab, toripalimab, retifanlimab, MEDI0680, budigalimab, and geptanolimab.

[0473] Embodiment 206. 203. The HDAC inhibitor for use according to embodiment 202, wherein each checkpoint inhibitor is independently selected from an anti-PD1 antibody and an anti-PD-L1 antibody.

[0474] Embodiment 207. 203. The HDAC inhibitor for use according to embodiment 202, wherein the checkpoint inhibitor is an anti-PD1 antibody.

[0475] Embodiment 208. 203. The HDAC inhibitor for use according to embodiment 202, wherein the checkpoint inhibitor is an anti-PD1-L1 antibody.

[0476] Embodiment 209. The HDAC inhibitor for use according to embodiment 203 or 204, wherein the anti-CTLA-4 antibody is ipilimumab.

[0477] Embodiment 210. The HDAC inhibitor for use according to any one of embodiments 203, 204, 206, and 207, wherein the anti-PD-1 antibody is pembrolizumab or nivolumab.

[0478] Embodiment 211. 208. The HDAC inhibitor for use according to any one of embodiments 203, 204, 206, and 207, wherein the anti-PD-1 antibody is pembrolizumab.

[0479] Embodiment 212. 208. The HDAC inhibitor for use according to any one of embodiments 203, 204, 206, and 207, wherein the anti-PD-1 antibody is nivolumab.

[0480] Embodiment 213. The HDAC inhibitor for use according to 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).

[0481] Embodiment 214. 194. The HDAC inhibitor for use according to any one of embodiments 180 to 193, wherein the immune checkpoint modulator is a T cell costimulatory receptor agonist or a dendritic cell costimulatory receptor agonist.

[0482] Embodiment 215. The HDAC inhibitor for use according to any one of embodiments 179 to 214, wherein at least one further therapeutic agent is a targeting agent.

[0483] Embodiment 216. 216. The HDAC inhibitor for use according to embodiment 215, wherein each targeting agent is independently selected from an anti-angiogenic agent (e.g., 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.

[0484] Embodiment 217. The HDAC inhibitor for use according to embodiment 215, wherein each targeted agent is independently selected from bevacizumab, ramucirumab, sotorasib, crizotinib, ceritinib, alectinib, brigutinib, lorlatinib, entrectinib, dabrafenib, trametinib, capmatinib, tepotinib, and larotrectinib.

[0485] Embodiment 218. The HDAC inhibitor for use according to any one of embodiments 179 to 217, wherein at least one further therapeutic agent is a chemotherapeutic agent.

[0486] Embodiment 219. The HDAC inhibitor for use according to embodiment 218, wherein each chemotherapeutic agent is independently selected from cisplatin, carboplatin, paclitaxel, albumin-bound paclitaxel (nab-paclitaxel), docetaxel, gemcitabine, vinorelbine, etoposide, and pemetrexed.

[0487] Embodiment 220. The HDAC inhibitor for use according to embodiment 218, wherein at least one chemotherapeutic agent is a platinum-containing therapeutic agent.

[0488] Embodiment 221. The HDAC inhibitor for use according to embodiment 218, wherein one chemotherapeutic agent is a platinum-containing chemotherapeutic agent (e.g., cisplatin) and the second chemotherapeutic agent is pemetrexed.

[0489] Embodiment 222. The HDAC inhibitor for use according to any one of embodiments 179 to 221, wherein at least one further therapeutic agent is radiation.

[0490] Embodiment 223. The HDAC inhibitor for use according to any one of embodiments 178 to 222, wherein the cancer is resistant to anti-PD1 therapy or anti-PD-L1 therapy.

[0491] Embodiment 224. 224. The HDAC inhibitor for use according to embodiment 223, wherein the cancer has natural resistance to anti-PD1 therapy or anti-PD-L1 therapy.

[0492] Embodiment 225. 224. The HDAC inhibitor for use according to embodiment 223, wherein the cancer has acquired resistance to anti-PD1 therapy or anti-PD-L1 therapy.

[0493] Embodiment 226. The HDAC inhibitor for use according to any one of embodiments 178 to 225, wherein the cancer is resistant to chemotherapy (e.g., platinum-containing chemotherapy).

[0494] Embodiment 227. The HDAC inhibitor for use according to embodiment 226, wherein the cancer has natural resistance to chemotherapy (e.g., platinum-containing chemotherapy).

[0495] Embodiment 228. The HDAC inhibitor for use according to embodiment 226, wherein the cancer has acquired resistance to chemotherapy (e.g., platinum-containing chemotherapy).

[0496] Embodiment 229. 229. The HDAC inhibitor for use according to any one of embodiments 178-228, wherein the cancer does not respond to or does not benefit from treatment with the immune checkpoint modulator when the immune checkpoint modulator is administered alone or as part of a treatment regimen that does not include the HDAC inhibitor.

[0497] Embodiment 230. The HDAC inhibitor for use according to any one of embodiments 178 to 229, wherein the cancer is selected from the group consisting of lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC), lung squamous cell carcinoma), 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 carcinoma (e.g., large cell neuroendocrine carcinoma), melanoma, non-melanoma skin cancer (e.g., cutaneous squamous cell carcinoma), bile duct carcinoma, gallbladder cancer, ovarian cancer (e.g., ovarian serous adenocarcinoma), bladder cancer (e.g., bladder urothelial carcinoma), prostate cancer (e.g., prostate adenocarcinoma), cervical cancer, cervical canal carcinoma, or cancer of unknown primary origin (e.g., adenocarcinoma of unknown primary origin).

[0498] Embodiment 231. The HDAC inhibitor for use according to embodiment 230, wherein the cancer is lung cancer.

[0499] Embodiment 232. 232. The HDAC inhibitor for use according to embodiment 231, wherein the cancer is lung adenocarcinoma.

[0500] Embodiment 233. 232. The HDAC inhibitor for use according to embodiment 231, wherein the cancer is non-small cell lung cancer (NSCLC).

[0501] Embodiment 234. The HDAC inhibitor for use according to embodiment 233, wherein the cancer is non-squamous non-small cell lung cancer (NSCLC).

[0502] Embodiment 235. 231. The HDAC inhibitor for use according to embodiment 230, wherein the cancer is colorectal cancer or colon adenocarcinoma.

[0503] Embodiment 236. The HDAC inhibitor for use according to any one of embodiments 178 to 235, wherein the cancer has been identified as having an STK11 mutation and one or more additional mutations.

[0504] Embodiment 237. 237. The HDAC inhibitor for use according to embodiment 236, wherein the further mutation is selected from a KRAS mutation and a KEAP1 mutation.

[0505] Embodiment 238. 237. The HDAC inhibitor for use according to embodiment 236, wherein the further mutation is a KRAS mutation.

[0506] Embodiment 239. 239. The HDAC inhibitor for use according to embodiment 238, wherein the KRAS mutation is a mutation at position G12, optionally the KRAS mutation is selected from a G12D mutation, a G12C mutation, a G12V mutation or a combination thereof.

[0507] Embodiment 240. 237. The HDAC inhibitor for use according to embodiment 236, wherein the further mutation is a KEAP1 mutation.

[0508] Embodiment 241. 237. The HDAC inhibitor for use according to embodiment 236, wherein the further mutations are a KRAS mutation and a KEAP1 mutation.

[0509] Embodiment 242. 242. The HDAC inhibitor for use according to any one of embodiments 178 to 241, wherein the cancer does not have an EGFR mutation.

[0510] Embodiment 243. The HDAC inhibitor for use according to any one of embodiments 178 to 242, wherein the cancer has increased or decreased STK11 expression.

[0511] Embodiment 244. The HDAC inhibitor for use according to embodiment 243, wherein an increase or decrease in STK expression is assessed by determining the copy number of the gene encoding STK11 compared to a control sample, wherein an increase in copy number indicates an increased expression level and a decrease in copy number indicates a decreased expression level.

[0512] Embodiment 245. 244. The HDAC inhibitor for use according to embodiment 243, wherein the increase or decrease in STK expression is assessed by determining the level of STK11 protein or mRNA compared to a control sample.

[0513] Embodiment 246. 246. The HDAC inhibitor for use according to embodiment 244 or 245, wherein the cancer has reduced STK11 expression.

[0514] Embodiment 247. The HDAC inhibitor for use according to any one of embodiments 178 to 242, wherein the cancer has an STK11 mutation.

[0515] Embodiment 248. STK11 mutations include: (i) a mutation in the nucleotide sequence encoding STK11; (ii) a mutation in a regulatory sequence controlling expression of the nucleotide sequence encoding STK11; (iii) a mutation in a nucleotide encoding a protein that interacts with the transcript of the STK11 gene; 248. The HDAC inhibitor for use according to embodiment 247, wherein the mutation is selected from:

[0516] Embodiment 249. 248. The HDAC inhibitor for use according to embodiment 247, wherein the STK11 mutation is a mutation in the translation product of the STK11 gene.

[0517] 250. 248. The HDAC inhibitor for use according to embodiment 247, wherein the STK11 mutation is a mutation in the transcript of the STK11 gene.

[0518] Embodiment 251. 251. The HDAC inhibitor for use according to any one of embodiments 247 to 250, wherein the STK11 mutation is an inactivating (loss-of-function) mutation.

[0519] Embodiment 252. The HDAC inhibitor for use according to any one of embodiments 243 to 246, wherein an increase or decrease in STK11 expression is measured in a sample derived from the subject.

[0520] Embodiment 253. The HDAC inhibitor for use according to embodiment 252, wherein an increase or decrease in STK11 expression is measured compared to a control.

[0521] Embodiment 254. The HDAC inhibitor for use according to embodiment 253, wherein the control is a healthy tissue, preferably of the same tissue type as the cancer tissue.

[0522] Embodiment 255. The HDAC inhibitor for use according to any one of embodiments 247 to 250, wherein an STK11 mutation has been identified in a sample derived from the subject.

[0523] Embodiment 256. 256. The HDAC inhibitor for use according to embodiment 255, wherein the STK11 mutation has been identified in a tumor sample derived from the subject.

[0524] Embodiment 257. 256. The HDAC inhibitor for use according to embodiment 255, wherein no STK11 mutation is identified in a healthy tissue sample derived from the subject.

[0525] Embodiment 258. The HDAC inhibitor for use according to any one of embodiments 178 to 257, wherein the STK11 mutation is not a germline mutation.

[0526] 259. The HDAC inhibitor for use according to any one of embodiments 179 to 258, wherein the HDAC inhibitor is administered simultaneously with the further therapeutic agent.

[0527] 260. The HDAC inhibitor for use according to any one of embodiments 179 to 258, wherein the HDAC inhibitor is administered separately from the further therapeutic agent.

[0528] Embodiment 261. The HDAC inhibitor for use according to any one of embodiments 179 to 258, wherein the HDAC inhibitor is administered sequentially with the further therapeutic agent.

[0529] Embodiment 262. The HDAC inhibitor for use according to any one of embodiments 179 to 258, wherein the HDAC inhibitor is administered before the further therapeutic agent.

[0530] Embodiment 263. The HDAC inhibitor for use according to any one of embodiments 179 to 258, wherein the HDAC inhibitor is administered after the further therapeutic agent.

[0531] Embodiment 264. The HDAC inhibitor for use according to any one of embodiments 179-258, wherein the method comprises administering to the subject an immune checkpoint modulator, and subsequently administering to the subject an HDAC inhibitor.

[0532] 265. The HDAC inhibitor for use according to any one of embodiments 179-258, wherein the method comprises administering to the subject an HDAC inhibitor, and subsequently administering to the subject an immune checkpoint modulator.

[0533] Embodiment 266. The HDAC inhibitor for use according to any one of embodiments 179-258, wherein the method comprises 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, followed by administering to the subject an HDAC inhibitor.

[0534] Embodiment 267. The HDAC inhibitor for use according to any one of embodiments 179-258, wherein the method comprises 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.

[0535] Embodiment 268. The HDAC inhibitor for use according to any one of embodiments 179-258, wherein 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.

[0536] 269. The HDAC inhibitor for use according to any one of embodiments 179-258, wherein 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.

[0537] 270. The HDAC inhibitor for use according to 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.

[0538] 271. The HDAC inhibitor for use according to 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 HDAC inhibitor, followed by administering to the subject an immune checkpoint modulator.

[0539] Embodiment 272. The HDAC inhibitor for use according to any one of embodiments 178 to 271, wherein the subject has a cancer identified as having altered STK11 activity or expression.

[0540] Embodiment 273. 273. The HDAC inhibitor for use according to any one of embodiments 178 to 272, wherein the histone deacetylase inhibitor is a selective inhibitor of histone deacetylase 1 (HDAC1 selective inhibitor).

[0541] Embodiment 274. The HDAC inhibitor for use according to any one of embodiments 178 to 272, wherein the histone deacetylase inhibitor is a selective inhibitor of histone deacetylase 1 and histone deacetylase 2 (HDAC1,2 selective inhibitor).

[0542] 275. The HDAC inhibitor for use according to any one of embodiments 178 to 272, wherein the histone deacetylase inhibitor is a selective HDAC class I inhibitor.

[0543] Embodiment 276. The HDAC inhibitor for use according to any one of embodiments 178 to 272, wherein the histone deacetylase inhibitor is a CoREST selective deacetylase inhibitor.

[0544] Embodiment 277. Use of an HDAC inhibitor in the manufacture of a medicament for treating a subject having cancer or at risk of developing cancer, wherein the treatment comprises administering to the subject an effective amount of a histone deacetylase (HDAC) inhibitor, and the cancer has been identified as having altered STK11 activity or expression.

[0545] Embodiment 278. The use of embodiment 277, wherein the histone deacetylase inhibitor is administered in combination with one or more additional therapeutic agents.

[0546] Embodiment 279. The use of embodiment 278, wherein at least one of the additional therapeutic agents is an immune checkpoint modulator.

[0547] 280. 1. Use of an HDAC inhibitor in the manufacture of a medicament for treating cancer in a subject, the treatment comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, the treatment modulating and / or improving the ratio of Teff cells to Treg cells in a tumor or tumor microenvironment, and the cancer has been identified as having altered STK11 activity or expression.

[0548] Embodiment 281. 1. Use of an HDAC inhibitor in the manufacture of a medicament for treating cancer in a subject, the treatment comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, the treatment reducing or depleting Treg cells in a tumor or tumor microenvironment, and the cancer has been identified as having altered STK11 activity or expression.

[0549] Embodiment 282. 1. Use of an HDAC inhibitor in the manufacture of a medicament for treating cancer in a subject, wherein the treatment comprises administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein the treatment induces or increases expression of a cytokine that promotes anti-tumor activity, and the cancer has been identified as having altered STK11 activity or expression.

[0550] Embodiment 283. 283. The use according to embodiment 282, wherein the cytokine is selected from the group of CXCL9, CXCL10, and CXCL11.

[0551] Embodiment 284. 1. Use of an HDAC inhibitor in the manufacture of a medicament for treating cancer in a subject, the treatment comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, the treatment reducing expression of cytokines that promote Treg cell recruitment, and the cancer being identified as having altered STK11 activity or expression.

[0552] Embodiment 285. The use of embodiment 284, wherein the cytokine is CCL1 or CCL22.

[0553] 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 administration of the HDAC inhibitor does not reduce the viability of erythroid or myeloid cells, and the cancer has been identified as having altered STK11 activity or expression.

[0554] Embodiment 287. Use of an HDAC inhibitor in the manufacture of a medicament for treating cancer in a subject, comprising administering an HDAC1,2 selective inhibitor, wherein the cancer exhibits an immune evasion phenotype characterized by STK11 mutant expression, and the HDAC1,2 selective inhibitor can attenuate or reverse the immune evasion phenotype.

[0555] Embodiment 288. The use of embodiment 286 or 287, further comprising administering an immune checkpoint modulator.

[0556] 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, an immune checkpoint modulator has been administered, is being administered, or will be administered to the subject, and the cancer has been identified as having altered STK11 activity or expression.

[0557] 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 administered, is being administered, or will be administered to the subject, and the cancer has been identified as having altered STK11 activity or expression.

[0558] 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.

[0559] Embodiment 292. The use of any one of embodiments 279-290, wherein each immune checkpoint modulator is independently a checkpoint inhibitor, a T cell costimulatory receptor agonist, or a dendritic cell costimulatory receptor agonist.

[0560] Embodiment 293. The use of any one of embodiments 279-292, wherein at least one immune checkpoint modulator is independently a T cell costimulatory receptor agonist or a dendritic cell costimulatory receptor agonist.

[0561] Embodiment 294. The use according to any one of embodiments 279 to 292, wherein at least one immune checkpoint modulator is a checkpoint inhibitor.

[0562] Embodiment 295. 295. The use of embodiment 294, 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.

[0563] Embodiment 296. 295. The use of embodiment 294, wherein each checkpoint inhibitor is independently selected from an anti-CTLA-4 agent, an anti-PD-1 agent, and an anti-PD-L1 agent.

[0564] Embodiment 297. 295. The use of embodiment 294, wherein each checkpoint inhibitor is independently selected from an anti-PD1 agent and an anti-PD-L1 agent.

[0565] Embodiment 298. 295. The use of embodiment 294, wherein the checkpoint inhibitor is an anti-PD1 agent.

[0566] Embodiment 299. 295. The use of embodiment 294, wherein the checkpoint inhibitor is an anti-PD-L1 agent.

[0567] Embodiment 300. The use of 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.

[0568] Embodiment 301. 300. The use of any one of embodiments 294 to 299, wherein each immune checkpoint inhibitor is independently an antibody.

[0569] Embodiment 302. 302. The use of embodiment 301, wherein each checkpoint inhibitor is independently selected from an anti-CTLA-4 antibody, an anti-PD-1 antibody, an anti-PD-L1 antibody, an anti-4-1BB antibody, an anti-OX-40 antibody, an anti-GITR antibody, an anti-CD27 antibody, an anti-CD28 antibody, an anti-CD40 antibody, an anti-LAG3 antibody, an anti-ICOS antibody, an anti-TWEAKR antibody, an anti-HVEM antibody, an anti-TIM-1 antibody, an anti-TIM-3 antibody, an anti-VISTA antibody, and an anti-TIGIT antibody.

[0570] Embodiment 303. The use of 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.

[0571] Embodiment 304. The use of embodiment 301, wherein each immune checkpoint inhibitor is independently selected from nivolumab, CT-011, AMP-224, pembrolizumab, pidilizumab, cemiplimab, dostallimab, prorugolimab, spartalizumab, camrelizumab, sasanlimab, sintilimab, tislelizumab, toripalimab, retifanlimab, MEDI0680, budigalimab, and geptanolimab.

[0572] Embodiment 305. 302. The use of embodiment 301, wherein each checkpoint inhibitor is independently selected from an anti-PD1 antibody and an anti-PD-L1 antibody.

[0573] Embodiment 306. 302. The use of embodiment 301, wherein the checkpoint inhibitor is an anti-PD1 antibody.

[0574] Embodiment 307. 302. The use of embodiment 301, wherein the checkpoint inhibitor is an anti-PD1-L1 antibody.

[0575] Embodiment 308. The use of embodiment 302 or 303, wherein the anti-CTLA-4 antibody is ipilimumab.

[0576] Embodiment 309. The use of any one of embodiments 302, 303, 305, and 306, wherein the anti-PD-1 antibody is pembrolizumab or nivolumab.

[0577] Embodiment 310. The use of any one of embodiments 302, 303, 305, and 306, wherein the anti-PD-1 antibody is pembrolizumab.

[0578] Embodiment 311. The use of any one of embodiments 302, 303, 305, and 306, wherein the anti-PD-1 antibody is nivolumab.

[0579] 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).

[0580] Embodiment 313. 292. The use of any one of embodiments 279 to 291, wherein the immune checkpoint modulator is a T cell costimulatory receptor agonist or a dendritic cell costimulatory receptor agonist.

[0581] Embodiment 314. The use according to any one of embodiments 278 to 313, wherein at least one further therapeutic agent is a targeting agent.

[0582] Embodiment 315. The use of embodiment 314, wherein each targeting agent is independently selected from an anti-angiogenic agent (e.g., 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.

[0583] Embodiment 316. The use of embodiment 314, wherein each targeted agent is independently selected from bevacizumab, ramucirumab, sotorasib, crizotinib, ceritinib, alectinib, brigutinib, lorlatinib, entrectinib, dabrafenib, trametinib, capmatinib, tepotinib, and larotrectinib.

[0584] Embodiment 317. The use according to any one of embodiments 278 to 316, wherein at least one further therapeutic agent is a chemotherapeutic agent.

[0585] Embodiment 318. The use of embodiment 317, wherein each chemotherapeutic agent is independently selected from cisplatin, carboplatin, paclitaxel, albumin-bound paclitaxel (nab-paclitaxel), docetaxel, gemcitabine, vinorelbine, etoposide, and pemetrexed.

[0586] Embodiment 319. The use of embodiment 317, wherein at least one chemotherapeutic agent is a platinum-containing therapeutic agent.

[0587] Embodiment 320. The use of embodiment 317, wherein one chemotherapeutic agent is a platinum-containing chemotherapeutic agent (e.g., cisplatin) and the second chemotherapeutic agent is pemetrexed.

[0588] Embodiment 321. The use according to any one of embodiments 278 to 320, wherein at least one further therapeutic agent is radiation.

[0589] Embodiment 322. The use of any one of embodiments 278 to 321, wherein the cancer is resistant to anti-PD1 therapy or anti-PD-L1 therapy.

[0590] Embodiment 323. The use of embodiment 322, wherein the cancer has natural resistance to anti-PD1 therapy or anti-PD-L1 therapy.

[0591] Embodiment 324. The use of embodiment 322, wherein the cancer has acquired resistance to anti-PD1 therapy or anti-PD-L1 therapy.

[0592] Embodiment 325. The use of any one of embodiments 277 to 324, wherein the cancer is resistant to chemotherapy (e.g., platinum-containing chemotherapy).

[0593] Embodiment 326. The use of embodiment 325, wherein the cancer has natural resistance to chemotherapy (e.g., platinum-containing chemotherapy).

[0594] Embodiment 327. The use of embodiment 325, wherein the cancer has acquired resistance to chemotherapy (e.g., platinum-containing chemotherapy).

[0595] Embodiment 328. The use of any one of embodiments 277-327, wherein the cancer does not respond 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.

[0596] Embodiment 329. The use of any one of embodiments 277 to 328, wherein the cancer is selected from the group consisting of lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC), lung squamous cell carcinoma), 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 carcinoma (e.g., large cell neuroendocrine carcinoma), melanoma, non-melanoma skin cancer (e.g., cutaneous squamous cell carcinoma), bile duct carcinoma, gallbladder carcinoma, ovarian cancer (e.g., ovarian serous adenocarcinoma), bladder cancer (e.g., bladder urothelial carcinoma), prostate cancer (e.g., prostate adenocarcinoma), cervical cancer, cervical carcinoma, or cancer of unknown primary origin (e.g., adenocarcinoma of unknown primary origin).

[0597] Embodiment 330. The use according to embodiment 329, wherein the cancer is lung cancer.

[0598] Embodiment 331. The use according to embodiment 330, wherein the cancer is lung adenocarcinoma.

[0599] Embodiment 332. The use of embodiment 330, wherein the cancer is non-small cell lung cancer (NSCLC).

[0600] Embodiment 333. The use of embodiment 332, wherein the cancer is non-squamous non-small cell lung cancer (NSCLC).

[0601] Embodiment 334. The use of embodiment 329, wherein the cancer is colorectal cancer or colon adenocarcinoma.

[0602] Embodiment 335. The use of any one of embodiments 277 to 334, wherein the cancer has been identified as having an STK11 mutation and one or more additional mutations.

[0603] Embodiment 336. 336. The use of embodiment 335, wherein the further mutation is selected from a KRAS mutation and a KEAP1 mutation.

[0604] Embodiment 337. 336. The use of embodiment 335, wherein the further mutation is a KRAS mutation.

[0605] Embodiment 338. The use of 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.

[0606] 339. 336. The use of embodiment 335, wherein the further mutation is a KEAP1 mutation.

[0607] 340. The use of embodiment 335, wherein the further mutations are a KRAS mutation and a KEAP1 mutation.

[0608] Embodiment 341. The use according to any one of embodiments 277 to 340, wherein the cancer does not have an EGFR mutation.

[0609] Embodiment 342. The use of any one of embodiments 277 to 341, wherein the cancer has increased or decreased STK11 expression.

[0610] Embodiment 343. The use described in embodiment 342, wherein an increase or decrease in STK expression is assessed by determining the copy number of the gene encoding STK11 compared to a control sample, wherein an increase in copy number indicates an increased expression level and a decrease in copy number indicates a decreased expression level.

[0611] Embodiment 344. The use of embodiment 342, wherein the increase or decrease in STK expression is assessed by determining the level of STK11 protein or mRNA compared to a control sample.

[0612] 345. The use of embodiment 343 or 344, wherein the cancer has reduced STK11 expression.

[0613] Embodiment 346. The use of any one of embodiments 277 to 311, wherein the cancer has an STK11 mutation.

[0614] Embodiment 347. STK11 mutations include: (i) a mutation in the nucleotide sequence encoding STK11; (ii) a mutation in a regulatory sequence controlling expression of the nucleotide sequence encoding STK11; (iii) a mutation in a nucleotide encoding a protein that interacts with the transcript of the STK11 gene; The use of embodiment 346, wherein the mutation is selected from:

[0615] Embodiment 348. The use of embodiment 346, wherein the STK11 mutation is a mutation in the translation product of the STK11 gene.

[0616] 349. The use of embodiment 346, wherein the STK11 mutation is a mutation in the transcript of the STK11 gene.

[0617] 350. The use according to any one of embodiments 346 to 349, wherein the STK11 mutation is an inactivating (loss-of-function) mutation.

[0618] Embodiment 351. The use according to any one of embodiments 342 to 345, wherein an increase or decrease in STK11 expression is measured in a sample derived from the subject.

[0619] Embodiment 352. The use of embodiment 351, wherein an increase or decrease in STK11 expression is measured compared to a control.

[0620] Embodiment 353. The use of embodiment 352, wherein the control is a healthy tissue, preferably of the same tissue type as the cancer tissue.

[0621] Embodiment 354. The use according to any one of embodiments 346 to 350, wherein the STK11 mutation has been identified in a sample derived from the subject.

[0622] 355. The use of embodiment 354, wherein the STK11 mutation has been identified in a tumor sample derived from the subject.

[0623] Embodiment 356. The use of embodiment 354, wherein the STK11 mutation is not identified in a healthy tissue sample derived from the subject.

[0624] Embodiment 357. The use according to any one of embodiments 277 to 356, wherein the STK11 mutation is not a germline mutation.

[0625] Embodiment 358. The use according to any one of embodiments 277 to 357, wherein the HDAC inhibitor is administered simultaneously with the further therapeutic agent.

[0626] 359. The use according to any one of embodiments 277 to 357, wherein the HDAC inhibitor is administered separately from the further therapeutic agent.

[0627] 360. The use according to any one of embodiments 277 to 357, wherein the HDAC inhibitor is administered sequentially with the further therapeutic agent.

[0628] Embodiment 361. The use according to any one of embodiments 277 to 357, wherein the HDAC inhibitor is administered before the further therapeutic agent.

[0629] Embodiment 362. The use according to any one of embodiments 277 to 357, wherein the HDAC inhibitor is administered after the further therapeutic agent.

[0630] Embodiment 363. The use of any one of embodiments 277 to 357, wherein the method comprises administering to the subject an immune checkpoint modulator, and subsequently administering to the subject an HDAC inhibitor.

[0631] Embodiment 364. The use of any one of embodiments 277 to 357, wherein the method comprises administering to the subject an HDAC inhibitor, and subsequently administering to the subject an immune checkpoint modulator.

[0632] 365. The use of any one of embodiments 277-357, wherein the method comprises 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, followed by administering to the subject an HDAC inhibitor.

[0633] Embodiment 366. The use of any one of embodiments 277-357, wherein the method comprises 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.

[0634] Embodiment 367. The use of any one of embodiments 277-357, wherein 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.

[0635] Embodiment 368. The use of any one of embodiments 277-357, wherein 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.

[0636] 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.

[0637] 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.

[0638] Embodiment 371. The use of any one of embodiments 277 to 370, wherein the subject has a cancer identified as having altered STK11 activity or expression.

[0639] Embodiment 372. The use according to any one of embodiments 277 to 371, wherein the histone deacetylase inhibitor is a selective inhibitor of histone deacetylase 1 (HDAC1 selective inhibitor).

[0640] Embodiment 373. The use according to any one of embodiments 277 to 371, wherein the histone deacetylase inhibitor is a selective inhibitor of histone deacetylase 1 and histone deacetylase 2 (HDAC1,2 selective inhibitor).

[0641] 374. The use according to any one of embodiments 277 to 371, wherein the histone deacetylase inhibitor is a selective HDAC class I inhibitor.

[0642] 375. The use according to any one of embodiments 277 to 371, wherein the histone deacetylase inhibitor is a CoREST selective deacetylase inhibitor.

[0643] 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 an 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 the STK11 mutation and / or an altered level of STK11 activity or expression indicates sensitivity to treatment with an HDAC inhibitor.

[0644] Embodiment 377. 1. 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 an 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 the STK11 mutation and / or altered level of STK11 activity or expression indicates sensitivity to treatment with a combination of an HDAC inhibitor and an immune checkpoint modulator.

[0645] Embodiment 378. A method for confirming the susceptibility of a subject having or diagnosed with cancer to treatment with a method described in any one of embodiments 1 to 99, wherein the confirmation method comprises determining i) the presence or absence of an 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 an STK11 mutation and / or an altered level of STK11 activity or expression indicates susceptibility to treatment with a method described in any one of embodiments 1 to 99.

[0646] 379. The histone deacetylase inhibitor is a compound of formula (I) [ka] or a pharmaceutically acceptable salt thereof. [Example]

[0647] The following examples are given for the purpose of illustrating various embodiments of the invention and are not intended to limit the invention in any manner. The examples, together with the methods described herein, are representative of presently preferred embodiments and are illustrative, not limiting, of the scope of the invention. Modifications and other uses which are encompassed within the spirit of the invention as defined by the claims will occur to those skilled in the art.

[0648] Example 1: Antitumor activity of anti-PD1 in combination with Compound I in a mouse subcutaneous MC38_sgStk11 tumor model Summary: We investigated the in vivo antitumor effects of dual combination treatment with anti-PD1 and HDAC1,2 selective inhibitors in a mouse subcutaneous MC38_sgStk11 tumor model in C57BL / 6 mice.

[0649] Experimental Design: A summary of the experimental design is provided in Table 1-1.

[0650] [Table 1-7]

[0651] material: animal The 96 mice and 39 spare mice were as follows: species: Mus musculus, strain: C57BL / 6, age: 8-10 weeks, sex: female, weight: 16.9-20.0 g. Animal supplier:Shanghai SLAC Laboratory Animal Co.,Ltd

[0652] Mice were housed in individual ventilated cages, four per cage, at constant temperature (approximately 20-26°C) and humidity (approximately 40-70%). Each cage measured approximately 300 mm x 200 mm x 180 mm. The bedding in each cage was corncob, which was changed twice weekly. Each cage's identification label contained the following information: number, sex, strain, date of receipt, treatment, study number, group number, and start date of treatment.

[0653] Throughout the study, animals were fed radiation-sterilized dry granular feed ad libitum. Animals had free access to sterilized drinking water. Animals were identified by ear tags.

[0654] compound 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 shows greater than 10-fold selectivity for HDAC1 over HDAC3 in intact cells. Compound I used in Example 1 shows significant selectivity for CoREST deacetylase over NCoR, NuRD, and Sin3 as described herein.

[0655] method cell culture MC38_sgStk11 tumor cells were maintained in vitro as monolayer cultures in DMEM + 2 mM glutamine supplemented with approximately 10% heat-inactivated fetal bovine serum, approximately 100 U / ml penicillin, and 100 μg / ml streptomycin at approximately 37°C in an atmosphere of approximately 5% CO2 in air. Tumor cells were routinely passaged twice weekly by trypsin-EDTA treatment. For tumor inoculation, growing cells in the exponential growth phase were harvested and counted.

[0656] Tumor inoculation and animal grouping Each mouse was subcutaneously inoculated with MC38_sgStk11 tumor cells (0.5 × 106) in 0.1 ml of PBS into the upper right flank, and tumors were allowed to develop. Four days after tumor inoculation, the average tumor size was 52 mm 3 Treatment began when tumor volume reached 100 μg / kg. Animals were assigned to groups according to standard operating procedures based on tumor volume. Each group consisted of eight tumor-bearing mice. Mice were administered the test article according to a predetermined regimen, as shown in the experimental design table (Table 1-1).

[0657] Observations All procedures related to the handling, housing, and treatment of animals in this study were conducted in accordance with guidelines approved by the vendor's Institutional Animal Care and Use Committee (IACUC) in accordance with the Association for the Accreditation of Laboratory Animal Care (AAALAC) guidelines. During routine monitoring, animals were checked daily for the effects of tumor growth and treatment on normal behavior, including mobility, food and water intake, weight gain or loss (weight was measured three times weekly), eye / hair matting, and other abnormal effects as described in the protocol. Mortality and observed clinical signs were recorded based on the number of animals in each subset.

[0658] Tumor measurements and endpoints The primary endpoint was to determine whether tumor growth could be delayed or whether the mice could be cured. Tumor size was measured in two dimensions using calipers three times a week, and the volume was expressed in mm using the formula: V = 0.5a × b2 (where a and b are the long and short diameters of the tumor, respectively). The T / C value (percent) is an indicator of antitumor effect, where T and C are the mean volumes of the treatment and control groups on a given day, respectively. TGI was calculated for each group using the formula: TGI (%) = [1 - (Ti - T0) / (Vi - V0)] × 100. Ti is the mean tumor volume of the treatment group on a given day, T0 is the mean tumor volume of the treatment group on the start of treatment, Vi is the mean tumor volume of the vehicle control group on the same day as Ti, and V0 is the mean tumor volume of the vehicle group on the start of treatment.

[0659] statistical analysis Statistical analysis of differences in tumor volume between groups was performed on data obtained at the best treatment time point, 11 days after the start of treatment. One-way analysis of variance was performed for comparison between groups. Survival analysis between groups was performed using the Kaplan-Meier test. p<0.05 was considered statistically significant.

[0660] result The mean tumor volumes over time in MC38_sgStk11 tumor-bearing C57BL / 6 mice receiving combination treatments are shown in Table 1-2 (anti-IgG2a) and Table 1-3 (anti-PD1).

[0661] [Table 1-8]

[0662] [Table 1-9]

[0663] [Table 1-10] [Table 1-11]

[0664] [Table 1-12] [Table 1-13]

[0665] Combined treatment with Compound I and anti-PD1 resulted in significant antitumor activity against the MC38_sgStk11 tumor model. The mean tumor size in vehicle-treated animals was 2,132 mm 11 days after the start of treatment. 3 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) resulted in significant antitumor activity, with the mean tumor size reaching approximately 708 mm at the same time point. 3 , 884m 3 , 399mm 3 , and 542 mm 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 with the vehicle group).

[0666] Tumor volume and survival were monitored over the treatment period, and tumor volumes were plotted by treatment group (Figure 1A) and by individual animal (Figure 1B).

[0667] Survival rates were plotted by tumor group (Figure 2A shows groups 1, 7, 2, 3, 4, 5, and 6; Figure 2B shows groups 1, 7, 8, 9, 10, 11, and 12; and Figure 2C shows groups 1, 4, 7, and 10).

[0668] Example 2: Re-challenge test of Example 1 Summary: A re-challenge study of Example 1 was conducted to assess whether the surviving animals in Example 1 had acquired T memory against the same tumor.

[0669] Experimental Design and Materials: Animals surviving the efficacy part were re-challenged with MC38_sgStk11 cells on the opposite side of the primary tumor.

[0670] A summary of the surviving animals in Example 1 is provided in Table 2-1.

[0671] [Table 2-1]

[0672] method cell culture MC38_sgStk11 tumor cells were maintained in vitro as monolayer cultures in DMEM + 2 mM glutamine supplemented with approximately 10% heat-inactivated fetal bovine serum, 100 U / ml penicillin, and 100 μg / ml streptomycin at approximately 37°C in an atmosphere of approximately 5% CO2 in air. Tumor cells were routinely passaged twice weekly by trypsin-EDTA treatment. For tumor inoculation, growing cells in the exponential growth phase were harvested and counted.

[0673] Tumor inoculation and animal grouping Mice were subcutaneously inoculated with MC38_sgStk11 tumor cells (0.5 × 10) in 0.1 ml of PBS into the lower left flank, allowing tumors to develop. The number of mice and cells in each group is shown in the experimental design (Table 2-1). Animals that survived in Example 1 were monitored for 21 days after treatment before rechallenge.

[0674] Observations All procedures for animal handling, housing, and treatment in this study were conducted in accordance with guidelines approved by the vendor's Institutional Animal Care and Use Committee (IACUC) in accordance with the Association for the Accreditation of Laboratory Animal Care (AAALAC) guidelines. During routine monitoring, animals were checked daily for the effects of tumor growth and treatment on normal behavior, including mobility, food and water intake, weight gain or loss (weight was measured twice weekly), eye / hair matting, and any other abnormal effects described in the protocol. Mortality and observed clinical signs were recorded based on the number of animals in each subset.

[0675] Tumor measurements and endpoints Tumor size was measured in three dimensions three times a week using calipers, and the volume was expressed in mm3 using the formula: V = 0.5a × b2, where a and b are the long and short diameters of the tumor, respectively.

[0676] result The mean tumor volume over time in C57BL / 6 mice re-challenged with MC38_sgStk11 is shown in Table 2-2.

[0677] [Table 2-2]

[0678] There was no tumor growth in surviving animals that were rechallenged with MC38_sgStk11 cells. These results may suggest that the surviving animals acquired T memory against the MC38_sgStk11 tumor.

[0679] All animals remained off treatment, and tumor size was plotted over time after rechallenge. Figure 3A shows tumor size by group. All previously treated groups overlap with no tumor growth. Figure 3B shows tumor size for a pooled group of previously treated mice compared to an untreated control group. Figure 4 shows the complete timeline and tumor size at the indicated time points for Experiments 1 and 2.

[0680] Example 3: Identification of anti-PD1 antibody sensitizer genes in STK-11-deficient tumors In this example, we determined the genes whose inhibition reverses anti-PD1 resistance driven by loss of STK11. Briefly, genes encoding HDAC1, HDAC2, or HDAC3 were deleted or disabled by CRISPR in an in vivo knockout screen in STK11-deficient MC38 tumor cells grown in C57Bl / 6 mice and then treated with an anti-PD1 antibody. Results indicate that HDAC1 is a sensitizing factor to anti-PD1 in STK11-deficient cancers (Figure 5A). Furthermore, we tested the toxicity of HDAC1, HDAC2, or HDAC3 by CRISPR-mediated deletion / disruption in several cell lines. Results showed a reduction in cell toxicity with HDAC1, HDAC2, or HDAC3 knockout, with HDAC3 knockout showing the highest toxicity within the panel of cell lines (Figure 5B).

[0681] Example 4: Identification of CoREST selective deacetylase inhibitors In this example, CoREST complex-selective compound I was identified using a NanoBRET (bioluminescence resonance energy transfer) target binding 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 their respective IC50 values were determined. The results show that the IC50 values of compound I for HDAC1 are 0.01 μM, for HDAC2 0.17 μM, and for HDAC3 1.07 μM (Figures 6A-6C and Table 3-1).

[0682] [Table 3-1]

[0683] The HDAC inhibition of the HDAC complexes CoREST, NCoR, NuRD, and Sin3 by Compound I was determined using a fluorescence-based deacetylase assay. Briefly, the HDAC complexes CoREST, NCoR, NuRD, and Sin3 were co-immunoprecipitated from A549 cells (a model of lung adenocarcinoma) using a complex-selective antibody, and the complexes were incubated with Compound I or the less selective HDAC inhibitors vorinostat, tucidinostat, and domatinostat. Suberoylanilide hydroxamic acid, a pan-HDAC inhibitor that targets all four complexes, was used as a positive control for complex activity to demonstrate that the isolated complexes retain functional deacetylase activity and to establish background assay fluorescence. HDAC inhibition was profiled using a fluorescence-based deacetylase assay. Exemplary IC 50 are shown in Table 3-2. The results in Table 3-2 demonstrate that Compound I is selective for the CoREST complex.

[0684] [Table 3-2]

[0685] Example 5: Antitumor activity of anti-PD1 in combination with Compound I in a mouse subcutaneous CT26 STK11-deficient tumor model In this example, the antitumor activity of combined treatment with anti-PD1 antibody and Compound I was determined in vivo in a syngeneic STK11-deficient mouse model.

[0686] Briefly, mice were inoculated with an STK11-deficient CT26 (a murine colorectal cancer cell line) tumor model using a method similar to that described in Example 1. This tumor model is resistant to murine anti-PD1 antibodies due to knockout of STK11. Mice were orally administered Compound I once daily and anti-PD1, anti-IgG2a control, or anti-PD1 control twice weekly, as indicated. Tumor volume and survival rates were monitored over the treatment period and plotted by individual animal for tumor volume ( FIG. 7A ) and by group for survival rate ( FIG. 7B ).

[0687] The results of Examples 1 and 5 demonstrate that Compound I reverses resistance to immune checkpoint blockade caused by loss of STK11 in colon adenocarcinoma and colorectal cancer tumor models.

[0688] Example 6: Efficacy of Compound I in Combination with Anti-PD1 Antibody in Mouse Models with and without T Cells The efficacy of Compound I in combination with anti-PD1 antibodies was determined in vivo in mouse models with and without T cells.

[0689] Briefly, athymic BALB / c nude mice and C57BL / 6 animals bearing STK11-deficient MC38 tumors were orally administered compound I at 30 mg / kg or 75 mg / kg once daily alone or twice weekly in combination with anti-PD1 (Figures 8A and 8B). The results indicate that the efficacy of compound I and anti-PD1 requires an intact T cell compartment.

[0690] Example 7: Cytokine profiling of tumors treated with Compound I Cytokine expression in tumors from mice treated with Compound I was determined by Nanostring PanCancer IO 360 assay.

[0691] Briefly, STK11- / - MC38 tumors from mice treated with 30 mg / kg of Compound I or anti-PD1 antibody alone or in combination for 7 days were harvested 8 hours after the final dose. The gene expression profiles of CXCL9, CXCL10, and CXCL11 in the tumors were determined using Nanostring PanCancer IO 360 (Figure 9A). Furthermore, the gene expression profiles of the Treg-attracting chemokines CCL1 and CCL22 in the tumors were determined using Nanostring PanCancer IO 360 (Figure 9B).

[0692] STK11-deficient MC38 cells were also profiled for HLA gene expression in vitro with the Nanostring IO360 panel after treatment with 0.2 uM Compound I for 4 days compared to DMSO vehicle control (Figure 9C).

[0693] The results show that treatment with an HDAC1,2-selective inhibitor drives cytokine expression, which promotes antitumor activity. Furthermore, treatment with Compound I reverses immune evasion on tumor cells by altering the expression of cytokines and antigen-presenting genes.

[0694] Example 8: T cell activity after treatment with a combination of Compound I and anti-PD1 antibody In this example, the ability of Compound I in combination with an anti-PD1 antibody to increase T cell activity was determined.

[0695] 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 harvested 8 hours after the final dose, and tumor-infiltrating lymphocytes (TILs) were profiled by flow cytometry. T cell populations were analyzed for total CD45+ cells, CD4+ cells, CD8+ cells, and CD8+ T effector memory (TEM) cells, as well as Treg cells (Figures 10A and 10B). Flow cytometry of regulatory T (Treg) cells showed a significant decrease in the frequency of Treg cells in the combination group (Figure 10B). The ratio of effector CD8+ T cells to regulatory T cells in each treatment group showed a significantly increased ratio in the combination group (Figure 10B).

[0696] IFNγ levels were assessed by Luminex analysis of tumors treated with 30 mg / kg Compound I or in combination with anti-PD1 (FIG. 10C).

[0697] Cocultures of human NSCLC cells with PBMCs and fibroblasts were treated with Compound I alone or in combination with a fixed dose of anti-PD1 in a dose-response fashion for 72 hours. IFNγ levels were quantified by ELISA from tissue culture supernatants (FIG. 10D).

[0698] These results indicate that the combination of Compound I and anti-PD1 antibody increased T cell activity and reduced Tregs in the tumor microenvironment.

[0699] To determine immune correlates of response to Compound I in combination with anti-PD-1 in the Stk11 mutant tumor microenvironment, MC38_sgStk11 tumor-bearing mice were treated for 7 days with vehicle (5% DMA + 30% PEG 400 + 65% of 30% HPβCD in water and 10 mg / kg anti-IgG2a), 30 mg / kg Compound I, 10 mg / kg anti-PD-1, or a combination thereof. After 7 days, tumors were harvested and flash-frozen for analysis using a gene expression panel of mouse tissues.

[0700] The total number of T cells was increased by anti-PD-1 alone and in combination with Compound I (Figure 10E). The abundance of regulatory T cells (Tregs) was also increased by anti-PD-1. However, combined treatment with anti-PD-1 and Compound I 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 indicate that combined treatment with Compound I and anti-PD-1 uncouples the recruitment of effector T cells and Tregs, increasing the effector / regulatory T cell ratio, which strongly favors immune cell-mediated tumor cell killing.

[0701] Example 9: Analysis of gene regulation by Compound I In this example, changes in gene expression between CoreDAC and other HDAC inhibitors were determined by Nanostring profiling.

[0702] Briefly, A549 cells were treated in vitro for 96 hours with the HDAC inhibitors vorinostat, domatinostat, and Compound I. To select comparable doses for each compound, H3K9Ac AlphaLISA was performed, and the dose resulting in a two-fold increase in H3K9Ac was selected for each inhibitor. Cells were harvested, and Nanostring profiling using the PanCancer IO360 panel was performed on the three treatment groups (Figures 11A-C). The three highest-ranked Gene Ontology groups for each compound, as determined from the Nanostring data (Figures 11A-C, top panels), were determined using nSolver software (Figures 11A-C, bottom panels). The results show that Compound I regulates the expression of fewer genes than the less selective HDAC inhibitors vorinostat and domatinostat.

[0703] Example 10: Analysis of the therapeutic index and cytotoxicity of Compound I In this example, the toxicity and therapeutic index of Compound I were determined in vitro and in vivo.

[0704] Briefly, colony-forming unit assays were performed in vitro to evaluate the effects of HDAC inhibitors on the viability of erythroid and myeloid cells. Cells were treated with a dose-response of each compound for 14 days. At the end of the experiment, cell colonies were quantified and compared to the solvent control. The effective dose range of Compound I was also plotted (range: 3 mg / kg to 75 mg / kg) (Figure 12A). The IC50 of each compound was calculated from the erythroid and myeloid colony-forming unit assays. These IC50s were normalized to the compound's potency against HDAC1 in the intracellular NanoBRET assay, allowing for head-to-head compound comparisons (Table 4-1).

[0705] [Table 4-1]

[0706] Clinically relevant doses of vorinostat for mice were calculated using body surface area equivalents. Mice bearing STK11-deficient MC38 tumors were treated in vivo with vorinostat or Compound I alone, or with vorinostat or Compound I in combination with anti-PD1. Tumor volume was monitored over the treatment period (Figure 12B for vorinostat and Figure 12C for Compound 1). The mean concentrations (C) of vorinostat or Compound I at the doses used in Figures 12B and 12C are shown. average ) and the C for HDAC1 IC50 at that dose average The coverage of the above is shown in Table 4-2.

[0707] [Table 4-2]

[0708] The concentration of Compound I versus inhibition of HDAC1 or HDAC3 in vivo is plotted in Figure 12D. The shaded boxes indicate the tolerated dose and effective dose range of Compound I. Non-tolerated exposure was above 150 mg / kg.

[0709] These results demonstrate that Compound I is less cytotoxic and has an improved therapeutic index compared to less selective HDAC inhibitors such as vorinostat. CoreDAC Compound I has an improved therapeutic index compared to previously developed HDAC inhibitors.

[0710] Example 11: Pharmacological properties of Compound I The pharmacokinetics (PK) of Compound I in rats was determined after a single intravenous bolus dose of 1 mg / kg of 20% w / v HPβCD, 1% v / v DMSO in saline or a single oral dose of 3 mg / kg of 0.5% methylcellulose (MC) in water was administered to male Sprague Dawley rats (fed for intravenous administration, fasted for oral administration). Plasma samples were collected from three rats per group at 0.05, 0.25, 0.5, 1, 2, 3, 4, 8, and 24 hours post-dose. Selected PK parameters of Compound I are presented in Table 5. Oral bioavailability was 95.4%.

[0711] The pharmacokinetics of Compound I in beagle dogs was determined in plasma after single intravenous bolus and oral administration to non-naive male and female beagle dogs. The vehicle used for intravenous administration was saline containing 20% w / v 2-hydroxypropyl β-cyclodextrin (HPβCD) and 1% v / v DMSO. For oral administration, the vehicle was 5% DMA, 30% PEG400, and 65% (30% HPβCD aqueous solution) (solution) or 0.5% MC (suspension). Plasma samples were collected from three dogs per group at 0.083, 0.25, 0.5, 1, 3, 6, 9, 12, 24, and 48 hours post-dose. Selected pharmacokinetic parameters of Compound I are presented in Table 5. When Compound I was administered as a solution at 3 mg / kg under fasting conditions, oral bioavailability was 67.4%.

[0712] The PK of Compound I in male cynomolgus monkeys was determined in plasma after a single intravenous bolus dose and oral administration to non-naive male cynomolgus monkeys. The vehicle used for intravenous administration was saline containing 20% w / v HPβCD and 1% v / v DMSO, and for oral administration, 0.5% MC (suspension). Plasma samples were collected from three animals per group at 0.083, 0.25, 0.5, 1, 3, 6, 9, 12, 24, and 48 hours post-dose. Selected PK parameters of Compound I are presented in Table 5. When Compound I was administered as a suspension at 3 mg / kg under fed conditions, oral bioavailability was 83%.

[0713] The effect of Compound I on the cloned human delayed rectifier potassium ion channel gene (hERG) stably expressed in human embryonic kidney (HEK) 293 cells was measured using manual patch clamp technique. Briefly, Compound I was soluble at 100 μM in 0.3% DMSO, pH 6.9. Dose range-finding (DRF) assays were performed using Compound I at concentrations of 3, 30, and 100 μM. Compound I inhibited hERG current by 15.67%, 45.85%, and 73.57% at 3, 30, and 100 μM, respectively. A definitive hERG assay was used to determine the IC50 of Compound I. In the definitive hERG assay, each concentration was measured in triplicate. The IC50 value of the inhibitory effect of Compound I on hERG potassium current was 71.07 μM.

[0714] The 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 (more than 93% remained after 240 minutes of incubation at an HLM protein concentration of 0.6 mg / ml). CYP-selective inhibitor experiments were not performed because the turnover of Compound I was not appreciable. Compound I was hardly metabolized by recombinant human CYPs (rh CYPs; CYP1A2, 2B6, 2C8, 2C9, 2C19, 2D6, and 3A4 / 5) with terminal half-lives (T 1 / 2 ) more than 60 minutes).

[0715] [Table 5]

[0716] Example 12: Predicted Human PK of Compound I Human PK parameters for predicted effective doses of Compound I were calculated based on data from rodent and dog studies and are presented in Table 6.

[0717] [Table 6]

[0718] The predicted human pharmacokinetics and therapeutic window are modeled in FIG.

[0719] Example 13: Mouse PK / PD of Compound I The formation and accumulation of acetylated histone 3 lysine 9 (H3K9Ac) in MC38 tumor tissues from mice treated with Compound I was measured by Western blot. Briefly, female C57BL / 6 mice bearing MC38 tumors were treated with Compound I for 7 days at the indicated doses (3 mg / kg, 10 mg / kg, and 30 mg / kg). Tissues were harvested 8 hours after the final administration, and the accumulation of H3K9Ac was quantified by Western blot (Figure 14A) and normalized to total histone H3 (Figure 14B). These results indicate that incubation with Compound I results in a dose-dependent accumulation of H3K9Ac.

[0720] In another PK / PD study, MC38 tumor-bearing female C57BL / 6 mice (12 / group) were cultured with similar mean tumor volumes of approximately 430 mm 3 Mice were assigned to treatment groups with the following formula: 1) vehicle (5% N,N-dimethylacetamide [DMA] + 30% polyethylene glycol [PEG] 400 + 65% 30% 2-hydroxypropyl-β-cyclodextrin [HP-β-CD] in water) or 30, 100, and 300 mg / kg Compound I once daily (QD) for 2 days. Plasma samples were collected 1, 2, 8, and 24 hours after the final dose and analyzed for Compound I concentrations. Peripheral blood mononuclear cells (PBMCs) and tumor samples were collected 2, 8, and 24 hours after the final dose. PBMC samples were processed for determination of mean fluorescence levels of acetyl histone H2B by flow cytometry. Tumor samples were processed for determination of protein levels of acetyl histone H3 by Western blot. No significant weight loss greater than 5% or adverse clinical signs were observed with Compound I treatment during this study.

[0721] Plasma concentrations of Compound I were dose-proportional, with the maximum observed 1 hour after the final dose (Figure 14C). Based on a free fraction of 10.05% in C57BL / 6 mouse plasma, the unbound free plasma exposures were 5470, 17238, and 69665 h.ng / mL for QD doses of 30, 100, and 300 mg / kg, respectively, demonstrating that dose-proportionality was achieved within this dose range. Compound I treatment at 30, 100, and 300 mg / kg QD resulted in a dose-dependent increase in tumor acetyl histone protein levels beginning 2 hours after the final dose. Following 300 mg / kg QD of Compound I (2 days of treatment), a maximum 8-fold and 3.7-fold induction of histone acetylation was observed in PBMCs and tumors, respectively, 24 hours after the final dose compared to vehicle controls (Figures 14D and 14E).

[0722] Overall, the PK / PD relationship was dose-dependent, and induction of histone acetylation was sustainable throughout the 24-hour treatment period while plasma concentrations of Compound I were above the in vitro IC50 of HDAC1.

[0723] Example 14: Antitumor activity of anti-PD-1 and Compound I combination in a colon cancer model with KRAS mutation and STK11 KO (CT26_STK11KO) and a colon cancer model with STK11 alteration (parental CT26 or wild-type CT26) The in vivo antitumor efficacy of combined anti-PD1 and compound I treatment was evaluated in the CT26 mouse model. CT26 is a colon cancer cell line harboring an endogenous KRAS G12D mutation. Experiments were performed in the parental / wild-type line and in a line in which STK11 was knocked out (CT26_STK11KO), resulting in an anti-PD1-resistant model with reduced CD8+ T cell infiltration.

[0724] In each experiment, animals (8 animals / group) were divided into four groups. Group I 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 rate were monitored over the treatment period. For the CT26_STK11KO model, tumor volume was plotted by individual animal (Figure 15A) and treatment group (Figure 15B). Survival rate was plotted by treatment group (Figure 15C).

[0725] For the CT26 parental model, tumor volumes were plotted by treatment group (FIG. 15D) and by individual animals in groups 1 and 4 (FIG. 15E).

[0726] The study demonstrated that Compound I as a single agent had superior efficacy in the parental model (84% TGI) compared to the STK11KO model (39% TGI), while combination treatment showed similar efficacy: ORR rates (%) were 86% (6 / 7) and 88% (7 / 8) in the parental and STK11KO models, respectively.

[0727] Example 15: Antitumor activity of anti-CTLA4 in combination with Compound I in a colon cancer model The in vivo antitumor effect of combined treatment with anti-CTLA4 and Compound I was evaluated in the CT26 mouse model. CT26 is a colon cancer cell line harboring an endogenous KRAS G12D mutation. Experiments were performed in the parental / wild-type line and in a line in which STK11 knockout (CT26_STK11KO) was introduced to generate an anti-CTLA4-resistant model.

[0728] The in vivo antitumor effect of dual combination treatment with anti-CTLA4 and Compound I was investigated in the CT26 syngeneic model. CT26 is a colon cancer cell line. Experiments were also performed in the STK11-null CT26 model, which is resistant to CTLA4.

[0729] There were 8 mice per group. Group I 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 over the treatment period. For the parent model, tumor volume was plotted by treatment group (Figure 16A) and for individual animals in Groups 1 and 4 (Figure 16B). For the STK11 knockout model, tumor volume was plotted by treatment group (Figure 16C) and for individual animals in Groups 1 and 4 (Figure 16D).

[0730] Compound I demonstrated superior efficacy in the parental model (84% TGI) compared to the STK11KO model (39% TGI). 100% of mice responded to combination treatment in the parental model, while 75% (6 / 8) of mice responded in the STK11KO model.

[0731] Table 7 summarizes the results of the combined treatments of Examples 14 and 15.

[0732] [Table 7]

[0733] Example 16: Antitumor activity of anti-PD-1 and Compound I combination in the Lewis lung cancer model In the PD-1-resistant STK11-null 3LL model, we investigated the in vivo antitumor effect of dual combination treatment with anti-PD1 and Compound I. The parental (non-STK11KO) 3LL line is relatively resistant to anti-PD1 treatment.

[0734] Animals (8 animals / group) were divided into four groups. Group I 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 rate were monitored over the treatment period. Tumor volume and survival rate were plotted by treatment group (Figures 17A and 17B, respectively). Combination treatment with Compound I reduced the PD-1 resistance caused by the SKT11 knockout in this model to baseline characteristics of the parental strain. This is shown by the decreased tumor volume and increased survival rate over time in Group 4 compared to the other groups.

[0735] Median times to events (TTE) and P values compared to control Group 1 (vehicle) are summarized in Table 8.

[0736] [Table 8]

Claims

1. 1. An HDAC inhibitor for use in a method of treating a subject having cancer or at risk of developing cancer, said method comprising administering to said subject an effective amount of a histone deacetylase (HDAC) inhibitor, said cancer being identified as having altered STK11 activity or expression.

2. The HDAC inhibitor for use according to claim 1, wherein the histone deacetylase inhibitor is administered in combination with one or more additional therapeutic agents.

3. 3. The HDAC inhibitor for use according to claim 2, wherein at least one of the additional therapeutic agents is an immune checkpoint modulator.

4. 1. An HDAC inhibitor for use in a method of treating cancer in a subject comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein said treatment modulates and / or improves the ratio of Teff cells to Treg cells in a tumor or tumor microenvironment, and said cancer has been identified as having altered STK11 activity or expression.

5. 1. An HDAC inhibitor for use in a method of treating cancer in a subject comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein said treatment reduces or depletes Treg cells in a tumor or tumor microenvironment, and said cancer has been identified as having altered STK11 activity or expression.

6. 1. An HDAC inhibitor for use in a method of treating cancer in a subject comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein said treatment induces or increases expression of a cytokine that promotes anti-tumor activity, and said cancer has been identified as having altered STK11 activity or expression.

7. 7. The HDAC inhibitor for use in the method of claim 6, wherein the cytokine is selected from the group of CXCL9, CXCL10, and CXCL11.

8. 1. An HDAC inhibitor for use in a method of treating cancer in a subject comprising administering to the subject an immune checkpoint modulator and an HDAC inhibitor, wherein said treatment reduces expression of cytokines that promote Treg cell recruitment, and said cancer has been identified as having altered STK11 activity or expression.

9. 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 comprising administering the HDAC inhibitor to the subject, wherein the administration of the HDAC inhibitor does not reduce the viability of erythroid or myeloid cells, and the cancer has been identified as having altered STK11 activity or expression.

11. An HDAC inhibitor for use in a method of treating cancer in a subject comprising administering an HDAC1,2 selective inhibitor, wherein the cancer exhibits an immune evasion phenotype characterized by mutant STK11 expression, and the HDAC1,2 selective inhibitor is capable of attenuating or reversing the immune evasion phenotype.

12. 12. An HDAC inhibitor for use in the method of claim 10 or 11, further comprising administering an immune checkpoint modulator.

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

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

15. 2. The HDAC inhibitor for use according to claim 1, wherein the HDAC inhibitor is administered in combination with two or more additional therapeutic agents, at least two of the additional therapeutic agents being immune checkpoint modulators.

16. 16. The HDAC inhibitor for use according to any one of claims 3 to 9 and 12 to 15, wherein each immune checkpoint modulator is independently a checkpoint inhibitor, a T cell costimulatory receptor agonist, or a dendritic cell costimulatory receptor agonist.

17. 16. The HDAC inhibitor for use according to any one of claims 3 to 9 and 12 to 15, wherein the at least one immune checkpoint modulator is independently a T cell costimulatory receptor agonist or a dendritic cell costimulatory receptor agonist.

18. 16. The HDAC inhibitor for use according to any one of claims 3 to 9 and 12 to 15, wherein said at least one immune checkpoint modulator is a checkpoint inhibitor.

19. 19. The HDAC inhibitor for use according to claim 18, 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.

20. 19. The HDAC inhibitor for use according to 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. 19. The HDAC inhibitor for use according to claim 18, wherein the checkpoint inhibitor is an anti-CTLA-4 agent.

22. 19. The HDAC inhibitor for use according to 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. The HDAC inhibitor for use according to any one of claims 3 to 9 and 12 to 24, wherein each immune checkpoint inhibitor is independently an antibody.

26. 26. The HDAC inhibitor for use according to claim 25, wherein each checkpoint inhibitor is independently selected from an anti-CTLA-4 antibody, an anti-PD-1 antibody, an anti-PD-L1 antibody, an anti-4-1BB antibody, an anti-OX-40 antibody, an anti-GITR antibody, an anti-CD27 antibody, an anti-CD28 antibody, an anti-CD40 antibody, an anti-LAG3 antibody, an anti-ICOS antibody, an anti-TWEAKR antibody, an anti-HVEM antibody, an anti-TIM-1 antibody, an anti-TIM-3 antibody, an anti-VISTA antibody, and an anti-TIGIT antibody.

27. 26. The HDAC inhibitor for use according to claim 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.

28. 26. The HDAC inhibitor for use according to claim 25, wherein each said immune checkpoint inhibitor is independently selected from nivolumab, CT-011, AMP-224, pembrolizumab, pidilizumab, cemiplimab, dostallimab, prorugolimab, spartalizumab, camrelizumab, sasanlimab, sintilimab, tislelizumab, toripalimab, retifanlimab, MEDI0680, budigalimab, and geptanolimab.

29. 26. The HDAC inhibitor for use according to claim 25, wherein each checkpoint inhibitor is independently selected from an anti-PD1 antibody and an anti-PD-L1 antibody.

30. 26. The HDAC inhibitor for use according to claim 25, wherein the checkpoint inhibitor is an anti-CTLA-4 antibody.

31. 26. The HDAC inhibitor for use according to claim 25, wherein the checkpoint inhibitor is an anti-PD1 antibody.

32. The HDAC inhibitor for use according to claim 25, wherein the checkpoint inhibitor is an anti-PD1-L1 antibody.

33. The HDAC inhibitor for use according to claims 26, 27 and 30, wherein the anti-CTLA-4 antibody is ipilimumab.

34. 32. 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. 32. 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. 32. 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. 33. 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. 25. The HDAC inhibitor for use according to any one of claims 3 to 9 and 12 to 24, wherein the immune checkpoint modulator is a T cell costimulatory receptor agonist or a dendritic cell costimulatory receptor agonist.

39. The HDAC inhibitor for use according to any one of claims 2 to 9 and 12 to 38, wherein the at least one further therapeutic agent is a targeting agent.

40. 40. The HDAC inhibitor for use according to claim 39, wherein each said targeting agent is independently selected from an anti-angiogenic agent (e.g., 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.

41. 40. The HDAC inhibitor for use according to claim 39, wherein each said targeting agent is independently selected from bevacizumab, ramucirumab, sotorasib, crizotinib, ceritinib, alectinib, brigutinib, lorlatinib, entrectinib, dabrafenib, trametinib, capmatinib, tepotinib, and larotrectinib.

42. The HDAC inhibitor for use according to any one of claims 3 to 9 and 12 to 41, wherein said at least one further therapeutic agent is a chemotherapeutic agent.

43. 43. The HDAC inhibitor for use according to claim 42, wherein each said chemotherapeutic agent is independently selected from cisplatin, carboplatin, paclitaxel, albumin-bound paclitaxel (nab-paclitaxel), docetaxel, gemcitabine, vinorelbine, etoposide, and pemetrexed.

44. 43. The HDAC inhibitor for use according to claim 42, wherein said at least one chemotherapeutic agent is a platinum-containing therapeutic agent.

45. 43. The HDAC inhibitor for use according to claim 42, wherein one said chemotherapeutic agent is a platinum-containing chemotherapeutic agent (e.g., cisplatin) and a second said chemotherapeutic agent is pemetrexed.

46. The HDAC inhibitor for use according to any one of claims 3 to 9 and 12 to 45, wherein said at least one further therapeutic agent is radiation.

47. The 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. 48. The HDAC inhibitor for use according to any one of claims 1 to 47, wherein the cancer is resistant to chemotherapy (e.g. platinum-containing chemotherapy).

49. 49. The HDAC inhibitor for use according to any one of claims 1 to 48, wherein the cancer does not respond to or does not benefit from treatment with said immune checkpoint modulator when administered alone or as part of a treatment regimen that does not include said HDAC inhibitor.

50. 50. The HDAC inhibitor for use according to any one of claims 1 to 49, wherein the cancer is selected from the group consisting of lung cancer (e.g., lung adenocarcinoma, non-small cell lung cancer (NSCLC), lung squamous cell carcinoma), 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 carcinoma (e.g., large cell neuroendocrine carcinoma), melanoma, non-melanoma skin cancer (e.g., cutaneous squamous cell carcinoma), 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, cervical canal carcinoma, or cancer of unknown primary origin (e.g., adenocarcinoma of unknown primary origin).

51. 51. The HDAC inhibitor for use according to claim 50, wherein the cancer is lung cancer.

52. 52. The HDAC inhibitor for use according to claim 51, wherein the cancer is lung adenocarcinoma.

53. 52. The HDAC inhibitor for use according to claim 51, wherein the cancer is non-small cell lung cancer (NSCLC).

54. 54. The HDAC inhibitor for use according to claim 53, wherein the cancer is non-squamous non-small cell lung cancer (NSCLC).

55. 51. The HDAC inhibitor for use according to claim 50, wherein the cancer is colorectal cancer or colon adenocarcinoma.

56. 56. The HDAC inhibitor for use according to any one of claims 1 to 55, wherein the cancer has reduced STK11 expression.

57. 56. The HDAC inhibitor for use according to any one of claims 1 to 55, wherein the cancer has an STK11 mutation.

58. 56. The HDAC inhibitor for use according to any one of claims 1 to 55, wherein the cancer is identified as having an STK11 mutation and one or more additional mutations.

59. 59. The HDAC inhibitor for use according to claim 58, wherein said further mutation is selected from a KRAS mutation and a KEAP1 mutation.

60. 59. The HDAC inhibitor for use according to claim 58, wherein the further mutation is a KRAS mutation.

61. 61. The HDAC inhibitor for use according to claim 59 or 60, wherein the KRAS mutation is a mutation at position G12, optionally the KRAS mutation is selected from a G12D mutation, a G12C mutation, a G12V mutation or a combination thereof.

62. 60. The HDAC inhibitor for use according to claim 59, wherein said further mutation is a KEAP1 mutation.

63. 60. The HDAC inhibitor for use according to claim 59, wherein said further mutations are a KRAS mutation and a KEAP1 mutation.

64. 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. 65. The HDAC inhibitor for use according to any one of claims 1 to 64, wherein said histone deacetylase inhibitor is a selective inhibitor of histone deacetylase 1 (HDAC1 selective inhibitor).

66. The 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. 65. The HDAC inhibitor for use according to any one of claims 1 to 64, wherein said histone deacetylase inhibitor is a selective HDAC class I inhibitor.

68. 68. The HDAC inhibitor for use according to any one of claims 1 to 67, wherein said 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 an STK11 mutation and / or ii) the STK11 activity or expression level in the subject or a sample derived from the subject, wherein the presence of the STK11 mutation and / or an altered level of STK11 activity or expression indicates sensitivity to treatment with the HDAC inhibitor.

70. The HDAC inhibitor is a compound of formula (I) 【Chemistry 4】 69. The HDAC inhibitor for use according to any one of claims 1 to 68, which is: or a pharmaceutically acceptable salt thereof.

71. 1. 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 an 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 the STK11 mutation and / or altered level of STK11 activity or expression is indicative of sensitivity to treatment with the combination of the HDAC inhibitor and the immune checkpoint modulator.

72. A method for confirming the susceptibility 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, said confirmation method comprising determining i) the presence or absence of an STK11 mutation and / or ii) the level of STK11 activity or expression in said subject or in a sample derived from said subject, wherein the presence of said STK11 mutation and / or altered level of STK11 activity or expression indicates susceptibility to the use of an HDAC inhibitor in the treatment method of any one of claims 1 to 70.

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