STING agonist biomarkers and methods of use thereof

Abstract

The present disclosure relates to methods of identifying, selecting, monitoring and / or treating cancer patients with STING agonists.

Description

[Technical field]

[0001] This application claims the benefit of and priority to U.S. Provisional Patent Application No. 63 / 261,048, entitled "BIOMARKERS FOR STING AGONISTS AND METHODS OF USING THE SAME," filed September 9, 2021, the contents of which are expressly incorporated by reference in their entirety into this specification. [Background technology]

[0002] The innate immune system provides the first line of defense against infectious pathogens. Studies have shown that the stimulator-of-interferon-genes (STING) protein plays a central role in this response by mediating type I interferon (IFNα and IFNβ) production through both the NFk-B and IRF3 transcriptional pathways in response to intracellular double-stranded DNA, intracellular pathogens, and mitochondrial damage (Ishikawa et al. (2008) Nature 455:674-678; Burdette et al. (2013) Nat. Immunol. 14:19-26; Zhong et al. (2008) Immunity 29:538-550; Sun et al. (2009) Proc. Natl. Acad. Sci. USA 106:8653-8658). The innate immune system also plays a role in both tumor-promoting and antitumor immunity (Rakoff-Nahoum et al. (2009) Nat. Rev. Cancer. 9:57-63; Rakoff-Nahoum et al. (2008) Biochemistry (Mosc). 73:555-561). It has been demonstrated that intratumoral administration of STING agonists into the tumor microenvironment can elicit antitumor immune T cell responses through the cyclic guanosine monophosphate-adenosine monophosphate synthase-stimulator of interferon genes (cGAS-STING) pathway (Woo et al. (2014) Immunity. 41:830-842; Deng et al. (2014) Immunity. 41:843-852). Thus, STING and its activation are emerging as promising therapeutic targets in oncology.

[0003] Cancer cell nuclei and mitochondria tend to release genomic contents into the cytosol in the form of double-stranded (ds) DNA. The conformational change that accompanies the recognition of this dsDNA by cyclic GMP-AMP synthase (cGAS) and its binding to dsDNA promotes the production of cyclic Gp(2',5')Ap(3',5') (cGAMP). STING (also called transmembrane protein 173 or TMEM173) is a transmembrane protein that undergoes a conformational change upon binding to cyclic dinucleotides (CDNs), such as cGAMP, and thus serves as a direct sensor of CDNs on both cancer cells and antigen-presenting cells (Shih et al. (2018) Biophys. J. 114(1):32-39). Activation of STING by CDNs is associated with the downstream production of many proinflammatory cytokines and chemokines, such as INFβ, and the induction of antiviral genes, such as type I IFNs and IFN-stimulated genes (ISGs).

[0004] STING typically consists of an N-terminal transmembrane region, a C-terminal region containing a dimerization domain, and a carboxy-terminal tail. STING mutants have evolved to distinguish non-canonical CDNs produced by mammalian cyclic GMP-AMP synthase from conventional (3'-5') CDNs, which are primarily produced by bacteria (Burdette et al. (2011) Nature 478:515-518; Corrales et al. (2015) Cell Rep. 11:1018-1030; Diner et al. (2013) Cell Reports 3:1355-1361).

[0005] STING agonists as potential therapeutic agents have been reported, which consist mostly of either CDN analogues or non-nucleotidyl small molecule agonists. Synthetic or naturally derived CDN analogues function by locking STING into an active conformation (Motedayen et al. (2020) J. Clin. Med. 9, 3323). Several STING agonists have been reported to have potent inhibitors of IFN-γ ... STING, OX-401, SITX-799, STACT-TREX1, XMT-2056, ONM-500, MV-626, PF 06928215, DN-15089, HH18202, STI-001, and E7766 or pharma- ceutically acceptable salts thereof are in clinical trials. E7766 is a CDN analogue from a novel class of macrocyclic bridged STING agonists (MBSAs). STING agonists are being evaluated or considered for the treatment of tumors, including melanoma, head and neck squamous cell carcinoma (HNSCC), upper aerodigestive tract cancer, breast cancer, colorectal cancer, and / or lymphoma. STING agonists are also being evaluated in combination with additional therapies, such as anti-PD-1 antibodies, such as the treatment regimens described in PCT / US2019 / 034933 (published as WO 2019 / 232392A1), which is incorporated by reference herein.

[0006] Despite the established antitumor efficacy of STING agonists in various preclinical models, many early clinical trials have failed to demonstrate similar antitumor efficacy (Meric-Bernstam et al., J. Clin. Oncol. 2019, 37, 2507-2507; Harrington et al., Ann. Oncol. 2018, 29, viii712). One of the challenges facing the development of STING agonists is the effect of human genetic mutations in proteins involved in the cGAS-STING pathway and their ability to mediate antitumor responses. Single nucleotide variants (SNVs) in innate immune receptors have been found to reduce the production of type 1 interferons and cytokines (Yi et al. PloS one 8.10(2013):e77846). Thus, genetic analysis of patients prior to treatment may be advantageous to identify patients who will respond well to STING agonists and thus benefit from the treatment. Summary of the Invention [Means for solving the problem]

[0007] The present disclosure relates to a method for identifying, selecting, monitoring, and / or treating cancer patients with STING agonists based on the patient's genotype. In some embodiments, the present disclosure relates to a method for identifying cancer patients suitable for treatment with a STING agonist by determining the patient's genotype. In some embodiments, patients identified as suitable for treatment with a STING agonist are administered a therapeutically effective amount of a STING agonist, such as E7766, or a pharma- ceutically acceptable salt thereof. In some embodiments, patients identified as suitable for treatment with a STING agonist are also administered an additional therapy, such as a checkpoint inhibitor.

[0008] In some embodiments, the disclosure provides a method of treating cancer in a patient, comprising administering a therapeutically effective amount of a STING agonist to a patient carrying (i) a reference or heterozygous DNA sequence for TMEM173 V48V (rs7447927); and (ii) a reference or heterozygous for TLR6 S249P (rs5743810); or a reference for TLR10 I775V (rs4129009). In some embodiments, the disclosure provides a use of one or more single nucleotide variants rs7447927, rs5743810, and / or rs4129009 as biomarkers of a patient's genotype for the manufacture of a medicament for treating cancer in a patient. In some embodiments, the disclosure provides a use of one or more single nucleotide variants rs7447927, rs5743810, and / or rs4129009 as biomarkers of a patient's genotype for the manufacture of a medicament for treating cancer in a patient. In some embodiments, the treatment comprises administering a therapeutically effective amount of a STING agonist to a patient carrying: (i) a reference or heterozygous DNA sequence for TMEM173 V48V (rs7447927); and (ii) a reference or heterozygous for TLR6 S249P (rs5743810); or a reference for TLR10 I775V (rs4129009).

[0009] In some embodiments, the disclosure provides a method of treating cancer in a patient, comprising: (a) determining that the patient possesses (i) a reference or heterozygous DNA sequence for TMEM173 V48V (rs7447927); and (ii) a reference or heterozygous DNA sequence for TLR6 S249P (rs5743810); or a reference DNA sequence for TLR10 I775V (rs4129009); and (b) administering to the patient a therapeutically effective amount of a STING agonist. In some embodiments, the disclosure provides the use of one or more single nucleotide variants rs7447927, rs5743810, and / or rs4129009 as biomarkers of the patient's genotype in the manufacture of a medicament for treating cancer in the patient. In some embodiments, the disclosure provides for the use of one or more single nucleotide variants rs7447927, rs5743810, and / or rs4129009 as biomarkers of a patient's genotype for treating cancer in the patient. In some embodiments, the treatment comprises (a) determining that the patient possesses (i) a reference or heterozygous DNA sequence for TMEM173 V48V (rs7447927); and (ii) a reference or heterozygous DNA sequence for TLR6 S249P (rs5743810); or a reference DNA sequence for TLR10 I775V (rs4129009); and (b) administering to the patient a therapeutically effective amount of a STING agonist.

[0010] In some embodiments, the disclosure provides a method of identifying a cancer patient suitable for treatment with a STING agonist, comprising: (a) determining that the patient possesses (i) a reference or heterozygous DNA sequence for TMEM173 V48V (rs7447927); and (ii) a reference or heterozygous DNA sequence for TLR6 S249P (rs5743810); or a reference DNA sequence for TLR10 I775V (rs4129009); and (b) identifying the patient as suitable for treatment with a STING agonist. In some embodiments, the disclosure provides the use of one or more single nucleotide variants rs7447927, rs5743810, and / or rs4129009 as biomarkers of a patient's genotype in the manufacture of a composition for identifying a cancer patient suitable for treatment with a STING agonist. In some embodiments, the disclosure provides for the use of a patient's genotype with respect to one or more single nucleotide variants rs7447927, rs5743810, and / or rs4129009 as a biomarker to identify cancer patients suitable for treatment with a STING agonist. In some embodiments, identifying comprises (a) determining that the patient possesses (i) a reference or heterozygous DNA sequence for TMEM173 V48V (rs7447927); and (ii) a reference or heterozygous DNA sequence for TLR6 S249P (rs5743810); or a reference DNA sequence for TLR10 I775V (rs4129009); and (b) identifying the patient as suitable for treatment with a STING agonist.

[0011] In other embodiments, the disclosure provides a STING agonist for use in treating cancer in a patient. In some embodiments, the treatment comprises administering a therapeutically effective amount of a STING agonist to a patient carrying (i) a reference or heterozygous DNA sequence for TMEM173 V48V (rs7447927); and (ii) a reference or heterozygous DNA sequence for TLR6 S249P (rs5743810); or a reference DNA sequence for TLR10 I775V (rs4129009).

[0012] In some embodiments, the methods and uses described herein include obtaining a biological sample from a patient and determining the patient's genotype for one or more single nucleotide variants rs7447927, rs5743810, and / or rs4129009 from the sample. In some embodiments, the biological sample includes a buccal sample, a blood sample, and / or a tumor sample. In some embodiments, the biological sample is obtained from the patient by buccal swab, phlebotomy, and / or tumor biopsy. In some embodiments, a treatment decision, for example, whether to administer a STING agonist such as E7766 or a pharma- ceutically acceptable salt thereof, is based on determining whether one or more single nucleotide variants rs7447927, rs5743810, and / or rs4129009 are present in the sample.

[0013] In some embodiments, the patient's genotype for one or more single nucleotide variants rs7447927, rs5743810, and / or rs4129009 is determined by DNA mutation testing. In some embodiments, DNA mutation testing comprises next generation sequencing (NGS), polymerase chain reaction (PCR), and / or pyrosequencing. In some embodiments, the patient is a reference for rs7447927 and a reference for rs5743810. In some embodiments, the patient is a reference for rs7447927 and a heterozygote for rs5743810. In some embodiments, the patient is a heterozygote for rs7447927 and a reference for rs5743810. In some embodiments, the patient is a heterozygote for rs7447927 and a heterozygote for rs5743810. In some embodiments, the patient is a reference for rs7447927 and a reference for rs4129009. In some embodiments, the patient is heterozygous for rs7447927 and reference for rs4129009.

[0014] In some embodiments, the patient has or is suspected of having upper aerodigestive tract cancer. In some embodiments, the cancer comprises lip cancer, buccal mucosa cancer, floor of mouth cancer, oral cavity cancer, hard palate cancer, base of tongue cancer, oral tongue cancer, tonsil cancer, oropharynx cancer, salivary gland cancer, gallbladder cancer, esophageal cancer, gastric cancer, and / or biliary tract cancer. In some embodiments, the cancer comprises head and neck squamous cell carcinoma (HNSCC). In some embodiments, the cancer comprises esophageal cancer. In some embodiments, the cancer is a recurrent cancer. In some embodiments, the cancer is a metastatic cancer.

[0015] In some embodiments, the STING agonist is selected from the group consisting of E7766 or a pharma- ceutically acceptable salt thereof, ADU-S100, BI 1387446, MK-1454, MK-2118, BMS-986301, CDK-002, GSK-3745417, idronoxyl, SB-11285, IMSA-101, SNX-281, SYNB-1891, TAK-676, DMXAA, FAA, CMA, α-mangostin, BNBC, DSDP, diABZI, bicyclic benzamides, benzothiophenes, MSA-2, SR-717, MAVU-104, TTI-10001, SRCB-0001, CRD 5500, ALG-031048, JNJ-'6196, IACS-8803, IACS-8779, NZ-IO-STING, OX-401, SITX-799, STACT-TREX1, XMT-2056, ONM-500, MV-626, PF-06928215, DN-15089, HH18202, and / or STI-001. In some embodiments, the STING agonist comprises one or more of E7766 or a pharma- ceutically acceptable salt thereof, ADU-S100, BI 1387446, MK-1454, MK-2118, BMS-986301, CDK-002, GSK-3745417, idronoxyl, SB-11285, IMSA-101, SNX-281, SYNB-1891, and / or TAK-676. In some embodiments, the STING agonist comprises a diammonium salt of E7766.

[0016] In some embodiments, the STING agonist is administered intratumorally to the patient. In some embodiments, the STING agonist is administered to the patient by intratumoral injection. In some embodiments, the injection is administered into a solid tumor, for example, where the tumor has a major axis diameter of at least 1 centimeter. In some embodiments, the injection is administered into a lymph node, for example, where the lymph node has a minor axis diameter of at least 1.5 centimeters. In some embodiments, the STING agonist is administered systemically. In some embodiments, the STING agonist is administered to the patient by intravenous infusion. In some embodiments, the STING agonist is administered subcutaneously to the patient.

[0017] In some embodiments, the STING agonist is administered to the patient in combination with at least one additional therapy. In some embodiments, the at least one additional therapy comprises administering one or more checkpoint inhibitors. In some embodiments, the checkpoint inhibitor targets PD1, PDL1, and / or CTLA4. In some embodiments, the checkpoint inhibitor comprises a programmed death-1 pathway (PD1) inhibitor. In some embodiments, the PD1 inhibitor comprises an anti-PD1 antibody. In some embodiments, the anti-PD1 antibody comprises pembrolizumab, nivolumab, and / or spartalizumab. In some embodiments, the PD1 inhibitor comprises an anti-PDL1 antibody. In some embodiments, the checkpoint inhibitor comprises a cytotoxic T-lymphocyte-associated antigen 4 pathway (CTLA4) inhibitor. In some embodiments, the CTLA4 inhibitor comprises an anti-CTLA4 antibody. In some embodiments, the anti-CTLA4 antibody comprises ipilimumab.

[0018] In some embodiments, the STING agonist is administered to the patient in combination with at least one additional therapy. In some embodiments, the additional therapy is administered to the subject prior to administration of the STING agonist. In some embodiments, the additional therapy is administered to the subject simultaneously with administration of the STING agonist. In some embodiments, the additional therapy is administered to the subject after administration of the STING agonist. In some embodiments, the additional therapy is administered intratumorally to the patient. In some embodiments, the additional therapy is administered to the patient by intratumoral injection. In some embodiments, the injection is administered into a solid tumor, e.g., where the tumor has a major axis diameter of at least 1 centimeter. In some embodiments, the injection is administered into a lymph node, e.g., where the lymph node has a minor axis diameter of at least 1.5 centimeters. In some embodiments, the additional therapy is administered systemically. In some embodiments, the additional therapy is administered to the patient by intravenous infusion.

[0019] In some embodiments, treatment with a STING agonist (e.g., any of the exemplary STING agonists described herein or incorporated by reference) reduces or inhibits the growth of the patient's tumor compared to the growth of the tumor before treatment. In some embodiments, treatment reduces the size of the patient's tumor compared to the size of the tumor before treatment. In some embodiments, treatment reduces the size of the patient's tumor by about 5%, 10%, 15%, 20% or more compared to the size of the tumor before treatment. In some embodiments, treatment reduces the size of the patient's tumor by about 20% or more compared to the size of the tumor before treatment. In some embodiments, treatment increases or decreases the expression or activity of at least one protein in the patient compared to the expression or activity of the same protein or proteins before treatment. In some embodiments, the at least one protein comprises a cytokine and / or a chemokine. In some embodiments, the at least one protein comprises IFNα, IFNβ, IFNγ, IP-10, MCP-1, MIP-1b, IL-6, and / or TNFα. [Brief description of the drawings]

[0020] [Figure 1] Hazard ratio plots of life expectancy for patients with upper aerodigestive tract (oral cavity, oropharynx, esophagus, stomach, biliary tract) tumors carrying reference / heterozygote TLR6 S249 and / or reference TLR10 I775 in combination with Neanderthal-associated STING1 rs7447927 are shown. [Diagram 2] A and B show circulating cytokine levels in patients following the first dose of STING agonist Compound 1. [Diagram 3] 1 shows changes in gene expression in leukocytes from patients administered the first dose of STING agonist Compound 1. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0021] The following detailed description and examples illustrate specific embodiments of the present disclosure. Those skilled in the art will recognize that there are numerous variations and modifications thereof that are encompassed within the scope of the present disclosure. Thus, the description of a specific embodiment should not be considered as limiting the scope of the present disclosure.

[0022] In order to facilitate understanding of this disclosure, certain terms are defined throughout the detailed description. Unless otherwise defined herein, all technical and scientific terms used in connection with this disclosure have the same meaning as commonly understood by those of ordinary skill in the art.

[0023] All references cited herein, including but not limited to published and unpublished patent applications, issued patents, and literature references, are hereby incorporated by reference and made a part hereof. To the extent that a cited reference conflicts with the disclosure of this specification, the present specification shall control.

[0024] As used herein, the singular forms of words also include the plural forms unless the context clearly dictates otherwise; by way of example, the terms "a," "an," and "the" are understood to be either singular or plural. By way of example, "an element" means one or more elements. The term "or" is intended to mean "and / or" unless the specific context dictates otherwise.

[0025] The term "agent" as used herein refers to a chemical compound, a mixture of chemical compounds, a biological macromolecule (e.g., an antibody), an extract from biological material, or a combination or conjugate thereof. The term "therapeutic agent" refers to an agent capable of providing a therapeutic benefit, e.g., regulating a biological process and / or providing a biological activity. In some embodiments, the agent is a STING agonist.

[0026] The term "STING agonist" refers to an agent that can directly act on STING or on upstream or downstream components of the cGAS-STING pathway to provide an agonist effect. Such agonist effects can include increasing the concentration of CDNs, such as cGAMP. In some embodiments, STING agonists are synthetic or naturally occurring CDN analogs that increase STING activation by locking STING in an active conformation. In some embodiments, STING agonists indirectly increase STING activation, for example, by preventing cGAMP degradation by ENPP1. In some embodiments, STING agonists increase the concentration of cytokines (e.g., INFβ) that are downstream of STING in the cGAS-STING pathway. In some embodiments, STING agonists increase the expression of antiviral genes (e.g., INF).

[0027] Treating a patient with a STING agonist can result in a biological response. In some embodiments, the biological response is a reduction in tumor growth rate or tumor volume. In some embodiments, the biological response is a reduction in cancer symptoms. In some embodiments, the STING agonist has the ability to bind to human STING or a functional variant or fragment thereof to provide an agonist effect, such as increasing or enhancing STING activity and / or stabilizing circulating STING (e.g., human STING). In some embodiments, the STING agonist has the ability to bind to an upstream or downstream molecule of the cGAS-STING pathway to provide an agonist effect. In some embodiments, the STING agonist is a small molecule. In some embodiments, the STING agonist is a biomolecule, such as an antibody or an antigen-binding fragment. In some embodiments, the STING agonist is a conjugate of an antibody and a small molecule.

[0028] As used herein, a "functional variant" or "fragment" refers to a peptide or nucleic acid that differs from a parent polypeptide or nucleic acid by one or more amino acid or nucleic acid deletions, substitutions, or additions, but still retains one or more specific functions or biological activities of the parent molecule. Nucleic acid substitutions include changes in which a single nucleic acid is replaced with a different nucleic acid. Such substitutions can be classified as "synonymous variants," in which the amino acid residue encoded by the nucleic acid sequence is not changed by the substitution. Substitutions can also be classified as "missense variants," in which the amino acid residue encoded by the nucleic acid sequence is changed by the substitution. Also included within the scope of the term variant when used in reference to a polynucleotide or polypeptide refers to a polynucleotide or polypeptide that may differ in terms of primary, secondary, or tertiary structure when compared to a reference polynucleotide or polypeptide (e.g., when compared to a wild-type polynucleotide or polypeptide), respectively.

[0029] "E7766" as used herein refers to a macrocycle-bridged STING agonist (MBSA) as described in Kim et al., ChemMedChem. 2021 Jun 7;16(11):1740-1743 and PCT / US2020 / 040515 (published as WO 2021003279A1), which are incorporated herein by reference. Its structure is shown as follows: [ka]

[0030] E7766 is (1R,3R,15E,28R,29R,30R,31R,34R,36R,39S,41R)-29,41-difluoro-34,39-bis(sulfanyl)-2,33,35,38,40,42-hexaoxa-4,6,9,11,13,18,20,22,25,27-decaaza-34k 5 ,39k 5 -Diphosphaoctacyclo[28.6.4.1 3,36 .1 28,31 .0 4,8 .0 7,12 .0 19,24 .0 23,27 ]dotetraconta-5,7,9,11,15,19,21,23,25-nonane-34,39-dione. In the event of any discrepancy between this chemical name and the structure provided above, the structure provided above shall prevail. Compound 1, the diammonium salt of E7766, has a molecular weight of 780.7. In the examples reported herein, compound 1, the diammonium salt, was used.

[0031] The term "pharmaceutical acceptable" as used herein means approved or expected to be approved by a federal or state regulatory agency for use in animals, and more particularly in humans, or listed in the United States Pharmacopeia or other generally recognized pharmacopoeias.

[0032] A "pharmaceutically acceptable salt", as used herein, is a salt that retains the desired biological activity of the parent compound to which it is added and does not impart undesired toxicological effects. Examples of such salts are (a) acid addition salts formed with inorganic acids, such as hydrochloric acid, hydrobromic acid, sulfuric acid, phosphoric acid, nitric acid, etc.; and salts formed with organic acids, such as acetic acid, oxalic acid, tartaric acid, succinic acid, maleic acid, fumaric acid, gluconic acid, citric acid, malic acid, ascorbic acid, benzoic acid, tannic acid, palmitic acid, alginic acid, polyglutamic acid, naphthalenesulfonic acid, methanesulfonic acid, p-toluenesulfonic acid, naphthalenedisulfonic acid, polygalacturonic acid, etc.; and (b) salts formed from anionic elements such as chlorine, bromine, and iodine. See, e.g., Haynes et al., "Commentary: Occurrence of Pharmaceutically Acceptable Anions and Cations in the Cambridge Structural Database," J Pharmaceutical Sciences, Vol. 94, No. 10 (2005), and Berge et al., "Pharmaceutical Salts," J Pharmaceutical Sciences, Vol. 66, No. 1 (1977), which are incorporated herein by reference.

[0033] "Pharmaceutical excipient" refers to materials such as auxiliary agents, carriers, pH adjusting and buffering agents, tonicity adjusting agents, wetting agents, preservatives, etc.

[0034] A "pharmaceutical composition" refers to a preparation in a form that allows for administration and subsequently provides the intended biological activity of one or more active ingredients and / or achieves a therapeutic effect, and that does not contain additional components that are unacceptably toxic to the patient to whom the formulation will be administered. The pharmaceutical composition may be sterile.

[0035] For example, an "effective amount" of a STING agonist, e.g., E7766 or a pharma- ceutically acceptable salt thereof, is an amount sufficient to achieve a specifically stated purpose, e.g., an amount sufficient to produce a therapeutic effect, such as a reduction in tumor growth rate or tumor volume, a reduction in a symptom of cancer, or some other indicator of therapeutic efficacy, following administration to a patient. The term "therapeutically effective amount" refers to, for example, an amount of a STING agonist, e.g., E7766 or a pharma- ceutically acceptable salt thereof, effective to provide a desired therapeutic effect, such as treating a disease or disorder in a patient. In the case of cancer, a therapeutically effective amount of a STING agonist, e.g., E7766 or a pharma- ceutically acceptable salt thereof, may result in a measurable change (e.g., an increase or decrease) in one or more clinically measured parameters of the cancer (e.g., one or more phenotypes and / or biomarkers modulated by STING), a reduction in the number of cancer cells, a reduction in tumor size, an inhibition (e.g., slowing or stopping) of tumor metastasis, an inhibition (e.g., slowing or stopping) of tumor growth, and / or an alleviation of one or more symptoms. A "prophylactically effective amount" refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired prophylactic result. Typically, since a prophylactic dose is used in patients prior to or at an earlier stage of disease, the prophylactically effective amount will be lower than the therapeutically effective amount.

[0036] As used herein, the term "treat" or "treatment" or "therapeutic" (and grammatically related terms) refers to any improvement in any outcome of a disease, such as extending survival, slowing disease progression (e.g., slowing or reducing tumor volume growth), ameliorating (e.g., reducing tumor volume), reducing morbidity, and / or reducing side effects caused by another treatment modality. Complete eradication of a disease or its symptoms or outcomes is included, but is not required for therapeutic action. Treatment may refer to the administration of one or more agents, such as a STING agonist (e.g., E7766 or a pharma- ceutically acceptable salt thereof), to a patient, e.g., a cancer patient. Treatment may prevent, cure, ameliorate, alleviate, palliate, alter, treat, ameliorate, inhibit, reverse, or affect a disease, one or more symptoms or outcomes of a disease, or a predisposition to a disease, e.g., cancer.

[0037] The terms "sample" and "biological sample" refer to any biological specimen from a subject or patient, e.g., a human patient. Exemplary biological samples include, but are not limited to, cells, tissues, and bodily fluids, such as blood, serum, plasma, intestinal fluids, as well as stool, organ, and venous samples. Biological samples are generally representative of any other sample taken from the same source, and can be preserved such that the preserved sample remains biologically equivalent to the sample at the time of its collection. In some embodiments, biological samples include buccal samples, blood samples, and / or tumor samples. In some embodiments, biological samples are obtained from patients by buccal swabs, phlebotomy, and / or tumor biopsy.

[0038] In some embodiments, a biological response is detected or monitored in a patient or in a sample from a patient. The term "biological response" as used herein refers to a response in a patient (or sample) after administration of (or contact with) an agent, such as a STING agonist (e.g., E7766 or a pharma- ceutically acceptable salt thereof). Biological responses can include, for example, any response related to cell signaling or signal transduction (e.g., phosphorylation of protein kinases), gene transcription, protein expression, toxicity, cytokine release, cell proliferation, cell motility or morphology, cell growth arrest, and / or cell death (e.g., apoptosis).

[0039] As used herein, the term "cytokine" refers to any molecule produced by a cell that affects the function of other cells to mediate an immune response. The term "chemokine" as used herein refers to certain cytokines that induce chemotaxis and / or specifically affect the migration of cells to the site of infection / inflammation. Exemplary cytokines and / or chemokines include, but are not limited to, IFNα, IFNβ, IFNγ, IP-10, MCP-1, MIP-1b, IL-6, and / or TNFα.

[0040] As used herein, the term "gene" refers to a nucleic acid molecule that contains an open reading frame that encodes a polypeptide. Natural allelic variation can typically result in 1-5% variation in the nucleotide sequence of a given gene. Alternative alleles can be identified by sequencing the gene of interest in a number of different individuals. This can be readily accomplished using methods known in the art.

[0041] As used herein, "allele" refers to a nucleic acid sequence that is present on one of the two chromosomes for a given genetic locus.

[0042] As used herein, the term "wild type allele," "reference allele," or "standard allele" refers to the nucleic acid sequence of the allele that is most frequently found in the human population. In some embodiments, a patient is considered the "reference" for a locus if both alleles are wild type.

[0043] As used herein, "wild-type" and "WT" may be used interchangeably herein to refer to a wild-type allele, gene, locus, or gene product.

[0044] As used herein, the term "allelic variant" or "variant" refers to a non-wild-type allele, gene, locus, or gene product.

[0045] As used herein, "DNA mutation testing" refers to the determination of the sequence of an allele using DNA sequencing and comparison with a wild-type allele or direct detection of the presence of nucleotides that are altered compared to a wild-type sequence in a given reference sequence. In some embodiments, DNA mutation testing includes the use of next generation sequencing (NGS). In some embodiments, DNA mutation testing includes the use of polymerase chain reaction (PCR). In some embodiments, DNA mutation testing includes the use of pyrosequencing. Other DNA sequencing methods are known in the art and may be used.

[0046] As used herein, "genotype" refers to the two alleles that exist for a particular genetic locus of interest.

[0047] As used herein, a "single nucleotide variant" (SNV) is an allelic variant that differs by a single nucleotide at a particular genomic location compared to a reference allele. In some embodiments, a single nucleotide variant can be identified by a reference number (Reference SNP (rs)).

[0048] As used herein, if two identical wild type alleles for a locus are found in a patient, then the patient is said to be the "reference" with respect to an allele at that locus.

[0049] As used herein, a patient is said to be "heterozygous" for an allele at a locus if the patient has two different alleles for that locus, and one of the alleles is the wild-type allele.

[0050] As used herein, if two identical non-wild-type alleles for a given locus are found in a patient, the patient is said to be "homozygous" for an allele at that locus.

[0051] As used herein, the term "human STING gene" (STING gene also referred to as "TMEM173") refers to a nucleic acid molecule comprising an open reading frame encoding human STING or any functional variant or fragment thereof (i.e., variants and fragments are encompassed, unless the context dictates that the term is used to refer exclusively to the wild-type gene). As used herein, a "wild-type human STING gene" comprises or consists of the nucleotide sequence of SEQ ID NO:2.

[0052] An allelic variant of the human STING gene comprises or consists of a nucleotide sequence that is not SEQ ID NO: 2. In some embodiments, an allelic variant of the human STING gene comprises or consists of the nucleotide sequence of SEQ ID NO: 3 or SEQ ID NO: 4. In some embodiments, an allelic variant of human STING may comprise or consist of the reference sequence TMEM173 (rs7447927).

[0053] As used herein, the term "human STING" refers to any naturally occurring form of human stimulator-of-interferon-genes (STING) protein. The term encompasses full-length human STING, as well as any form of human STING that may result from cellular processing. The term also encompasses functional variants or fragments of human STING, including but not limited to allelic variants, splice variants, and isoforms that retain one or more biological functions of human STING (i.e., variants and fragments are included unless the context dictates that the term is used to refer only to the wild-type protein).

[0054] As used herein, the term "wild-type human STING" refers to the gene product of the wild-type allele found in the human STING locus.As used herein, wild-type human STING is encoded by the nucleotide sequence of SEQ ID NO:2.As used herein, wild-type human STING is the amino acid sequence of SEQ ID NO:1.

[0055] As used herein, the term "allelic variant of human STING" refers to the gene product of a non-wild type allele found at the human STING locus and encompasses any allelic variant of human STING. Exemplary allelic variants of human STING are described in Patel and Lin ((2019) Genes & Immunity 20:82-89), which is incorporated herein by reference for its disclosure and sequences of such variants. Exemplary allelic variants of human STING include, but are not limited to, HAQ (R71H-G230A-R293Q), AQ (G230A-R293Q), Q293, and H232 (Patel and Lin (2019) Genes & Immunity 20:82-89). In some embodiments, the allelic variant of human STING is a synonymous variant. In some embodiments, the synonymous variant of human STING may be encoded by TMEM173 (rs7447927).

[0056] Exemplary STING sequences are shown in Table 1.

[0057] As used herein, the term "human TLR6 gene" (TLR6 gene, also referred to as "TLR6") refers to a nucleic acid molecule comprising an open reading frame encoding the human Toll-like receptor 6 protein, or any functional variant or fragment thereof (i.e., variants and fragments are encompassed, unless the context dictates that the term is used to refer only to the wild-type gene). As used herein, the wild-type human TLR6 gene comprises or consists of the nucleotide sequence of SEQ ID NO:6.

[0058] An allelic variant of the human TLR6 gene comprises or consists of a nucleotide sequence that is not SEQ ID NO: 6. In some embodiments, an allelic variant of the human TLR6 gene comprises or consists of the nucleotide sequence of SEQ ID NO: 8. In some embodiments, an allelic variant of the human TLR6 gene may comprise or consist of the reference sequence TLR6 (rs5743810).

[0059] As used herein, the term "human TLR6" refers to any naturally occurring form of human TLR6 protein. The term encompasses full-length human TLR6, as well as any form of human TLR6 that may result from cellular processing. The term also encompasses functional variants or fragments of human TLR6, including, but not limited to, allelic variants, splice variants, and isoforms that retain one or more biological functions of human TLR6 (i.e., variants and fragments are included unless the context dictates that the term is used to refer only to the wild-type protein).

[0060] As used herein, the term "wild-type human TLR6" refers to the gene product of the wild-type allele found in the human TLR6 locus. As used herein, wild-type human TLR6 is encoded by the nucleotide sequence of SEQ ID NO:6. As used herein, wild-type human TLR6 is the amino acid sequence of SEQ ID NO:5.

[0061] As used herein, the term "allelic variant of human TLR6" refers to a gene or gene product of a non-wild type allele found at the human TLR6 locus and encompasses any allelic variant of human TLR6. In some embodiments, the human TLR6 is an allelic variant of human TLR6 comprising a S249P mutation. In some embodiments, the allelic variant of human TLR6 comprising a S249P mutation comprises SEQ ID NO: 7. In some embodiments, the allelic variant of human TLR6 may be encoded by TLR6(rs5743810).

[0062] Exemplary TLR6 sequences are shown in Table 2.

[0063] As used herein, the term "human TLR10 gene" (TLR10 gene also referred to as "TLR10") refers to a nucleic acid molecule comprising an open reading frame encoding the human Toll-like receptor 10 protein, or any functional variant or fragment thereof (i.e., variants and fragments are encompassed, unless the context dictates that the term is used to refer only to the wild-type gene). In some embodiments, the wild-type human TLR10 gene comprises or consists of the nucleotide sequence of SEQ ID NO:10.

[0064] An allelic variant of the human TLR10 gene comprises or consists of a nucleotide sequence that is not SEQ ID NO: 10. In some embodiments, an allelic variant of the human TLR10 gene comprises or consists of the nucleotide sequence of SEQ ID NO: 12. In some embodiments, an allelic variant of the human TLR10 gene may comprise or consist of the reference sequence TLR10 (rs4129009).

[0065] As used herein, the term "human TLR10" refers to any naturally occurring form of human TLR10 protein. The term encompasses full-length human TLR10, as well as any form of human TLR10 that may result from cellular processing. The term also encompasses functional variants or fragments of human TLR10, including, but not limited to, allelic variants, splice variants, and isoforms that retain one or more biological functions of human TLR10 (i.e., variants and fragments are included unless the context dictates that the term is used to refer only to the wild-type protein).

[0066] As used herein, the term "wild-type human TLR10" refers to the gene product of the wild-type allele found at the human TLR10 locus. As used herein, wild-type human TLR10 is encoded by the nucleotide sequence of SEQ ID NO: 10. As used herein, wild-type human TLR10 is the amino acid sequence of SEQ ID NO: 9.

[0067] As used herein, the term "allelic variant of human TLR10" refers to a gene or gene product of a non-wild type allele found at the human TLR10 locus and encompasses any allelic variant of human TLR10. In some embodiments, the human TLR10 is an allelic variant of human TLR10 comprising an I775V mutation. In some embodiments, the allelic variant of human TLR10 comprising an I775V mutation comprises SEQ ID NO: 11. In some embodiments, the allelic variant of human TLR10 may be encoded by TLR10(rs4129009).

[0068] Exemplary TLR10 sequences are shown in Table 3.

[0069] Residues of two or more polypeptides are said to "correspond" if the residues occupy similar positions in the polypeptide structure. Similar positions in two or more polypeptides may be determined by aligning the polypeptide sequences based on amino acid sequence or structural similarity. One of skill in the art will appreciate that it may be necessary to introduce gaps in either sequence to produce a satisfactory alignment. Unless otherwise indicated, residue positions are designated with reference to the amino acid numbering of wild-type human STING (SEQ ID NO:1). For example, a variant of human STING (e.g., an allelic variant of human STING) may contain a modification to an arginine at position 232, as counted from the N-terminus of SEQ ID NO:1. In this example, the arginine at position 232 of SEQ ID NO:1 is designated as "R232". If the arginine at position 232 of SEQ ID NO:1 is replaced with, for example, histidine, the histidine modification at position 232 is designated as "R232H".

[0070] [Table 1]

[0071] [Table 2]

[0072]

Table 3

[0073]

Table 4

[0074]

Table 5

[0075]

Table 6

[0076]

Table 7

[0077]

Table 8

[0078]

Table 9

[0079]

Table 10

[0080]

Table 11

[0081]

Table 12

[0082]

Table 13

[0083] [Table 14]

[0084] [Table 15]

[0085] [Table 16]

[0086] [Table 17]

[0087] [Table 18]

[0088] [Table 19]

[0089] [Table 20]

[0090] The terms "subject" and "patient" may be used interchangeably herein to refer to any animal, such as any mammal, including, but not limited to, humans, non-human primates, rodents, etc. In some embodiments, the subject or patient is a mammal. In some embodiments, the subject or patient is a human.

[0091] As used herein, "intratumoral administration" and "intratumoral injection" are used interchangeably to refer to the delivery of an agent directly to tumor tissue.

[0092] As used herein, "long axis diameter" refers to the length of a tumor as measured on its longest axis using, for example, CT / MRI and / or photography according to Modified Response Evaluation Criteria in Solid Tumors (RECIST) 1.1. In some embodiments, a STING agonist is administered to a patient suffering from a solid tumor, where the long axis diameter of the solid tumor is 1 cm or greater. In some embodiments, a STING agonist is administered to a patient suffering from a lymphoma, where the long axis diameter of the lymphoma is 1 cm or greater.

[0093] As used herein, "short axis diameter" refers to the length of a tumor as measured on the short axis using, for example, CT / MRI and / or photography according to Modified Response Evaluation Criteria in Solid Tumors (RECIST) 1.1. In some embodiments, a STING agonist is administered to a patient with lymph node disease, where the short axis diameter of the lymph node is 1.5 cm or greater.

[0094] Administration "in combination" or "co-administration" as used herein means that two or more different therapies are delivered to a patient while the patient is suffering from a disease or disorder (e.g., cancer). For example, in some embodiments, two or more therapies are delivered after the patient is diagnosed with a disease or disorder and before the disease or disorder is cured or eliminated. In some embodiments, there is an overlap, since the delivery of one treatment is still occurring at the beginning of the delivery of the second treatment. In some embodiments, the first and second treatments are started at the same time. This type of delivery is sometimes referred to herein as "simultaneous," "concurrent," or "combined" delivery. In other embodiments, the delivery of a dose of the second treatment is started after the delivery of at least one dose of one treatment is completed. This type of delivery is sometimes referred to herein as "sequential" or "sequential" delivery. In some embodiments, a STING agonist is administered to a patient alone or in combination with at least one additional therapy. In some embodiments of the combination therapy, at least one additional therapy includes administering a checkpoint inhibitor. In some embodiments, the STING agonist and the checkpoint inhibitor are administered simultaneously. In some embodiments, the STING agonist and checkpoint inhibitor are administered sequentially, in either case, the two treatments must be administered close enough in time to provide the desired therapeutic effect.

[0095] As used herein, the term "checkpoint inhibitor" refers to any therapeutic agent, including any small molecule chemical compound, antibody, nucleic acid molecule, or polypeptide, or any fragment thereof, or any conjugate thereof, that inhibits one or more immune checkpoint pathways, thereby allowing broader immune activity. Immune checkpoints are signaling pathways that limit the activity of immune responses. Inhibiting immune checkpoint pathways can result in an increase in immune response. In some embodiments, checkpoint inhibitors target PD1, PDL1, and / or CTLA4.

[0096] As used herein, the terms "cancer," "neoplasm," and "tumor" are used interchangeably and refer to cells that have undergone malignant transformation and become pathological to the host organism, whether in the singular or plural form. Primary cancer cells can be easily distinguished from non-cancerous cells by well-established techniques, such as histological examination. As used herein, the definition of cancer cells includes not only primary cancer cells, but also any cells derived from a cancer cell ancestor. This includes metastasized cancer cells, as well as in vitro cultures and cell lines derived from cancer cells. Cancer may manifest as a solid tumor, e.g., tumors detectable by techniques such as computed tomography (CT) scan, magnetic resonance imaging (MRI), x-ray, ultrasound, or palpation during physical examination, based on the tumor mass, and / or tumors detectable because of the expression of one or more cancer-specific antigens in a sample available from the patient. Cancer may also be a hematological (or hematopoietic or blood-related) malignancy, e.g., cancer derived from blood cells or immune cells, which may also be referred to as a liquid tumor. Specific examples of hematological malignancies include leukemia; plasma cell malignancies; lymphomas, and the like. In some embodiments, the human subject is diagnosed with cancer prior to treatment or is concurrently diagnosed. In some embodiments, the cancer described herein may be any solid tumor and / or hematological malignancy. In some embodiments, the cancer comprises upper aerodigestive tract cancer. In some embodiments, the cancer comprises lip cancer, buccal mucosa cancer, floor of the mouth cancer, oral cavity cancer, hard palate cancer, base of tongue cancer, oral tongue cancer, tonsil cancer, oropharynx cancer, salivary gland cancer, gallbladder cancer, esophageal cancer, gastric cancer, and / or biliary tract cancer. In some embodiments, the cancer comprises head and neck squamous cell carcinoma (e.g., lip cancer, buccal mucosa cancer, floor of the mouth cancer, oral cavity cancer, hard palate cancer, base of tongue cancer, oral tongue cancer, tonsil cancer, and / or oropharynx cancer). In some embodiments, the cancer comprises esophageal cancer. In some embodiments, the cancer is a recurrent cancer. In some embodiments, the cancer is a metastatic cancer.

[0097] As used herein, "upper aerodigestive tract cancer" includes cancers of the organs and tissues of the upper respiratory and digestive tract. In some embodiments, upper aerodigestive tract cancer refers to lip cancer. In some embodiments, upper aerodigestive tract cancer includes oral cavity cancer. In some embodiments, upper aerodigestive tract cancer includes tongue cancer. In some embodiments, upper aerodigestive tract cancer includes nasal cancer. In some embodiments, upper aerodigestive tract cancer includes pharyngeal cancer. In some embodiments, upper aerodigestive tract cancer includes vocal cord cancer. In some embodiments, upper aerodigestive tract cancer includes esophageal cancer. In some embodiments, upper aerodigestive tract cancer includes tracheal cancer. In some embodiments, upper aerodigestive tract cancer includes stomach cancer. In some embodiments, upper aerodigestive tract cancer includes biliary tract cancer.

[0098] As used herein, "head and neck squamous cell carcinoma" or "HNSCC" includes cancer of the lip, buccal mucosa, floor of the mouth, oral cavity, hard palate, base of tongue, oral tongue, tonsil, and / or oropharyngeal cancer.

[0099] In some embodiments, a "recurrent" cancer is one that has returned after a period during which the cancer could not be detected.

[0100] In some embodiments, a "metastatic" cancer is one that has spread from its primary site to another location in the human organism.

[0101] Treatment Methods and Uses In various embodiments, the methods and uses described herein include obtaining a biological sample from a patient and determining from the sample whether the patient's genotype includes one or more of the single nucleotide variants rs7447927, rs5743810, and / or rs4129009. In some embodiments, the biological sample includes a buccal sample, a blood sample, and / or a tumor sample. In some embodiments, the biological sample is obtained from the patient by buccal swab, phlebotomy, and / or tumor biopsy. In some embodiments, a treatment decision, for example, whether to administer a STING agonist such as E7766 or a pharma- ceutically acceptable salt thereof, is based on determining whether one or more of the single nucleotide variants rs7447927, rs5743810, and / or rs4129009 are present in the sample. In some embodiments, the patient is administered a treatment including a STING agonist (e.g., alone or in combination with at least one additional agent, such as a checkpoint inhibitor) based on the genotyping from the sample.

[0102] Single nucleotide variants, detection methods, and patient selection In some embodiments, the methods and uses described herein include obtaining a biological sample from a patient and determining from the sample the patient's genotype at TMEM173 and TLR6, a combination of genotypes at TMEM173 and TLR10, or all three genes, for example to determine a decision to treat with a STING agonist. In some embodiments, the assessment of the genotype includes examining one or more single nucleotide variants rs7447927, rs5743810, and / or rs4129009. In some embodiments, the biological sample includes a buccal sample, a blood sample, and / or a tumor sample. In some embodiments, the biological sample is obtained from the patient by buccal swab, phlebotomy, and / or tumor biopsy. Such samples can be obtained by methods known to those skilled in the art.

[0103] In some embodiments, the patient's genotype for one or more of the single nucleotide variants rs7447927, rs5743810, and / or rs4129009 is determined by DNA mutation testing. In some embodiments, DNA mutation testing comprises next generation sequencing (NGS), polymerase chain reaction (PCR), and / or pyrosequencing.

[0104] In some embodiments, assessing the genotype in the patient sample comprises determining whether the sample is reference (i.e., wild type or standard for both alleles), mutant (non-wild type for both alleles), or heterozygous (one wild type allele and one mutant allele) for TMEM173. In some embodiments, assessing the genotype in the patient sample comprises determining whether the sample is wild type, mutant, or heterozygous for TLR6. In some embodiments, assessing the genotype in the patient sample comprises determining whether the sample is wild type, mutant, or heterozygous for TLR10. In some embodiments, assessing the sample comprises determining the presence or absence of the rs7447927 genotype for TMEM173 and the presence or absence of the rs5743810 genotype for TLR6. In some embodiments, assessing the sample comprises determining the presence or absence of the rs7447927 genotype for TMEM173 and the presence or absence of the rs4129009 genotype for TLR10. In some embodiments, evaluating the sample comprises determining the presence or absence of rs7447927 genotype for TMEM173, the presence or absence of rs5743810 genotype for TLR6, and the presence or absence of rs4129009 genotype for TLR10. In some embodiments, evaluating the sample comprises determining the presence or absence of rs7447927 genotype for TMEM173, and the presence or absence of rs5743810 genotype for TLR6. In some embodiments, evaluating the sample comprises determining the presence or absence of rs7447927 genotype for TMEM173, and the presence or absence of rs4129009 genotype for TLR10. In some embodiments, evaluating the sample comprises determining the presence or absence of rs7447927 genotype for TMEM173, the presence or absence of rs5743810 genotype of TLR6, and the presence or absence of rs4129009 genotype for TLR10.

[0105] In some embodiments, the wild type TMEM173 allele comprises or consists of SEQ ID NO:2. In some embodiments, the allelic variant of the human TMEM173 gene (TMEM173 V48V) comprises or consists of any sequence other than SEQ ID NO:2, e.g., SEQ ID NO:3 or 4. In some embodiments, the wild type TLR6 allele comprises or consists of SEQ ID NO:6. In some embodiments, the allelic variant of the human TLR6 gene (TLR6 S249P) comprises or consists of any sequence other than SEQ ID NO:6, e.g., SEQ ID NO:8. In some embodiments, the wild type TLR10 allele comprises or consists of SEQ ID NO:10. In some embodiments, the allelic variant of the human TLR10 gene (TLR10 I775V) comprises or consists of any sequence other than SEQ ID NO:10, e.g., SEQ ID NO:12. In some embodiments, the variant comprises any of those listed in Table 4 below.

[0106] [Table 21]

[0107] [Table 22]

[0108] In some embodiments, the patient is a candidate for treatment based on the patient's genotype for one or more single nucleotide variants rs7447927, rs5743810, and / or rs4129009 as described in Table 5. In some embodiments, the patient is a reference for rs7447927 and a reference for rs5743810. In some embodiments, the patient is a reference for rs7447927 and a heterozygote for rs5743810. In some embodiments, the patient is a heterozygote for rs7447927 and a reference for rs5743810. In some embodiments, the patient is a heterozygote for rs7447927 and a heterozygote for rs5743810. In some embodiments, the patient is a reference for rs7447927 and a reference for rs4129009. In some embodiments, the patient is a heterozygote for rs7447927 and a reference for rs4129009.

[0109] In some embodiments, the disclosure provides a method of treating cancer in a patient, comprising: (a) determining that the patient possesses (i) a reference or heterozygous DNA sequence for TMEM173 V48V (rs7447927); and (ii) a reference or heterozygous DNA sequence for TLR6 S249P (rs5743810); or a reference DNA sequence for TLR10 I775V (rs4129009); and (b) administering to the patient a therapeutically effective amount of a STING agonist. In some embodiments, the disclosure provides a method of treating cancer in a patient, comprising administering a therapeutically effective amount of a STING agonist to a patient carrying (i) a reference or heterozygous DNA sequence for TMEM173 V48V (rs7447927); and (ii) a reference or heterozygous DNA sequence for TLR6 S249P (rs5743810); or a reference DNA sequence for TLR10 I775V (rs4129009). In some embodiments, the disclosure provides a use of one or more single nucleotide variants rs7447927, rs5743810, and / or rs4129009 as biomarkers of a patient's genotype for the patient in the manufacture of a medicament for treating cancer in a patient. In some embodiments, the disclosure provides a use of one or more single nucleotide variants rs7447927, rs5743810, and / or rs4129009 as biomarkers of a patient's genotype for the patient in the manufacture of a medicament for treating cancer in a patient. In some embodiments, the disclosure provides for the use of one or more single nucleotide variants rs7447927, rs5743810, and / or rs4129009 as biomarkers of a patient's genotype for treating cancer in the patient. In some embodiments, the treatment comprises (a) determining that the patient possesses (i) a reference or heterozygous DNA sequence for TMEM173 V48V (rs7447927); and (ii) a reference or heterozygous DNA sequence for TLR6 S249P (rs5743810); or a reference DNA sequence for TLR10 I775V (rs4129009); and (b) administering to the patient a therapeutically effective amount of a STING agonist.

[0110] In various embodiments, the STING agonist may be administered in a pharmaceutical composition. The pharmaceutical composition may include a second agent, for example, at least one checkpoint inhibitor. In some embodiments, the at least one checkpoint inhibitor is in a second pharmaceutical composition that is administered simultaneously or sequentially with the STING agonist, or in a pharmaceutical composition that includes the STING agonist. In some embodiments, the at least one checkpoint inhibitor is in a second pharmaceutical composition that is administered separately from the STING agonist (e.g., at a separate clinical visit), or in a pharmaceutical composition that includes the STING agonist.

[0111] therapeutic compounds In various embodiments, the methods disclosed herein include administering a STING agonist or a pharmaceutical composition comprising a STING agonist to a patient in need thereof, e.g., a patient identified as suitable for treatment with a STING agonist according to the methods disclosed herein. In some embodiments, the STING agonist is selected from the group consisting of E7766 or a pharma- ceutically acceptable salt thereof, ADU-S100, BI 1387446, MK-1454, MK-2118, BMS-986301, CDK-002, GSK-3745417, idronoxyl, SB-11285, IMSA-101, SNX-281, SYNB-1891, TAK-676, DMXAA, FAA, CMA, α-mangostin, BNBC, DSDP, diABZI, bicyclic benzamides, benzothiophenes, MSA-2, SR-717, MAVU-104, TTI-10001, SRCB-0001, CRD 5500, ALG-031048, JNJ-'6196, IACS-8803, IACS-8779, NZ-IO-STING, OX-401, SITX-799, STACT-TREX1, XMT-2056, ONM-500, MV-626, PF-06928215, DN-15089, HH18202, and / or STI-001. In some embodiments, the STING agonist comprises one or more of E7766 or a pharma- ceutically acceptable salt thereof, ADU-S100, BI 1387446, MK-1454, MK-2118, BMS-986301, CDK-002, GSK-3745417, idronoxyl, SB-11285, IMSA-101, SNX-281, SYNB-1891, and / or TAK-676. In some embodiments, the STING agonist comprises E7766 or a pharma- ceutically acceptable salt thereof, such as a diammonium salt thereof.

[0112] In some embodiments, the methods disclosed herein include administering a STING agonist or a pharmaceutical composition comprising a STING agonist to a patient in need thereof in combination with at least one additional agent, such as a checkpoint inhibitor or a pharmaceutical composition comprising a checkpoint inhibitor. In some embodiments, the checkpoint inhibitor is an inhibitor of the programmed death-1 (PD1) pathway. The programmed cell death 1 (PD1) pathway represents an immune control switch that can evade active T cell immune surveillance upon tumor cell engagement. The ligands of the PD1 receptor (PDL1 and PDL2) can be constitutively expressed or induced in various tumors. As used herein, the term "PD1 inhibitor" refers to any inhibitor of PD1 and / or the PD1 pathway, unless the context dictates that it specifically refers to an inhibitor that acts directly on the PD1 receptor. Exemplary PD1 inhibitors include, but are not limited to, anti-PD1 and anti-PDL1 antibodies.

[0113] In some embodiments, the checkpoint inhibitor is an anti-PD1 antibody that binds to the PD-1 receptor. Exemplary anti-PD1 antibodies include, but are not limited to, pembrolizumab (MK-3475), nivolumab, and / or spartalizumab.

[0114] In some embodiments, the checkpoint inhibitor is an anti-PDL1 antibody. Exemplary anti-PDL1 antibodies include, but are not limited to, atezolizumab, avelumab, and durvalumab.

[0115] In another embodiment, the checkpoint inhibitor is an inhibitor of cytotoxic T-lymphocyte-associated antigen (CTLA4) pathway.CTLA4, also known as CD152, is a protein receptor that downregulates immune response.CTLA4 is constitutively expressed on regulatory T cells, but is only upregulated on conventional T cells after activation.

[0116] As used herein, the term "CTLA4 inhibitor" refers to any inhibitor of CTLA4 and / or the CTLA4 pathway, unless the context dictates that it specifically refers to an inhibitor that acts directly on CTLA4. Exemplary CTLA4 inhibitors include, but are not limited to, anti-CTLA4 antibodies. In some embodiments, the CTLA4 inhibitor comprises an anti-CTLA4 antibody.

[0117] In some embodiments, checkpoint inhibitors are targeted to PD1 / PDL1, CTLA4, OX40, CD40, LAG3, TIM3, GITR, and / or KIR (including multispecific antibodies that can bind to two or more epitopes on one or more checkpoint antigen targets). In some embodiments, checkpoint inhibitors are targeted to CTLA4, OX40, CD40, and / or GITR. In some embodiments, checkpoint inhibitors are targeted by administering inhibitory antibodies or other similar inhibitory molecules (e.g., inhibitory anti-CTLA4 or anti-PD1 / PDL1 antibodies). In some embodiments, checkpoint inhibitors are targeted by administering agonists against the target; examples of targets in this class include stimulatory targets OX40, CD40, and / or GITR. In some embodiments, checkpoint inhibitors are agonist antibodies against OX40, CD40, and / or GITR. Agonistic antibodies directed against OX40 may have a dual role, inhibiting regulatory T cell suppression while enhancing effector cell function. Agonistic anti-GITR antibodies have also been shown to enhance the resistance of effector T cells to the inhibition induced by regulatory T cells (Karaki et al. (2016) Vaccines (Basel) 4(4):37). Similarly, agonistic CD40 antibodies also demonstrate T cell-dependent antitumor activity. Activation of CD40 on dendritic cells increases cross-presentation of tumor antigens, resulting in an increase in the number of effector T cells directed towards activated tumors (Ellmark et al. (2015) Oncoimmunol. 4(7):e1011484).

[0118] Treatment regimen By virtue of their agonistic activity, STING agonists may be useful in the treatment of cancer in subjects in need of such treatment, including various cancerous growths, oncogenic processes, metastatic tissues, or malignantly transformed cells, tissues, or organs. The inventors have discovered that STING agonists may be particularly effective in the treatment of cancer in patients exhibiting certain genotypes, such as those discussed above.

[0119] As used herein, a patient is "suitable" for or "in need of" a treatment if the patient would benefit biologically, medically, and / or in terms of quality of life from the treatment. In some embodiments, a patient suitable for treatment with a STING agonist (e.g., E7766 or a pharmaceutically acceptable salt thereof) is a cancer patient with a particular genotype that includes a combination of one or more single nucleotide variants rs7447927, rs5743810, and / or rs4129009. In some embodiments, a patient's genotype for one or more single nucleotide variants rs7447927, rs5743810, and / or rs4129009 is used as a biomarker to predict or determine whether a patient is likely to respond to or benefit from treatment with a STING agonist (e.g., E7766 or a pharmaceutically acceptable salt thereof). In some embodiments, the patient carries (i) a reference or heterozygous DNA sequence for TMEM173 V48V (rs7447927); and (ii) a reference or heterozygous DNA sequence for TLR6 S249P (rs5743810); or a reference DNA sequence for TLR10 I775V (rs4129009). In some embodiments, the patient is a reference for rs7447927 and a reference for rs5743810. In some embodiments, the patient is a reference for rs7447927 and a heterozygous for rs5743810. In some embodiments, the patient is a heterozygous for rs7447927 and a reference for rs5743810. In some embodiments, the patient is a heterozygous for rs7447927 and a heterozygous for rs5743810. In some embodiments, the patient is a reference for rs7447927 and a reference for rs4129009. In some embodiments, the patient is heterozygous for rs7447927 and reference for rs4129009. In some embodiments, the patient's genotype for one or more single nucleotide variants rs7447927, rs5743810, and / or rs4129009 is determined by DNA mutation testing.

[0120] In some embodiments, the STING agonist is administered intratumorally to the patient. In some embodiments, the STING agonist is administered subcutaneously to the patient. In some embodiments, the STING agonist is administered to the patient by intratumoral injection. In some embodiments, the injection is administered into a solid tumor, e.g., where the tumor has a major axis diameter of at least 1 centimeter. In some embodiments, the injection is administered into a lymph node, e.g., where the lymph node has a minor axis diameter of at least 1.5 centimeters. In some embodiments, the STING agonist is administered systemically. In some embodiments, the STING agonist is administered to the patient by intravenous infusion. In some embodiments, a person skilled in the art will be able to select a suitable concentration and frequency of administration of the STING agonist to be administered to the patient.

[0121] In some embodiments, the STING agonist is administered to the patient in combination with at least one additional therapy. In some embodiments, there is an overlap, since the delivery of one therapy is still occurring at the beginning of the delivery of the second therapy. In some embodiments, the first and second therapies are initiated at the same time. This type of delivery is sometimes referred to herein as "simultaneous," "concurrent," or "combined" delivery. In other embodiments, the delivery of a dose of the second therapy is initiated after the delivery of at least one dose of one therapy has ended. This type of delivery is sometimes referred to herein as "sequential" or "sequential" delivery. In some embodiments, the STING agonist is administered to the patient alone or in combination with at least one additional therapy. In some embodiments of the combination therapy, at least one additional therapy includes administering a checkpoint inhibitor. In some embodiments, the STING agonist and the checkpoint inhibitor are administered simultaneously. In some embodiments, the STING agonist and the checkpoint inhibitor are administered sequentially. In either case, the two therapies must be administered close enough in time to provide the desired therapeutic effect.

[0122] In some embodiments, the at least one additional therapy comprises administering one or more checkpoint inhibitors. In some embodiments, the checkpoint inhibitor targets PD1, PDL1, and / or CTLA4. In some embodiments, the checkpoint inhibitor comprises a programmed death-1 pathway (PD1) inhibitor. In some embodiments, the PD1 inhibitor comprises an anti-PD1 antibody. In some embodiments, the anti-PD1 antibody comprises pembrolizumab, nivolumab, and / or spartalizumab. In some embodiments, the PD1 inhibitor comprises an anti-PDL1 antibody. In some embodiments, the checkpoint inhibitor comprises a cytotoxic T-lymphocyte-associated antigen 4 pathway (CTLA4) inhibitor. In some embodiments, the CTLA4 inhibitor comprises an anti-CTLA4 antibody. In some embodiments, the anti-CTLA4 antibody comprises ipilimumab.

[0123] In some embodiments, the checkpoint inhibitor is an anti-PD1 antibody that binds to the PD-1 receptor. Exemplary anti-PD1 antibodies include, but are not limited to, pembrolizumab (MK-3475), nivolumab, and / or spartalizumab. For example, pembrolizumab and spartalizumab are both humanized monoclonal antibodies of the IgG4 / kappa isotype designed to block the interaction between PD1 and its ligands, PDL1 and PDL2 (Kao and Lou (2019) Head Neck 41 Suppl 1:4-18; Naing et al. (2020) J Immunother Cancer 8(1):e000530). Pembrolizumab enhances T lymphocyte immune responses in cultured blood cells from healthy human donors, cancer patients, and primates. Pembrolizumab has also been reported to regulate the levels of interleukin-2 (IL-2), tumor necrosis factor alpha (TNFα), interferon gamma (IFNγ), and other cytokines. For example, nivolumab is a fully-length human IgG4 anti-PD1 monoclonal antibody that disrupts the interaction of the PD1 receptor with its ligands PDL1 and PDL2, thereby inhibiting the cellular immune response (Guo et al. (2017) J Cancer 8(3):410-6). In some embodiments, the anti-PD1 antibody is pembrolizumab. In some embodiments, the anti-PD1 antibody is spartalizumab. In some embodiments, the anti-PD1 antibody is nivolumab.

[0124] In some embodiments, the checkpoint inhibitor is an anti-PDL1 antibody. Exemplary anti-PDL1 antibodies include, but are not limited to, atezolizumab, avelumab, and durvalumab. For example, atezolizumab is an IgG1 humanized monoclonal antibody that has been reported to block PD1 / PDL1 interaction by targeting PDL1 expression on many types of malignant cells. This blockade of the PD1 / PDL1 pathway may stimulate immune defense mechanisms against tumors (Abdin et al. (2018) Cancers (Basel) 10(2):32). In some embodiments, the anti-PDL1 antibody is atezolizumab.

[0125] In another embodiment, the checkpoint inhibitor is an inhibitor of cytotoxic T-lymphocyte-associated antigen (CTLA4) pathway.CTLA4, also known as CD152, is a protein receptor that downregulates immune response.CTLA4 is constitutively expressed on regulatory T cells, but is only upregulated on conventional T cells after activation.

[0126] As used herein, the term "CTLA4 inhibitor" refers to any inhibitor of CTLA4 and / or the CTLA4 pathway, unless the context dictates that it specifically refers to an inhibitor that acts directly on CTLA4. Exemplary CTLA4 inhibitors include, but are not limited to, anti-CTLA4 antibodies. In some embodiments, a CTLA4 inhibitor comprises an anti-CTLA4 antibody. Exemplary anti-CTLA4 antibodies include, but are not limited to, ipilimumab (MDX-010) and tremelimumab (CP-675,206), both of which are fully human. Ipilimumab is an IgG1 with a plasma half-life of about 12-14 days; tremelimumab is an IgG2 with a plasma half-life of about 22 days. See, e.g., Phan et al. (2003) Proc Natl Acad Sci USA. 100:8372-7; Ribas et al. (2005) J Clin Oncol. 23:8968-77; Weber et al. (2008) J Clin Oncol. 26:5950-6. In some embodiments, the anti-CTLA4 antibody comprises ipilimumab.

[0127] In some embodiments, the checkpoint inhibitors are targeted to PD1 / PDL1, CTLA4, OX40, CD40, LAG3, TIM3, GITR, and / or KIR (including multispecific antibodies that can bind to two or more epitopes on one or more checkpoint antigen targets). In some embodiments, the checkpoint inhibitors are targeted to CTLA4, OX40, CD40, and / or GITR. In some embodiments, the checkpoint inhibitors are inhibitory antibodies or other similar inhibitory molecules (e.g., inhibitory anti-CTLA4 or anti-PD1 / PDL1 antibodies). In some embodiments, the checkpoint inhibitors are agonists for their targets; examples of targets in this class include stimulatory targets OX40, CD40, and / or GITR. In some embodiments, the checkpoint inhibitors are agonist antibodies for OX40, CD40, and / or GITR. Agonistic antibodies directed against OX40 may have a dual role of inhibiting regulatory T cell suppression while enhancing effector cell function. Agonistic anti-GITR antibodies have also been shown to enhance the resistance of effector T cells to the inhibition induced by regulatory T cells (Karaki et al. (2016) Vaccines (Basel) 4(4):37). Similarly, agonistic CD40 antibodies may also demonstrate T cell-dependent antitumor activity. Activation of CD40 on dendritic cells may increase cross-presentation of tumor antigens, resulting in an increase in the number of effector T cells directed toward activated tumors (Ellmark et al. (2015) Oncoimmunol. 4(7):e1011484).

[0128] In some embodiments, the STING agonist is administered to the patient in combination with at least one additional therapy. In some embodiments, the additional therapy is administered to the subject prior to administration of the STING agonist. In some embodiments, the additional therapy is administered to the subject simultaneously with administration of the STING agonist. In some embodiments, the additional therapy is administered to the subject after administration of the STING agonist. In some embodiments, the additional therapy is administered to the patient intratumorally or intravascularly. In some embodiments, the additional therapy is administered to the patient by intratumoral injection. In some embodiments, the injection is administered into a solid tumor, e.g., where the tumor has a major axis diameter of at least 1 centimeter. In some embodiments, the injection is administered into a lymph node, e.g., where the lymph node has a minor axis diameter of at least 1.5 centimeters. In some embodiments, the additional therapy is administered systemically. In some embodiments, the additional therapy is administered to the patient by intravenous infusion. In some embodiments, one of skill in the art will be able to select a suitable route of administration, concentration, and frequency of administration of the additional therapeutic agent to be administered to the patient.

[0129] In some embodiments, a biological response is evaluated in a sample after contact with one or more agents, e.g., a STING agonist (e.g., E7766 or a pharma- ceutically acceptable salt thereof), measured using any of the exemplary assays described herein or known in the art. In some embodiments, the assay involves contacting a subject (e.g., a patient), a cell, or a culture of cells with a STING agonist (e.g., E7766 or a pharma- ceutically acceptable salt thereof) and determining whether one or more characteristics of the subject, cell, or culture are altered after contact. In some embodiments, the alteration may be detected in RNA expression levels, protein expression levels, protein activity levels, protein modification (e.g., protein phosphorylation) levels, one or more cell function levels, reporter signal levels, toxicity, cytokine release, cell proliferation, cell motility or morphology, cell growth, cell death (e.g., apoptosis), and / or tumor growth.

[0130] In some embodiments, the biological response is detected using one or more assays to assess protein expression, activity, and / or phosphorylation levels. In some embodiments, the biological response is detected using one or more assays, such as kinase or enzyme activity assays, radiolabeling, or the like. 32 The response is detected using one or more assays selected from incubation of whole cells with P-orthophosphate, two-dimensional gel electrophoresis, immunoblot assays (e.g., Western blots), AlphaLISA® assays, enzyme-linked immunosorbent assays (ELISAs), cell-based ELISA assays, intracellular flow cytometry, immunocytochemistry (ICC), immunohistochemistry (IHC), mass spectrometry, multianalyte profiling (e.g., phosphoprotein multiplex assays), and fluorescent in situ hybridization (FISH). In some embodiments, the biological response is detected by measuring or monitoring tumor growth over a period of time.

[0131] In some embodiments, the biological response is an increase or decrease in expression or activity of at least one protein in the patient compared to the expression or activity of the same protein or proteins in the patient prior to administration of the STING agonist. In some embodiments, the biological response is an increase or decrease in expression or activity of at least one protein in a sample from the patient compared to the expression or activity of the same protein or proteins in a sample prior to contact with the STING agonist. In some embodiments, the at least one protein exhibiting increased or decreased expression or activity comprises a cytokine and / or a chemokine.

[0132] In some embodiments, the biological response is detected using imaging of the patient. In some embodiments, the biological response is detected by measuring or monitoring tumor growth over a period of time. In some embodiments, the biological response is detected by measuring or monitoring using CT / MRI and / or photography of the patient. In some embodiments, if a biological response is detected, treatment is continued. EXAMPLES

[0133] The following examples provide exemplary embodiments of the present disclosure. Those skilled in the art will recognize numerous improvements and modifications that may be made without changing the spirit or scope of the present disclosure. Such improvements and modifications are encompassed within the scope of the present disclosure. The examples provided are not intended to limit the present disclosure in any way.

[0134] Example 1. STING agonist Compound 1 administered intratumorally and dose extension cohorts in patients with advanced solid tumors or lymphoma. A Phase 1 / 1b open-label, multicenter study will be conducted to determine the safety / tolerability and preliminary clinical activity of Compound 1 administered intratumorally as a single agent in patients with advanced solid tumors or lymphomas. In the dose escalation and dose expansion part, patients will receive Compound 1 intratumorally in advanced solid tumors or lymphomas to determine the safety / tolerability profile of Compound 1 and determine the maximum tolerated dose (MTD) and / or recommended phase 2 dose (RP2D). Toxicity will be assessed according to the National Cancer Institute Common Terminology Criteria for Adverse Events, version 5.0 (NCI CTCAE v.5.0). Patients will also be evaluated for the incidence of adverse events (AEs) and serious adverse events (SAEs) for up to 90 days after the last dose of Compound 1.

[0135] In the dose expansion part, patients with tumors including melanoma, head and neck squamous cell carcinoma (HNSCC), breast cancer, colorectal cancer, and / or other lymphomas will receive intratumoral administration of Compound 1 to confirm the safety of Compound 1 as a single agent and to determine its preliminary clinical activity. Clinical activity will be evaluated by objective response rate (ORR), duration of response (DOR), and disease control rate (DCR) associated with treatment with Compound 1. Patients will also be evaluated for the incidence of adverse events (AEs) and serious adverse events (SAEs) for up to 90 days after the last dose of Compound 1.

[0136] Example 2. Biomarkers for STING agonist treatment. Context: Admixture of archaic (Neanderthal and Denisovan) and ancestral genes may modulate susceptibility to autoimmunity and cancer. By investigating functional interactions between archaic and ancestral STING1 and TLR genes, we identified vulnerabilities that could be addressed by STING agonist therapy.

[0137] Methods: Genetic variants from 10,389 cancer patients were obtained from TCGA. Archaic sequences were accessed using UCSD Genome Browser v410. Linkage disequilibrium was examined using LDlink v5.0. Patient 1 was treated according to the procedure discussed in Example 1. See also ClinicalTrials.gov Identifier: NCT04144140, which is incorporated herein by reference.

[0138] Results: STING1 variants were overrepresented in cancer patients. The common V48V (rs7447927-C>G) variant was in linkage disequilibrium with the reference alleles of the partially active HAQ and REF variants, as well as with rs13153461, present in the Neanderthal sequence. STING1 rs7447927-G was also associated with HLA A mutations of Neanderthal origin. * 24:02 (p<0.001), A * 02:06 (p=0.01), and A *31:01 (p=0.02). Possible epistasis between the STING1 rs7447927-G variant and TLR variants associated with reduced H. pylori carriage rates (e.g., Neanderthal-associated TLR10 I775V (rs4129009) and ancestral TLR6 P249S (rs5743810)) was also examined. In 32 TCGA legacy studies, no independent prognosis was identified; however, in patients with upper aerodigestive tract (oral cavity, oropharynx, esophagus, stomach, biliary tract) tumors carrying reference / heterozygous TLR6 S249 and / or reference TLR10 I775, rs7447927-G zygosity status was prognostic for survival in combination with Neanderthal-associated STING1. Hazard ratios for rs7447927-GG vs. GC (median survival 4.8 vs. 2.7 years) and GG vs. CC (4.8 vs. 1.8 years) were 0.71 and 0.53 (N=713, p=0.0003), respectively (Figure 1).

[0139] An initial case study of the first patient (patient 1) to receive a STING agonist was evaluated. Patient 1 is a 75-year-old esophageal cancer patient with a history of gastroesophageal reflux disease (GERD), Barrett's esophagus, and TLR6 S249, TLR10 I775V, and STING1 rs7447927-GC, progressing from anti-PD1 and chemotherapy, who received 11 intratumoral injections of 75 μg of STING agonist compound 1. Patient 1 received the first injection on day 1, followed by three weekly doses and seven doses at 3-week intervals. Treatment-related grade 2 anemia and hyponatremia, serum IFN-β and IP10 induction, a 20% tumor size reduction including an abscopal effect, and a progression-free survival (PFS) benefit of 6.3 months were observed (Figures 2 and 3).

Claims

1. 1. A pharmaceutical composition comprising a STING agonist for treating cancer in a patient, wherein a therapeutically effective amount of the STING agonist is administered to the patient, wherein the patient: (i) a reference or heterozygous DNA sequence for TMEM173 V48V (rs7447927) and a reference or heterozygous DNA sequence for TLR6 S249P (rs5743810); or (ii) a reference or heterozygous DNA sequence for TMEM173 V48V (rs7447927) and a reference DNA sequence for TLR10 I775V (rs4129009); A pharmaceutical composition comprising:

2. 10. The pharmaceutical composition of claim 1, wherein a biological sample is obtained from the patient to determine the patient's genotype with respect to one or more single nucleotide variants rs7447927, rs5743810, and / or rs4129009.

3. 3. The pharmaceutical composition of claim 2, wherein the biological sample comprises a buccal sample, a blood sample, and / or a tumor sample, optionally obtained by oral swab, phlebotomy, or tumor biopsy.

4. 2. The pharmaceutical composition of claim 1, wherein the patient's genotype for one or more single nucleotide variants rs7447927, rs5743810, and / or rs4129009 is determined by DNA mutation testing, optionally wherein the DNA mutation testing comprises next generation sequencing (NGS), polymerase chain reaction (PCR), or pyrosequencing.

5. The patient: (a) reference for rs7447927 and reference for rs5743810; (b) reference for rs7447927 and heterozygous for rs5743810; (c) heterozygous for rs7447927 and reference for rs5743810; (d) heterozygous for rs7447927 and heterozygous for rs5743810; (e) a reference to rs7447927 and a reference to rs4129009; or (f) the pharmaceutical composition of claim 1, which is heterozygous for rs7447927 and reference for rs4129009.

6. The pharmaceutical composition of claim 1 , wherein the cancer comprises upper aerodigestive tract cancer.

7. 7. The pharmaceutical composition of claim 6, wherein the cancer comprises lip cancer, buccal mucosa cancer, floor of mouth cancer, oral cancer, hard palate cancer, base of tongue cancer, oral tongue cancer, tonsil cancer, oropharynx cancer, salivary gland cancer, gallbladder cancer, esophageal cancer, stomach cancer, and / or biliary tract cancer.

8. 8. The pharmaceutical composition of claim 7, wherein the cancer comprises head and neck squamous cell carcinoma (HNSCC) or esophageal cancer, optionally wherein the cancer is recurrent cancer, and further optionally wherein the cancer is metastatic cancer.

9. The STING agonist is selected from the group consisting of E7766, ADU-S100, BI 1387446, MK-1454, MK-2118, BMS-986301, CDK-002, GSK-3745417, idronoxyl, SB-11285, IMSA-101, SNX-281, SYNB-1891, TAK-676, DMXAA, FAA, CMA, α-mangostin, BNBC, DSDP, diABZI, bicyclic benzamide, benzothiophene, MSA-2, SR-717, MAVU-104, TTI-10001, SRCB-0001, CRD 5500, ALG-031048, JNJ-'6196, IACS-8803, IACS-8779, NZ-IO-STING, OX-401, SITX-799, STACT-TREX1, XMT-2056, ONM-500, MV-626, PF-06928215, DN-15089, HH18202, STI-001, and pharmaceutically acceptable salts thereof.

10. 10. The pharmaceutical composition of claim 9, wherein the STING agonist comprises one or more of E7766, ADU-S100, BI 1387446, MK-1454, MK-2118, BMS-986301, CDK-002, GSK-3745417, idronoxyl, SB-11285, IMSA-101, SNX-281, SYNB-1891, TAK-676, and pharmaceutically acceptable salts thereof.

11. The pharmaceutical composition of claim 9, wherein the STING agonist comprises E7766 or a pharmaceutically acceptable salt thereof.

12. 10. The pharmaceutical composition of claim 9, wherein the STING agonist comprises a diammonium salt of E7766.

13. 9. The pharmaceutical composition of any one of claims 1 to 8, wherein the composition is adapted to be administered intratumorally to the patient, optionally wherein the composition is adapted to be administered to the patient by intratumoral injection.

14. The injection (a) adapted to be administered into a solid tumor, the solid tumor having a major axis diameter of at least 1 centimeter; or (b) The pharmaceutical composition of claim 13, which is adapted to be administered into a lymph node, the lymph node having a short axis diameter of at least 1.5 centimeters.

15. The pharmaceutical composition according to any one of claims 1 to 8, wherein the composition is adapted to be administered to the patient in combination with at least one additional therapy.

16. 16. The pharmaceutical composition of claim 15, wherein the at least one additional therapy comprises a checkpoint inhibitor.

17. the checkpoint inhibitor comprises a programmed death-1 pathway (PD1) inhibitor, a PDL1 inhibitor, and / or a cytotoxic T-lymphocyte-associated antigen 4 pathway (CTLA4) inhibitor, and optionally (a) the PD1 inhibitor comprises an anti-PD1 antibody, and further optionally, the anti-PD1 antibody comprises pembrolizumab, nivolumab, and / or spartalizumab; (b) the PDL1 inhibitor comprises an anti-PDL1 antibody; and / or (c) The pharmaceutical composition of claim 16, wherein the CTLA4 inhibitor comprises an anti-CTLA4 antibody, and further optionally, the anti-CTLA4 antibody comprises ipilimumab.

18. The administration of the composition to the patient, (a) the growth of a tumor in said patient is reduced or inhibited as compared to the growth of said tumor prior to administration; (b) a reduction in the size of a tumor in said patient compared to the size of said tumor before administration; and / or (c) the size of the tumor in the patient is reduced by at least 20% or more compared to the size of the tumor before administration.

19. The pharmaceutical composition described in claim 18, wherein administration of the composition to the patient reduces the size of the patient's tumor by at least 20% or more compared to the size of the tumor before administration.

20. The method of claim 20, wherein administration of said composition to said patient increases or decreases the expression or activity of at least one protein in said patient compared to the expression or activity of the same one or more proteins prior to administration, and optionally, said at least one protein: (a) cytokines and / or chemokines; and / or (b) IFNα, IFNβ, IFNγ, IP-10, MCP-1, MIP-1b, IL-6, and / or TNFα The pharmaceutical composition according to any one of claims 1 to 8, comprising:

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