RNA-aided immunotherapeutics

SUMMARY [0006] Immunotherapy of cancers is a desirable therapeutic alternative in lieu of or in addition to the standard chemotherapy and radiation therapy protocols. Immune checkpoint inhibitors have been satisfactory in overall response rate for several different tumors and in particular EBV-associated tumors. In the context of EBV-associated tumors, viral proteins like EBNA2 and LMP1 affect immune checkpoint genes, such as, PD-L1 and ICOSL expression by altering miRNAs. Thus, a combination of miRNA, their mimics or chemically modified antisense oligonucleotides targeting miRNAs (i.e., a locked nucleic acid (LNA)), and immune checkpoints inhibitors on nanoparticles, provide a unique method for silencing immune checkpoints both from outside and within the tumor cell. [0007] In one aspect, the present disclosure provides a method for treating an EBV-related cancer in a subject in need thereof, comprising administering an effective amount of one or more of (a) an agent that increases an amount of miR-34a in the subject and (b) an agent that decreases an amount of miR-l29 in the subject, wherein: the subject is undergoing treatment with an immune checkpoint immunotherapy selected from an agent that modulates one or more of programmed cell death protein-l (PD-l), programmed death-ligand 1 (PD-L1), programmed death-ligand 2 (PD-L2), inducible T-cell costimulator (ICOS), inducible T-cell costimulator ligand (ICOSL), and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4). [0008] In some embodiments, the EBV-related cancer is selected from one or more of Non-Hodgkin lymphoma (NHL), B- cell Lymphoma (BL), Burkitt lymphoma, Hodgkin lymphoma (HL), nasopharyngeal carcinoma, gastric carcinoma, human T-lymphotropic virus 1 (HTLV-1), and adult T-cell leukemia (ATL)/lymphoma. [0009] In some embodiments, the agent that increases an amount of miR-34a is selected from one or more of miR-34a and a miR-34a mimetic. In some embodiments, the agent that increases an amount of miR-34a is an inhibitor of Early B-cell factor (EBF1). [0010] In some embodiments, the agent that decreases an amount of miR-l29 is selected from one or more of an antisense oligonucleotide, an antagomir and a construct expressing a miRNA inhibitor. In some embodiments, the antisense oligonucleotide comprises a sequence that is at least partially complementary to a mature sequence of miR-l29. In some embodiments, the agent is chemically modified. In some embodiments, the chemical modification is selected from locked nucleic acid (LNA), phosphorothioate, 2'-0-Methyl, 2'-0-Methoxyethyl, 2'-0-alkyl-RNA unit, 2'-OMe-RNA unit, 2'-amino-DNA unit, 2'-fluoro-DNA unit, peptide nucleic acid (PNA) unit, hexitol nucleic acids (HNA) unit, INA unit, and a 2'-0-(2-Methoxyethyl)-RNA (2' MOE RNA) unit. [0011] In some embodiments, the agent that modulates PD-l is an antibody or antibody format specific for PD-l. In some embodiments, the antibody or antibody format specific for PD-l is selected from one or more of a monoclonal antibody, polyclonal antibody, antibody fragment, Fab, Fab', Fab'-SH, F(ab')2, Fv, single chain Fv, diabody, linear antibody, bispecific antibody, multispecific antibody, chimeric antibody, humanized antibody, human antibody, and fusion protein comprising the antigen-binding portion of an antibody. In some embodiments, the antibody or antibody format specific for PD-l is selected from Nivolumab, Pembrolizumab, Pidilizumab, BMS-936559, Atezolizumab, or Avelumab. [0012] In some embodiments, the agent that modulates PD-L1 is an antibody or antibody format specific for PD-L1. In some embodiments, the antibody or antibody format specific for PD-L1 is selected from one or more of a monoclonal antibody, polyclonal antibody, antibody fragment, Fab, Fab', Fab'-SH, F(ab')2, Fv, single chain Fv, diabody, linear antibody, bispecific antibody, multispecific antibody, chimeric antibody, humanized antibody, human antibody, and fusion protein comprising the antigen-binding portion of an antibody. In some embodiments, the antibody or antibody format specific for PD-L1 is selected from Nivolumab, Pembrolizumab, Pidilizumab, BMS-936559, Atezolizumab, Avelumab or Durvalumab. [0013] In some embodiments, the agent that modulates PD-L2 is an antibody or antibody format specific for PD-L2. In some embodiments, the antibody or antibody format specific for PD-L2 is selected from one or more of a monoclonal antibody, polyclonal antibody, antibody fragment, Fab, Fab', Fab'-SH, F(ab')2, Fv, single chain Fv, diabody, linear antibody, bispecific antibody, multispecific antibody, chimeric antibody, humanized antibody, human antibody, and fusion protein comprising the antigen-binding portion of an antibody. [0014] In some embodiments, the agent that modulates ICOS is an antibody or antibody format specific for ICOS. In some embodiments, the antibody or antibody format specific for ICOS is selected from one or more of a monoclonal antibody, polyclonal antibody, antibody fragment, Fab, Fab', Fab'-SH, F(ab')2, Fv, single chain Fv, diabody, linear antibody, bispecific antibody, multispecific antibody, chimeric antibody, humanized antibody, human antibody, and fusion protein comprising the antigen-binding portion of an antibody. In some embodiments, the antibody or antibody format specific for ICOS comprises JTX-2011. [0015] In some embodiments, the agent that modulates ICOSL is an antibody or antibody format specific for ICOSL. In some embodiments, the antibody or antibody format specific for ICOSL is selected from one or more of a monoclonal antibody, polyclonal antibody, antibody fragment, Fab, Fab', Fab'-SH, F(ab')2, Fv, single chain Fv, diabody, linear antibody, bispecific antibody, multispecific antibody, chimeric antibody, humanized antibody, human antibody, and fusion protein comprising the antigen-binding portion of an antibody. [0016] In some embodiments, the agent that modulates CTLA-4 is an antibody or antibody format specific for CTLA-4. In some embodiments, the antibody or antibody format specific for CTLA-4 is selected from one or more of a monoclonal antibody, polyclonal antibody, antibody fragment, Fab, Fab', Fab'-SH, F(ab')2, Fv, single chain Fv, diabody, linear antibody, bispecific antibody, multispecific antibody, chimeric antibody, humanized antibody, human antibody, and fusion protein comprising the antigen-binding portion of an antibody. In some embodiments, the antibody or antibody format specific for CTLA-4 is selected from tremelimumab or Ipilimumab. [0017] In some embodiments, administration is by intratumoral, intradermal, subcutaneous, intramuscular, intraperitoneal or intravenous injection, or direct injection into cancer tissue. [0018] In one aspect, the disclosure provides a method for treating an EBV-related cancer in a subject in need thereof, comprising administering (i) an effective amount of one or more of (a) an agent that increases an amount of miR-34a in the subject and (b) an agent that decreases an amount of miR-l29 in the subject, and (ii) an effective amount of an immune checkpoint immunotherapy selected from an agent that modulates one or more of PD-l, PD-L1, PD-L2, ICOS, ICOSL, and CTLA-4. [0019] In one aspect, the disclosure provides a method for potentiating an immune checkpoint immunotherapy of an EBV-related cancer in a subject in need thereof, comprising administering an agent that increases an amount of miR-34a in the subject, wherein: the immune checkpoint immunotherapy is an agent that modulates one or more of PD-l, PD-L1, and PD-L2 and the subject is predicted to be poorly responsive or non-responsive to the immune checkpoint immunotherapy or has presented as poorly responsive or non-responsive to the immune checkpoint immunotherapy. [0020] In one aspect, the disclosure provides a method for potentiating immune checkpoint immunotherapy of an EBV-related cancer in a subject in need thereof, comprising administering an agent that decreases an amount of miR-l29 in the subject, wherein the immune checkpoint immunotherapy is an agent that modulates one or more of ICOS, ICOSL, and CTLA-4 and the subject is predicted to be poorly responsive or non-responsive to the immune checkpoint immunotherapy or has presented as poorly responsive or non-responsive to the immune checkpoint immunotherapy. [0021] In some embodiments, the method reduces and/or mitigates one or more side effects of the immune checkpoint immunotherapy. In some embodiments, the side effect is selected from decreased appetite, rashes, fatigue, pneumonia, pleural effusion, pneumonitis, pyrexia, nausea, dyspnea, cough, constipation, diarrhea, immune-mediated pneumonitis, colitis, hepatitis, endocrinopathies, hypophysitis, iridocyclitis, and nephritis. [0022] In some embodiments, the method reduces the dose of immune checkpoint immunotherapy. In some embodiments, method reduces number of administrations of the immune checkpoint immunotherapy. In some embodiments, the method increases a therapeutic window of the immune checkpoint immunotherapy. [0023] In some embodiments, the method elicits a potent immune response in less-immunogenic tumors. In some embodiments, the method converts a tumor with reduced inflammation (“cold tumor”) to a responsive, inflamed tumor (“hot tumor”). [0024] In some embodiments, the method makes the cancer responsive or more responsive to a combination therapy of the immune checkpoint immunotherapy and one or more chemotherapeutic agents and/or radiotherapy. In some embodiments, the subject is predicted to be poorly responsive or non-responsive to the immune checkpoint immunotherapy based on expression of one or more of PD-l, PD-L1, PD-L2, ICOS, ICOSL, and CTLA-4 in a tumor specimen. In some embodiments, the subject is predicted to be poorly responsive or non-responsive to an agent that modulates one or more of PD-l, PD-L1, and PD-L2 based on low on expression of PD-l, PD-L1, and PD-L2 in a tumor specimen. [0025] In some embodiments, the subject is predicted to be poorly responsive or non-responsive to an agent that modulates one or more of PD-l, PD-L1, and PD-L2 tumor proportion score (TPS) of less than about 49% for PD-L1 staining. [0026] In one aspect, the disclosure provides a method for treating an EBV-related cancer in a subject in need thereof, comprising administering (i) an effective amount of one or more of (a) an agent that increases an amount of miR-34a in the subject and (b) an agent that decreases an amount of miR-l29 in the subject, and (ii) an effective amount of an immune checkpoint immunotherapy selected from an agent that modulates one or more of PD-l, PD-L1, PD-L2, ICOS, ICOSL, and CTLA-4. [0027] In one aspect, the disclosure provides a method for evaluating an EBV-related cancer subject’s likelihood of response to an immune checkpoint immunotherapy, comprising evaluating a level of one or more of miR-34a and miR-l29 in a biological sample from the subject, wherein a low level of miR-34a and/or high level of miR-l29 is indicative of a cancer that is suitable for immune checkpoint immunotherapy. [0028] In one aspect, the disclosure provides a method for treating an EBV-related cancer, comprising: (a) evaluating a subject’s likelihood of response to an immune checkpoint immunotherapy, comprising evaluating a level of one or more of miR-34a and miR-l29 in a biological sample from the subject, wherein a low level of miR-34a and/or high level of miR-129 is indicative of a cancer that is suitable for immune checkpoint immunotherapy and (b) administering an immune checkpoint immunotherapy selected from an agent that modulates one or more of PD-l, PD-L1, and PD-L2 based on low on expression of PD-l, PD-L1, and PD-L2 to the subject having a low level of miR-34a and/or high level of miR-l29.