Gene-regulating compositions and methods for improved immunotherapy
Inventors
Benson, Micah • Merkin, Jason • Kryukov, Gregory V. • Shenker, Solomon Martin • Schlabach, Michael • Tubo, Noah • Kaberna, II, James Martin
Assignees
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Publication Number
US-11332713-B2
Publication Date
2022-05-17
Expiration Date
Abstract
The present disclosure provides methods and compositions related to the modification of immune effector cells to increase therapeutic efficacy. In some embodiments, immune effector cells modified to reduce expression of one or more endogenous target genes, or to reduce one or more functions of an endogenous protein to enhance effector functions of the immune cells are provided. In some embodiments, immune effector cells further modified by introduction of transgenes conferring antigen specificity, such as exogenous T cell receptors (TCRs) or chimeric antigen receptors (CARs) are provided. Methods of treating a cell proliferative disorder, such as a cancer, using the modified immune effector cells described herein are also provided.
Core Innovation
The invention relates to non-naturally occurring modified human immune effector cells in which endogenous SOCS1 gene expression and/or function is reduced relative to an unmodified human immune effector cell. In particular, the modified human immune effector cell comprises an inactivating nucleic acid mutation in an SH2 domain of an endogenous SOCS1 gene, where the inactivating nucleic acid mutation is an insertion, deletion, or mutation in the SH2 domain.
The invention also provides gene-regulating systems for targeting endogenous SOCS1, including one or more guide RNA (gRNA) and a Cas endonuclease. In these systems, the gRNA comprises a targeting domain nucleic acid sequence that binds to a target nucleic acid sequence in an SH2 domain of an endogenous SOCS1 gene, and the target nucleic acid sequence and/or targeting-domain nucleic acid sequence is selected from enumerated SEQ ID NOs, including SEQ ID NOs: 1101-1232.
The invention also includes human immune effector cells and kits that incorporate the SOCS1-targeting gene-regulating system. The system and kit comprise one or more gRNA and a Cas endonuclease configured for SH2-domain SOCS1 targeting, and the overall approach is positioned for generating modified immune effector cells with enhanced effector functions, including proliferation, tumor infiltration, persistence, cytotoxicity, cytokine production, and resistance to exhaustion.
Claims Coverage
The independent claims cover engineered SOCS1 SH2-domain targeting via modified human immune effector cells, gene-regulating systems with gRNA and a Cas endonuclease, enumerated SOCS1 target or targeting-domain sequences, human immune effector cells comprising the gRNA/Cas components, and a kit comprising the gRNA and Cas endonuclease. Across the independent claims, four core inventive features are present: SOCS1 SH2-domain inactivation in immune effector cells, gRNA/Cas targeting to the SOCS1 SH2 domain, restriction to enumerated SOCS1 target/encoding sequences, and kit/system formats.
Inactivating SOCS1 SH2-domain mutation in a modified human immune effector cell
A non-naturally occurring modified human immune effector cell comprising an inactivating nucleic acid mutation in an SH2 domain of an endogenous SOCS1 gene, wherein endogenous SOCS1 gene expression and/or function in the modified human immune effector cell is reduced relative to endogenous SOCS1 gene expression and/or function in an unmodified human immune effector cell, and wherein the inactivating nucleic acid mutation is an insertion, deletion, or mutation in the SH2 domain.
gRNA/Cas targeting of the SOCS1 SH2 domain
A gene-regulating system comprising one or more guide RNA (gRNA) and a Cas endonuclease, wherein the one or more gRNA comprises a targeting domain nucleic acid sequence that binds to a target nucleic acid sequence in an SH2 domain of an endogenous SOCS1 gene.
Enumerated SOCS1 SH2 target/encoding sequences for gRNA targeting
A gene-regulating system comprising one or more guide RNA (gRNA) and a Cas endonuclease, wherein the one or more gRNA comprises a targeting domain nucleic acid sequence that binds to a target nucleic acid sequence in an endogenous SOCS1 gene, and wherein the target nucleic acid sequence is selected from the group consisting of SEQ ID NOs: 1101-1232; or the targeting domain nucleic acid sequence is encoded by a sequence selected from the group consisting of SEQ ID NOs: 1101-1232.
Human immune effector cell with gRNA/Cas for SOCS1 SH2 targeting
A human immune effector cell comprising a guide RNA (gRNA) and a Cas endonuclease, wherein the gRNA comprises a targeting domain nucleic acid sequence that binds to a target nucleic acid sequence in an SH2 domain of an endogenous SOCS1 gene.
Kit containing gRNA and Cas endonuclease for SOCS1 SH2 targeting
A kit comprising one or more guide RNA (gRNA) and a Cas endonuclease, wherein the one or more gRNA comprises a targeting domain nucleic acid sequence that binds to a target nucleic acid sequence in an SH2 domain of an endogenous SOCS1 gene.
Overall, the independent claims center on SOCS1 SH2-domain targeting and inactivation in modified human immune effector cells using gRNA and a Cas endonuclease, with additional independent-claim scope that includes enumerated SOCS1 target or targeting-domain sequence identifiers and corresponding system, cell, and kit embodiments.
Stated Advantages
Enhanced effector functions including proliferation, tumor infiltration, persistence, cytotoxicity, cytokine production, and resistance to exhaustion.
Improved anti-tumor activity when immune effector cells are dual gene edited, including enhanced tumor growth inhibition in described models.
Increased CAR-T accumulation after BCOR/CBLB dual editing.
Enhanced IL-2 and IFNγ cytokine production after BCOR/CBLB dual editing.
Near-complete inhibition of tumor growth with Socs1/Cblb dual edits in B16-F10.
Documented Applications
Therapeutic use for cancer, including immunotherapy based on modified immune effector cells with reduced SOCS1 expression and/or function.
Therapeutic use for other disorders, including immunotherapy based on reduced SOCS1 expression and/or function in modified immune effector cells.
CD19 CAR-T Raji model evaluations showing improved anti-tumor efficacy with combined editing of BCOR and CBLB.
Murine syngeneic tumor model validation using dual-edited T cells, including B16Ova OT1 and MC38gp100 PMEL models.
B16-F10 lung metastasis model evaluations, including tumor growth inhibition categories and near-complete inhibition with Socs1/Cblb dual edits.
Validation and contrast experiments involving SOCS1 with Cblb and examples involving Ankrd11, including PD-1/Lag3 as a contrasting case.
SOCS1 pharmacology evaluation via downstream clinical-study design elements and assay concepts.
Discovery of SOCS1 inhibitors targeting the SH2 domain and assessment of activation-marker changes after SOCS1/ANKRD11/CBL2-related editing.
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