Intracellular genomic transplant and methods of therapy
Inventors
Moriarity, Branden • Webber, Beau • Choudhry, Modassir • Rosenberg, Steven A. • Palmer, Douglas C. • Restifo, Nicholas P.
Assignees
USA REPRESENTED BY SECRETARY Department F Health And Human Services AS • Intima Bioscience Inc • University of Minnesota System • US Department of Health and Human Services
Publication Number
US-11903966-B2
Publication Date
2024-02-20
Expiration Date
2036-07-29
Interested in licensing this patent?
MTEC can help explore whether this patent might be available for licensing for your application.
Abstract
Genetically modified compositions, such as non-viral vectors and T cells, for treating cancer are disclosed. Also disclosed are the methods of making and using the genetically modified compositions in treating cancer.
Core Innovation
Despite remarkable advances in cancer therapeutics over the last 50 years, many tumor types, particularly in advanced stages, remain recalcitrant to chemotherapy, radiotherapy, or biotherapy, and cannot be addressed through surgical techniques. Recent advances in genetic engineering of lymphocytes to recognize molecular targets on tumors in vivo have resulted in remarkable cases of remission, but these successes have been largely limited to hematologic tumors. Broad application to solid tumors is limited by the lack of identifiable molecules expressed by tumor cells that can be used to specifically bind and mediate tumor destruction.
The disclosed compositions and methods enable the identification of cancer-specific T Cell Receptors (TCRs) that recognize unique immunogenic mutations in a patient's cancer and allow for treatment of any cancer type within a patient. Transgenes encoding these cancer-specific TCRs can be inserted into T cells using non-viral methods such as CRISPR, TALEN, transposon-based, ZEN, meganuclease, or Mega-TAL. This non-viral integration system facilitates reliable expression of TCR transgenes in engineered T cells with preserved immunologic and anti-tumor potency.
The invention includes engineered cells comprising at least one gene disruption and at least one non-virally integrated TCR sequence, where the gene disruption can be caused by the integration of the TCR sequence. Disrupted genes can be immune checkpoint genes, such as PD-1, CD276, CTLA-4, LAG3, and others. The engineered TCR may recognize antigen in the context of major histocompatibility complex (MHC) class I or II, including neoantigens identified through whole-exome sequencing. The engineered cells can be primary immune cells, such as T cells, stem cells, or progenitor cells, and can be autologous or non-autologous (allogenic) to the subject.
Claims Coverage
The patent includes multiple independent claims focusing on genetically engineered human primary cells for cancer treatment, involving specific genomic disruptions and expression of exogenous neoantigen-targeting receptors.
Engineered neoantigen-targeting primary cells with CIS-1 gene disruption
A method of treating cancer by administering ex vivo engineered human primary CD4+ T cells comprising an endonuclease-mediated genomic disruption (indel) within exon 2 or 3 of the cytokine inducible SH2-containing protein gene (CIS-1), suppressing CIS-1 protein expression, and expressing an exogenous functional neoantigen-targeting T cell receptor (TCR) or chimeric antigen receptor (CAR) specific for a neoantigen expressed by the cancer.
Genomic disruption of TCR alpha or beta loci in engineered cells
Engineered cell populations additionally comprising cells with genomic disruption in T Cell Receptor Alpha Constant (TRAC) or Beta Locus (TRB) genes, where exogenous neoantigen-targeting receptors are expressed from DNA integrated into the disrupted TCR gene loci.
Use of CRISPR-Cas9 for gene disruption and transgene integration
Genomic disruption is performed by Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) system, specifically using Cas9 protein to create double strand breaks facilitating insertion of exogenous neoantigen-targeting receptors.
Engineered cells include diverse immune cell populations
The engineered cell populations may further comprise CD8+ T cells, dendritic cells, B cells, natural killer (NK) cells, tumor infiltrating lymphocytes (TILs), or peripheral blood lymphocytes (PBLs), either autologous or allogeneic to the subject.
Exogenous neoantigen-targeting receptors introduced by viral vectors
Exogenous functional neoantigen targeting TCRs or CARs expressed from DNA molecules integrated into disrupted endogenous genes, which can be introduced into CD4+ T cells using viral vectors such as adeno-associated virus (AAV).
Treatment of various cancers using engineered cells
Methods for treating neoantigen-expressing cancers including gastrointestinal, breast, prostate cancers, bladder, bone, brain, esophageal, lung, ovarian, prostate, and multiple other cancer types by administration of engineered cells with CIS-1 disruption and exogenous neoantigen-targeting receptors.
The independent claims cover methods of treating cancer by administering human primary immune cells engineered ex vivo to disrupt CIS-1 and optionally TCR loci using CRISPR-Cas9, and expressing exogenous neoantigen-targeting TCRs or CARs. The claims specify the genomic disruptions, receptor expression, methods of gene editing, cell populations, delivery vectors, and cancers treated.
Stated Advantages
The method enables identification and targeting of unique immunogenic mutations in a patient's cancer for more effective immunotherapy.
Non-viral integration of TCR transgenes preserves physiologic and immunologic anti-tumor potency of engineered T cells.
Use of homologous recombination enhancers and toxicity-modulating compounds improves cell viability and efficiency of genomic editing.
The approach facilitates versatile engineering of various immune cell types, including autologous and allogeneic cells.
Targeting immune checkpoint genes like PD-1 and CIS-1 enhances therapeutic potential by suppressing inhibitory signaling pathways.
Compatibility with good manufacturing practices (GMP) enables scalable production of engineered cells for clinical use.
Documented Applications
Use of engineered cells expressing cancer-specific TCRs for adoptive cell therapy in treating various hematologic and solid tumors.
Treatment of neoantigen-expressing cancers including bladder, bone, brain, esophageal, gastrointestinal, liver, lung, ovarian, prostate, and other cancers using engineered T cells.
Application of engineered tumor infiltrating lymphocytes (TILs) and peripheral blood lymphocytes (PBLs) with genomic disruptions and exogenous receptor expression in immunotherapy.
Compositions and methods for reducing cellular toxicity during genomic engineering using modifying compounds to enhance viability and gene integration efficiency.
Interested in licensing this patent?