Combination of CRISPR/Cas9 System and CAR-T Cell Therapy: A New Era for Refractory and Relapsed Hematological Malignancies

Abstract

Chimeric antigen receptor T (CAR-T) cell therapy is the novel treatment strategy for hematological malignancies such as acute lymphoblastic leukemia (ALL), lymphoma and multiple myeloma. However, treatment-related toxicities such as cytokine release syndrome (CRS) and immune effector cell-associated neurotoxicity syndrome (ICANS) have become significant hurdles to CAR-T treatment. Multiple strategies were established to alter the CAR structure on the genomic level to improve efficacy and reduce toxicities. Recently, the innovative gene-editing technology–clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease9 (Cas9) system, which particularly exhibits preponderance in knock-in and knockout at specific sites, is widely utilized to manufacture CAR-T products. The application of CRISPR/Cas9 to CAR-T cell therapy has shown promising clinical results with minimal toxicity. In this review, we summarized the past achievements of CRISPR/Cas9 in CAR-T therapy and focused on the potential CAR-T targets.

Keywords

chimeric antigen receptor T cell treatment / clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease9 / gene editing / immunotherapy / hematologic malignancy

References

[1] WiedenheftB, SternbergSH, DoudnaJA. RNA-guided genetic silencing systems in bacteria and archaea. Nature, 2012, 482(7385): 331-338

[2] DeltchevaE, ChylinskiK, SharmaCM, et al.. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature, 2011, 471(7340): 602-607

[3] JinekM, ChylinskiK, FonfaraI, et al.. A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity. Science, 2012, 337(6096): 816-821

[4] DoudnaJA. The promise and challenge of therapeutic genome editing. Nature, 2020, 578(7794): 229-236

[5] MollanooriH, ShahrakiH, RahmatiY, et al.. CRISPR/Cas9 and CAR-T cell, collaboration of two revolutionary technologies in cancer immunotherapy, an instruction for successful cancer treatment. Hum Immunol, 2018, 79(12): 876-882

[6] ElsallabM, LevineBL, WayneAS, et al.. CAR T-cell product performance in haematological malignancies before and after marketing authorisation. Lancet Oncol, 2020, 21(2): e104-e116

[7] ReaganPM, FriedbergJW. Axicabtagene ciloleucel and brexucabtagene autoleucel in relapsed and refractory diffuse large B-cell and mantle cell lymphomas. Future Oncol, 2021, 17(11): 1269-1283

[8] AbramsonJS, PalombaML, GordonLI, et al.. Lisocabtagene maraleucel for patients with relapsed or refractory large B-cell lymphomas (TRANSCEND NHL 001): a multicentre seamless design study. Lancet, 2020, 396(10254): 839-852

[9] MunshiNC, AndersonLDJr., ShahN, et al.. Idecabtagene Vicleucel in Relapsed and Refractory Multiple Myeloma. N Engl J Med, 2021, 384(8): 705-716

[10] SinghAK, McguirkJP. CAR T cells: continuation in a revolution of immunotherapy. Lancet Oncol, 2020, 21(3): e168-e178

[11] KuwanaY, AsakuraY, UtsunomiyaN, et al.. Expression of chimeric receptor composed of immunoglobulin-derived V regions and T-cell receptor-derived C regions. Biochem Biophys Res Commun, 1987, 149(3): 960-968

[12] JuneCH, SadelainM. Chimeric Antigen Receptor Therapy. N Engl J Med, 2018, 379(1): 64-73

[13] GongMC, LatoucheJB, KrauseA, et al.. Cancer patient T cells genetically targeted to prostate-specific membrane antigen specifically lyse prostate cancer cells and release cytokines in response to prostate-specific membrane antigen. Neoplasia, 1999, 1(2): 123-127

[14] KershawMH, WestwoodJA, ParkerLL, et al.. A phase I study on adoptive immunotherapy using gene-modified T cells for ovarian cancer. Clin Cancer Res, 2006, 12(20): 6106-6115 Pt 1

[15] LamersCH, SleijferS, VultoAG, et al.. Treatment of metastatic renal cell carcinoma with autologous T-lymphocytes genetically retargeted against carbonic anhydrase IX: first clinical experience. J Clin Oncol, 2006, 24(13): e20-22

[16] TillBG, JensenMC, WangJ, et al.. Adoptive immunotherapy for indolent non-Hodgkin lymphoma and mantle cell lymphoma using genetically modified autologous CD20-specific T cells. Blood, 2008, 112(6): 2261-2271

[17] ImaiC, MiharaK, AndreanskyM, et al.. Chimeric receptors with 4-1BB signaling capacity provoke potent cytotoxicity against acute lymphoblastic leukemia. Leukemia, 2004, 18(4): 676-684

[18] GerstmayerB, HoffmannM, AltenschmidtU, et al.. Costimulation of T-cell proliferation by a chimeric B7-antibody fusion protein. Cancer Immunol Immunother, 1997, 45(3–4): 156-158

[19] SadelainM, BrentjensR, RivièreI. The basic principles of chimeric antigen receptor design. Cancer Discov, 2013, 3(4): 388-398

[20] HuangD, MillerM, AshokB, et al.. CRISPR/Cas systems to overcome challenges in developing the next generation of T cells for cancer therapy. Adv Drug Deliv Rev, 2020, 158: 17-35

[21] DepilSP, DuchateauS, GruppA, et al.. ‘Off-the-shelf’ allogeneic CAR T cells: development and challenges. Nat Rev Drug Discov, 2020, 19(3): 185-199

[22] RenJ, LiuC, FangC, et al.. Multiplex Genome Editing to Generate Universal CAR T Cells Resistant to PD1 Inhibition. Clin Cancer Res, 2017, 23(9): 2255-2266

[23] LiuX, ZhangY, ChengC, et al.. CRISPR-Cas9-mediated multiplex gene editing in CAR-T cells. Cell Res, 2017, 27(1): 154-157

[24] EyquemJ, Mansilla-sotoJ, GiavridisT, et al.. Targeting a CAR to the TRAC locus with CRISPR/Cas9 enhances tumour rejection. Nature, 2017, 543(7643): 113-117

[25] WiebkingV, LeeCM, MostrelN, et al.. Genome editing of donor-derived T-cells to generate allogenic chimeric antigen receptor-modified T cells: Optimizing αβ T cell-depleted haploidentical hematopoietic stem cell transplantation. Haematologica, 2021, 106(3): 847-858

[26] Mosti L, Langner LM, Chmielewski KO, et al. Targeted multi-epitope switching enables straightforward positive/negative selection of CAR T cells. Gene Ther, 2021. doi: https://doi.org/10.1038/s41434-021-00220-6

[27] RothTL, Puig-sausC, YuR, et al.. Reprogramming human T cell function and specificity with non-viral genome targeting. Nature, 2018, 559(7714): 405-409

[28] OdéZ, CondoriJ, PetersonN, et al.. CRISPR-Mediated Non-Viral Site-Specific Gene Integration and Expression in T Cells: Protocol and Application for T-Cell Therapy. Cancers (Basel), 2020, 12(6): 1704

[29] ZhaoY, SuH, ShenX, et al.. The immunological function of CD52 and its targeting in organ transplantation. Inflamm Res, 2017, 66(7): 571-578

[30] RowanWC, HaleG, TiteJP, et al.. Cross-linking of the CAMPATH-1 antigen (CD52) triggers activation of normal human T lymphocytes. Int Immunol, 1995, 7(1): 69-77

[31] PoirotL, PhilipB, Schiffer-manniouiC, et al.. Multiplex Genome-Edited T-cell Manufacturing Platform for “Off-the-Shelf” Adoptive T-cell Immunotherapies. Cancer Res, 2015, 75(18): 3853-3864

[32] QasimW, ZhanH, SamarasingheS, et al.. Molecular remission of infant B-ALL after infusion of universal TALEN gene-edited CAR T cells. Sci Transl Med, 2017, 9(374): eaaj2013

[33] HuY, ZhouY, ZhangM, et al.. CRISPR/Cas9-Engineered Universal CD19/CD22 Dual-Targeted CAR-T Cell Therapy for Relapsed/Refractory B-cell Acute Lymphoblastic Leukemia. Clin Cancer Res, 2021, 27(10): 2764-2772

[34] RabinovichGA, GabrilovichD, SotomayorEM. Immunosuppressive strategies that are mediated by tumor cells. Annu Rev Immunol, 2007, 25: 267-296

[35] SuS, ZouZ, ChenF, et al.. CRISPR-Cas9-mediated disruption of PD-1 on human T cells for adoptive cellular therapies of EBV positive gastric cancer. Oncoimmunology, 2017, 6(1): e1249558

[36] SuS, HuB, ShaoJ, et al.. CRISPR-Cas9 mediated efficient PD-1 disruption on human primary T cells from cancer patients. Sci Rep, 2016, 6: 20070

[37] RuppLJ, SchumannK, RoybalKT, et al.. CRISPR/Cas9-mediated PD-1 disruption enhances anti-tumor efficacy of human chimeric antigen receptor T cells. Sci Rep, 2017, 7(1): 737

[38] DaiX, ParkJJ, DuY, et al.. One-step generation of modular CAR-T cells with AAV-Cpf1. Nat Methods, 2019, 16(3): 247-254

[39] SchumannK, LinS, BoyerE, et al.. Generation of knock-in primary human T cells using Cas9 ribonucleoproteins. Proc Natl Acad Sci U S A, 2015, 112(33): 10 437-10 442

[40] HuB, ZouY, ZhangL, et al.. Nucleofection with Plasmid DNA for CRISPR/Cas9-Mediated Inactivation of Programmed Cell Death Protein 1 in CD133-Specific CAR T Cells. Hum Gene Ther, 2019, 30(4): 446-458

[41] StadtmauerEA, FraiettaJA, DavisMM, et al.. CRISPR-engineered T cells in patients with refractory cancer. Science, 2020, 367(6481): eaba7365

[42] ZhangY, ZhangX, ChengC, et al.. CRISPR-Cas9 mediated LAG-3 disruption in CAR-T cells. Front Med, 2017, 11(4): 554-562

[43] JungIY, KimYY, YuHS, et al.. CRISPR/Cas9-Mediated Knockout of DGK Improves Antitumor Activities of Human T Cells. Cancer Res, 2018, 78(16): 4692-4703

[44] RenJ, ZhangX, LiuX, et al.. A versatile system for rapid multiplex genome-edited CAR T cell generation. Oncotarget, 2017, 8(10): 17002-17011

[45] TangN, ChengC, ZhangX, et al.. TGF-β inhibition via CRISPR promotes the long-term efficacy of CAR T cells against solid tumors. JCI Insight, 2020, 5(4): e133977

[46] LiN, TangN, ChengC, et al.. Improving the anti-solid tumor efficacy of CAR-T cells by inhibiting adenosine signaling pathway. Oncoimmunology, 2020, 9(1): 1824643

[47] FraiettaJA, NoblesCL, SammonsMA, et al.. Disruption of TET2 promotes the therapeutic efficacy of CD19-targeted T cells. Nature, 2018, 558(7709): 307-312

[48] LiuX, RanganathanR, JiangS, et al.. A Chimeric Switch-Receptor Targeting PD1 Augments the Efficacy of Second-Generation CAR T Cells in Advanced Solid Tumors. Cancer Res, 2016, 76(6): 1578-1590

[49] SuarezER, ChangDK, SunJ, et al.. Chimeric antigen receptor T cells secreting anti-PD-L1 antibodies more effectively regress renal cell carcinoma in a humanized mouse model. Oncotarget, 2016, 7(23): 34 341-34 355

[50] YekuOO, PurdonTJ, KoneruM, et al.. Armored CAR T cells enhance antitumor efficacy and overcome the tumor microenvironment. Sci Rep, 2017, 7(1): 10541

[51] AvanziMP, YekuO, LiX, et al.. Engineered Tumor-Targeted T Cells Mediate Enhanced Anti-Tumor Efficacy Both Directly and through Activation of the Endogenous Immune System. Cell Rep, 2018, 23(7): 2130-2141

[52] HurtonLV, SinghH, NajjarAM, et al.. Tethered IL-15 augments antitumor activity and promotes a stem-cell memory subset in tumor-specific T cells. Proc Natl Acad Sci U S A, 2016, 113(48): e7788-e7797

[53] AdachiK, KanoY, NagaiT, et al.. IL-7 and CCL19 expression in CAR-T cells improves immune cell infiltration and CAR-T cell survival in the tumor. Nat Biotechnol, 2018, 36(4): 346-351

[54] BoiceM, SalloumD, MourcinF, et al.. Loss of the HVEM Tumor Suppressor in Lymphoma and Restoration by Modified CAR-T Cells. Cell, 2016, 167(2): 405-418.e413

[55] KuhnNF, PurdonTJ, Van LeeuwenDG, et al.. CD40 Ligand-Modified Chimeric Antigen Receptor T Cells Enhance Antitumor Function by Eliciting an Endogenous Antitumor Response. Cancer Cell, 2019, 35(3): 473-488.e476

[56] LynnRC, WeberEW, SotilloE, et al.. c-Jun overexpression in CAR T cells induces exhaustion resistance. Nature, 2019, 576(7786): 293-300

[57] ChenJ, López-moyadoIF, SeoH, et al.. NR4A transcription factors limit CAR T cell function in solid tumours. Nature, 2019, 567(7749): 530-534

[58] SeoH, ChenJ, González-avalosE, et al.. TOX and TOX2 transcription factors cooperate with NR4A transcription factors to impose CD8(+) T cell exhaustion. Proc Natl Acad Sci USA, 2019, 116(25): 12 410-12 415

[59] NeelapuSS, TummalaS, KebriaeiP, et al.. Chimeric antigen receptor T-cell therapy—assessment and management of toxicities. Nat Rev Clin Oncol, 2018, 15(1): 47-62

[60] SternerRM, SakemuraR, CoxMJ, et al.. GM-CSF inhibition reduces cytokine release syndrome and neuroinflammation but enhances CAR-T cell function in xenografts. Blood, 2019, 133(7): 697-709

[61] HoyosV, SavoldoB, QuintarelliC, et al.. Engineering CD19-specific T lymphocytes with interleukin-15 and a suicide gene to enhance their anti-lymphoma/leukemia effects and safety. Leukemia, 2010, 24(6): 1160-1170

[62] DiaconuI, BallardB, ZhangM, et al.. Inducible Caspase-9 Selectively Modulates the Toxicities of CD19-Specific Chimeric Antigen Receptor-Modified T Cells. Mol Ther, 2017, 25(3): 580-592

[63] Gomes-silvaD, SrinivasanM, SharmaS, et al.. CD7-edited T cells expressing a CD7-specific CAR for the therapy of T-cell malignancies. Blood, 2017, 130(3): 285-296

[64] CooperML, ChoiJ, StaserK, et al.. An “off-the-shelf” fratricide-resistant CAR-T for the treatment of T cell hematologic malignancies. Leukemia, 2018, 32(9): 1970-1983

[65] RaikarSS, FleischerLC, MootR, et al.. Development of chimeric antigen receptors targeting T-cell malignancies using two structurally different anti-CD5 antigen binding domains in NK and CRISPR-edited T cell lines. Oncoimmunology, 2018, 7(3): e1407898

[66] ChoSW, KimS, KimY, et al.. Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res, 2014, 24(1): 132-141

[67] FuY, SanderJD, ReyonD, et al.. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol, 2014, 32(3): 279-284

[68] CromwellCR, SungK, ParkJ, et al.. Incorporation of bridged nucleic acids into CRISPR RNAs improves Cas9 endonuclease specificity. Nat Commun, 2018, 9(1): 1448

[69] KleinstiverBP, PattanayakV, PrewMS, et al.. High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature, 2016, 529(7587): 490-495

[70] SlaymakerIM, GaoL, ZetscheB, et al.. Rationally engineered Cas9 nucleases with improved specificity. Science, 2016, 351(6268): 84-88

[71] ChenJS, DagdasYS, KleinstiverBP, et al.. Enhanced proofreading governs CRISPR-Cas9 targeting accuracy. Nature, 2017, 550(7676): 407-410

[72] FuBX, HansenLL, ArtilesKL, et al.. Landscape of target:guide homology effects on Cas9-mediated cleavage. Nucleic Acids Res, 2014, 42(22): 13 778-13 787

[73] HaapaniemiE, BotlaS, PerssonJ, et al.. CRISPR-Cas9 genome editing induces a p53-mediated DNA damage response. Nat Med, 2018, 24(7): 927-930

[74] BrandénLJ, MohamedAJ, SmithCI. A peptide nucleic acid-nuclear localization signal fusion that mediates nuclear transport of DNA. Nat Biotechnol, 1999, 17(8): 784-787

[75] WangHX, SongZ, LaoYH, et al.. Nonviral gene editing via CRISPR/Cas9 delivery by membrane-disruptive and endosomolytic helical polypeptide. Proc Natl Acad Sci USA, 2018, 115(19): 4903-4908

[76] HemmiH, TakeuchiO, KawaiT, et al.. A Toll-like receptor recognizes bacterial DNA. Nature, 2000, 408(6813): 740-745

[77] CrudeleJM, ChamberlainJS. Cas9 immunity creates challenges for CRISPR gene editing therapies. Nat Commun, 2018, 9(1): 3497

[78] MendellJR, Al-zaidyS, ShellR, et al.. Single-Dose Gene-Replacement Therapy for Spinal Muscular Atrophy. N Engl J Med, 2017, 377(18): 1713-1722

[79] GhaemiA, BagherI E, AbnousK, et al.. CRISPR-cas9 genome editing delivery systems for targeted cancer therapy. Life Sci, 2021, 267: 118969

[80] Salas-mckeeJ, KongW, GladneyWL, et al.. CRISPR/Cas9-based genome editing in the era of CAR T cell immunotherapy. Hum Vaccin Immunother, 2019, 15(5): 1126-1132

[81] Agarwal S, Wellhausen N, Levine BL, et al. Production of Human CRISPR-Engineered CAR-T Cells. J Vis Exp, 2021,169. doi: https://doi.org/10.3791/62299

[82] ShifrutE, CarnevaleJ, TobinV, et al.. Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function. Cell, 2018, 175(7): 1958-1971.e1915

[83] HinterleitnerR, GruberT, Pfeifhofer-obermairC, et al.. Adoptive transfer of siRNA Cblb-silenced CD8+ T lymphocytes augments tumor vaccine efficacy in a B16 melanoma model. PLoS One, 2012, 7(9): e44295

[84] LiauNPD, LaktyushinA, LucetIS, et al.. The molecular basis of JAK/STAT inhibition by SOCS1. Nat Commun, 2018, 9(1): 1558

[85] WangD, PragerBC, GimpleRC, et al.. CRISPR Screening of CAR T Cells and Cancer Stem Cells Reveals Critical Dependencies for Cell-Based Therapies. Cancer Discov, 2020, 11(5): 1192-1211

[86] SchmidtsA, MarshLC, SrivastavaAA, et al.. Cell-based artificial APC resistant to lentiviral transduction for efficient generation of CAR-T cells from various cell sources. J Immunother Cancer, 2020, 8(2): e000990

[87] TahmasebiS, ElahiR, KhoshE, et al.. Programmable and multi-targeted CARs: a new breakthrough in cancer CAR-T cell therapy. Clin Transl Oncol, 2021, 23(6): 1003-1019

[88] Hou AJ, Chen LC, Chen YY. Navigating CAR-T cells through the solid-tumour microenvironment. Nat Rev Drug Discov, 2021. doi: https://doi.org/10.1038/s41573-021-00189-2