Non-viral precision T cell receptor replacement for personalized cell therapy.
Humans
Antigens, Neoplasm
/ genetics
Biopsy
Cell- and Tissue-Based Therapy
/ adverse effects
Cytokine Release Syndrome
/ complications
Disease Progression
Encephalitis
/ complications
Gene Editing
Gene Knock-In Techniques
Gene Knockout Techniques
Genes, T-Cell Receptor alpha
Genes, T-Cell Receptor beta
Mutation
Neoplasms
/ complications
Patient Safety
Precision Medicine
/ adverse effects
Receptors, Antigen, T-Cell
/ genetics
T-Lymphocytes
/ immunology
Transgenes
/ genetics
HLA Antigens
/ immunology
CRISPR-Cas Systems
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
03 2023
03 2023
Historique:
received:
16
06
2022
accepted:
04
11
2022
pubmed:
11
11
2022
medline:
25
3
2023
entrez:
10
11
2022
Statut:
ppublish
Résumé
T cell receptors (TCRs) enable T cells to specifically recognize mutations in cancer cells
Identifiants
pubmed: 36356599
doi: 10.1038/s41586-022-05531-1
pii: 10.1038/s41586-022-05531-1
pmc: PMC9768791
doi:
Substances chimiques
Antigens, Neoplasm
0
Receptors, Antigen, T-Cell
0
HLA Antigens
0
Banques de données
ClinicalTrials.gov
['NCT03970382']
Types de publication
Clinical Trial, Phase I
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
687-696Subventions
Organisme : NIAID NIH HHS
ID : K08 AI139375
Pays : United States
Organisme : NCI NIH HHS
ID : P01 CA244118
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA008748
Pays : United States
Organisme : NCI NIH HHS
ID : R35 CA197633
Pays : United States
Organisme : NCI NIH HHS
ID : T32 CA009120
Pays : United States
Commentaires et corrections
Type : CommentIn
Type : CommentIn
Informations de copyright
© 2022. The Author(s).
Références
Matsushita, H. et al. Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting. Nature 482, 400–404 (2012).
pubmed: 22318521
pmcid: 3874809
doi: 10.1038/nature10755
van Rooij, N. et al. Tumor exome analysis reveals neoantigen-specific T-cell reactivity in an ipilimumab-responsive melanoma. J. Clin. Oncol. 31, e439–e442 (2013).
pubmed: 24043743
doi: 10.1200/JCO.2012.47.7521
Schumacher, T. N. & Schreiber, R. D. Neoantigens in cancer immunotherapy. Science 348, 69–74 (2015).
pubmed: 25838375
doi: 10.1126/science.aaa4971
Gros, A. et al. Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients. Nat. Med. 22, 433–438 (2016).
pubmed: 26901407
pmcid: 7446107
doi: 10.1038/nm.4051
Tran, E. et al. Cancer immunotherapy based on mutation-specific CD4
pubmed: 24812403
pmcid: 6686185
doi: 10.1126/science.1251102
Sahin, U. et al. Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer. Nature 547, 222–226 (2017).
pubmed: 28678784
doi: 10.1038/nature23003
Sahin, U. & Tureci, O. Personalized vaccines for cancer immunotherapy. Science 359, 1355–1360 (2018).
pubmed: 29567706
doi: 10.1126/science.aar7112
Hu, Z. et al. Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in patients with melanoma. Nat. Med. 27, 515–525 (2021).
pubmed: 33479501
pmcid: 8273876
doi: 10.1038/s41591-020-01206-4
Lowery, F. J. et al. Molecular signatures of antitumor neoantigen-reactive T cells from metastatic human cancers. Science https://doi.org/10.1126/science.abl5447 (2022).
Ott, P. A. et al. An immunogenic personal neoantigen vaccine for patients with melanoma. Nature 547, 217–221 (2017).
pubmed: 28678778
pmcid: 5577644
doi: 10.1038/nature22991
Robinson, J. et al. The IPD and IMGT/HLA database: allele variant databases. Nucleic Acids Res. 43, D423–D431 (2015).
pubmed: 25414341
doi: 10.1093/nar/gku1161
Greenbaum, U., Dumbrava, E. I., Biter, A. B., Haymaker, C. L. & Hong, D. S. Engineered T-cell receptor T cells for cancer immunotherapy. Cancer Immunol. Res. 9, 1252–1261 (2021).
pubmed: 34728535
doi: 10.1158/2326-6066.CIR-21-0269
Peng, S. et al. Sensitive detection and analysis of neoantigen-specific T cell populations from tumors and blood. Cell Rep. 28, 2728–2738.e7 (2019).
pubmed: 31484081
pmcid: 6774618
doi: 10.1016/j.celrep.2019.07.106
Rosenberg, S. A., Restifo, N. P., Yang, J. C., Morgan, R. A. & Dudley, M. E. Adoptive cell transfer: a clinical path to effective cancer immunotherapy. Nat. Rev. Cancer 8, 299–308 (2008).
pubmed: 18354418
pmcid: 2553205
doi: 10.1038/nrc2355
Roth, T. L. et al. Reprogramming human T cell function and specificity with non-viral genome targeting. Nature 559, 405–409 (2018).
pubmed: 29995861
pmcid: 6239417
doi: 10.1038/s41586-018-0326-5
Oh, S. A. et al. High-efficiency nonviral CRISPR/Cas9-mediated gene editing of human T cells using plasmid donor DNA. J. Exp. Med. 219, e20211530 (2022).
pubmed: 35452075
pmcid: 9040063
doi: 10.1084/jem.20211530
Eyquem, J. et al. Targeting a CAR to the TRAC locus with CRISPR/Cas9 enhances tumour rejection. Nature 543, 113–117 (2017).
pubmed: 28225754
pmcid: 5558614
doi: 10.1038/nature21405
Muller, T. R. et al. Targeted T cell receptor gene editing provides predictable T cell product function for immunotherapy. Cell Rep. Med. 2, 100374 (2021).
pubmed: 34467251
pmcid: 8385324
doi: 10.1016/j.xcrm.2021.100374
Ruggiero, E. et al. CRISPR-based gene disruption and integration of high-avidity, WT1-specific T cell receptors improve antitumor T cell function. Sci. Transl Med. 14, eabg8027 (2022).
pubmed: 35138911
doi: 10.1126/scitranslmed.abg8027
Puig-Saus, C. et al. Landscape analysis of neoepitope-specific T cell responses to immunotherapy. Cancer Res. https://doi.org/10.1158/1538-7445.AM2020-NG11 (2020).
Johnson, L. A. et al. Gene therapy with human and mouse T-cell receptors mediates cancer regression and targets normal tissues expressing cognate antigen. Blood 114, 535–546 (2009).
pubmed: 19451549
pmcid: 2929689
doi: 10.1182/blood-2009-03-211714
Robbins, P. F. et al. Tumor regression in patients with metastatic synovial cell sarcoma and melanoma using genetically engineered lymphocytes reactive with NY-ESO-1. J. Clin. Oncol. 29, 917–924 (2011).
pubmed: 21282551
pmcid: 3068063
doi: 10.1200/JCO.2010.32.2537
Tran, E. et al. T-cell transfer therapy targeting mutant KRAS in cancer. N. Engl. J. Med. 375, 2255–2262 (2016).
pubmed: 27959684
pmcid: 5178827
doi: 10.1056/NEJMoa1609279
Malekzadeh, P. et al. Neoantigen screening identifies broad TP53 mutant immunogenicity in patients with epithelial cancers. J. Clin. Invest. 129, 1109–1114 (2019).
pubmed: 30714987
doi: 10.1172/JCI123791
Jin, B. Y. et al. Engineered T cells targeting E7 mediate regression of human papillomavirus cancers in a murine model. JCI Insight 3, e99488 (2018).
pubmed: 29669936
pmcid: 5931134
doi: 10.1172/jci.insight.99488
Sanderson, J. P. et al. Preclinical evaluation of an affinity-enhanced MAGE-A4-specific T-cell receptor for adoptive T-cell therapy. Oncoimmunology 9, 1682381 (2020).
pubmed: 32002290
doi: 10.1080/2162402X.2019.1682381
Draper, L. M. et al. Targeting of HPV-16
pubmed: 26429982
pmcid: 4603283
doi: 10.1158/1078-0432.CCR-14-3341
Poirot, L. et al. Multiplex genome-edited T-cell manufacturing platform for “off-the-shelf” adoptive T-cell immunotherapies. Cancer Res. 75, 3853–3864 (2015).
pubmed: 26183927
doi: 10.1158/0008-5472.CAN-14-3321
Stadtmauer, E. A. et al. CRISPR-engineered T cells in patients with refractory cancer. Science 367, eaba7365 (2020).
pubmed: 32029687
doi: 10.1126/science.aba7365
Mujib, S. et al. Antigen-independent induction of Tim-3 expression on human T cells by the common γ-chain cytokines IL-2, IL-7, IL-15, and IL-21 is associated with proliferation and is dependent on the phosphoinositide 3-kinase pathway. J. Immunol. 188, 3745–3756 (2012).
pubmed: 22422881
doi: 10.4049/jimmunol.1102609
Shevchenko, I. et al. Enhanced expression of CD39 and CD73 on T cells in the regulation of anti-tumor immune responses. Oncoimmunology 9, 1744946 (2020).
pubmed: 33457090
pmcid: 7790505
doi: 10.1080/2162402X.2020.1744946
Teachey, D. T. et al. Identification of predictive biomarkers for cytokine release syndrome after chimeric antigen receptor T-cell therapy for acute lymphoblastic leukemia. Cancer Discov. 6, 664–679 (2016).
pubmed: 27076371
pmcid: 5448406
doi: 10.1158/2159-8290.CD-16-0040
Wang, M. et al. KTE-X19 CAR T-cell therapy in relapsed or refractory mantle-cell lymphoma. N. Engl. J. Med. 382, 1331–1342 (2020).
pubmed: 32242358
pmcid: 7731441
doi: 10.1056/NEJMoa1914347
Venkatesan, S. et al. Perspective: APOBEC mutagenesis in drug resistance and immune escape in HIV and cancer evolution. Ann. Oncol. 29, 563–572 (2018).
pubmed: 29324969
pmcid: 5888943
doi: 10.1093/annonc/mdy003
Zhang, J. et al. Non-viral, specifically targeted CAR-T cells achieve high safety and efficacy in B-NHL. Nature 609, 369–374 (2022).
pubmed: 36045296
pmcid: 9452296
doi: 10.1038/s41586-022-05140-y
Swanton, C., McGranahan, N., Starrett, G. J. & Harris, R. S. APOBEC enzymes: mutagenic fuel for cancer evolution and heterogeneity. Cancer Discov. 5, 704–712 (2015).
pubmed: 26091828
pmcid: 4497973
doi: 10.1158/2159-8290.CD-15-0344
McGranahan, N. et al. Allele-specific HLA loss and immune escape in lung cancer evolution. Cell 171, 1259–1271.e11 (2017).
pubmed: 29107330
pmcid: 5720478
doi: 10.1016/j.cell.2017.10.001
Doran, S. L. et al. T-cell receptor gene therapy for human papillomavirus-associated epithelial cancers: a first-in-human, phase I/II study. J. Clin. Oncol. 37, 2759–2768 (2019).
pubmed: 31408414
pmcid: 6800280
doi: 10.1200/JCO.18.02424
Nagarsheth, N. B. et al. TCR-engineered T cells targeting E7 for patients with metastatic HPV-associated epithelial cancers. Nat. Med. 27, 419–425 (2021).
pubmed: 33558725
pmcid: 9620481
doi: 10.1038/s41591-020-01225-1
Kalbasi, A. & Ribas, A. Tumour-intrinsic resistance to immune checkpoint blockade. Nat. Rev. Immunol. 20, 25–39 (2020).
pubmed: 31570880
doi: 10.1038/s41577-019-0218-4
Schober, K. et al. Reverse TCR repertoire evolution toward dominant low-affinity clones during chronic CMV infection. Nat. Immunol. 21, 434–441 (2020).
pubmed: 32205883
doi: 10.1038/s41590-020-0628-2
Wermke, M. et al. Safety and anti-tumor activity of TCR-engineered autologous, PRAME-directed T cells across multiple advanced solid cancers at low doses—clinical update on the ACTengine® IMA203 trial. J. Immunother. Cancer https://doi.org/10.1136/jitc-2021-SITC2021.959 (2021).
Hong, D. S. et al.Updated safety and efficacy from SURPASS, the phase I trial of ADP-A2M4CD8, a next-generation autologous T-cell receptor T-cell therapy, in previously treated patients with unresectable or metastatic tumors. Ann. Oncol. 33, S331–S355 (2022).
doi: 10.1016/j.annonc.2022.07.861
Provasi, E. et al. Editing T cell specificity towards leukemia by zinc finger nucleases and lentiviral gene transfer. Nat. Med. 18, 807–815 (2012).
pubmed: 22466705
pmcid: 5019824
doi: 10.1038/nm.2700
Fraietta, J. A. et al. Disruption of TET2 promotes the therapeutic efficacy of CD19-targeted T cells. Nature 558, 307–312 (2018).
pubmed: 29849141
pmcid: 6320248
doi: 10.1038/s41586-018-0178-z
Sen, D. R. et al. The epigenetic landscape of T cell exhaustion. Science 354, 1165–1169 (2016).
pubmed: 27789799
pmcid: 5497589
doi: 10.1126/science.aae0491
Li, M. O., Wan, Y. Y., Sanjabi, S., Robertson, A. K. & Flavell, R. A. Transforming growth factor-β regulation of immune responses. Annu. Rev. Immunol. 24, 99–146 (2006).
pubmed: 16551245
doi: 10.1146/annurev.immunol.24.021605.090737
Schmidt, R. et al. CRISPR activation and interference screens decode stimulation responses in primary human T cells. Science 375, eabj4008 (2022).
pubmed: 35113687
pmcid: 9307090
doi: 10.1126/science.abj4008
Kalbasi, A. et al. Potentiating adoptive cell therapy using synthetic IL-9 receptors. Nature 607, 360–365 (2022).
pubmed: 35676488
pmcid: 9283313
doi: 10.1038/s41586-022-04801-2
Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://doi.org/10.48550/arXiv.1303.3997 (2013).
Koboldt, D. C. et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 22, 568–576 (2012).
pubmed: 22300766
pmcid: 3290792
doi: 10.1101/gr.129684.111
Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat. Biotechnol. 31, 213–219 (2013).
pubmed: 23396013
pmcid: 3833702
doi: 10.1038/nbt.2514
Saunders, C. T. et al. Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics 28, 1811–1817 (2012).
pubmed: 22581179
doi: 10.1093/bioinformatics/bts271
Lai, Z. et al. VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research. Nucleic Acids Res. 44, e108 (2016).
pubmed: 27060149
pmcid: 4914105
doi: 10.1093/nar/gkw227
Dobin, A. & Gingeras, T. R. Mapping RNA-seq reads with STAR. Curr. Protoc Bioinformatics 51, 11.14.1–11.14.19 (2015).
pubmed: 26334920
doi: 10.1002/0471250953.bi1114s51
Szolek, A. et al. OptiType: precision HLA typing from next-generation sequencing data. Bioinformatics 30, 3310–3316 (2014).
pubmed: 25143287
pmcid: 4441069
doi: 10.1093/bioinformatics/btu548
Reynisson, B., Alvarez, B., Paul, S., Peters, B. & Nielsen, M. NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data. Nucleic Acids Res. 48, W449–W454 (2020).
pubmed: 32406916
pmcid: 7319546
doi: 10.1093/nar/gkaa379
Favero, F. et al. Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data. Ann. Oncol. 26, 64–70 (2015).
pubmed: 25319062
doi: 10.1093/annonc/mdu479
Roth, A. et al. PyClone: statistical inference of clonal population structure in cancer. Nat. Methods 11, 396–398 (2014).
pubmed: 24633410
pmcid: 4864026
doi: 10.1038/nmeth.2883
Chang, M. T. et al. Accelerating discovery of functional mutant alleles in cancer. Cancer Discov. 8, 174–183 (2018).
pubmed: 29247016
doi: 10.1158/2159-8290.CD-17-0321
Power, R. P. et al. A diagnostic platform for precision cancer therapy enabling composite biomarkers by combining tumor and immune features from an enhanced exome and transcriptome. Cancer Res. 80, 1334 (2020).
doi: 10.1158/1538-7445.AM2020-1334
Bolotin, D. A. et al. MiXCR: software for comprehensive adaptive immunity profiling. Nat. Methods 12, 380–381 (2015).
pubmed: 25924071
doi: 10.1038/nmeth.3364
Diaz-Gay, M. et al. Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples. BMC Bioinformatics 19, 224 (2018).
pubmed: 29898651
pmcid: 6001047
doi: 10.1186/s12859-018-2234-y
Alexandrov, L. B. et al. The repertoire of mutational signatures in human cancer. Nature 578, 94–101 (2020).
pubmed: 32025018
pmcid: 7054213
doi: 10.1038/s41586-020-1943-3
Smith, C., Ma, Y., Campbell, K. M., Pan, Z. & Stawiski, E. Uncovering HLA loss of heterozygosity in cancer for the improvement of personalized neoTCR immunotherapy with PACT-ESCAPE. Cancer Res. https://doi.org/10.1158/1538-7445.AM2022-1213 (2022).
Robinson, J. et al. IPD-IMGT/HLA database. Nucleic Acids Res. 48, D948–D955 (2020).
pubmed: 31667505
Bratman, S. V. et al. Personalized circulating tumor DNA analysis as a predictive biomarker in solid tumor patients treated with pembrolizumab. Nat. Cancer 1, 873–881 (2020).
pubmed: 35121950
doi: 10.1038/s43018-020-0096-5
Lybarger, L. et al. Enhanced immune presentation of a single-chain major histocompatibility complex class I molecule engineered to optimize linkage of a C-terminally extended peptide. J. Biol. Chem. 278, 27105–27111 (2003).
pubmed: 12732632
doi: 10.1074/jbc.M303716200
Lefranc, M. P. et al. IMGT®, the international ImMunoGeneTics information system® 25 years on. Nucleic Acids Res. 43, D413–D422 (2015).
pubmed: 25378316
doi: 10.1093/nar/gku1056
Bethune, M. T., Comin-Anduix, B., Hwang Fu, Y. H., Ribas, A. & Baltimore, D. Preparation of peptide–MHC and T-cell receptor dextramers by biotinylated dextran doping. BioTechniques 62, 123–130 (2017).
pubmed: 28298179
doi: 10.2144/000114525