A dormant TIL phenotype defines non-small cell lung carcinomas sensitive to immune checkpoint blockers
S N Gettinger, J Choi, N Mani, M F Sanmamed, I Datar, Ryan Sowell, Victor Y Du, E Kaftan, S Goldberg, W Dong, D Zelterman, K Politi, P Kavathas, S Kaech, X Yu, H Zhao, J Schlessinger, R Lifton, D L Rimm, L Chen, R S Herbst, K A Schalper, S N Gettinger, J Choi, N Mani, M F Sanmamed, I Datar, Ryan Sowell, Victor Y Du, E Kaftan, S Goldberg, W Dong, D Zelterman, K Politi, P Kavathas, S Kaech, X Yu, H Zhao, J Schlessinger, R Lifton, D L Rimm, L Chen, R S Herbst, K A Schalper
Abstract
The biological determinants of sensitivity and resistance to immune checkpoint blockers are not completely understood. To elucidate the role of intratumoral T-cells and their association with the tumor genomic landscape, we perform paired whole exome DNA sequencing and multiplexed quantitative immunofluorescence (QIF) in pre-treatment samples from non-small cell lung carcinoma (NSCLC) patients treated with PD-1 axis blockers. QIF is used to simultaneously measure the level of CD3+ tumor infiltrating lymphocytes (TILs), in situ T-cell proliferation (Ki-67 in CD3) and effector capacity (Granzyme-B in CD3). Elevated mutational load, candidate class-I neoantigens or intratumoral CD3 signal are significantly associated with favorable response to therapy. Additionally, a "dormant" TIL signature is associated with survival benefit in patients treated with immune checkpoint blockers characterized by elevated TILs with low activation and proliferation. We further demonstrate that dormant TILs can be reinvigorated upon PD-1 blockade in a patient-derived xenograft model.
Conflict of interest statement
In the last 12 months Dr. Kurt Schalper has been speaker or consultant for Merck, Takeda Pharmaceuticals, Shattuck Labs and Celgene. His laboratory has received research funding from Vasculox/Tioma, Navigate Biopharma, Tesaro Inc, Onkaido Therapeutics/Moderna, Takeda Pharmaceuticals and Surface Oncology. Dr. David Rimm is consultant or advisor to AstraZeneca, Agendia, Agilent, Biocept, Bristo-Myers-Squibb, Cell Signaling Technology. Cepheid, Merck, Optrascan, Perkinelmer and Ultivue. His laboratory has received research funding from AstraZeneca, Cepheid, Navigate/Novartis, NextCure, Gilead Sciences, Ultivue and Perkinelmer. Dr. Rimm also holds equity in PixelGear. Dr. Katerina Politi serves as consultant or advisor for AstraZeneca, Merck, Novartis and Tocagen. Her laboratory received research funds from AstraZeneca, Roche, Kolltan and Symphogen. Dr. Politi also holds royalties in IP licenced from Memorial Sloan Kettering Cancer Center to Molecular MD. Dr. Sarah Goldberg serves as consultant or advisor for AstraZeneca, Bristol-Myers Squibb, Lilly and Boehringer Ingelheim. She received research support from AstraZeneca. Lieping Chen serves as consultant or advisor for Pfizer, Vcanbio and GenomiCare. He is a scientific founder of NextCure and Tayu Biotech. His laboratory receives research funding from NextCure. The remaining authors declare no competing interests. with the content of this work.
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References
- Herbst RS, et al. Predictive correlates of response to the anti-PD-L1 antibody MPDL3280A in cancer patients. Nature. 2014;515:563–567. doi: 10.1038/nature14011.
- Borghaei H, et al. Nivolumab versus docetaxel in advanced nonsquamous non-small-cell lung cancer. N. Engl. J. Med. 2015;373:1627–1639. doi: 10.1056/NEJMoa1507643.
- Garon EB, et al. Pembrolizumab for the treatment of non-small-cell lung cancer. N. Engl. J. Med. 2015;372:2018–2028. doi: 10.1056/NEJMoa1501824.
- Herbst RS, et al. Pembrolizumab versus docetaxel for previously treated, PD-L1-positive, advanced non-small-cell lung cancer (KEYNOTE-010): a randomised controlled trial. Lancet. 2016;387:1540–1550. doi: 10.1016/S0140-6736(15)01281-7.
- Wolchok JD, et al. Nivolumab plus ipilimumab in advanced melanoma. N. Engl. J. Med. 2013;369:122–133. doi: 10.1056/NEJMoa1302369.
- Postow MA, et al. Nivolumab and ipilimumab versus ipilimumab in untreated melanoma. N. Engl. J. Med. 2015;372:2006–2017. doi: 10.1056/NEJMoa1414428.
- Larkin J, et al. Combined Nivolumab and Ipilimumab or Monotherapy in Untreated Melanoma. N. Engl. J. Med. 2015;373:23–34. doi: 10.1056/NEJMoa1504030.
- Antonia S, et al. Safety and antitumour activity of durvalumab plus tremelimumab in non-small cell lung cancer: a multicentre, phase 1b study. Lancet Oncol. 2016;17:299–308. doi: 10.1016/S1470-2045(15)00544-6.
- Velcheti V, et al. Programmed death ligand-1 expression in non-small cell lung cancer. Lab. Invest. 2014;94:107–116. doi: 10.1038/labinvest.2013.130.
- Taube JM, et al. Colocalization of inflammatory response with B7-h1 expression in human melanocytic lesions supports an adaptive resistance mechanism of immune escape. Sci. Transl. Med. 2012;4:127ra37. doi: 10.1126/scitranslmed.3003689.
- Tumeh PC, et al. PD-1 blockade induces responses by inhibiting adaptive immune resistance. Nature. 2014;515:568–571. doi: 10.1038/nature13954.
- Le DT, et al. PD-1 blockade in tumors with mismatch-repair deficiency. N. Engl. J. Med. 2015;372:2509–2520. doi: 10.1056/NEJMoa1500596.
- Rizvi NA, et al. Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science. 2015;348:124–128. doi: 10.1126/science.aaa1348.
- Hugo W, et al. Genomic and transcriptomic features of response to anti-PD-1 Therapy in metastatic melanoma. Cell. 2015;165:35–44. doi: 10.1016/j.cell.2016.02.065.
- Riaz N, et al. The role of neoantigens in response to immune checkpoint blockade. Int. Immunol. 2016;28:411–419. doi: 10.1093/intimm/dxw019.
- Snyder A, et al. Genetic basis for clinical response to CTLA-4 blockade in melanoma. N. Engl. J. Med. 2014;371:2189–2199. doi: 10.1056/NEJMoa1406498.
- Van Allen EM, et al. Genomic correlates of response to CTLA-4 blockade in metastatic melanoma. Science. 2015;350:207–211. doi: 10.1126/science.aad0095.
- McGranahan N, et al. Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade. Science. 2016;351:1463–1469. doi: 10.1126/science.aaf1490.
- Linnemann C, et al. High-throughput epitope discovery reveals frequent recognition of neo-antigens by CD4+ T cells in human melanoma. Nat. Med. 2015;21:81–85. doi: 10.1038/nm.3773.
- Tran E, et al. Immunogenicity of somatic mutations in human gastrointestinal cancers. Science. 2015;350:1387–1390. doi: 10.1126/science.aad1253.
- Gros A, et al. Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients. Nat. Med. 2016;22:433–438. doi: 10.1038/nm.4051.
- Motzer RJ, et al. Nivolumab versus everolimus in advanced renal-cell carcinoma. N. Engl. J. Med. 2015;373:1803–1813. doi: 10.1056/NEJMoa1510665.
- Rooney MS, Shukla SA, Wu CJ, Getz G, Hacohen N. Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell. 2015;160:48–61. doi: 10.1016/j.cell.2014.12.033.
- Alexandrov LB, et al. Signatures of mutational processes in human cancer. Nature. 2013;500:415–421. doi: 10.1038/nature12477.
- Calis JJ, et al. Properties of MHC class I presented peptides that enhance immunogenicity. PLoS Comput. Biol. 2013;9:e1003266. doi: 10.1371/journal.pcbi.1003266.
- van der Bruggen P, et al. A gene encoding an antigen recognized by cytolytic T lymphocytes on a human melanoma. Science. 1991;254:1643–1647. doi: 10.1126/science.1840703.
- Zarling AL, et al. Identification of class I MHC-associated phosphopeptides as targets for cancer immunotherapy. Proc. Natl Acad. Sci. USA. 2006;103:14889–14894. doi: 10.1073/pnas.0604045103.
- Cobbold M, et al. MHC class I-associated phosphopeptides are the targets of memory-like immunity in leukemia. Sci. Transl. Med. 2013;5:203ra125. doi: 10.1126/scitranslmed.3006061.
- Kumai T, et al. Induction of tumor-reactive T helper responses by a posttranslational modified epitope from tumor protein p53. Cancer Immunol. Immunother. 2014;63:469–p478. doi: 10.1007/s00262-014-1533-z.
- Brentville VA, et al. Citrullinated vimentin presented on MHC-II in tumor cells is a target for CD4+ T-cell-mediated antitumor immunity. Cancer Res. 2016;76:548–560. doi: 10.1158/0008-5472.CAN-15-1085.
- Rosenberg JE, et al. Atezolizumab in patients with locally advanced and metastatic urothelial carcinoma who have progressed following treatment with platinum-based chemotherapy: a single-arm, multicentre, phase 2 trial. Lancet. 2016;387:1909–1920. doi: 10.1016/S0140-6736(16)00561-4.
- Raulet DH, Guerra N. Oncogenic stress sensed by the immune system: role of natural killer cell receptors. Nat. Rev. Immunol. 2009;9:568–580. doi: 10.1038/nri2604.
- Härtlova A, et al. DNA damage primes the type I interferon system via the cytosolic DNA sensor STING to promote anti-microbial innate immunity. Immunity. 2015;42:332–343. doi: 10.1016/j.immuni.2015.01.012.
- Giannakis M, et al. Genomic correlates of immune-cell infiltrates in colorectal carcinoma. Cell Rep. 2016;17:1206. doi: 10.1016/j.celrep.2016.10.009.
- Chabanon RM, et al. Mutational landscape and sensitivity to immune checkpoint blockers. Clin. Cancer Res. 2016;22:4309–4321. doi: 10.1158/1078-0432.CCR-16-0903.
- Schumacher TN, Hacohen N. Neoantigens encoded in the cancer genome. Curr. Opin. Immunol. 2016;41:98–103. doi: 10.1016/j.coi.2016.07.005.
- Hundal J, et al. pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens. Genome Med. 2016;8:11. doi: 10.1186/s13073-016-0264-5.
- Strønen E, et al. Targeting of cancer neoantigens with donor-derived T cell receptor repertoires. Science. 2016;352:1337–1341. doi: 10.1126/science.aaf2288.
- Daud AI, et al. Tumor immune profiling predicts response to anti-PD-1 therapy in human melanoma. J. Clin. Invest. 2016;126:3447–3452. doi: 10.1172/JCI87324.
- Salmon H, et al. Matrix architecture defines the preferential localization and migration of T cells into the stroma of human lung tumors. J. Clin. Invest. 2012;122:899–910. doi: 10.1172/JCI45817.
- Khazen R, et al. Melanoma cell lysosome secretory burst neutralizes the CTL-mediated cytotoxicity at the lytic synapse. Nat. Commun. 2016;7:10823. doi: 10.1038/ncomms10823.
- Hillert R, et al. Large molecular systems landscape uncovers T cell trapping in human skin cancer. Sci. Rep. 2016;6:19012. doi: 10.1038/srep19012.
- Ho PC, et al. Phosphoenolpyruvate is a metabolic checkpoint of anti-tumor T cell responses. Cell. 2015;162:1217–1228. doi: 10.1016/j.cell.2015.08.012.
- Im SJ, et al. Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy. Nature. 2016;537:417–421. doi: 10.1038/nature19330.
- Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–1760. doi: 10.1093/bioinformatics/btp324.
- Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38:e164. doi: 10.1093/nar/gkq603.
- Magi A, et al. EXCAVATOR: detecting copy number variants from whole-exome sequencing data. Genome Biol. 2013;14:R120. doi: 10.1186/gb-2013-14-10-r120.
- Zhao S, et al. Landscape of somatic single-nucleotide and copy-number mutations in uterine serous carcinoma. Proc. Natl Acad. Sci. USA. 2013;110:2916–2921. doi: 10.1073/pnas.1222577110.
- Liu C, et al. ATHLATES: accurate typing of human leukocyte antigen through exome sequencing. Nucleic Acids Res. 2013;41:e142. doi: 10.1093/nar/gkt481.
- Ceman S, Rudersdorf RA, Petersen JM, DeMars RDMA. and DMB are the only genes in the class II region of the human MHC needed for class II-associated antigen processing. J. Immunol. 1995;154:2545–2556.
- Wolfl M, Greenberg PD. Antigen-specific activation and cytokine-facilitated expansion of naive, human CD8+ T cells. Nat. Protoc. 2014;9:950–966. doi: 10.1038/nprot.2014.064.
- Du VY, et al. HIV-1-specific CD8 T cells exhibit limited cross-reactivity during acute infection. J. Immunol. 2016;196:3276–3286. doi: 10.4049/jimmunol.1502411.
- Schalper K. A., et al. Objective measurement and clinical significance of TILs in non-small cell lung cancer. J. Natl Cancer. Inst. 107, pii: dju435 (2015).
- Finck R, et al. Normalization of mass cytometry data with bead standards. Cytom. A. 2013;83:483–494. doi: 10.1002/cyto.a.22271.
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