Computational immunogenomic approaches to predict response to cancer immunotherapies

Sun, C. et al. Reversible and adaptive resistance to BRAF(V600E) inhibition in melanoma. Nature 508, 118–122 (2014).

Article  CAS  PubMed  Google Scholar 

Buchbinder, E. I. & Desai, A. CTLA-4 and PD-1 pathways: similarities, differences, and implications of their inhibition. Am. J. Clin. Oncol. 39, 98–106 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

McDermott, D., Haanen, J., Chen, T. T., Lorigan, P. & O’Day, S. Efficacy and safety of ipilimumab in metastatic melanoma patients surviving more than 2 years following treatment in a phase III trial (MDX010-20). Ann. Oncol. 24, 2694–2698 (2013).

Article  CAS  PubMed  Google Scholar 

Eggermont, A. M. M. et al. Prolonged survival in stage III melanoma with ipilimumab adjuvant therapy. N. Engl. J. Med. 375, 1845–1855 (2016).

Article  CAS  PubMed  Google Scholar 

Hammers, H. J. et al. Safety and efficacy of nivolumab in combination with ipilimumab in metastatic renal cell carcinoma: the CheckMate 016 study. J. Clin. Oncol. 35, 3851–3858 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Motzer, R. J. et al. Nivolumab versus everolimus in advanced renal-cell carcinoma. N. Engl. J. Med. 373, 1803–1813 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Overman, M. J. et al. Nivolumab in patients with metastatic DNA mismatch repair-deficient or microsatellite instability-high colorectal cancer (CheckMate 142): an open-label, multicentre, phase 2 study. Lancet Oncol. 18, 1182–1191 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Brahmer, J. et al. Nivolumab versus docetaxel in advanced squamous-cell non-small-cell lung cancer. N. Engl. J. Med. 373, 123–135 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ansell, S. M. et al. PD-1 blockade with nivolumab in relapsed or refractory Hodgkin’s lymphoma. N. Engl. J. Med. 372, 311–319 (2014).

Article  PubMed  Google Scholar 

Sharma, P. et al. Nivolumab in metastatic urothelial carcinoma after platinum therapy (CheckMate 275): a multicentre, single-arm, phase 2 trial. Lancet Oncol. 18, 312–322 (2017).

Article  CAS  PubMed  Google Scholar 

El-Khoueiry, A. B. et al. Nivolumab in patients with advanced hepatocellular carcinoma (CheckMate 040): an open-label, non-comparative, phase 1/2 dose escalation and expansion trial. Lancet 389, 2492–2502 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen, R. et al. Phase II study of the efficacy and safety of pembrolizumab for relapsed/refractory classic Hodgkin lymphoma. J. Clin. Oncol. 35, 2125–2132 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Diaz, L. et al. 386P—efficacy of pembrolizumab in phase 2 KEYNOTE-164 and KEYNOTE-158 studies of microsatellite instability high cancers. Ann. Oncol. 28, v128–v129 (2017).

Article  Google Scholar 

Chung, H. C. et al. Efficacy and safety of pembrolizumab in previously treated advanced cervical cancer: results from the phase II KEYNOTE-158 study. J. Clin. Oncol. 37, 1470–1478 (2019).

Article  CAS  PubMed  Google Scholar 

Zhu, A. X. et al. Pembrolizumab in patients with advanced hepatocellular carcinoma previously treated with sorafenib (KEYNOTE-224): a non-randomised, open-label phase 2 trial. Lancet Oncol. 19, 940–952 (2018).

Article  PubMed  Google Scholar 

Nghiem, P. et al. Durable tumor regression and overall survival in patients with advanced Merkel cell carcinoma receiving pembrolizumab as first-line therapy. J. Clin. Oncol. 37, 693–702 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Alley, E. W. et al. Clinical safety and activity of pembrolizumab in patients with malignant pleural mesothelioma (KEYNOTE-028): preliminary results from a non-randomised, open-label, phase 1b trial. Lancet Oncol. 18, 623–630 (2017).

Article  CAS  PubMed  Google Scholar 

Patel, S. P. & Kurzrock, R. PD-L1 expression as a predictive biomarker in cancer immunotherapy. Mol. Cancer Ther. 14, 847 (2015).

Article  CAS  PubMed  Google Scholar 

Duffy, M. J. & Crown, J. Biomarkers for predicting response to immunotherapy with immune checkpoint inhibitors in cancer patients. Clin. Chem. 65, 1228–1238 (2019).

Article  CAS  PubMed  Google Scholar 

Fundytus, A., Booth, C. M. & Tannock, I. F. How low can you go? PD-L1 expression as a biomarker in trials of cancer immunotherapy. Ann. Oncol. 32, 833–836 (2021).

Article  CAS  PubMed  Google Scholar 

Hellmann, M. D. et al. Nivolumab plus ipilimumab in lung cancer with a high tumor mutational burden. N. Engl. J. Med. 378, 2093–2104 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Marabelle, A. et al. Association of tumour mutational burden with outcomes in patients with advanced solid tumours treated with pembrolizumab: prospective biomarker analysis of the multicohort, open-label, phase 2 KEYNOTE-158 study. Lancet Oncol. 21, 1353–1365 (2020).

Article  CAS  PubMed  Google Scholar 

FDA. FDA Approves Pembrolizumab for Adults and Children with TMB-H Solid Tumors, https://www.fda.gov/drugs/drug-approvals-and-databases/fda-approves-pembrolizumab-adults-and-children-tmb-h-solid-tumors (2020).

Hugo, W. et al. Genomic and transcriptomic features of response to anti-PD-1 therapy in metastatic melanoma. Cell 165, 35–44 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ayers, M. et al. IFN-γ-related mRNA profile predicts clinical response to PD-1 blockade. J. Clin. Investig. 127, 2930–2940 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Cristescu, R. et al. Pan-tumor genomic biomarkers for PD-1 checkpoint blockade-based immunotherapy. Science 362, eaar3593 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Van Allen, E. M. et al. Genomic correlates of response to CTLA-4 blockade in metastatic melanoma. Science 350, 207 (2015).

Article  PubMed  PubMed Central  Google Scholar 

Liu, D. et al. Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma. Nat. Med. 25, 1916–1927 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rizvi, N. A. et al. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science 348, 124 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Anagnostou, V. et al. Multimodal genomic features predict outcome of immune checkpoint blockade in non-small-cell lung cancer. Nat. Cancer 1, 99–111 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

McGranahan, N. et al. Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade. Science 351, 1463 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kim, S. T. et al. Comprehensive molecular characterization of clinical responses to PD-1 inhibition in metastatic gastric cancer. Nat. Med. 24, 1449–1458 (2018).

Article  CAS  PubMed  Google Scholar 

Aran, D., Sirota, M. & Butte, A. J. Systematic pan-cancer analysis of tumour purity. Nat. Commun. 6, 8971 (2015).

Article  CAS  PubMed  Google Scholar 

Carter, S. L. et al. Absolute quantification of somatic DNA alterations in human cancer. Nat. Biotechnol. 30, 413–421 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Raine, K. M. et al. ascatNgs: identifying somatically acquired copy-number alterations from whole-genome sequencing data. Curr. Protoc. Bioinformatics 56, 15.19.11–15.19.17 (2016).

Article  Google Scholar 

Song, S. et al. qpure: a tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles. PLoS ONE 7, e45835 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yoshihara, K. et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat. Commun. 4, 2612 (2013).

Article  PubMed 

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