Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors

Diana Miao ¹, Claire A Margolis ¹, Natalie I Vokes ¹, David Liu ¹, Amaro Taylor-Weiner ¹, Stephanie M Wankowicz ¹, Dennis Adeegbe ², Daniel Keliher ¹, Bastian Schilling ³, Adam Tracy ⁴, Michael Manos ¹, Nicole G Chau ¹, Glenn J Hanna ¹, Paz Polak ⁴, Scott J Rodig ¹, Sabina Signoretti ¹, Lynette M Sholl ¹, Jeffrey A Engelman ⁵, Gad Getz ⁴, Pasi A Jänne ¹, Robert I Haddad ¹, Toni K Choueiri ¹, David A Barbie ¹, Rizwan Haq ¹, Mark M Awad ¹, Dirk Schadendorf ¹, F Stephen Hodi ¹, Joaquim Bellmunt ¹, Kwok-Kin Wong ¹, Peter Hammerman ¹, Eliezer M Van Allen ⁶

Affiliations

¹ Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
² Perlmutter Cancer Center at NYU Langone Medical Center, New York, NY, USA.
³ Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, Germany.
⁴ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁵ Massachusetts General Hospital Cancer Center, Boston, MA, USA.
⁶ Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. eliezerm_vanallen@dfci.harvard.edu.

PMID: 30150660
61 References
172 citations

Abstract

Tumor mutational burden correlates with response to immune checkpoint blockade in multiple solid tumors, although in microsatellite-stable tumors this association is of uncertain clinical utility. Here we uniformly analyzed whole-exome sequencing (WES) of 249 tumors and matched normal tissue from patients with clinically annotated outcomes to immune checkpoint therapy, including radiographic response, across multiple cancer types to examine additional tumor genomic features that contribute to selective response. Our analyses identified genomic correlates of response beyond mutational burden, including somatic events in individual driver genes, certain global mutational signatures, and specific HLA-restricted neoantigens. However, these features were often interrelated, highlighting the complexity of identifying genetic driver events that generate an immunoresponsive tumor environment. This study lays a path forward in analyzing large clinical cohorts in an integrated and multifaceted manner to enhance the ability to discover clinically meaningful predictive features of response to immune checkpoint blockade.

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Integrated molecular drivers coordinate biological and clinical states in melanoma. Jake R Conway, Felix Dietlein, +13 authors, Eliezer M Van Allen. less Nat Genet, 2020 Nov 25; 52(12). PMID: 33230298 Free PMC article.
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Three Immune-Associated Subtypes of Diffuse Glioma Differ in Immune Infiltration, Immune Checkpoint Molecules, and Prognosis. Quanwei Zhou, Xuejun Yan, +5 authors, Caiping Ren. less Front Oncol, 2021 Jan 12; 10. PMID: 33425739 Free PMC article.
Apolipoprotein C1 stimulates the malignant process of renal cell carcinoma via the Wnt3a signaling. Hao Jiang, Jing-Yuan Tang, +4 authors, Xiao-Zhou He. less Cancer Cell Int, 2021 Jan 13; 21(1). PMID: 33430855 Free PMC article.
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Atezolizumab prolongs overall survival over docetaxel in advanced non-small-cell lung cancer patients harboring STK11 or KEAP1 mutation. Wei Nie, Lu Gan, +17 authors, Bao-Hui Han. less Oncoimmunology, 2021 Feb 05; 10(1). PMID: 33537171 Free PMC article.
Comprehensive Characterization of Immunological Profiles and Clinical Significance in Hepatocellular Carcinoma. Ping Tao, Liang Hong, +5 authors, Ruyi Xue. less Front Oncol, 2021 Feb 09; 10. PMID: 33552954 Free PMC article.
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Circulating mucosal-associated invariant T cells identify patients responding to anti-PD-1 therapy. Sara De Biasi, Lara Gibellini, +16 authors, Andrea Cossarizza. less Nat Commun, 2021 Mar 17; 12(1). PMID: 33723257 Free PMC article.
Tumor mutational burden as a predictor of immunotherapy response in breast cancer. Tess A O'Meara, Sara M Tolaney. Oncotarget, 2021 Mar 23; 12(5). PMID: 33747355 Free PMC article.
Targeting natural splicing plasticity of APOBEC3B restricts its expression and mutagenic activity. A Rouf Banday, Olusegun O Onabajo, +10 authors, Ludmila Prokunina-Olsson. less Commun Biol, 2021 Mar 24; 4(1). PMID: 33753867 Free PMC article.
Advanced Melanoma: Resistance Mechanisms to Current Therapies. Alexandra M Haugh, April K S Salama, Douglas B Johnson. Hematol Oncol Clin North Am, 2021 Mar 25; 35(1). PMID: 33759769 Free PMC article. Review.
Effect of NCOR1 Mutations on Immune Microenvironment and Efficacy of Immune Checkpoint Inhibitors in Patient with Bladder Cancer. Anqi Lin, Zhengang Qiu, Jian Zhang, Peng Luo. Front Immunol, 2021 Mar 26; 12. PMID: 33763074 Free PMC article.
[Tumor biology of oropharyngeal carcinoma]. S Laban, M Brand, +5 authors, T K Hoffmann. less HNO, 2020 Nov 21; 69(4). PMID: 33215226 Review.
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Germline variants predictive of tumor mutational burden and immune checkpoint inhibitor efficacy. Ajay Chatrath, Aakrosh Ratan, Anindya Dutta. iScience, 2021 Apr 01; 24(3). PMID: 33786423 Free PMC article.
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Molecular profiling of long-term responders to immune checkpoint inhibitors in advanced non-small cell lung cancer. Joan Frigola, Alejandro Navarro, +17 authors, Ramon Amat. less Mol Oncol, 2020 Dec 21; 15(4). PMID: 33342055 Free PMC article.
High tumor mutation burden fails to predict immune checkpoint blockade response across all cancer types. D J McGrail, P G Pilié, +13 authors, S-Y Lin. less Ann Oncol, 2021 Mar 20; 32(5). PMID: 33736924 Free PMC article.
Curative-Intent Treatment with Durvalumab in Early-Stage Cancers. Giovanni Melillo, Vikram Chand, +2 authors, Alejandro Yovine, Ashok Gupta, Cristian Massacesi. less Adv Ther, 2021 Apr 22; 38(6). PMID: 33881745 Free PMC article. Review.
RB1 and TP53 co-mutations correlate strongly with genomic biomarkers of response to immunity checkpoint inhibitors in urothelial bladder cancer. Ramon Gonzalez Manzano, Ana Catalan-Latorre, Antonio Brugarolas. BMC Cancer, 2021 Apr 22; 21(1). PMID: 33879103 Free PMC article.
MGA Mutation as a Novel Biomarker for Immune Checkpoint Therapies in Non-Squamous Non-Small Cell Lung Cancer. Lei Sun, Man Li, +4 authors, Linlang Guo. less Front Pharmacol, 2021 May 01; 12. PMID: 33927616 Free PMC article.
Cytotoxic lymphocytes target characteristic biophysical vulnerabilities in cancer. Maria Tello-Lafoz, Katja Srpan, +12 authors, Ekrem Emrah Er. less Immunity, 2021 Mar 24; 54(5). PMID: 33756102 Free PMC article.
Strategies for the Construction of Mouse Models With Humanized Immune System and Evaluation of Tumor Immune Checkpoint Inhibitor Therapy. Wenwen Guo, Caiqin Zhang, +2 authors, Tianyun Qiao, Jumei Zhao, Changhong Shi. less Front Oncol, 2021 May 18; 11. PMID: 33996603 Free PMC article. Review.
Identification of combinations of somatic mutations that predict cancer survival and immunotherapy benefit. Ayal B Gussow, Eugene V Koonin, Noam Auslander. NAR Cancer, 2021 May 25; 3(2). PMID: 34027407 Free PMC article.
The temporal mutational and immune tumour microenvironment remodelling of HER2-negative primary breast cancers. Leticia De Mattos-Arruda, Javier Cortes, +17 authors, Carlos Caldas. less NPJ Breast Cancer, 2021 Jun 09; 7(1). PMID: 34099718 Free PMC article.
Association Between FSIP2 Mutation and an Improved Efficacy of Immune Checkpoint Inhibitors in Patients With Skin Cutaneous Melanoma. Haoxuan Ying, Anqi Lin, +2 authors, Junyi Liang, Jian Zhang, Peng Luo. less Front Mol Biosci, 2021 Jun 12; 8. PMID: 34113648 Free PMC article.
Peripheral CD8+ T cell characteristics associated with durable responses to immune checkpoint blockade in patients with metastatic melanoma. Benjamin P Fairfax, Chelsea A Taylor, +12 authors, Mark R Middleton. less Nat Med, 2020 Feb 12; 26(2). PMID: 32042196 Free PMC article.
Catenin Alpha-2 Mutation Changes the Immune Microenvironment in Lung Adenocarcinoma Patients Receiving Immune Checkpoint Inhibitors. Yang Wen, Anqi Lin, +4 authors, Jian Zhang. less Front Pharmacol, 2021 Jun 25; 12. PMID: 34163353 Free PMC article.
Pan-cancer analysis of SETD2 mutation and its association with the efficacy of immunotherapy. Mingdong Lu, Bin Zhao, +4 authors, Xian Shen. less NPJ Precis Oncol, 2021 Jun 16; 5(1). PMID: 34127768 Free PMC article.
Massive PD-L1 and CD8 double positive TILs characterize an immunosuppressive microenvironment with high mutational burden in lung cancer. Libin Zhang, Yanhui Chen, +10 authors, Hao Peng. less J Immunother Cancer, 2021 Jun 19; 9(6). PMID: 34140315 Free PMC article.
Multi-omics analysis reveals prognostic value of tumor mutation burden in hepatocellular carcinoma. Qianhui Xu, Hao Xu, +5 authors, Wen Huang. less Cancer Cell Int, 2021 Jul 05; 21(1). PMID: 34217320 Free PMC article.
Prognostic and immunological role of CD36: A pan-cancer analysis. Yong-Jian Chen, Wei-Xin Liao, +7 authors, Xing Li. less J Cancer, 2021 Jul 09; 12(16). PMID: 34234847 Free PMC article.
Identification of NOTCH4 mutation as a response biomarker for immune checkpoint inhibitor therapy. Junyu Long, Dongxu Wang, +8 authors, Haitao Zhao. less BMC Med, 2021 Jul 22; 19(1). PMID: 34284787 Free PMC article.
Emerging targets for anticancer vaccination: IDH. M Platten, L Bunse, W Wick. ESMO Open, 2021 Jul 17; 6(4). PMID: 34271312 Free PMC article. Review.
The Impact of NOTCH Pathway Alteration on Tumor Microenvironment and Clinical Survival of Immune Checkpoint Inhibitors in NSCLC. Xiaohua Li, Yuntao Wang, +3 authors, Xuebing Li, Gang Feng, Sheng Hu, Yifeng Bai. less Front Immunol, 2021 Jul 27; 12. PMID: 34305884 Free PMC article.
Immunogenomic determinants of tumor microenvironment correlate with superior survival in high-risk neuroblastoma. Riyue Bao, Stefani Spranger, +7 authors, Ami V Desai. less J Immunother Cancer, 2021 Jul 18; 9(7). PMID: 34272305 Free PMC article.
Epidemiology, Risk Assessment, and Biomarkers for Patients with Advanced Renal Cell Carcinoma. Kyrollis Attalla, Stanley Weng, Martin H Voss, A Ari Hakimi. Urol Clin North Am, 2020 Jul 01; 47(3). PMID: 32600532 Free PMC article. Review.
The Promises and Challenges of Tumor Mutation Burden as an Immunotherapy Biomarker: A Perspective from the International Association for the Study of Lung Cancer Pathology Committee. Lynette M Sholl, Fred R Hirsch, +35 authors, John W Longshore. less J Thorac Oncol, 2020 Jun 12; 15(9). PMID: 32522712 Free PMC article. Review.
TGFBR2 mutation predicts resistance to immune checkpoint inhibitors in patients with non-small cell lung cancer. Teng Li, Han Wang, +8 authors, Zhijie Wang. less Ther Adv Med Oncol, 2021 Aug 20; 13. PMID: 34408796 Free PMC article.
Predictive Value of the TP53/PIK3CA/ATM Mutation Classifier for Patients With Bladder Cancer Responding to Immune Checkpoint Inhibitor Therapy. Yi-Hui Pan, Jia-Xing Zhang, +5 authors, Jun-Hang Luo. less Front Immunol, 2021 Aug 24; 12. PMID: 34421886 Free PMC article.
Nivolumab in combination with cabozantinib for metastatic triple-negative breast cancer: a phase II and biomarker study. Romualdo Barroso-Sousa, Tanya E Keenan, +13 authors, Sara M Tolaney. less NPJ Breast Cancer, 2021 Aug 27; 7(1). PMID: 34433812 Free PMC article.
The current issues and future perspective of artificial intelligence for developing new treatment strategy in non-small cell lung cancer: harmonization of molecular cancer biology and artificial intelligence. Ichidai Tanaka, Taiki Furukawa, Masahiro Morise. Cancer Cell Int, 2021 Aug 28; 21(1). PMID: 34446006 Free PMC article. Review.
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Pan-Cancer Analysis of PARP1 Alterations as Biomarkers in the Prediction of Immunotherapeutic Effects and the Association of Its Expression Levels and Immunotherapy Signatures. Xinke Zhang, Yingying Wang, +2 authors, Gari A, Chunhua Qu, Jiewei Chen. less Front Immunol, 2021 Sep 18; 12. PMID: 34531868 Free PMC article.
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Identification of immune-related subtypes of colorectal cancer to improve antitumor immunotherapy. Xiaobo Zheng, Yong Gao, +5 authors, Mingqing Xu. less Sci Rep, 2021 Oct 02; 11(1). PMID: 34593914 Free PMC article.
CD177 modulates the function and homeostasis of tumor-infiltrating regulatory T cells. Myung-Chul Kim, Nicholas Borcherding, +32 authors, Weizhou Zhang. less Nat Commun, 2021 Oct 03; 12(1). PMID: 34599187 Free PMC article.
Identification and validation of tissue or ctDNA PTPRD phosphatase domain deleterious mutations as prognostic and predictive biomarkers for immune checkpoint inhibitors in non-squamous NSCLC. Yiting Sun, Jianchun Duan, +10 authors, Jie Wang. less BMC Med, 2021 Oct 08; 19(1). PMID: 34615542 Free PMC article.
Prevalence and Landscape of Actionable Genomic Alterations in Renal Cell Carcinoma. Kyrollis Attalla, Renzo G DiNatale, +17 authors, A Ari Hakimi. less Clin Cancer Res, 2021 Jul 16; 27(20). PMID: 34261695 Free PMC article.
Weighted Gene Co-expression Network Analysis Identifies a Cancer-Associated Fibroblast Signature for Predicting Prognosis and Therapeutic Responses in Gastric Cancer. Hang Zheng, Heshu Liu, +2 authors, Huayu Li, Weidong Dou, Xin Wang. less Front Mol Biosci, 2021 Oct 26; 8. PMID: 34692770 Free PMC article.
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Sex Disparities of Genomic Determinants in Response to Immune Checkpoint Inhibitors in Melanoma. Fuyan Shi, Wenjing Zhang, +6 authors, Qinghua Wang. less Front Immunol, 2021 Nov 20; 12. PMID: 34795662 Free PMC article.
Single-Cell RNA Sequencing Reveals the Heterogeneity of Tumor-Associated Macrophage in Non-Small Cell Lung Cancer and Differences Between Sexes. Qi Yang, Hongman Zhang, +4 authors, Jian Zhang. less Front Immunol, 2021 Nov 23; 12. PMID: 34804043 Free PMC article.
Emerging biomarkers in metastatic urothelial carcinoma: tumour mutational burden, PD-L1 expression and APOBEC polypeptide-like signature in a patient with complete response to anti-programmed cell death protein-1 inhibitor. Marcello Moro Queiroz, Zenaide Silva de Souza, +8 authors, Diogo Assed Bastos. less Ecancermedicalscience, 2021 Nov 27; 15. PMID: 34824629 Free PMC article.
Potential Biomarkers for the Efficacy of PD-1-PD-L Blockade in Cancer. Miruna Grecea, Olga Soritau, +2 authors, Daniel Dulf, Tudor Eliade Ciuleanu, Mihnea Zdrenghea. less Onco Targets Ther, 2021 Dec 02; 14. PMID: 34848970 Free PMC article. Review.
Combination of Tumor Mutational Burden and Specific Gene Mutations Stratifies Outcome to Immunotherapy Across Recurrent and Metastatic Head and Neck Squamous Cell Carcinoma. Ying-Peng Peng, Rong Wang, +5 authors, Zhi-Gang Liu. less Front Genet, 2021 Dec 07; 12. PMID: 34868231 Free PMC article.
Evaluation of 30 DNA damage response and 6 mismatch repair gene mutations as biomarkers for immunotherapy outcomes across multiple solid tumor types. Zhe Gong, Yue Yang, Jieyun Zhang, Weijian Guo. Cancer Biol Med, 2021 May 08;. PMID: 33960179 Free PMC article.
The developing landscape of combinatorial therapies of immune checkpoint blockade with DNA damage repair inhibitors for the treatment of breast and ovarian cancers. Lingling Zhu, Jiewei Liu, Jiang Chen, Qinghua Zhou. J Hematol Oncol, 2021 Dec 22; 14(1). PMID: 34930377 Free PMC article. Review.
Cell cycle on the crossroad of tumorigenesis and cancer therapy. Jing Liu, Yunhua Peng, Wenyi Wei. Trends Cell Biol, 2021 Jul 27; 32(1). PMID: 34304958 Free PMC article. Review.
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SNF5, a core subunit of SWI/SNF complex, regulates melanoma cancer cell growth, metastasis, and immune escape in response to matrix stiffness. Ying Chen, Meilian Zhao, +4 authors, Liling Tang. less Transl Oncol, 2022 Jan 10; 17. PMID: 34999540 Free PMC article.
Analysis of N6-Methyladenosine Modification Patterns and Tumor Immune Microenvironment in Pancreatic Adenocarcinoma. Yong Liu, Guangbing Li, +4 authors, Jun Liu. less Front Genet, 2022 Jan 21; 12. PMID: 35046996 Free PMC article.
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Novel Molecular Determinants of Response or Resistance to Immune Checkpoint Inhibitor Therapies in Melanoma. Wenjing Zhang, Yujia Kong, +5 authors, Qinghua Wang. less Front Immunol, 2022 Jan 29; 12. PMID: 35087523 Free PMC article.
Inactivation of Fbxw7 Impairs dsRNA Sensing and Confers Resistance to PD-1 Blockade. Cécile Gstalder, David Liu, +21 authors, Rizwan Haq. less Cancer Discov, 2020 May 07; 10(9). PMID: 32371478 Free PMC article.
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Immune checkpoint inhibitors and driver oncogenes in non-small cell lung cancer. Yosuke Miura, Norimitsu Kasahara, Noriaki Sunaga. Transl Cancer Res, 2019 Dec 01; 8(Suppl 6). PMID: 35117146 Free PMC article.
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Multi-omic analysis reveals significantly mutated genes and DDX3X as a sex-specific tumor suppressor in cutaneous melanoma. Rached Alkallas, Mathieu Lajoie, +9 authors, Ian R Watson. less Nat Cancer, 2020 Jun 01; 1(6). PMID: 35121978 Free PMC article.
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