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Transcriptional Mechanisms of Resistance to Anti-PD-1 Therapy

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Transcriptional Mechanisms of Resistance to Anti-PD-1 Therapy Author Manuscript Published OnlineFirst on February 13, 2017; DOI: 10.1158/1078-0432.CCR-17-0270 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Transcriptional mechanisms of resistance to anti-PD-1 therapy Maria L. Ascierto1, Alvin Makohon-Moore2, 11, Evan J. Lipson1, Janis M. Taube3,4, Tracee L. McMiller5, Alan E. Berger6, Jinshui Fan6, Genevieve J. Kaunitz3, Tricia R. Cottrell4, Zachary A. Kohutek7, Alexander Favorov8,10, Vladimir Makarov7,11, Nadeem Riaz7,11, Timothy A. Chan7,11, Leslie Cope8, Ralph H. Hruban4,9, Drew M. Pardoll1, Barry S. Taylor11,12,13, David B. Solit13, Christine A Iacobuzio-Donahue2,11, and Suzanne L. Topalian5 From the 1Departments of Oncology, 3Dermatology, 4Pathology, 5Surgery, 6The Lowe Family Genomics Core, 8Oncology Bioinformatics Core, and the 9 Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287; the 10Laboratory of System Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, Moscow, Russia; and 2Pathology, 7Radiation Oncology, 11Human Oncology and Pathogenesis Program, 12Department of Epidemiology and Biostatistics, and the 13Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York NY 10065. MLA, AM-M, EJL, and JMT contributed equally to this work Running title: Transcriptional mechanisms of resistance to anti-PD-1 Key Words: melanoma, cancer genetics, immunotherapy, anti-PD-1 Financial Support: This study was supported by the Melanoma Research Alliance (to SLT and CI-D), the Bloomberg~Kimmel Institute for Cancer Immunotherapy (to JMT, DMP, and SLT), the Barney Family Foundation (to SLT), Moving for Melanoma of Delaware (to SLT), the 1 Downloaded from clincancerres.aacrjournals.org on October 2, 2021. © 2017 American Association for Cancer Research. Author Manuscript Published OnlineFirst on February 13, 2017; DOI: 10.1158/1078-0432.CCR-17-0270 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Laverna Hahn Charitable Trust (to SLT), the National Cancer Institute (R01 CA142779 to JMT, DMP and SLT; 5T32 CA193145 to TRC; R01 CA179991 to CI-D; P30-CA008748 to Memorial Sloan Kettering Cancer Center), the MSKCC TROT Fellowship (to AM-M), the Starr Cancer Consortium (to TAC), the Pershing Square Sohn Cancer Research Foundation (to TAC), the Immunogenomics and Precision Oncology Platform (to TAC), and the Marie-Josée and Henry R. Kravis Center for Molecular Oncology (to DBS). To whom correspondence should be addressed: SLT at 1550 Orleans St., CRB2 room 508, Baltimore, MD 21287; phone 410-502-8218; FAX 410-502-1958; email [email protected]; and to CI-D, 1275 York Avenue PO Box 20, New York, NY 10065; email [email protected]. The following authors have declared relevant financial relationships: EJL receives research funding from Genentech and Merck, and consults for Amgen, Bristol-Myers Squibb and Merck. JMT receives research funding from Bristol-Myers Squibb and serves on advisory boards for Bristol-Myers Squibb, Merck, and AstraZeneca. RHH receives royalty payments through his institution, from Myriad Genetics, and serves on the board of directors of MiDiagnostics. TAC receives research funding from Bristol-Myers Squibb, and is a co-founder of and holds equity in Gritstone Oncology. DMP receives research grants from Bristol-Myers Squibb; consults for Five Prime Therapeutics, GlaxoSmithKline, Jounce Therapeutics, MedImmune, Pfizer, Potenza Therapeutics, and Sanofi; holds stock options in Jounce and Potenza; and is entitled to receive patent royalties through his institution, from Bristol-Myers Squibb and Potenza. DBS consults for Pfizer and Loxo Oncology. SLT receives research funding from Bristol-Myers Squibb. MLA, AM-M, TLM, AEB, JF, GJK, TRC, ZAK, AF, VM, NR, LC, BST, and CI-D do not declare any conflicts. Word count: 6000 Tables: 2 Figures: 5 Supplementary files: 8 (Supplementary Methods, 3 tables, 4 figures) 2 Downloaded from clincancerres.aacrjournals.org on October 2, 2021. © 2017 American Association for Cancer Research. Author Manuscript Published OnlineFirst on February 13, 2017; DOI: 10.1158/1078-0432.CCR-17-0270 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. ABSTRACT Purpose: To explore factors associated with response and resistance to anti-PD-1 therapy, we analyzed multiple disease sites at autopsy in a patient with widely metastatic melanoma who had a heterogeneous response. Materials and Methods: Twenty-six melanoma specimens (four pre-mortem, 22 post-mortem) were subjected to whole-exome sequencing. Candidate immunologic markers and gene expression were assessed in ten cutaneous metastases showing response or progression during therapy. Results: The melanoma was driven by biallelic inactivation of NF1. All lesions had highly concordant mutational profiles and copy number alterations, indicating linear clonal evolution. Expression of candidate immunologic markers was similar in responding and progressing lesions. However, progressing cutaneous metastases were associated with over-expression of genes associated with extracellular matrix and neutrophil function. Conclusions: Although mutational and immunologic differences have been proposed as the primary determinants of heterogeneous response/resistance to targeted therapies and immunotherapies, respectively, differential lesional gene expression profiles may also dictate anti-PD-1 outcomes. STATEMENT OF SIGNIFICANCE: This rapid autopsy study of a patient with widespread melanoma experiencing a mixed response to anti-PD-1 therapy revealed highly homogeneous genomic and immunologic characteristics in responding and non-responding lesions. However, a distinct gene expression profile was associated with non-response, suggesting that intratumoral transcriptional programs can determine response/resistance to anti-PD-1 therapy. 3 Downloaded from clincancerres.aacrjournals.org on October 2, 2021. © 2017 American Association for Cancer Research. Author Manuscript Published OnlineFirst on February 13, 2017; DOI: 10.1158/1078-0432.CCR-17-0270 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. INTRODUCTION Complex interactions between the immune system and melanoma influence tumor invasion and metastasis, and ultimately define patient survival. Immunologic and genetic factors may contribute independently to prognosis and treatment resistance in melanoma, however, a deeper knowledge of their interactions is central to understanding disease evolution and developing synergistic combination treatment regimens. Melanoma has the capacity to metastasize to virtually any organ in the body; often, the full extent of metastasis is discovered only on postmortem examination. To date, studies of melanoma heterogeneity and metastatic evolution have been hampered by the limited availability of tissues from readily accessible anatomic sites in living patients. This limitation can be overcome by a rapid autopsy approach.1 This approach has been applied to pancreatic and other cancer types, revealing diverse patterns of clonal evolution from the primary lesion to metastases, in which intratumoral subclones and metastatic tumors accumulate private mutations superimposed on shared or ubiquitous mutations.2-4 In some cases, an unexpectedly long chronology from primary lesion to the development of metastasis has been observed. Immune checkpoint blockade with PD-1/PD-L1 antibodies, recently approved for treating metastatic melanoma, Hodgkin lymphoma, and cancers of the lung, kidney, bladder, and head and neck, unleashes endogenous antitumor immunity to eliminate cancer cells.5 To date, most research into anti-PD-1 treatment resistance has focused on immunologic factors such as intratumoral PD-L1 expression and infiltration of cytolytic CD8+ T cells.6-8 However, the extent to which genetic and other factors may play equally important roles is unknown. We therefore combined genetic and immunologic analyses of tumor evolution within one patient’s cutaneous melanoma over a 5-year clinical course from diagnosis to metastasis and death. This patient received anti-PD-1 therapy up to the time of death, at which time some metastases were responding to therapy while others were progressing. Surprisingly, genetic and immunologic factors were relatively homogenous among responding and progressing lesions, while a non- genomic program characterized the progressing metastases. RESULTS Clinical history and tumor specimens 4 Downloaded from clincancerres.aacrjournals.org on October 2, 2021. © 2017 American Association for Cancer Research. Author Manuscript Published OnlineFirst on February 13, 2017; DOI: 10.1158/1078-0432.CCR-17-0270 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. A 60-year-old man presented with a primary cutaneous melanoma of the left upper extremity, 7 mm in Breslow thickness. Clinical testing indicated that no mutations were present in the most frequently mutated regions of BRAF, KIT, NRAS, and PIK3CA. Over the ensuing 2 years, the patient underwent surgical resection of locoregional recurrences, including lymph node and in-transit cutaneous metastases. Distant metastases then appeared, for which he received two 4-dose courses of ipilimumab (anti-CTLA-4) over 15 months. The patient’s disease was initially stable
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