Abstract 1011: RNAseq analysis obtained from on-purpose tumor biopsies of patients in the MATCH-R trial allows the identification of potential mechanisms of acquired resistance to PD(L)1 therapies
Authors: Verlingue Loic , Mahjoubi Linda , Aspeslagh Sandrine , Pedrero Marion , Buzzatti Giulia , Brandao David , Balogh Zsofia , Rouleau Etienne , Lacroix Ludovic , Bahleda Rastislav , Massard Christophe , Hollebecque Antoine , Gazzah Anas , Lefebvre Céline , Koscielny Serge , Scoazec Jean Yves , Angevin Eric , André Fabrice , Marabelle Aurélien , Soria Jean Charles 
Published: July 2017

Abstract
Background: MATCH-R is a prospective molecular characterization trial (NCT02517892) aiming at defining the molecular basis of acquired resistance to targeted agents and immune checkpoint blockers. RNA sequencing (RNAseq) has been used to identify mechanisms of secondary resistance to immunotherapy.
Patients and methods: Patients’ metastatic tumors were multi-site biopsied at relapse under immunotherapies after a period of clinical benefit, defined by a partial response or a stable disease of more than 6 months. Genome-wide RNAseq counts were intra-patient normalized and a score of each gene’s expression was computed in comparison to a cohort of 450 metastatic cancer patients with RNAseq available at the time of analysis.
Results: To date, 10 patients treated by immunotherapies have had a successful RNAseq in the MATCH-R trial. Five patients were treated with PD-1 inhibitors and 5 with PD-L1 inhibitors. Three patients had NSCLC, 2 MSI high endometrial carcinoma, 2 anal carcinoma, 2 urothelial carcinoma and 1 TNBC. Eight out off ten patients had an expression of IDO1 higher than the median expression of IDO1 in our 450 controls (p value = 0.005). A patient with endometrial carcinoma had one of the highest expressions of IDO1 in the cohort. Consistently, IDO1 activation has previously been reported as a mechanism of secondary resistance to immunotherapies. A 40 year old smoker NSCLC patient with a TP53 mutation has been treated during 11 months with anti-PD1. RNAseq analysis on the biopsy of a progressive lesion showed decreased expression of different actors of the JAK-STAT pathway (biopsy composed of 40% tumor cells and 60% microenvironment). Of the 78 genes signatures used (including 52 immunogenes signatures), the interferon gamma signature had the lowest expression (p value = 0.004), consistent with a previous report of JAK-STAT-induced resistance to immunotherapy. Two more patients had an altered immune profile that could be involved in resistance to immunotherapies, but was not yet reported in the litterature. Confirmation of the RNAseq analysis with immunohistochemistry is currently ongoing. The gene signatures of the 10 patients, composed of immunogenes, DNA repair genes and epigenes, were compared to the whole cohort in order to deduce corresponding false discovery rates. As such we could identify 2 gene clusters, one enriched in T cells, dendritic cells and macrophages, and the other enriched in epigenes and DNA repair genes. Analysis of more patients is currently ongoing in order to cluster the results with clinical characteristics.
Conclusion: Gene expression in the biopsy of patients that relapsed after initial benefit to immunotherapy is informative and helps to identify the mechanism of acquired resistance.
Citation Format: Loic Verlingue, Linda Mahjoubi, Sandrine Aspeslagh, Marion Pedrero, Giulia Buzzatti, David Brandao, Zsofia Balogh, Etienne Rouleau, Ludovic Lacroix, Rastislav Bahleda, Christophe Massard, Antoine Hollebecque, Anas Gazzah, Céline Lefebvre, Serge Koscielny, Jean Yves Scoazec, Eric Angevin, Fabrice André, Aurélien Marabelle, Jean Charles Soria. RNAseq analysis obtained from on-purpose tumor biopsies of patients in the MATCH-R trial allows the identification of potential mechanisms of acquired resistance to PD(L)1 therapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1011. doi:10.1158/1538-7445.AM2017-1011