Abstract 6425: Functional roles of enhancers in immune microenvironment & immunotherapy response
Authors: Rai Kunal , Maitituoheti Mayinuer , Shi Alvin , Tang Ming , Ho Li-Lun , Kreidieh Firas Youssef , Terranova Christopher , Galani Kyriakitsa , Keung Emily Z. , Creasy Caitlin A. , Wu Manrong , Chen Jiajia , Chen Nana , Singh Anand K. , Chaudhri Apoorvi , Anvar Nazanin E. , Tarrantino Giuseppe , Yang Jiekun , Sarkar Sharmistha , Jiang Shan , Malke Jared , Haydu Lauren , Burton Elizabeth , Davies Michael A. , Gershenwald Jeffrey E. , Hwu Patrick , Lazar Alexander , Cheah Jaime H. , Soule Christian K. , Levine Stuart S. , Bernatchez Chantale , Saladi Srinivas V. , Liu David , Tawbi Hussein , Wargo Jennifer , Boland Genevieve M. , Kellis Manolis 
Published: April 2023

Immune checkpoint blockade (ICB) therapy has improved long-term survival for patients with advanced melanoma. However, there is critical need to identify potential biomarkers of response and actionable strategies to improve response rates. Through generation and analysis of over 200 chromatin modification maps for ICB-treated melanoma patient samples, melanoma cells and T cells, we identified significant enrichment of active enhancer states in non-responders at baseline. Enhancer mapping by bulk ChIP-Seq or single cell ATAC-Seq methods in two independent cohorts of ICB-treated melanoma samples identified an enhancer signature that predicted response to anti-PD-1 therapy. The activated non-responder enhancers marked a group of key regulators of several pathways in melanoma cells (including c-MET, TGFβ, EMT and AKT) that are known to mediate resistance to ICB therapy. In addition, several checkpoint receptors were alternatively activated by aberrant enhancers in T cells. Unbiased CRISPRi screening in melanoma cells and T cells identified novel functional enhancers, such as one upstream of c-MET, that mediate ICB response or T cell mediated killing. Finally, inhibition of enhancers and repression of these pathways using bromodomain inhibitors along with anti-PD-1 therapy significantly decreased melanoma tumor burden and increased T-cell infiltration. Epigenomic experiments identified a signature of 107 genes that could be used as pharmacodynamic marker for BET inhibitor response. Together, these findings identify enhancer upregulation as a key mechanism of adaptive resistance to ICB response, a potential enhancer-based biomarker of resistance to anti-PD-1 and enhancer blockade in combination with ICB as a potential strategy to improve responses.

Citation Format: Kunal Rai, Mayinuer Maitituoheti, Alvin Shi, Ming Tang, Li-Lun Ho, Firas Youssef Kreidieh, Christopher Terranova, Kyriakitsa Galani, Emily Z. Keung, Caitlin A. Creasy, Manrong Wu, Jiajia Chen, Nana Chen, Anand K. Singh, Apoorvi Chaudhri, Nazanin E. Anvar, Giuseppe Tarrantino, Jiekun Yang, Sharmistha Sarkar, Shan Jiang, Jared Malke, Lauren Haydu, Elizabeth Burton, Michael A. Davies, Jeffrey E. Gershenwald, Patrick Hwu, Alexander Lazar, Jaime H. Cheah, Christian K. Soule, Stuart S. Levine, Chantale Bernatchez, Srinivas V. Saladi, David Liu, Hussein Tawbi, Jennifer Wargo, Genevieve M. Boland, Manolis Kellis. Functional roles of enhancers in immune microenvironment & immunotherapy response. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6425.