Histone Methylation Mark Analyses Distinguish Carts Manufactured from Distinct Sources and Uncover Novel Transcription Factors Associated with In Vivo Function of Carts after Infusion into DLBCL Patients That Are Not Identified By RNA-Seq

Abstract

Chimeric antigen receptor-modified T cell (CART) therapy has heralded a revolution in cancer immunotherapy. Yet, understanding the qualities that govern effects on in vivo function of CART infusion products (IP) has been challenging. RNA sequencing (RNA-seq), albeit high dimensional in scope, is limited by the dynamic nature of transcription, especially in T cells and CARTs where activation may hinder identification of transiently or minimally expressed genes. We investigated whether epigenomic analyses of histone 3 lysine methylation marks (H3Kme) might uncover genes associated with the potential of starting T cell subsets and CART IP that could not be identified by RNA-seq. We used Cleavage Under Targets and Restriction Using Nuclease (CUT&RUN) to assess whole genome transcriptionally permissive H3K4me2 and repressive H3K27me3 marks in naïve (N), central memory (CM) and effector memory (EM) CD8+ T cells and in CARTs of different potencies and manufactured from different sources. We identify, for the first time, epigenetic predictors of CART cell expansion in a clinical trial (NCT01865617).

Publication
Blood