124P Targeting neoantigens in chronic lymphocytic leukemia (CLL) for personalized T cell therapy

Abstract

Background: Cancer cells are known to express unique tumor associated antigens (TAA) or novel neoantigens (NeoAg). The latter arise from somatic mutations (SNPs, ins/dels, frameshifts, neoORFs). Such antigens are considered as potential targets of T cell therapy & were investigated in CLL using paired whole exome (WES) & transcriptome (WTS) next generation sequencing (NGS) in this study. The main aim of this study was to identify TAA / personalized NeoAgs in CLL patients for T cell therapy using NGS approach. Methods: This study was approved by the institute’s ethics committee. WES (Twist Whole Exome library prep kit) & WTS (NEB Ultra II directional RNA-Seq Library Prep kit) on Illumina NovaSeq6000 was performed on malignant CLL B cells (CD45+CD19+CD5+) & paired Neutrophils (CD45+CD15+CD16+CD56-) in 51 CLL patients. Data was processed with in-house neoantigen discovery pipeline that identified somatic variants, differential expression, predicted HLA– neopeptide binding & coanalyzed TCR CDR3 motifs. Results The topmost highly expressed genes in CLL included FMOD, SFTPB, IGSF3 that could be considered as putative TAAs & explored further. Several somatic mutations were identified in TP53(8%), SF3B1(19%), NOTCH1(15%), CHD2(6%) & others. Further analysis revealed a series of HLA-A2 restricted putative neoepitopes derived from C16ORF57, FNDC3B, SF3B1, NFKB1E & other NeoAgs. The NFKB1E neoepitope, for example, originated from a frameshift deletion in exon 1 in two patients & was predicted to be restricted not only by HLA-A*02:11 (most common A2 allele in North Indians) but also other versatile subtypes A*02:01 (Caucasian, Gambian, Japanese) /*02:02 (Gambian) /*02:05 (Gambian, N Indians) /*02:06 (Japanese) /*02:07 (Japanese, N Indians). The CD8+T cell TCRαβ CDR3 motifs were also coanalyzed in these patients. Conclusions Immunogenic potential of TAA & NeoAgs identified in this study warrant further investigations & could offer promising personalized immunotherapeutic approach for treatment of CLL. Activation of NeoAg specific cytotoxic T cells in conjunction with checkpoint blockage/ CART/ adjuvants/ conventional therapies could augment anti tumor immune responses. Acknowledgements ICMR 2020-0012, 5/13/4/2020/NCD-III for funding.