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

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.

Editorial acknowledgement

Clinical trial identification

Legal entity responsible for the study

All India Institute of Medical Sciences.

Funding

Indian Council of Medical Research.

Disclosure

All authors have declared no conflicts of interest.