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2963 Frequent Copy Gains of Viral LMP-1 Confers Radiosensitivity in Natural-Killer/T Cell Lymphoma

Program: Oral and Poster Abstracts
Session: 621. Lymphomas: Translational – Molecular and Genetic: Poster II
Hematology Disease Topics & Pathways:
Research, Translational Research, Lymphomas, Non-Hodgkin lymphoma, Clinical Research, Genomics, Bioinformatics, Diseases, Therapy sequence, Aggressive lymphoma, Treatment Considerations, Lymphoid Malignancies, Non-Biological therapies, Survivorship, Biological Processes, Molecular biology, Technology and Procedures, Radiation Therapy, Study Population, Human
Sunday, December 8, 2024, 6:00 PM-8:00 PM

Jing Quan Lim, PhD1,2*, Dachuan Huang, PhD, BSc, MSc1*, Kelila Xin Ye Chai, MSc2*, Phyu The, BSc3*, Kerry May Huifen Lim2*, Wendy Lee, PhD4*, Liang Wei Wang5*, Nur Ayuni Muhammad Taib6*, Beng Hooi Phang6*, Wee-Joo Chng7,8, Olaf Rötzschke, PhD4*, Jason Yongsheng Chan2, Soon Thye Lim9*, Jin-Xin BEI, PhD10*, Siok-Bian Ng11* and Choon Kiat Ong12*

1Duke-NUS Medical School, Singapore, Singapore
2National Cancer Centre Singapore, Singapore, Singapore
3Pathology, National University of Singapore, Singapore, Singapore
4Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
5Singapore Immunology Network, Singapore, SGP
6National Cancer Centre Singapore, Singapore, SGP
7Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
8Department of Haematology-Oncology, National University Cancer Institute, Singapore, Singapore
9Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
10SKL of Oncology In South China, Sun Yat-Sen University Cancer Center, Guangzhou, CHN
11Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
12National Cancer Centre Singapore, Singapore, Singapore, SGP

Introduction

Discovered from Burkitt’s lymphoma (BL) in 1964, the Epstein-Barr Virus (EBV) was the first virus to associate with human cancers. EBV associated malignancies of particular significance in Asia include natural-killer/T cell lymphoma (NKTCL) and nasopharyngeal carcinoma (NPC), where their neoplastic cells are ubiquitously infected with EBV. Recently, numerous studies have reported somatic mutations altering immune-evasion, JAK-STAT, NF-κB, epigenetic, and MAPK pathways in NKTCL. In addition, we have also reported germline single-nucleotide polymorphisms (SNPs) of HLA-DPB1, IL18RAP and HLA-DRB1 that conferred increased risk of NKTCL and prognostic models that could contribute to the progression of NKTCL. Although frequent copy-number variations (CNV) of chromosome 6q21 implicating PRDM1, ATG5 and AIM1 genes were reported in NKTCL, there is still a general lack of research of CNV on oncogenic EBV genes in NKTCL.

Materials

To detect non-reference CNV events within the EBV genomes, we used whole-genome sequencing (WGS) to comprehensively profile the genomic landscape of 77 high quality tumor-normal matched samples from patients with NKTCL and 10 NK/T lymphoma/leukaemia cell lines. We also included whole-transcriptome (n=36) sequencing data, with matching WGS data, to analyse dysregulated pathways within mutations-of-interest.

Results

We used a step-wise analytical methodology to detect viral copy-gains and discovered frequent copy-gains of LMP-1 in 22.1% (18/77) of NKTCL tumors and 10% (1/10) of cell lines. The recurrently gained locus encapsulated the viral LMP-1, BNLF2a, and BNLF2b genes, which led to increased expressions of LMP-1. This recurrence rate supersedes the frequencies of most previously reported mutated human-genes in NKTCL. We also further validated these genomic alterations with both Nanopore long-read sequencing and Sanger sequencing. Gene-set enrichment analysis also showed that the “P53_PATHWAY” gene-set was the most enriched (FDR<0.001) within the LMP-1copy-gain samples. Importantly, we found that patients with tumors harbouring LMP-1copy-gain were significantly associated with better progression-free survival (P=0.028) and overall survival (P=0.026), when treated with radiation, regardless of early or late tumor staging. Experimentally, we showed that overexpression of LMP-1 rendered radiosensitivity and, inversely, shLMP-1 rendered radioresistance in two NKTCL cell lines. Mechanistically, expression of LMP-1 increased double stranded breaks as evident by increased γH2AX and drove anti-tumoral activity by GADD45a-induced apoptosis.

Conclusion

In conclusion, this study reports on the frequent copy-gains of viral LMP-1 in NKTCL. The experiments also reports on the mechanistic link between an unexpected relationship between increased LMP-1 and better survivals from better sensitization to DNA damaging therapeutic agents.

Disclosures: Chng: Celgene: Honoraria, Research Funding; Abbvie: Honoraria; Hummingbird: Research Funding; J&J: Honoraria, Research Funding; Amgen: Honoraria; BMS: Honoraria; Novartis: Honoraria; Takeda: Honoraria. Chan: SymBio Pharmaceuticals: Research Funding.

*signifies non-member of ASH