EBV-Associated Lymphoma Consortium Annual Meeting (Abstract): Submission #9

Abstract Summary Diffuse large B-cell lymphoma (DLBCL) is the most common form of non-Hodgkin lymphoma and the leading cause of cancer-related death in HIV-infected individuals. Up to 40% of individuals have refractory or relapsing DLBCL, and associated Epstein-Bar virus (EBV) coincides with even higher rates of mortality. Earlier, we showed that EBV activates Signal transducer and activator of transcription 3 (STAT3) leading to loss of the DNA damage response checkpoint and homologous recombination repair. While this ensures proliferation despite damage, it also increases reliance on alternate dsDNA break repair mechanisms. Targeting such parallel pathways represents a promising new approach to treatment known as synthetic lethality. Here, we investigate the gene expression profiles of EBV+-DLBCL tumors from HIV positive individuals to identify additional codependent DNA replication/repair pathways that may be targetable by synthetic lethal strategies. Five EBV+-DLBCL biopsies along with two matched normal tissue controls were obtained from the AIDS Cancer Specimen Resource. Immunohistochemistry confirmed the presence of CD20+ cells, EBV’s LMP-1, and proliferating cells marked by Ki67. Single nuclei suspensions were isolated from the frozen samples and subjected to barcoded cDNA amplification and sequencing using the PARSE single-nucleus RNA-seq protocol. Sequencing was performed on an Illumina NovaSeq to a depth of ~50,000–200,000 reads per nucleus. Only nuclei with >100 detected genes and < 15% mitochondrial gene content were retained for analysis. Data were processed by log-normalization and analyzed by shared near-neighbor and UMAP in Seurat. Analysis revealed varying cell types within and between the different samples as well as different degrees of malignant B cells. While ongoing, highly expressed genes enriched in malignant B cell populations varied greatly across samples. In addition to anticipated oncogenes, comparisons across samples and between the tumor tissues and matched normal control tissues reveal several genes involved in DNA replication, repair or metabolism.