Neuropilin-1 is involved in lytic replication in a subset of primary effusion lymphoma cell lines and for KSHV gene expression in primary endothelial cells

ABSTRACT Primary effusion lymphoma (PEL) is a B cell lymphoma that occurs most often in people living with HIV/AIDS and is caused by Kaposi sarcoma herpesvirus (KSHV). Most are also infected with Epstein-Barr virus (EBV). While newer regimens now exist, PEL still has poorer outcomes compared to other HIV-associated lymphomas. Since PEL B cells lack typical B cell markers, we aim to identify other surface proteins in disease cells that may act as possible diagnostic or prognostic markers. We performed single cell DNA-seq and antibody derived tag-seq on BCBL1 (KSHV+/EBV−) and LCL (KSHV−/EBV+ lymphoblastoid cell line) cells to determine which surface markers are specific for KSHV+ PEL. We identified neuropilin-1 (NRP1) as a surface marker that is overexpressed in KSHV+ PEL cell lines (BCBL1, JSC1), but not in EBV+ LCL cells. NRP1 depletion during reactivation reduced lytic transcription, virion production, and infectivity of NRP1+ PEL cell lines. Selected NRP1+ PEL cells also expressed higher levels of NANOG and OCT3/4 compared to controls. NRP1+ PEL cells had higher amounts of lytic transcripts. Conversely, lytic cells express higher amounts of NRP1 transcripts at the single-cell level. Overexpression of NRP1 resulted in significantly higher lytic transcripts during lytic induction. Our findings suggest that NRP1 is a surface marker expressed for a subtype of PEL cells that is required for efficient lytic replication. It is also associated with increased expression of stemness markers, denoting poor prognosis in cancer. IMPORTANCE KSHV is a cancer-causing herpesvirus that is the etiologic agent for primary effusion lymphoma (PEL), with half of patients who are chemotherapy-resistant and have poor prognosis overall. Here, we present our discovery of NRP1 as a surface marker for a proposed subtype of PEL cell lines. We present data that support a role for NRP1 in generating infectious progeny virions and that NRP1 is associated with viral gene expression during its lytic phase. Due to NRP1’s role in cancer as studied by others, it is possible that NRP1 is contributing toward worse clinical outcomes in a subgroup of people with PEL. We propose that NRP1 is a potential prognostic marker for a certain category of PEL and can be targeted in chemotherapy-resistant PEL since small molecule inhibitors against NRP1 are already available.