Project description:Defective viral genomes of the copy-back type (cbDVGs) are generated during RSV infectin and are suggested to impact the clinical outcome. Here in this study we selected the nasal secretions from 13 hospitalized pediatric pateints, including both cnDVG+ and cbDVG-, to perform RNA-seq to understand the impact of cbDVGs on patient transcriptome.
Project description:Epstein-Barr virus (EBV) is a human gamma-herpesvirus that is causally associated with various lymphomas and carcinomas. Although EBV is not typically associated with multiple myeloma (MM), it can be found in some B-cell lines derived from multiple myeloma patients. Here, we analyzed two EBV+ MM-patient derived cell lines IM9 and ARH77 and found defective viral genomes and atypical viral gene expression patterns. We performed RNA-seq transcriptomics to characterize the viral and cellular properties of the two EBV+ cell lines compared to canonical MM cell line 8226. Principal component analyses indicated that IM9 and ARH77 clustered together and distinct from 8226. ImmGen analysis designate these cells as stem-cell and bone marrow derived. IM9 and ARH77 displayed atypical viral gene expression, including a leaky lytic cycle gene expression with absence of lytic DNA amplification. Genome sequencing revealed that EBV genomes in ARH77 contain large deletions, while IM9 has copy number losses in multiple EBV loci. Both IM9 and ARH77 have numerous EBV genome heterogeneity suggestive of cell harboring multiple and variant viral genomes. Among the lytic genes, we identified atypical high-level expression of BLRF2 and BLRF1. BRLF2 encodes a tegument protein previously shown to bind BNRF1 and to also interact with cGAS, similar to KSHV ORF52, also known as the inhibitor of cGAS (KicGAS). We demonstrate the shRNA depletion of BLRF2 alters viral and host gene expression, including a reduction in lytic gene activation and DNA amplification. These findings demonstrate that aberrant viral genomes and lytic gene expression persist in rare B-cells derived from MM tumors, and suggest that EBV may contribute to etiology of MM.
Project description:Epstein-Barr virus (EBV) is a human gamma-herpesvirus that is causally associated with various lymphomas and carcinomas. Although EBV is not typically associated with multiple myeloma (MM), it can be found in some B-cell lines derived from multiple myeloma patients. Here, we analyzed two EBV+ MM-patient derived cell lines IM9 and ARH77 and found defective viral genomes and atypical viral gene expression patterns. We performed RNA-seq transcriptomics to characterize the viral and cellular properties of the two EBV+ cell lines compared to canonical MM cell line 8226. Principal component analyses indicated that IM9 and ARH77 clustered together and distinct from 8226. ImmGen analysis designate these cells as stem-cell and bone marrow derived. IM9 and ARH77 displayed atypical viral gene expression, including a leaky lytic cycle gene expression with absence of lytic DNA amplification. Genome sequencing revealed that EBV genomes in ARH77 contain large deletions, while IM9 has copy number losses in multiple EBV loci. Both IM9 and ARH77 have numerous EBV genome heterogeneity suggestive of cell harboring multiple and variant viral genomes. Among the lytic genes, we identified atypical high-level expression of BLRF2 and BLRF1. BRLF2 encodes a tegument protein previously shown to bind BNRF1 and to also interact with cGAS, similar to KSHV ORF52, also known as the inhibitor of cGAS (KicGAS). We demonstrate the shRNA depletion of BLRF2 alters viral and host gene expression, including a reduction in lytic gene activation and DNA amplification. These findings demonstrate that aberrant viral genomes and lytic gene expression persist in rare B-cells derived from MM tumors, and suggest that EBV may contribute to etiology of MM.
