High-throughput sequence analysis of peripheral T-cell lymphomas indicates subtype specific viral gene expression patterns and immune cell microenvironments
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA543084 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9059111.fastq.gz | Fastqsanger.gz | |||
| SRR9059112.fastq.gz | Fastqsanger.gz | |||
| SRR9059113.fastq.gz | Fastqsanger.gz | |||
| SRR9059114.fastq.gz | Fastqsanger.gz | |||
| SRR9059115.fastq.gz | Fastqsanger.gz |
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Project description:Certain peripheral T-cell lymphomas (PTCLs) have been associated with viral infection, particularly infection with Epstein-Barr virus (EBV). However, a comprehensive virome analysis across PTCLs has not previously been reported, and viral gene expression profiles have been studied only in certain PTCL subtypes. In this study we utilized published RNA-seq data sets from seven different PTCL studies as well as new RNA-seq data from our laboratory to screen for virus association, to analyze viral gene expression, and to assess B- and T-cell receptor diversity paradigms across these tumor types. In addition to identifying EBV in angioimmunoblastic T-cell lymphoma (AITL) and extranodal NK/T cell lymphoma (ENKTL), two PTCL subtypes with well-established EBV associations, we also detected EBV in several cases of anaplastic large cell lymphoma (ALCL), and we found evidence of infection by the oncogenic viruses KSHV and HTLV-1 in isolated PTCL cases. In AITLs, EBV gene expression analysis showed expression of immediate early, early and late lytic genes, suggesting either abortive lytic replication and/or productive infection in a subset of the EBV infected infiltrating B-lymphocytes. Deconvolution of immune cell subpopulations demonstrated a greater B-cell signal in AITLs than in other PTCL subtypes, consistent with a larger role for B-cell support in the pathogenesis of AITL. T-cell receptor (TCR) and B-cell receptor (BCR) repertoires reconstructed from RNA-seq data demonstrated increased BCR diversity in AITLs, consistent with a possible EBV-driven polyclonal response. These findings indicate potential alternative roles for EBV in PTCLs in addition to the canonical oncogenic mechanisms associated with EBV latent infection. The findings also suggest the involvement of other viruses in T-cell lymphoma pathogenesis and demonstrate immunological alterations associated with these cancers.
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