Metagenomic analysis to identify novel infectious agents in systemic anaplastic large cell lymphoma

Anaplastic large cell lymphoma (ALCL) is a rare CD30-expressing T-cell non-Hodgkin lymphoma (NHL). Risk of systemic ALCL is highly increased among immunosuppressed individuals. Because risk of cancers associated with viruses is increased with immunosuppression, we conducted a metagenomic analysis of microbial associations with systemic ALCL to determine whether a known or novel pathogen is associated with the tumor. Total RNA from specimens of 29 systemic ALCLs (28 cases from the general population, 1 case from an HIV-infected individual), 3 Epstein-Barr virus (EBV)-positive diffuse large B-cell lymphomas occurring in transplant recipients (positive controls), and 5 breast cancers (negative controls) was extracted and sequenced. We utilized a stepwise bioinformatic approach to comprehensively characterize RNA sequencing reads and identify sequences related to viruses and other microorganisms. Although we detected EBV in the positive controls, we did not find evidence of a biologically-relevant microorganism associated specifically with ALCL samples or the negative control specimens. Therefore, our results do not support a viral etiology for ALCL. Additional studies of ALCL cases arising among immunosuppressed people individuals are warranted.

This repository contains PathSeq and virID output files and an R notebook sufficient to reproduce figures in the manuscript "Metagenomic analysis to identify novel infectious agents in systemic anaplastic large cell lymphoma"