Metagenomic analysis of DNA viruses from posttransplant lymphoproliferative disorders

Abstract

Posttransplant lymphoproliferative disorders (PTLDs), 50%‐80% of which are strongly associated with Epstein‐Barr virus (EBV), carry a high morbidity and mortality. Most clinical/epidemiological/tumor characteristics do not consistently associate with worse patient survival, so our aim was to identify if other viral genomic characteristics associated better with survival. We extracted DNA from stored paraffin‐embedded PTLD tissues at our center, identified viral sequences by metagenomic shotgun sequencing (MSS), and analyzed the data in relation to clinical outcomes. Our study population comprised 69 PTLD tissue samples collected between 1991 and 2015 from 60 subjects. Nucleotide sequences from at least one virus were detected by MSS in 86% (59/69) of the tissues (EBV in 61%, anelloviruses 52%, gammapapillomaviruses 14%, CMV 7%, and HSV in 3%). No viruses were present in higher proportion in EBV‐negative PTLD (compared to EBV‐positive PTLD). In univariable analysis, death within 5 years of PTLD diagnosis was associated with anellovirus (P = 0.037) and gammapapillomavirus (P = 0.036) detection by MSS, higher tissue qPCR levels of the predominant human anellovirus species torque teno virus (TTV; P = 0.016), T cell type PTLD, liver, brain or bone marrow location. In multivariable analyses, T cell PTLD (P = 0.006) and TTV PCR level (P = 0.012) remained significant. In EBV‐positive PTLD, EBNA‐LP, EBNA1 and EBNA3C had significantly higher levels of nonsynonymous gene variants compared to the other EBV genes. Multiple viruses are detectable in PTLD tissues by MSS. Anellovirus positivity, not EBV positivity,was associated with worse patient survival in our series. Confirmation and extension of this work in larger multicenter studies is desirable.

Genomic variations in EBNA3C of EBV associate with posttransplant lymphoproliferative disorder

“…Previous full genome sequencing studies of EBV in PTLD were restricted to cell lines derived from PTLD patients (9) or FFPE PTLD specimens (16) and did not include non-PTLD transplant controls. Consistent with our findings, Dharnidharka et al (16) also found that EBNA3C, as well as EBNA1 and EBNA-LP, isolated from FFPE specimens had increased numbers of variations compared with other EBV genes; however, the specific variations were not reported. Interestingly, the Ala-683Val and Glu701Gln variations in EBNA3C that we identified from the blood of PTLD subjects were also identified in some PTLD-derived B cell lines (9).…”

“…These variant peptides may constitute tumor neoantigens that could be exploited to augment cellular immunotherapy approaches. Using previously established classification schemes for EBV strains, we found that all EBV genomes isolated from the blood of PTLD patients were type 1, consistent with prior reports that type 1 is prevalent in EBV isolated from FFPE specimens of PTLD patients (16,34). In contrast, 4 of the 6 strain types defined by LMP1 diversity were represented in PTLD-derived EBV genomes (11).…”

ViroMatch: A Computational Pipeline for the Detection of Viral Sequences from Complex Metagenomic Data

“…We developed ViroMatch to analyze data sets of millions of short metagenomic sequence reads to identify viruses by sensitive sequence alignment using pragmatic system resources. We have modified and refined our analysis pipeline workflow over time, primarily applied to the analysis of vertebrate viruses ( 9 – 16 ). The latest version is made available to the public for the first time here.…”

Semi-Quantitative Characterization of Post-Transplant Lymphoproliferative Disorder Morphological Subtypes with [18F]FDG PET/CT

“…Post-transplant lymphoproliferative disorder (PTLD) is a complication of hematopoietic stem cell (HSCT) and solid organ transplantation associated with high morbidity and mortality [ 1 , 2 , 3 , 4 ]. These lymphoid and/or plasmacytic proliferations comprise a broad morphological spectrum, ranging from Epstein–Barr virus drive hyperplasia to malignant monoclonal proliferations, histologically indistinguishable from B-cell (or less commonly T/NK-cell) lymphomas in immunocompetent patients [ 5 ].…”