Genomic insights into the pathogenesis of Epstein–Barr virus-associated diffuse large B-cell lymphoma by whole-genome and targeted amplicon sequencing

Abstract

Epstein–Barr virus (EBV)-associated diffuse large B-cell lymphoma not otherwise specified (DLBCL NOS) constitute a distinct clinicopathological entity in the current World Health Organization (WHO) classification. However, its genomic features remain sparsely characterized. Here, we combine whole-genome sequencing (WGS), targeted amplicon sequencing (tNGS), and fluorescence in situ hybridization (FISH) from 47 EBV + DLBCL (NOS) cases to delineate the genomic landscape of this rare disease. Integrated WGS and tNGS analysis clearly distinguished this tumor type from EBV-negative DLBCL due to frequent mutations in ARID1A (45%), KMT2A/KMT2D (32/30%), ANKRD11 (32%), or NOTCH2 (32%). WGS uncovered structural aberrations including 6q deletions (5/8 patients), which were subsequently validated by FISH (14/32 cases). Expanding on previous reports, we identified recurrent alterations in CCR6 (15%), DAPK1 (15%), TNFRSF21 (13%), CCR7 (11%), and YY1 (6%). Lastly, functional annotation of the mutational landscape by sequential gene set enrichment and network propagation predicted an effect on the nuclear factor κB (NFκB) pathway (CSNK2A2, CARD10), IL6/JAK/STAT (SOCS1/3, STAT3), and WNT signaling (FRAT1, SFRP5) alongside aberrations in immunological processes, such as interferon response. This first comprehensive description of EBV + DLBCL (NOS) tumors substantiates the evidence of its pathobiological independence and helps stratify the molecular taxonomy of aggressive lymphomas in the effort for future therapeutic strategies.

EBV-positive Diffuse Large B-Cell Lymphoma, NOS in a Filipino Patient

“…It may be useful in the future, once these technologies are more widely available. 24,25 The prognosis and appropriate treatment of EBV+ DLBCL is markedly different between these closely related entities. 2,26 EBV positivity is associated with more advanced stage, extranodal involvement, and poorer response to treatment.…”

Integrative genomic and transcriptomic analysis in plasmablastic lymphoma identifies disruption of key regulatory pathways

“…As described in Gebauer et al, 24 raw fastq reads trimmed (adapter and quality values) using fastp 25 (version 0.20.0; minimum length, 50 bp; maximum unqualified bases, 30%; trim tail set to 1) and trimmed reads were mapped to GRCh37/hg19 by using bwa mem (version 0.7.15). 26 Resulting SAM files were cleaned and sorted and converted into BAM format using P icard T ools (version 2.18.4).…”

CCR7 in Blood Cancers – Review of Its Pathophysiological Roles and the Potential as a Therapeutic Target

“…Therefore, it is not surprising that chemokine receptor (CKR) expression varies between these subtypes and in association with disease location (91,92). Up to 62% of DLBCL express CCR7, both in analyses of flow cytometry and immunohistochemistry (IHC), with a preferential mRNA and protein expression in the non-GCB subtypes, especially in patients with both LN and BM involvement (79,85,93,94). In EBV-positive DLBCL of the elderly, in primary effusion lymphoma, in gastric extranodal DLBCL, and in transformation of gastric mucosa-associated lymphoid tissue (MALT) lymphomas to gastric extranodal DLBCL, up-regulation of CCR7 mRNA, among other CKR, was reported (32,91,(94)(95)(96).…”

“…Up to 62% of DLBCL express CCR7, both in analyses of flow cytometry and immunohistochemistry (IHC), with a preferential mRNA and protein expression in the non-GCB subtypes, especially in patients with both LN and BM involvement (79,85,93,94). In EBV-positive DLBCL of the elderly, in primary effusion lymphoma, in gastric extranodal DLBCL, and in transformation of gastric mucosa-associated lymphoid tissue (MALT) lymphomas to gastric extranodal DLBCL, up-regulation of CCR7 mRNA, among other CKR, was reported (32,91,(94)(95)(96). Notably, in EBV-associated DLBCL recurrent mutations in the CCR7 gene are found in 11% of patients (94).…”

“…In EBV-positive DLBCL of the elderly, in primary effusion lymphoma, in gastric extranodal DLBCL, and in transformation of gastric mucosa-associated lymphoid tissue (MALT) lymphomas to gastric extranodal DLBCL, up-regulation of CCR7 mRNA, among other CKR, was reported (32,91,(94)(95)(96). Notably, in EBV-associated DLBCL recurrent mutations in the CCR7 gene are found in 11% of patients (94). These alterations seem exclusive to this subtype and could enable homing of tumor cells to SLOs where the virus in turn propagates infection or establishes latency, thereby driving lymphomagenesis (97).…”