Molecular distinctiveness of duodenal-type follicular lymphoma revealed by integrated multi-omic analysis

Abstract

Abstract Follicular lymphoma (FL) is the most common indolent B-cell non-Hodgkin lymphoma, typically presenting with widespread nodal involvement and an incurable clinical course. In contrast, duodenal-type follicular lymphoma (DTFL) is a rare and distinct FL subtype that is characteristically localized to the duodenum, shows minimal systemic dissemination, and is associated with excellent long-term survival. Due to the limited use of endoscopic practices, DTFL has a low incidence of diagnosis, leaving its biology largely unexplored. While previous transcriptomic studies have suggested similarities between DTFL and gastric MALT lymphoma—particularly in the overexpression of CCL20 and MAdCAM-1—many such analyses were conducted on biopsy specimens, raising concerns regarding contamination by gastrointestinal tissue and the resulting misinterpretation of tumor-intrinsic gene expression. In this study, we aimed to define the molecular characteristics of DTFL through a comprehensive genomic and transcriptomic approach. We analyzed fresh-frozen endoscopic biopsy specimens from 23 patients with DTFL and 8 with gastric MALT lymphoma as controls. We performed whole-exome sequencing (WES) and RNA sequencing (RNA-seq). Mutation calling was conducted using our in-house pipeline, and driver gene analysis was performed with dNdScv. RNA-seq reads were processed using STAR for alignment and RSEM for quantification. Differential gene expression and pathway enrichment analyses were conducted to identify subtype-specific molecular features. To eliminate the influence of gastrointestinal tract-derived transcripts, we utilized tissue expression profiles from the GTEx database and defined a set of 4,943 genes specifically expressed in normal stomach and intestinal tissues. These lineage-associated genes were excluded from downstream analyses. Additionally, two samples with extremely low tumor purity (as determined by WES) and ten with high expression of gastrointestinal-specific genes (by RNA-seq) were excluded from transcriptome analysis to ensure accurate tumor profiling. Fusion gene detection was performed using the Arriba algorithm on RNA-seq data. We identified CREBBP (85.7%), BCL2 (71.4%), KMT2D (42.8%), CARD11 (42.8%), HVCN1 (35.7%), and EEF1A1 (21.4%) as the most frequently mutated genes in DTFL. Among them, CREBBP was identified as a significant driver gene. While KMT2D mutations were significantly less frequent than in advanced nodal FL (52% vs. 79%), EEF1A1 and HVCN1 mutations were significantly enriched in DTFL. Importantly, TNFRSF14 mutations, which have been reported in 32% of DTFL cases in other cohorts, were absent in our cohorts. In contrast, none of these mutations were found in gastric MALT lymphoma samples. Unsupervised hierarchical clustering of RNA-seq data from 14 DTFL and 5 gastric MALT lymphoma cases—after exclusion of gastrointestinal-specific genes—segregated the two diseases into clearly distinct molecular groups. We identified 98 genes upregulated in DTFL and 98 upregulated in gastric MALT lymphoma. Gene set enrichment analysis revealed that chromatin remodeling-related genes were enriched in gastric MALT lymphoma, while WNT signaling, PI3K-AKT pathway, and neutrophil-mediated immune response were enriched in DTFL. Notably, DTFL samples showed significantly higher expression of AKT1, PIK3CA, and NFKB1, suggesting activation of survival and inflammatory pathways. In conclusion, our integrated genomic and transcriptomic profiling demonstrates that DTFL is molecularly distinct from gastric MALT lymphoma, despite prior suggestions of similarity. Also, DTFL is distinct from nodal FL. The application of strict filtering to eliminate contaminating gastrointestinal signatures allowed us to delineate tumor-intrinsic characteristics with high specificity. Our findings provide new insights into the biology of DTFL and lay the groundwork for future diagnostic and therapeutic strategies.