Whole-Genome Analysis Revealed the Genetic Landscape of Intravascular Large B-Cell Lymphoma

• Published in: Blood 2024-11, Vol.144 (Supplement 1), p.2983-2983
• Main Authors: Mori, Takuto, Shimada, Kazuyuki, Mimura, Kaito, Kakiuchi, Nobuyuki, Maeda, Hirona, Takaori-Kondo, Akifumi, Ogawa, Seishi, Tomita, Akihiro, Yoshida, Kenichi
• Format: Article
• Language: English
• ISSN: 0006-4971; 1528-0020
• DOI: 10.1182/blood-2024-204466

Introduction Intravascular large B-cell lymphoma (IVLBCL) is a rare subtype of aggressive lymphoma characterized by selective growth of large malignant cells within small vessels in multiple organs. Previous studies using targeted sequencing and exome sequencing of IVLBCLs revealed a similar mutational landscape with that of activated B-cell (ABC) type of DLBCLs. However, the mechanism of exclusive localization of lymphoma cells within blood vessels and molecular pathogenesis of tumor development in IVLBCL remains unclear. Recent reports showed the usefulness of cell-free DNA (cfDNA) for genetic analysis due to the enrichment of tumor-cell derived DNA in cfDNA in patients with IVLBCL rather than biopsy samples with tumor cell scarcity. Method To reveal the mutational landscape of IVLBCLs, we perform whole-genome sequencing of 12 patients with IVLBCL using plasma-derived cfDNA with peripheral blood mononuclear cells as controls. Single-nucleotide variants (SNVs) and small insertion-deletions (indels) were analyzed with G-CAT pipeline; copy number alterations with ASCAT; and structural variations (SVs) with GRIDSS. Mutational signatures were analyzed with SigProfiler and its associated packages. Results The median of 32,699 SNVs and indels were detected, 0.78% of which were exonic mutations. IGLL5, PIM1, CD79B, ETV6, TBL1XR1, MYD88, HIST1H1E, KLHL14, MPEG1, VMP1, BCL11A, BTG1, DTX1, KMT2D, PRDM1, TTN, and OSBPL10 genes were recurrently (≥33%) mutated in coding regions. Although previous studies identified 3'UTR region of NFIKIZ gene in ABC-type DLBCLs, no NFIKIZ mutations were found in IVLBCL samples. We identified foci affected by Kataegis, which is a form of hypermutations characterized by clustered SNVs, including IGLL5, PIM1, BTG2 and BCL6 genes. Cony number analysis showed enrichment of focal gain in 1q32 involving MDM4 and BTG1, 9p24 involving CD274, and 19q13. Focal deletions were detected in 3p13 involving FOXP1, 6p21 involving PRDM1, 6q24, and 9p21 involving CDKN2A/B. As for structural variants, we detected recurrent deletions in CDKN2A/B, FHIT, ETV6, TOX, and CD58. Various type of SVs involving CD274 were found, including deletions in 3'-UTR, tandem duplication, and translocation. Mutational signature analysis of overall single base substitutions identified SBS1, SBS5, and SBS40a, signatures caused by endogenous mutational process, and SBS9 derived from somatic mutations caused by polymerase eta. By contrast, Kataegic mutations had enrichment of SB