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

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 SBS5 and SBS84 caused by activity of activation-induced cytidine deaminase (AID), suggesting that different mutational processes related to somatic hypermutations (SHMs) operated independently.

To trace the development of IVLBCLs, we analyzed the relative timing of the acquisition of CNAs and SNVs using MutationTimeR package. Most of the recurrent exonic mutations were classified as early clonal mutations or intermediate clonal mutations. Loss-of-heterozygosity (LOH) of 9p involving CDKN2A was identified in 6 of 12 cases and all these changes were acquired in the earlier phase relative to overall SNVs.

Conclusion

Our data provide a mutational landscape of the whole genome in IVLBCLs. SHMs are deeply involved in the mutagenesis of IVLBCLs, where multiple mutational processes independently occurred in different target genes or regions. Genetic abnormalities frequently occurred in chromosome 9p, which contribute to the early development of IVLBCLs. Our genetic analysis can provide a deep insight into the disease characteristic of IVLBCL.

Shimada:BeiGene: Consultancy; Chigai: Consultancy, Honoraria; Daiichi Sankyo: Consultancy, Honoraria; Gilead: Consultancy, Honoraria; Jannsen: Consultancy, Honoraria; Eli Lilly: Consultancy; Ohara: Consultancy; Kyowa Kirin: Honoraria, Research Funding; Eisai: Honoraria; Takeda: Honoraria; Bristol-Myers Squibb: Honoraria; Nippon Shinyaku: Honoraria; Meiji Seika Pharma: Honoraria; Ono: Honoraria; AbbVie: Honoraria; Novartis: Honoraria; Genmab: Honoraria; Mundi Pharma: Honoraria; Sanofi: Honoraria. Mimura:Takeda Science Foundation: Research Funding. Kakiuchi:Sumitomo Pharma: Research Funding. Takaori-Kondo:Janssen Pharmaceutical K.K.: Honoraria; Otsuka Pharmaceutical Co., Ltd.: Honoraria; Megakaryon Co., Ltd.: Consultancy, Honoraria; AstraZeneca K.K.: Honoraria; Gilead Sciences: Honoraria; Bristol Myers Squibb: Honoraria; Nippon Shinyaku Co., Ltd.: Research Funding; Japanese Society of Hematology: Research Funding; CHUGAI PHARMACEUTICAL CO., LTD.: Research Funding; AbbVie Inc.: Honoraria, Research Funding; Eisai Co., Ltd: Research Funding; Otsuka Pharmaceutical Co., Ltd.: Research Funding; Kyowa Kirin Co., Ltd.: Research Funding; Shionogi & Co., Ltd.: Research Funding; ASAHI KASEI PHARMA CORPORATION: Research Funding; PhamaEssentia Japan: Research Funding; Dai-ichi Kogyo Seiyaku Co., Ltd.: Research Funding; ONO PHARMACEUTICAL CO., LTD.: Research Funding. Ogawa:Nakatani Foundation: Speakers Bureau; Nihonshinyaku Co., Ltd.: Other: Donation; Otsuka Pharmaceutical Co., Ltd.: Research Funding; The Mitsubishi Foundation: Speakers Bureau; Nanpuh Hospital: Other: Endowed chair; Asahi Genomics Inc: Current equity holder in publicly-traded company; Chordia Therapeutics Inc.: Consultancy, Other: Endowed chair, Research Funding; Eisai Co., Ltd.: Consultancy, Research Funding. Tomita:Chugai Pharmaceutical: Honoraria, Research Funding; Astellas Pharma: Honoraria, Research Funding; Eisai: Honoraria, Research Funding; Otsuka Pharmaceutical: Research Funding; Ono Pharmaceutical: Research Funding; Shionogi: Research Funding; Sumitomo Dainippon Pharma: Research Funding; Taiho Pharmaceutical: Research Funding; Takeda Pharmaceutical: Honoraria, Research Funding; Teijin: Research Funding; Nippon Shinyaku: Honoraria, Research Funding; Nihon Pharmaceutical: Research Funding; Pfizer Japan: Research Funding; Mochida Pharmaceutical: Research Funding; Yakult Honsha: Research Funding; Perseus Proteomics: Research Funding; AstraZeneca: Honoraria; AbbVie GK: Honoraria; Kyowa Kirin: Honoraria, Research Funding; Janssen Pharmaceutical: Honoraria; Zenyaku Kogyo: Honoraria; Bristol-Myers Squibb: Honoraria; SymBio Pharmaceutical: Honoraria. Yoshida:Takeda Science Foundation: Research Funding; The Naito Foundation: Research Funding.