The mutational landscape of ocular marginal zone lymphoma identifies frequent alterations in TNFAIP3 followed by mutations in TBL1XR1 and CREBBP
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Hyunchul Jung1,4,*, Hae Yong Yoo2,*, Seung Ho Lee2,*, Sohyun Shin3, Sang Cheol Kim4, Sejoon Lee4, Je-Gun Joung4, Jae-Yong Nam2,4, Daeun Ryu2,4, Jae Won Yun4,5, Jung Kyoon Choi1, Ambarnil Ghosh5, Kyeong Kyu Kim5, Seok Jin Kim6, Won Seog Kim6, Woong-Yang Park1 and Young Hyeh Ko3
1Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
2Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
3Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
4Samsung Genome Institute, Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea
5Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
6Division of Hematology and Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
*These authors have contributed equally to this work
Young Hyeh Ko, email: email@example.com
Woong-Yang Park, email: firstname.lastname@example.org
Keywords: marginal zone lymphoma, ocular, whole-genome sequencing, RNA sequencing, mutation
Received: October 17, 2016 Accepted: November 30, 2016 Published: August 28, 2018
Ocular marginal zone lymphoma is a common type of low-grade B-cell lymphoma. To investigate the genomic changes that occur in ocular marginal zone lymphoma, we analyzed 10 cases of ocular marginal zone lymphoma using whole-genome and RNA sequencing and an additional 38 cases using targeted sequencing. Major genetic alterations affecting genes involved in nuclear factor (NF)-κB pathway activation (60%), chromatin modification and transcriptional regulation (44%), and B-cell differentiation (23%) were identified. In whole-genome sequencing, the 6q23.3 region containing TNFAIP3 was deleted in 5 samples (50%). In addition, 5 structural variation breakpoints in the first intron of IL20RA located in the 6q23.3 region was found in 3 samples (30%). In targeted sequencing, a disruptive mutation of TNFAIP3 was the most common alteration (54%), followed by mutations of TBL1XR1 (18%), cAMP response element binding proteins (CREBBP) (17%) and KMT2D (6%). All TBL1XR1 mutations were located within the WD40 domain, and TBL1XR1 mutants transfected into 293T cells increased TBL1XR1 binding with nuclear receptor corepressor (NCoR), leading to increased degradation of NCoR and the activation of NF-kB and JUN target genes. This study confirms genes involving in the activation of the NF-kB signaling pathway is the major driver in the oncogenesis of ocular MZL.
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