An integrated genomic and expression analysis of 7q deletion in splenic marginal zone lymphoma

• Published in: PloS one Vol. 7; no. 9; p. e44997
• Main Authors: Watkins, A James, Hamoudi, Rifat A, Zeng, Naiyan, Yan, Qingguo, Huang, Yuanxue, Liu, Hongxiang, Zhang, Jianzhong, Braggio, Esteban, Fonseca, Rafael, de Leval, Laurence, Isaacson, Peter G, Wotherspoon, Andrew, McPhail, Ellen D, Dogan, Ahmet, Du, Ming-Qing
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 13.09.2012; Public Library of Science (PLoS)
• Subjects: Artificial chromosomes; Biology; Cancer; Chromosome Deletion; Chromosomes, Human, Pair 7 - genetics; Clonal deletion; Comparative analysis; Comparative Genomic Hybridization; Cytogenetics; Deoxyribonucleic acid; DNA; DNA methylation; Epigenesis, Genetic; Epigenetic inheritance; Gene deletion; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; Gene sequencing; Genes; Genes, Neoplasm - genetics; Genetic analysis; Genetic aspects; Genome, Human - genetics; Genomics; Heterozygote; Histopathology; Humans; Hybridization; Interferon Regulatory Factors - genetics; Laboratories; Lymphocytes; Lymphocytes B; Lymphoma; Lymphoma, B-Cell, Marginal Zone - genetics; Medicine; MicroRNA; MicroRNAs; MicroRNAs - genetics; MicroRNAs - metabolism; miRNA; Mutation; Mutation - genetics; Non-Hodgkin's lymphomas; Oligonucleotide Array Sequence Analysis; Open Reading Frames - genetics; Pathology; Polymorphism, Genetic; Prostate; Reverse Transcriptase Polymerase Chain Reaction; Sequence Analysis, DNA; Sequence Analysis, RNA; Skin cancer; Spleen; Splenic Neoplasms - genetics; Studies; Minnesota; United Kingdom > UK; United States > US; China; Arizona
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0044997

Splenic marginal zone lymphoma (SMZL) is an indolent B-cell lymphoproliferative disorder characterised by 7q32 deletion, but the target genes of this deletion remain unknown. In order to elucidate the genetic target of this deletion, we performed an integrative analysis of the genetic, epigenetic, transcriptomic and miRNomic data. High resolution array comparative genomic hybridization of 56 cases of SMZL delineated a minimally deleted region (2.8 Mb) at 7q32, but showed no evidence of any cryptic homozygous deletion or recurrent breakpoint in this region. Integrated transcriptomic analysis confirmed significant under-expression of a number of genes in this region in cases of SMZL with deletion, several of which showed hypermethylation. In addition, a cluster of 8 miRNA in this region showed under-expression in cases with the deletion, and three (miR-182/96/183) were also significantly under-expressed (P<0.05) in SMZL relative to other lymphomas. Genomic sequencing of these miRNA and IRF5, a strong candidate gene, did not show any evidence of somatic mutation in SMZL. These observations provide valuable guidance for further characterisation of 7q deletion.