title: An integrated genomic and expression analysis of 7q deletion in splenic marginal zone lymphoma.
abstract: 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.
authors.affiliation: Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom.
authors.forename: A James
authors.initials: AJ
authors.lastname: Watkins
authors.forename: Rifat A
authors.initials: RA
authors.lastname: Hamoudi
authors.forename: Naiyan
authors.initials: N
authors.lastname: Zeng
authors.forename: Qingguo
authors.initials: Q
authors.lastname: Yan
authors.forename: Yuanxue
authors.initials: Y
authors.lastname: Huang
authors.forename: Hongxiang
authors.initials: H
authors.lastname: Liu
authors.forename: Jianzhong
authors.initials: J
authors.lastname: Zhang
authors.forename: Esteban
authors.initials: E
authors.lastname: Braggio
authors.forename: Rafael
authors.initials: R
authors.lastname: Fonseca
authors.forename: Laurence
authors.initials: L
authors.lastname: de Leval
authors.forename: Peter G
authors.initials: PG
authors.lastname: Isaacson
authors.forename: Andrew
authors.initials: A
authors.lastname: Wotherspoon
authors.forename: Ellen D
authors.initials: ED
authors.lastname: McPhail
authors.forename: Ahmet
authors.initials: A
authors.lastname: Dogan
authors.forename: Ming-Qing
authors.initials: MQ
authors.lastname: Du
mesh_terms: D002872:Chromosome Deletion; D002897:Chromosomes, Human, Pair 7 / Q000235:genetics*; D055028:Comparative Genomic Hybridization; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D052138:Genes, Neoplasm / Q000235:genetics; D015894:Genome, Human / Q000235:genetics*; D006579:Heterozygote; D006801:Humans; D050835:Interferon Regulatory Factors / Q000235:genetics; D018442:Lymphoma, B-Cell, Marginal Zone / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D009154:Mutation / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames / Q000235:genetics; D011110:Polymorphism, Genetic; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D013160:Splenic Neoplasms / Q000235:genetics*
chemical_list: C431713:IRF5 protein, human; D050835:Interferon Regulatory Factors; D035683:MicroRNAs