An Integrated Genomic and Expression Analysis of 7q Deletion in Splenic Marginal Zone Lymphoma

A. James Watkins, Rifat A. Hamoudi, Naiyan Zeng, Qingguo Yan, Yuanxue Huang, Hongxiang Liu, Jianzhong Zhang, Esteban D Braggio, Rafael Fonseca, Laurence de Leval, Peter G. Isaacson, Andrew Wotherspoon, Ellen McPhail, Ahmet Dogan, Ming Qing Du

Research output: Contribution to journalArticle

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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.

Original languageEnglish (US)
Article numbere44997
JournalPLoS One
Volume7
Issue number9
DOIs
StatePublished - Sep 13 2012

Fingerprint

lymphoma
Lymphoma
Genes
MicroRNAs
genomics
transcriptomics
microRNA
Cells
comparative genomic hybridization
somatic mutation
lymphatic diseases
Comparative Genomic Hybridization
Lymphoproliferative Disorders
gene deletion
Gene Deletion
Epigenomics
epigenetics
B-lymphocytes
genetic techniques and protocols
B-Lymphocytes

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Watkins, A. J., Hamoudi, R. A., Zeng, N., Yan, Q., Huang, Y., Liu, H., ... Du, M. Q. (2012). An Integrated Genomic and Expression Analysis of 7q Deletion in Splenic Marginal Zone Lymphoma. PLoS One, 7(9), [e44997]. https://doi.org/10.1371/journal.pone.0044997

An Integrated Genomic and Expression Analysis of 7q Deletion in Splenic Marginal Zone Lymphoma. / Watkins, A. James; Hamoudi, Rifat A.; Zeng, Naiyan; Yan, Qingguo; Huang, Yuanxue; Liu, Hongxiang; Zhang, Jianzhong; Braggio, Esteban D; Fonseca, Rafael; de Leval, Laurence; Isaacson, Peter G.; Wotherspoon, Andrew; McPhail, Ellen; Dogan, Ahmet; Du, Ming Qing.

In: PLoS One, Vol. 7, No. 9, e44997, 13.09.2012.

Research output: Contribution to journalArticle

Watkins, AJ, Hamoudi, RA, Zeng, N, Yan, Q, Huang, Y, Liu, H, Zhang, J, Braggio, ED, Fonseca, R, de Leval, L, Isaacson, PG, Wotherspoon, A, McPhail, E, Dogan, A & Du, MQ 2012, 'An Integrated Genomic and Expression Analysis of 7q Deletion in Splenic Marginal Zone Lymphoma', PLoS One, vol. 7, no. 9, e44997. https://doi.org/10.1371/journal.pone.0044997
Watkins, A. James ; Hamoudi, Rifat A. ; Zeng, Naiyan ; Yan, Qingguo ; Huang, Yuanxue ; Liu, Hongxiang ; Zhang, Jianzhong ; Braggio, Esteban D ; Fonseca, Rafael ; de Leval, Laurence ; Isaacson, Peter G. ; Wotherspoon, Andrew ; McPhail, Ellen ; Dogan, Ahmet ; Du, Ming Qing. / An Integrated Genomic and Expression Analysis of 7q Deletion in Splenic Marginal Zone Lymphoma. In: PLoS One. 2012 ; Vol. 7, No. 9.
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