Uniparental disomies, homozygous deletions, amplifications, and target genes in mantle cell lymphoma revealed by integrative high-resolution whole-genome profiling

Sílvia Beà, Itziar Salaverria, Lluís Armengol, Magda Pinyol, Verónica Fernández, Elena M. Hartmann, Pedro Jares, Virginia Amador, Luís Hernández, Alba Navarro, German Ott, Andreas Rosenwald, Xavier P. Estivill, Elias Campo

Research output: Contribution to journalArticle

118 Citations (Scopus)

Abstract

Mantle cell lymphoma(MCL) is genetically characterized by the t(11;14)(q13;q32) translocation and a high number of secondary chromosomal alterations.However, only a limited number of target genes have been identified. We have studied 10 MCL cell lines and 28 primary tumors with a combination of a high-density single-nucleotide polymorphism array and gene expression profiling. We detected highly altered genomes in the majority of the samples with a high number of partial uniparental disomies(UPDs).The UPD at 17p was one of the most common, and it was associated with TP53 gene inactivation. Homozygous deletions targeted 4 known tumor suppressor genes(CDKN2C, BCL2L11, CDKN2A, and RB1) and 6 new genes(FAF1, MAP2, SP100,MOBKL2B, ZNF280A, and PRAME). Gene amplification coupled with overexpres-sion was identified in 35 different regions. The most recurrent amplified regions were 11q13.3-q13.5, 13q31.3, and 18q21.33, which targeted CCND1, C13orf25, and BCL2, respectively. Interestingly, the breakpoints flanking all the genomic alterations, including UPDs, were significantly associated with genomic regions enriched in copy number variants and segmental duplications, suggesting that the recombination at these regions may play a role in the genomic instability of MCL. This integrative genomic analysis has revealed target genes that may be potentially relevant in MCL pathogenesis.

Original languageEnglish
Pages (from-to)3059-3069
Number of pages11
JournalBlood
Volume113
Issue number13
DOIs
Publication statusPublished - 26 Mar 2009
Externally publishedYes

Fingerprint

Uniparental Disomy
Mantle-Cell Lymphoma
Gene Amplification
Amplification
Genes
Genome
Genomic Segmental Duplications
Tumors
Genomic Instability
p53 Genes
Gene Silencing
Gene Expression Profiling
Tumor Suppressor Genes
Genetic Recombination
Single Nucleotide Polymorphism
Polymorphism
Gene expression
Cell Line
Nucleotides
Cells

ASJC Scopus subject areas

  • Immunology
  • Biochemistry
  • Hematology
  • Cell Biology

Cite this

Uniparental disomies, homozygous deletions, amplifications, and target genes in mantle cell lymphoma revealed by integrative high-resolution whole-genome profiling. / Beà, Sílvia; Salaverria, Itziar; Armengol, Lluís; Pinyol, Magda; Fernández, Verónica; Hartmann, Elena M.; Jares, Pedro; Amador, Virginia; Hernández, Luís; Navarro, Alba; Ott, German; Rosenwald, Andreas; Estivill, Xavier P.; Campo, Elias.

In: Blood, Vol. 113, No. 13, 26.03.2009, p. 3059-3069.

Research output: Contribution to journalArticle

Beà, S, Salaverria, I, Armengol, L, Pinyol, M, Fernández, V, Hartmann, EM, Jares, P, Amador, V, Hernández, L, Navarro, A, Ott, G, Rosenwald, A, Estivill, XP & Campo, E 2009, 'Uniparental disomies, homozygous deletions, amplifications, and target genes in mantle cell lymphoma revealed by integrative high-resolution whole-genome profiling', Blood, vol. 113, no. 13, pp. 3059-3069. https://doi.org/10.1182/blood-2008-07-170183
Beà, Sílvia ; Salaverria, Itziar ; Armengol, Lluís ; Pinyol, Magda ; Fernández, Verónica ; Hartmann, Elena M. ; Jares, Pedro ; Amador, Virginia ; Hernández, Luís ; Navarro, Alba ; Ott, German ; Rosenwald, Andreas ; Estivill, Xavier P. ; Campo, Elias. / Uniparental disomies, homozygous deletions, amplifications, and target genes in mantle cell lymphoma revealed by integrative high-resolution whole-genome profiling. In: Blood. 2009 ; Vol. 113, No. 13. pp. 3059-3069.
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abstract = "Mantle cell lymphoma(MCL) is genetically characterized by the t(11;14)(q13;q32) translocation and a high number of secondary chromosomal alterations.However, only a limited number of target genes have been identified. We have studied 10 MCL cell lines and 28 primary tumors with a combination of a high-density single-nucleotide polymorphism array and gene expression profiling. We detected highly altered genomes in the majority of the samples with a high number of partial uniparental disomies(UPDs).The UPD at 17p was one of the most common, and it was associated with TP53 gene inactivation. Homozygous deletions targeted 4 known tumor suppressor genes(CDKN2C, BCL2L11, CDKN2A, and RB1) and 6 new genes(FAF1, MAP2, SP100,MOBKL2B, ZNF280A, and PRAME). Gene amplification coupled with overexpres-sion was identified in 35 different regions. The most recurrent amplified regions were 11q13.3-q13.5, 13q31.3, and 18q21.33, which targeted CCND1, C13orf25, and BCL2, respectively. Interestingly, the breakpoints flanking all the genomic alterations, including UPDs, were significantly associated with genomic regions enriched in copy number variants and segmental duplications, suggesting that the recombination at these regions may play a role in the genomic instability of MCL. This integrative genomic analysis has revealed target genes that may be potentially relevant in MCL pathogenesis.",
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AU - Beà, Sílvia

AU - Salaverria, Itziar

AU - Armengol, Lluís

AU - Pinyol, Magda

AU - Fernández, Verónica

AU - Hartmann, Elena M.

AU - Jares, Pedro

AU - Amador, Virginia

AU - Hernández, Luís

AU - Navarro, Alba

AU - Ott, German

AU - Rosenwald, Andreas

AU - Estivill, Xavier P.

AU - Campo, Elias

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N2 - Mantle cell lymphoma(MCL) is genetically characterized by the t(11;14)(q13;q32) translocation and a high number of secondary chromosomal alterations.However, only a limited number of target genes have been identified. We have studied 10 MCL cell lines and 28 primary tumors with a combination of a high-density single-nucleotide polymorphism array and gene expression profiling. We detected highly altered genomes in the majority of the samples with a high number of partial uniparental disomies(UPDs).The UPD at 17p was one of the most common, and it was associated with TP53 gene inactivation. Homozygous deletions targeted 4 known tumor suppressor genes(CDKN2C, BCL2L11, CDKN2A, and RB1) and 6 new genes(FAF1, MAP2, SP100,MOBKL2B, ZNF280A, and PRAME). Gene amplification coupled with overexpres-sion was identified in 35 different regions. The most recurrent amplified regions were 11q13.3-q13.5, 13q31.3, and 18q21.33, which targeted CCND1, C13orf25, and BCL2, respectively. Interestingly, the breakpoints flanking all the genomic alterations, including UPDs, were significantly associated with genomic regions enriched in copy number variants and segmental duplications, suggesting that the recombination at these regions may play a role in the genomic instability of MCL. This integrative genomic analysis has revealed target genes that may be potentially relevant in MCL pathogenesis.

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