Limits...
Integrated genomic analysis implicates haploinsufficiency of multiple chromosome 5q31.2 genes in de novo myelodysplastic syndromes pathogenesis.

Graubert TA, Payton MA, Shao J, Walgren RA, Monahan RS, Frater JL, Walshauser MA, Martin MG, Kasai Y, Walter MJ - PLoS ONE (2009)

Bottom Line: We found no somatic nucleotide changes in the 46 MDS samples, and no cytogenetically silent 5q31.2 deletions in 20/20 samples analyzed by array CGH.The mRNA levels of 7 genes in the commonly deleted interval were reduced by 50% in CD34+ cells from del(5q) MDS samples, and no gene showed complete loss of expression.Taken together, these data show that small deletions and/or point mutations in individual 5q31.2 genes are not common events in MDS, and implicate haploinsufficiency of multiple genes as the relevant genetic consequence of this common deletion.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America.

ABSTRACT
Deletions spanning chromosome 5q31.2 are among the most common recurring cytogenetic abnormalities detectable in myelodysplastic syndromes (MDS). Prior genomic studies have suggested that haploinsufficiency of multiple 5q31.2 genes may contribute to MDS pathogenesis. However, this hypothesis has never been formally tested. Therefore, we designed this study to systematically and comprehensively evaluate all 28 chromosome 5q31.2 genes and directly test whether haploinsufficiency of a single 5q31.2 gene may result from a heterozygous nucleotide mutation or microdeletion. We selected paired tumor (bone marrow) and germline (skin) DNA samples from 46 de novo MDS patients (37 without a cytogenetic 5q31.2 deletion) and performed total exonic gene resequencing (479 amplicons) and array comparative genomic hybridization (CGH). We found no somatic nucleotide changes in the 46 MDS samples, and no cytogenetically silent 5q31.2 deletions in 20/20 samples analyzed by array CGH. Twelve novel single nucleotide polymorphisms were discovered. The mRNA levels of 7 genes in the commonly deleted interval were reduced by 50% in CD34+ cells from del(5q) MDS samples, and no gene showed complete loss of expression. Taken together, these data show that small deletions and/or point mutations in individual 5q31.2 genes are not common events in MDS, and implicate haploinsufficiency of multiple genes as the relevant genetic consequence of this common deletion.

Show MeSH

Related in: MedlinePlus

5q31.2 SNP loss of heterozygosity in del(5q) samples.A. Sequence traces for SNP rs1059110 in tumor samples from an individual homozygous for the common allele (left), a heterozygote (middle) with a normal allele trace peak height ratio = 0.44 (i.e., no allelic imbalance), and a heterozygote (right) with an abnormal allele trace peak height ratio = 0.20 (i.e., allelic imbalance). B. Heat map of allelic imbalance for 23 SNPs from 8 del(5q) and 9 non-del(5q) MDS samples. Each column represents a sample, and each row represents a SNP. red, allelic imbalance; yellow, no evidence of allelic imbalance; grey, homozygous SNP; white, no data. Base pair location is listed in the left column. C. (left panel) Proportion of abnormal metaphases is highly correlated with allelic skewing in heterozygous SNPs. (right panel) Blast count is a poor predictor of clonality. Two samples with bone marrow myeloblast counts less than 5% are clonal, indicated by marked SNP allelic skewing. In contrast, four samples with myeloblast counts greater than or equal to 5% were non-clonal as measured by SNP allelic ratio.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2642994&req=5

pone-0004583-g002: 5q31.2 SNP loss of heterozygosity in del(5q) samples.A. Sequence traces for SNP rs1059110 in tumor samples from an individual homozygous for the common allele (left), a heterozygote (middle) with a normal allele trace peak height ratio = 0.44 (i.e., no allelic imbalance), and a heterozygote (right) with an abnormal allele trace peak height ratio = 0.20 (i.e., allelic imbalance). B. Heat map of allelic imbalance for 23 SNPs from 8 del(5q) and 9 non-del(5q) MDS samples. Each column represents a sample, and each row represents a SNP. red, allelic imbalance; yellow, no evidence of allelic imbalance; grey, homozygous SNP; white, no data. Base pair location is listed in the left column. C. (left panel) Proportion of abnormal metaphases is highly correlated with allelic skewing in heterozygous SNPs. (right panel) Blast count is a poor predictor of clonality. Two samples with bone marrow myeloblast counts less than 5% are clonal, indicated by marked SNP allelic skewing. In contrast, four samples with myeloblast counts greater than or equal to 5% were non-clonal as measured by SNP allelic ratio.

Mentions: To assess whether preferential retention of a SNP allele occurred in the 9 monosomy 5 or del(5q) samples, we examined their sequence traces for 64 SNPs (12 SNPs in Table 3, 47 SNPs in Table S3, and 5 SNPs without race-matched control data). DNA extracted from a homogeneous population of tumor cells harboring a deletion of one copy of chromosome 5q31.2 will contain complete loss of heterozygosity for all SNPs in 5q31.2 genes that are heterozygous in the germline. Sequence traces from these bone marrow samples display only one peak at each SNP, which represents the retained SNP allele in the tumor cells (Figure 2). In contrast, DNA extracted from a heterogeneous population of cells containing both tumor cells with a del(5q), and normal cells without del(5q), produce sequence traces displaying two alleles of unequal peak heights indicating allele skewing. There were 5 SNPs that had allele skewing in 3 or more del(5q) samples, but 0/5 SNPs displayed uniform retention of the same allele (data not shown).


Integrated genomic analysis implicates haploinsufficiency of multiple chromosome 5q31.2 genes in de novo myelodysplastic syndromes pathogenesis.

Graubert TA, Payton MA, Shao J, Walgren RA, Monahan RS, Frater JL, Walshauser MA, Martin MG, Kasai Y, Walter MJ - PLoS ONE (2009)

5q31.2 SNP loss of heterozygosity in del(5q) samples.A. Sequence traces for SNP rs1059110 in tumor samples from an individual homozygous for the common allele (left), a heterozygote (middle) with a normal allele trace peak height ratio = 0.44 (i.e., no allelic imbalance), and a heterozygote (right) with an abnormal allele trace peak height ratio = 0.20 (i.e., allelic imbalance). B. Heat map of allelic imbalance for 23 SNPs from 8 del(5q) and 9 non-del(5q) MDS samples. Each column represents a sample, and each row represents a SNP. red, allelic imbalance; yellow, no evidence of allelic imbalance; grey, homozygous SNP; white, no data. Base pair location is listed in the left column. C. (left panel) Proportion of abnormal metaphases is highly correlated with allelic skewing in heterozygous SNPs. (right panel) Blast count is a poor predictor of clonality. Two samples with bone marrow myeloblast counts less than 5% are clonal, indicated by marked SNP allelic skewing. In contrast, four samples with myeloblast counts greater than or equal to 5% were non-clonal as measured by SNP allelic ratio.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2642994&req=5

pone-0004583-g002: 5q31.2 SNP loss of heterozygosity in del(5q) samples.A. Sequence traces for SNP rs1059110 in tumor samples from an individual homozygous for the common allele (left), a heterozygote (middle) with a normal allele trace peak height ratio = 0.44 (i.e., no allelic imbalance), and a heterozygote (right) with an abnormal allele trace peak height ratio = 0.20 (i.e., allelic imbalance). B. Heat map of allelic imbalance for 23 SNPs from 8 del(5q) and 9 non-del(5q) MDS samples. Each column represents a sample, and each row represents a SNP. red, allelic imbalance; yellow, no evidence of allelic imbalance; grey, homozygous SNP; white, no data. Base pair location is listed in the left column. C. (left panel) Proportion of abnormal metaphases is highly correlated with allelic skewing in heterozygous SNPs. (right panel) Blast count is a poor predictor of clonality. Two samples with bone marrow myeloblast counts less than 5% are clonal, indicated by marked SNP allelic skewing. In contrast, four samples with myeloblast counts greater than or equal to 5% were non-clonal as measured by SNP allelic ratio.
Mentions: To assess whether preferential retention of a SNP allele occurred in the 9 monosomy 5 or del(5q) samples, we examined their sequence traces for 64 SNPs (12 SNPs in Table 3, 47 SNPs in Table S3, and 5 SNPs without race-matched control data). DNA extracted from a homogeneous population of tumor cells harboring a deletion of one copy of chromosome 5q31.2 will contain complete loss of heterozygosity for all SNPs in 5q31.2 genes that are heterozygous in the germline. Sequence traces from these bone marrow samples display only one peak at each SNP, which represents the retained SNP allele in the tumor cells (Figure 2). In contrast, DNA extracted from a heterogeneous population of cells containing both tumor cells with a del(5q), and normal cells without del(5q), produce sequence traces displaying two alleles of unequal peak heights indicating allele skewing. There were 5 SNPs that had allele skewing in 3 or more del(5q) samples, but 0/5 SNPs displayed uniform retention of the same allele (data not shown).

Bottom Line: We found no somatic nucleotide changes in the 46 MDS samples, and no cytogenetically silent 5q31.2 deletions in 20/20 samples analyzed by array CGH.The mRNA levels of 7 genes in the commonly deleted interval were reduced by 50% in CD34+ cells from del(5q) MDS samples, and no gene showed complete loss of expression.Taken together, these data show that small deletions and/or point mutations in individual 5q31.2 genes are not common events in MDS, and implicate haploinsufficiency of multiple genes as the relevant genetic consequence of this common deletion.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America.

ABSTRACT
Deletions spanning chromosome 5q31.2 are among the most common recurring cytogenetic abnormalities detectable in myelodysplastic syndromes (MDS). Prior genomic studies have suggested that haploinsufficiency of multiple 5q31.2 genes may contribute to MDS pathogenesis. However, this hypothesis has never been formally tested. Therefore, we designed this study to systematically and comprehensively evaluate all 28 chromosome 5q31.2 genes and directly test whether haploinsufficiency of a single 5q31.2 gene may result from a heterozygous nucleotide mutation or microdeletion. We selected paired tumor (bone marrow) and germline (skin) DNA samples from 46 de novo MDS patients (37 without a cytogenetic 5q31.2 deletion) and performed total exonic gene resequencing (479 amplicons) and array comparative genomic hybridization (CGH). We found no somatic nucleotide changes in the 46 MDS samples, and no cytogenetically silent 5q31.2 deletions in 20/20 samples analyzed by array CGH. Twelve novel single nucleotide polymorphisms were discovered. The mRNA levels of 7 genes in the commonly deleted interval were reduced by 50% in CD34+ cells from del(5q) MDS samples, and no gene showed complete loss of expression. Taken together, these data show that small deletions and/or point mutations in individual 5q31.2 genes are not common events in MDS, and implicate haploinsufficiency of multiple genes as the relevant genetic consequence of this common deletion.

Show MeSH
Related in: MedlinePlus