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Analysis of positional candidate genes in the AAA1 susceptibility locus for abdominal aortic aneurysms on chromosome 19.

Lillvis JH, Kyo Y, Tromp G, Lenk GM, Li M, Lu Q, Igo RP, Sakalihasan N, Ferrell RE, Schworer CM, Gatalica Z, Land S, Kuivaniemi H - BMC Med. Genet. (2011)

Bottom Line: Several SNPs were nominally associated with AAA (p < 0.05).Haplotype analysis found a nominally associated 5-SNP haplotype in the CEBPG/PEPD locus, as well as a nominally associated 2-SNP haplotype in the CD22 locus.PEPD and CD22 were considered the most promising candidate genes for altering AAA risk, based on gene function, association evidence, gene expression, and protein expression.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA.

ABSTRACT

Background: Abdominal aortic aneurysm (AAA) is a complex disorder with multiple genetic risk factors. Using affected relative pair linkage analysis, we previously identified an AAA susceptibility locus on chromosome 19q13. This locus has been designated as the AAA1 susceptibility locus in the Online Mendelian Inheritance in Man (OMIM) database.

Methods: Nine candidate genes were selected from the AAA1 locus based on their function, as well as mRNA expression levels in the aorta. A sample of 394 cases and 419 controls was genotyped for 41 SNPs located in or around the selected nine candidate genes using the Illumina GoldenGate platform. Single marker and haplotype analyses were performed. Three genes (CEBPG, PEPD and CD22) were selected for DNA sequencing based on the association study results, and exonic regions were analyzed. Immunohistochemical staining of aortic tissue sections from AAA and control individuals was carried out for the CD22 and PEPD proteins with specific antibodies.

Results: Several SNPs were nominally associated with AAA (p < 0.05). The SNPs with most significant p-values were located near the CCAAT enhancer binding protein (CEBPG), peptidase D (PEPD), and CD22. Haplotype analysis found a nominally associated 5-SNP haplotype in the CEBPG/PEPD locus, as well as a nominally associated 2-SNP haplotype in the CD22 locus. DNA sequencing of the coding regions revealed no variation in CEBPG. Seven sequence variants were identified in PEPD, including three not present in the NCBI SNP (dbSNP) database. Sequencing of all 14 exons of CD22 identified 20 sequence variants, five of which were in the coding region and six were in the 3'-untranslated region. Five variants were not present in dbSNP. Immunohistochemical staining for CD22 revealed protein expression in lymphocytes present in the aneurysmal aortic wall only and no detectable expression in control aorta. PEPD protein was expressed in fibroblasts and myofibroblasts in the media-adventitia border in both aneurysmal and non-aneurysmal tissue samples.

Conclusions: Association testing of the functional positional candidate genes on the AAA1 locus on chromosome 19q13 demonstrated nominal association in three genes. PEPD and CD22 were considered the most promising candidate genes for altering AAA risk, based on gene function, association evidence, gene expression, and protein expression.

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Sequence variants identified by candidate gene sequencing. Variants in PEPD (A) and CD22 (B) plotted to show their relative chromosomal positions and positions relative to gene features. Exons are indicated by the boxes above the x-axis. PEPD is transcribed right to left (minus strand) and CD22 is transcribed left to right (plus strand). Chromosomal coordinates are in kilobase pairs (kb).
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Figure 2: Sequence variants identified by candidate gene sequencing. Variants in PEPD (A) and CD22 (B) plotted to show their relative chromosomal positions and positions relative to gene features. Exons are indicated by the boxes above the x-axis. PEPD is transcribed right to left (minus strand) and CD22 is transcribed left to right (plus strand). Chromosomal coordinates are in kilobase pairs (kb).

Mentions: PEPD contains 15 small exons that are spaced over a large genomic distance. cDNA was used as a template for sequencing since the spliced transcript could be covered in only three PCR reactions. Seven sequence variants were identified in PEPD when 21 AAA cases and two controls were analyzed (Table 4; Figure 2A; Additional file 9, Table S7; Additional file 10, Table S8). Six individuals showed no variation in their PEPD sequence, 12 were heterozygous for one variant, four were heterozygous for two variants and one individual was homozygous for the minor allele of one variant (Additional file 9, Table S7). Four of the seven variants were present in only 1/23 (1/46 alleles) individuals, one was present in 3/23 (3/46 alleles), one in 5/23 (5/46 alleles) and one in 9/23 (10/46 alleles) (Additional file 9, Table S7).


Analysis of positional candidate genes in the AAA1 susceptibility locus for abdominal aortic aneurysms on chromosome 19.

Lillvis JH, Kyo Y, Tromp G, Lenk GM, Li M, Lu Q, Igo RP, Sakalihasan N, Ferrell RE, Schworer CM, Gatalica Z, Land S, Kuivaniemi H - BMC Med. Genet. (2011)

Sequence variants identified by candidate gene sequencing. Variants in PEPD (A) and CD22 (B) plotted to show their relative chromosomal positions and positions relative to gene features. Exons are indicated by the boxes above the x-axis. PEPD is transcribed right to left (minus strand) and CD22 is transcribed left to right (plus strand). Chromosomal coordinates are in kilobase pairs (kb).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3037298&req=5

Figure 2: Sequence variants identified by candidate gene sequencing. Variants in PEPD (A) and CD22 (B) plotted to show their relative chromosomal positions and positions relative to gene features. Exons are indicated by the boxes above the x-axis. PEPD is transcribed right to left (minus strand) and CD22 is transcribed left to right (plus strand). Chromosomal coordinates are in kilobase pairs (kb).
Mentions: PEPD contains 15 small exons that are spaced over a large genomic distance. cDNA was used as a template for sequencing since the spliced transcript could be covered in only three PCR reactions. Seven sequence variants were identified in PEPD when 21 AAA cases and two controls were analyzed (Table 4; Figure 2A; Additional file 9, Table S7; Additional file 10, Table S8). Six individuals showed no variation in their PEPD sequence, 12 were heterozygous for one variant, four were heterozygous for two variants and one individual was homozygous for the minor allele of one variant (Additional file 9, Table S7). Four of the seven variants were present in only 1/23 (1/46 alleles) individuals, one was present in 3/23 (3/46 alleles), one in 5/23 (5/46 alleles) and one in 9/23 (10/46 alleles) (Additional file 9, Table S7).

Bottom Line: Several SNPs were nominally associated with AAA (p < 0.05).Haplotype analysis found a nominally associated 5-SNP haplotype in the CEBPG/PEPD locus, as well as a nominally associated 2-SNP haplotype in the CD22 locus.PEPD and CD22 were considered the most promising candidate genes for altering AAA risk, based on gene function, association evidence, gene expression, and protein expression.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA.

ABSTRACT

Background: Abdominal aortic aneurysm (AAA) is a complex disorder with multiple genetic risk factors. Using affected relative pair linkage analysis, we previously identified an AAA susceptibility locus on chromosome 19q13. This locus has been designated as the AAA1 susceptibility locus in the Online Mendelian Inheritance in Man (OMIM) database.

Methods: Nine candidate genes were selected from the AAA1 locus based on their function, as well as mRNA expression levels in the aorta. A sample of 394 cases and 419 controls was genotyped for 41 SNPs located in or around the selected nine candidate genes using the Illumina GoldenGate platform. Single marker and haplotype analyses were performed. Three genes (CEBPG, PEPD and CD22) were selected for DNA sequencing based on the association study results, and exonic regions were analyzed. Immunohistochemical staining of aortic tissue sections from AAA and control individuals was carried out for the CD22 and PEPD proteins with specific antibodies.

Results: Several SNPs were nominally associated with AAA (p < 0.05). The SNPs with most significant p-values were located near the CCAAT enhancer binding protein (CEBPG), peptidase D (PEPD), and CD22. Haplotype analysis found a nominally associated 5-SNP haplotype in the CEBPG/PEPD locus, as well as a nominally associated 2-SNP haplotype in the CD22 locus. DNA sequencing of the coding regions revealed no variation in CEBPG. Seven sequence variants were identified in PEPD, including three not present in the NCBI SNP (dbSNP) database. Sequencing of all 14 exons of CD22 identified 20 sequence variants, five of which were in the coding region and six were in the 3'-untranslated region. Five variants were not present in dbSNP. Immunohistochemical staining for CD22 revealed protein expression in lymphocytes present in the aneurysmal aortic wall only and no detectable expression in control aorta. PEPD protein was expressed in fibroblasts and myofibroblasts in the media-adventitia border in both aneurysmal and non-aneurysmal tissue samples.

Conclusions: Association testing of the functional positional candidate genes on the AAA1 locus on chromosome 19q13 demonstrated nominal association in three genes. PEPD and CD22 were considered the most promising candidate genes for altering AAA risk, based on gene function, association evidence, gene expression, and protein expression.

Show MeSH
Related in: MedlinePlus