Molecular signatures of cardiac defects in down syndrome lymphoblastoid cell lines suggest altered ciliome and hedgehog pathways

Forty percent of people with Down syndrome exhibit heart defects, most often an atrioventricular septal defect (AVSD) and less frequently a ventricular septal defect (VSD) or atrial septal defect (ASD). Lymphoblastoid cell lines (LCLs) were established from lymphocytes of individuals with trisomy 21, the chromosomal abnormality causing Down syndrome. Gene expression profiles generated from DNA microarrays of LCLs from individuals without heart defects (CHD-; n = 22) were compared with those of LCLs from patients with cardiac malformations (CHD+; n = 21). After quantile normalization, principal component analysis revealed that AVSD carriers could be distinguished from a combined group of ASD or VSD (ASD+VSD) carriers. From 9,758 expressed genes, we identified 889 and 1,016 genes differentially expressed between CHD- and AVSD and CHD- and ASD+VSD, respectively, with only 119 genes in common. A specific chromosomal enrichment was found in each group of affected genes. Among the differentially expressed genes, more than 65% are expressed in human or mouse fetal heart tissues (GEO dataset). Additional LCLs from new groups of AVSD and ASD+VSD patients were analyzed by quantitative PCR; observed expression ratios were similar to microarray results. Analysis of GO categories revealed enrichment of genes from pathways regulating clathrin-mediated endocytosis in patients with AVSD and of genes involved in semaphorin-plexin-driven cardiogenesis and the formation of cytoplasmic microtubules in patients with ASD-VSD. A pathway-oriented search revealed enrichment in the ciliome for both groups and a specific enrichment in Hedgehog and Jak-stat pathways among ASD+VSD patients. These genes or related pathways are therefore potentially involved in normal cardiogenesis as well as in cardiac malformations observed in individuals with trisomy 21. © 2012 Ripoll et al

Transcriptome signature of heart defects.

<p>Comparison of ratios for DE genes up- or down-regulated in the AVSD or ASD+VSD group between (1) array ratio in the Ts21 CHD⁻ vs 2N, (2) array ratio in CHD⁺ vs CHD⁻, (3) q-PCR ratio from different experiments in CHD⁺ vs CHD⁻ using additional samples (total number in parentheses). Gene nomenclature, <i>AUTS2</i>: autism susceptibility candidate 2; <i>CNN2</i>: calponin 2; <i>DSCR3</i>: Down syndrome critical region gene 3; <i>DYNLT3</i>: dynein, light chain, Tctex-type 3; <i>NQO1</i>: NAD(P)H dehydrogenase, quinone 1; <i>OFD1</i>: oral-facial-digital syndrome 1; <i>PDIA4</i>: protein disulfide isomerase family A, member 4; <i>PIGP</i>: phosphatidylinositol glycan anchor biosynthesis, class P; <i>TTC3</i>: tetratricopeptide repeat domain 3; <i>TUBB2B</i>: tubulin, beta 2B; <i>ACTG1</i>: actin, gamma 1; <i>ALDOC</i>: aldolase C, fructose-bisphosphate; <i>CACYBP</i>: calcyclin binding protein; <i>DTYMK</i>: deoxythymidylate kinase (thymidylate kinase); <i>ENO2</i>: enolase 2 (gamma, neuronal); <i>GART</i>: phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase; <i>IFNAR1</i>: interferon (alpha, beta, and omega) receptor 1; <i>PLTP</i>: phospholipid transfer protein; <i>RPL10A</i>: ribosomal protein L10a; <i>TNFAIP2</i>: tumor necrosis factor, alpha-induced protein 2.</p

Classification of heart defects (CHD+) according to the distribution frequency of their p-values.

<p>Empirical cumulative distributions of p-values for the 2-by-2 Student tests A: AVSD/ASD; B: AVSD/VSD; C: ASD/VSD. Comparisons were obtained for 11 224 tests. The comparison to the uniform distribution shows that there is no overall differential expression between ASD and VSD (less small p-values than for an uniform distribution). Cdf: cumulative distribution function.</p

GO categories in the CDH⁺ DE genes.

<p>Analysis of the enrichment of GO categories for the genes DE in the comparison between AVSD or ASD+VSD set of genes and CHD⁻ set of genes compared to the genes expressed in LCLs. Analysis used GOrilla software with a p-value threshold at 10⁻³. N - is the total number of genes, B - is the total number of genes associated with a specific null, n - is the number of genes in the group with heart defect, b - is the number of genes in the intersection.</p

Principal component analysis of gene expression profiles of LCLs from individuals with DS and with CHD: red- AVSD (n = 7); green- ASD (n = 8); blue- VSD (n = 6).

<p>Red circle indicates AVSD, blue circle indicates ASD and VSD.</p

Genotype–phenotype correlations in Down syndrome identified by array CGH in 30 cases of partial trisomy and partial monosomy chromosome 21

Down syndrome (DS) is one of the most frequent congenital birth defects, and the most common genetic cause of mental retardation. In most cases, DS results from the presence of an extra copy of chromosome 21. DS has a complex phenotype, and a major goal of DS research is to identify genotype–phenotype correlations. Cases of partial trisomy 21 and other HSA21 rearrangements associated with DS features could identify genomic regions associated with specific phenotypes. We have developed a BAC array spanning HSA21q and used array comparative genome hybridization (aCGH) to enable high-resolution mapping of pathogenic partial aneuploidies and unbalanced translocations involving HSA21. We report the identification and mapping of 30 pathogenic chromosomal aberrations of HSA21 consisting of 19 partial trisomies and 11 partial monosomies for different segments of HSA21. The breakpoints have been mapped to within ∼85 kb. The majority of the breakpoints (26 of 30) for the partial aneuploidies map within a 10-Mb region. Our data argue against a single DS critical region. We identify susceptibility regions for 25 phenotypes for DS and 27 regions for monosomy 21. However, most of these regions are still broad, and more cases are needed to narrow down the phenotypic maps to a reasonable number of candidate genomic elements per phenotype