Molecular Signatures of Cardiac Defects in Down Syndrome Lymphoblastoid Cell Lines Suggest Altered Ciliome and Hedgehog Pathways

Abstract

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.

Bioinformatic Analysis of Genes and MicroRNAs Associated With Atrioventricular Septal Defect in Down Syndrome Patients

“…In comparison with a previous study based on the same microarray profiling, 10) a different DEG screening method and criteria were utilized in our study. The limma package 18) used in the present study is the most widely used software in DEG screening, and the criteria of P < 0.05 and |log 2 FC| > 0.5 are strict enough to ensure the significance of DEGs.…”

“…Microarray data: Gene expression profiling of GSE34457 10) was downloaded from the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/), based on the platform of GPL6102 (Illumina human-6 v2.0 expression beadchip). A total of 22 samples from DS patients without congenital heart disease and 7 samples from DS patients with AVSD were utilized in this study.…”

“…The mutation of COL6A1 in exon 35 genes has been identified in DS patients with AVSD. 8) Reportedly, Ciliome 10) and VEGF-A pathways 11) are involved in the genetic underpinnings of AVSD in humans. Ripoll, et al identified several GO (gene ontology) functions and pathways associated with AVSD in DS patients by using gene expression profiling.…”

“…Ripoll, et al identified several GO (gene ontology) functions and pathways associated with AVSD in DS patients by using gene expression profiling. 10) However, no in-depth studies have identified the protein-protein interactions (PPIs) between candidate genes of AVSD. In addition, there is evidence that microRNAs (miRNAs) play crucial roles in heart development and diseases, 12) such as miR-155, 13) miR-652, 14) microRNA-340-5p, 15) and miR-210.…”

Identification of altered pathways in Down syndrome-associated congenital heart defects using an individualized pathway aberrance score

“…A study of rare partial trisomy 21 cases suggested the presence of a minimal, 1.77-Mb CHD candidate region at 21q22.3, between markers D21S3 and PFKL (Korbel et al, 2009). Recent studies have also suggested the potential contribution of VEGFA (Ackerman et al, 2012), cleome and Hedgehog (Ripoll et al, 2012), and folate (Locke et al, 2010) pathways to the pathogenicity of DS-CHD. The transcription profile of DS-CHD was obtained based on the Hsa21 genes in the heart of 18-22-week-old human fetuses (Conti et al, 2007).…”