Classification of human chromosome 21 gene-expression variations in Down syndrome: impact on disease phenotypes

Abstract

Down syndrome caused by chromosome 21 trisomy is the most common genetic cause of mental retardation in humans. Disruption of the phenotype is thought to be the result of gene-dosage imbalance. Variations in chromosome 21 gene expression in Down syndrome were analyzed in lymphoblastoid cells derived from patients and control individuals. Of the 359 genes and predictions displayed on a specifically designed high-content chromosome 21 microarray, one-third were expressed in lymphoblastoid cells. We performed a mixed-model analysis of variance to find genes that are differentially expressed in Down syndrome independent of sex and interindividual variations. In addition, we identified genes with variations between Down syndrome and control samples that were significantly different from the gene-dosage effect (1.5). Microarray data were validated by quantitative polymerase chain reaction. We found that 29% of the expressed chromosome 21 transcripts are overexpressed in Down syndrome and correspond to either genes or open reading frames. Among these, 22% are increased proportional to the gene-dosage effect, and 7% are amplified. The other 71% of expressed sequences are either compensated (56%, with a large proportion of predicted genes and antisense transcripts) or highly variable among individuals (15%). Thus, most of the chromosome 21 transcripts are compensated for the gene-dosage effect. Overexpressed genes are likely to be involved in the Down syndrome phenotype, in contrast to the compensated genes. Highly variable genes could account for phenotypic variations observed in patients. Finally, we show that alternative transcripts belonging to the same gene are similarly regulated in Down syndrome but sense and antisense transcripts are not.

Figure 1.

Classification of HSA21 genes according to the expression ratio between DS and control LCLs. The sum of classified genes is 136 genes minus 2 (C21ORF108 and PRMT2) that appear twice, depending on the oligonucleotide probe considered (see the “Results” section for details).

Figure 2.

Distribution of DS/control ratios for class I, II, III, and IV genes and non-HSA21 reference genes. The plot represents the minimum and maximum values (whiskers), the first and third quartiles (box), and the median value (midline) of DS/control ratios for each class of genes.

Figure 3.

PCA of HSA21 genes (A) and non-HSA21 genes (B). Red and blue symbols represent DS and control samples, respectively. Squares represent samples extracted from females, and diamonds represent samples extracted from males.

Figure 4.

Distribution of the variance of M for class I, II, III, and IV genes. The plot represents the minimum and maximum values (whiskers), the first and third quartiles (box), and the median value (midline) of the variances of M for each class of genes, where M is the mean of .

Figure 5.

Distribution of expressed, class I, II, III, and IV genes along HSA21. The left Y-axis indicates the proportion of expressed genes in each 5-Mb interval, and the right Y-axis indicates the proportion of class I, II, III, and IV genes in each 5-Mb interval.