Whole genome microarray analysis of gene expression in subjects with fragile X syndrome

Purpose: Fragile X syndrome, the most common inherited form of human mental retardation, arises as a consequence of a large expansion of a CGG trinucleotide repeat in 5 untranslated region of the fragile X mental retardation 1 (FMR1) gene located on the X chromosome. Although the FMR1 gene was cloned 15 years ago, the mechanisms that cause fragile X syndrome remain to be elucidated. Multiple studies have identified proteins that potentially interact with FMRP, the product of FMR1, and differentially expressed genes in an Fmr1 knockout mouse. To assess the impact of fragile X syndrome on gene expression in humans and to attempt to identify disturbed genes and gene interactive pathways relevant to fragile X syndrome, we performed gene expression microarray analysis using RNA isolated from lymphoblastoid cells derived from males with fragile X syndrome with and similarly aged control males. Methods: We used whole genome microarrays consisting of 57,000 probes to analyze global changes to the transcriptome in readily available lymphoblastoid cell lines derived from males with fragile X syndrome and healthy comparison males with normal intelligence. We verified the differential expression of several of these genes with known biological function relevant to fragile X syndrome using quantitative reverse transcription polymerase chain reaction using RNA from lymphoblastoid cells from fragile X syndrome and control males as well as RNA from human brain tissue (frontal cortex) of other affected fragile X syndrome males. Results: We identified more than 90 genes that had significant differences in probe intensity of at least 1.5-fold with a false discovery rate of 5% in cells from males with fragile X syndrome relative to comparison males. The list of 90 differentially expressed genes contained an overrepresentation of genes involved in signaling (e.g., UNC13B [-3.3-fold change in expression in lymphoblasts by quantitative reverse transcription polymerase chain reaction), GABRD [+2.0-fold change] EEF1A2 [+4.3-fold change]), morphogenesis (e.g., MAP1B [-7.5-fold change], ACCN1 [-8.0-fold change]), and neurodevelopment and function (e.g., PPP1R9B [+3.5-fold change], HES1 [+2.8-fold change]). Conclusions: These genes may represent members of candidate networks disturbed by the loss of FMR1 and consequently fragile X mental retardation protein function, thus lending support for altered fragile X mental retardation protein function resulting in an abnormal transcriptome. Further analyses of the genes, especially those that have been identified in multiple studies, are warranted to develop a more integrated description of the alterations in gene processing that lead to fragile X syndrome.