Gene-network analysis identifies susceptibility genes related to glycobiology in autism

Abstract

The recent identification of copy-number variation in the human genome has opened up new avenues for the discovery of positional candidate genes underlying complex genetic disorders, especially in the field of psychiatric disease. One major challenge that remains is pinpointing the susceptibility genes in the multitude of disease-associated loci. This challenge may be tackled by reconstruction of functional gene-networks from the genes residing in these loci. We applied this approach to autism spectrum disorder (ASD), and identified the copy-number changes in the DNA of 105 ASD patients and 267 healthy individuals with Illumina Humanhap300 Beadchips. Subsequently, we used a human reconstructed gene-network, Prioritizer, to rank candidate genes in the segmental gains and losses in our autism cohort. This analysis highlighted several candidate genes already known to be mutated in cognitive and neuropsychiatric disorders, including RAI1, BRD1, and LARGE. In addition, the LARGE gene was part of a sub-network of seven genes functioning in glycobiology, present in seven copy-number changes specifically identified in autism patients with limited co-morbidity. Three of these seven copy-number changes were de novo in the patients. In autism patients with a complex phenotype and healthy controls no such sub-network was identified. An independent systematic analysis of 13 published autism susceptibility loci supports the involvement of genes related to glycobiology as we also identified the same or similar genes from those loci. Our findings suggest that the occurrence of genomic gains and losses of genes associated with glycobiology are important contributors to the development of ASD.

Figure 1. Expression analysis during mouse brain development of glycobiology-related genes overrepresented in autism-associated CNVs.

a–c: mLarge, d–f: mGalnt9, g–i: mArsa, j,k: mGcnt2, l: mB3galt6. a) At E14.5 mLarge is expressed throughout the nervous system. The expression in the interior of the medial ganglionic eminence (MGE, (arrow), and in the dorsal root ganglia (DRG's, arrowheads) is higher then in surrounding tissues. b) At E18.5 expression is maintained in the nervous system, more intense expression was observed in the cortical plate and the developing cornu ammonis (CA) regions of the hippocampus (arrow), and in the mitral cells of the olfactory bulb (arrowhead). c) In the adult brain mLarge expression is high in the cerebral cortex and hippocampus. The anterior cerebral cortex (arrow) and the CA2 region of the hippocampus (arrowhead) show more intense staining than adjacent cells. In the cerebellum mLARGE is highly expressed in the Purkinje cell layer (asterisk). d) A low level of mGalnt9 expression was observed in the cortical plate at E14.5, stronger staining was present in the region of the future hypothalamus (arrow), and in a stripe of cells adjacent to the central canal of the spinal cord (arrowheads). e) At E18.5 neural expression of mGalnt9 has become restricted to the forebrain, with the exception of the thalamus (asterisk), and some hindbrain nuclei (not shown). The arrowhead and arrow indicate higher levels of mGalnt9 expression in the anterior cortical plate, and in the hippocampus, respectively. The transition between high and low level expression in the cortical plate is marked by a dotted line. f) In the adult brain mGalnt9 was expressed in layer II/III pyramidal neurons of the cerebral cortex, and in the CA1 and CA2 region of the hippocampus. Expression at a lower level was present in the thalamus and in the Purkinje and granular cell layer of the cerebellum. g) At E14.5 mArsa expression was observed in the floorplate neuroepithelium of the midbrain (arrow), extending caudally into the spinal cord (arrowheads). A low intensity signal was also present in the thalamus. h) At E18.5 expression of mArsa was maintained throughout the nervous system, with highest expression in the cortical plate, and thalamus (asterisk). i) In adult brain a low level of mArsa expression was observed in the CA and DG regions of the hippocampus, and in the granular cell layer of the cerebellum. Additionally, the medial vestibular nucleus showed expression of mArsa. j) Expression of mGcnt2 in the cerebellar anlage (arrow) at E14.5. k) In the adult brain, mGcnt2 was expressed in the CA regions of the hippocampus, and in the lateral portion of the caudate putamen. l) mB3galt6 was ubiquitously expressed from E14.5 onwards. Magnifications: 12.5×, except j: 25×. Abbreviations: aon: anterior olfactory nucleus, cb: cerebellum, cp: cortical plate, cpu: caudate putamen, dg: dentate gyrus, hip: hippocampus, liv: liver, lv: lateral ventricle, mb: midbrain, med: medulla oblongata, mf: mesencephalic flexure, nc: neocortex, ob: olfactory bulb, oe: olfactory epithelium, pf: pontine flexure, thal: thalamus, to: tongue, tri: trigeminal ganglion, sc: spinal cord, smc: primary somatosensory cortex.