Association of autism with polymorphisms in the paired-like homeodomain transcription factor 1 (PITX1) on chromosome 5q31: a candidate gene analysis

Abstract

Background: Autism is a complex, heterogeneous, behaviorally-defined disorder characterized by disruptions of the nervous system and of other systems such as the pituitary-hypothalamic axis. In a previous genome wide screen, we reported linkage of autism with a 1.2 Megabase interval on chromosome 5q31. For the current study, we hypothesized that 3 of the genes in this region could be involved in the development of autism: 1) paired-like homeodomain transcription factor 1 (PITX1), which is a key regulator of hormones within the pituitary-hypothalamic axis, 2) neurogenin 1, a transcription factor involved in neurogenesis, and 3) histone family member Y (H2AFY), which is involved in X-chromosome inactivation in females and could explain the 4:1 male:female gender distortion present in autism.

Methods: A total of 276 families from the Autism Genetic Resource Exchange (AGRE) repository composed of 1086 individuals including 530 affected children were included in the study. Single nucleotide polymorphisms tagging the three candidate genes were genotyped on the initial linkage sample of 116 families. A second step of analysis was performed using tightly linked SNPs covering the PITX1 gene. Association was evaluated using the FBAT software version 1.7.3 for single SNP analysis and the HBAT command from the same package for haplotype analysis respectively.

Results: Association between SNPs and autism was only detected for PITX1. Haplotype analysis within PITX1 showed evidence for overtransmission of the A-C haplotype of markers rs11959298 - rs6596189 (p = 0.0004). Individuals homozygous or heterozygous for the A-C haplotype risk allele were 2.54 and 1.59 fold more likely to be autistic than individuals who were not carrying the allele, respectively.

Conclusion: Strong and consistent association was observed between a 2 SNPs within PITX1 and autism. Our data suggest that PITX1, a key regulator of hormones within the pituitary-hypothalamic axis, may be implicated in the etiology of autism.

Figure 1

Genomic organization of the linkage region on chromosome 5q31 and haplotype heat-map of PITX1. A) Five clones in the region showed elevated identity-by-descent sharing values. The highest p-value was observed for clone FE0DBACA4ZA08 (p = 6.40 * 10^-7, position (built 34) = chr5:134.467.793 – 134.639.841). Orientation of gene transcription is indicated by arrows. The bottom panel shows the exon-intron structure of the PITX1 gene. Two transcripts have been described for the gene, which make use of the same start and stop codons but differ in their respective 5' and 3' UTR regions.

Figure 2

Linkage disequilibrium (LD) map of the PITX1.gene. Thirteen SNP markers within the 6.5 kb of genomic sequence span the 5' and 3' UTRs of PITX1. Pair-wise LD among SNPs was investigated using D'. Haplotype blocks were determined by identifying the first and last markers in a block, which are in strong LD with all intermediate markers. The structure and position of the PITX1 gene, the positions of the 5 SNPs from the first step genotyping and the 9 SNPS from the second step genotyping are indicated (SNP markers in bold), respectively. LD, linkage disequilibrium; SNP, small nucleotide polymorphism; UTR, 5'-untranslated regions.