Identification of causal genes and cellular pathways for idiopathic achalasia on the basis of genome-wide association studies (GWAS)
Final Report Abstract
The aim of the project was the worldwide first genome-wide association study (GWAS) in idiopathic achalasia using 5,000 patients and more than 6,000 controls from six different European populations, namely from Central Europe, Sweden, Poland, Greece, Italy, and Spain. This should lead to the identification of genetic risk variants for achalasia and allow genetic downstream analyses. However, for the following reasons the project deviated from the initial research plan and was considerably more time-consuming than expected: (i) At the project start, DNA samples from only 4,600 achalasia cases were available because the recruitment of patients in the participating clinical centers was less effective than expected. These samples − together with the control samples from Greece and Poland − were genome-wide genotyped at the applicants’ laboratories in Bonn in early 2018. (ii) Also in 2018, it was planned to use already genotyped control samples from Italy and Spain through a collaboration with the European Alzheimer Disease Biobank (EADB). However, the genotyping of both control samples was considerably delayed, so that the transfer of the genotype data not occurred until the end of 2019. (iii) In 2020, the GWAS meta-analysis was then performed and revealed four loci that were genome-wide significantly associated with achalasia. However, in the meantime, the clinical project partners expected to recruit 500 additional achalasia patients by mid-2021. To achieve the initial envisaged size of the patient cohort and to increase the statistical GWAS power, these additional samples were then subjected to genome-wide genotyping in Bonn. The corresponding data are available since September 2022 and are currently being analyzed together with the GWAS data from 2020. In the following, we summarize our GWAS findings from 2020, which are based on a case-control sample of 4,585 achalasia patients and 10,317 controls. In total, we could identify four genome-wide significant associated risk loci for achalasia. SNP rs28688207 on chromosome 6p21 within the HLA region showed the strongest disease association (P = 4.54 x 10-42, odds ratio (OR) of 1.42 (95% confidence interval (CI) 1.34-1.47)). The variant is located in the splice acceptor site of HLA-DQβ1 exon 5 and leads to an 8-amino-acid insertion at position 227-234 in the cytoplasmic tail of HLA-DQB1. It has been speculated that the insertion might lead to an altered intracellular trafficking, as the C-terminal tails of HLA molecules are thought to promote these processes. SNP rs2138653 on chromosome 18p11 represents the strongest achalasia associated risk variant at the second GWAS locus (P = 8.41 x 10^-09, OR 1.09 (95% CI 1.06-1.12)). The risk SNP is located nearby PTPN2, which encodes for the protein tyrosine phosphatase non-receptor type 2 and has a regulatory role in a variety of immune-relevant signaling pathways. PTPN2 has attracted much attention previously because GWAS for numerous autoimmune diseases showed association at this locus. Among others, this refers to inflammatory bowel disease (IBD), Crohn’s disease (CD), rheumatoid arthritis, type-1 diabetes, and psoriasis. The third strongest disease associated locus is located on chromosome 9q32. Here, rs1126711 was achalasia associated with P = 2.33 x 10^-08 (OR 1.07 (95% CI 1.04-1.09)). The variant is located in close proximity to TNFSF15, which encodes for the tumor necrosis factor (TNF)-like cytokine 1A and plays a pivotal role in autoimmune diseases. Accordingly, elevated TNFSF15 levels have been observed in patients with various autoimmune diseases and the locus showed previously GWAS associations in IBD, CD, and primary biliary cirrhosis. In contrast to all three loci above, the fourth genome-wide significantly associated achalasia locus on chromosome 19p13 has not been previously implicated in autoimmune diseases. Here, rs150926484, which is located in exon 6 of the gene ZFP30, showed disease association with P = 3.27 x 10^-08 (OR 1.34 (95% CI 1.21-1.49)). So far, the function of ZFP30 is poorly understood. Future studies are warranted to identify a promising candidate gene for achalasia at this locus. On the polygenic level, we estimated the SNP-based heritability of achalasia to be 18.7±8.6% standard deviation (SD) using the existing GWAS data and LD score regression. All other analyses at the polygenic level − for example, correlations with other phenotypes − will be carried out once we have the final data from the extended achalasia GWAS cohort. Based on these data we will also carry out all downstream analyses in order to characterize the GWAS loci and the genetic architecture of achalasia.
Publications
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(2019) First genotype-phenotype study reveals HLA-DQβ1 insertion heterogeneity in high-resolution manometry achalasia subtypes. United European Gastroenterol J 7: 45-51
Vackova Z, Niebisch S, Triantafyllou T, Becker J, Hess T, Kreuser N, Kanoni S, Deloukas P, Schüller V, Heinrichs SK, Thieme R, Nöthen MM, Knapp M, Spicak J, Gockel I, Schumacher J, Theodorou D, Martinek J
