학술논문
Functional characterisation of the amyotrophic lateral sclerosis risk locus GPX3/TNIP1
Document Type
article
Author
Restuadi, Restuadi; Steyn, Frederik J; Kabashi, Edor; Ngo, Shyuan T; Cheng, Fei-Fei; Nabais, Marta F; Thompson, Mike J; Qi, Ting; Wu, Yang; Henders, Anjali K; Wallace, Leanne; Bye, Chris R; Turner, Bradley J; Ziser, Laura; Mathers, Susan; McCombe, Pamela A; Needham, Merrilee; Schultz, David; Kiernan, Matthew C; van Rheenen, Wouter; van den Berg, Leonard H; Veldink, Jan H; Ophoff, Roel; Gusev, Alexander; Zaitlen, Noah; McRae, Allan F; Henderson, Robert D; Wray, Naomi R; Giacomotto, Jean; Garton, Fleur C
Source
Genome Medicine. 14(1)
Subject
Language
Abstract
BackgroundAmyotrophic lateral sclerosis (ALS) is a complex, late-onset, neurodegenerative disease with a genetic contribution to disease liability. Genome-wide association studies (GWAS) have identified ten risk loci to date, including the TNIP1/GPX3 locus on chromosome five. Given association analysis data alone cannot determine the most plausible risk gene for this locus, we undertook a comprehensive suite of in silico, in vivo and in vitro studies to address this.MethodsThe Functional Mapping and Annotation (FUMA) pipeline and five tools (conditional and joint analysis (GCTA-COJO), Stratified Linkage Disequilibrium Score Regression (S-LDSC), Polygenic Priority Scoring (PoPS), Summary-based Mendelian Randomisation (SMR-HEIDI) and transcriptome-wide association study (TWAS) analyses) were used to perform bioinformatic integration of GWAS data (Ncases = 20,806, Ncontrols = 59,804) with 'omics reference datasets including the blood (eQTLgen consortium N = 31,684) and brain (N = 2581). This was followed up by specific expression studies in ALS case-control cohorts (microarray Ntotal = 942, protein Ntotal = 300) and gene knockdown (KD) studies of human neuronal iPSC cells and zebrafish-morpholinos (MO).ResultsSMR analyses implicated both TNIP1 and GPX3 (p < 1.15 × 10-6), but there was no simple SNP/expression relationship. Integrating multiple datasets using PoPS supported GPX3 but not TNIP1. In vivo expression analyses from blood in ALS cases identified that lower GPX3 expression correlated with a more progressed disease (ALS functional rating score, p = 5.5 × 10-3, adjusted R2 = 0.042, Beffect = 27.4 ± 13.3 ng/ml/ALSFRS unit) with microarray and protein data suggesting lower expression with risk allele (recessive model p = 0.06, p = 0.02 respectively). Validation in vivo indicated gpx3 KD caused significant motor deficits in zebrafish-MO (mean difference vs. control ± 95% CI, vs. control, swim distance = 112 ± 28 mm, time = 1.29 ± 0.59 s, speed = 32.0 ± 2.53 mm/s, respectively, p for all