Functional characterisation of the amyotrophic lateral sclerosis risk locus GPX3/TNIP1

Authors

Restuadi Restuadi
Frederik J. Steyn
Edor Kabashi
Shyuan T. Ngo
Fei-Fei Cheng
Marta F. Nabais
Mike J. Thompson
Ting Qi
Yang Wu
Anjali K. Henders
Leanne Wallace
Chris R. Bye
Bradley J. Turner
Laura Ziser
Susan Mathers
Pamela A. McCombe
Merrilee Needham, The University of Notre Dame AustraliaFollow
David Schultz
Matthew C. Kiernan
Wouter van Rheenen
Leonard H. van den Berg
Jan H. Veldink
Roel Ophoff
Alexander Gusev
Noah Zaitlen
Allan F. McRae
Robert D. Henderson
Naomi R. Wray
Jean Giacomotto
Fleur C. Garton

Publication Details

Restuadi, R., Steyn, F. J., Kabashi, E., Ngo, S. T., Cheng, F., Nabais, M. F., Thompson, M. J., Qi, T., Wu, Y., Henders, A. K., Wallace, L., Bye, C. R., Turner, B. J., Ziser, L., Mathers, S., McCombe, P. A., Needham, M., Schultz, D., Kiernan, M. C., van Rheenen, W., van den Berg, L. H., Veldink, J. H., Ophoff, R., Gusev, A., Zaitlen, N., McRae, A. F., Henderson, R. D., Wray, N. R., Giacomotto, J., & Garton, F. C. (2022). Functional characterisation of the amyotrophic lateral sclerosis risk locus GPX3/TNIP1. Genome Medicine, 14.

Abstract

Background: Amyotrophic 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.

Methods: The 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 (N_cases = 20,806, N_controls = 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 N_total = 942, protein N_total = 300) and gene knockdown (KD) studies of human neuronal iPSC cells and zebrafish-morpholinos (MO).

Results: SMR 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, B_effect = 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 < 0.0001), which were rescued with gpx3 expression, with no phenotype identified with tnip1 KD or gpx3 overexpression.

Keywords

motor neurone disease, MND, genome-wide association study, computational biology, Zebrafish, neurodegenerative diseases, quantitative trait loci, genes, regulator, disease progression

Link to Publisher Version (URL)

10.1186/s13073-021-01006-6