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Lookup NU author(s): Dr Jérémie NsengimanaORCiD
This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).
© 2025 The Author(s). Transcriptome-wide association studies (TWASs) have the potential to identify susceptibility genes associated with testicular germ cell tumors (TGCTs). We conducted a comprehensive TGCT TWAS by integrating genome-wide association study (GWAS) summary data with predicted expression models from normal testis, TGCT tissues, and a cross-tissue panel that encompasses shared regulatory features across 22 normal tissues, including the testis. Gene associations were evaluated while accounting for variant-level effects from GWASs, followed by fine-mapping analyses in regions exhibiting multiple TWAS signals, and finally supplemented by colocalization analysis. Expression and protein patterns of identified TWAS genes were further examined in relevant tissues. Our analysis tested 19,805 gene-disease links, revealing 165 TGCT-associated genes with a false discovery rate of less than 0.01. We prioritized 46 candidate genes by considering GWAS-inflated signals, correlations between neighboring genes, and evidence of colocalization. Among these, 23 genes overlap with 22 GWAS loci, with 7 being associations not previously implicated in TGCT risk. Additionally, 23 genes located within 21 loci are at least 1 Mb away from published GWAS index variants. The 46 prioritized genes display expression levels consistent with expected expression levels in human gonadal cell types and precursor tumor cells and significant enrichment in TGCTs. Additionally, immunohistochemistry revealed protein-level accumulation of two candidate genes, ARID3B and GINM1, in both precursor and tumor cells. These findings enhance our understanding of the genetic predisposition to TGCTs and underscore the importance of further functional investigations into these candidate genes.
Author(s): Ugalde-Morales E, Wilf R, Pluta J, Ploner A, Fan M, Damra M, Aben KK, Anson-Cartwright L, Chen C, Cortessis VK, Daneshmand S, Ferlin A, Gamulin M, Gietema JA, Gonzalez-Niera A, Grotmol T, Hamilton RJ, Harland M, Haugen TB, Hauser R, Hildebrandt MAT, Karlsson R, Kiemeney LA, Kim J, Lessel D, Lothe RA, Loveday C, Chanock SJ, McGlynn KA, Meijer C, Nead KT, Nsengimana J, Popovic M, Rafnar T, Richiardi L, Rocca MS, Schwartz SM, Skotheim RI, Stefansson K, Stewart DR, Turnbull C, Vaughn DJ, Winge SB, Zheng T, Monteiro AN, Almstrup K, Kanetsky PA, Nathanson KL, Wiklund F
Publication type: Article
Publication status: Published
Journal: American Journal of Human Genetics
Year: 2025
Volume: 112
Issue: 3
Pages: 630-643
Print publication date: 06/03/2025
Online publication date: 24/02/2025
Acceptance date: 28/01/2025
Date deposited: 10/03/2025
ISSN (print): 0002-9297
ISSN (electronic): 1537-6605
Publisher: Cell Press
URL: https://doi.org/10.1016/j.ajhg.2025.01.022
DOI: 10.1016/j.ajhg.2025.01.022
Data Access Statement: The code used in this analysis is available at https://github.com/emiuga/TGCT_TWAS. Fusion software, prediction models, and reference LD are available at http://gusevlab.org/projects/fusion/. TGCT GWAS summary data used in this study are available at https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001349.v2.p1
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