Identification of genes associated with testicular germ cell tumor susceptibility through a transcriptome-wide association study
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| Názov: | Identification of genes associated with testicular germ cell tumor susceptibility through a transcriptome-wide association study |
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| Autori: | Ugalde-Morales, E., Wilf, R., Pluta, J., Ploner, A., Fan, M., Damra, M., Aben, K.K.H., Anson-Cartwright, L., Chen, C., Cortessis, V.K., Daneshmand, S., Ferlin, A., Gamulin, M., Gietema, J.A., Gonzalez-Niera, A., Grotmol, T., Hamilton, R.J., Harland, M., Haugen, T.B., Hauser, R., Hildebrandt, M.A., Karlsson, R., Kiemeney, B., Kim, Jung, Lessel, D., Lothe, R.A., Loveday, C., Chanock, S.J., McGlynn, K.A., Meijer, C., Nead, K.T., Nsengimana, J., Popovic, M., Rafnar, T., Richiardi, L., Rocca, M.S., Schwartz, S.M., Skotheim, R.I., Stefansson, K., Stewart, D.R., Turnbull, C., Vaughn, D.J., Winge, S.B., Zheng, T., Monteiro, Ana, Almstrup, K., Kanetsky, P.A., Nathanson, K.L., Wiklund, F. |
| Zdroj: | Am J Hum Genet American Journal of Human Genetics, 112, 3, pp. 630-643 Ugalde-Morales, E, Wilf, R, Pluta, J, Ploner, A, Fan, M, Damra, M, Aben, K K, Anson-Cartwright, L, Chen, C, Cortessis, V K, Daneshmand, S, Ferlin, A, Gamulin, M, Gietema, J A, Gonzalez-Niera, A, Grotmol, T, Hamilton, R J, Harland, M, Haugen, T B, Hauser, R, Hildebrandt, M A T, Karlsson, R, Kiemeney, L A, Kim, J, Lessel, D, Lothe, R A, Loveday, C, Chanock, S J, McGlynn, K A, Meijer, C, Nead, K T, Nsengimana, J, Popovic, M, Rafnar, T, Richiardi, L, Rocca, M S, Schwartz, S M, Skotheim, R I, Stefansson, K, Stewart, D R, Turnbull, C, Vaughn, D J, Winge, S B, Zheng, T, Monteiro, A N, Almstrup, K, Kanetsky, P A, Nathanson, K L, Wiklund, F & The Testicular Cancer Consortium 2025, ' Identification of genes associated with testicular germ cell tumor susceptibility through a transcriptome-wide association study ', American Journal of Human Genetics, vol. 112, no. 3, pp. 630-643 . https://doi.org/10.1016/j.ajhg.2025.01.022 |
| Informácie o vydavateľovi: | Elsevier BV, 2025. |
| Rok vydania: | 2025 |
| Predmety: | Male, Primary and Community Care - Radboud University Medical Center, Gene Expression Profiling, colocalization analysis, testicular germ cell tumors, transcriptome-wide association study, Neoplasms, Germ Cell and Embryonal, Polymorphism, Single Nucleotide, Transcriptome / genetics, Article, Gene Expression Regulation, Neoplastic, Testicular Neoplasms / genetics, Testicular Neoplasms, Neoplasms, Germ Cell and Embryonal / genetics, IQ health - Radboud University Medical Center, Urology - Radboud University Medical Center, Humans, Genetic Predisposition to Disease, Transcriptome, Polymorphism, Single Nucleotide / genetics, Genome-Wide Association Study |
| Popis: | 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. |
| Druh dokumentu: | Article Other literature type |
| Popis súboru: | application/pdf |
| Jazyk: | English |
| ISSN: | 0002-9297 |
| DOI: | 10.1016/j.ajhg.2025.01.022 |
| Prístupová URL adresa: | https://pubmed.ncbi.nlm.nih.gov/39999848 https://hdl.handle.net/https://repository.ubn.ru.nl/handle/2066/317614 https://doi.org/10.1016/j.ajhg.2025.01.022 https://hdl.handle.net/11370/b6938e82-8f31-4cb3-b558-d341748fad39 https://research.rug.nl/en/publications/b6938e82-8f31-4cb3-b558-d341748fad39 https://doi.org/10.1016/j.ajhg.2025.01.022 https://repository.ubn.ru.nl//bitstream/handle/2066/317614/317614.pdf https://hdl.handle.net/2066/317614 https://curis.ku.dk/ws/files/431467687/1_s2.0_S0002929725000229_main.pdf https://urn.nsk.hr/urn:nbn:hr:105:918624 https://doi.org/10.1016/j.ajhg.2025.01.022 |
| Rights: | CC BY |
| Prístupové číslo: | edsair.doi.dedup.....08f697d230853243381b360a3e091887 |
| Databáza: | OpenAIRE |
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Nájsť tento článok vo Web of Science | Abstrakt: | 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. |
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| ISSN: | 00029297 |
| DOI: | 10.1016/j.ajhg.2025.01.022 |