Systematically identification of survival-associated eQTLs in a Japanese kidney cancer cohort.
<h4>Background</h4>Clear cell renal carcinoma (ccRCC) is the predominant form of kidney cancer, but the prognostic value of expression quantitative trait loci (eQTLs) remains underexplored, particularly in Asian populations.<h4>Objective</h4>We analyzed whole-exome sequencing...
Saved in:
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2025-07-01
|
| Series: | PLoS Genetics |
| Online Access: | https://doi.org/10.1371/journal.pgen.1011770 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850113979546861568 |
|---|---|
| author | Xiya Song Han Jin Xiangyu Li Meng Yuan Hong Yang Yusuke Sato Haruki Kume Seishi Ogawa Cheng Zhang Adil Mardinoglu |
| author_facet | Xiya Song Han Jin Xiangyu Li Meng Yuan Hong Yang Yusuke Sato Haruki Kume Seishi Ogawa Cheng Zhang Adil Mardinoglu |
| author_sort | Xiya Song |
| collection | DOAJ |
| description | <h4>Background</h4>Clear cell renal carcinoma (ccRCC) is the predominant form of kidney cancer, but the prognostic value of expression quantitative trait loci (eQTLs) remains underexplored, particularly in Asian populations.<h4>Objective</h4>We analyzed whole-exome sequencing and RNA sequencing data from 100 Japanese ccRCC patients to identify eQTLs. Multiple Cox proportional hazard models assessed survival associations, with validation in the Cancer Genome Atlas ccRCC cohort (n = 287).<h4>Results</h4>We identified 805 eGenes and 4,558 cis-eQTLs in the Japanese cohort. Survival analysis revealed a total of 9 eGenes significantly associated with overall survival (FDR < 0.05). Further exploratory analysis were performed using 158 eGenes and 711 eQTLs (p-value <0.05) as potential prognostic signals. Among these, 223 eQTLs regulating 54 eGenes showed consistent prognostic effects at both expression and genetic levels. Cross-population validation identified eight eQTLs regulating 11 eGenes with reproducible survival associations across ethnicities, including a missense mutation in ERV3-1 and regulatory variants near ANKRD20A7P. These variants demonstrated consistent allelic effects on both gene expression and patient survival in both cohorts. |
| format | Article |
| id | doaj-art-c11239dadd5b442083df0113f79d3a05 |
| institution | OA Journals |
| issn | 1553-7390 1553-7404 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj-art-c11239dadd5b442083df0113f79d3a052025-08-20T02:37:01ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042025-07-01217e101177010.1371/journal.pgen.1011770Systematically identification of survival-associated eQTLs in a Japanese kidney cancer cohort.Xiya SongHan JinXiangyu LiMeng YuanHong YangYusuke SatoHaruki KumeSeishi OgawaCheng ZhangAdil Mardinoglu<h4>Background</h4>Clear cell renal carcinoma (ccRCC) is the predominant form of kidney cancer, but the prognostic value of expression quantitative trait loci (eQTLs) remains underexplored, particularly in Asian populations.<h4>Objective</h4>We analyzed whole-exome sequencing and RNA sequencing data from 100 Japanese ccRCC patients to identify eQTLs. Multiple Cox proportional hazard models assessed survival associations, with validation in the Cancer Genome Atlas ccRCC cohort (n = 287).<h4>Results</h4>We identified 805 eGenes and 4,558 cis-eQTLs in the Japanese cohort. Survival analysis revealed a total of 9 eGenes significantly associated with overall survival (FDR < 0.05). Further exploratory analysis were performed using 158 eGenes and 711 eQTLs (p-value <0.05) as potential prognostic signals. Among these, 223 eQTLs regulating 54 eGenes showed consistent prognostic effects at both expression and genetic levels. Cross-population validation identified eight eQTLs regulating 11 eGenes with reproducible survival associations across ethnicities, including a missense mutation in ERV3-1 and regulatory variants near ANKRD20A7P. These variants demonstrated consistent allelic effects on both gene expression and patient survival in both cohorts.https://doi.org/10.1371/journal.pgen.1011770 |
| spellingShingle | Xiya Song Han Jin Xiangyu Li Meng Yuan Hong Yang Yusuke Sato Haruki Kume Seishi Ogawa Cheng Zhang Adil Mardinoglu Systematically identification of survival-associated eQTLs in a Japanese kidney cancer cohort. PLoS Genetics |
| title | Systematically identification of survival-associated eQTLs in a Japanese kidney cancer cohort. |
| title_full | Systematically identification of survival-associated eQTLs in a Japanese kidney cancer cohort. |
| title_fullStr | Systematically identification of survival-associated eQTLs in a Japanese kidney cancer cohort. |
| title_full_unstemmed | Systematically identification of survival-associated eQTLs in a Japanese kidney cancer cohort. |
| title_short | Systematically identification of survival-associated eQTLs in a Japanese kidney cancer cohort. |
| title_sort | systematically identification of survival associated eqtls in a japanese kidney cancer cohort |
| url | https://doi.org/10.1371/journal.pgen.1011770 |
| work_keys_str_mv | AT xiyasong systematicallyidentificationofsurvivalassociatedeqtlsinajapanesekidneycancercohort AT hanjin systematicallyidentificationofsurvivalassociatedeqtlsinajapanesekidneycancercohort AT xiangyuli systematicallyidentificationofsurvivalassociatedeqtlsinajapanesekidneycancercohort AT mengyuan systematicallyidentificationofsurvivalassociatedeqtlsinajapanesekidneycancercohort AT hongyang systematicallyidentificationofsurvivalassociatedeqtlsinajapanesekidneycancercohort AT yusukesato systematicallyidentificationofsurvivalassociatedeqtlsinajapanesekidneycancercohort AT harukikume systematicallyidentificationofsurvivalassociatedeqtlsinajapanesekidneycancercohort AT seishiogawa systematicallyidentificationofsurvivalassociatedeqtlsinajapanesekidneycancercohort AT chengzhang systematicallyidentificationofsurvivalassociatedeqtlsinajapanesekidneycancercohort AT adilmardinoglu systematicallyidentificationofsurvivalassociatedeqtlsinajapanesekidneycancercohort |