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Hwang J, Lee HE, Han JS, Choi MH, Hong SH, Kim SW, Yang JH, Park U, Jung ES, Choi YJ. Sex-specific survival gene mutations are discovered as clinical predictors of clear cell renal cell carcinoma. Sci Rep 2024; 14:15800. [PMID: 38982123 PMCID: PMC11233666 DOI: 10.1038/s41598-024-66525-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024] Open
Abstract
Although sex differences have been reported in patients with clear cell renal cell carcinoma (ccRCC), biological sex has not received clinical attention and genetic differences between sexes are poorly understood. This study aims to identify sex-specific gene mutations and explore their clinical significance in ccRCC. We used data from The Cancer Genome Atlas-Kidney Renal Clear Cell Carcinoma (TCGA-KIRC), The Renal Cell Cancer-European Union (RECA-EU) and Korean-KIRC. A total of 68 sex-related genes were selected from TCGA-KIRC through machine learning, and 23 sex-specific genes were identified through verification using the three databases. Survival differences according to sex were identified in nine genes (ACSS3, ALG13, ASXL3, BAP1, JADE3, KDM5C, KDM6A, NCOR1P1, and ZNF449). Female-specific survival differences were found in BAP1 in overall survival (OS) (TCGA-KIRC, p = 0.004; RECA-EU, p = 0.002; and Korean-KIRC, p = 0.003) and disease-free survival (DFS) (TCGA-KIRC, p = 0.001 and Korean-KIRC, p = 0.000004), and NCOR1P1 in DFS (TCGA-KIRC, p = 0.046 and RECA-EU, p = 0.00003). Male-specific survival differences were found in ASXL3 (OS, p = 0.017 in TCGA-KIRC; and OS, p = 0.005 in RECA-EU) and KDM5C (OS, p = 0.009 in RECA-EU; and DFS, p = 0.016 in Korean-KIRC). These results suggest that biological sex may be an important predictor and sex-specific tailored treatment may improve patient care in ccRCC.
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Affiliation(s)
- Jia Hwang
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-Gu, Seoul, 06591, Republic of Korea
| | - Hye Eun Lee
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-Gu, Seoul, 06591, Republic of Korea
| | - Jin Seon Han
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-Gu, Seoul, 06591, Republic of Korea
| | - Moon Hyung Choi
- Department of Radiology, College of Medicine, Eunpyeong St. Mary's Hospital, The Catholic University of Korea, Seoul, 03312, Republic of Korea
| | - Sung Hoo Hong
- Department of Urology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Sae Woong Kim
- Department of Urology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Ji Hoon Yang
- Department of Computer Science and Engineering, Sogang University, Seoul, 04107, Republic of Korea
| | - Unsang Park
- Department of Computer Science and Engineering, Sogang University, Seoul, 04107, Republic of Korea
| | - Eun Sun Jung
- Department of Hospital Pathology, College of Medicine, Eunpyeong St. Mary's Hospital, The Catholic University of Korea, Seoul, 03312, Republic of Korea
| | - Yeong Jin Choi
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-Gu, Seoul, 06591, Republic of Korea.
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Gong H, Liu W, Wu Z, Zhang M, Sun Y, Ling Z, Xiao S, Ai H, Xin Y, Yang B, Huang L. Evolutionary insights into porcine genomic structural variations based on a novel constructed dataset from 24 worldwide diverse populations. Evol Appl 2022. [DOI: 10.1111/eva.13455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Huanfa Gong
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences Zhejiang University Hangzhou P.R. China
- Key Laboratory of Animal Nutrition and Feed Science in Eastern China, Ministry of Agriculture, College of Animal Sciences Zhejiang University Hangzhou P.R. China
| | - Weiwei Liu
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Zhongzi Wu
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Mingpeng Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Yingchun Sun
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Ziqi Ling
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Shijun Xiao
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Huashui Ai
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Yuyun Xin
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
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Okada K, Fukai A, Mori D, Hosaka Y, Yano F, Chung UI, Kawaguchi H, Tanaka S, Ikeda T, Saito T. Identification of SCAN domain zinc-finger gene ZNF449 as a novel factor of chondrogenesis. PLoS One 2014; 9:e115169. [PMID: 25546433 PMCID: PMC4278888 DOI: 10.1371/journal.pone.0115169] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 11/19/2014] [Indexed: 11/21/2022] Open
Abstract
Transcription factors SOX9, SOX5 and SOX6 are indispensable for generation and differentiation of chondrocytes. However, molecular mechanisms to induce the SOX genes are poorly understood. To address this issue, we previously determined the human embryonic enhancer of SOX6 by 5′RACE analysis, and identified the 46-bp core enhancer region (CES6). We initially performed yeast one-hybrid assay for screening other chondrogenic factors using CES6 as bait, and identified a zinc finger protein ZNF449. ZNF449 and Zfp449, a counterpart in mouse, transactivated enhancers or promoters of SOX6, SOX9 and COL2A1. Zfp449 was expressed in mesenchyme-derived tissues including cartilage, calvaria, muscle and tendon, as well as in other tissues including brain, lung and kidney. In limb cartilage of mouse embryo, Zfp449 protein was abundantly located in periarticular chondrocytes, and decreased in accordance with the differentiation. Zfp449 protein was also detected in articular cartilage of an adult mouse. During chondrogenic differentiation of human mesenchymal stem cells, ZNF449 was increased at an early stage, and its overexpression enhanced SOX9 and SOX6 only at the initial stage of the differentiation. We further generated Zfp449 knockout mice to examine the in vivo roles; however, no obvious abnormality was observed in skeletal development or articular cartilage homeostasis. ZNF449 may regulate chondrogenic differentiation from mesenchymal progenitor cells, although the underlying mechanisms are still unknown.
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Affiliation(s)
- Keita Okada
- Sensory & Motor System Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Atsushi Fukai
- Sensory & Motor System Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
- Sports Medicine and Orthopedics, Kanto Rosai Hospital, Japan Labour Health and Welfare Organization, Kanagawa, Japan
| | - Daisuke Mori
- Bone and Cartilage Regenerative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoko Hosaka
- Sensory & Motor System Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
- Orthopedic Surgery, Tokyo Metropolitan Bokutoh Hospital, Tokyo, Japan
| | - Fumiko Yano
- Bone and Cartilage Regenerative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
- Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ung-il Chung
- Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Kawaguchi
- Sensory & Motor System Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
- Spine Center, Tokyo Shinjuku Medical Center, Japan Community Health care Organization, Tokyo, Japan
| | - Sakae Tanaka
- Sensory & Motor System Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshiyuki Ikeda
- Sensory & Motor System Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
- Division of Transfusion Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Taku Saito
- Sensory & Motor System Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
- Bone and Cartilage Regenerative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
- * E-mail:
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