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Yu Y, Zuo X, He M, Gao J, Fu Y, Qin C, Meng L, Wang W, Song Y, Cheng Y, Zhou F, Chen G, Zheng X, Wang X, Liang B, Zhu Z, Fu X, Sheng Y, Hao J, Liu Z, Yan H, Mangold E, Ruczinski I, Liu J, Marazita ML, Ludwig KU, Beaty TH, Zhang X, Sun L, Bian Z. Genome-wide analyses of non-syndromic cleft lip with palate identify 14 novel loci and genetic heterogeneity. Nat Commun 2017; 8:14364. [PMID: 28232668 PMCID: PMC5333091 DOI: 10.1038/ncomms14364] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 12/20/2016] [Indexed: 01/08/2023] Open
Abstract
Non-syndromic cleft lip with palate (NSCLP) is the most serious sub-phenotype of non-syndromic orofacial clefts (NSOFC), which are the most common craniofacial birth defects in humans. Here we conduct a GWAS of NSCLP with multiple independent replications, totalling 7,404 NSOFC cases and 16,059 controls from several ethnicities, to identify new NSCLP risk loci, and explore the genetic heterogeneity between sub-phenotypes of NSOFC. We identify 41 SNPs within 26 loci that achieve genome-wide significance, 14 of which are novel (RAD54B, TMEM19, KRT18, WNT9B, GSC/DICER1, PTCH1, RPS26, OFCC1/TFAP2A, TAF1B, FGF10, MSX1, LINC00640, FGFR1 and SPRY1). These 26 loci collectively account for 10.94% of the heritability for NSCLP in Chinese population. We find evidence of genetic heterogeneity between the sub-phenotypes of NSOFC and among different populations. This study substantially increases the number of genetic susceptibility loci for NSCLP and provides important insights into the genetic aetiology of this common craniofacial malformation. Non-syndromic cleft lip with palate is a common birth defect of unknown aetiology. Here, the authors discover 14 new genes associated with this condition, and show genetic heterogeneity in this and other non-syndromic orofacial clefting disorders.
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Affiliation(s)
- Yanqin Yu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China
| | - Xianbo Zuo
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230032, China.,State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, China.,Key Lab of Dermatology, Ministry of Education, Heifei, China.,Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China.,Collaborative Innovation Center of Complex and Severe skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
| | - Miao He
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China.,Department of Pediatric Dentistry, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China
| | - Jinping Gao
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230032, China.,State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, China.,Key Lab of Dermatology, Ministry of Education, Heifei, China.,Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China.,Collaborative Innovation Center of Complex and Severe skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
| | - Yuchuan Fu
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China
| | - Chuanqi Qin
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China.,Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China
| | - Liuyan Meng
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China
| | - Wenjun Wang
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230032, China.,State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, China.,Key Lab of Dermatology, Ministry of Education, Heifei, China.,Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China.,Collaborative Innovation Center of Complex and Severe skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
| | - Yaling Song
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China
| | - Yong Cheng
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China
| | - Fusheng Zhou
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230032, China.,State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, China.,Key Lab of Dermatology, Ministry of Education, Heifei, China.,Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China.,Collaborative Innovation Center of Complex and Severe skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
| | - Gang Chen
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230032, China.,State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, China.,Key Lab of Dermatology, Ministry of Education, Heifei, China.,Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China.,Collaborative Innovation Center of Complex and Severe skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
| | - Xiaodong Zheng
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230032, China.,State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, China.,Key Lab of Dermatology, Ministry of Education, Heifei, China.,Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China.,Collaborative Innovation Center of Complex and Severe skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
| | - Xinhuan Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China
| | - Bo Liang
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230032, China.,State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, China.,Key Lab of Dermatology, Ministry of Education, Heifei, China.,Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China.,Collaborative Innovation Center of Complex and Severe skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
| | - Zhengwei Zhu
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230032, China.,State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, China.,Key Lab of Dermatology, Ministry of Education, Heifei, China.,Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China.,Collaborative Innovation Center of Complex and Severe skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
| | - Xiazhou Fu
- Department of Genetics and Centre for Developmental Biology, College of Life Science, Wuhan University, Wuhan, Hubei 430072, China
| | - Yujun Sheng
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230032, China.,State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, China.,Key Lab of Dermatology, Ministry of Education, Heifei, China.,Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China.,Collaborative Innovation Center of Complex and Severe skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
| | - Jiebing Hao
- The Second Charity Hospital of Henan Province, Jiaozuo, Henan 454000, China
| | - Zhongyin Liu
- Stomatological Hospital of Nanyang, Nanyang, Henan 473013, China
| | - Hansong Yan
- Stomatological Hospital of Xiangyang, Xiangyang, Hubei 441011, China
| | - Elisabeth Mangold
- Institute of Human Genetics, Life and Brain Center, University of Bonn, 53127 Bonn, Germany
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Jianjun Liu
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230032, China.,State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, China.,Key Lab of Dermatology, Ministry of Education, Heifei, China.,Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China.,Collaborative Innovation Center of Complex and Severe skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
| | - Mary L Marazita
- Department of Oral Biology and Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15219, USA.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA.,Clinical and Translational Science, Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Kerstin U Ludwig
- Institute of Human Genetics, Life and Brain Center, University of Bonn, 53127 Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, 53127 Bonn, Germany
| | - Terri H Beaty
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Xuejun Zhang
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230032, China.,State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, China.,Key Lab of Dermatology, Ministry of Education, Heifei, China.,Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China.,Collaborative Innovation Center of Complex and Severe skin Disease, Anhui Medical University, Hefei, Anhui 230032, China.,Department of Dermatology at No. 2 Hospital, Anhui Medical University, Hefei, Anhui 230022, China.,Institute of Dermatology and Department of Dermatology, Huashan Hospital of Fudan University, Shanghai 200040, China
| | - Liangdan Sun
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230032, China.,State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, China.,Key Lab of Dermatology, Ministry of Education, Heifei, China.,Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China.,Collaborative Innovation Center of Complex and Severe skin Disease, Anhui Medical University, Hefei, Anhui 230032, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui Province, Anhui 230032, China
| | - Zhuan Bian
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China
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6
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Nagai Y, Yamamoto Y, Yasuhara T, Hata K, Nishikawa T, Tanaka T, Tanaka J, Kiyomatsu T, Kawai K, Nozawa H, Kazama S, Yamaguchi H, Ishihara S, Sunami E, Yamanaka T, Miyagawa K, Watanabe T. High RAD54B expression: an independent predictor of postoperative distant recurrence in colorectal cancer patients. Oncotarget 2016; 6:21064-73. [PMID: 26046797 PMCID: PMC4673250 DOI: 10.18632/oncotarget.4222] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 05/09/2015] [Indexed: 01/05/2023] Open
Abstract
We recently reported a specific mechanism that RAD54B, an important factor in homologous recombination, promotes genomic instability via the degradation of p53 protein in vitro. However, clinical significance of RAD54Bin colorectal cancer (CRC) remains unclear. Thus we analyzed RAD54B geneexpression in CRC patients. Using the training set (n = 123), the optimal cut-off value for stratification was determined, and validated in another cohort (n = 89). Kaplan-Meier plots showed that distant recurrence free survival was significantly lesser in high RAD54B expression group compared with that of low expression group in both training (P = 0.0013) and validation (P = 0.024) set. Multivariate analysis using Cox proportional-hazards model showed that high RAD54B expression was an independent predictor in both training (hazard ratio, 4.31; 95% CI, 1.53-13.1; P = 0.0060) and validation (hazard ratio, 3.63; 95% CI, 1.23-10.7; P = 0.021) set. In addition, a negative significant correlation between RAD54B and CDKN1A, a target gene of p53, was partially confirmed, suggesting that RAD54B functions via the degradation of p53 protein even in clinical samples. This study first demonstrated RAD54B expression has potential to serve as a novel prognostic biomarker, particularly for distant recurrence in CRC patients.
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Affiliation(s)
- Yuzo Nagai
- Department of Surgical Oncology, Faculty of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Yoko Yamamoto
- Department of Surgical Oncology, Faculty of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Takaaki Yasuhara
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Keisuke Hata
- Department of Surgical Oncology, Faculty of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Takeshi Nishikawa
- Department of Surgical Oncology, Faculty of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Toshiaki Tanaka
- Department of Surgical Oncology, Faculty of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Junichiro Tanaka
- Department of Surgical Oncology, Faculty of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Tomomichi Kiyomatsu
- Department of Surgical Oncology, Faculty of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Kazushige Kawai
- Department of Surgical Oncology, Faculty of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Hiroaki Nozawa
- Department of Surgical Oncology, Faculty of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Shinsuke Kazama
- Department of Surgical Oncology, Faculty of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Hironori Yamaguchi
- Department of Surgical Oncology, Faculty of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Soichiro Ishihara
- Department of Surgical Oncology, Faculty of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Eiji Sunami
- Department of Surgical Oncology, Faculty of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Takeharu Yamanaka
- Department of Biostatistics, Graduate School of Medicine, Yokohama City University, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Kiyoshi Miyagawa
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Toshiaki Watanabe
- Department of Surgical Oncology, Faculty of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
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