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Chen Z, Lei Y, Finnell RH, Ding Y, Su Z, Wang Y, Xie H, Chen F. Whole-exome sequencing study of hypospadias. iScience 2023; 26:106663. [PMID: 37168556 PMCID: PMC10165268 DOI: 10.1016/j.isci.2023.106663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/01/2023] [Accepted: 04/07/2023] [Indexed: 05/13/2023] Open
Abstract
Hypospadias results from the impaired urethral development, which is influenced by androgens, but its genetic etiology is still unknown. Through whole exome sequencing analysis, we identified NR5A1, SRD5A2, and AR as mutational hotspots in the etiology of severe hypospadias, as these genes are related to androgen signaling. Additionally, rare damaging variants in cilia-related outer dynein arm heavy chain (ODNAH) genes (DNAH5, DNAH8, DNAH9, DNAH11, and DNAH17) (p = 8.5 × 10-47) were significantly enriched in hypospadias cases. The Dnah8 KO mice exhibited significantly decreased testosterone levels, which had an impact on urethral development and disrupted steroid biosynthesis. Combined with trios data, transcriptomic, and phenotypical and proteomic characterization of a mouse model, our work links ciliary genes with hypospadias. Overall, a panel of ODNAH genes with rare damaging variants was identified in 24% of hypospadias patients, providing significant insights into the underlying pathogenesis of hypospadias as well as genetic counseling.
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Affiliation(s)
- Zhongzhong Chen
- Department of Urology, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Urogenital Development Research Center, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Yunping Lei
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard H. Finnell
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Departments of Molecular and Human Genetics and Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yu Ding
- Department of Urology, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Zhixi Su
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yaping Wang
- Department of Urology, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Hua Xie
- Department of Urology, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Fang Chen
- Department of Urology, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Clinical Research Center For Hypospadias Pediatric College, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
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Chen Z, Li P, Lyu Y, Wang Y, Gao K, Wang J, Lan F, Chen F. Molecular genetics and general management of androgen insensitivity syndrome. Intractable Rare Dis Res 2023; 12:71-77. [PMID: 37287652 PMCID: PMC10242393 DOI: 10.5582/irdr.2023.01024] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/25/2023] [Accepted: 05/15/2023] [Indexed: 06/09/2023] Open
Abstract
Androgen insensitivity syndrome (AIS) is a rare genetic disorder that affects the development of the male reproductive system in individuals with a 46,XY karyotype. In addition to physical impacts, patients with AIS may face psychological distress and social challenges related to gender identity and acceptance. The major molecular etiology of AIS results from hormone resistance caused by mutations in the X-linked androgen receptor (AR) gene. Depending on the severity of androgen resistance, the wide spectrum of AIS can be divided into complete AIS (CAIS), partial AIS (PAIS), or mild AIS (MAIS). Open issues in the treatment and management of AIS include decisions about reconstructive surgery, genetic counseling, gender assignment, timing of gonadectomy, fertility and physiological outcomes. Although new genomic approaches have improved understanding of the molecular causes of AIS, identification of individuals with AIS can be challenging, and molecular genetic diagnosis is often not achievable. The relationship between AIS genotype and phenotype is not well established. Therefore, the optimal management remains uncertain. The objective of this review is to outline the recent progress and promote understanding of AIS related to the clinical manifestation, molecular genetics and expert multidisciplinary approach, with an emphasis on genetic etiology.
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Affiliation(s)
- Zhongzhong Chen
- Department of Urology, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Clinical Research Center for Hypospadias Pediatric College, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Urogenital Development Research Center, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Pin Li
- Department of Endocrinology, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yiqing Lyu
- Department of Urology, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yaping Wang
- Department of Urology, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Kexin Gao
- Department of Urology, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jing Wang
- Department of Urology, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fuying Lan
- Department of Urology, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fang Chen
- Department of Urology, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Clinical Research Center for Hypospadias Pediatric College, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Zeng L, Fan X, Wang X, Deng H, Zhang X, Zhang K, He S, Li N, Han Q, Liu Z. Involvement of NEK2 and its interaction with NDC80 and CEP250 in hepatocellular carcinoma. BMC Med Genomics 2020; 13:158. [PMID: 33109182 PMCID: PMC7590453 DOI: 10.1186/s12920-020-00812-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/25/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND NEK2 has an established involvement in hepatocellular carcinoma (HCC) but the roles of NEK2 and its interacting proteins in HCC have not been systematically explored. METHODS This study examined NEK2 and its interacting proteins in HCC based on multiple databases. RESULTS NEK2 mRNA was highly expressed in HCC tissues compared with normal liver tissues. The survival of HCC patients with high NEK2 mRNA expression was shorter than those with low expression. MAD1L1, CEP250, MAPK1, NDC80, PPP1CA, PPP1R2 and NEK11 were the interacting proteins of NEK2. Among them, NDC80 and CEP250 were the key interacting proteins of NEK2. Mitotic prometaphase may be the key pathway that NEK2 and its interacting proteins contributed to HCC pathogenesis. NEK2, NDC80 and CEP250 mRNAs were highly expressed in HCC tissues compared with normal liver tissues. The mRNA levels of NEK2 were positively correlated with those of NDC80 or CEP250. Univariate regression showed that NEK2, NDC80 and CEP250 mRNA expressions were significantly associated with HCC patients' survival. Multivariate regression showed that NDC80 mRNA expression was an independent predictor for HCC patients' survival. Methylations and genetic alterations of NEK2, NDC80 and CEP250 were observed in HCC samples. The alterations of NEK2, NDC80 and CEP250 genes were co-occurrence. Patients with high mRNA expression and genetic alterations of NEK2, NDC80 and CEP250 had poor prognosis. CONCLUSIONS NEK2 and its interacting proteins NDC80 and CEP250 play important roles in HCC development and progression and thus may be potentially used as biomarkers and therapeutic targets of HCC.
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Affiliation(s)
- Lu Zeng
- Department of Infectious Diseases, First Affiliated Hospital of Xi’an Jiaotong University, No. 277 Yanta West Road, Xi’an, 710061 Shaanxi Province People’s Republic of China
- Xi’an Medical University, Xi’an, 710021 Shaanxi Province People’s Republic of China
| | - Xiude Fan
- Department of Infectious Diseases, First Affiliated Hospital of Xi’an Jiaotong University, No. 277 Yanta West Road, Xi’an, 710061 Shaanxi Province People’s Republic of China
| | - Xiaoyun Wang
- Department of Infectious Diseases, First Affiliated Hospital of Xi’an Jiaotong University, No. 277 Yanta West Road, Xi’an, 710061 Shaanxi Province People’s Republic of China
| | - Huan Deng
- Department of Infectious Diseases, First Affiliated Hospital of Xi’an Jiaotong University, No. 277 Yanta West Road, Xi’an, 710061 Shaanxi Province People’s Republic of China
| | - Xiaoge Zhang
- Department of Infectious Diseases, First Affiliated Hospital of Xi’an Jiaotong University, No. 277 Yanta West Road, Xi’an, 710061 Shaanxi Province People’s Republic of China
| | - Kun Zhang
- Department of Infectious Diseases, First Affiliated Hospital of Xi’an Jiaotong University, No. 277 Yanta West Road, Xi’an, 710061 Shaanxi Province People’s Republic of China
| | - Shan He
- Department of Infectious Diseases, First Affiliated Hospital of Xi’an Jiaotong University, No. 277 Yanta West Road, Xi’an, 710061 Shaanxi Province People’s Republic of China
- Xi’an Medical University, Xi’an, 710021 Shaanxi Province People’s Republic of China
| | - Na Li
- Department of Infectious Diseases, First Affiliated Hospital of Xi’an Jiaotong University, No. 277 Yanta West Road, Xi’an, 710061 Shaanxi Province People’s Republic of China
| | - Qunying Han
- Department of Infectious Diseases, First Affiliated Hospital of Xi’an Jiaotong University, No. 277 Yanta West Road, Xi’an, 710061 Shaanxi Province People’s Republic of China
| | - Zhengwen Liu
- Department of Infectious Diseases, First Affiliated Hospital of Xi’an Jiaotong University, No. 277 Yanta West Road, Xi’an, 710061 Shaanxi Province People’s Republic of China
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Chen Z, Lin X, Wang Y, Xie H, Chen F. Dysregulated expression of androgen metabolism genes and genetic analysis in hypospadias. Mol Genet Genomic Med 2020; 8:e1346. [PMID: 32515122 PMCID: PMC7434757 DOI: 10.1002/mgg3.1346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 12/18/2022] Open
Abstract
Background The aberrant expression of genes involved in androgen metabolism and genetic contribution are unclear in hypospadias. Methods We compared gene expression profiles by RNA sequencing from five non‐hypospadiac foreskins, five mild hypospadiac foreskins, and five severe hypospadiac foreskins. In addition, to identify rare coding variants with large effects on hypospadias risk, we carried out whole exome sequencing in three patients in a hypospadias family. Results The average expression of androgen receptor (AR) and CYP19A1 were significantly decreased in severe hypospadias (p < .01) and mild hypospadias (p < .05), whereas expression of several other androgen metabolism enzymes, including CYP3A4, HSD17B14, HSD3B7, HSD17B7, CYP11A1 were exclusively significantly expressed in severe hypospadias (p < .05). Compound rare damaging mutants of AR gene with HSD3B1 and SLC25A5 genes were identified in the different severe hypospadias. Conclusions In conclusion, our findings demonstrated that dysregulation of AR and CYP19A1 could play a crucial role in the development of hypospadias. Inconsistent AR expression may be caused by the feedback loop of ESR1 signaling or combined genetic effects with other risk genes. This findings complement the possible role of AR triggered mechanism in the development of hypospadias.
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Affiliation(s)
- Zhongzhong Chen
- Department of Urology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoling Lin
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yaping Wang
- Department of Urology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Hua Xie
- Department of Urology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Fang Chen
- Department of Urology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Department of Urology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.,Shanghai Eastern Urological Reconstruction and Repair Institute, Shanghai, China
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Chen Z, Lin X, Lei Y, Chen H, Finnell RH, Wang Y, Xu J, Lu D, Xie H, Chen F. Genome-wide association study in Chinese cohort identifies one novel hypospadias risk associated locus at 12q13.13. BMC Med Genomics 2019; 12:196. [PMID: 31856834 PMCID: PMC6923877 DOI: 10.1186/s12920-019-0642-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 12/04/2019] [Indexed: 12/21/2022] Open
Abstract
Background Hypospadias risk–associated gene variants have been reported in populations of European descent using genome-wide association studies (GWASs). There is little known at present about any possible hypospadias risk associations in Han Chinese populations. Methods To systematically investigate hypospadias risk–associated gene variants in Chinese patients, we performed the first GWAS in a Han Chinese cohort consisting of 197 moderate-severe hypospadias cases and 933 unaffected controls. Suggestive loci (p < 1 × 10− 4) were replicated in 118 cases and 383 controls, as well as in a second independent validation population of 137 cases and 190 controls. Regulatory and protein-protein interactions (PPIs) were then conducted for the functional analyses of candidate variants. Results We identified rs11170516 with the risk allele G within the SP1/SP7 region that was independently associated with moderate-severe hypospadias [SP1/SP7, rs11170516, Pcombine = 3.5 × 10− 9, odds ratio (OR) = 1.96 (1.59–2.44)]. Results also suggested that rs11170516 is associated with the expression of SP1 as a cis-expression quantitative trait locus (cis-eQTL). Protein SP1 could affect the risk of hypospadias via PPIs. Conclusions We performed the first GWAS of moderate-severe hypospadias in a Han Chinese cohort, and identified one novel susceptibility cis-acting regulatory locus at 12q13.13, which may regulate a variety of hypospadias-related pathways by affecting proximal SP1 gene expression and subsequent PPIs. This study complements known common hypospadias risk-associated variants and provides the possible role of cis-acting regulatory variant in causing hypospadias.
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Affiliation(s)
- Zhongzhong Chen
- Department of Urology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200062, China
| | - Xiaoling Lin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China.,Department of Urology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Yunping Lei
- Center for Precision Environmental Health, Departments of Molecular and Cellular Biology and Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Haitao Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Richard H Finnell
- Center for Precision Environmental Health, Departments of Molecular and Cellular Biology and Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yaping Wang
- Department of Urology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200062, China
| | - Jianfeng Xu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China.,Department of Urology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Hua Xie
- Department of Urology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200062, China.
| | - Fang Chen
- Department of Urology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200062, China. .,Department of Urology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China. .,Shanghai Eastern Urological Reconstruction and Repair institute, Shanghai, 200233, China.
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Lenart J, Zieminska E, Diamandakis D, Lazarewicz JW. Altered expression of genes involved in programmed cell death in primary cultured rat cerebellar granule cells acutely challenged with tetrabromobisphenol A. Neurotoxicology 2017; 63:126-136. [PMID: 28970181 DOI: 10.1016/j.neuro.2017.09.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/22/2017] [Accepted: 09/28/2017] [Indexed: 12/19/2022]
Abstract
In the present study, primary cultures of rat cerebellar granule cells (CGC) and the RT2 Profiler PCR array were used to examine the effect of acutely applied brominated flame retardant tetrabromobisphenol A (TBBPA) on the expression of 84 genes related to the main modes of programmed cell death. CGC, at the 7th day of culture, were exposed to 10 or 25μM TBBPA for 30min. Then, 3, 6, and 24h later, the viability of the cells was examined by the staining with propidium iodide (PI) or using the calcein/ethidium homodimer (CA/ET) live/dead kit, and RNA was extracted for the evaluation of gene expression by RT-PCR. At 3, 6 and 24h after the treatment, the number of viable neurons decreased, according to the PI staining method, to 75%, 58% and 41%, respectively, and with the CA/ET method to 65%, 58% and 28%, respectively. In CGC analyzed 3h after the treatment with 25μM TBBPA or 6h after 10μM TBBPA, the only change in the gene expression was a reduction in the expression of Tnf, which is associated with autophagy and may activate some pro-apoptotic proteins. Six hours after 25μM TBBPA, only 2 genes were over-expressed, a pro-apoptotic Tnfrsf10b and Irgm, which is related to autophagy, and the genes that were suppressed included the anti-apoptotic gene Xiap, the necrosis-related Commd4, pro-apoptotic Abl1, 5 genes involved in autophagy (App, Atg3, Mapk8, Pten, and Snca) and 2 genes that participate in two metabolic pathways: Atp6v1g2 (pro-apoptotic and necrosis) and Tnf (pro-apoptotic, autophagy). Autophagy-related Snca and Tnf remained under-expressed 24h after treatment with 25μM TBBPA, which was accompanied by the over-expression of the pro-apoptotic Casp6, the anti-apoptotic Birc3, 2 genes related to autophagy (Htt and Irgm) and 2 genes (Fas and Tp53) that are involved in both apoptosis (pro-apoptotic) and autophagy. These results show a complex pattern of TBBPA-evoked changes in the expression of the genes involved in the programmed neuronal death, indicating no induction of programmed necrosis, an early suppression of the autophagy and anti-apoptotic genes, followed by a delayed activation of genes associated with apoptosis.
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Affiliation(s)
- Jacek Lenart
- Department of Neurochemistry, Mossakowski Medical Research Centre, Polish Academy of Sciences, Pawinskiego 5, 02-106, Warsaw, Poland.
| | - Elzbieta Zieminska
- Department of Neurochemistry, Mossakowski Medical Research Centre, Polish Academy of Sciences, Pawinskiego 5, 02-106, Warsaw, Poland
| | - Dominik Diamandakis
- Department of Neurochemistry, Mossakowski Medical Research Centre, Polish Academy of Sciences, Pawinskiego 5, 02-106, Warsaw, Poland
| | - Jerzy W Lazarewicz
- Department of Neurochemistry, Mossakowski Medical Research Centre, Polish Academy of Sciences, Pawinskiego 5, 02-106, Warsaw, Poland
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Yue J, Xu W, Ban R, Huang S, Miao M, Tang X, Liu G, Liu Y. PTIR: Predicted Tomato Interactome Resource. Sci Rep 2016; 6:25047. [PMID: 27121261 PMCID: PMC4848565 DOI: 10.1038/srep25047] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 04/08/2016] [Indexed: 01/18/2023] Open
Abstract
Protein-protein interactions (PPIs) are involved in almost all biological processes and form the basis of the entire interactomics systems of living organisms. Identification and characterization of these interactions are fundamental to elucidating the molecular mechanisms of signal transduction and metabolic pathways at both the cellular and systemic levels. Although a number of experimental and computational studies have been performed on model organisms, the studies exploring and investigating PPIs in tomatoes remain lacking. Here, we developed a Predicted Tomato Interactome Resource (PTIR), based on experimentally determined orthologous interactions in six model organisms. The reliability of individual PPIs was also evaluated by shared gene ontology (GO) terms, co-evolution, co-expression, co-localization and available domain-domain interactions (DDIs). Currently, the PTIR covers 357,946 non-redundant PPIs among 10,626 proteins, including 12,291 high-confidence, 226,553 medium-confidence, and 119,102 low-confidence interactions. These interactions are expected to cover 30.6% of the entire tomato proteome and possess a reasonable distribution. In addition, ten randomly selected PPIs were verified using yeast two-hybrid (Y2H) screening or a bimolecular fluorescence complementation (BiFC) assay. The PTIR was constructed and implemented as a dedicated database and is available at http://bdg.hfut.edu.cn/ptir/index.html without registration.
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Affiliation(s)
- Junyang Yue
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei 230009, China
| | - Wei Xu
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei 230009, China
| | - Rongjun Ban
- School of Information Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Shengxiong Huang
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei 230009, China
| | - Min Miao
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei 230009, China
| | - Xiaofeng Tang
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei 230009, China
| | - Guoqing Liu
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yongsheng Liu
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei 230009, China
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
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Olow A, Chen Z, Niedner RH, Wolf DM, Yau C, Pankov A, Lee EPR, Brown-Swigart L, van 't Veer LJ, Coppé JP. An Atlas of the Human Kinome Reveals the Mutational Landscape Underlying Dysregulated Phosphorylation Cascades in Cancer. Cancer Res 2016; 76:1733-45. [PMID: 26921330 DOI: 10.1158/0008-5472.can-15-2325-t] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 01/04/2016] [Indexed: 12/14/2022]
Abstract
Kinase inhibitors are used widely to treat various cancers, but adaptive reprogramming of kinase cascades and activation of feedback loop mechanisms often contribute to therapeutic resistance. Determining comprehensive, accurate maps of kinase circuits may therefore help elucidate mechanisms of response and resistance to kinase inhibitor therapies. In this study, we identified and validated phosphorylatable target sites across human cell and tissue types to generate PhosphoAtlas, a map of 1,733 functionally interconnected proteins comprising the human phospho-reactome. A systematic curation approach was used to distill protein phosphorylation data cross-referenced from 38 public resources. We demonstrated how a catalog of 2,617 stringently verified heptameric peptide regions at the catalytic interface of kinases and substrates could expose mutations that recurrently perturb specific phospho-hubs. In silico mapping of 2,896 nonsynonymous tumor variants identified from thousands of tumor tissues also revealed that normal and aberrant catalytic interactions co-occur frequently, showing how tumors systematically hijack, as well as spare, particular subnetworks. Overall, our work provides an important new resource for interrogating the human tumor kinome to strategically identify therapeutically actionable kinase networks that drive tumorigenesis. Cancer Res; 76(7); 1733-45. ©2016 AACR.
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Affiliation(s)
- Aleksandra Olow
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, California
| | - Zhongzhong Chen
- The State Key Laboratory of Genetic Engineering, Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - R Hannes Niedner
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, California
| | - Denise M Wolf
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, California
| | - Christina Yau
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, California
| | - Aleksandr Pankov
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, California
| | - Evelyn Pei Rong Lee
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, California
| | - Lamorna Brown-Swigart
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, California
| | - Laura J van 't Veer
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, California
| | - Jean-Philippe Coppé
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, California.
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9
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Ghosh A, De RK. Fuzzy Correlated Association Mining: Selecting altered associations among the genes, and some possible marker genes mediating certain cancers. Appl Soft Comput 2016. [DOI: 10.1016/j.asoc.2015.09.057] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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