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Xiang H, Luo R, Wang Y, Yang B, Xu S, Huang W, Tang S, Fang R, Chen L, Zhu N, Yu Z, Akesu S, Wei C, Xu C, Zhou Y, Gu J, Zhao J, Hou Y, Ding C. Proteogenomic insights into the biology and treatment of pan-melanoma. Cell Discov 2024; 10:78. [PMID: 39039072 PMCID: PMC11263678 DOI: 10.1038/s41421-024-00688-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 05/03/2024] [Indexed: 07/24/2024] Open
Abstract
Melanoma is one of the most prevalent skin cancers, with high metastatic rates and poor prognosis. Understanding its molecular pathogenesis is crucial for improving its diagnosis and treatment. Integrated analysis of multi-omics data from 207 treatment-naïve melanomas (primary-cutaneous-melanomas (CM, n = 28), primary-acral-melanomas (AM, n = 81), primary-mucosal-melanomas (MM, n = 28), metastatic-melanomas (n = 27), and nevi (n = 43)) provides insights into melanoma biology. Multivariate analysis reveals that PRKDC amplification is a prognostic molecule for melanomas. Further proteogenomic analysis combined with functional experiments reveals that the cis-effect of PRKDC amplification may lead to tumor proliferation through the activation of DNA repair and folate metabolism pathways. Proteome-based stratification of primary melanomas defines three prognosis-related subtypes, namely, the ECM subtype, angiogenesis subtype (with a high metastasis rate), and cell proliferation subtype, which provides an essential framework for the utilization of specific targeted therapies for particular melanoma subtypes. The immune classification identifies three immune subtypes. Further analysis combined with an independent anti-PD-1 treatment cohort reveals that upregulation of the MAPK7-NFKB signaling pathway may facilitate T-cell recruitment and increase the sensitivity of patients to immunotherapy. In contrast, PRKDC may reduce the sensitivity of melanoma patients to immunotherapy by promoting DNA repair in melanoma cells. These results emphasize the clinical value of multi-omics data and have the potential to improve the understanding of melanoma treatment.
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Affiliation(s)
- Hang Xiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rongkui Luo
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yunzhi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bing Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sha Xu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Wen Huang
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shaoshuai Tang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rundong Fang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lingli Chen
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Na Zhu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zixiang Yu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sujie Akesu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chuanyuan Wei
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chen Xu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Yuhong Zhou
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Jianying Gu
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital (Xiamen), Fudan University, Shanghai, China.
| | - Jianyuan Zhao
- Institute for Developmental and Regenerative Cardiovascular Medicine, MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
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2
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Proteogenomics of diffuse gliomas reveal molecular subtypes associated with specific therapeutic targets and immune-evasion mechanisms. Nat Commun 2023; 14:505. [PMID: 36720864 PMCID: PMC9889805 DOI: 10.1038/s41467-023-36005-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 01/12/2023] [Indexed: 02/02/2023] Open
Abstract
Diffuse gliomas are devastating brain tumors. Here, we perform a proteogenomic profiling of 213 retrospectively collected glioma tumors. Proteogenomic analysis reveals the downstream biological events leading by EGFR-, IDH1-, TP53-mutations. The comparative analysis illustrates the distinctive features of GBMs and LGGs, indicating CDK2 inhibitor might serve as a promising drug target for GBMs. Further proteogenomic integrative analysis combined with functional experiments highlight the cis-effect of EGFR alterations might lead to glioma tumor cell proliferation through ERK5 medicates nucleotide synthesis process. Proteome-based stratification of gliomas defines 3 proteomic subgroups (S-Ne, S-Pf, S-Im), which could serve as a complement to WHO subtypes, and would provide the essential framework for the utilization of specific targeted therapies for particular glioma subtypes. Immune clustering identifies three immune subtypes with distinctive immune cell types. Further analysis reveals higher EGFR alteration frequencies accounts for elevation of immune check point protein: PD-L1 and CD70 in T-cell infiltrated tumors.
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Sharma N, Kumari D, Panigrahi I, Khetarpal P. A systematic review of the monogenic causes of Non-Syndromic Hearing Loss (NSHL) and discussion of Current Diagnosis and Treatment options. Clin Genet 2023; 103:16-34. [PMID: 36089522 DOI: 10.1111/cge.14228] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 12/13/2022]
Abstract
Hearing impairment is one of the most widespread inheritable sensory disorder affecting at least 1 in every 1000 born. About two-third of hereditary hearing loss (HHL) disorders are non-syndromic. To provide comprehensive update of monogenic causes of non-syndromic hearing loss (NSHL), literature search has been carried out with appropriate keywords in the following databases-PubMed, Google Scholar, Cochrane library, and Science Direct. Out of 2214 papers, 271 papers were shortlisted after applying inclusion and exclusion criterion. Data extracted from selected papers include information about gene name, identified pathogenic variants, ethnicity of the patient, age of onset, gender, title, authors' name, and year of publication. Overall, pathogenic variants in 98 different genes have been associated with NSHL. These genes have important role to play during early embryonic development in ear structure formation and hearing development. Here, we also review briefly the recent information about diagnosis and treatment approaches. Understanding pathogenic genetic variants are helpful in the management of affected and may offer targeted therapies in future.
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Affiliation(s)
- Nandita Sharma
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Divya Kumari
- Department of Pediatrics Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Inusha Panigrahi
- Department of Pediatrics Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Preeti Khetarpal
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
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4
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Tong Y, Sun M, Chen L, Wang Y, Li Y, Li L, Zhang X, Cai Y, Qie J, Pang Y, Xu Z, Zhao J, Zhang X, Liu Y, Tian S, Qin Z, Feng J, Zhang F, Zhu J, Xu Y, Lou W, Ji Y, Zhao J, He F, Hou Y, Ding C. Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma. J Hematol Oncol 2022; 15:168. [PMID: 36434634 PMCID: PMC9701038 DOI: 10.1186/s13045-022-01384-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/02/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with poor prognosis. Proteogenomic characterization and integrative proteomic analysis provide a functional context to annotate genomic abnormalities with prognostic value. METHODS We performed an integrated multi-omics analysis, including whole-exome sequencing, RNA-seq, proteomic, and phosphoproteomic analysis of 217 PDAC tumors with paired non-tumor adjacent tissues. In vivo functional experiments were performed to further illustrate the biological events related to PDAC tumorigenesis and progression. RESULTS A comprehensive proteogenomic landscape revealed that TP53 mutations upregulated the CDK4-mediated cell proliferation process and led to poor prognosis in younger patients. Integrative multi-omics analysis illustrated the proteomic and phosphoproteomic alteration led by genomic alterations such as KRAS mutations and ADAM9 amplification of PDAC tumorigenesis. Proteogenomic analysis combined with in vivo experiments revealed that the higher amplification frequency of ADAM9 (8p11.22) could drive PDAC metastasis, though downregulating adhesion junction and upregulating WNT signaling pathway. Proteome-based stratification of PDAC revealed three subtypes (S-I, S-II, and S-III) related to different clinical and molecular features. Immune clustering defined a metabolic tumor subset that harbored FH amplicons led to better prognosis. Functional experiments revealed the role of FH in altering tumor glycolysis and in impacting PDAC tumor microenvironments. Experiments utilizing both in vivo and in vitro assay proved that loss of HOGA1 promoted the tumor growth via activating LARP7-CDK1 pathway. CONCLUSIONS This proteogenomic dataset provided a valuable resource for researchers and clinicians seeking for better understanding and treatment of PDAC.
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Affiliation(s)
- Yexin Tong
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Mingjun Sun
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Lingli Chen
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Yunzhi Wang
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Yan Li
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Lingling Li
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Xuan Zhang
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Yumeng Cai
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Jingbo Qie
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Yanrui Pang
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Ziyan Xu
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Jiangyan Zhao
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Xiaolei Zhang
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Yang Liu
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Sha Tian
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Zhaoyu Qin
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Jinwen Feng
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Fan Zhang
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Jiajun Zhu
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Yifan Xu
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Wenhui Lou
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Yuan Ji
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Jianyuan Zhao
- grid.16821.3c0000 0004 0368 8293Institute for Development and Regenerative Cardiovascular Medicine, MOE-Shanghai Key Laboratory of Children’s Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China ,grid.207374.50000 0001 2189 3846Department of Anatomy and Neuroscience Research Institute, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001 China
| | - Fuchu He
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China ,grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, 102206 China ,grid.506261.60000 0001 0706 7839Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing, 102206 China
| | - Yingyong Hou
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Chen Ding
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
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Torkamandi S, Bayat S, Mirfakhraie R, Rezaei S, Askari M, Piltan S, Gholami M. Targeted sequencing of CDH23 and GJB2 genes in an Iranian pedigree with Usher syndrome and non-syndromic hearing loss. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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6
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Jiang H, Niu Y, Qu L, Huang X, Zhu X, Tang G. A novel compound heterozygous mutation in the GJB2 gene is associated with non-syndromic hearing loss in a Chinese family. Biosci Trends 2019; 12:470-475. [PMID: 30473554 DOI: 10.5582/bst.2018.01156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Autosomal recessive (AR) non-syndromic hearing loss (NSHL) is the most common form of hereditary deafness. Mutations in the gap junction protein beta 2 (GJB2) gene encoding connexin 26 (Cx26) account for about 50% of cases of ARNSHL. In the current study, a combination of exome sequencing and Sanger sequencing in a Chinese Dong family with ARNSHL allowed identification of a novel compound heterozygous mutation c.240G>C(p. Q80H)/C.109G>A(p.V37I) in exon 2 of the GJB2 gene, which co-segregated with the disease phenotype in this family and was not evident in 100 healthy controls. Bioinformatic analysis revealed that the two mutations in the GJB2 gene were probably pathogenic. Results indicated that the compound heterozygous variants, p.Q80H and p.V37I, in the GJB2 gene are associated with ARNSHL. The Q80H variant was initially identified in patients of Dong Chinese origin with NSHL. The current results broaden the spectrum of GJB2 mutations responsible for NSHL and have important implications for molecular diagnosis, treatment, and genetic counseling for this family.
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Affiliation(s)
- Haiou Jiang
- Department of Cellular Biology and Genetics, Hunan Provincial Key Laboratory of Dong Medicine, Hunan University of Medicine
| | - Youya Niu
- Department of Cellular Biology and Genetics, Hunan Provincial Key Laboratory of Dong Medicine, Hunan University of Medicine
| | - Lingfeng Qu
- Department of Cellular Biology and Genetics, Hunan Provincial Key Laboratory of Dong Medicine, Hunan University of Medicine
| | - Xueshuang Huang
- Department of Cellular Biology and Genetics, Hunan Provincial Key Laboratory of Dong Medicine, Hunan University of Medicine
| | - Xinlong Zhu
- Department of Cellular Biology and Genetics, Hunan Provincial Key Laboratory of Dong Medicine, Hunan University of Medicine
| | - Genyun Tang
- Department of Cellular Biology and Genetics, Hunan Provincial Key Laboratory of Dong Medicine, Hunan University of Medicine
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7
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Xia H, Huang X, Xu H, Zhou YA, Gong L, Yang Z, Lv J, Deng H. GJB2 c.235delC variant associated with autosomal recessive nonsyndromic hearing loss and auditory neuropathy spectrum disorder. Genet Mol Biol 2019; 42:48-51. [PMID: 30816908 PMCID: PMC6428124 DOI: 10.1590/1678-4685-gmb-2017-0318] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 06/19/2018] [Indexed: 11/22/2022] Open
Abstract
Autosomal recessive nonsyndromic hearing loss (ARNSHL) is a genetically heterogeneous neurosensory disorder, usually characterized by congenital or prelingual hearing loss. We report a Han Chinese male, born to consanguineous parents, presenting with nonsyndromic sensorineural hearing loss, whose clinical phenotype was also consistent with auditory neuropathy spectrum disorder (ANSD). After exome sequencing, a gap junction protein beta 2 gene (GJB2) c.235delC variant in the homozygous state was detected in the patient. Both parents were heterozygous for this variant, as documented by Sanger sequencing. The known pathogenic GJB2 c.235delC variant was not detected in 200 healthy controls. It is predicted to be a disease-causing alteration by generating a truncated protein p.(L79Cfs*3), disturbing the appropriate folding and/or oligomerization of connexins and leading to defective gap junction channels. This study shows that the association of homozygosity of the GJB2 c.235delC variant with ARNSHL and ANSD in a patient.
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Affiliation(s)
- Hong Xia
- Third Xiangya Hospital, Center for Experimental Medicine and Department of Neurology, Central South University, Changsha, Hunan, China
| | - Xiangjun Huang
- First Affiliated Hospital, Department of General Surgery, Hunan University, Changsha, Hunan, China
| | - Hongbo Xu
- Third Xiangya Hospital, Center for Experimental Medicine and Department of Neurology, Central South University, Changsha, Hunan, China
| | - Yong-An Zhou
- Second Affiliated Hospital, Department of Blood Transfusion, Shaanxi Normal University, Taiyuan, Shanxi, China
| | - Lina Gong
- Third Xiangya Hospital, Center for Experimental Medicine and Department of Neurology, Central South University, Changsha, Hunan, China
| | - Zhijian Yang
- Third Xiangya Hospital, Center for Experimental Medicine and Department of Neurology, Central South University, Changsha, Hunan, China
| | - Jingyan Lv
- Third Xiangya Hospital, Center for Experimental Medicine and Department of Neurology, Central South University, Changsha, Hunan, China
| | - Hao Deng
- Third Xiangya Hospital, Center for Experimental Medicine and Department of Neurology, Central South University, Changsha, Hunan, China
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8
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Cui M, Hu Y, Bi Y, Wang W, Wang M, Zhang X, Zhang R, Wang P, Su Z, Gao X, Wang J, Li Q, Liao Q, Zhao Y. Preliminary exploration of potential molecular therapeutic targets in recurrent and metastatic parathyroid carcinomas. Int J Cancer 2018; 144:525-532. [PMID: 30362515 DOI: 10.1002/ijc.31948] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/17/2018] [Accepted: 10/17/2018] [Indexed: 12/20/2022]
Abstract
Parathyroid carcinoma (PC) is a rare endocrine malignancy. Surgical resection is curative for local lesions, while effective therapies are lacking for recurrent or metastatic PCs. To study whether targeted therapies could be applied in recurrent or metastatic PCs, potential therapeutic targets were identified with next-generation sequencing (NGS). DNA was extracted from formalin-fixed, paraffin-embedded (FFPE) sections from 19 recurrent or metastatic PC samples. A panel of 560 genes was sequenced with NGS to identify genomic alterations at an average sequencing depth of 581×. In total, 190 genomic alterations were identified. Nine PC samples (47%) harbored at least one potentially actionable genomic alteration including in the after genes: ROS1 (5/19; 26%), PTEN (3/19; 16%), TSC1 (2/19; 11%), PIK3CA (1/19; 5%), AKT1 (1/19; 5%), MTOR (1/19; 5%), ERBB2 (1/19; 5%), NTRK1 (1/19; 5%), IDH1 (1/19; 5%) and FGFR3 (1/19; 5%). CDC73 mutations were detected in 9/19 (47%) PC samples. Additional recurrent genomic alterations were identified in MSH2 (15/19; 79%), AR (9/19; 47%), BCR (8/19; 42%), SLC45A3 (6/19; 32%), MAGI1 (5/19; 26%), ZNF521 (4/19; 21%), KMT2C (4/19; 21%) and NOTCH4 (4/19; 21%). Our study identified a relatively high frequency of potentially actionable genomic alterations in PC patients in a Chinese population for the first time. A series of recurrent mutant genes was detected as well. Our study contributes to both the selection of novel targeted therapies for PC and further molecular understanding of this refractory malignancy.
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Affiliation(s)
- Ming Cui
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ya Hu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yalan Bi
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Weiwei Wang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Mengyi Wang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiang Zhang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ronghua Zhang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Peipei Wang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhe Su
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiang Gao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jiali Wang
- The Scientific and Technical Department, Novogene Bioinformatics Institute, Beijing, China
| | - Qing Li
- The Scientific and Technical Department, Novogene Bioinformatics Institute, Beijing, China
| | - Quan Liao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yupei Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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9
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Li W, Sun J, Ling J, Li J, He C, Liu Y, Chen H, Men M, Niu Z, Deng Y, Li M, Li T, Wen J, Sang S, Li H, Wan Z, Richard EM, Chapagain P, Yan D, Liu XZ, Mei L, Feng Y. ELMOD3, a novel causative gene, associated with human autosomal dominant nonsyndromic and progressive hearing loss. Hum Genet 2018; 137:329-342. [PMID: 29713870 DOI: 10.1007/s00439-018-1885-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/16/2018] [Indexed: 11/26/2022]
Abstract
Autosomal dominant nonsyndromic hearing loss (ADNSHL) is a highly genetically heterogeneous disorder. Up to date only approximately 37 ADNSHL-causing genes have been identified. The goal of this study was to determine the causative gene in a five-generation Chinese family with ADNSHL. A Chinese family was ascertained. Simultaneously, two affected individuals and one normal hearing control from the family were analyzed by whole exome capture sequencing. To assess the functional effect of the identified variant, in-vitro studies were performed. novel missense variant, c.512A>G (p.His171Arg) in exon 8 of the ELMO domain-containing 3 (ELMOD3) gene, was identified as a causative variant in this family affected by late-onset and progressive ADNSHL. The variant was validated by Sanger sequencing and found to co-segregate with the phenotype within the pedigree and was absent in 500 ethnically matched unrelated normal hearing control subjects. To our knowledge, this is the first report of a family with ADNSHL caused by ELMOD3 mutation. Western blots and immunofluorescence staining demonstrated that p.His171Arg resulted in abnormal expression levels of ELMOD3 and abnormal subcellular localization. Furthermore, the analysis of the stability of the wild-type (WT) and mutant ELMOD3 protein shows that the decay of p.His171Arg is faster than that of the WT, suggesting a shorter halflife of the c.512A > G variant. A novel variant in the ELMOD3 gene, encoding a member of the engulfment and cell motility (ELMO) family of GTPase-activating proteins, was identified for the first time as responsible for ADNSHL.
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Affiliation(s)
- Wu Li
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Jie Sun
- Department of Otolaryngology, The Eight Affiliated Hospital, Sun Yat-sen University, 3025 Shennan Middle Road, Shenzhen, Guangdong, China
| | - Jie Ling
- Institute of Precision Medicine, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
| | - Jiada Li
- Center for Medical Genetics, Central South University, 110 Xiangya Road, Changsha, Hunan, China
- School of Life Sciences, Central South University of China, 110 Xiangya Road, Changsha, Hunan, China
| | - Chufeng He
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Yalan Liu
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Hongsheng Chen
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Meichao Men
- Health Management Center, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
| | - Zhijie Niu
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Yuyuan Deng
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Meng Li
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Taoxi Li
- Center for Medical Genetics, Central South University, 110 Xiangya Road, Changsha, Hunan, China
- School of Life Sciences, Central South University of China, 110 Xiangya Road, Changsha, Hunan, China
| | - Jie Wen
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Shushan Sang
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Haibo Li
- Department of Ophthalmology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
| | - Zhengqing Wan
- Center for Medical Genetics, Central South University, 110 Xiangya Road, Changsha, Hunan, China
- School of Life Sciences, Central South University of China, 110 Xiangya Road, Changsha, Hunan, China
| | - Elodie M Richard
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, Florida, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, USA
| | - Xue Zhong Liu
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, USA
- Dr. John T. Macdonald Foundation, Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Lingyun Mei
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China.
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China.
| | - Yong Feng
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China.
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China.
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10
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Identification of a Novel Mutation in the ABCA4 Gene in a Chinese Family with Retinitis Pigmentosa Using Exome Sequencing. Biosci Rep 2018; 38:BSR20171300. [PMID: 29437900 PMCID: PMC5857910 DOI: 10.1042/bsr20171300] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/08/2017] [Accepted: 01/29/2018] [Indexed: 11/26/2022] Open
Abstract
Retinitis pigmentosa (RP) is a group of hereditary, degenerative retinal disorders characterized by progressive retinal dysfunction, outer retina cell loss, and retinal tissue atrophy. It eventually leads to tunnel vision and legal or total blindness. Here, we aimed to reveal the causal gene and mutation contributing to the development of autosomal recessive RP (arRP) in a consanguineous family. A novel homozygous mutation, c.4845delT (p.K1616Rfs*46), in the ATP-binding cassette subfamily A member 4 gene (ABCA4) was identified. It may reduce ABCA4 protein activity, leading to progressive degeneration of both rod and cone photoreceptors. The study extends the arRP genotypic spectrum and confirms a genotype–phenotype relationship. The present study may also disclose some new clues for RP genetic causes and pathogenesis, as well as clinical and genetic diagnosis. The research findings may contribute to improvement in clinical care, therapy, genetic screening, and counseling.
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11
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Mittal R, Nguyen D, Patel AP, Debs LH, Mittal J, Yan D, Eshraghi AA, Van De Water TR, Liu XZ. Recent Advancements in the Regeneration of Auditory Hair Cells and Hearing Restoration. Front Mol Neurosci 2017; 10:236. [PMID: 28824370 PMCID: PMC5534485 DOI: 10.3389/fnmol.2017.00236] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/11/2017] [Indexed: 12/18/2022] Open
Abstract
Neurosensory responses of hearing and balance are mediated by receptors in specialized neuroepithelial sensory cells. Any disruption of the biochemical and molecular pathways that facilitate these responses can result in severe deficits, including hearing loss and vestibular dysfunction. Hearing is affected by both environmental and genetic factors, with impairment of auditory function being the most common neurosensory disorder affecting 1 in 500 newborns, as well as having an impact on the majority of elderly population. Damage to auditory sensory cells is not reversible, and if sufficient damage and cell death have taken place, the resultant deficit may lead to permanent deafness. Cochlear implants are considered to be one of the most successful and consistent treatments for deaf patients, but only offer limited recovery at the expense of loss of residual hearing. Recently there has been an increased interest in the auditory research community to explore the regeneration of mammalian auditory hair cells and restoration of their function. In this review article, we examine a variety of recent therapies, including genetic, stem cell and molecular therapies as well as discussing progress being made in genome editing strategies as applied to the restoration of hearing function.
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Affiliation(s)
- Rahul Mittal
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Desiree Nguyen
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Amit P. Patel
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Luca H. Debs
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Jeenu Mittal
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Adrien A. Eshraghi
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Thomas R. Van De Water
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Xue Z. Liu
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
- Department of Otolaryngology, Xiangya Hospital, Central South UniversityChangsha, China
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