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Panagiotou E, Vathiotis IA, Makrythanasis P, Hirsch F, Sen T, Syrigos K. Biological and therapeutic implications of the cancer-related germline mutation landscape in lung cancer. THE LANCET. RESPIRATORY MEDICINE 2024:S2213-2600(24)00124-3. [PMID: 38885686 DOI: 10.1016/s2213-2600(24)00124-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 06/20/2024]
Abstract
Although smoking is the primary cause of lung cancer, only about 15% of lifelong smokers develop the disease. Moreover, a substantial proportion of lung cancer cases occur in never-smokers, highlighting the potential role of inherited genetic factors in the cause of lung cancer. Lung cancer is significantly more common among those with a positive family history, especially for early-onset disease. Therefore, the presence of pathogenic germline variants might act synergistically with environmental factors. The incorporation of next-generation sequencing in routine clinical practice has led to the identification of cancer-predisposing mutations in an increasing proportion of patients with lung cancer. This Review summarises the landscape of germline susceptibility in lung cancer and highlights the importance of germline testing in patients diagnosed with the disease, which has the potential to identify individuals at risk, with implications for tailored therapeutic approaches and successful prevention through genetic counselling and screening.
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Affiliation(s)
- Emmanouil Panagiotou
- Third Department of Internal Medicine, Sotiria General Hospital for Chest Diseases, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis A Vathiotis
- Third Department of Internal Medicine, Sotiria General Hospital for Chest Diseases, National and Kapodistrian University of Athens, Athens, Greece.
| | - Periklis Makrythanasis
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece; Department of Genetic Medicine and Development, Medical School, University of Geneva, Geneva, Switzerland; Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Fred Hirsch
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Triparna Sen
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Konstantinos Syrigos
- Third Department of Internal Medicine, Sotiria General Hospital for Chest Diseases, National and Kapodistrian University of Athens, Athens, Greece
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Zhang R, Jiang W, Wang G, Zhang Y, Liu W, Li M, Yu J, Yan X, Zhou F, Du W, Qian K, Xiao Y, Liu T, Ju L, Wang X. Parkin inhibits proliferation and migration of bladder cancer via ubiquitinating Catalase. Commun Biol 2024; 7:245. [PMID: 38424181 PMCID: PMC10904755 DOI: 10.1038/s42003-024-05935-x] [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: 06/12/2023] [Accepted: 02/19/2024] [Indexed: 03/02/2024] Open
Abstract
PRKN is a key gene involved in mitophagy in Parkinson's disease. However, recent studies have demonstrated that it also plays a role in the development and metastasis of several types of cancers, both in a mitophagy-dependent and mitophagy-independent manner. Despite this, the potential effects and underlying mechanisms of Parkin on bladder cancer (BLCA) remain unknown. Therefore, in this study, we investigated the expression of Parkin in various BLCA cohorts derived from human. Here we show that PRKN expression was low and that PRKN acts as a tumor suppressor by inhibiting the proliferation and migration of BLCA cells in a mitophagy-independent manner. We further identified Catalase as a binding partner and substrate of Parkin, which is an important antioxidant enzyme that regulates intracellular ROS levels during cancer progression. Our data showed that knockdown of CAT led to increased intracellular ROS levels, which suppressed cell proliferation and migration. Conversely, upregulation of Catalase decreased intracellular ROS levels, promoting cell growth and migration. Importantly, we found that Parkin upregulation partially restored these effects. Moreover, we discovered that USP30, a known Parkin substrate, could deubiquitinate and stabilize Catalase. Overall, our study reveals a novel function of Parkin and identifies a potential therapeutic target in BLCA.
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Affiliation(s)
- Renjie Zhang
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wenyu Jiang
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Gang Wang
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yi Zhang
- Euler Technology, ZGC Life Sciences Park, Beijing, China
- Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing, China
| | - Wei Liu
- Department of Urology, Peking University Aerospace Center Hospital, Beijing, China
| | - Mingxing Li
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jingtian Yu
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xin Yan
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Fenfang Zhou
- Department of Radiology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wenzhi Du
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yu Xiao
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Tongzu Liu
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - Lingao Ju
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - Xinghuan Wang
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China.
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Wei B, Zhao J, Li J, Feng J, Sun M, Wang Z, Shi C, Yang K, Qin Y, Zhang J, Ma J, Dong H. Pathogenic germline variants in BRCA1 and TP53 increase lung cancer risk in Chinese. Cancer Med 2023; 12:21219-21228. [PMID: 37930190 PMCID: PMC10726856 DOI: 10.1002/cam4.6692] [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: 06/07/2023] [Revised: 10/07/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUD Multiple studies have identified pathogenic germline variants in cancer susceptibility genes (CSGs) in Chinese lung cancer patients; however, accurate assessment of these variants' contributions to cancer predisposition is always hampered by the absence of data on the prevalence of these variants in the general population. It is necessary to conduct a large-scale case-control study to identify CSGs that significantly increase the risk of lung cancer. MATERIALS AND METHODS We performed targeted sequencing of a CSGs panel in 1117 lung cancer patients and 16,327 controls from the general Chinese population. RESULTS In comparison to controls, lung cancer patients had a considerably higher prevalence of pathogenic and likely pathogenic (P/LP) variations. Among lung cancer patients, 72% of P/LP variants carriers did not have a family cancer history, who would be ignored if germline testing was only provided for patients meeting family history-based criteria. Furthermore, compared to individuals with late-onset lung cancer, patients with early-onset lung cancer had a considerably higher prevalence of P/LP variations. With odds ratios (ORs) ranging from 4-fold (BRCA1: OR, 4.193; 95%CI, 1.382-10.768) to 29-fold (TP53: OR, 29.281; 95%CI, 1.523-1705.506), P/LP variants in the BRCA1 and TP53 genes were discovered to be strongly related to increased lung cancer risk. Additionally, with ORs ranging from 7.322-fold to infinity, we discovered 23 variations previously categorized as non-P/LP variants were highly enriched in lung cancer patients. CONCLUSION Our findings indicated that P/LP variants in BRCA1 and TP53 conferred increased risk of lung cancer in Chinese.
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Affiliation(s)
- Bing Wei
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Jiadong Zhao
- Nanjing Shenyou Institute of Genome ResearchNanjingJiangsuChina
| | - Jun Li
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Junnan Feng
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Manman Sun
- Nanjing Shenyou Institute of Genome ResearchNanjingJiangsuChina
| | - Zhizhong Wang
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Chao Shi
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Ke Yang
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Yue Qin
- Nanjing Shenyou Institute of Genome ResearchNanjingJiangsuChina
| | - Jing Zhang
- Nanjing Shenyou Institute of Genome ResearchNanjingJiangsuChina
| | - Jie Ma
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Hui Dong
- Department of Gastroenterology, Shanghai Key Laboratory of Pancreatic DiseasesShanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
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Persson M, Andersson MK, Sahlin PE, Mitani Y, Brandwein-Weber MS, Frierson HF, Moskaluk C, Fonseca I, Ferrarotto R, Boecker W, Loening T, El-Naggar AK, Stenman G. Comprehensive molecular characterization of adenoid cystic carcinoma reveals tumor suppressors as novel drivers and prognostic biomarkers. J Pathol 2023; 261:256-268. [PMID: 37565350 DOI: 10.1002/path.6172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 06/19/2023] [Accepted: 06/28/2023] [Indexed: 08/12/2023]
Abstract
Adenoid cystic carcinoma (ACC) is a MYB-driven head and neck malignancy with high rates of local recurrence and distant metastasis and poor long-term survival. New effective targeted therapies and clinically useful biomarkers for patient stratification are needed to improve ACC patient survival. Here, we present an integrated copy number and transcriptomic analysis of ACC to identify novel driver genes and prognostic biomarkers. A total of 598 ACCs were studied. Clinical follow-up was available from 366 patients, the largest cohort analyzed to date. Copy number losses of 1p36 (70/492; 14%) and of the tumor suppressor gene PARK2 (6q26) (85/343; 25%) were prognostic biomarkers; patients with concurrent losses (n = 20) had significantly shorter overall survival (OS) than those with one or no deletions (p < 0.0001). Deletion of 1p36 independently predicted short OS in multivariate analysis (p = 0.02). Two pro-apoptotic genes, TP73 and KIF1B, were identified as putative 1p36 tumor suppressor genes whose reduced expression was associated with poor survival and increased resistance to apoptosis. PARK2 expression was markedly reduced in tumors with 6q deletions, and PARK2 knockdown increased spherogenesis and decreased apoptosis, indicating that PARK2 is a tumor suppressor in ACC. Moreover, analysis of the global gene expression pattern in 30 ACCs revealed a transcriptomic signature associated with short OS, multiple copy number alterations including 1p36 deletions, and reduced expression of TP73. Taken together, the results indicate that TP73 and PARK2 are novel putative tumor suppressor genes and potential prognostic biomarkers in ACC. Our studies provide new important insights into the pathogenesis of ACC. The results have important implications for biomarker-driven stratification of patients in clinical trials. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Marta Persson
- Sahlgrenska Center for Cancer Research, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
| | - Mattias K Andersson
- Sahlgrenska Center for Cancer Research, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
| | - Per-Erik Sahlin
- Department of Plastic Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Yoshitsugu Mitani
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Henry F Frierson
- Department of Pathology, University of Virginia Health System, Charlottesville, VA, USA
| | - Christopher Moskaluk
- Department of Pathology, University of Virginia Health System, Charlottesville, VA, USA
| | - Isabel Fonseca
- Serviço de Anatomia Patológica, Instituto Português de Oncologia de Francisco Gentil - Lisboa and Instituto de Anatomia Patológica, Faculdade de Medicina de Lisboa, Lisbon, Portugal
| | - Renata Ferrarotto
- Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Werner Boecker
- Gerhard Domagk Institute of Pathology, University of Muenster, Muenster, Germany
- Gerhard-Seifert Reference Centre, Hamburg, Germany
| | | | - Adel K El-Naggar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Göran Stenman
- Sahlgrenska Center for Cancer Research, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
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Cannon-Albright LA, Teerlink CC, Stevens J, Facelli JC, Carr SR, Allen-Brady K, Puri S, Bailey-Wilson JE, Musolf AM, Akerley W. A rare FGF5 candidate variant (rs112475347) for predisposition to nonsquamous, nonsmall-cell lung cancer. Int J Cancer 2023; 153:364-372. [PMID: 36916144 PMCID: PMC10182245 DOI: 10.1002/ijc.34510] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/16/2023]
Abstract
A unique approach with rare resources was used to identify candidate variants predisposing to familial nonsquamous nonsmall-cell lung cancers (NSNSCLC). We analyzed sequence data from NSNSCLC-affected cousin pairs belonging to high-risk lung cancer pedigrees identified in a genealogy of Utah linked to statewide cancer records to identify rare, shared candidate predisposition variants. Variants were tested for association with lung cancer risk in UK Biobank. Evidence for linkage with lung cancer was also reviewed in families from the Genetic Epidemiology of Lung Cancer Consortium. Protein prediction modeling compared the mutation with reference. We sequenced NSNSCLC-affected cousin pairs from eight high-risk lung cancer pedigrees and identified 66 rare candidate variants shared in the cousin pairs. One variant in the FGF5 gene also showed significant association with lung cancer in UKBiobank. This variant was observed in 3/163 additional sampled Utah lung cancer cases, 2 of whom were related in another independent pedigree. Modeling of the predicted protein predicted a second binding site for SO4 that may indicate binding differences. This unique study identified multiple candidate predisposition variants for NSNSCLC, including a rare variant in FGF5 that was significantly associated with lung cancer risk and that segregated with lung cancer in the two pedigrees in which it was observed. FGF5 is an oncogenic factor in several human cancers, and the mutation found here (W81C) changes the binding ability of heparan sulfate to FGF5, which might lead to its deregulation. These results support FGF5 as a potential NSNSCLC predisposition gene and present additional candidate predisposition variants.
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Affiliation(s)
- Lisa A Cannon-Albright
- Genetic Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
- Huntsman Cancer Institute, Salt Lake City, Utah, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah, USA
| | - Craig C Teerlink
- Genetic Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah, USA
| | - Jeff Stevens
- Genetic Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Julio C Facelli
- Department of BioMedical Informatics, University of Utah School of Medicine, Salt Lake City, Utah, USA
- Clinical and Translational Science Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Shamus R Carr
- Thoracic Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kristina Allen-Brady
- Genetic Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Sonam Puri
- Huntsman Cancer Institute, Salt Lake City, Utah, USA
- Medical Oncology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, USA
| | - Anthony M Musolf
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, USA
| | - Wallace Akerley
- Huntsman Cancer Institute, Salt Lake City, Utah, USA
- Medical Oncology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
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Hong CS, Alanya H, DiStasio M, Boulware SD, Rimmer RA, Omay SB, Erson-Omay EZ. Sporadic pituitary adenoma with somatic double-hit loss of MEN1. Pituitary 2023:10.1007/s11102-023-01336-1. [PMID: 37438451 DOI: 10.1007/s11102-023-01336-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/25/2023] [Indexed: 07/14/2023]
Abstract
PURPOSE Pituitary adenomas commonly arise in patients with MEN1 syndrome, an autosomal dominant condition predisposing to neuroendocrine tumor formation, and typically diagnosed in patients with a relevant family cancer history. In these patients with existing germline loss of MEN1 on one allele, somatic loss of the second MEN1 allele leads to complete loss of the MEN1 protein, menin, and subsequent tumor formation. METHODS Whole exome sequencing was performed on the tumor and matching blood under an institutional board approved protocol. DNA extraction and analysis was conducted according to previously described methods. RESULTS We describe a 23 year-old patient with no significant past medical history or relevant family history who underwent surgical resection of a symptomatic and medically resistant prolactinoma. Whole exome sequencing of tumor and blood samples revealed somatic loss of MEN1 at both alleles, suggesting a double hit mechanism, with no underlying germline MEN1 mutation. CONCLUSION To our knowledge, this is the first case of pituitary adenoma to arise from somatic loss of MEN1 and in the absence of an underlying germline MEN1 mutation.
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Affiliation(s)
- Christopher S Hong
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Hasan Alanya
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Marcello DiStasio
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Susan D Boulware
- Department of Pediatrics, Section of Endocrinology and Diabetes, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Ryan A Rimmer
- Department of Surgery, Division of Otolaryngology, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Sacit Bulent Omay
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, 06510, USA
| | - E Zeynep Erson-Omay
- Department of Neurosurgery, Yale School of Medicine, 300 Cedar Street, TAC S327, New Haven, CT, 06511, USA.
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The RING finger protein family in health and disease. Signal Transduct Target Ther 2022; 7:300. [PMID: 36042206 PMCID: PMC9424811 DOI: 10.1038/s41392-022-01152-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/31/2022] [Accepted: 08/09/2022] [Indexed: 02/05/2023] Open
Abstract
Ubiquitination is a highly conserved and fundamental posttranslational modification (PTM) in all eukaryotes regulating thousands of proteins. The RING (really interesting new gene) finger (RNF) protein, containing the RING domain, exerts E3 ubiquitin ligase that mediates the covalent attachment of ubiquitin (Ub) to target proteins. Multiple reviews have summarized the critical roles of the tripartite-motif (TRIM) protein family, a subgroup of RNF proteins, in various diseases, including cancer, inflammatory, infectious, and neuropsychiatric disorders. Except for TRIMs, since numerous studies over the past decades have delineated that other RNF proteins also exert widespread involvement in several diseases, their importance should not be underestimated. This review summarizes the potential contribution of dysregulated RNF proteins, except for TRIMs, to the pathogenesis of some diseases, including cancer, autoimmune diseases, and neurodegenerative disorder. Since viral infection is broadly involved in the induction and development of those diseases, this manuscript also highlights the regulatory roles of RNF proteins, excluding TRIMs, in the antiviral immune responses. In addition, we further discuss the potential intervention strategies targeting other RNF proteins for the prevention and therapeutics of those human diseases.
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8
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Li M, Meng GX, Liu XW, Ma T, Sun G, He H. Deep-LC: A Novel Deep Learning Method of Identifying Non-Small Cell Lung Cancer-Related Genes. Front Oncol 2022; 12:949546. [PMID: 35936745 PMCID: PMC9353732 DOI: 10.3389/fonc.2022.949546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 06/16/2022] [Indexed: 12/15/2022] Open
Abstract
According to statistics, lung cancer kills 1.8 million people each year and is the main cause of cancer mortality worldwide. Non-small cell lung cancer (NSCLC) accounts for over 85% of all lung cancers. Lung cancer has a strong genetic predisposition, demonstrating that the susceptibility and survival of lung cancer are related to specific genes. Genome-wide association studies (GWASs) and next-generation sequencing have been used to discover genes related to NSCLC. However, many studies ignored the intricate interaction information between gene pairs. In the paper, we proposed a novel deep learning method named Deep-LC for predicting NSCLC-related genes. First, we built a gene interaction network and used graph convolutional networks (GCNs) to extract features of genes and interactions between gene pairs. Then a simple convolutional neural network (CNN) module is used as the decoder to decide whether the gene is related to the disease. Deep-LC is an end-to-end method, and from the evaluation results, we can conclude that Deep-LC performs well in mining potential NSCLC-related genes and performs better than existing state-of-the-art methods.
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Affiliation(s)
| | | | | | | | - Ge Sun
- *Correspondence: Ge Sun, ; HongMei He,
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9
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Mukherjee S, Bandlamudi C, Hellmann MD, Kemel Y, Drill E, Rizvi H, Tkachuk K, Khurram A, Walsh MF, Zauderer MG, Mandelker D, Topka S, Zehir A, Srinivasan P, Selvan ME, Carlo MI, Cadoo KA, Latham A, Hamilton JG, Liu YL, Lipkin SM, Belhadj S, Bond GL, Gümüş ZH, Klein RJ, Ladanyi M, Solit DB, Robson ME, Jones DR, Kris MG, Vijai J, Stadler ZK, Amos CI, Taylor BS, Berger MF, Rudin CM, Offit K. Germline Pathogenic Variants Impact Clinicopathology of Advanced Lung Cancer. Cancer Epidemiol Biomarkers Prev 2022; 31:1450-1459. [PMID: 35477182 PMCID: PMC9250622 DOI: 10.1158/1055-9965.epi-21-1287] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/31/2022] [Accepted: 04/25/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The genetic factors that modulate risk for developing lung cancer have not been fully defined. Here, we sought to determine the prevalence and clinical significance of germline pathogenic/likely pathogenic variants (PV) in patients with advanced lung cancer. METHODS We studied clinical and tumor characteristics of germline PV in 5,118 patients who underwent prospective genomic profiling using paired tumor-normal tissue samples in 468 cancer genes. RESULTS Germline PV in high/moderate-penetrance genes were observed in 222 (4.3%) patients; of these, 193 patients had PV in DNA damage repair (DDR) pathway genes including BRCA2 (n = 54), CHEK2 (n = 30), and ATM (n = 26) that showed high rate of biallelic inactivation in tumors. BRCA2 heterozygotes with lung adenocarcinoma were more likely to be never smokers and had improved survival compared with noncarriers. Fourteen patients with germline PV in lung cancer predisposing genes (TP53, EGFR, BAP1, and MEN1) were diagnosed at younger age compared with noncarriers, and of tumor suppressors, 75% demonstrated biallelic inactivation in tumors. A significantly higher proportion of germline PV in high/moderate-penetrance genes were detected in high-risk patients who had either a family history of any cancer, multiple primary tumors, or early age at diagnosis compared with unselected patients (10.5% vs. 4.1%; P = 1.7e-04). CONCLUSIONS These data underscore the biological and clinical importance of germline mutations in highly penetrant DDR genes as a risk factor for lung cancer. IMPACT The family members of lung cancer patients harboring PV in cancer predisposing genes should be referred for genetic counseling and may benefit from proactive surveillance.
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Affiliation(s)
| | | | | | - Yelena Kemel
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Esther Drill
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Hira Rizvi
- Memorial Sloan Kettering Cancer Center, United States
| | - Kaitlyn Tkachuk
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Aliya Khurram
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Michael F Walsh
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | - Diana Mandelker
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Sabine Topka
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | | | - Maria I Carlo
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Karen A Cadoo
- St. James’s Hospital, Trinity College Dublin, Trinity St. James’s Cancer Institute, Dublin 8, Ireland
| | - Alicia Latham
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, United States
| | - Jada G Hamilton
- Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Ying L Liu
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | - Sami Belhadj
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Gareth L Bond
- University of Birmingham, Birmingham, United Kingdom
| | - Zeynep H Gümüş
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Robert J Klein
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - David B Solit
- Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Mark E Robson
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - David R Jones
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Mark G Kris
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Joseph Vijai
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Zsofia K Stadler
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, United States
| | | | - Barry S Taylor
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Michael F Berger
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Charles M Rudin
- Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
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10
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Wang M, Banik I, Shain AH, Yeh I, Bastian BC. Integrated genomic analyses of acral and mucosal melanomas nominate novel driver genes. Genome Med 2022; 14:65. [PMID: 35706047 PMCID: PMC9202124 DOI: 10.1186/s13073-022-01068-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 06/03/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Acral and mucosal melanomas are aggressive subtypes of melanoma, which have a significantly lower burden of somatic mutations than cutaneous melanomas, but more frequent copy number variations, focused gene amplifications, and structural alterations. The landscapes of their genomic alterations remain to be fully characterized. METHODS We compiled sequencing data of 240 human acral and mucosal melanoma samples from 11 previously published studies and applied a uniform pipeline to call tumor cell content, ploidy, somatic and germline mutations, as well as CNVs, LOH, and SVs. We identified genes that are significantly mutated or recurrently affected by CNVs and implicated in oncogenesis. We further examined the difference in the frequency of recurrent pathogenic alterations between the two melanoma subtypes, correlation between pathogenic alterations, and their association with clinical features. RESULTS We nominated PTPRJ, mutated and homozygously deleted in 3.8% (9/240) and 0.8% (2/240) of samples, respectively, as a probable tumor suppressor gene, and FER and SKP2, amplified in 3.8% and 11.7% of samples, respectively, as probable oncogenes. We further identified a long tail of infrequent pathogenic alterations, involving genes such as CIC and LZTR1. Pathogenic germline mutations were observed on MITF, PTEN, ATM, and PRKN. We found BRAF V600E mutations in acral melanomas with fewer structural variations, suggesting that they are distinct and related to cutaneous melanomas. Amplifications of PAK1 and GAB2 were more commonly observed in acral melanomas, whereas SF3B1 R625 codon mutations were unique to mucosal melanomas (12.9%). Amplifications at 11q13-14 were frequently accompanied by fusion to a region on chromosome 6q12, revealing a recurrent novel structural rearrangement whose role remains to be elucidated. CONCLUSIONS Our meta-analysis expands the catalog of driver mutations in acral and mucosal melanomas, sheds new light on their pathogenesis and broadens the catalog of therapeutic targets for these difficult-to-treat cancers.
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Affiliation(s)
- Meng Wang
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Ishani Banik
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - A Hunter Shain
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Iwei Yeh
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
| | - Boris C Bastian
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
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11
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Al-Bari AA. Inhibition of autolysosomes by repurposing drugs as a promising therapeutic strategy for the treatment of cancers. ALL LIFE 2022. [DOI: 10.1080/26895293.2022.2078894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Abdul Alim Al-Bari
- Department of Pharmacy, Faculty of Science, University of Rajshahi, Rajshahi, Bangladesh
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12
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Benusiglio PR, Fallet V, Cadranel J. Invited editorial: Q and A on hereditary lung cancer. Respir Med Res 2022; 81:100881. [DOI: 10.1016/j.resmer.2021.100881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/09/2021] [Indexed: 11/30/2022]
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13
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Rosas I, Morís G, Coto E, Blázquez M, Suárez E, García-Fernández C, Siso P, Martínez C, Pérez-Oliveira S, Álvarez V, Menéndez-González M. Cancer in Parkinson's Disease: An Approximation to the Main Risk Factors. NEURODEGENER DIS 2021; 21:36-41. [PMID: 34673649 DOI: 10.1159/000520301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 10/18/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Many evidences suggest a pathological link between neurodegenerative diseases and cancer. In fact, several epidemiologic studies indicate a decreased incidence of most cancer types in Parkinson's disease (PD) patients and some PD genes are involved in cancer networks. OBJECTIVE The aim of this study is to assess the influence of several factors in the risk of cancer in a cohort of 753 PD patients and to study how these variables interact with each other. METHODS We analyzed the effect of gender, tobacco, alcohol, type of PD (genetic or idiopathic PD), and two genetic variants, previously associated with cancer, rs5848-GRN and rs1042522-TP53. RESULTS A higher age at PD onset was observed in patients who develop cancer before PD (p < 0.001). Alcohol consumption was a risk factor to develop cancer in PD patients (p = 0.011), while smoking was not a cancer risk factor in our cohort (p = 0.098). Among the genetic factors, the genotype TT GRN-rs5848 was statistically more frequent in PD patients without cancer (p = 0.05). CONCLUSIONS Our study identified several factors, genetic and nongenetic, which contribute to the risk for cancer in PD.
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Affiliation(s)
- Irene Rosas
- Laboratorio de Genética, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Germán Morís
- Servicio de Neurología, Hospital Universitario Central de Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Eliecer Coto
- Laboratorio de Genética, Hospital Universitario Central de Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Marta Blázquez
- Servicio de Neurología, Hospital Universitario Central de Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Esther Suárez
- Servicio de Neurología, Hospital Universitario Central de Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Ciara García-Fernández
- Servicio de Neurología, Hospital Universitario Central de Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Pablo Siso
- Servicio de Neurología, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Carmen Martínez
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Servicio de Neurología, Hospital Universitario de Cabueñes, Gijón, Spain
| | | | - Victoria Álvarez
- Laboratorio de Genética, Hospital Universitario Central de Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Manuel Menéndez-González
- Servicio de Neurología, Hospital Universitario Central de Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
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14
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Rammal S, Kourie HR, Jalkh N, Mehawej C, Chouery E, Moujaess E, Dabar G. Molecular pathogenesis of hereditary lung cancer: a literature review. Pharmacogenomics 2021; 22:791-803. [PMID: 34410147 DOI: 10.2217/pgs-2020-0150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Among all cancer types, pulmonary cancer has the highest mortality rate. Tobacco consumption remains the major risk factor for the development of lung cancer. However, many studies revealed a correlation between inherited genetic variants and predisposition to lung cancer, especially in nonsmokers. To date, genetic testing for the detection of germline mutations is not yet recommended in patients with lung cancer and testing is focused on somatic alterations given their implication in the treatment choice. Understanding the impact of genetic predisposition on the occurrence of lung cancer is essential to enable the introduction of accurate guidelines and recommendations that might reduce mortality. In this review paper, we describe familial lung cancer, and expose germline mutations that are linked to this type of cancer. We also report pathogenic genetic variants linked to syndromes associated with lung cancer.
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Affiliation(s)
- Souraya Rammal
- Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon
| | - Hampig Raphael Kourie
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon
| | - Nadine Jalkh
- Medical Genetics Unit, Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon
| | - Cybel Mehawej
- Medical Genetics Unit, Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon
| | - Eliane Chouery
- Medical Genetics Unit, Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon
| | - Elissar Moujaess
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon
| | - Georges Dabar
- Pulmonary & Critical Care Division, Hotel Dieu de France, Saint Joseph University of Beirut, Beirut, Lebanon
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15
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McInerney-Leo AM, Chew HY, Inglis PL, Leo PJ, Joseph SR, Cooper CL, Okano S, Hassall T, Anderson L, Bowman RV, Gattas M, Harris JE, Marshall MS, Shaw JG, Wheeler L, Yang IA, Brown MA, Fong KM, Simpson F, Duncan EL. Germline ERBB3 mutation in familial non-small cell lung carcinoma: Expanding ErbB's role in oncogenesis. Hum Mol Genet 2021; 30:2393-2401. [PMID: 34274969 PMCID: PMC8643496 DOI: 10.1093/hmg/ddab172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/12/2021] [Accepted: 06/21/2021] [Indexed: 11/22/2022] Open
Abstract
Lung cancer is the commonest cause of cancer deaths worldwide. Although strongly associated with smoking, predisposition to lung cancer is also heritable, with multiple common risk variants identified. Rarely, dominantly inherited non-small-cell lung cancer (NSCLC) has been reported due to somatic mutations in EGFR/ErbB1 and ERBB2. Germline exome sequencing was performed in a multi-generation family with autosomal dominant NSCLC, including an affected child. Tumour samples were also sequenced. Full-length wild-type (wtErbB3) and mutant ERBB3 (mutErbB3) constructs were transfected into HeLa cells. Protein expression, stability, and subcellular localization were assessed, and cellular proliferation, pAkt/Akt and pERK levels determined. A novel germline variant in ERBB3 (c.1946 T > G: p.Iso649Arg), coding for receptor tyrosine-protein kinase erbB-3 (ErbB3), was identified, with appropriate segregation. There was no loss-of-heterozygosity in tumour samples. Both wtErbB3 and mutErbB3 were stably expressed. MutErbB3-transfected cells demonstrated an increased ratio of the 80 kDa form (which enhances proliferation) compared with the full-length (180 kDa) form. MutErbB3 and wtErbB3 had similar punctate cytoplasmic localization pre- and post-epidermal growth factor stimulation; however, epidermal growth factor receptor (EGFR) levels decreased faster post-stimulation in mutErbB3-transfected cells, suggesting more rapid processing of the mutErbB3/EGFR heterodimer. Cellular proliferation was increased in mutErbB3-transfected cells compared with wtErbB3 transfection. MutErbB3-transfected cells also showed decreased pAkt/tAkt ratios and increased pERK/tERK 30 min post-stimulation compared with wtErbB3 transfection, demonstrating altered signalling pathway activation. Cumulatively, these results support this mutation as tumorogenic. This is the first reported family with a germline ERBB3 mutation causing heritable NSCLC, furthering understanding of the ErbB family pathway in oncogenesis.
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Affiliation(s)
- Aideen M McInerney-Leo
- The Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102
| | - Hui Yi Chew
- The Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102
| | - Po-Ling Inglis
- Medical Oncology, Royal Brisbane and Women's Hospital, Herston, QLD, 4029
| | - Paul J Leo
- Australian Translational Genomics Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, 37 Kent St, Woolloongabba, QLD, 4102
| | - Shannon R Joseph
- The Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102
| | - Caroline L Cooper
- Department of Anatomical Pathology, Pathology Queensland, Princess Alexandra Hospital, Brisbane.,UQTRC, Faculty of Medicine, The University of Queensland, 288 Herston Road, Herston, QLD, 4006
| | - Satomi Okano
- The Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102
| | - Tim Hassall
- Queensland Children's Hospital, South Brisbane, QLD, 4101
| | - Lisa Anderson
- Medical Oncology, Royal Brisbane and Women's Hospital, Herston, QLD, 4029
| | - Rayleen V Bowman
- UQTRC, Faculty of Medicine, The University of Queensland, 288 Herston Road, Herston, QLD, 4006.,Department of Thoracic Medicine, The Prince Charles Hospital, Rode Road, Chermside, QLD, 4032
| | - Michael Gattas
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, 4029
| | - Jessica E Harris
- Australian Translational Genomics Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, 37 Kent St, Woolloongabba, QLD, 4102
| | - Mhairi S Marshall
- Australian Translational Genomics Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, 37 Kent St, Woolloongabba, QLD, 4102
| | - Janet G Shaw
- UQTRC, Faculty of Medicine, The University of Queensland, 288 Herston Road, Herston, QLD, 4006.,Department of Thoracic Medicine, The Prince Charles Hospital, Rode Road, Chermside, QLD, 4032
| | - Lawrie Wheeler
- Australian Translational Genomics Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, 37 Kent St, Woolloongabba, QLD, 4102
| | - Ian A Yang
- UQTRC, Faculty of Medicine, The University of Queensland, 288 Herston Road, Herston, QLD, 4006.,Department of Thoracic Medicine, The Prince Charles Hospital, Rode Road, Chermside, QLD, 4032
| | - Matthew A Brown
- Australian Translational Genomics Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, 37 Kent St, Woolloongabba, QLD, 4102.,Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom.,King's College London NIHR Biomedical Research Centre, King's College London, United Kingdom
| | - Kwun M Fong
- UQTRC, Faculty of Medicine, The University of Queensland, 288 Herston Road, Herston, QLD, 4006.,Department of Thoracic Medicine, The Prince Charles Hospital, Rode Road, Chermside, QLD, 4032
| | - Fiona Simpson
- The Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102
| | - Emma L Duncan
- Australian Translational Genomics Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, 37 Kent St, Woolloongabba, QLD, 4102.,UQTRC, Faculty of Medicine, The University of Queensland, 288 Herston Road, Herston, QLD, 4006.,Department of Twin Research and Genetic Epidemiology, Faculty of Life Sciences and Medicine, King's College London, United Kingdom
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16
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Comprehensive Genomic and Transcriptomic Analysis of Three Synchronous Primary Tumours and a Recurrence from a Head and Neck Cancer Patient. Int J Mol Sci 2021; 22:ijms22147583. [PMID: 34299215 PMCID: PMC8305204 DOI: 10.3390/ijms22147583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 11/17/2022] Open
Abstract
Synchronous primary malignancies occur in a small proportion of head and neck squamous cell carcinoma (HNSCC) patients. Here, we analysed three synchronous primaries and a recurrence from one patient by comparing the genomic and transcriptomic profiles among the tumour samples and determining the recurrence origin. We found remarkable levels of heterogeneity among the primary tumours, and through the patterns of shared mutations, we traced the origin of the recurrence. Interestingly, the patient carried germline variants that might have predisposed him to carcinogenesis, together with a history of alcohol and tobacco consumption. The mutational signature analysis confirmed the impact of alcohol exposure, with Signature 16 present in all tumour samples. Characterisation of immune cell infiltration highlighted an immunosuppressive environment in all samples, which exceeded the potential activity of T cells. Studies such as the one described here have important clinical value and contribute to personalised treatment decisions for patients with synchronous primaries and matched recurrences.
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17
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Griffin Waller R, Madsen MJ, Gardner J, Sborov DW, Camp NJ. Duo Shared Genomic Segment analysis identifies a genome-wide significant risk locus at 18q21.33 in myeloma pedigrees. JOURNAL OF TRANSLATIONAL GENETICS AND GENOMICS 2021; 5:112-123. [PMID: 34888494 PMCID: PMC8654160 DOI: 10.20517/jtgg.2021.09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIM High-risk pedigrees (HRPs) are a powerful design to map highly penetrant risk genes. We previously described Shared Genomic Segment (SGS) analysis, a mapping method for single large extended pedigrees that also addresses genetic heterogeneity inherent in complex diseases. SGS identifies shared segregating chromosomal regions that may inherit in only a subset of cases. However, single large pedigrees that are individually powerful (at least 15 meioses between studied cases) are scarce. Here, we expand the SGS strategy to incorporate evidence from two extended HRPs by identifying the same segregating risk locus in both pedigrees and allowing for some relaxation in the size of each HRP. METHODS Duo-SGS is a procedure to combine single-pedigree SGS evidence. It implements statistically rigorous duo-pedigree thresholding to determine genome-wide significance levels that account for optimization across pedigree pairs. Single-pedigree SGS identifies optimal segments shared by case subsets at each locus across the genome, with nominal significance assessed empirically. Duo-SGS combines the statistical evidence for SGS segments at the same genomic location in two pedigrees using Fisher's method. One pedigree is paired with all others and the best duo-SGS evidence at each locus across the genome is established. Genome-wide significance thresholds are determined through distribution-fitting and the Theory of Large Deviations. We applied the duoSGS strategy to eleven extended, myeloma HRPs. RESULTS We identified one genome-wide significant region at 18q21.33 (0.85 Mb, P = 7.3 × 10-9) which contains one gene, CDH20. Thirteen regions were genome-wide suggestive: 1q42.2, 2p16.1, 3p25.2, 5q21.3, 5q31.1, 6q16.1, 6q26, 7q11.23, 12q24.31, 13q13.3, 18p11.22, 18q22.3 and 19p13.12. CONCLUSION Our results provide novel risk loci with segregating evidence from multiple HRPs and offer compelling targets and specific segment carriers to focus a future search for functional variants involved in inherited risk formyeloma.
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Affiliation(s)
- Rosalie Griffin Waller
- Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
- University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | | | - John Gardner
- Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Douglas W. Sborov
- Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
- University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Nicola J. Camp
- Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
- University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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18
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Yang J, Li H, Li B, Li W, Guo Q, Hu L, Song Z, Zhou B. Profiling Oncogenic Germline Mutations in Unselected Chinese Lung Cancer Patients. Front Oncol 2021; 11:647598. [PMID: 33898318 PMCID: PMC8058453 DOI: 10.3389/fonc.2021.647598] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/16/2021] [Indexed: 12/24/2022] Open
Abstract
Introduction Emerging evidence has suggested that inherited factors are also involved in lung cancer development. However, most studies focused on well-elucidated cancer predisposition genes, the majority of which are tumor suppressor genes. The profile of germline mutations in oncogenic driver genes remains unrevealed, which might also provide potential clinical implications for lung cancer management. Methods Sequencing data from 36,813 unselected lung cancer patients who underwent somatic mutation profiling were retrospectively reviewed. All recruited patients had matched white blood cell samples sequenced in parallel using a capture-based panel including eight key lung cancer driver genes (epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK), MET proto-oncogene, receptor tyrosine kinase (MET), Kirsten rat sarcoma viral oncogene homolog (KRAS), Erb-B2 receptor tyrosine kinase 2(ERBB2), ROS proto-oncogene 1, receptor tyrosine kinase (ROS1), ret proto-oncogene (RET), and B-Raf proto-oncogene, serine/threonine kinase (BRAF)). Likely pathogenic/pathogenic (LP/P) variants were called according to the classification criteria of the American College of Medical Genetics and Genomics. Variants of uncertain significance (VUS) located in the kinase domains of driver genes and occurring recurrently (n ≥3) were also included for further analyses. Results Seven different LP/P variants in EGFR, MET, or RET were identified in 0.03% of lung cancer patients (n = 14) and 25 different VUS in the kinase domains of seven driver genes (except KRAS) were found with a prevalence of 0.3% (n = 117).Collectively, germline mutations were most frequently seen in ROS1 (n = 31, 0.084%), followed by MET (n = 23, 0.062%), EGFR (n = 22, 0.06%), ALK (n = 22, 0.06%) and RET (n = 17, 0.046%). LP/P variants and VUS fell the most commonly in EGFR (n = 10, 72%) and ROS1 (n = 31, 26%), respectively. Of the 10 patients with EGFR LP/P germline mutation, 70% also acquired somatic EGFR driver mutation exon21 p.L858R or exon19 deletion at baseline; while the three patients with pathogenic germline RET mutation displayed distinct baseline somatic profiles of rare EGFR mutation or KRAS exon2 p.G12C. We discovered 11 germline mutations that also occurred somatically, including four LP/P variants and seven VUS. Conclusion We present the first study to systemically characterize the germline mutation in oncogenic driver genes in a large cohort of unselected patients with lung cancers.
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Affiliation(s)
- Jie Yang
- Radiotherapy Department, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Hefei Li
- Department of Thoracic Surgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Ben Li
- Department of Thoracic Surgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Wei Li
- Department of Thoracic Surgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Qiang Guo
- Department of Thoracic Surgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Ling Hu
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Baoding, China
| | - Zizheng Song
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Baoding, China
| | - Bin Zhou
- Department of Thoracic Surgery, Affiliated Hospital of Hebei University, Baoding, China
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19
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Perwez A, Wahabi K, Rizvi MA. Parkin: A targetable linchpin in human malignancies. Biochim Biophys Acta Rev Cancer 2021; 1876:188533. [PMID: 33785381 DOI: 10.1016/j.bbcan.2021.188533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/21/2021] [Accepted: 03/21/2021] [Indexed: 12/16/2022]
Abstract
Parkin, an E3 ubiquitin ligase has been found to be deregulated in a variety of human cancers. Our current understanding is endowed with strong evidences that Parkin plays crucial role in the pathogenesis of cancer by controlling/interfering with major hallmarks of cancer delineated till today. Consistent with the idea of mitophagy, the existing studies imitates the tumor suppressive potential of Parkin, resolved by its capacity to regulate cell proliferation, cell migration, angiogenesis, apoptosis and overall cellular survival. Dysfunction of Parkin has resulted in the loss of ubiquitination of cell cycle components followed by their accumulation leading to genomic instability, perturbed cell cycle and eventually tumor progression. In this review, we provide an overview of current knowledge about the critical role of Parkin in cancer development and progression and have focussed on its therapeutic implications highlighting the diagnostic and prognostic value of Parkin as a biomarker. We earnestly hope that an in-depth knowledge of Parkin will provide a linchpin to target in various cancers that will open a new door of clinical applications and therapeutics.
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Affiliation(s)
- Ahmad Perwez
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Khushnuma Wahabi
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Moshahid A Rizvi
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India.
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20
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Liu Y, Xia J, McKay J, Tsavachidis S, Xiao X, Spitz MR, Cheng C, Byun J, Hong W, Li Y, Zhu D, Song Z, Rosenberg SM, Scheurer ME, Kheradmand F, Pikielny CW, Lusk CM, Schwartz AG, Wistuba II, Cho MH, Silverman EK, Bailey-Wilson J, Pinney SM, Anderson M, Kupert E, Gaba C, Mandal D, You M, de Andrade M, Yang P, Liloglou T, Davies MPA, Lissowska J, Swiatkowska B, Zaridze D, Mukeria A, Janout V, Holcatova I, Mates D, Stojsic J, Scelo G, Brennan P, Liu G, Field JK, Hung RJ, Christiani DC, Amos CI. Rare deleterious germline variants and risk of lung cancer. NPJ Precis Oncol 2021; 5:12. [PMID: 33594163 PMCID: PMC7887261 DOI: 10.1038/s41698-021-00146-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 12/11/2020] [Indexed: 01/19/2023] Open
Abstract
Recent studies suggest that rare variants exhibit stronger effect sizes and might play a crucial role in the etiology of lung cancers (LC). Whole exome plus targeted sequencing of germline DNA was performed on 1045 LC cases and 885 controls in the discovery set. To unveil the inherited causal variants, we focused on rare and predicted deleterious variants and small indels enriched in cases or controls. Promising candidates were further validated in a series of 26,803 LCs and 555,107 controls. During discovery, we identified 25 rare deleterious variants associated with LC susceptibility, including 13 reported in ClinVar. Of the five validated candidates, we discovered two pathogenic variants in known LC susceptibility loci, ATM p.V2716A (Odds Ratio [OR] 19.55, 95%CI 5.04-75.6) and MPZL2 p.I24M frameshift deletion (OR 3.88, 95%CI 1.71-8.8); and three in novel LC susceptibility genes, POMC c.*28delT at 3' UTR (OR 4.33, 95%CI 2.03-9.24), STAU2 p.N364M frameshift deletion (OR 4.48, 95%CI 1.73-11.55), and MLNR p.Q334V frameshift deletion (OR 2.69, 95%CI 1.33-5.43). The potential cancer-promoting role of selected candidate genes and variants was further supported by endogenous DNA damage assays. Our analyses led to the identification of new rare deleterious variants with LC susceptibility. However, in-depth mechanistic studies are still needed to evaluate the pathogenic effects of these specific alleles.
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Grants
- R01 CA060691 NCI NIH HHS
- U19 CA203654 NCI NIH HHS
- R01 CA084354 NCI NIH HHS
- R01 HL110883 NHLBI NIH HHS
- U01 CA076293 NCI NIH HHS
- R01 CA080127 NCI NIH HHS
- R01 CA141769 NCI NIH HHS
- P30 ES006096 NIEHS NIH HHS
- P50 CA090578 NCI NIH HHS
- P30 CA022453 NCI NIH HHS
- S10 RR024574 NCRR NIH HHS
- HHSN261201300011C NCI NIH HHS
- R01 CA134682 NCI NIH HHS
- R01 CA134433 NCI NIH HHS
- R01 HL113264 NHLBI NIH HHS
- R01 HL082487 NHLBI NIH HHS
- R01 CA250905 NCI NIH HHS
- U19 CA148127 NCI NIH HHS
- P20 GM103534 NIGMS NIH HHS
- R01 CA092824 NCI NIH HHS
- R01 CA087895 NCI NIH HHS
- U01 HL089897 NHLBI NIH HHS
- K07 CA181480 NCI NIH HHS
- HHSN268201100011I NHLBI NIH HHS
- HHSN268201100011C NHLBI NIH HHS
- R01 CA127219 NCI NIH HHS
- R01 CA074386 NCI NIH HHS
- P30 CA023108 NCI NIH HHS
- U01 HL089856 NHLBI NIH HHS
- P30 ES030285 NIEHS NIH HHS
- P30 CA125123 NCI NIH HHS
- DP1 AG072751 NIA NIH HHS
- U01 CA243483 NCI NIH HHS
- HHSN268200782096C NHLBI NIH HHS
- HHSN268201200007C NHLBI NIH HHS
- N01HG65404 NHGRI NIH HHS
- R35 GM122598 NIGMS NIH HHS
- U01 CA209414 NCI NIH HHS
- R03 CA077118 NCI NIH HHS
- 001 World Health Organization
- DP1 CA174424 NCI NIH HHS
- This work was supported by grants from the National Institutes of Health (R01CA127219, R01CA141769, R01CA060691, R01CA87895, R01CA80127, R01CA84354, R01CA134682, R01CA134433, R01CA074386, R01CA092824, R01CA250905, R01HL113264, R01HL082487, R01HL110883, R03CA77118, P20GM103534, P30CA125123, P30CA023108, P30CA022453, P30ES006096, P50CA090578, U01CA243483, U01HL089856, U01HL089897, U01CA76293, U19CA148127, U01CA209414, K07CA181480, N01-HG-65404, HHSN268200782096C, HHSN261201300011I, HHSN268201100011, HHSN268201 200007C, DP1-CA174424, DP1-AG072751, CA125123, RR024574, Intramural Research Program of the National Human Genome Research Institute (JEB-W), and Herrick Foundation. Dr. Amos is an Established Research Scholar of the Cancer Prevention Research Institute of Texas (RR170048). We also want to acknowledge the Cytometry and Cell Sorting Core support by the Cancer Prevention and Research Institute of Texas Core Facility (RP180672). At Toronto, the study is supported by The Canadian Cancer Society Research Institute (# 020214) to R. H., Ontario Institute for Cancer Research to R. H, and the Alan Brown Chair to G. L. and Lusi Wong Programs at the Princess Margaret Hospital Foundation. The Liverpool Lung Project is supported by Roy Castle Lung Cancer Foundation.
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Affiliation(s)
- Yanhong Liu
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jun Xia
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - James McKay
- International Agency for Research on Cancer, Lyon, France
| | - Spiridon Tsavachidis
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Xiangjun Xiao
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Margaret R Spitz
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Chao Cheng
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Jinyoung Byun
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Wei Hong
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Yafang Li
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Dakai Zhu
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Zhuoyi Song
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Michael E Scheurer
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Farrah Kheradmand
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, USA
| | - Claudio W Pikielny
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA
| | - Christine M Lusk
- Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Ann G Schwartz
- Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Susan M Pinney
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Elena Kupert
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Colette Gaba
- The University of Toledo College of Medicine, Toledo, OH, USA
| | - Diptasri Mandal
- Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Ming You
- Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Ping Yang
- Mayo Clinic College of Medicine, Scottsdale, AZ, USA
| | - Triantafillos Liloglou
- Roy Castle Lung Cancer Research Programme, The University of Liverpool, Department of Molecular and Clinical Cancer Medicine, Liverpool, UK
| | - Michael P A Davies
- Roy Castle Lung Cancer Research Programme, The University of Liverpool, Department of Molecular and Clinical Cancer Medicine, Liverpool, UK
| | - Jolanta Lissowska
- M. Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Beata Swiatkowska
- Nofer Institute of Occupational Medicine, Department of Environmental Epidemiology, Lodz, Poland
| | - David Zaridze
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Anush Mukeria
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Vladimir Janout
- Faculty of Health Sciences, Palacky University, Olomouc, Czech Republic
| | - Ivana Holcatova
- Institute of Public Health and Preventive Medicine, Charles University, 2nd Faculty of Medicine, Prague, Czech Republic
| | - Dana Mates
- National Institute of Public Health, Bucharest, Romania
| | - Jelena Stojsic
- Department of Thoracopulmonary Pathology, Service of Pathology, Clinical Center of Serbia, Belgrade, Serbia
| | | | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - Geoffrey Liu
- Princess Margaret Cancer Center, Toronto, ON, Canada
| | - John K Field
- Roy Castle Lung Cancer Research Programme, The University of Liverpool, Department of Molecular and Clinical Cancer Medicine, Liverpool, UK
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | | | - Christopher I Amos
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA.
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21
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Lebrett MB, Crosbie EJ, Smith MJ, Woodward ER, Evans DG, Crosbie PAJ. Targeting lung cancer screening to individuals at greatest risk: the role of genetic factors. J Med Genet 2021; 58:217-226. [PMID: 33514608 PMCID: PMC8005792 DOI: 10.1136/jmedgenet-2020-107399] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 12/06/2020] [Accepted: 12/08/2020] [Indexed: 12/24/2022]
Abstract
Lung cancer (LC) is the most common global cancer. An individual’s risk of developing LC is mediated by an array of factors, including family history of the disease. Considerable research into genetic risk factors for LC has taken place in recent years, with both low-penetrance and high-penetrance variants implicated in increasing or decreasing a person’s risk of the disease. LC is the leading cause of cancer death worldwide; poor survival is driven by late onset of non-specific symptoms, resulting in late-stage diagnoses. Evidence for the efficacy of screening in detecting cancer earlier, thereby reducing lung-cancer specific mortality, is now well established. To ensure the cost-effectiveness of a screening programme and to limit the potential harms to participants, a risk threshold for screening eligibility is required. Risk prediction models (RPMs), which provide an individual’s personal risk of LC over a particular period based on a large number of risk factors, may improve the selection of high-risk individuals for LC screening when compared with generalised eligibility criteria that only consider smoking history and age. No currently used RPM integrates genetic risk factors into its calculation of risk. This review provides an overview of the evidence for LC screening, screening related harms and the use of RPMs in screening cohort selection. It gives a synopsis of the known genetic risk factors for lung cancer and discusses the evidence for including them in RPMs, focusing in particular on the use of polygenic risk scores to increase the accuracy of targeted lung cancer screening.
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Affiliation(s)
- Mikey B Lebrett
- Division of Infection, Immunity and Respiratory Medicine, The University of Manchester Faculty of Biology Medicine and Health, Manchester, UK.,Prevention and Early Detection Theme, NIHR Manchester Biomedical Research Centre, Manchester, UK
| | - Emma J Crosbie
- Prevention and Early Detection Theme, NIHR Manchester Biomedical Research Centre, Manchester, UK.,Division of Cancer Sciences, The University of Manchester Faculty of Biology Medicine and Health, Manchester, UK
| | - Miriam J Smith
- Prevention and Early Detection Theme, NIHR Manchester Biomedical Research Centre, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Emma R Woodward
- Prevention and Early Detection Theme, NIHR Manchester Biomedical Research Centre, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - D Gareth Evans
- Prevention and Early Detection Theme, NIHR Manchester Biomedical Research Centre, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Philip A J Crosbie
- Division of Infection, Immunity and Respiratory Medicine, The University of Manchester Faculty of Biology Medicine and Health, Manchester, UK .,Prevention and Early Detection Theme, NIHR Manchester Biomedical Research Centre, Manchester, UK.,Manchester Thoracic Oncology Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
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22
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Liu M, Liu X, Suo P, Gong Y, Qu B, Peng X, Xiao W, Li Y, Chen Y, Zeng Z, Lu Y, Huang T, Zhao Y, Liu M, Li L, Chen Y, Zhou Y, Liu G, Yao J, Chen S, Song L. The contribution of hereditary cancer-related germline mutations to lung cancer susceptibility. Transl Lung Cancer Res 2020; 9:646-658. [PMID: 32676327 PMCID: PMC7354149 DOI: 10.21037/tlcr-19-403] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Background Germline variations may contribute to lung cancer susceptibility besides environmental factors. The influence of germline mutations on lung cancer susceptibility and their correlation with somatic mutations has not been systematically investigated. Methods In this study, germline mutations from 1,026 non-small cell lung cancer (NSCLC) patients were analyzed with a 58-gene next-generation sequencing (NGS) panel containing known hereditary cancer-related genes, and were categorized based on American College of Medical Genetics and Genomics (ACMG) guidelines in pathogenicity, and the corresponding somatic mutations were analyzed using a 605-gene NGS panel containing known cancer-related genes. Results Plausible genetic susceptibility was found in 4.7% of lung cancer patients, in which 14 patients with pathogenic mutations (P group) and 34 patients with likely-pathogenic mutations (LP group) were identified. The ratio of the first degree relatives with lung cancer history of the P groups was significantly higher than the Non-P group (P=0.009). The ratio of lung cancer patients with history of other cancers was higher in P (P=0.0007) or LP (P=0.017) group than the Non-P group. Pathogenic mutations fell most commonly in BRCA2, followed by CHEK2 and ATM. Likely-pathogenic mutations fell most commonly in NTRK1 and EXT2, followed by BRIP1 and PALB2. These genes are involved in DNA repair, cell cycle regulation and tumor suppression. By comparing the germline mutation frequency from this study with that from the whole population or East Asian population (gnomAD database), we found that the overall odds ratio (OR) for P or LP group was 17.93 and 15.86, respectively, when compared with the whole population, and was 2.88 and 3.80, respectively, when compared with the East Asian population, suggesting the germline mutations of the P and LP groups were risk factors for lung cancer. Somatic mutation analysis revealed no significant difference in tumor mutation burden (TMB) among the groups, although a trend of lower TMB in the pathogenic group was found. The SNV/INDEL mutation frequency of TP53 in the P group was significantly lower than the other two groups, and the copy number variation (CNV) mutation frequency of PIK3CA and MET was significantly higher than the Non-P group. Pathway enrichment analysis found no significant difference in aberrant pathways among the three groups. Conclusions A proportion of 4.7% of patients carrying germline variants may be potentially linked to increased susceptibility to lung cancer. Patients with pathogenic germline mutations exhibited stronger family history and higher lung cancer risk.
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Affiliation(s)
- Mengyuan Liu
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Xinyi Liu
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Peisu Suo
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Yuan Gong
- The Second Medical Center of the Chinese PLA General Hospital, Beijing 100853, China
| | - Baolin Qu
- The Second Medical Center of the Chinese PLA General Hospital, Beijing 100853, China
| | - Xiumei Peng
- The Fourth Medical Center of the Chinese PLA General Hospital, Beijing 100037, China
| | - Wenhua Xiao
- The Fourth Medical Center of the Chinese PLA General Hospital, Beijing 100037, China
| | - Yuemin Li
- The Eighth Medical Center of the Chinese PLA General Hospital, Beijing 100091, China
| | - Yan Chen
- The Fifth Medical Center of the Chinese PLA General Hospital, Beijing 100039, China
| | - Zhen Zeng
- The Fifth Medical Center of the Chinese PLA General Hospital, Beijing 100039, China
| | - Yinying Lu
- The Fifth Medical Center of the Chinese PLA General Hospital, Beijing 100039, China
| | - Tanxiao Huang
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Yingshen Zhao
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Ming Liu
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Lifeng Li
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Yaru Chen
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Yanqing Zhou
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Guifeng Liu
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Jianfei Yao
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Shifu Chen
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Lele Song
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China.,The Eighth Medical Center of the Chinese PLA General Hospital, Beijing 100091, China
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23
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Rotunno M, Barajas R, Clyne M, Hoover E, Simonds NI, Lam TK, Mechanic LE, Goldstein AM, Gillanders EM. A Systematic Literature Review of Whole Exome and Genome Sequencing Population Studies of Genetic Susceptibility to Cancer. Cancer Epidemiol Biomarkers Prev 2020; 29:1519-1534. [PMID: 32467344 DOI: 10.1158/1055-9965.epi-19-1551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 03/17/2020] [Accepted: 05/13/2020] [Indexed: 01/03/2023] Open
Abstract
The application of next-generation sequencing (NGS) technologies in cancer research has accelerated the discovery of somatic mutations; however, progress in the identification of germline variation associated with cancer risk is less clear. We conducted a systematic literature review of cancer genetic susceptibility studies that used NGS technologies at an exome/genome-wide scale to obtain a fuller understanding of the research landscape to date and to inform future studies. The variability across studies on methodologies and reporting was considerable. Most studies sequenced few high-risk (mainly European) families, used a candidate analysis approach, and identified potential cancer-related germline variants or genes in a small fraction of the sequenced cancer cases. This review highlights the importance of establishing consensus on standards for the application and reporting of variants filtering strategies. It also describes the progress in the identification of cancer-related germline variation to date. These findings point to the untapped potential in conducting studies with appropriately sized and racially diverse families and populations, combining results across studies and expanding beyond a candidate analysis approach to advance the discovery of genetic variation that accounts for the unexplained cancer heritability.
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Affiliation(s)
- Melissa Rotunno
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland.
| | - Rolando Barajas
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Mindy Clyne
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Elise Hoover
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | | | - Tram Kim Lam
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Leah E Mechanic
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Alisa M Goldstein
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Elizabeth M Gillanders
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
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24
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Wang P, Dai X, Jiang W, Li Y, Wei W. RBR E3 ubiquitin ligases in tumorigenesis. Semin Cancer Biol 2020; 67:131-144. [PMID: 32442483 DOI: 10.1016/j.semcancer.2020.05.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/28/2020] [Accepted: 05/04/2020] [Indexed: 02/06/2023]
Abstract
RING-in-between-RING (RBR) E3 ligases are one class of E3 ligases that is characterized by the unique RING-HECT hybrid mechanism to function with E2s to transfer ubiquitin to target proteins for degradation. Emerging evidence has demonstrated that RBR E3 ligases play essential roles in neurodegenerative diseases, infection, inflammation and cancer. Accumulated evidence has revealed that RBR E3 ligases exert their biological functions in various types of cancers by modulating the degradation of tumor promoters or suppressors. Hence, we summarize the differential functions of RBR E3 ligases in a variety of human cancers. In general, ARIH1, RNF14, RNF31, RNF144B, RNF216, and RBCK1 exhibit primarily oncogenic roles, whereas ARIH2, PARC and PARK2 mainly have tumor suppressive functions. Moreover, the underlying mechanisms by which different RBR E3 ligases are involved in tumorigenesis and progression are also described. We discuss the further investigation is required to comprehensively understand the critical role of RBR E3 ligases in carcinogenesis. We hope our review can stimulate the researchers to deeper explore the mechanism of RBR E3 ligases-mediated carcinogenesis and to develop useful inhibitors of these oncogenic E3 ligases for cancer therapy.
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Affiliation(s)
- Peter Wang
- School of Laboratory Medicine, Bengbu Medical College, Anhui, 233030, China
| | - Xiaoming Dai
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave., Boston, MA, USA
| | - Wenxiao Jiang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Yuyun Li
- School of Laboratory Medicine, Bengbu Medical College, Anhui, 233030, China.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave., Boston, MA, USA.
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25
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Wang Y, Su GF, Huang ZX, Wang ZG, Zhou PJ, Fan JL, Wang YF. Cepharanthine hydrochloride induces mitophagy targeting GPR30 in hepatocellular carcinoma (HCC). Expert Opin Ther Targets 2020; 24:389-402. [PMID: 32106726 DOI: 10.1080/14728222.2020.1737013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Objectives: Cepharanthine exhibits a wide range of therapeutic effects against numerous cancers by virtue of its pleiotropic mechanisms. However, cepharanthine monotherapy has insufficient drug efficacy for cancers in animal models and clinical trials. The mechanism of its limited efficacy is unknown.Methods: We investigated the possible mechanism for the limited drug efficacy of cepharanthine in cancer therapy using both hepatocellular carcinoma (HCC) primary cells and cell lines, in vitro and in mouse xenograft models.Results: We found that cepharanthine hydrochloride (CH), a semi-synthetic derivative of cepharanthine, induced mitophagy independent of mTOR signaling, and played an AMPK-dependent protective role in the cell fate of HCC in vitro and in vivo. Mechanistically, we demonstrated that CH may bind to GPR30 receptor to activate the subsequent signal cascade involving mitochondrial fission, thus facilitating mitophagy. Therefore, we proposed a new therapeutic regimen for HCC involving CH combined with an autophagy inhibitor. This regimen exhibited remarkable anti-cancer effects in HCC xenograft mouse model.Conclusion: These results identify CH as a new mitophagy inducer targeting GPR30 receptor. The combination therapy of CH and an autophagy inhibitor may become a novel strategy for enhancing the anti-tumor potential of cepharanthine in HCC.
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Affiliation(s)
- Yao Wang
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, P. R. China.,Guangzhou Jinan Biomedicine Research and Development Center Co.ltd, Guangzhou, Guangdong, P. R. China
| | - Gui-Feng Su
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, P. R. China
| | - Ze-Xiu Huang
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, P. R. China
| | - Zhen-Guang Wang
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Peng-Jun Zhou
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, P. R. China.,The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Jiang-Lin Fan
- Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo-City, Japan
| | - Yi-Fei Wang
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, P. R. China.,Guangzhou Jinan Biomedicine Research and Development Center Co.ltd, Guangzhou, Guangdong, P. R. China
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26
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Cetani F, Pardi E, Aretini P, Saponaro F, Borsari S, Mazoni L, Apicella M, Civita P, La Ferla M, Caligo MA, Lessi F, Mazzanti CM, Torregossa L, Oppo A, Marcocci C. Whole exome sequencing in familial isolated primary hyperparathyroidism. J Endocrinol Invest 2020; 43:231-245. [PMID: 31486992 DOI: 10.1007/s40618-019-01107-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/29/2019] [Indexed: 12/14/2022]
Abstract
PURPOSE Familial isolated hyperparathyroidism (FIHP) is a rare inherited disease accounting for 1% of all cases of primary hyperparathyroidism (PHPT). It is genetically heterogeneous being associated with mutations in different genes, including MEN1, CDC73, CASR, and recently GCM2. The aim of the study was to further investigate the molecular pathogenesis in Italian FIHP kindreds. METHODS We used whole exome sequencing (WES) in the probands of seven unrelated FIHP kindreds. We carried out a separate family-based exome analysis in a large family characterized by the co-occurrence of PHPT with multiple tumors apparently unrelated to the disease. Selected variants were also screened in 18 additional FIHP kindreds. The clinical, biochemical, and pathological characteristics of the families were also investigated. RESULTS Three different variants in GCM2 gene were found in two families, but only one (p.Tyr394Ser), already been shown to be pathogenic in vitro, segregated with the disease. Six probands carried seven heterozygous missense mutations segregating with the disease in the FAT3, PARK2, HDAC4, ITPR2 and TBCE genes. A genetic variant in the APC gene co-segregating with PHPT (p.Val530Ala) was detected in a family whose affected relatives had additional tumors, including colonic polyposis. CONCLUSION We confirm the role of GCM2 germline mutations in the pathogenesis of FIHP, although at a lower rate than in the previous WES study. Further studies are needed to establish the prevalence and the role in the predisposition to FIHP of the novel variants in additional genes.
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Affiliation(s)
- F Cetani
- University Hospital of Pisa, Endocrine Unit 2, Via Paradisa 2, 56124, Pisa, Italy.
| | - E Pardi
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - P Aretini
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
| | - F Saponaro
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - S Borsari
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - L Mazoni
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - M Apicella
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - P Civita
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
| | - M La Ferla
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
| | - M A Caligo
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - F Lessi
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
| | - C M Mazzanti
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
| | - L Torregossa
- Division of Surgical Pathology, University Hospital of Pisa, Pisa, Italy
| | - A Oppo
- Endocrinology Unit, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - C Marcocci
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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27
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Zhang ZL, Wang NN, Ma QL, Chen Y, Yao L, Zhang L, Li QS, Shi MH, Wang HF, Ying Z. Somatic and germline mutations in the tumor suppressor gene PARK2 impair PINK1/Parkin-mediated mitophagy in lung cancer cells. Acta Pharmacol Sin 2020; 41:93-100. [PMID: 31285534 PMCID: PMC7470868 DOI: 10.1038/s41401-019-0260-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/21/2019] [Indexed: 12/11/2022] Open
Abstract
PARK2, which encodes Parkin, is a disease-causing gene for both neurodegenerative disorders and cancer. Parkin can function as a neuroprotector that plays a crucial role in the regulation of mitophagy, and germline mutations in PARK2 are associated with Parkinson's disease (PD). Intriguingly, recent studies suggest that Parkin can also function as a tumor suppressor and that somatic and germline mutations in PARK2 are associated with various human cancers, including lung cancer. However, it is presently unknown how the tumor suppressor activity of Parkin is affected by these mutations and whether it is associated with mitophagy. Herein, we show that wild-type (WT) Parkin can rapidly translocate onto mitochondria following mitochondrial damage and that Parkin promotes mitophagic clearance of mitochondria in lung cancer cells. However, lung cancer-linked mutations inhibit the mitochondrial translocation and ubiquitin-associated activity of Parkin. Among all lung cancer-linked mutants that we tested, A46T Parkin failed to translocate onto mitochondria and could not recruit downstream mitophagic regulators, including optineurin (OPTN) and TFEB, whereas N254S and R275W Parkin displayed slower mitochondrial translocation than WT Parkin. Moreover, we found that deferiprone (DFP), an iron chelator that can induce mitophagy, greatly increased the death of A46T Parkin-expressing lung cancer cells. Taken together, our results reveal a novel mitophagic mechanism in lung cancer, suggesting that lung cancer-linked mutations in PARK2 are associated with impaired mitophagy and identifying DFP as a novel therapeutic agent for PARK2-linked lung cancer and possibly other types of cancers driven by mitophagic dysregulation.
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28
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Duan H, Lei Z, Xu F, Pan T, Lu D, Ding P, Zhu C, Pan C, Zhang S. PARK2 Suppresses Proliferation and Tumorigenicity in Non-small Cell Lung Cancer. Front Oncol 2019; 9:790. [PMID: 31508359 PMCID: PMC6716169 DOI: 10.3389/fonc.2019.00790] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/06/2019] [Indexed: 12/26/2022] Open
Abstract
Aims: PARK2 mutation is originally associated with the progression of Parkinson's disease. In recent years, PARK2 has been reported as a tumor suppressor gene in various cancers, including lung cancer. However, the biological functions and potential molecular mechanisms of PARK2 in non-small cell lung cancer (NSCLC) are still unclear. Methods: The level of PARK2 expression in 32 tissue samples of NSCLC and matched non-tumor lung tissues was detected by Western blot, and 64 specimens of NSCLC tissues were detected by immunohistochemistry. H1299 and H460 cell lines were used to PARK2 overexpression models, and H460 cell line was also used to PARK2 knockdown model. Using cell viability, colony formation, cell cycle, apoptosis, migration, and invasion assay, the biological functions of PARK2 were evaluated and the potential molecular mechanism of PARK2 was investigated in vitro. Meanwhile, 22 nude mice were employed for in vivo studies. Results: Western blot analysis revealed a decrease of PARK2 protein expression in human NSCLC samples. Immunohistochemistry also identified a vastly reduced expression of PARK2 in NSCLC (72%) and low PARK2 expression was significantly associated with tumor histological grade, lymph node metastasis and advanced TNM stage. Overexpression of PARK2 suppressed cell proliferation, colony formation, migration, and invasion, arrested cell cycle progression in the G1 phase, and induced apoptosis in human non-small cell lines H1299 and H460 in vitro. Meanwhile, knockdown of PARK2 had the opposite biological functions. In addition, PARK2 significantly decreased the tumor volumes in subcutaneous xenograft model and reduced the incidence of metastatic tumors in the transfer model. Exploration of the molecular mechanism of PARK2 in NSCLC showed that PARK2 negatively regulated the EGFR/AKT/mTOR signaling pathway. Conclusions: PARK2 was an important tumor suppressor in NSCLC, which might inhibit cancer growth and metastases through the down regulation of the EGFR/AKT/mTOR signaling pathway.
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Affiliation(s)
- Huijie Duan
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, The Second Affiliated Hospital, School of Medicine, Cancer Institute, Zhejiang University, Hangzhou, China
| | - Zhong Lei
- Department of Orthopedics Research Institute, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Fei Xu
- Department of Oncology, Municipal Hospital of Qingdao, Qingdao, China
| | - Tao Pan
- Department of Breast Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Demin Lu
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, The Second Affiliated Hospital, School of Medicine, Cancer Institute, Zhejiang University, Hangzhou, China
| | - Peili Ding
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, The Second Affiliated Hospital, School of Medicine, Cancer Institute, Zhejiang University, Hangzhou, China
| | - Chunpeng Zhu
- Department of Gastroenterology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chi Pan
- Department of Breast Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Suzhan Zhang
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, The Second Affiliated Hospital, School of Medicine, Cancer Institute, Zhejiang University, Hangzhou, China.,Research Center for Air Pollution and Health, School of Medicine, Zhejiang University, Hangzhou, China
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29
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Shao L, Zuo X, Yang Y, Zhang Y, Yang N, Shen B, Wang J, Wang X, Li R, Jin G, Yu D, Chen Y, Sun L, Li Z, Fu Q, Hu Z, Han X, Song X, Shen H, Sun Y. The inherited variations of a p53-responsive enhancer in 13q12.12 confer lung cancer risk by attenuating TNFRSF19 expression. Genome Biol 2019; 20:103. [PMID: 31126313 PMCID: PMC6533720 DOI: 10.1186/s13059-019-1696-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 04/22/2019] [Indexed: 12/20/2022] Open
Abstract
Background Inherited factors contribute to lung cancer risk, but the mechanism is not well understood. Defining the biological consequence of GWAS hits in cancers is a promising strategy to elucidate the inherited mechanisms of cancers. The tag-SNP rs753955 (A>G) in 13q12.12 is highly associated with lung cancer risk in the Chinese population. Here, we systematically investigate the biological significance and the underlying mechanism behind 13q12.12 risk locus in vitro and in vivo. Results We characterize a novel p53-responsive enhancer with lung tissue cell specificity in a 49-kb high linkage disequilibrium block of rs753955. This enhancer harbors 3 highly linked common inherited variations (rs17336602, rs4770489, and rs34354770) and six p53 binding sequences either close to or located between the variations. The enhancer effectively protects normal lung cell lines against pulmonary carcinogen NNK-induced DNA damages and malignant transformation by upregulating TNFRSF19 through chromatin looping. These variations significantly weaken the enhancer activity by affecting its p53 response, especially when cells are exposed to NNK. The effect of the mutant enhancer alleles on TNFRSF19 target gene in vivo is supported by expression quantitative trait loci analysis of 117 Chinese NSCLC samples and GTEx data. Differentiated expression of TNFRSF19 and its statistical significant correlation with tumor TNM staging and patient survival indicate a suppressor role of TNFRSF19 in lung cancer. Conclusion This study provides evidence of how the inherited variations in 13q12.12 contribute to lung cancer risk, highlighting the protective roles of the p53-responsive enhancer-mediated TNFRSF19 activation in lung cells under carcinogen stress. Electronic supplementary material The online version of this article (10.1186/s13059-019-1696-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lipei Shao
- Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126, China.,Department of Cell Biology, Nanjing Medical University, Nanjing, 211126, China
| | - Xianglin Zuo
- Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126, China.,Department of Cell Biology, Nanjing Medical University, Nanjing, 211126, China
| | - Yin Yang
- Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126, China.,Department of Cell Biology, Nanjing Medical University, Nanjing, 211126, China
| | - Yu Zhang
- Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126, China.,Department of Cell Biology, Nanjing Medical University, Nanjing, 211126, China
| | - Nan Yang
- Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211126, China
| | - Jianying Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211126, China
| | - Xuchun Wang
- Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126, China.,Department of Cell Biology, Nanjing Medical University, Nanjing, 211126, China
| | - Ruilei Li
- Department of Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, 650000, Yunnan, China
| | - Guangfu Jin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211126, China.,Collaborative Innovation Center for Cancer Personalized Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Cancer Center, Nanjing Medical University, Nanjing, 211126, China
| | - Dawei Yu
- Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126, China.,Department of Cell Biology, Nanjing Medical University, Nanjing, 211126, China
| | - Yuan Chen
- Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126, China.,Department of Cell Biology, Nanjing Medical University, Nanjing, 211126, China
| | - Luan Sun
- Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126, China.,Department of Cell Biology, Nanjing Medical University, Nanjing, 211126, China
| | - Zhen Li
- Department of Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, 650000, Yunnan, China
| | - Qiaofen Fu
- Department of Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, 650000, Yunnan, China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211126, China.,Collaborative Innovation Center for Cancer Personalized Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Cancer Center, Nanjing Medical University, Nanjing, 211126, China
| | - Xiao Han
- Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126, China
| | - Xin Song
- Department of Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, 650000, Yunnan, China.
| | - Hongbin Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211126, China. .,Collaborative Innovation Center for Cancer Personalized Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Cancer Center, Nanjing Medical University, Nanjing, 211126, China.
| | - Yujie Sun
- Key laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211126, China. .,Collaborative Innovation Center for Cancer Personalized Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Cancer Center, Nanjing Medical University, Nanjing, 211126, China. .,Department of Cell Biology, Nanjing Medical University, Nanjing, 211126, China.
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30
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Shukuya T, Takahashi K. Germline mutations in lung cancer. Respir Investig 2019; 57:201-206. [PMID: 30639082 DOI: 10.1016/j.resinv.2018.12.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 11/29/2018] [Accepted: 12/12/2018] [Indexed: 06/09/2023]
Abstract
Genetic testing for alterations in oncogenic driver genes has become essential and standard in the clinical practice of the treatment of lung cancer. Germline mutations potentially predisposing patients to lung cancer are rare; however, with the introduction of next-generation sequencing in the clinical practice of lung cancer, the identification of potentially predisposing germline abnormalities is becoming more common. In addition, liquid biopsy, which analyzes cell-free DNA in blood, increases the possibility of detecting these germline mutations. In this review, we summarize the germline mutations detected in lung cancer patients and briefly describe the future perspectives.
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Affiliation(s)
- Takehito Shukuya
- Department of Respiratory Medicine, Juntendo University School of Medicine, Tokyo, Japan; Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.
| | - Kazuhisa Takahashi
- Department of Respiratory Medicine, Juntendo University School of Medicine, Tokyo, Japan
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31
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Kishinevsky S, Wang T, Rodina A, Chung SY, Xu C, Philip J, Taldone T, Joshi S, Alpaugh ML, Bolaender A, Gutbier S, Sandhu D, Fattahi F, Zimmer B, Shah SK, Chang E, Inda C, Koren J, Saurat NG, Leist M, Gross SS, Seshan VE, Klein C, Tomishima MJ, Erdjument-Bromage H, Neubert TA, Henrickson RC, Chiosis G, Studer L. HSP90-incorporating chaperome networks as biosensor for disease-related pathways in patient-specific midbrain dopamine neurons. Nat Commun 2018; 9:4345. [PMID: 30341316 PMCID: PMC6195591 DOI: 10.1038/s41467-018-06486-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/29/2018] [Indexed: 12/21/2022] Open
Abstract
Environmental and genetic risk factors contribute to Parkinson’s Disease (PD) pathogenesis and the associated midbrain dopamine (mDA) neuron loss. Here, we identify early PD pathogenic events by developing methodology that utilizes recent innovations in human pluripotent stem cells (hPSC) and chemical sensors of HSP90-incorporating chaperome networks. We show that events triggered by PD-related genetic or toxic stimuli alter the neuronal proteome, thereby altering the stress-specific chaperome networks, which produce changes detected by chemical sensors. Through this method we identify STAT3 and NF-κB signaling activation as examples of genetic stress, and phospho-tyrosine hydroxylase (TH) activation as an example of toxic stress-induced pathways in PD neurons. Importantly, pharmacological inhibition of the stress chaperome network reversed abnormal phospho-STAT3 signaling and phospho-TH-related dopamine levels and rescued PD neuron viability. The use of chemical sensors of chaperome networks on hPSC-derived lineages may present a general strategy to identify molecular events associated with neurodegenerative diseases. The early molecular events that ultimately lead to neuronal cell death in pathologies such as Parkinson’s disease are poorly understood. Here the authors use pluripotent stem-cell-derived human midbrain neurons and chemical biology tools to gain molecular level insight into the events induced by toxic and genetic stresses that mimic those occurring during neurodegeneration.
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Affiliation(s)
- Sarah Kishinevsky
- The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA.,Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA.,Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.,Neuroscience Graduate Program of Weill Cornell Graduate School of Biomedical Sciences, Weill Cornell Medical College, 1300 York Avenue, Box 65, New York, NY, 10065, USA
| | - Tai Wang
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Anna Rodina
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Sun Young Chung
- The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA.,Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA
| | - Chao Xu
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - John Philip
- Proteomics Core Facility, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Tony Taldone
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Suhasini Joshi
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Mary L Alpaugh
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.,Department of Molecular and Cellular Biosciences, Rowan University, 1275 York Avenue, Glassboro, NJ, 08028, USA
| | - Alexander Bolaender
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Simon Gutbier
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Konstanz, 78464, Germany
| | - Davinder Sandhu
- Department of Pharmacology, Weill Cornell College of Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Faranak Fattahi
- The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA.,Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA
| | - Bastian Zimmer
- The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA.,Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA
| | - Smit K Shah
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Elizabeth Chang
- Proteomics Core Facility, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Carmen Inda
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.,Hostos Community College, City University of New York, Bronx, NY, 10453, USA
| | - John Koren
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.,Department of Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Nathalie G Saurat
- The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA.,Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA
| | - Marcel Leist
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Konstanz, 78464, Germany
| | - Steven S Gross
- Department of Pharmacology, Weill Cornell College of Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Venkatraman E Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, 10017, USA
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, 23538, Germany
| | - Mark J Tomishima
- The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA.,Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA.,SKI Stem Cell Research Facility, 1275 York Avenue, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Hediye Erdjument-Bromage
- Department of Cell Biology, NYU School of Medicine, New York, NY, 10016, USA.,Kimmel Center for Biology and Medicine at the Skirball Institute, NYU School of Medicine, New York, NY, 10016, USA
| | - Thomas A Neubert
- Department of Cell Biology, NYU School of Medicine, New York, NY, 10016, USA.,Kimmel Center for Biology and Medicine at the Skirball Institute, NYU School of Medicine, New York, NY, 10016, USA
| | - Ronald C Henrickson
- Proteomics Core Facility, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Gabriela Chiosis
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA. .,Department of Medicine, Memorial Hospital, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
| | - Lorenz Studer
- The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA.,Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA
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32
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Liu Y, Lusk CM, Cho MH, Silverman EK, Qiao D, Zhang R, Scheurer ME, Kheradmand F, Wheeler DA, Tsavachidis S, Armstrong G, Zhu D, Wistuba II, Chow CWB, Behrens C, Pikielny CW, Neslund-Dudas C, Pinney SM, Anderson M, Kupert E, Bailey-Wilson J, Gaba C, Mandal D, You M, de Andrade M, Yang P, Field JK, Liloglou T, Davies M, Lissowska J, Swiatkowska B, Zaridze D, Mukeriya A, Janout V, Holcatova I, Mates D, Milosavljevic S, Scelo G, Brennan P, McKay J, Liu G, Hung RJ, Christiani DC, Schwartz AG, Amos CI, Spitz MR. Rare Variants in Known Susceptibility Loci and Their Contribution to Risk of Lung Cancer. J Thorac Oncol 2018; 13:1483-1495. [PMID: 29981437 PMCID: PMC6366341 DOI: 10.1016/j.jtho.2018.06.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/06/2018] [Accepted: 06/17/2018] [Indexed: 10/28/2022]
Abstract
BACKGROUND Genome-wide association studies are widely used to map genomic regions contributing to lung cancer (LC) susceptibility, but they typically do not identify the precise disease-causing genes/variants. To unveil the inherited genetic variants that cause LC, we performed focused exome-sequencing analyses on genes located in 121 genome-wide association study-identified loci previously implicated in the risk of LC, chronic obstructive pulmonary disease, pulmonary function level, and smoking behavior. METHODS Germline DNA from 260 case patients with LC and 318 controls were sequenced by utilizing VCRome 2.1 exome capture. Filtering was based on enrichment of rare and potential deleterious variants in cases (risk alleles) or controls (protective alleles). Allelic association analyses of single-variant and gene-based burden tests of multiple variants were performed. Promising candidates were tested in two independent validation studies with a total of 1773 case patients and 1123 controls. RESULTS We identified 48 rare variants with deleterious effects in the discovery analysis and validated 12 of the 43 candidates that were covered in the validation platforms. The top validated candidates included one well-established truncating variant, namely, BRCA2, DNA repair associated gene (BRCA2) K3326X (OR = 2.36, 95% confidence interval [CI]: 1.38-3.99), and three newly identified variations, namely, lymphotoxin beta gene (LTB) p.Leu87Phe (OR = 7.52, 95% CI: 1.01-16.56), prolyl 3-hydroxylase 2 gene (P3H2) p.Gln185His (OR = 5.39, 95% CI: 0.75-15.43), and dishevelled associated activator of morphogenesis 2 gene (DAAM2) p.Asp762Gly (OR = 0.25, 95% CI: 0.10-0.79). Burden tests revealed strong associations between zinc finger protein 93 gene (ZNF93), DAAM2, bromodomain containing 9 gene (BRD9), and the gene LTB and LC susceptibility. CONCLUSION Our results extend the catalogue of regions associated with LC and highlight the importance of germline rare coding variants in LC susceptibility.
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Affiliation(s)
- Yanhong Liu
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christine M. Lusk
- Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ruyang Zhang
- Harvard University School of Public Health, Boston, MA 02115, USA
| | - Michael E. Scheurer
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Farrah Kheradmand
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Michael E. DeBakey Veterans Affairs Medical Center; Houston, TX 77030, USA
| | - David A. Wheeler
- Department of Molecular and Human Genetics, Human Genome Sequence Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Spiridon Tsavachidis
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Georgina Armstrong
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dakai Zhu
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ignacio I. Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chi-Wan B. Chow
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Claudio W. Pikielny
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Lebanon, NH 03755, USA
| | | | - Susan M. Pinney
- University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Marshall Anderson
- University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Elena Kupert
- University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | | | - Colette Gaba
- The University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Diptasri Mandal
- Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Ming You
- Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Ping Yang
- Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - John K. Field
- Roy Castle Lung Cancer Research Programme, The University of Liverpool, Department of Molecular and Clinical Cancer Medicine, Liverpool, UK
| | - Triantafillos Liloglou
- Roy Castle Lung Cancer Research Programme, The University of Liverpool, Department of Molecular and Clinical Cancer Medicine, Liverpool, UK
| | - Michael Davies
- Roy Castle Lung Cancer Research Programme, The University of Liverpool, Department of Molecular and Clinical Cancer Medicine, Liverpool, UK
| | - Jolanta Lissowska
- The M. Sklodowska-Curie Institute of Oncology Center, Warsaw 02781, Poland
| | - Beata Swiatkowska
- Nofer Institute of Occupational Medicine, Department of Environmental Epidemiology, Lodz 91348, Poland
| | - David Zaridze
- Russian N.N. Blokhin Cancer Research Centre, Moscow 115478, Russian Federation
| | - Anush Mukeriya
- Russian N.N. Blokhin Cancer Research Centre, Moscow 115478, Russian Federation
| | - Vladimir Janout
- Faculty of Health Sciences, Palacky University, Olomouc 77515, Czech Republic
| | - Ivana Holcatova
- Institute of Public Health and Preventive Medicine, Charles University, 2nd Faculty of Medicine, Prague 12800, Czech Republic
| | - Dana Mates
- National Institute of Public Health, Bucharest 050463, Romania
| | - Sasa Milosavljevic
- International Organization for Cancer Prevention and Research (IOCPR), Belgrade, Serbia
| | | | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - James McKay
- International Agency for Research on Cancer, Lyon, France
| | - Geoffrey Liu
- Princess Margaret Cancer Center, Toronto, ON, M5G 2M9, Canada
| | - Rayjean J. Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5 Canada
| | | | | | - Ann G. Schwartz
- Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA
| | - Christopher I Amos
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX 77030, USA
| | - Margaret R. Spitz
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
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Byun J, Schwartz AG, Lusk C, Wenzlaff AS, de Andrade M, Mandal D, Gaba C, Yang P, You M, Kupert EY, Anderson MW, Han Y, Li Y, Qian D, Stilp A, Laurie C, Nelson S, Zheng W, Hung RJ, Gaborieau V, Mckay J, Brennan P, Caporaso NE, Landi MT, Wu X, McLaughlin JR, Brhane Y, Bossé Y, Pinney SM, Bailey-Wilson JE, Amos CI. Genome-wide association study of familial lung cancer. Carcinogenesis 2018; 39:1135-1140. [PMID: 29924316 PMCID: PMC6148967 DOI: 10.1093/carcin/bgy080] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/12/2018] [Accepted: 06/18/2018] [Indexed: 12/27/2022] Open
Abstract
To identify genetic variation associated with lung cancer risk, we performed a genome-wide association analysis of 685 lung cancer cases that had a family history of two or more first or second degree relatives compared with 744 controls without lung cancer that were genotyped on an Illumina Human OmniExpressExome-8v1 array. To ensure robust results, we further evaluated these findings using data from six additional studies that were assembled through the Transdisciplinary Research on Cancer of the Lung Consortium comprising 1993 familial cases and 33 690 controls. We performed a meta-analysis after imputation of all variants using the 1000 Genomes Project Phase 1 (version 3 release date September 2013). Analyses were conducted for 9 327 222 SNPs integrating data from the two sources. A novel variant on chromosome 4p15.31 near the LCORL gene and an imputed rare variant intergenic between CDKN2A and IFNA8 on chromosome 9p21.3 were identified at a genome-wide level of significance for squamous cell carcinomas. Additionally, associations of CHRNA3 and CHRNA5 on chromosome 15q25.1 in sporadic lung cancer were confirmed at a genome-wide level of significance in familial lung cancer. Previously identified variants in or near CHRNA2, BRCA2, CYP2A6 for overall lung cancer, TERT, SECISPB2L and RTEL1 for adenocarcinoma and RAD52 and MHC for squamous carcinoma were significantly associated with lung cancer.
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Affiliation(s)
- Jinyoung Byun
- Department of Biomedical Data Science, Dartmouth Geisel School of Medicine, Lebanon, NH, USA
| | - Ann G Schwartz
- Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Christine Lusk
- Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | | | - Mariza de Andrade
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Diptasri Mandal
- Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Colette Gaba
- University of Toledo Dana Cancer Center, Toledo, OH, USA
| | - Ping Yang
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Ming You
- Medical College of Wisconsin, Milwaukee, WI, USA
| | | | | | - Younghun Han
- Department of Biomedical Data Science, Dartmouth Geisel School of Medicine, Lebanon, NH, USA
| | - Yafang Li
- Department of Biomedical Data Science, Dartmouth Geisel School of Medicine, Lebanon, NH, USA
| | - David Qian
- Department of Biomedical Data Science, Dartmouth Geisel School of Medicine, Lebanon, NH, USA
| | - Adrienne Stilp
- Genetic Analysis Center, University of Washington, Seattle, WA, USA
| | - Cathy Laurie
- Genetic Analysis Center, University of Washington, Seattle, WA, USA
| | - Sarah Nelson
- Genetic Analysis Center, University of Washington, Seattle, WA, USA
| | - Wenying Zheng
- Genetic Analysis Center, University of Washington, Seattle, WA, USA
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Valerie Gaborieau
- Genetic Epidemiology Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - James Mckay
- Genetic Epidemiology Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xifeng Wu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Yonathan Brhane
- Genetic Analysis Center, University of Washington, Seattle, WA, USA
| | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Molecular Medicine, Laval University, Québec, Canada
| | - Susan M Pinney
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Joan E Bailey-Wilson
- National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA
| | - Christopher I Amos
- Department of Biomedical Data Science, Dartmouth Geisel School of Medicine, Lebanon, NH, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
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Donner I, Katainen R, Sipilä LJ, Aavikko M, Pukkala E, Aaltonen LA. Germline mutations in young non-smoking women with lung adenocarcinoma. Lung Cancer 2018; 122:76-82. [DOI: 10.1016/j.lungcan.2018.05.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 05/28/2018] [Accepted: 05/30/2018] [Indexed: 02/06/2023]
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Yamamoto H, Yatabe Y, Toyooka S. Inherited lung cancer syndromes targeting never smokers. Transl Lung Cancer Res 2018; 7:498-504. [PMID: 30225213 DOI: 10.21037/tlcr.2018.06.01] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Lung cancer is the leading cause of cancer death worldwide. Most of lung cancers develop sporadically and thus inherited lung cancers are rare. Several reports show that germline mutations in the kinase domain of epidermal growth factor receptor (EGFR) such as R776G, R776H, T790M, V843I and P848L, predispose to develop lung cancer. Most lung cancer cases with germline EGFR T790M mutations had secondary EGFR somatic mutations. Never smokers with germline EGFR T790M mutations develop lung cancer more frequently than ever smokers. In addition, germline EGFR T790M mutations favored female gender. Therefore, germline EGFR T790M mutations result in a unique inherited lung cancer syndrome targeting never smokers. The authors previously reported a Japanese familial lung cancer pedigree with germline mutations in the transmembrane domain of human epidermal growth factor receptor 2 (HER2). The female proband and her mother in this pedigree, who were light or never smokers, developed multiple lung adenocarcinomas, and had germline HER2 G660D mutations. They had no EGFR somatic mutations or other genes known to cause lung cancers. Although we know only one pedigree with germline HER2 mutations, these mutations may also cause inherited lung cancers targeting female never smokers. Based on our in vitro analyses, we administered HER2 inhibitor afatinib to the proband and achieved partial response. These lung cancers arising from germline mutations of receptor tyrosine kinases such as EGFR and HER2 may have different features from those with sporadic mutations.
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Affiliation(s)
- Hiromasa Yamamoto
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan
| | - Shinichi Toyooka
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
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Koeller DR, Chen R, Oxnard GR. Hereditary Lung Cancer Risk: Recent Discoveries and Implications for Genetic Counseling and Testing. CURRENT GENETIC MEDICINE REPORTS 2018. [DOI: 10.1007/s40142-018-0140-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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37
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Bossé Y, Amos CI. A Decade of GWAS Results in Lung Cancer. Cancer Epidemiol Biomarkers Prev 2018; 27:363-379. [PMID: 28615365 PMCID: PMC6464125 DOI: 10.1158/1055-9965.epi-16-0794] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/06/2016] [Accepted: 04/20/2017] [Indexed: 01/03/2023] Open
Abstract
Genome-wide association studies (GWAS) were successful to identify genetic factors robustly associated with lung cancer. This review aims to synthesize the literature in this field and accelerate the translation of GWAS discoveries into results that are closer to clinical applications. A chronologic presentation of published GWAS on lung cancer susceptibility, survival, and response to treatment is presented. The most important results are tabulated to provide a concise overview in one read. GWAS have reported 45 lung cancer susceptibility loci with varying strength of evidence and highlighted suspected causal genes at each locus. Some genetic risk loci have been refined to more homogeneous subgroups of lung cancer patients in terms of histologic subtypes, smoking status, gender, and ethnicity. Overall, these discoveries are an important step for future development of new therapeutic targets and biomarkers to personalize and improve the quality of care for patients. GWAS results are on the edge of offering new tools for targeted screening in high-risk individuals, but more research is needed if GWAS are to pay off the investment. Complementary genomic datasets and functional studies are needed to refine the underlying molecular mechanisms of lung cancer preliminarily revealed by GWAS and reach results that are medically actionable. Cancer Epidemiol Biomarkers Prev; 27(4); 363-79. ©2018 AACRSee all articles in this CEBP Focus section, "Genome-Wide Association Studies in Cancer."
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Affiliation(s)
- Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec, Canada.
- Department of Molecular Medicine, Laval University, Quebec, Canada
| | - Christopher I Amos
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
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Abstract
Osteosarcoma (OS) is the most common primary malignant bone tumor mainly occurring in children and adolescents. In past decades, studies revealed that PARK2 was a vital tumor suppressor gene in many malignant solid tumors. However, the role of PARK2 in OS remains largely unclear. Therefore, we assessed PARK2 expression in OS tissue and adjacent non-tumor tissues by immunohistochemical (IHC) analysis, and evaluated PARK2 mRNA expression in OS cell lines by real-time PCR analysis. The HOS and U2OS cell lines were employed to establish a PARK2 overexpression model. Using this model, we investigated the potential role of PARK2 in OS and explored the underlying molecular mechanisms. Our study showed PARK2 was downregulated in OS tissue and cell lines, which was significantly associated with higher tumor stage (P < 0.05). Overexpression of PARK2 arrested the cell cycle, inhibited cell proliferation, migration, and invasion, induced cell apoptosis, and reduced tube formation in vitro. Moreover, overexpression of PARK2 significantly suppressed tumor growth and angiogenesis in vivo. Additionally, PARK2 negatively regulated OS development through the JAK2/STAT3/VEGF pathway. Our findings demonstrate that PARK2 is a tumor suppressor gene that may negatively affect OS growth and angiogenesis via partly inhibiting the JAK2/STAT3/VEGF signaling pathway.
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Bennett CW, Berchem G, Kim YJ, El-Khoury V. Cell-free DNA and next-generation sequencing in the service of personalized medicine for lung cancer. Oncotarget 2018; 7:71013-71035. [PMID: 27589834 PMCID: PMC5342606 DOI: 10.18632/oncotarget.11717] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/11/2016] [Indexed: 12/13/2022] Open
Abstract
Personalized medicine has emerged as the future of cancer care to ensure that patients receive individualized treatment specific to their needs. In order to provide such care, molecular techniques that enable oncologists to diagnose, treat, and monitor tumors are necessary. In the field of lung cancer, cell free DNA (cfDNA) shows great potential as a less invasive liquid biopsy technique, and next-generation sequencing (NGS) is a promising tool for analysis of tumor mutations. In this review, we outline the evolution of cfDNA and NGS and discuss the progress of using them in a clinical setting for patients with lung cancer. We also present an analysis of the role of cfDNA as a liquid biopsy technique and NGS as an analytical tool in studying EGFR and MET, two frequently mutated genes in lung cancer. Ultimately, we hope that using cfDNA and NGS for cancer diagnosis and treatment will become standard for patients with lung cancer and across the field of oncology.
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Affiliation(s)
- Catherine W Bennett
- Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
| | - Guy Berchem
- Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg.,Centre Hospitalier de Luxembourg, L-1210 Luxembourg, Luxembourg
| | - Yeoun Jin Kim
- Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
| | - Victoria El-Khoury
- Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
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Lee S, She J, Deng B, Kim J, de Andrade M, Na J, Sun Z, Wampfler JA, Cunningham JM, Wu Y, Limper AH, Aubry MC, Wendt C, Biterman P, Yang P, Lou Z. Multiple-level validation identifies PARK2 in the development of lung cancer and chronic obstructive pulmonary disease. Oncotarget 2018; 7:44211-44223. [PMID: 27329585 PMCID: PMC5190090 DOI: 10.18632/oncotarget.9954] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 05/09/2016] [Indexed: 12/31/2022] Open
Abstract
An important precursor to lung cancer development is chronic obstructive pulmonary disease (COPD), independent of exposure to tobacco smoke. Both diseases are associated with increased host susceptibility, inflammation, and genomic instability. However, validation of the candidate genes and functional confirmation to test shared genetic contribution and cellular mechanisms to the development of lung cancer in patients with COPD remains underexplored. Here, we show that loss of PARK2 (encoding Parkin) increases the expression of proinflammation factors as well as nuclear NF-κB localization, suggesting a role of PARK2 loss in inflammation. Additional exploration showed that PARK2 deficiency promotes genomic instability and cell transformation. This role of PARK2 in inflammation and chromosome instability provides a potential link among Parkin, COPD and lung cancer. A further comprehensive validation of 114 informative single nucleotide polymorphism (SNP) variants of PARK2, in 2,484 cases and controls with well-defined lung cancer and COPD phenotypes, found rs577876, rs6455728 and rs9346917 (p<0.01) to be significantly associated with lung cancer development in people with COPD. Our findings support the evidence that PARK2 might have a tumor suppressor role in the development of COPD and lung cancer.
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Affiliation(s)
- SeungBaek Lee
- Division of Oncology Research, Mayo Clinic, Rochester, MN, USA
| | - Jun She
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, China.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Bo Deng
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.,Department of Thoracic Surgery, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing, China
| | - JungJin Kim
- Division of Oncology Research, Mayo Clinic, Rochester, MN, USA
| | - Mariza de Andrade
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Jie Na
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Zhifu Sun
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Jason A Wampfler
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | | | - Yanhong Wu
- Genomics Shared Resource, Mayo Clinic, Rochester, MN, USA
| | - Andrew H Limper
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Chris Wendt
- Department of Medicine, Pulmonary Division, University of Minnesota, Minneapolis, MN, USA.,Department of Medicine, Pulmonary Section, Minneapolis VA Medical Center, Minneapolis, MN, USA
| | - Peter Biterman
- Department of Medicine, Pulmonary Division, University of Minnesota, Minneapolis, MN, USA
| | - Ping Yang
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Zhenkun Lou
- Division of Oncology Research, Mayo Clinic, Rochester, MN, USA
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Parry EM, Gable DL, Stanley SE, Khalil SE, Antonescu V, Florea L, Armanios M. Germline Mutations in DNA Repair Genes in Lung Adenocarcinoma. J Thorac Oncol 2017; 12:1673-1678. [PMID: 28843361 DOI: 10.1016/j.jtho.2017.08.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 07/31/2017] [Accepted: 08/05/2017] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Although lung cancer is generally thought to be environmentally provoked, anecdotal familial clustering has been reported, suggesting that there may be genetic susceptibility factors. We systematically tested whether germline mutations in eight candidate genes may be risk factors for lung adenocarcinoma. METHODS We studied lung adenocarcinoma cases for which germline sequence data had been generated as part of The Cancer Genome Atlas project but had not been previously analyzed. We selected eight genes, ATM serine/threonine kinase gene (ATM), BRCA2, DNA repair associated gene (BRCA2), checkpoint kinase 2 gene (CHEK2), EGFR, parkin RBR E3 ubiquitin protein ligase gene (PARK2), telomerase reverse transcriptase gene (TERT), tumor protein p53 gene (TP53), and Yes associated protein 1 gene (YAP1), on the basis of prior anecdotal association with lung cancer or genome-wide association studies. RESULTS Among 555 lung adenocarcinoma cases, we detected 14 pathogenic mutations in five genes; they occurred at a frequency of 2.5% and represented an OR of 66 (95% confidence interval: 33-125, p < 0.0001 [chi-square test]). The mutations fell most commonly in ATM (50%), followed by TP53, BRCA2, EGFR, and PARK2. Most (86%) of these variants had been reported in other familial cancer syndromes. Another 12 cases (2%) carried ultrarare variants that were predicted to be deleterious by three protein prediction programs; these most frequently involved ATM and BRCA2. CONCLUSIONS A subset of patients with lung adenocarcinoma, at least 2.5% to 4.5%, carry germline variants that have been linked to cancer risk in Mendelian syndromes. The genes fall most frequently in DNA repair pathways. Our data indicate that patients with lung adenocarcinoma, similar to other solid tumors, include a subset of patients with inherited susceptibility.
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Affiliation(s)
- Erin M Parry
- Osler Medical Housestaff Training Program, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Dustin L Gable
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Susan E Stanley
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sara E Khalil
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Valentin Antonescu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Liliana Florea
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Mary Armanios
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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Abstract
OBJECTIVE To review current risk factors for lung cancer, identify screening and early detection guidelines while describing new approaches that use genomic technologies. DATA SOURCES Published scientific literature, clinical literature, and published lung cancer screening guidelines from the United States and Canada. CONCLUSION Nurses are caring for lung cancer patients who, historically, do not live for long periods after diagnosis. Research is revealing promising screening methodologies that can detect lung cancer 1 to 4 years earlier than the current approaches. IMPLICATIONS FOR NURSING PRACTICE Current knowledge about screening for lung cancer is a vital tool for nurses working with persons at high risk for this potentially aggressive and life-threatening malignancy. While old methods remain the standard of care, new detection methods use a variety of genomic-based technologies. These developing approaches emphasize the need for nurses at all levels of practice to have a working knowledge of genetics to educate patients and conference with colleagues.
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Ni H, Zhou Z, Jiang B, Yuan X, Cao X, Huang G, Li Y. Inactivation of parkin by promoter methylation correlated with lymph node metastasis and genomic instability in nasopharyngeal carcinoma. Tumour Biol 2017; 39:1010428317695025. [PMID: 28351314 DOI: 10.1177/1010428317695025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This study aimed to investigate the inactivation of the parkin gene by promoter methylation and its relationship with genome instability in nasopharyngeal carcinoma. Parkin was considered as a tumor suppressor gene in various types of cancers. However, its role in nasopharyngeal carcinoma is unexplored. Genomic instabilities were detected in nasopharyngeal carcinoma tissues by the random amplified polymorphic DNA. The methylation-specific polymerase chain reaction, semi-quantitative reverse transcription polymerase chain reaction, and immunohistochemical analysis were used to detect methylation and mRNA and protein expression of parkin in 54 cases of nasopharyngeal carcinoma tissues and 16 cases of normal nasopharyngeal epithelia tissues, and in 5 nasopharyngeal carcinoma cell lines (CNE1, CNE2, TWO3, C666, and HONE1) and 1 normal nasopharyngeal epithelia cell line (NP69). mRNA expression of parkin in CNE1 and CNE2 was analyzed before and after methyltransferase inhibitor 5-aza-2-deoxycytidine treatment. The relationship between promoter methylation and mRNA expression, demethylation and mRNA expression, and mRNA and protein expression of the gene and clinical factors and genomic instabilities were analyzed. The mRNA and protein expression levels were significantly reduced in 54 cases of human nasopharyngeal carcinoma compared with 16 cases of normal nasopharyngeal epithelia. Parkin-methylated cases showed significantly lower mRNA and protein expression levels compared with unmethylated cases. After 5-aza-2-deoxycytidine treatment, parkin mRNA expression was restored in CNE1 and CNE2; 92.59% (50/54) of nasopharyngeal carcinoma demonstrated genomic instability. Parkin is frequently inactivated by promoter methylation, and its mRNA and protein expression correlate with lymph node metastasis and genomic instability. Parkin deficiency probably promotes tumorigenesis in nasopharyngeal carcinoma.
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Affiliation(s)
- Haifeng Ni
- Department of Otolaryngology, Hangzhou First People’s Hospital, Nanjing Medical University, Hangzhou, China
| | - Zhen Zhou
- Department of Otolaryngology, Hangzhou First People’s Hospital, Nanjing Medical University, Hangzhou, China
| | - Bo Jiang
- Department of Otolaryngology, Hangzhou First People’s Hospital, Nanjing Medical University, Hangzhou, China
| | - Xiaoyang Yuan
- Department of Otolaryngology, Hangzhou First People’s Hospital, Nanjing Medical University, Hangzhou, China
| | - Xiaolin Cao
- Department of Otolaryngology, Hangzhou First People’s Hospital, Nanjing Medical University, Hangzhou, China
| | - Guangwu Huang
- Department of Otolaryngology, First Affiliated Hospital, Guangxi Medical University, Nanning, China
| | - Yong Li
- Department of Otolaryngology, Hangzhou First People’s Hospital, Nanjing Medical University, Hangzhou, China
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44
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Genetic susceptibility variants for lung cancer: replication study and assessment as expression quantitative trait loci. Sci Rep 2017; 7:42185. [PMID: 28181565 PMCID: PMC5299838 DOI: 10.1038/srep42185] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/06/2017] [Indexed: 12/13/2022] Open
Abstract
Many single nucleotide polymorphisms (SNPs) have been associated with lung cancer but lack confirmation and functional characterization. We retested the association of 56 candidate SNPs with lung adenocarcinoma risk and overall survival in a cohort of 823 Italian patients and 779 healthy controls, and assessed their function as expression quantitative trait loci (eQTLs). In the replication study, eight SNPs (rs401681, rs3019885, rs732765, rs2568494, rs16969968, rs6495309, rs11634351, and rs4105144) associated with lung adenocarcinoma risk and three (rs9557635, rs4105144, and rs735482) associated with survival. Five of these SNPs acted as cis-eQTLs, being associated with the transcription of IREB2 (rs2568494, rs16969968, rs11634351, rs6495309), PSMA4 (rs6495309) and ERCC1 (rs735482), out of 10,821 genes analyzed in lung. For these three genes, we obtained experimental evidence of differential allelic expression in lung tissue, pointing to the existence of in-cis genomic variants that regulate their transcription. These results suggest that these SNPs exert their effects on cancer risk/outcome through the modulation of mRNA levels of their target genes.
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Musolf AM, Simpson CL, de Andrade M, Mandal D, Gaba C, Yang P, Li Y, You M, Kupert EY, Anderson MW, Schwartz AG, Pinney SM, Amos CI, Bailey-Wilson JE. Familial Lung Cancer: A Brief History from the Earliest Work to the Most Recent Studies. Genes (Basel) 2017; 8:genes8010036. [PMID: 28106732 PMCID: PMC5295030 DOI: 10.3390/genes8010036] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 12/29/2016] [Accepted: 01/11/2017] [Indexed: 02/06/2023] Open
Abstract
Lung cancer is the deadliest cancer in the United States, killing roughly one of four cancer patients in 2016. While it is well-established that lung cancer is caused primarily by environmental effects (particularly tobacco smoking), there is evidence for genetic susceptibility. Lung cancer has been shown to aggregate in families, and segregation analyses have hypothesized a major susceptibility locus for the disease. Genetic association studies have provided strong evidence for common risk variants of small-to-moderate effect. Rare and highly penetrant alleles have been identified by linkage studies, including on 6q23-25. Though not common, some germline mutations have also been identified via sequencing studies. Ongoing genomics studies aim to identify additional high penetrance germline susceptibility alleles for this deadly disease.
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Affiliation(s)
- Anthony M Musolf
- National Human Genome Research Institute, National Institutes of Health, Baltimore, MD 21224, USA.
| | - Claire L Simpson
- National Human Genome Research Institute, National Institutes of Health, Baltimore, MD 21224, USA.
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38103, USA.
| | | | - Diptasri Mandal
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA.
| | - Colette Gaba
- Department of Medicine, University of Toledo Dana Cancer Center, Toledo, OH 43604, USA.
| | - Ping Yang
- Mayo Clinic, Rochester, MN 55904, USA.
| | - Yafang Li
- Geisel School of Medicine, Dartmouth College, Lebanon, NH 03766, USA.
| | - Ming You
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53202, USA.
| | - Elena Y Kupert
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53202, USA.
| | | | - Ann G Schwartz
- Karmanos Cancer Institute, Wayne State University, Detroit, MI 48226, USA.
| | - Susan M Pinney
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45202, USA.
| | | | - Joan E Bailey-Wilson
- National Human Genome Research Institute, National Institutes of Health, Baltimore, MD 21224, USA.
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Pan-Cancer Analysis Links PARK2 to BCL-XL-Dependent Control of Apoptosis. Neoplasia 2016; 19:75-83. [PMID: 28038320 PMCID: PMC5198112 DOI: 10.1016/j.neo.2016.12.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 12/04/2016] [Accepted: 12/06/2016] [Indexed: 11/23/2022] Open
Abstract
Mutation of the PARK2 gene can promote both Parkinson's Disease and cancer, yet the underlying mechanisms of how PARK2 controls cellular physiology is incompletely understood. Here, we show that the PARK2 tumor suppressor controls the apoptotic regulator BCL-XL and modulates programmed cell death. Analysis of approximately 10,000 tumor genomes uncovers a striking pattern of mutual exclusivity between PARK2 genetic loss and amplification of BCL2L1, implicating these genes in a common pathway. PARK2 directly binds to and ubiquitinates BCL-XL. Inactivation of PARK2 leads to aberrant accumulation of BCL-XL both in vitro and in vivo, and cancer-specific mutations in PARK2 abrogate the ability of the ubiquitin E3 ligase to target BCL-XL for degradation. Furthermore, PARK2 modulates mitochondrial depolarization and apoptosis in a BCL-XL-dependent manner. Thus, like genes at the nodal points of growth arrest pathways such as p53, the PARK2 tumor suppressor is able to exert its antiproliferative effects by regulating both cell cycle progression and programmed cell death.
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Xie X, Luo X, Xie M, Liu Y, Wu T. Risk of lung cancer in Parkinson's disease. Oncotarget 2016; 7:77319-77325. [PMID: 27801674 PMCID: PMC5363588 DOI: 10.18632/oncotarget.12964] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/14/2016] [Indexed: 01/11/2023] Open
Abstract
Recently, growing evidence has revealed the significant association between Parkinson's disease (PD) and cancer. However, controversy still exists concerning the association between PD and lung cancer. A comprehensive article search for relevant studies published was performed using the following online databases: PubMed, Web of Science and Embase up to August 31, 2016. The pooled risk ratio (RR) and their 95 % confidence intervals (CI) were calculated using the method of inverse variance with the random-effects model. Fifteen studies comprising 348,780 PD patients were included in this study. The pooled result indicated that patients with PD were significantly associated with a decreased risk of lung cancer (RR: 0.53, 95% CI: 0.41-0.70, P < 0.001). In addition, subgroup analyses performed in Western population also confirmed the significant inverse relationship between PD and risk of lung cancer (RR: 0.48, 95% CI: 0.39-0.60, P < 0.001). In the subgroup analysis, a reduced risk of lung cancer in PD patients from Western population was consistent regardless of study design, gender, or study quality. In conclusion, PD patients were significantly associated with a reduced risk of lung cancer in Western population. The relationship between them in Asian population needs to be confirmed by future studies.
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Affiliation(s)
- Xin Xie
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang City 110001, PR China
| | - Xiaoguang Luo
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang City 110001, PR China
| | - Mingliang Xie
- Clinics of the People's Armed Police Command College, Tianjin City, 300000, PR China
| | - Yang Liu
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang City 110001, PR China
| | - Ting Wu
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang City 110001, PR China
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Tang CF, Lu MK, Muo CH, Tsai CH, Kao CH. Increased risk of brain tumor in patients with Parkinson's disease: a nationwide cohort study in Taiwan. Acta Neurol Scand 2016; 134:148-53. [PMID: 26508469 DOI: 10.1111/ane.12524] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2015] [Indexed: 12/29/2022]
Abstract
OBJECTIVES Parkinson's disease (PD) is a neurodegenerative disease. A decreased risk of cancer, except for melanoma, has been observed in patients with PD. The aim of this study was to evaluate the association between brain tumor and PD in a Taiwanese population. MATERIALS AND METHODS We used data from the National Health Insurance program of Taiwan. The PD cohort contained 2998 patients, and each patient was frequency-matched, based on age and sex, with 4 people without PD, who were randomly selected from the general population. Cox's proportional hazard regression analysis was conducted to estimate the effects of PD on the risk of brain tumor. RESULTS The risk of developing brain tumor was significantly higher in patients with PD than in those without PD (adjusted hazard ratio = 2.11; 95% confidence interval (CI) = 1.24-3.59), and benign brain tumor exhibited a particularly elevated risk of 2.16-fold (95% CI = 1.26-3.68). The hazard ratio (HR) for developing a benign brain tumor was higher in female patients with PD than in female patients without PD, with the risk being 2.65-fold (95% CI = 1.30-5.43). An analysis of the two age groups, 50-64 years and ≥65 years, showed that the HR of only the 50-64-year group was significantly higher between the PD and non-PD groups (HR = 2.77, 95% CI = 1.07-7.14). CONCLUSION The present study showed that Taiwanese patients with PD are at a higher risk of developing brain tumor than the general population. The exact underlying etiologies require further investigation.
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Affiliation(s)
- C.-F. Tang
- Department of Neurology; China Medical University Hospital; Taichung Taiwan
- School of Medicine; Medical College; China Medical University; Taichung Taiwan
| | - M.-K. Lu
- Department of Neurology; China Medical University Hospital; Taichung Taiwan
- School of Medicine; Medical College; China Medical University; Taichung Taiwan
- Graduate Institute of Neural and Cognitive Sciences; China Medical University; Taichung Taiwan
| | - C.-H. Muo
- School of Medicine; Medical College; China Medical University; Taichung Taiwan
- Management Office for Health Data; China Medical University Hospital; Taichung Taiwan
| | - C.-H. Tsai
- Department of Neurology; China Medical University Hospital; Taichung Taiwan
- School of Medicine; Medical College; China Medical University; Taichung Taiwan
- Graduate Institute of Neural and Cognitive Sciences; China Medical University; Taichung Taiwan
| | - C.-H. Kao
- Department of Nuclear Medicine and PET Center; China Medical University Hospital; Taichung Taiwan
- Graduate Institute of Clinical Medical Science and School of Medicine; College of Medicine; China Medical University; Taichung Taiwan
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Levin L, Srour S, Gartner J, Kapitansky O, Qutob N, Dror S, Golan T, Dayan R, Brener R, Ziv T, Khaled M, Schueler-Furman O, Samuels Y, Levy C. Parkin Somatic Mutations Link Melanoma and Parkinson's Disease. J Genet Genomics 2016; 43:369-79. [DOI: 10.1016/j.jgg.2016.05.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 12/31/2022]
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Xiong D, Wang Y, You M. PARK2 gene and familial lung cancer: what is the link? Future Oncol 2016; 11:1707-10. [PMID: 26075437 DOI: 10.2217/fon.15.79] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Donghai Xiong
- Department of Pharmacology & Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Yian Wang
- Department of Pharmacology & Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ming You
- Department of Pharmacology & Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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