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Malfait J, Wan J, Spicuglia S. Epromoters are new players in the regulatory landscape with potential pleiotropic roles. Bioessays 2023; 45:e2300012. [PMID: 37246247 DOI: 10.1002/bies.202300012] [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: 01/17/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/30/2023]
Abstract
Precise spatiotemporal control of gene expression during normal development and cell differentiation is achieved by the combined action of proximal (promoters) and distal (enhancers) cis-regulatory elements. Recent studies have reported that a subset of promoters, termed Epromoters, works also as enhancers to regulate distal genes. This new paradigm opened novel questions regarding the complexity of our genome and raises the possibility that genetic variation within Epromoters has pleiotropic effects on various physiological and pathological traits by differentially impacting multiple proximal and distal genes. Here, we discuss the different observations pointing to an important role of Epromoters in the regulatory landscape and summarize the evidence supporting a pleiotropic impact of these elements in disease. We further hypothesize that Epromoter might represent a major contributor to phenotypic variation and disease.
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Affiliation(s)
- Juliette Malfait
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, LIGUE, Marseille, France
| | - Jing Wan
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, LIGUE, Marseille, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, LIGUE, Marseille, France
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2
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Alsheikh AJ, Wollenhaupt S, King EA, Reeb J, Ghosh S, Stolzenburg LR, Tamim S, Lazar J, Davis JW, Jacob HJ. The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases. BMC Med Genomics 2022; 15:74. [PMID: 35365203 PMCID: PMC8973751 DOI: 10.1186/s12920-022-01216-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/17/2022] [Indexed: 02/08/2023] Open
Abstract
Background The remarkable growth of genome-wide association studies (GWAS) has created a critical need to experimentally validate the disease-associated variants, 90% of which involve non-coding variants. Methods To determine how the field is addressing this urgent need, we performed a comprehensive literature review identifying 36,676 articles. These were reduced to 1454 articles through a set of filters using natural language processing and ontology-based text-mining. This was followed by manual curation and cross-referencing against the GWAS catalog, yielding a final set of 286 articles. Results We identified 309 experimentally validated non-coding GWAS variants, regulating 252 genes across 130 human disease traits. These variants covered a variety of regulatory mechanisms. Interestingly, 70% (215/309) acted through cis-regulatory elements, with the remaining through promoters (22%, 70/309) or non-coding RNAs (8%, 24/309). Several validation approaches were utilized in these studies, including gene expression (n = 272), transcription factor binding (n = 175), reporter assays (n = 171), in vivo models (n = 104), genome editing (n = 96) and chromatin interaction (n = 33). Conclusions This review of the literature is the first to systematically evaluate the status and the landscape of experimentation being used to validate non-coding GWAS-identified variants. Our results clearly underscore the multifaceted approach needed for experimental validation, have practical implications on variant prioritization and considerations of target gene nomination. While the field has a long way to go to validate the thousands of GWAS associations, we show that progress is being made and provide exemplars of validation studies covering a wide variety of mechanisms, target genes, and disease areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01216-w.
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Affiliation(s)
- Ammar J Alsheikh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA.
| | - Sabrina Wollenhaupt
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Emily A King
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jonas Reeb
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Sujana Ghosh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | | | - Saleh Tamim
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jozef Lazar
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - J Wade Davis
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Howard J Jacob
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
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Gong H, Ren J, Xu J, Zhong X, Abudureheman Z, Yilamujiang S, Xie C, Ma T, Li F, Tang L, Xu A, Li L. SMAD3 rs36221701 T>C polymorphism impacts COPD susceptibility in the Kashi population. Gene 2022; 808:145970. [PMID: 34547372 DOI: 10.1016/j.gene.2021.145970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/14/2021] [Indexed: 01/20/2023]
Abstract
Small mother against decapentaplegic (SMAD) family member 3 (SMAD3) is well correlated with the inflammatory response of chronic obstructive pulmonary disease (COPD). A previous study indicated that the single nucleotide polymorphism (SNP) rs36221701 of SMAD3 was related to the risk of inflammatory disease. Hence, given the pathogenesis of COPD is intently associated with smoking and gene polymorphism, this study aims to analyze the relationship between SMAD3 rs36221701 and COPD susceptibility, and to explore whether the interaction is related to smoking status. We studied the association between the rs36221701 and rs34307601 of SMAD3 and COPD susceptibility, a total of 541 COPD patients and 534 controls of the Uyghur population were recruited at the First People's Hospital and the village of Kashi. The interrelation of the two SNPs with the risk of COPD was determined by calculating odds ratio (OR) and 95% confidence interval (95% CI). We found a significant association between the rs36221701 and COPD risk in the non-smoking population. TC genotype showed a significant decreased association with COPD risk (OR = 0.59, 95% CI = 0.41-0.83, P < 0.05), but CC genotype can increased the COPD risk (OR > 1, P < 0.05). In addition, COPD susceptibility was not related to the genetic variations in the rs34307601 (P > 0.05). In conclusion, we confirmed that the SMAD3 rs36221701 may be associated with COPD susceptibility in the Chinese Uyghur population, especially among non-smokers. Our data provide new light for the relationship between SMAD3 gene polymorphisms and COPD susceptibility in the Chinese Uyghur population.
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Affiliation(s)
- Hui Gong
- Clinical Research Center of Infectious Diseases (Pulmonary Tuberculosis), First People's Hospital of Kashi, Kashi, Xinjiang, PR China
| | - Jie Ren
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashi, Kashi, Xinjiang, PR China
| | - Jingran Xu
- Clinical Research Center of Infectious Diseases (Pulmonary Tuberculosis), First People's Hospital of Kashi, Kashi, Xinjiang, PR China
| | - Xuemei Zhong
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashi, Kashi, Xinjiang, PR China
| | - Zulipikaer Abudureheman
- Clinical Research Center of Infectious Diseases (Pulmonary Tuberculosis), First People's Hospital of Kashi, Kashi, Xinjiang, PR China
| | - Subinuer Yilamujiang
- Clinical Research Center of Infectious Diseases (Pulmonary Tuberculosis), First People's Hospital of Kashi, Kashi, Xinjiang, PR China
| | - Chengxin Xie
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashi, Kashi, Xinjiang, PR China
| | - Tao Ma
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashi, Kashi, Xinjiang, PR China
| | - Feifei Li
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashi, Kashi, Xinjiang, PR China
| | - Lifeng Tang
- Clinical Research Center of Infectious Diseases (Pulmonary Tuberculosis), First People's Hospital of Kashi, Kashi, Xinjiang, PR China
| | - Aimin Xu
- Department of Clinical Laboratory, First People's Hospital of Kashi, Kashi, Xinjiang, PR China.
| | - Li Li
- Clinical Research Center of Infectious Diseases (Pulmonary Tuberculosis), First People's Hospital of Kashi, Kashi, Xinjiang, PR China; Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashi, Kashi, Xinjiang, PR China.
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Hu Y, Liang D, Chen X, Chen L, Bai J, Li H, Yin C, Zhong W. [MiR-671-5p negatively regulates SMAD3 to inhibit migration and invasion of osteosarcoma cells]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:1562-1568. [PMID: 34755673 DOI: 10.12122/j.issn.1673-4254.2021.10.16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE To explore the role of miR-671-5p in regulating the migration and invasion of osteosarcoma and the underlying mechanisms. METHODS The differentially expressed microRNAs (miRNAs) in osteosarcoma were screened in the NCBI online database, and the target proteins of these miRNAs were predicted and their functions were analyzed. Osteosarcoma cells were transfected with a plasmid overexpressing miR-671-5p, and the transfection efficiency was assessed using quantitative real-time PCR (qRT-PCR). The changes in the migration and invasion of the transfected cells were examined with Transwell assay, and the expressions of proteins related with epithelial-mesenchymal transition (EMT) were detected using Western blotting. Dual-luciferase reporter assay was performed to determine whether the 3'UTR of SMAD3 contained a targeted binding site of miR-671-5p. RESULTS MiR-671-5p was significantly down-regulated in both osteosarcoma tissues and osteosarcoma cells (P < 0.05). The osteosarcoma cells overexpressing miR-671-5p showed significantly reduced migration and invasion abilities (P < 0.05) with obviously lowered expressions of EMT-related proteins (P < 0.05). SMAD3 was highly expressed in osteosarcoma cells (P < 0.05), and dual-luciferase reporter assay confirmed the presence of a targeted binding site between miR-671-5p and the 3'UTR of SMAD3 (P < 0.05). In osteosarcoma cells transfected with a SMAD3-overexpressing plasmid (P < 0.05), the high expression of SMAD3 significantly inhibited by miR-671-5p overexpression (P < 0.05). Transwell assay demonstrated that SMAD3 overexpression significantly promoted the migration and invasion of osteosarcoma cells (P < 0.05), and while miR-671-5p overexpression obviously reversed this effect (P < 0.05). CONCLUSION MiR-671-5p can inhibit the invasion and migration of osteosarcoma cells by negatively regulating SMAD3.
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Affiliation(s)
- Y Hu
- Department of Pathology, Weifang Medical University, Weifang 261053, China
| | - D Liang
- First Department of Joint Surgery, Weifang Medical University, Weifang 261053, China
| | - X Chen
- Department of Pathology, Weifang Medical University, Weifang 261053, China
| | - L Chen
- Department of Pathology, Weifang Medical University, Weifang 261053, China
| | - J Bai
- Department of Pathology, Weifang Medical University, Weifang 261053, China
| | - H Li
- Medicine Research Center, Weifang Medical University, Weifang 261053, China
| | - C Yin
- College of Nursing, Weifang Medical University, Weifang 261053, China
| | - W Zhong
- First Department of Joint Surgery, Weifang Medical University, Weifang 261053, China
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Kunc V, Kléma J. On transformative adaptive activation functions in neural networks for gene expression inference. PLoS One 2021; 16:e0243915. [PMID: 33444316 PMCID: PMC7808640 DOI: 10.1371/journal.pone.0243915] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 12/01/2020] [Indexed: 11/19/2022] Open
Abstract
Gene expression profiling was made more cost-effective by the NIH LINCS program that profiles only ∼1, 000 selected landmark genes and uses them to reconstruct the whole profile. The D-GEX method employs neural networks to infer the entire profile. However, the original D-GEX can be significantly improved. We propose a novel transformative adaptive activation function that improves the gene expression inference even further and which generalizes several existing adaptive activation functions. Our improved neural network achieves an average mean absolute error of 0.1340, which is a significant improvement over our reimplementation of the original D-GEX, which achieves an average mean absolute error of 0.1637. The proposed transformative adaptive function enables a significantly more accurate reconstruction of the full gene expression profiles with only a small increase in the complexity of the model and its training procedure compared to other methods.
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Affiliation(s)
- Vladimír Kunc
- Department of Computer Science, Czech Technical University in Prague, Faculty of Electrical Engineering, Prague, Czech Republic
| | - Jiří Kléma
- Department of Computer Science, Czech Technical University in Prague, Faculty of Electrical Engineering, Prague, Czech Republic
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Kunc V, Kléma J. On tower and checkerboard neural network architectures for gene expression inference. BMC Genomics 2020; 21:454. [PMID: 33327945 PMCID: PMC7739475 DOI: 10.1186/s12864-020-06821-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/12/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND One possible approach how to economically facilitate gene expression profiling is to use the L1000 platform which measures the expression of ∼1,000 landmark genes and uses a computational method to infer the expression of another ∼10,000 genes. One such method for the gene expression inference is a D-GEX which employs neural networks. RESULTS We propose two novel D-GEX architectures that significantly improve the quality of the inference by increasing the capacity of a network without any increase in the number of trained parameters. The architectures partition the network into individual towers. Our best proposed architecture - a checkerboard architecture with a skip connection and five towers - together with minor changes in the training protocol improves the average mean absolute error of the inference from 0.134 to 0.128. CONCLUSIONS Our proposed approach increases the gene expression inference accuracy without increasing the number of weights of the model and thus without increasing the memory footprint of the model that is limiting its usage.
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Affiliation(s)
- Vladimír Kunc
- Department of Computer Science, Karlovo náměstí 13, Prague, 121 35 Czech Republic
| | - Jiří Kléma
- Department of Computer Science, Karlovo náměstí 13, Prague, 121 35 Czech Republic
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Comiskey DF, He H, Liyanarachchi S, Sheikh MS, Hendrickson IV, Yu L, Brock PL, de la Chapelle A. Characterizing the function of EPB41L4A in the predisposition to papillary thyroid carcinoma. Sci Rep 2020; 10:19984. [PMID: 33203992 PMCID: PMC7672090 DOI: 10.1038/s41598-020-76606-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/20/2020] [Indexed: 12/21/2022] Open
Abstract
Papillary thyroid carcinoma (PTC) is the most common histotype of thyroid carcinoma. The heritability of PTC is high compared to other cancers, but its underlying causes are unknown. A recent genome-wide association study revealed the association of a variant at the 5q22 locus, rs73227498, with PTC predisposition. We report that rs17134155, a variant in high linkage disequilibrium with rs73227498, is located in an enhancer region downstream of coding transcripts of EPB41L4A. Rs17134155 showed significant enhancer activity in luciferase assays, and haplotypes containing the protective allele of this variant conferred a significantly lower risk of PTC. While the index SNP, rs73227498, acted as a significant cis-eQTL for expression of EPB41L4A, rs17134155 was a significant cis-sQTL for the alternative splicing of a non-coding transcript of EPB41L4A, called EPB41L4A-203. We also performed knockdown of EPB41L4A followed by microarray analysis. Some of the top differentially-expressed genes were represented among regulators of the WNT/β-catenin signaling pathway. Our results indicate that an enhancer region at 5q22 regulates the expression and splicing of EPB41L4A transcripts. We also provide evidence that EPB41L4A expression is involved in regulating growth and differentiation pathways, suggesting that decreased expression of EPB41L4A is a mechanism in the predisposition to PTC.
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Affiliation(s)
- Daniel F Comiskey
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, Comprehensive Cancer Center, College of Medicine, The Ohio State University Wexner Medical Center, 804 Biomedical Research Tower, 460 W 12th Ave., Columbus, OH, 43210, USA
| | - Huiling He
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, Comprehensive Cancer Center, College of Medicine, The Ohio State University Wexner Medical Center, 804 Biomedical Research Tower, 460 W 12th Ave., Columbus, OH, 43210, USA
| | - Sandya Liyanarachchi
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, Comprehensive Cancer Center, College of Medicine, The Ohio State University Wexner Medical Center, 804 Biomedical Research Tower, 460 W 12th Ave., Columbus, OH, 43210, USA
| | - Mehek S Sheikh
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, Comprehensive Cancer Center, College of Medicine, The Ohio State University Wexner Medical Center, 804 Biomedical Research Tower, 460 W 12th Ave., Columbus, OH, 43210, USA
| | - Isabella V Hendrickson
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, Comprehensive Cancer Center, College of Medicine, The Ohio State University Wexner Medical Center, 804 Biomedical Research Tower, 460 W 12th Ave., Columbus, OH, 43210, USA
| | - Lianbo Yu
- Center for Biostatistics, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - Pamela L Brock
- Department of Internal Medicine, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - Albert de la Chapelle
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, Comprehensive Cancer Center, College of Medicine, The Ohio State University Wexner Medical Center, 804 Biomedical Research Tower, 460 W 12th Ave., Columbus, OH, 43210, USA.
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Morillo-Bernal J, Fernández LP, Santisteban P. FOXE1 regulates migration and invasion in thyroid cancer cells and targets ZEB1. Endocr Relat Cancer 2020; 27:137-151. [PMID: 31846430 PMCID: PMC6993207 DOI: 10.1530/erc-19-0156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/16/2019] [Indexed: 12/17/2022]
Abstract
FOXE1 is a thyroid-specific transcription factor essential for thyroid gland development and maintenance of the differentiated state. Interestingly, a strong association has been recently described between FOXE1 expression and susceptibility to thyroid cancer, but little is known about the mechanisms underlying FOXE1-induced thyroid tumorigenesis. Here, we used a panel of human thyroid cancer-derived cell lines covering the spectrum of thyroid cancer phenotypes to examine FOXE1 expression and to test for correlations between FOXE1 expression, the allele frequency of two SNPs and a length polymorphism in or near the FOXE1 locus associated with cancer susceptibility, and the migration ability of thyroid cancer cell lines. Results showed that FOXE1 expression correlated with differentiation status according to histological sub-type, but not with SNP genotype or cell migration ability. However, loss-and-gain-of-function experiments revealed that FOXE1 modulates cell migration, suggesting a role in epithelial-to-mesenchymal transition (EMT). Our previous genome-wide expression analysis identified Zeb1, a major EMT inducer, as a putative Foxe1 target gene. Indeed, gene silencing of FOXE1 decreased ZEB1 expression, whereas its overexpression increased ZEB1 transcriptional activity. FOXE1 was found to directly interact with the ZEB1 promoter. Lastly, ZEB1 silencing decreased the ability of thyroid tumoral cells to migrate and invade, pointing to its importance in thyroid tumor mestastases. In conclusion, we have identified ZEB1 as a bona fide target of FOXE1 in thyroid cancer cells, which provides new insights into the role of FOXE1 in regulating cell migration and invasion in thyroid cancer.
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Affiliation(s)
- Jesús Morillo-Bernal
- Instituto de Investigaciones Biomédicas ‘Alberto Sols’, Consejo Superior Investigaciones Científicas, and Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
| | - Lara P Fernández
- Instituto de Investigaciones Biomédicas ‘Alberto Sols’, Consejo Superior Investigaciones Científicas, and Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
- Molecular Oncology Group, IMDEA Food Institute, CEI UAM-CSIC, Madrid, Spain
| | - Pilar Santisteban
- Instituto de Investigaciones Biomédicas ‘Alberto Sols’, Consejo Superior Investigaciones Científicas, and Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Correspondence should be addressed to P Santisteban:
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Niu H, Huang Y, Yan L, Zhang L, Zhao M, Lu T, Yang X, Chen Z, Zhan C, Shi Y, Wang Q. Knockdown of SMAD3 inhibits the growth and enhances the radiosensitivity of lung adenocarcinoma via p21 in vitro and in vivo. Int J Biol Sci 2020; 16:1010-1022. [PMID: 32140069 PMCID: PMC7053338 DOI: 10.7150/ijbs.40173] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 12/26/2019] [Indexed: 01/09/2023] Open
Abstract
Radiotherapy is an effective approach for the treatment of lung adenocarcinoma. However, evidence suggests that lung adenocarcinoma can easily develop tolerance to radiotherapy. The purpose of this study was to investigate the effect and mechanism of SMAD3 on the radiosensitivity of lung adenocarcinoma in vitro and in vivo. We found that knockdown of SMAD3 using two short hairpin RNAs in lentivirus vectors significantly inhibited cell growth and increased radiosensitivity of the lung adenocarcinoma cell lines A549, H1299, and H1975. Using RNA sequencing and bioinformatics analyses, we found that the significantly differentially expressed genes in SMAD3 knockdown cells were mainly enriched in the cell cycle process. We then showed that knockdown of SMAD3 significantly reduced expression of cyclin-dependent kinase inhibitor 1 (p21) and increased the proportion of G2/M phase cells and the radiosensitivity of lung adenocarcinoma. Chromatin immunoprecipitation results in the Gene Expression Omnibus (GEO) database and our luciferase assay verified that SMAD3 directly bound the p21 promoter. A series of rescue experiments showed that overexpression of p21 partly reversed the effect of SMAD3 on proliferation and radioresistance in vitro and in vivo. Moreover, we found that the expression levels of SMAD3 and p21 were highly correlated, and both correlated with the patients' survival in online databases and clinical specimens. Expression of SMAD3 and p21 was also significantly different between radioresistant and radiosensitive patients in our hospital. Our results indicate that SMAD3 is a potential prognosis and radiosensitivity indicator as well as a target for radiotherapy and other treatments of patients with lung adenocarcinoma.
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Affiliation(s)
- Hao Niu
- Department of Radiation Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yiwei Huang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Li Yan
- Department of Radiation Oncology, Eye & ENT Hospital, Fudan University, Shanghai, China
| | - Li Zhang
- Department of Radiation Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Mengnan Zhao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tao Lu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaodong Yang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhengcong Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yu Shi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qun Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
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Wang Y, Liyanarachchi S, Miller KE, Nieminen TT, Comiskey DF, Li W, Brock P, Symer DE, Akagi K, DeLap KE, He H, Koboldt DC, de la Chapelle A. Identification of Rare Variants Predisposing to Thyroid Cancer. Thyroid 2019; 29:946-955. [PMID: 30957677 PMCID: PMC6648188 DOI: 10.1089/thy.2018.0736] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background: Familial non-medullary thyroid cancer (NMTC) accounts for a relatively small proportion of thyroid cancer cases, but it displays strong genetic predisposition. So far, only a few NMTC susceptible genes and low-penetrance variants contributing to NMTC have been described. This study aimed to identify rare germline variants that may predispose individuals to NMTC by sequencing a cohort of 17 NMTC families. Methods: Whole-genome sequencing and genome-wide linkage analysis were performed in 17 NMTC families. MendelScan and BasePlayer were applied to screen germline variants followed by customized filtering. The remaining candidate variants were subsequently validated by Sanger sequencing. A panel of 277 known cancer predisposition genes was also screened in these families. Results: A total of 41 rare coding candidate variants in 40 genes identified by whole-genome sequencing are reported, including 24 missense, five frameshift, five splice change, and seven nonsense variants. Sanger sequencing confirmed all 41 rare variants and proved their co-segregation with NMTC in the extended pedigrees. In silico functional analysis of the candidate genes using Ingenuity Pathway Analysis showed that cancer was the top category of "Diseases and Disorders." Additionally, a targeted search displayed six variants in known cancer predisposition genes, including one frameshift variant and five missense variants. Conclusions: The data identify rare germline variants that may play important roles in NMTC predisposition. It is proposed that in future research including functional characterization, these variants and genes be considered primary candidates for thyroid cancer predisposition.
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Affiliation(s)
- Yanqiang Wang
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Sandya Liyanarachchi
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Katherine E. Miller
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Taina T. Nieminen
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Daniel F. Comiskey
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Wei Li
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Pamela Brock
- Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - David E. Symer
- Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Keiko Akagi
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Katherine E. DeLap
- Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Huiling He
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Daniel C. Koboldt
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Albert de la Chapelle
- Human Cancer Genetics Program and Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
- Address correspondence to: Albert de la Chapelle, MD, PhD, Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, 804 Biomedical Research Tower, 460 W. 12th Avenue, Columbus, OH 43210
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Hińcza K, Kowalik A, Kowalska A. Current Knowledge of Germline Genetic Risk Factors for the Development of Non-Medullary Thyroid Cancer. Genes (Basel) 2019; 10:genes10070482. [PMID: 31247975 PMCID: PMC6678600 DOI: 10.3390/genes10070482] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/21/2019] [Accepted: 06/25/2019] [Indexed: 02/03/2023] Open
Abstract
The thyroid is the most common site of endocrine cancer. One type of thyroid cancer, non-medullary thyroid cancer (NMTC), develops from follicular cells and represents approximately 90% of all thyroid cancers. Approximately 5%–15% of NMTC cases are thought to be of familial origin (FNMTC), which is defined as the occurrence of the disease in three or more first-degree relatives of the patient. It is often divided into two groups: Syndrome-associated and non-syndromic. The associated syndromes include Cowden syndrome, familial adenomatous polyposis, Gardner syndrome, Carney complex and Werner syndrome. The hereditary factors contributing to the unfavorable course of FNMTC remain poorly understood; therefore, considerable effort is being expended to identify contributing loci. Research carried out to date identifies fourteen genes (DICER1, FOXE1, PTCSC2, MYH9, SRGAP1, HABP2, BRCA1, CHEK2, ATM, RASAL1, SRRM2, XRCC1, TITF-1/NKX2.1, PTCSC3) associated with vulnerability to FNMTC that are not related to hereditary syndromes. In this review, we summarize FNMTC studies to date, and provide information on genes involved in the development of non-syndromic familial non-medullary thyroid cancers, and the significance of mutations in these genes as risk factors. Moreover, we discuss whether the genetic polymorphism rs966423 in DIRC3 has any potential as a prognostic factor of papillary thyroid cancer.
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Affiliation(s)
- Kinga Hińcza
- Department Molecular Diagnostics, Holycross Centre, 25-734 Kielce, Poland.
| | - Artur Kowalik
- Department Molecular Diagnostics, Holycross Centre, 25-734 Kielce, Poland
| | - Aldona Kowalska
- The Faculty of Health Sciences of the Jan Kochanowski University, 25-317 Kielce, Poland
- Endocrinology Clinic of Holycross Cancer Centre, 25-734 Kielce, Poland
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