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Andalib KMS, Rahman MH, Habib A. Bioinformatics and cheminformatics approaches to identify pathways, molecular mechanisms and drug substances related to genetic basis of cervical cancer. J Biomol Struct Dyn 2023; 41:14232-14247. [PMID: 36852684 DOI: 10.1080/07391102.2023.2179542] [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: 10/17/2022] [Accepted: 02/07/2023] [Indexed: 03/01/2023]
Abstract
Cervical cancer (CC) is a global threat to women and our knowledge is frighteningly little about its underlying genomic contributors. Our research aimed to understand the underlying molecular and genetic mechanisms of CC by integrating bioinformatics and network-based study. Transcriptomic analyses of three microarray datasets identified 218 common differentially expressed genes (DEGs) within control samples and CC specimens. KEGG pathway analysis revealed pathways in cell cycle, drug metabolism, DNA replication and the significant GO terms were cornification, proteolysis, cell division and DNA replication. Protein-protein interaction (PPI) network analysis identified 20 hub genes and survival analyses validated CDC45, MCM2, PCNA and TOP2A as CC biomarkers. Subsequently, 10 transcriptional factors (TFs) and 10 post-transcriptional regulators were detected through TFs-DEGs and miRNAs-DEGs regulatory network assessment. Finally, the CC biomarkers were subjected to a drug-gene relationship analysis to find the best target inhibitors. Standard cheminformatics method including in silico ADMET and molecular docking study substantiated PD0325901 and Selumetinib as the most potent candidate-drug for CC treatment. Overall, this meticulous study holds promises for further in vitro and in vivo research on CC diagnosis, prognosis and therapies. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- K M Salim Andalib
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia, Bangladesh
- Center for Advanced Bioinformatics and Artificial Intelligent Research, Islamic University, Kushtia, Bangladesh
| | - Ahsan Habib
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
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2
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Ramachandran D, Dörk T. Genomic Risk Factors for Cervical Cancer. Cancers (Basel) 2021; 13:5137. [PMID: 34680286 PMCID: PMC8533931 DOI: 10.3390/cancers13205137] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/04/2021] [Accepted: 10/11/2021] [Indexed: 12/28/2022] Open
Abstract
Cervical cancer is the fourth common cancer amongst women worldwide. Infection by high-risk human papilloma virus is necessary in most cases, but not sufficient to develop invasive cervical cancer. Despite a predicted genetic heritability in the range of other gynaecological cancers, only few genomic susceptibility loci have been identified thus far. Various case-control association studies have found corroborative evidence for several independent risk variants at the 6p21.3 locus (HLA), while many reports of associations with variants outside the HLA region remain to be validated in other cohorts. Here, we review cervical cancer susceptibility variants arising from recent genome-wide association studies and meta-analysis in large cohorts and propose 2q14 (PAX8), 17q12 (GSDMB), and 5p15.33 (CLPTM1L) as consistently replicated non-HLA cervical cancer susceptibility loci. We further discuss the available evidence for these loci, knowledge gaps, future perspectives, and the potential impact of these findings on precision medicine strategies to combat cervical cancer.
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Affiliation(s)
| | - Thilo Dörk
- Gynaecology Research Unit, Department of Gynaecology and Obstetrics, Comprehensive Cancer Center, Hannover Medical School, D-30625 Hannover, Germany;
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3
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Jia M, Ren L, Hu L, Ma H, Jin G, Li D, Li N, Hu Z, Hang D. Association of long non-coding RNA HOTAIR and MALAT1 variants with cervical cancer risk in Han Chinese women. J Biomed Res 2019; 33:308. [PMCID: PMC6813535 DOI: 10.7555/jbr.33.20180096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 02/26/2019] [Indexed: 05/05/2024] Open
Abstract
Long noncoding RNA (lncRNA) HOTAIR and MALAT1 are implicated in the development of multiple cancers. Genetic variants within HOTAIR and MALAT1 may affect the gene expression, thereby modifying genetic susceptibility to cervical cancer. A case-control study was designed, including 1 486 cervical cancer patients and 1 536 healthy controls. Based on RegulomeDB database, 11 SNPs were selected and genotyped by using Sequenom's Mass ARRAY. Univariate and multivariate logistic regression models were used to calculate the odds ratio (OR) and 95% confidence interval (CI). We found that the A allele of rs35643724 in HOTAIR was associated with increased risk of cervical cancer, while the C allele of rs1787666 in MALAT1 was associated with decreased risk. Compared to individuals with 0–1 unfavorable allele, those with 3–4 unfavorable alleles showed 18% increased odds of having cervical cancer. Our findings suggest that HOTAIR rs35643724 and MALAT1 rs1787666 might represent potential biomarkers for cervical cancer susceptibility.
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Affiliation(s)
- Meiqun Jia
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Gynecologic Oncology, the Affiliated Tumor Hospital of Nantong University (Nantong Tumor Hospital), Nantong, Jiangsu 226361, China
| | - Lulu Ren
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Lingmin Hu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Reproduction, the Affiliated Changzhou Maternity and Child Health Care Hospital of Nanjing Medical University, Changzhou, Jiangsu 213003, China
| | - Hongxia Ma
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Guangfu Jin
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Dake Li
- Department of Gynecologic Oncology, Nanjing Maternity and Child Health Hospital, Nanjing, Jiangsu 210004, China
| | - Ni Li
- Program Office for Cancer Screening in Urban China, National Cancer Centre/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Zhibin Hu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211166, China
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Dong Hang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211166, China
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4
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Aterido A, Cañete JD, Tornero J, Ferrándiz C, Pinto JA, Gratacós J, Queiró R, Montilla C, Torre-Alonso JC, Pérez-Venegas JJ, Fernández Nebro A, Muñoz-Fernández S, González CM, Roig D, Zarco P, Erra A, Rodríguez J, Castañeda S, Rubio E, Salvador G, Díaz-Torné C, Blanco R, Willisch Domínguez A, Mosquera JA, Vela P, Sánchez-Fernández SA, Corominas H, Ramírez J, de la Cueva P, Fonseca E, Fernández E, Puig L, Dauden E, Sánchez-Carazo JL, López-Estebaranz JL, Moreno D, Vanaclocha F, Herrera E, Blanco F, Fernández-Gutiérrez B, González A, Pérez-García C, Alperi-López M, Olivé Marques A, Martínez-Taboada V, González-Álvaro I, Sanmartí R, Tomás Roura C, García-Montero AC, Bonàs-Guarch S, Mercader JM, Torrents D, Codó L, Gelpí JL, López-Corbeto M, Pluma A, López-Lasanta M, Tortosa R, Palau N, Absher D, Myers R, Marsal S, Julià A. Genetic variation at the glycosaminoglycan metabolism pathway contributes to the risk of psoriatic arthritis but not psoriasis. Ann Rheum Dis 2018; 78:annrheumdis-2018-214158. [PMID: 30552173 DOI: 10.1136/annrheumdis-2018-214158] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/16/2018] [Accepted: 11/16/2018] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Psoriatic arthritis (PsA) is a chronic inflammatory arthritis affecting up to 30% of patients with psoriasis (Ps). To date, most of the known risk loci for PsA are shared with Ps, and identifying disease-specific variation has proven very challenging. The objective of the present study was to identify genetic variation specific for PsA. METHODS We performed a genome-wide association study in a cohort of 835 patients with PsA and 1558 controls from Spain. Genetic association was tested at the single marker level and at the pathway level. Meta-analysis was performed with a case-control cohort of 2847 individuals from North America. To confirm the specificity of the genetic associations with PsA, we tested the associated variation using a purely cutaneous psoriasis cohort (PsC, n=614) and a rheumatoid arthritis cohort (RA, n=1191). Using network and drug-repurposing analyses, we further investigated the potential of the PsA-specific associations to guide the development of new drugs in PsA. RESULTS We identified a new PsA risk single-nucleotide polymorphism at B3GNT2 locus (p=1.10e-08). At the pathway level, we found 14 genetic pathways significantly associated with PsA (pFDR<0.05). From these, the glycosaminoglycan (GAG) metabolism pathway was confirmed to be disease-specific after comparing the PsA cohort with the cohorts of patients with PsC and RA. Finally, we identified candidate drug targets in the GAG metabolism pathway as well as new PsA indications for approved drugs. CONCLUSION These findings provide insights into the biological mechanisms that are specific for PsA and could contribute to develop more effective therapies.
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Affiliation(s)
- Adrià Aterido
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Juan D Cañete
- Rheumatology Department, Hospital Clínic de Barcelona and IDIBAPS, Barcelona, Spain
| | - Jesús Tornero
- Rheumatology Department, Hospital Universitario Guadalajara, Guadalajara, Spain
| | - Carlos Ferrándiz
- Dermatology Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - José Antonio Pinto
- Rheumatology Department, Complejo Hospitalario Juan Canalejo, A Coruña, Spain
| | - Jordi Gratacós
- Rheumatology Department, Hospital Parc Taulí, Sabadell, Spain
| | - Rubén Queiró
- Rheumatology Department, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Carlos Montilla
- Rheumatology Department, Hospital Virgen de la Vega, Salamanca, Spain
| | | | | | - Antonio Fernández Nebro
- Rheumatology Department, Instituto de Investigación Biomédica de Málaga, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Santiago Muñoz-Fernández
- Rheumatology Department, Hospital Universitario Infanta Sofía, Universidad Europea, Madrid, Spain
| | - Carlos M González
- Rheumatology Department, Hospital Universitario Gregorio Marañón, Madrid, Spain
| | - Daniel Roig
- Rheumatology Department, Hospital Moisès Broggi, Barcelona, Spain
| | - Pedro Zarco
- Rheumatology Department, Hospital Universitario Fundación Alcorcón, Madrid, Spain
| | - Alba Erra
- Rheumatology Department, Hospital Sant Rafael, Barcelona, Spain
| | - Jesús Rodríguez
- Rheumatology Department, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Santos Castañeda
- Rheumatology Department, Hospital Universitario La Princesa, IIS La Princesa, Madrid, Spain
| | - Esteban Rubio
- Rheumatology Department, Centro de Salud Virgen de los Reyes, Sevilla, Spain
| | - Georgina Salvador
- Rheumatology Department, Hospital Universitario Mútua de Terrassa, Terrassa, Spain
| | - Cesar Díaz-Torné
- Rheumatology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Ricardo Blanco
- Rheumatology Department, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | | | - José Antonio Mosquera
- Rheumatology Department, Complejo Hospitalario Hospital Provincial de Pontevedra, Pontevedra, Spain
| | - Paloma Vela
- Rheumatology Department, Hospital General Universitario de Alicante, Alicante, Spain
| | | | - Héctor Corominas
- Rheumatology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Rheumatology Department, Hospital Dos de Maig, Barcelona, Spain
| | - Julio Ramírez
- Rheumatology Department, Hospital Clínic de Barcelona and IDIBAPS, Barcelona, Spain
| | - Pablo de la Cueva
- Dermatology Department, Hospital Universitario Infanta Leonor, Madrid, Spain
| | - Eduardo Fonseca
- Dermatology Department, Complejo Hospitalario Universitario de A Coruña, A Coruña, Spain
| | - Emilia Fernández
- Dermatology Department, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Lluis Puig
- Dermatology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Esteban Dauden
- Dermatology Department, Hospital Universitario La Princesa, IIS La Princesa, Madrid, Spain
| | | | | | - David Moreno
- Dermatology Department, Hospital Virgen Macarena, Sevilla, Spain
| | | | - Enrique Herrera
- Dermatology Department, Hospital Universitario Virgen de la Victoria, Málaga, Spain
| | - Francisco Blanco
- Rheumatology Department, INIBIC-Hospital Universitario A Coruña, A Coruña, Spain
| | | | - Antonio González
- Instituto de Investigación Sanitaria Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
| | | | | | | | | | | | - Raimon Sanmartí
- Rheumatology Department, Hospital Clínic de Barcelona and IDIBAPS, Barcelona, Spain
| | | | | | - Sílvia Bonàs-Guarch
- Barcelona Supercomputing Centre (BSC), Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona, Spain
| | - Josep Maria Mercader
- Barcelona Supercomputing Centre (BSC), Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona, Spain
| | - David Torrents
- Barcelona Supercomputing Centre (BSC), Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Laia Codó
- Life Sciences Department, Barcelona Supercomputing Centre, Barcelona, Spain
| | - Josep Lluís Gelpí
- Life Sciences Department, Barcelona Supercomputing Centre, Barcelona, Spain
| | | | - Andrea Pluma
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Maria López-Lasanta
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Raül Tortosa
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Nuria Palau
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Richard Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Sara Marsal
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Antonio Julià
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, Spain
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5
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Xu Y, Cheng L, Dai H, Zhang R, Wang M, Shi T, Sun M, Cheng X, Wei Q. Variants in Notch signalling pathway genes, PSEN1 and MAML2, predict overall survival in Chinese patients with epithelial ovarian cancer. J Cell Mol Med 2018; 22:4975-4984. [PMID: 30055028 PMCID: PMC6156353 DOI: 10.1111/jcmm.13764] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 06/04/2018] [Indexed: 12/18/2022] Open
Abstract
To identify genetic variants in Notch signalling pathway genes that may predict survival of Han Chinese patients with epithelial ovarian cancer (EOC), we analysed a total of 1273 single nucleotide polymorphisms (SNPs) within 75 Notch genes in 480 patients from a published EOC genomewide association study (GWAS). We found that PSEN1 rs165934 and MAML2 rs76032516 were associated with overall survival (OS) of patients by multivariate Cox proportional hazards regression analysis. Specifically, the PSEN1 rs165934 AA genotype was associated with a poorer survival (adjusted hazards ratio [adjHR] = 1.41, 95% CI = 1.07-1.84, and P = .014), compared with the CC + CA genotype, while MAML2 rs76032516 AA + AC genotypes were associated with a poorer survival (adjHR = 1.58, 95% CI = 1.16-2.14, P = .004), compared with the CC genotype. The combined analysis of these two SNPs revealed that the death risk increased as the number of unfavourable genotypes increased in a dose-dependent manner (Ptrend < .001). Additionally, the expression quantitative trait loci analysis revealed that the SNP rs165932 in the rs165934 LD block (r2 = .946) was associated with expression levels of PSEN1, which might be responsible for the observed association with SNP rs165934. The associations of PSEN1 rs165934 and MAML2 rs76032516 of the Notch signalling pathway genes with OS in Chinese EOC patients are novel findings, which need to be validated in other large and independent studies.
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Affiliation(s)
- Yuan Xu
- Cancer InstituteFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Lei Cheng
- Cancer InstituteFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Hongji Dai
- Department of Epidemiology and BiostatisticsKey Laboratory of Cancer Prevention and TherapyTianjinChina
- Key Laboratory of Breast Cancer Prevention and TherapyMinistry of EducationNational Clinical Research Center for CancerTianjin Medical University Cancer Institute and HospitalTianjinChina
| | - Ruoxin Zhang
- Cancer InstituteFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Mengyun Wang
- Cancer InstituteFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Tingyan Shi
- Ovarian Cancer ProgramDivision of Gynecologic OncologyDepartment of Gynecology and ObstetricsFudan University Zhongshan HospitalShanghaiChina
| | - Menghong Sun
- Department of PathologyTissue BankFudan University Shanghai Cancer CenterShanghaiChina
| | - Xi Cheng
- Cancer InstituteFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghaiChina
| | - Qingyi Wei
- Cancer InstituteFudan University Shanghai Cancer CenterShanghaiChina
- Duke Cancer InstituteDuke University Medical CenterDurhamNCUSA
- Department of Population Health SciencesDuke University School of MedicineDurhamNCUSA
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6
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Chen D, Enroth S, Liu H, Sun Y, Wang H, Yu M, Deng L, Xu S, Gyllensten U. Pooled analysis of genome-wide association studies of cervical intraepithelial neoplasia 3 (CIN3) identifies a new susceptibility locus. Oncotarget 2018; 7:42216-42224. [PMID: 27285765 PMCID: PMC5173129 DOI: 10.18632/oncotarget.9916] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 05/13/2016] [Indexed: 01/09/2023] Open
Abstract
Recent genome-wide association studies (GWASs) in subjects of European descent have identified associations between cervical cancer risk and three independent loci as well as multiple classical human leukocyte antigen (HLA) alleles at 6p21.3. To search for novel loci associated with development of cervical cancer, we performed a pooled analysis of data from two GWASs by imputing over 10 million genetic variants and 424 classical HLA alleles, for 1,553 intraepithelial neoplasia 3 (CIN3), 81 cervical cancer and 4,442 controls from the Swedish population. Notable findings were validated in an independent study of 961 patients (827 with CIN3 and 123 with cervical cancer) and 1,725 controls. Our data provided increased support for previously identified loci at 6p21.3 (rs9271898, P = 1.2 × 10−24; rs2516448, 1.1 × 10−15; and rs3130196, 2.3 × 10−9, respectively) and also confirmed associations with reported classical HLA alleles including HLA-B*07:02, -B*15:01, -DRB1*13:01, -DRB1*15:01, -DQA1*01:03, -DQB1*06:03 and -DQB1*06:02. In addition, we identified and subsequently replicated an independent signal at rs73730372 at 6p21.3 (odds ratio = 0.60, 95% confidence interval = 0.54–0.67, P = 3.0 × 10−19), which was found to be an expression quantitative trait locus (eQTL) of both HLA-DQA1 and HLA-DQB1. This is one of the strongest common genetic protective variants identified so far for CIN3. We also found HLA-C*07:02 to be associated with risk of CIN3. The present study provides new insights into pathogenesis of CIN3.
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Affiliation(s)
- Dan Chen
- Ministry of Education and Shanghai Key Laboratory of Children's Environmental Health, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Uppsala, Sweden
| | - Stefan Enroth
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Uppsala, Sweden
| | - Han Liu
- Ministry of Education and Shanghai Key Laboratory of Children's Environmental Health, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yang Sun
- Laboratory of Biochemistry and Molecular Biology, School of Life Science,Yunnan University, Kunming, China
| | - Huibo Wang
- Department of Neurosurgery, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Min Yu
- Laboratory of Biochemistry and Molecular Biology, School of Life Science,Yunnan University, Kunming, China
| | - Lian Deng
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shuhua Xu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China.,Collaborative Innovation Center of Genetics and Development, Shanghai, China
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Uppsala, Sweden
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7
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Bahrami A, Hasanzadeh M, Shahidsales S, Farazestanian M, Hassanian SM, Moetamani Ahmadi M, Maftouh M, Gharib M, Yousefi Z, Kadkhodayan S, Ferns GA, Avan A. Genetic susceptibility in cervical cancer: From bench to bedside. J Cell Physiol 2017; 233:1929-1939. [PMID: 28542881 DOI: 10.1002/jcp.26019] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/18/2017] [Indexed: 01/21/2023]
Abstract
Cervical cancer (CC) is the third most common malignancy in women globally, and persistent infection with the oncogenic human papillomaviruses (HPV) is recognized as the major risk factor. The pathogenesis of CC relies on the interplay between the tumorigenic properties of the HPV and host factors. Host-related genetic factors, including the presence of susceptibility loci for cervix tumor is substantial importance. Preclinical and genome-wide association studies (GWAS) have reported the associations of genetic variations in several susceptibility loci for the development of cervical cancer. However, many of these reports are inconsistent. In this review, we discuss the findings to date of candidate gene association studies, and GWAS in cervical cancer. The associations between these genetic variations with response to chemotherapy are also discussed.
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Affiliation(s)
- Afsane Bahrami
- Department of Modern Sciences and Technologies, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Metabolic Syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.,Student research committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Malihe Hasanzadeh
- Department of Gynecology Oncology, Woman Health Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Marjaneh Farazestanian
- Department of Gynecology Oncology, Woman Health Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mahdi Hassanian
- Metabolic Syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mehrdad Moetamani Ahmadi
- Department of Modern Sciences and Technologies, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mina Maftouh
- Metabolic Syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Masoumeh Gharib
- Department of Pathology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zohreh Yousefi
- Department of Gynecology Oncology, Woman Health Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sima Kadkhodayan
- Department of Gynecology Oncology, Woman Health Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A Ferns
- Brighton & Sussex Medical School, Division of Medical Education, Falmer, Brighton, United Kingdom
| | - Amir Avan
- Metabolic Syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran
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8
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Identification of a serum-induced transcriptional signature associated with metastatic cervical cancer. PLoS One 2017; 12:e0181242. [PMID: 28854209 PMCID: PMC5576712 DOI: 10.1371/journal.pone.0181242] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 06/28/2017] [Indexed: 02/07/2023] Open
Abstract
Objective Tumor cells that escape local tissue control can convert inflammatory cells from tumor suppressors to tumor promoters. Moreover, soluble immune-modulating factors secreted from the tumor environment can be difficult to identify in patient serum due to their low abundance. We used an alternative strategy to infer a metastatic signature induced by sera of cervical cancer patients. Methods Sera from patients with local and metastatic cervical cancer were used to induce a disease-specific transcriptional signature in cultured, healthy peripheral blood mononuclear cells (PBMCs). An empirical Bayesian method, EBarrays, was used to identify differentially expressed (DE) genes with a target false discovery rate of <5%. Ingenuity Pathway Analysis (IPA) software was used to detect the top molecular and cellular functions associated with the DE genes. IPA and in silco analysis was used to pinpoint candidate upstream regulators, including cancer-related microRNAs (miRNAs). Results We identified enriched pathways in the metastatic cervical group related to immune surveillance functions, such as downregulation of engulfment, accumulation, and phagocytosis of hematopoietic cells. The predicted top upstream genes were IL-10 and immunoglobulins. In silco analysis identified miRNAs predicted to drive the transcriptional signature. Two of the 4 miRNAs (miR-23a-3p and miR-944) were validated in a cohort of women with local and metastatic cervical cancer. Conclusions This study supports the use of a cell-based assay that uses PBMC “reporters” to predict biologically relevant factors in patient serum. Further, disease-specific transcriptional signatures induced by patient sera have the potential to differentiate patients with local versus metastatic disease.
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Banister CE, Liu C, Pirisi L, Creek KE, Buckhaults PJ. Identification and characterization of HPV-independent cervical cancers. Oncotarget 2017; 8:13375-13386. [PMID: 28077784 PMCID: PMC5355105 DOI: 10.18632/oncotarget.14533] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/27/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Human papillomavirus (HPV) initiates cervical cancer, and continuous expression of HPV oncogenes E6 and E7 is thought to be necessary to maintain malignant growth. Current therapies target proliferating cells, rather than specific pathways, and most experimental therapies specifically target E6/E7. We investigated the presence and expression of HPV in cervical cancer, to correlate HPV oncogene expression with clinical and molecular features of these tumors that may be relevant to new targeted therapies. RESULTS While virtually all cervical cancers contained HPV DNA, and most expressed E6/E7 (HPV-active), a subset (8%) of HPV DNA-positive cervical cancers did not express HPV transcripts (HPV-inactive). HPV-inactive tumors occurred in older women (median 54 vs. 45 years, p = 0.02) and were associated with poorer survival (median 715 vs 3046 days, p = 0.0003). Gene expression profiles of HPV-active and -inactive tumors were distinct. HPV-active tumors expressed E2F target genes and increased AKT/MTOR signaling. HPV-inactive tumors had increased WNT/β-catenin and Sonic Hedgehog signaling. Substantial genome-wide differences in DNA methylation were observed. HPV-inactive tumors had a global decrease in DNA methylation; however, many promoter-associated CpGs were hypermethylated. Many inflammatory response genes showed promoter methylation and decreased expression. The somatic mutation landscapes were significantly different. HPV-active tumors carried few somatic mutations in driver genes, whereas HPV-inactive tumors were enriched for non-synonymous somatic mutations (p-value < 0.0000001) specifically targeting TP53, ARID, WNT, and PI3K pathways. MATERIALS AND METHODS The Cancer Genome Atlas (TCGA) cervical cancer data were analyzed. CONCLUSIONS Many of the gene expression changes and somatic mutations found in HPV-inactive tumors alter pathways for which targeted therapeutics are available. Treatment strategies focused on WNT, PI3K, or TP53 mutations may be effective against HPV-inactive tumors and could improve survival for these cervical cancer patients.
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Affiliation(s)
| | - Changlong Liu
- University of South Carolina College of Pharmacy, Columbia, SC, USA
| | - Lucia Pirisi
- University of South Carolina School of Medicine, Columbia, SC, USA
| | - Kim E Creek
- University of South Carolina College of Pharmacy, Columbia, SC, USA
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Gui H, Kwan JS, Sham PC, Cherny SS, Li M. Sharing of Genes and Pathways Across Complex Phenotypes: A Multilevel Genome-Wide Analysis. Genetics 2017; 206:1601-1609. [PMID: 28495956 PMCID: PMC5500153 DOI: 10.1534/genetics.116.198150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 04/20/2017] [Indexed: 12/15/2022] Open
Abstract
Evidence from genome-wide association studies (GWAS) suggest that pleiotropic effects on human complex phenotypes are very common. Recently, an atlas of genetic correlations among complex phenotypes has broadened our understanding of human diseases and traits. Here, we examine genetic overlap, from a gene-centric perspective, among the same 24 phenotypes previously investigated for genetic correlations. After adopting the multilevel pipeline (freely available at http://grass.cgs.hku.hk/limx/kgg/), which includes intragenic single nucleotide polymorphisms (SNPs), genes, and gene-sets, to estimate genetic similarities across phenotypes, a large amount of sharing of several biologically related phenotypes was confirmed. In addition, significant genetic overlaps were also found among phenotype pairs that were previously unidentified by SNP-level approaches. All these pairs with new genetic links are supported by earlier epidemiological evidence, although only a few of them have pleiotropic genes in the GWAS Catalog. Hence, our gene and gene-set analyses are able to provide new insights into cross-phenotype connections. The investigation on genetic sharing at three different levels presents a complementary picture of how common DNA sequence variations contribute to disease comorbidities and trait manifestations.
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Affiliation(s)
- Hongsheng Gui
- Center for Genomic Sciences, University of Hong Kong, Hong Kong SAR, China
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Michigan 48202
| | - Johnny S Kwan
- Department of Psychiatry, University of Hong Kong, Hong Kong SAR, China
| | - Pak C Sham
- Center for Genomic Sciences, University of Hong Kong, Hong Kong SAR, China
- Department of Psychiatry, University of Hong Kong, Hong Kong SAR, China
- The State Key Laboratory of Brain and Cognitive Sciences, University of Hong Kong, Hong Kong SAR, China
| | - Stacey S Cherny
- Center for Genomic Sciences, University of Hong Kong, Hong Kong SAR, China
- Department of Psychiatry, University of Hong Kong, Hong Kong SAR, China
- The State Key Laboratory of Brain and Cognitive Sciences, University of Hong Kong, Hong Kong SAR, China
| | - Miaoxin Li
- Center for Genomic Sciences, University of Hong Kong, Hong Kong SAR, China
- Department of Psychiatry, University of Hong Kong, Hong Kong SAR, China
- Department of Medical Genetics, Center for Genome Research, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510275 China
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11
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Aterido A, Julià A, Carreira P, Blanco R, López-Longo JJ, Venegas JJP, Olivé À, Andreu JL, Aguirre-Zamorano MÁ, Vela P, Nolla JM, Marenco-de la Fuente JL, Zea A, Pego JM, Freire M, Díez E, López-Lasanta M, López-Corbeto M, Palau N, Tortosa R, Gelpí JL, Absher D, Myers RM, Fernández-Nebro A, Marsal S. Genome-wide pathway analysis identifies VEGF pathway association with oral ulceration in systemic lupus erythematosus. Arthritis Res Ther 2017; 19:138. [PMID: 28619073 PMCID: PMC5471877 DOI: 10.1186/s13075-017-1345-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/22/2017] [Indexed: 02/06/2023] Open
Abstract
Background Systemic lupus erythematosus (SLE) is a genetically complex rheumatic disease characterized by heterogeneous clinical manifestations of unknown etiology. Recent studies have suggested the existence of a genetic basis for SLE heterogeneity. The objective of the present study was to identify new genetic variation associated with the clinically relevant phenotypes in SLE. Methods A two-stage pathway-based approach was used to identify the genetic variation associated with the main clinical phenotypes in SLE. In the discovery stage, 482 SLE patients were genotyped using Illumina Human Quad610 microarrays. Association between 798 reference genetic pathways from the Molecular Signatures Database and 11 SLE phenotypes was tested using the set-based method implemented in PLINK software. Pathways significantly associated after multiple test correction were subsequently tested for replication in an independent cohort of 425 SLE patients. Using an in silico approach, we analyzed the functional effects of common SLE therapies on the replicated genetic pathways. The association of known SLE risk variants with the development of the clinical phenotypes was also analyzed. Results In the discovery stage, we found a significant association between the vascular endothelial growth factor (VEGF) pathway and oral ulceration (P value for false discovery rate (PFDR) < 0.05), and between the negative regulation signaling pathway of retinoic acid inducible gene-I/melanoma differentiation associated gene 5 and the production of antinuclear antibodies (PFDR < 0.05). In the replication stage, we validated the association between the VEGF pathway and oral ulceration. Therapies commonly used to treat mucocutaneous phenotypes in SLE were found to strongly influence VEGF pathway gene expression (P = 4.60e-4 to 5.38e-14). Analysis of known SLE risk loci identified a strong association between PTPN22 and the risk of hematologic disorder and with the development of antinuclear antibodies. Conclusions The present study has identified VEGF genetic pathway association with the risk of oral ulceration in SLE. New therapies targeting the VEGF pathway could be more effective in reducing the severity of this phenotype. These findings represent a first step towards the understanding of the genetic basis of phenotype heterogeneity in SLE. Electronic supplementary material The online version of this article (doi:10.1186/s13075-017-1345-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adrià Aterido
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, 08035, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, 08005, Spain
| | - Antonio Julià
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, 08035, Spain.
| | - Patricia Carreira
- Rheumatology Department, Hospital Universitario 12 de Octubre, Madrid, 28041, Spain
| | - Ricardo Blanco
- Rheumatology Department, Hospital Universitario Marqués de Valdecilla, Santander, 39008, Spain
| | | | | | - Àlex Olivé
- Rheumatology Department, Hospital Universitari Germans Trias i Pujol, Badalona, 08916, Spain
| | - José Luís Andreu
- Rheumatology Department, Hospital Universitario Puerta de Hierro, Madrid, 28222, Spain
| | | | - Paloma Vela
- Rheumatology Department, Hospital General Universitario de Alicante, Alicante, 03010, Spain
| | - Joan M Nolla
- Rheumatology Department, Hospital Universitari de Bellvitge, Barcelona, 08907, Spain
| | | | - Antonio Zea
- Rheumatology Department, Hospital Universitario Ramón y Cajal, 28034, Madrid, Spain
| | - José María Pego
- Instituto de Investigación Biomédica de Vigo, Ourense y Pontevedra, 36204, Spain
| | - Mercedes Freire
- Rheumatology Department, Hospital Universitario A Coruña, A Coruña, 15006, Spain
| | - Elvira Díez
- Rheumatology Department, Hospital Complejo Asistencial Universitario de León, León, 24001, Spain
| | - María López-Lasanta
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, 08035, Spain
| | - Mireia López-Corbeto
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, 08035, Spain
| | - Núria Palau
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, 08035, Spain
| | - Raül Tortosa
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, 08035, Spain
| | - Josep Lluís Gelpí
- Life Sciences, Barcelona Supercomputing Centre, Barcelona, 08034, Spain
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, 35806, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, 35806, USA
| | - Antonio Fernández-Nebro
- Rheumatology Department, Hospital Regional Universitario de Málaga, Málaga, 29010, Spain. .,Instituto de Investigación Biomédica de Málaga, Universidad de Málaga, Málaga, 29010, Spain.
| | - Sara Marsal
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, 08035, Spain
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12
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Genome-Wide Pathway Analysis Identifies Genetic Pathways Associated with Psoriasis. J Invest Dermatol 2015; 136:593-602. [PMID: 26743605 DOI: 10.1016/j.jid.2015.11.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/27/2015] [Accepted: 11/12/2015] [Indexed: 11/22/2022]
Abstract
Psoriasis is a chronic inflammatory disease with a complex genetic architecture. To date, the psoriasis heritability is only partially explained. However, there is increasing evidence that the missing heritability in psoriasis could be explained by multiple genetic variants of low effect size from common genetic pathways. The objective of this study was to identify new genetic variation associated with psoriasis risk at the pathway level. We genotyped 598,258 single nucleotide polymorphisms in a discovery cohort of 2,281 case-control individuals from Spain. We performed a genome-wide pathway analysis using 1,053 reference biological pathways. A total of 14 genetic pathways (PFDR ≤ 2.55 × 10(-2)) were found to be significantly associated with psoriasis risk. Using an independent validation cohort of 7,353 individuals from the UK, a total of 6 genetic pathways were significantly replicated (PFDR ≤ 3.46 × 10(-2)). We found genetic pathways that had not been previously associated with psoriasis risk such as retinol metabolism (Pcombined = 1.84 × 10(-4)), the transport of inorganic ions and amino acids (Pcombined = 1.57 × 10(-7)), and post-translational protein modification (Pcombined = 1.57 × 10(-7)). In the latter pathway, MGAT5 showed a strong network centrality, and its association with psoriasis risk was further validated in an additional case-control cohort of 3,429 individuals (P < 0.05). These findings provide insights into the biological mechanisms associated with psoriasis susceptibility.
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13
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Yuan F, Sun R, Chen P, Liang Y, Ni S, Quan Y, Huang J, Zhang L, Gao L. Combined analysis of pri-miR-34b/c rs4938723 and TP53 Arg72Pro with cervical cancer risk. Tumour Biol 2015; 37:6267-73. [PMID: 26619844 DOI: 10.1007/s13277-015-4467-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 11/17/2015] [Indexed: 12/12/2022] Open
Abstract
miR-34 family members can form a p53-miR-34 positive feedback loop and induce apoptosis, DNA repair, angiogenesis, and cell cycle arrest. We conducted a case-control study to examine whether two polymorphisms (i.e., rs4938723 in the promoter of pri-miR-34b/c and TP53 Arg72Pro) were linked to the carcinogenesis of cervical cancer among Chinese Han women. Genotypes of the two polymorphisms in 328 cervical cancer patients and 568 control subjects were determined by using a polymerase chain reaction-restriction fragment length polymorphism assay. We found a significantly increased cervical cancer risk in the pri-miR-34b/c rs4938723 under dominant and overdominant model (CT/CC vs. TT: adjusted OR = 1.34, 95 % CI = 1.01-1.77; CT vs. TT/CC: adjusted OR = 1.37, 95 % CI = 1.05-1.80, respectively). Increased cervical cancer risks were also found in the TP53 Arg72Pro under a heterozygous comparison and overdominant model (CG vs. GG: adjusted OR = 1.44, 95 % CI = 1.06-1.95; CG vs. GG/CC: adjusted OR = 1.47, 95 % CI = 1.12-1.94, respectively). Stratification analysis showed that patients carrying the pri-miR-34b/c rs4938723 CT genotype had a significantly increased risk for developing poorly differential status and clinical stage I. Moreover, increased cancer risks were observed for the TP53 Arg72Pro polymorphism in patients with poorly differential status, clinical stage II, and without lymph node metastasis. Combined analysis revealed that the genotypes of rs4938723 CT/CC and TP53 Arg72Pro CG/CC had an increased cervical cancer risk (OR = 2.21, 95 % CI = 1.38-3.53). These findings suggest that the pri-miR-34b/c rs4938723 and TP53 Arg72Pro polymorphisms may contribute to the genesis of cervical cancer.
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Affiliation(s)
- Fang Yuan
- Department of Immunology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Ruifen Sun
- Department of Immunology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
- Central Laboratory, Yunnan University of Traditional Chinese Medicine, Kunming, 650500, Yunnan, People's Republic of China
| | - Peng Chen
- Laboratory of Molecular and Translational Medicine, West China Institute of Women and Children's Health, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
- Key Laboratory of Obstetric and Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Yundan Liang
- Laboratory of Molecular and Translational Medicine, West China Institute of Women and Children's Health, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
- Key Laboratory of Obstetric and Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Shanshan Ni
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Yi Quan
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Juan Huang
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Lin Zhang
- Department of Immunology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China.
- Laboratory of Molecular and Translational Medicine, West China Institute of Women and Children's Health, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China.
- Key Laboratory of Obstetric and Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China.
| | - Linbo Gao
- Laboratory of Molecular and Translational Medicine, West China Institute of Women and Children's Health, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China.
- Key Laboratory of Obstetric and Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China.
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14
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Chen D, Cui T, Ek WE, Liu H, Wang H, Gyllensten U. Analysis of the genetic architecture of susceptibility to cervical cancer indicates that common SNPs explain a large proportion of the heritability. Carcinogenesis 2015; 36:992-8. [PMID: 26045304 DOI: 10.1093/carcin/bgv083] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 05/20/2015] [Indexed: 11/14/2022] Open
Abstract
The genetic architecture of susceptibility to cervical cancer is not well-understood. By using a genome-wide association study (GWAS) of 1034 cervical cancer patients and 3948 controls with 632668 single-nucleotide polymorphisms (SNPs), we estimated that 24.0% [standard error (SE) = 5.9%, P = 3.19×10(-6)] of variation in liability to cervical cancer is captured by autosomal SNPs, a bit lower than the heritability estimated from family study (27.0%), suggesting that a substantial proportion of the heritability is tagged by common SNPs. The remaining missing heritability most probably reflects incomplete linkage disequilibrium between causal variants and the genotyped SNPs. The variance explained by each chromosome is not related to its length (R (2) = 0.020, P = 0.516). Published genome-wide significant variants only explain 2.1% (SE = 1.5%, P = 0) of phenotypic variance, which reveals that most of the heritability has not been detected, presumably due to small individual effects. Another 2.1% (SE = 1.1%, P = 0.013) of variation is attributable to biological pathways associated with risk of cervical cancer, supporting that pathway analysis can identify part of the hidden heritability. Except for human leukocyte antigen genes and MHC class I polypeptide-related sequence A (MICA), none of the 82 candidate genes/regions reported in other association studies contributes to the heritability of cervical cancer in our dataset. This study shows that risk of cervical cancer is influenced by many common germline genetic variants of small effects. The findings are important for further study design to identify the hiding heritability that has not yet been revealed. More susceptibility loci are yet to be found in GWASs with higher power.
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Affiliation(s)
- Dan Chen
- Ministry of Education and Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China, Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Uppsala 75108, Sweden and
| | - Tao Cui
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Uppsala 75108, Sweden and
| | - Weronica E Ek
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Uppsala 75108, Sweden and
| | - Han Liu
- Ministry of Education and Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Huibo Wang
- Department of Neurosurgery, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Uppsala 75108, Sweden and
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15
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Doan HQ, Nguyen HP, Rady P, Tyring SK. Expression patterns of immune-associated genes in external genital and perianal warts treated with sinecatechins. Viral Immunol 2015; 28:236-40. [PMID: 25774455 DOI: 10.1089/vim.2014.0144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The role of human papillomavirus (HPV) in human disease includes external genital and perianal warts (EGW), with some HPV genotypes having oncogenic potential (i.e., HPV-16 and -18). While green-tea extracts have antitumor and antiproliferative effects in vitro, the mechanism of action of sinecatechins in the treatment of EGW is not well understood. To investigate the role of immune-regulated genes further, an open-label, single institution, prospective study was conducted enrolling patients with clinically diagnosed EGW. Thirty subjects were enrolled, and 18 completed the trial. All patients applied sinecatechins 15% ointment to target lesions in the study. RNA expression microarrays were obtained from treated EGW lesions and analyzed for differential gene expression of immune-regulated genes. HPV types were analyzed and, based on copy number, were stratified into virological responders (VR) or nonresponders (VNR). Gene expression analysis of RNA samples was performed using TaqMan arrays for human T cell receptor and CD3 complex (TCR), Toll-like receptors (TLR) pathway, interferon (IFN) pathway, and antigen processing pathway. A total of 256 genes were analyzed across the four arrays. Genes that were significantly regulated between VRs and VNRs were CREB3L4, HIST1H3A, HIST1H3H, IFNA1, IFNA4, IFNA5, IFNA6, IFNA8, IFNA14, IFNG, IFNAR1, IL6, IRF9, MAPK4, MAPK5, MAPK14, NET1, and PIK3C2A in the IFN array. In the TCR array, HLA_B was found to be statistically significantly upregulated in both the VR and VNR groups; concomitantly, CD8A was found to be statistically significantly downregulated only in VRs. In the TLR array, only LBP and MAPK8 were found to be differentially regulated. In the antigen processing array, HLA-A, HLA-C, HLA-DMA, HLA-DMB, HLA-F, PSMA5, PSMB8, and PSMB9 were differentially downregulated. Based on these findings, it was determined that sinecatechins treatment modulates and downregulates genes involved in the pro-inflammatory response to HPV infection.
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Affiliation(s)
- Hung Q Doan
- 1 Department of Dermatology, University of Texas Health Science Center , Houston, Texas
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16
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Chen D, Gyllensten U. Lessons and implications from association studies and post-GWAS analyses of cervical cancer. Trends Genet 2014; 31:41-54. [PMID: 25467628 DOI: 10.1016/j.tig.2014.10.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/27/2014] [Accepted: 10/28/2014] [Indexed: 12/30/2022]
Abstract
Cervical cancer has a heritable genetic component. A large number of genetic associations with cervical cancer have been reported in hypothesis-driven candidate gene studies, but many of these results are either inconsistent or have failed to be independently replicated. Genome-wide association studies (GWAS) have identified additional susceptibility loci previously not implicated in cervical cancer development, highlighting the power of genome-wide unbiased association analyses. Post-GWAS analyses including pathway-based analysis and functional characterization of associated variants have provided new insights into the pathogenesis of cervical cancer. In this review we summarize findings from candidate gene association studies, GWAS, and post-GWAS analyses of cervical cancer. We also discuss gaps in our understanding, possible clinical implications of the findings, and lessons for studies of other complex diseases.
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Affiliation(s)
- Dan Chen
- Ministry of Education and Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Uppsala, Sweden.
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Uppsala, Sweden
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