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Olmedo-Suárez MÁ, Ramírez-Díaz I, Pérez-González A, Molina-Herrera A, Coral-García MÁ, Lobato S, Sarvari P, Barreto G, Rubio K. Epigenetic Regulation in Exposome-Induced Tumorigenesis: Emerging Roles of ncRNAs. Biomolecules 2022; 12:513. [PMID: 35454102 PMCID: PMC9032613 DOI: 10.3390/biom12040513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 02/06/2023] Open
Abstract
Environmental factors, including pollutants and lifestyle, constitute a significant role in severe, chronic pathologies with an essential societal, economic burden. The measurement of all environmental exposures and assessing their correlation with effects on individual health is defined as the exposome, which interacts with our unique characteristics such as genetics, physiology, and epigenetics. Epigenetics investigates modifications in the expression of genes that do not depend on the underlying DNA sequence. Some studies have confirmed that environmental factors may promote disease in individuals or subsequent progeny through epigenetic alterations. Variations in the epigenetic machinery cause a spectrum of different disorders since these mechanisms are more sensitive to the environment than the genome, due to the inherent reversible nature of the epigenetic landscape. Several epigenetic mechanisms, including modifications in DNA (e.g., methylation), histones, and noncoding RNAs can change genome expression under the exogenous influence. Notably, the role of long noncoding RNAs in epigenetic processes has not been well explored in the context of exposome-induced tumorigenesis. In the present review, our scope is to provide relevant evidence indicating that epigenetic alterations mediate those detrimental effects caused by exposure to environmental toxicants, focusing mainly on a multi-step regulation by diverse noncoding RNAs subtypes.
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Affiliation(s)
- Miguel Ángel Olmedo-Suárez
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Ivonne Ramírez-Díaz
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Facultad de Biotecnología, Campus Puebla, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla 72410, Mexico
| | - Andrea Pérez-González
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Alejandro Molina-Herrera
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Miguel Ángel Coral-García
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Decanato de Ciencias de la Salud, Campus Puebla, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla 72410, Mexico
| | - Sagrario Lobato
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Pouya Sarvari
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
| | - Guillermo Barreto
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Laboratoire IMoPA, CNRS, Université de Lorraine, UMR 73635 Nancy, France
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Karla Rubio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
- Laboratoire IMoPA, CNRS, Université de Lorraine, UMR 73635 Nancy, France
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
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Xie W, Sun H, Li X, Lin F, Wang Z, Wang X. Ovarian cancer: epigenetics, drug resistance, and progression. Cancer Cell Int 2021; 21:434. [PMID: 34404407 PMCID: PMC8369623 DOI: 10.1186/s12935-021-02136-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 08/03/2021] [Indexed: 03/05/2023] Open
Abstract
Ovarian cancer (OC) is one of the most common malignant tumors in women. OC is associated with the activation of oncogenes, the inactivation of tumor suppressor genes, and the activation of abnormal cell signaling pathways. Moreover, epigenetic processes have been found to play an important role in OC tumorigenesis. Epigenetic processes do not change DNA sequences but regulate gene expression through DNA methylation, histone modification, and non-coding RNA. This review comprehensively considers the importance of epigenetics in OC, with a focus on microRNA and long non-coding RNA. These types of RNA are promising molecular markers and therapeutic targets that may support precision medicine in OC. DNA methylation inhibitors and histone deacetylase inhibitors may be useful for such targeting, with a possible novel approach combining these two therapies. Currently, the clinical application of such epigenetic approaches is limited by multiple obstacles, including the heterogeneity of OC, insufficient sample sizes in reported studies, and non-optimized methods for detecting potential tumor markers. Nonetheless, the application of epigenetic approaches to OC patient diagnosis, treatment, and prognosis is a promising area for future clinical investigation.
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Affiliation(s)
- Weiwei Xie
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University School of Medicine Xinhua Hospital, 1665 Kongjiang Road, Yangpu District, Shanghai, China
| | - Huizhen Sun
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University School of Medicine Xinhua Hospital, 1665 Kongjiang Road, Yangpu District, Shanghai, China
| | - Xiaoduan Li
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Feikai Lin
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University School of Medicine Xinhua Hospital, 1665 Kongjiang Road, Yangpu District, Shanghai, China
| | - Ziliang Wang
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University School of Medicine Xinhua Hospital, 1665 Kongjiang Road, Yangpu District, Shanghai, China.
| | - Xipeng Wang
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University School of Medicine Xinhua Hospital, 1665 Kongjiang Road, Yangpu District, Shanghai, China.
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Zamaraev AV, Volik PI, Sukhikh GT, Kopeina GS, Zhivotovsky B. Long non-coding RNAs: A view to kill ovarian cancer. Biochim Biophys Acta Rev Cancer 2021; 1876:188584. [PMID: 34157315 DOI: 10.1016/j.bbcan.2021.188584] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 12/22/2022]
Abstract
An emerging role of long non-coding RNAs (lncRNAs) in tumor progression has been revealed in the last decade. Through interactions with nucleic acids and proteins, lncRNAs could act as enhancers, scaffolds or decoys for a number of oncoproteins and tumor suppressors. The aberrant lncRNA expression or mutations are often associated with changes in a variety of cellular processes, including proliferation, stress response and cell death. Here, we will focus on the tumor-associated lncRNAs in ovarian cancer according to their contribution to cancer hallmarks, such as intense proliferation, cell death resistance, altered energy metabolism, invasion and metastasis, and immune evasion. Moreover, the potential clinical implications of lncRNAs and their significance for the diagnosis, prognosis and therapy of ovarian cancer will be discussed.
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Affiliation(s)
- Alexey V Zamaraev
- Faculty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Pavel I Volik
- Faculty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Gennady T Sukhikh
- V. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, 117997 Moscow, Russia
| | - Gelina S Kopeina
- Faculty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia.
| | - Boris Zhivotovsky
- Faculty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia; Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 210, 17177 Stockholm, Sweden.
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Harvey G, Pham CT, Inacio MC, Laver K, Lynch EA, Jorissen RN, Karnon J, Bourke A, Forward J, Maddison J, Whitehead C, Rupa J, McNamara C, Crotty M. An integrated knowledge translation approach to address avoidable rehospitalisations and unplanned admissions for older people in South Australia: implementation and evaluation program plan. Implement Sci Commun 2021; 2:36. [PMID: 33827707 PMCID: PMC8025566 DOI: 10.1186/s43058-021-00141-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 03/22/2021] [Indexed: 12/20/2022] Open
Abstract
Background Repeated admission to hospital can be stressful for older people and their families and puts additional pressure on the health care system. While there is some evidence about strategies to better integrate care, improve older patients’ experiences at transitions of care, and reduce preventable hospital readmissions, implementing these strategies at scale is challenging. This program of research comprises multiple, complementary research activities with an overall goal of improving the care for older people after discharge from hospital. The program leverages existing large datasets and an established collaborative network of clinicians, consumers, academics, and aged care providers. Methods The program of research will take place in South Australia focusing on people aged 65 and over. Three inter-linked research activities will be the following: (1) analyse existing registry data to profile individuals at high risk of emergency department encounters and hospital admissions; (2) evaluate the cost-effectiveness of existing ‘out-of-hospital’ programs provided within the state; and (3) implement a state-wide quality improvement collaborative to tackle key interventions likely to improve older people’s care at points of transitions. The research is underpinned by an integrated approach to knowledge translation, actively engaging a broad range of stakeholders to optimise the relevance and sustainability of the changes that are introduced. Discussion This project highlights the uniqueness and potential value of bringing together key stakeholders and using a multi-faceted approach (risk profiling; evaluation framework; implementation and evaluation) for improving health services. The program aims to develop a practical and scalable solution to a challenging health service problem for frail older people and service providers.
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Affiliation(s)
- Gillian Harvey
- College of Nursing and Health Sciences, Flinders University, Adelaide, Australia
| | - Clarabelle T Pham
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, Australia
| | - Maria C Inacio
- Registry of Senior Australians, South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Kate Laver
- Division of Rehabilitation, Aged and Palliative Care, College of Medicine and Public Health, Flinders Medical Centre, Flinders University, Adelaide, Australia
| | - Elizabeth A Lynch
- College of Nursing and Health Sciences, Flinders University, Adelaide, Australia
| | - Robert N Jorissen
- Registry of Senior Australians, South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Jonathan Karnon
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, Australia
| | - Alice Bourke
- Department of Geriatric and Rehabilitation Medicine, Royal Adelaide Hospital, Adelaide, Australia
| | - John Forward
- Aged Care, Rehabilitation and Palliative Care Division, Northern Adelaide Local Health Network, Adelaide, Australia
| | - John Maddison
- Medical Services, Northern Adelaide Local Health Network, Adelaide, Australia
| | - Craig Whitehead
- Division of Rehabilitation, Aged and Palliative Care, College of Medicine and Public Health, Flinders Medical Centre, Flinders University, Adelaide, Australia
| | - Jesmin Rupa
- Division of Rehabilitation, Aged and Palliative Care, College of Medicine and Public Health, Flinders Medical Centre, Flinders University, Adelaide, Australia.
| | - Carmel McNamara
- Adelaide Nursing School, University of Adelaide, Adelaide, Australia
| | - Maria Crotty
- Division of Rehabilitation, Aged and Palliative Care, College of Medicine and Public Health, Flinders Medical Centre, Flinders University, Adelaide, Australia
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Liu J, Lv D, Wang X, Wang R, Li X. Systematic Profiling of Alternative Splicing Events in Ovarian Cancer. Front Oncol 2021; 11:622805. [PMID: 33763357 PMCID: PMC7982604 DOI: 10.3389/fonc.2021.622805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/15/2021] [Indexed: 12/02/2022] Open
Abstract
Alternative splicing (AS) is significantly related to the development of tumor and the clinical outcome of patients. In this study, our aim was to systematically analyze the survival-related AS signal in ovarian serous cystadenocarcinoma (OV) and estimate its prognostic validity in 48,049 AS events out of 21,854 genes. We studied 1,429 AS events out of 1,125 genes, which were significantly related to the overall survival (OS) in patients with OV. We established alternative splicing features on the basis of seven AS events and constructed a new comprehensive prognostic model. Kaplan-Meier curve analysis showed that seven AS characteristics and comprehensive prognostic models could strongly stratify patients with ovarian cancer and make them distinctive prognosis. ROC analysis from 0.781 to 0.888 showed that these models were highly efficient in distinguishing patient survival. We also verified the prognostic characteristics of these models in a testing cohort. In addition, uni-variate and multivariate Cox analysis showed that these models were superior independent risk factors for OS in patients with OV. Interestingly, AS events and splicing factor (SFs) networks revealed an important link between these prognostic alternative splicing genes and splicing factors. We also found that the comprehensive prognosis model signature had higher prediction ability than the mRNA signature. In summary, our study provided a possible prognostic prediction model for patients with OV and revealed the splicing network between AS and SFs, which could be used as a potential predictor and therapeutic target for patients with OV.
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Affiliation(s)
- Jia Liu
- Department of Gynecology, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, Shenyang, China
| | - Dekang Lv
- Cancer Center, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Xiaobin Wang
- Department of Gynecology, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, Shenyang, China
| | - Ruicong Wang
- Department of Gynecology and Obsterics, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xiaodong Li
- Cancer Center, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
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Liang H, Bai Y, Wang H, Yang X. Identification of LncRNA Prognostic Markers for Ovarian Cancer by Integration of Co-expression and CeRNA Network. Front Genet 2021; 11:566497. [PMID: 33664764 PMCID: PMC7920993 DOI: 10.3389/fgene.2020.566497] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 11/03/2020] [Indexed: 02/05/2023] Open
Abstract
Background Ovarian cancer (OC), one of the most prevalent gynecological malignancies, is characterized by late detection and dismal prognosis. Recent studies show that long non-coding RNAs (lncRNAs) in competitive endogenous RNA (ceRNA) networks influence immune infiltration and cancer prognosis. However, the function of lncRNA in OC immune infiltration and prognosis remains unclear. Methods Transcriptomes of 378 OC samples and clinical data were retrieved from the TCGA repository. Modules related to immune cells were identified using weighted gene co-expression network analysis (WGCNA). Functional enrichment analysis and survival analysis were then performed for the identification of immune-related lncRNAs in the brown module using Cox regression model. Finally, a ceRNA network was constructed by using the lncRNAs and mRNAs from the brown module. Results We found lncRNAs and mRNAs in the brown module to be significantly associated with immune cells in OC and identified 4 lncRNAs as potential OC prognostic markers. We further established that lncRNAs in the ceRNA network influence OC immune infiltration and prognosis by regulating miRNA, ultimately modulating mRNA levels. Conclusion We have identified 4 lncRNAs as independent immune prognostic factors for OC. Furthermore, our findings offer novel insight into lncRNAs as OC immune and prognostic biomarkers.
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Affiliation(s)
- Huisheng Liang
- Department of Gynecology and Obstetrics, The Affiliated Zhongshan Hospital of Xiamen University, Xiamen, China.,Organ Transplantation Institute, School of Medicine, Xiamen University, Xiamen, China
| | - Yuquan Bai
- Department of Thoracic Surgery, West China Hospital of Sichuan University, Chengdu, China
| | - Hailong Wang
- Organ Transplantation Institute, School of Medicine, Xiamen University, Xiamen, China.,Department of Basic Medicine, School of Medicine, Xiamen University, Xiamen, China
| | - Xiangjun Yang
- Department of Gynecology and Obstetrics, The Affiliated Zhongshan Hospital of Xiamen University, Xiamen, China
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Han Y, Wang J, Xu B. Novel biomarkers and prediction model for the pathological complete response to neoadjuvant treatment of triple-negative breast cancer. J Cancer 2021; 12:936-945. [PMID: 33403050 PMCID: PMC7778555 DOI: 10.7150/jca.52439] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/12/2020] [Indexed: 12/16/2022] Open
Abstract
Objective: To develop and validate a prediction model for the pathological complete response (pCR) to neoadjuvant chemotherapy (NCT) of triple-negative breast cancer (TNBC). Methods: We systematically searched Gene Expression Omnibus, ArrayExpress, and PubMed for the gene expression profiles of operable TNBC accessible to NCT. Molecular heterogeneity was detected with hierarchical clustering method, and the biological profiles of differentially expressed genes were investigated by Gene Ontology, Kyoto Encyclopedia of Genes and Genomes analyses, and Gene Set Enrichment Analysis (GSEA). Next, machine-learning algorithms including random-forest analysis and least absolute shrinkage and selection operator (LASSO) analysis were synchronously performed and, then, the intersected proportion of significant genes was undergone binary logistic regression to fulfill variables selection. The predictive response score (pRS) system was built as the product of the gene expression and coefficient obtained from the logistic analysis. Last, the cohorts were randomly divided in a 7:3 ratio into training cohort and validation cohort for the introduction of a robust model, and a nomogram was constructed with the independent predictors for pCR rate. Results: A total of 217 individuals from four cohort datasets (GSE32646, GSE25065, GSE25055, GSE21974) with complete clinicopathological information were included. Based on the microarray data, a six-gene panel (ATP4B, FBXO22, FCN2, RRP8, SMERK2, TET3) was identified. A robust nomogram, adopting pRS and clinical tumor size stage, was established and the performance was successively validated by calibration curves and receiver operating characteristic curves with the area under curve 0.704 and 0.756, respectively. Results of GSEA revealed that the biological processes including apoptosis, hypoxia, mTORC1 signaling and myogenesis, and oncogenic features of EGFR and RAF were in proactivity to attribute to an inferior response. Conclusions: This study provided a robust prediction model for pCR rate and revealed potential mechanisms of distinct response to NCT in TNBC, which were promising and warranted to further validate in the perspective.
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Affiliation(s)
- Yiqun Han
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College. No. 17, Panjiayuan Nanli, Chaoyang District, Beijing 100021, China
| | - Jiayu Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College. No. 17, Panjiayuan Nanli, Chaoyang District, Beijing 100021, China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College. No. 17, Panjiayuan Nanli, Chaoyang District, Beijing 100021, China
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Qing L, Gu P, Liu M, Shen J, Liu X, Guang R, Ke K, Huang Z, Lee W, Zhao H. Extracellular Matrix-Related Six-lncRNA Signature as a Novel Prognostic Biomarker for Bladder Cancer. Onco Targets Ther 2020; 13:12521-12538. [PMID: 33324071 PMCID: PMC7733340 DOI: 10.2147/ott.s284167] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/10/2020] [Indexed: 12/11/2022] Open
Abstract
Introduction Bladder cancer (BC) is the fourth-commones cancer and the sixth-leading cause of cancer-related death among men. However, a lack of reliable biomarkers remains a problem forprognosis and treatment of BC. lncRNAs have been shown to play important roles in various cancers, and have emerged as promising biomarkers for cancer prognosis and treatment. Methods In this study, using univariate and multivariate Cox regression analysis, we examined the differential expression profiles of 1,651 lncRNAs in the TCGA BLCA cohort and created a prognostic gene signature composed of six lncRNAs (for SNHG12, MAFG-DT, ASMTL-AS1, LINC02321, LINC01322, and LINC00922), designed the SMALLL signature. Results The SMALLL signature displayed significant prognostic power for overall survival for BC patients in multiple cohorts. Gene Ontology analysis showed that genes coexpressed with the SMALLL signature were associated with the extracellular matrix network, and immune cell–infiltration analysis showed that activated naïve B cells, regulatory T cells, M0 macrophages, eosinophils, resting memory CD4 T cells and resting NK cells were significantly different in high- and low-risk groups. We also confirmed differential expression of the lncRNAs of the SMALLL signature in BC tissue and paracancer normal tissue by qRT-PCR analysis. Cell-invasion and -migration experiments showed that MAFG-AS1, ASMTL-AS1, LINC02321, and LINC00922 significantly affected cell invasion and migration. Conclusion Our study revealed that the lncRNA signature is an important predictive factor of prognosis and provides a promising biomarker for BC.
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Affiliation(s)
- Liangliang Qing
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People's Republic of China
| | - Peng Gu
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People's Republic of China
| | - Mingsheng Liu
- Second Ward of Urology, Qujing Affiliated Hospital of Kunming Medical University, Qujing, Yunnan, People's Republic of China
| | - Jihong Shen
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People's Republic of China
| | - Xiaodong Liu
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People's Republic of China
| | - Runyun Guang
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People's Republic of China
| | - Kunbin Ke
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People's Republic of China
| | - Zhuo Huang
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People's Republic of China
| | - Wenhui Lee
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People's Republic of China.,Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming, Yunnan, People's Republic of China
| | - Hui Zhao
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People's Republic of China
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Zhao X, He M. Comprehensive pathway-related genes signature for prognosis and recurrence of ovarian cancer. PeerJ 2020; 8:e10437. [PMID: 33344083 PMCID: PMC7718801 DOI: 10.7717/peerj.10437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/06/2020] [Indexed: 12/14/2022] Open
Abstract
Background Ovarian cancer (OC) is a highly malignant disease with a poor prognosis and high recurrence rate. At present, there is no accurate strategy to predict the prognosis and recurrence of OC. The aim of this study was to identify gene-based signatures to predict OC prognosis and recurrence. Methods mRNA expression profiles and corresponding clinical information regarding OC were collected from The Cancer Genome Atlas (TCGA) database. Gene set enrichment analysis (GSEA) and LASSO analysis were performed, and Kaplan–Meier curves, time-dependent ROC curves, and nomograms were constructed using R software and GraphPad Prism7. Results We first identified several key signalling pathways that affected ovarian tumorigenesis by GSEA. We then established a nine-gene-based signature for overall survival (OS) and a five-gene-based-signature for relapse-free survival (RFS) using LASSO Cox regression analysis of the TCGA dataset and validated the prognostic value of these signatures in independent GEO datasets. We also confirmed that these signatures were independent risk factors for OS and RFS by multivariate Cox analysis. Time-dependent ROC analysis showed that the AUC values for OS and RFS were 0.640, 0.663, 0.758, and 0.891, and 0.638, 0.722, 0.813, and 0.972 at 1, 3, 5, and 10 years, respectively. The results of the nomogram analysis demonstrated that combining two signatures with the TNM staging system and tumour status yielded better predictive ability. Conclusion In conclusion, the two-gene-based signatures established in this study may serve as novel and independent prognostic indicators for OS and RFS.
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Affiliation(s)
- Xinnan Zhao
- Department of Rheumatology and Immunology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Miao He
- Department of Pharmacology, China Medical University, Shenyang, China
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10
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Chen Q, Hu L, Huang D, Chen K, Qiu X, Qiu B. Six-lncRNA Immune Prognostic Signature for Cervical Cancer. Front Genet 2020; 11:533628. [PMID: 33173530 PMCID: PMC7591729 DOI: 10.3389/fgene.2020.533628] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/21/2020] [Indexed: 12/13/2022] Open
Abstract
Background This study searched for immune-related long noncoding RNAs (lncRNAs) to predict the prognosis of patients with cervical cancer. Method We obtained immunologically relevant lncRNA expression profiles and clinical follow-up data from cervical cancer patients from The Cancer Genome Atlas database and the Molecular Signatures Database. Cervical cancer patients were randomly divided into a training group, testing group and combined group. The immune prognostic signature was constructed by Least Absolute Shrinkage and Selection Operator Cox regression, prognosis was analyzed by Kaplan-Meier curves between different groups, and the accuracy of the prognostic model was assessed by receiver operating characteristic-area under the curve (ROC-AUC) analysis. Results A six-lncRNA immune prognostic signature (LIPS) was constructed to predict the prognosis of cervical cancer. The six lncRNAs are as follows: AC009065.8, LINC01871, MIR210HG, GEMIN7-AS1, GAS5-AS1, and DLEU1. A ROC-AUC analysis indicated that the model could predict the prognosis of cervical cancer patients in different subgroups. A Kaplan-Meier analysis showed that patients with high risk scores had a poor prognosis; these results were equally meaningful in the subgroup analyses. Risk scores differed depending on the clinical pathology and tumor grade and were independent risk factors for cervical cancer prognosis. Gene set enrichment analysis revealed an association between the LIPS and the immune response, Wnt signaling pathway, and TGF beta signaling pathway. Conclusion Our study shows that the six-LIPS can predict the prognosis of cervical cancer and contribute to decisions regarding the immunotherapeutic strategy.
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Affiliation(s)
- Qian Chen
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Lang Hu
- Guangxi Medical University Cancer Hospital, Nanning, China
| | - Dongping Huang
- Department of Nutrition, School of Public Health, Guangxi Medical University, Nanning, China
| | - Kaihua Chen
- Department of Radiation Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Xiaoqiang Qiu
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, China
| | - Bingqing Qiu
- Department of Nuclear Medicine, Guangxi Medical University Cancer Hospital, Nanning, China
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11
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Calanca N, Abildgaard C, Rainho CA, Rogatto SR. The Interplay between Long Noncoding RNAs and Proteins of the Epigenetic Machinery in Ovarian Cancer. Cancers (Basel) 2020; 12:E2701. [PMID: 32967233 PMCID: PMC7563210 DOI: 10.3390/cancers12092701] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/09/2020] [Accepted: 09/16/2020] [Indexed: 12/19/2022] Open
Abstract
Comprehensive large-scale sequencing and bioinformatics analyses have uncovered a myriad of cancer-associated long noncoding RNAs (lncRNAs). Aberrant expression of lncRNAs is associated with epigenetic reprogramming during tumor development and progression, mainly due to their ability to interact with DNA, RNA, or proteins to regulate gene expression. LncRNAs participate in the control of gene expression patterns during development and cell differentiation and can be cell and cancer type specific. In this review, we described the potential of lncRNAs for clinical applications in ovarian cancer (OC). OC is a complex and heterogeneous disease characterized by relapse, chemoresistance, and high mortality rates. Despite advances in diagnosis and treatment, no significant improvements in long-term survival were observed in OC patients. A set of lncRNAs was associated with survival and response to therapy in this malignancy. We manually curated databases and used bioinformatics tools to identify lncRNAs implicated in the epigenetic regulation, along with examples of direct interactions between the lncRNAs and proteins of the epigenetic machinery in OC. The resources and mechanisms presented herein can improve the understanding of OC biology and provide the basis for further investigations regarding the selection of novel biomarkers and therapeutic targets.
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Affiliation(s)
- Naiade Calanca
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (N.C.); (C.A.R.)
| | - Cecilie Abildgaard
- Department of Oncology, University Hospital of Southern Denmark-Vejle, Institute of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark;
- Department of Clinical Genetics, University Hospital of Southern Denmark-Vejle, Institute of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Cláudia Aparecida Rainho
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (N.C.); (C.A.R.)
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, University Hospital of Southern Denmark-Vejle, Institute of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
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12
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Li X, Yu S, Yang R, Wang Q, Liu X, Ma M, Li Y, Wu S. Identification of lncRNA-associated ceRNA network in high-grade serous ovarian cancer metastasis. Epigenomics 2020; 12:1175-1191. [PMID: 32462930 DOI: 10.2217/epi-2020-0097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aim: To uncover a novel lncRNA-miRNA-mRNA network associated with high-grade serous ovarian cancer metastasis. Material & methods: The candidate differentially expressed lncRNAs were obtained from RNA-sequencing data and determined by functional experiments. The downstream miRNAs and mRNAs were identified by bioinformatic prediction and subjected to functional enrichment analysis. Results: The expression levels of lncRNA ENTPD1-AS1/PRANCR/NR2F2-AS1 were reduced in omental metastatic tissues. Similar differential expression patterns of these lncRNAs were also found in lnCAR database and we verified their tumor suppressive roles by performing functional experiments. Furthermore, we predicted miRNAs and mRNAs via bioinformatic tools and validated their alteration in expression levels in presence of lncRNA interference. Conclusion: We proposed a potential ceRNA regulatory mechanism in high-grade serous ovarian cancer omental metastasis.
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Affiliation(s)
- Xi Li
- Department of Obstetrics & Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sihui Yu
- Department of Obstetrics & Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rui Yang
- Department of Obstetrics & Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qi Wang
- Trauma Center, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiangnan Liu
- Department of Obstetrics & Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingjun Ma
- Department of Obstetrics & Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanli Li
- Department of Obstetrics & Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sufang Wu
- Department of Obstetrics & Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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