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Ma X, Chen L, Chen T, Chen K, Zhang H, Huang K, Zheng H, Jin H, Cheng Z, Xiao K, Guo J. Identification of a 24-gene panel and a novel marker of PODXL2 essential for the pathological diagnosis of early prostate cancer. Comput Struct Biotechnol J 2023; 21:5476-5490. [PMID: 38022698 PMCID: PMC10663703 DOI: 10.1016/j.csbj.2023.10.044] [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: 07/20/2023] [Revised: 10/13/2023] [Accepted: 10/22/2023] [Indexed: 12/01/2023] Open
Abstract
Precise diagnosis of early prostate cancer (PCa) is critical for preventing tumor progression. However, the diagnostic outcomes of currently used markers are far from satisfactory due to the low sensitivity or specificity. Here, we identified a diagnostic subpopulation in PCa tissue with the integrating analysis of single-cell and bulk RNA-seq. The representative markers of this subpopulation were extracted to perform intersection analysis with early-PCa-related gene module generated from weighted correlation network analysis (WGCNA). A total of 24 overlapping genes were obtained, the diagnostic roles of which were validated by distinguishing normal and tumorous prostate samples from the public dataset. A least absolute shrinkage and selection operator (LASSO) model was constructed based on these genes and the obtained 24-gene panel showed high sensitivity and specificity for PCa diagnosis, with better identifying capability of PCa than the commercially used gene panel of Oncotype DX. The top two risk factors, TRPM4 and PODXL2, were verified to be highly expressed in early PCa tissues by multiplex immunostaining, and PODXL2 was more sensitive and specific compared to TRPM4 and the pathologically used marker AMACR for early PCa diagnosis, suggesting a novel and promising pathology marker.
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Affiliation(s)
- Xiaoshi Ma
- Department of Urology, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
- Clinical Research Center for Geriatrtics, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
| | - Lipeng Chen
- Clinical Medical Research Center, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
| | - Tao Chen
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Kun Chen
- Department of Radiotherapy, Nanjing Medical University The Fourth School of Clinical Medicine, Nanjing 210000, Jiangsu, China
| | - Huirong Zhang
- Clinical Medical Research Center, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
| | - Kaipeng Huang
- Department of Pathology, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
| | - Han Zheng
- Department of Urology, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu 241000, Anhui, China
| | - Hongtao Jin
- Department of Radiotherapy, Nanjing Medical University The Fourth School of Clinical Medicine, Nanjing 210000, Jiangsu, China
| | - Zhiqiang Cheng
- Department of Pathology, Third People’s Hospital of Shenzhen (The Second Affiliated Hospital of Southern University of Science and Technology), Shenzhen 518100, Guangdong, China
| | - Kefeng Xiao
- Department of Urology, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
- Clinical Research Center for Geriatrtics, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
| | - Jinan Guo
- Department of Urology, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
- Clinical Research Center for Geriatrtics, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
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2
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Hu D, Cao Q, Tong M, Ji C, Li Z, Huang W, Jin Y, Tong G, Wang Y, Li P, Zhang H. A novel defined risk signature based on pyroptosis-related genes can predict the prognosis of prostate cancer. BMC Med Genomics 2022; 15:24. [PMID: 35135561 PMCID: PMC8822680 DOI: 10.1186/s12920-022-01172-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/31/2022] [Indexed: 11/23/2022] Open
Abstract
Background Pyroptosis can not only inhibit the occurrence and development of tumors but also develop a microenvironment conducive to cancer growth. However, pyroptosis research in prostate cancer (PCa) has rarely been reported. Methods The expression profile and corresponding clinical data were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Patients were divided into different clusters using consensus clustering analysis, and differential genes were obtained. We developed and validated a prognostic biomarker for biochemical recurrence (BCR) of PCa using univariate Cox analysis, Lasso-Cox analysis, Kaplan–Meier (K–M) survival analysis, and time-dependent receiver operating characteristics (ROC) curves. Results The expression levels of most pyroptosis-related genes (PRGs) are different not only between normal and tumor tissues but also between different clusters. Cluster 2 patients have a better prognosis than cluster 1 patients, and there are significant differences in immune cell content and biological pathway between them. Based on the classification of different clusters, we constructed an eight genes signature that can independently predict the progression-free survival (PFS) rate of a patient, and this signature was validated using a GEO data set (GSE70769). Finally, we established a nomogram model with good accuracy. Conclusions In this study, PRGs were used as the starting point and based on the expression profile and clinical data, a prognostic signature with a high predictive value for biochemical recurrence (BCR) following radical prostatectomy (RP) was finally constructed, and the relationship between pyroptosis, immune microenvironment, and PCa was explored, providing important clues for future research on pyroptosis and immunity. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01172-5.
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Affiliation(s)
- Ding Hu
- Department of Urology, Jinzhou Medical University, The First Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Qingfei Cao
- Department of Urology, Jinzhou Medical University, The First Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Ming Tong
- Department of Urology, Jinzhou Medical University, The First Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China.
| | - Chundong Ji
- Department of Urology, Affiliated Hospital of Panzhihua University, Panzhihua, Sichuan, China.
| | - Zizhi Li
- Department of Urology, Jinzhou Medical University, The First Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Weichao Huang
- Department of Urology, Jinzhou Medical University, The First Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Yanyang Jin
- Department of Urology, Jinzhou Medical University, The First Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Guangquan Tong
- Department of Urology, Jinzhou Medical University, The First Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Yutao Wang
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Pengfei Li
- Department of Urology, Jinzhou Medical University, The First Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Huashan Zhang
- Department of Urology, Jinzhou Medical University, The First Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
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Abstract
Optogenetics combines light and genetics to enable precise control of living cells, tissues, and organisms with tailored functions. Optogenetics has the advantages of noninvasiveness, rapid responsiveness, tunable reversibility, and superior spatiotemporal resolution. Following the initial discovery of microbial opsins as light-actuated ion channels, a plethora of naturally occurring or engineered photoreceptors or photosensitive domains that respond to light at varying wavelengths has ushered in the next chapter of optogenetics. Through protein engineering and synthetic biology approaches, genetically-encoded photoswitches can be modularly engineered into protein scaffolds or host cells to control a myriad of biological processes, as well as to enable behavioral control and disease intervention in vivo. Here, we summarize these optogenetic tools on the basis of their fundamental photochemical properties to better inform the chemical basis and design principles. We also highlight exemplary applications of opsin-free optogenetics in dissecting cellular physiology (designated "optophysiology"), and describe the current progress, as well as future trends, in wireless optogenetics, which enables remote interrogation of physiological processes with minimal invasiveness. This review is anticipated to spark novel thoughts on engineering next-generation optogenetic tools and devices that promise to accelerate both basic and translational studies.
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Affiliation(s)
- Peng Tan
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas, United States.,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Lian He
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas, United States
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, United States.,Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, Texas, United States
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas, United States.,Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, Texas, United States
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Pou Casellas C, Jansen K, Rookmaaker MB, Clevers H, Verhaar MC, Masereeuw R. Regulation of Solute Carriers OCT2 and OAT1/3 in the Kidney: A Phylogenetic, Ontogenetic and Cell Dynamic Perspective. Physiol Rev 2021; 102:993-1024. [PMID: 34486394 DOI: 10.1152/physrev.00009.2021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Over the course of more than 500 million years, the kidneys have undergone a remarkable evolution from primitive nephric tubes to intricate filtration-reabsorption systems that maintain homeostasis and remove metabolic end products from the body. The evolutionarily conserved solute carriers Organic Cation Transporter 2 (OCT2), and Organic Anion Transporters 1 and 3 (OAT1/3) coordinate the active secretion of a broad range of endogenous and exogenous substances, many of which accumulate in the blood of patients with kidney failure despite dialysis. Harnessing OCT2 and OAT1/3 through functional preservation or regeneration could alleviate the progression of kidney disease. Additionally, it would improve current in vitro test models that lose their expression in culture. With this review, we explore OCT2 and OAT1/3 regulation using different perspectives: phylogenetic, ontogenetic and cell dynamic. Our aim is to identify possible molecular targets to both help prevent or compensate for the loss of transport activity in patients with kidney disease, and to enable endogenous OCT2 and OAT1/3 induction in vitro in order to develop better models for drug development.
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Affiliation(s)
- Carla Pou Casellas
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, Netherlands.,Hubrecht Institute - Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands
| | - Katja Jansen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Maarten B Rookmaaker
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, Netherlands
| | - Hans Clevers
- Hubrecht Institute - Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands
| | - Marianne C Verhaar
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, Netherlands
| | - Rosalinde Masereeuw
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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Su Q, Liu Z, Chen C, Gao H, Zhu Y, Wang L, Pan M, Liu J, Yang X, Tian J. Gene signatures predict biochemical recurrence-free survival in primary prostate cancer patients after radical therapy. Cancer Med 2021; 10:6492-6502. [PMID: 34453418 PMCID: PMC8446568 DOI: 10.1002/cam4.4092] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/16/2021] [Accepted: 06/05/2021] [Indexed: 12/27/2022] Open
Abstract
Background This study evaluated the predictive value of gene signatures for biochemical recurrence (BCR) in primary prostate cancer (PCa) patients. Methods Clinical features and gene expression profiles of PCa patients were attained from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets, which were further classified into a training set (n = 419), a validation set (n = 403). The least absolute shrinkage and selection operator Cox (LASSO‐Cox) method was used to select discriminative gene signatures in training set for biochemical recurrence‐free survival (BCRFS). Selected gene signatures established a risk score system. Univariate and multivariate analyses of prognostic factors about BCRFS were performed using the Cox proportional hazards regression models. A nomogram based on multivariate analysis was plotted to facilitate clinical application. Kyoto Encyclopedia of Gene and Genomes (KEGG) and Gene Ontology (GO) analyses were then executed for differentially expressed genes (DEGs). Results Notably, the risk score could significantly identify BCRFS by time‐dependent receiver operating characteristic (t‐ROC) curves in the training set (3‐year area under the curve (AUC) = 0.820, 5‐year AUC = 0.809) and the validation set (3‐year AUC = 0.723, 5‐year AUC = 0.733). Conclusions Clinically, the nomogram model, which incorporates Gleason score and the risk score, could effectively predict BCRFS and potentially be utilized as a useful tool for the screening of BCRFS in PCa.
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Affiliation(s)
- Qiang Su
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine and Engineering, Beihang University, Beijing, China.,Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing, China.,Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China
| | - Zhenyu Liu
- CAS Key Laboratory of Molecular Imaging, Beijing Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Automation, Chinese Academy of Sciences, Beijing, China.,School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Chi Chen
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine and Engineering, Beihang University, Beijing, China.,Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China
| | - Han Gao
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine and Engineering, Beihang University, Beijing, China.,Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China
| | - Yongbei Zhu
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine and Engineering, Beihang University, Beijing, China.,Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China
| | - Liusu Wang
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine and Engineering, Beihang University, Beijing, China.,Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China
| | - Meiqing Pan
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine and Engineering, Beihang University, Beijing, China.,Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China
| | - Jiangang Liu
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine and Engineering, Beihang University, Beijing, China.,Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China
| | - Xin Yang
- CAS Key Laboratory of Molecular Imaging, Beijing Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China.,School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Jie Tian
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine and Engineering, Beihang University, Beijing, China.,Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China.,CAS Key Laboratory of Molecular Imaging, Beijing Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Automation, Chinese Academy of Sciences, Beijing, China.,Engineering Research Center of Molecular and Neuro Imaging of Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, China
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Timofte AD, Giuşcă SE, Lozneanu L, Manole MB, Prutianu I, Gafton B, Rusu A, Căruntu ID. HOXB13 and TFF3 can contribute to the prognostic stratification of prostate adenocarcinoma. ROMANIAN JOURNAL OF MORPHOLOGY AND EMBRYOLOGY = REVUE ROUMAINE DE MORPHOLOGIE ET EMBRYOLOGIE 2021; 62:41-52. [PMID: 34609407 PMCID: PMC8597359 DOI: 10.47162/rjme.62.1.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
Homeobox B13 (HOXB13) and trefoil factor 3 (TFF3) are novel candidates for the classification of prostate cancer (PC) in molecular subtypes that could predict the clinical evolution of patients. The aim of our study was to analyze the possible associations between HOXB13 and TFF3 immunohistochemical (IHC) expression in sporadic prostate adenocarcinoma (PAC), the potential prognostic value in relation to the classical clinico-pathological parameters, as well as their role in defining distinct molecular subtypes of this malignancy. The study group comprised 105 patients diagnosed with PAC who underwent radical prostatectomy. IHC exam was performed using anti-HOXB13 and anti-TFF3 antibodies and a scoring system that permit the separation of the cases into two subgroups, with low and high immunoexpression, respectively. The statistical analysis evaluated the relationship between the two immunomarkers and clinico-pathological parameters. The Kaplan-Meier curves and log-rank Mantel-Cox test were used for assessing the prostate-specific antigen (PSA)-progression free survival. Four subgroups of PAC were defined based on the IHC overexpression and low immunoexpression of HOXB13 and TFF3. High HOXB13 and TFF3 immunoexpression was commonly identified in cases characterized by a Gleason score over 7, a G4 or G5 dominant pattern, a grade group of 3 or 4 and a preoperatory PSA serum level over 20 ng/mL. HOXB13 overexpression was also associated with pathological tumor-node-metastasis (pTNM) stage. The subgroup with both low HOXB13 and TFF3 immunoexpression had the highest PSA-progression free interval, whereas the subgroup with high HOXB13 immunoexpression and low TFF3 immunoexpression presented the lowest rate, but no statistically significant differences were registered. Our results sustain the role of HOXB13 and TFF3 in the stratification of PAC. Further investigations in larger cohorts are imposed to validate the clinical significance of these subgroups in the diagnostic and prognostic of PAC.
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Affiliation(s)
- Andrei Daniel Timofte
- Department of Morphofunctional Sciences I, Grigore T. Popa University of Medicine and Pharmacy, Iaşi, Romania;
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Lam D, Clark S, Stirzaker C, Pidsley R. Advances in Prognostic Methylation Biomarkers for Prostate Cancer. Cancers (Basel) 2020; 12:E2993. [PMID: 33076494 PMCID: PMC7602626 DOI: 10.3390/cancers12102993] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 12/24/2022] Open
Abstract
There is a major clinical need for accurate biomarkers for prostate cancer prognosis, to better inform treatment strategies and disease monitoring. Current clinically recognised prognostic factors, including prostate-specific antigen (PSA) levels, lack sensitivity and specificity in distinguishing aggressive from indolent disease, particularly in patients with localised intermediate grade prostate cancer. There has therefore been a major focus on identifying molecular biomarkers that can add prognostic value to existing markers, including investigation of DNA methylation, which has a known role in tumorigenesis. In this review, we will provide a comprehensive overview of the current state of DNA methylation biomarker studies in prostate cancer prognosis, and highlight the advances that have been made in this field. We cover the numerous studies into well-established candidate genes, and explore the technological transition that has enabled hypothesis-free genome-wide studies and the subsequent discovery of novel prognostic genes.
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Affiliation(s)
- Dilys Lam
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
| | - Susan Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Clare Stirzaker
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Ruth Pidsley
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, New South Wales 2010, Australia
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Romero-Garcia S, Prado-Garcia H, Carlos-Reyes A. Role of DNA Methylation in the Resistance to Therapy in Solid Tumors. Front Oncol 2020; 10:1152. [PMID: 32850327 PMCID: PMC7426728 DOI: 10.3389/fonc.2020.01152] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022] Open
Abstract
Despite the recent advances in chemotherapeutic treatments against cancer, some types of highly aggressive and invasive cancer develop drug resistance against conventional therapies, which continues to be a major problem in the fight against cancer. In recent years, studies of alterations of DNA methylome have given us a better understanding of the role of DNA methylation in the development of tumors. DNA methylation (DNAm) is an epigenetic change that promotes the covalent transfer of methyl groups to DNA. This process suppresses gene expression through the modulation of the transcription machinery access to the chromatin or through the recruitment of methyl binding proteins. DNAm is regulated mainly by DNA methyltransferases. Aberrant DNAm contributes to tumor progression, metastasis, and resistance to current anti-tumoral therapies. Aberrant DNAm may occur through hypermethylation in the promoter regions of tumor suppressor genes, which leads to their silencing, while hypomethylation in the promoter regions of oncogenes can activate them. In this review, we discuss the impact of dysregulated methylation in certain genes, which impact signaling pathways associated with apoptosis avoidance, metastasis, and resistance to therapy. The analysis of methylome has revealed patterns of global methylation, which regulate important signaling pathways involved in therapy resistance in different cancer types, such as breast, colon, and lung cancer, among other solid tumors. This analysis has provided gene-expression signatures of methylated region-specific DNA that can be used to predict the treatment outcome in response to anti-cancer therapy. Additionally, changes in cancer methylome have been associated with the acquisition of drug resistance. We also review treatments with demethylating agents that, in combination with standard therapies, seem to be encouraging, as tumors that are in early stages can be successfully treated. On the other hand, tumors that are in advanced stages can be treated with these combination schemes, which could sensitize tumor cells that are resistant to the therapy. We propose that rational strategies, which combine specific demethylating agents with conventional treatment, may improve overall survival in cancer patients.
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Affiliation(s)
- Susana Romero-Garcia
- Department of Chronic-Degenerative Diseases, National Institute of Respiratory Diseases "Ismael Cosío Villegas", Mexico City, Mexico
| | - Heriberto Prado-Garcia
- Department of Chronic-Degenerative Diseases, National Institute of Respiratory Diseases "Ismael Cosío Villegas", Mexico City, Mexico
| | - Angeles Carlos-Reyes
- Department of Chronic-Degenerative Diseases, National Institute of Respiratory Diseases "Ismael Cosío Villegas", Mexico City, Mexico
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9
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Epigenetic Analysis of Circulating Tumor DNA in Localized and Metastatic Prostate Cancer: Evaluation of Clinical Biomarker Potential. Cells 2020; 9:cells9061362. [PMID: 32486483 PMCID: PMC7349912 DOI: 10.3390/cells9061362] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/25/2020] [Accepted: 05/28/2020] [Indexed: 12/19/2022] Open
Abstract
Novel and minimally-invasive prostate cancer (PCa)-specific biomarkers are needed to improve diagnosis and risk stratification. Here, we investigated the biomarker potential in localized and de novo metastatic PCa (mPCa) of methylated circulating tumor DNA (ctDNA) in plasma. Using the Marmal-aid database and in-house datasets, we identified three top candidates specifically hypermethylated in PCa tissue: DOCK2, HAPLN3, and FBXO30 (specificity/sensitivity: 80%-100%/75-94%). These candidates were further analyzed in plasma samples from 36 healthy controls, 61 benign prostatic hyperplasia (BPH), 102 localized PCa, and 65 de novo mPCa patients using methylation-specific droplet digital PCR. Methylated ctDNA for DOCK2/HAPLN3/FBXO30 was generally not detected in healthy controls, BPH patients, nor in patients with localized PCa despite a positive signal in 98%-100% of matched radical prostatectomy tissue samples. However, ctDNA methylation of DOCK2, HAPLN3, and/or FBXO30 was detected in 61.5% (40/65) of de novo mPCa patients and markedly increased in high- compared to low-volume mPCa (89.3% (25/28) vs. 32.1% (10/31), p < 0.001). Moreover, detection of methylated ctDNA was associated with significantly shorter time to progression to metastatic castration resistant PCa, independent of tumor-volume. These results indicate that methylated ctDNA (DOCK2/HAPLN3/FBXO30) may be potentially useful for identification of hormone-naïve mPCa patients who could benefit from intensified treatment.
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10
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Jahan R, Shah A, Kisling SG, Macha MA, Thayer S, Batra SK, Kaur S. Odyssey of trefoil factors in cancer: Diagnostic and therapeutic implications. Biochim Biophys Acta Rev Cancer 2020; 1873:188362. [PMID: 32298747 DOI: 10.1016/j.bbcan.2020.188362] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/01/2020] [Accepted: 04/01/2020] [Indexed: 02/07/2023]
Abstract
Trefoil factors 1, 2, and 3 (TFFs) are a family of small secretory molecules involved in the protection and repair of the gastrointestinal tract (GI). TFFs maintain and restore epithelial structural integrity via transducing key signaling pathways for epithelial cell migration, proliferation, and invasion. In recent years, TFFs have emerged as key players in the pathogenesis of multiple diseases, especially cancer. Initially recognized as tumor suppressors, emerging evidence demonstrates their key role in tumor progression and metastasis, extending their actions beyond protection. However, to date, a comprehensive understanding of TFFs' mechanism of action in tumor initiation, progression and metastasis remains obscure. The present review discusses the structural, functional and mechanistic implications of all three TFF family members in tumor progression and metastasis. Also, we have garnered information from studies on their structure and expression status in different organs, along with lessons from their specific knockout in mouse models. In addition, we highlight the emerging potential of using TFFs as a biomarker to stratify tumors for better therapeutic intervention.
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Affiliation(s)
- Rahat Jahan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, NE, 68198, USA
| | - Ashu Shah
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, NE, 68198, USA
| | - Sophia G Kisling
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, NE, 68198, USA
| | - Muzafar A Macha
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, NE, 68198, USA; Department of Otolaryngology-Head & Neck Surgery, University of Nebraska Medical Center, NE, 68198, USA; Department of Biotechnology, Central University of Kashmir, Ganderbal, Jammu and Kashmir, India -191201
| | - Sarah Thayer
- Division of Surgical Oncology, Department of Surgery, University of Nebraska Medical Center, NE, 68198, USA; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, NE, 68198, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, NE, 68198, USA; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, NE, 68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, NE 68198, USA.
| | - Sukhwinder Kaur
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, NE, 68198, USA.
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Zhang M, Wang B, Chong QY, Pandey V, Guo Z, Chen RM, Wang L, Wang Y, Ma L, Kumar AP, Zhu T, Wu ZS, Yin Z, Basappa, Goh BC, Lobie PE. A novel small-molecule inhibitor of trefoil factor 3 (TFF3) potentiates MEK1/2 inhibition in lung adenocarcinoma. Oncogenesis 2019; 8:65. [PMID: 31685806 PMCID: PMC6828705 DOI: 10.1038/s41389-019-0173-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 02/08/2023] Open
Abstract
TFF3 has been identified as a novel biomarker to distinguish between lung adenocarcinoma (ADC) and lung squamous-cell carcinoma (SCC). Herein, we determined the oncogenic functions of TFF3 and demonstrated the potential of pharmacological inhibition of TFF3 in lung ADC using a novel small-molecule inhibitor of TFF3 dimerization (AMPC). Forced expression of TFF3 in lung ADC cells enhanced cell proliferation and survival, increased anchorage-independent growth, cancer stem cell behavior, growth in 3D Matrigel, and cell migration and invasion. In contrast, depleted expression of TFF3 suppressed these cellular functions. Mechanistically, TFF3 exerted its oncogenic function through upregulation of ARAF and hence enhanced downstream activation of MEK1/2 and ERK1/2. Pharmacological inhibition of TFF3 by AMPC, resulted in markedly decreased cell survival, proliferation, 3D growth and foci formation, and impaired tumor growth in a xenograft mouse model. Moreover, the combination of various MEK1/2 inhibitors with AMPC exhibited synergistic inhibitory effects on lung ADC cell growth. In conclusion, this study provides the first evidence that TFF3 is a potent promoter of lung ADC progression. Targeting TFF3 with a novel small-molecule inhibitor alone or in combination with conventional MEK1/2 inhibitors are potential strategies to improve the outcome of lung ADC.
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Affiliation(s)
- Mengyi Zhang
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Baocheng Wang
- Biomedical Translational Research Institute, Jinan University, Guangzhou, China.,Tsinghua Berkeley Shenzhen Institute (TBSI), Tsinghua University, Shenzhen, China
| | - Qing-Yun Chong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Vijay Pandey
- Tsinghua Berkeley Shenzhen Institute (TBSI), Tsinghua University, Shenzhen, China.,Shenzhen Bay Laboratory, Shenzhen, Guangzhou, China
| | - Zhirong Guo
- Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Ru-Mei Chen
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Lingzhi Wang
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yanxin Wang
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Lan Ma
- Tsinghua Berkeley Shenzhen Institute (TBSI), Tsinghua University, Shenzhen, China
| | - Alan P Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Cancer Program, Medical Science Cluster, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tao Zhu
- Department of Oncology of the First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Zheng-Sheng Wu
- Department of Pathology, Anhui Medical University, Hefei, Anhui, China
| | - Zhinan Yin
- Biomedical Translational Research Institute, Jinan University, Guangzhou, China
| | - Basappa
- Laboratory of Chemical Biology, Department of Studies in Organic Chemistry, University of Mysore, Manasagangotri, Mysore, 570006, Karnataka, India
| | - Boon-Cher Goh
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Haematology-Oncology, National University Health System, Singapore, Singapore
| | - Peter E Lobie
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore. .,Tsinghua Berkeley Shenzhen Institute (TBSI), Tsinghua University, Shenzhen, China. .,Shenzhen Bay Laboratory, Shenzhen, Guangzhou, China.
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12
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Nørgaard M, Haldrup C, Bjerre MT, Høyer S, Ulhøi B, Borre M, Sørensen KD. Epigenetic silencing of MEIS2 in prostate cancer recurrence. Clin Epigenetics 2019; 11:147. [PMID: 31640805 PMCID: PMC6805635 DOI: 10.1186/s13148-019-0742-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 09/10/2019] [Indexed: 01/23/2023] Open
Abstract
Background Current diagnostic and prognostic tools for prostate cancer (PC) are suboptimal, resulting in overdiagnosis and overtreatment of clinically insignificant tumors. Thus, to improve the management of PC, novel biomarkers are urgently needed. Results In this study, we integrated genome-wide methylome (Illumina 450K DNA methylation array (450K)) and RNA sequencing (RNAseq) data performed in a discovery set of 27 PC and 15 adjacent normal (AN) prostate tissue samples to identify candidate driver genes involved in PC development and/or progression. We found significant enrichment for homeobox genes among the most aberrantly methylated and transcriptionally dysregulated genes in PC. Specifically, homeobox gene MEIS2 (Myeloid Ecotropic viral Insertion Site 2) was significantly hypermethylated (p < 0.0001, Mann-Whitney test) and transcriptionally downregulated (p < 0.0001, Mann-Whitney test) in PC compared to non-malignant prostate tissue in our discovery sample set, which was also confirmed in an independent validation set including > 500 PC and AN tissue samples in total (TCGA cohort analyzed by 450K and RNAseq). Furthermore, in three independent radical prostatectomy (RP) cohorts (n > 700 patients in total), low MEIS2 transcriptional expression was significantly associated with poor biochemical recurrence (BCR) free survival (p = 0.0084, 0.0001, and 0.0191, respectively; log-rank test). Next, we analyzed another RP cohort consisting of > 200 PC, AN, and benign prostatic hyperplasia (BPH) samples by quantitative methylation-specific PCR (qMSP) and found that MEIS2 was significantly hypermethylated (p < 0.0001, Mann-Whitney test) in PC compared to non-malignant prostate tissue samples (AN and BPH) with an AUC > 0.84. Moreover, in this cohort, aberrant MEIS2 hypermethylation was significantly associated with post-operative BCR (p = 0.0068, log-rank test), which was subsequently confirmed (p = 0.0067; log-rank test) in the independent TCGA validation cohort (497 RP patients; 450K data). Conclusions To the best of our knowledge, this is the first study to investigate, demonstrate, and independently validate a prognostic biomarker potential for MEIS2 at the transcriptional expression level and at the DNA methylation level in PC.
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Affiliation(s)
- Maibritt Nørgaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Christa Haldrup
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Marianne Trier Bjerre
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Høyer
- Department of Histopathology, Aarhus University Hospital, Aarhus, Denmark
| | - Benedicte Ulhøi
- Department of Histopathology, Aarhus University Hospital, Aarhus, Denmark
| | - Michael Borre
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Karina D Sørensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark. .,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
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13
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Song C, Chen H, Song C. Research status and progress of the RNA or protein biomarkers for prostate cancer. Onco Targets Ther 2019; 12:2123-2136. [PMID: 30962694 PMCID: PMC6434918 DOI: 10.2147/ott.s194138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Prostate cancer is a kind of male malignancy. Recently, a large number of studies have reported many potential biomarkers for the diagnosis and prognosis of prostate cancer. In this literature review, we have collected a number of potential biomarkers for prostate cancer reported in the last 5 years. Among them, some are undergoing Phase III clinical trials, and others have been approved by the US Food and Drug Administration. However, most are still in the period of basic research. The review will contribute to future research to find the biomarkers to guide clinicians to make personalized treatment decisions for each prostate cancer patient.
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Affiliation(s)
- Chunjiao Song
- Medical Research Center, Shaoxing People's Hospital/Shaoxing Hospital, Zhejiang University School of Medicine, Shaoxing, Zhejiang Province, China,
| | - Huan Chen
- Key Laboratory of Microorganism Technology and Bioinformatics Research of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, Zhejiang, China
| | - Chunyu Song
- Department of Anesthesia, The Second Clinical Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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14
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Carlos-Reyes Á, López-González JS, Meneses-Flores M, Gallardo-Rincón D, Ruíz-García E, Marchat LA, Astudillo-de la Vega H, Hernández de la Cruz ON, López-Camarillo C. Dietary Compounds as Epigenetic Modulating Agents in Cancer. Front Genet 2019; 10:79. [PMID: 30881375 PMCID: PMC6406035 DOI: 10.3389/fgene.2019.00079] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 01/28/2019] [Indexed: 12/15/2022] Open
Abstract
Epigenetic mechanisms control gene expression during normal development and their aberrant regulation may lead to human diseases including cancer. Natural phytochemicals can largely modulate mammalian epigenome through regulation of mechanisms and proteins responsible for chromatin remodeling. Phytochemicals are mainly contained in fruits, seeds, and vegetables as well as in foods supplements. These compounds act as powerful cellular antioxidants and anti-carcinogens agents. Several dietary compounds such as catechins, curcumin, genistein, quercetin and resveratrol, among others, exhibit potent anti-tumor activities through the reversion of epigenetic alterations associated to oncogenes activation and inactivation of tumor suppressor genes. In this review, we summarized the actual knowledge about the role of dietary phytochemicals in the restoration of aberrant epigenetic alterations found in cancer cells with a particular focus on DNA methylation and histone modifications. Furthermore, we discussed the mechanisms by which these natural compounds modulate gene expression at epigenetic level and described their molecular targets in diverse types of cancer. Modulation of epigenetic activities by phytochemicals will allow the discovery of novel biomarkers for cancer prevention, and highlights its potential as an alternative therapeutic approach in cancer.
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Affiliation(s)
- Ángeles Carlos-Reyes
- Laboratorio de Cáncer de Pulmón, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosio Villegas”, Mexico City, Mexico
| | - José Sullivan López-González
- Laboratorio de Cáncer de Pulmón, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosio Villegas”, Mexico City, Mexico
| | - Manuel Meneses-Flores
- Laboratorio de Cáncer de Pulmón, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosio Villegas”, Mexico City, Mexico
| | - Dolores Gallardo-Rincón
- Laboratorio de Medicina Traslacional, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Erika Ruíz-García
- Laboratorio de Medicina Traslacional, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Laurence A. Marchat
- Programa en Biomedicina Molecular y Red de Biotecnología, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Horacio Astudillo-de la Vega
- Laboratorio de Investigación Traslacional en Cáncer y Terapia Celular, Hospital de Oncología, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | | | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
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