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Wang W, Feng Y, Dong J, Zhou Z, Jing J, Li Z, Chen L, Lin X, Ma J, Yao B. A Novel Compound Heterozygous Mutation in TDRD9 Causes Oligozoospermia. Reprod Sci 2024:10.1007/s43032-024-01665-x. [PMID: 39174853 DOI: 10.1007/s43032-024-01665-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 07/26/2024] [Indexed: 08/24/2024]
Abstract
Oligozoospermia is an important cause of male infertility for which treatment options are limited. Spermatogenesis is complex, and the causes of oligozoospermia remain largely unknown. Because genetic mutations are important factors of oligozoospermia pathogenesis, our study aimed to explore the genetic causes of oligozoospermia. Whole- exome sequencing (WES) was performed on one proband from a Chinese family who was diagnosed with oligozoospermia. The pathogenic mutations were confirmed by Sanger sequencing, and a minigene assay was used to determine the effect of the identified splicing mutation. We identified a novel compound heterozygous mutation in the TDRD9 gene, comprising a splicing mutation (c.1115 + 3A > G) and a frameshift mutation (c.958delC), in the proband; neither of these mutations were found in 50 unrelated healthy people. In addition, a minigene assay demonstrated that the frameshift produced partially truncated protein, and the splicing mutation led to a frameshift mutation and premature termination due to abnormal alternative splicing of TDRD9. These findings indicate that deleterious compound heterozygous mutation in TDRD9 could lead to oligozoospermia, highlighting the crucial role of TDRD9 in spermatogenesis and further clarifying the genetic causes of male infertility resulting from oligozoospermia. Our study expands the spectrum of TDRD9-related phenotypes and provides a new specific target for future genetic counseling.
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Affiliation(s)
- Wenhua Wang
- Center of Reproductive Medicine, Affiliated Jinling Hospital, Nanjing Medical University, Nanjing, 210002, Jiangsu, China
| | - Yuming Feng
- Center of Reproductive Medicine, Clinical School of Medical College, Nanjing Jinling Hospital, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Jie Dong
- Center of Reproductive Medicine, Clinical School of Medical College, Nanjing Jinling Hospital, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Zheng Zhou
- Center of Reproductive Medicine, Clinical School of Medical College, Nanjing Jinling Hospital, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Jun Jing
- Center of Reproductive Medicine, Affiliated Jinling Hospital, Nanjing Medical University, Nanjing, 210002, Jiangsu, China
- Center of Reproductive Medicine, Clinical School of Medical College, Nanjing Jinling Hospital, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Zixiong Li
- Department of Oncology, Nanjing Jinling Hospital of Nanjing University, Nanjing, 210002, China
| | - Li Chen
- Center of Reproductive Medicine, Affiliated Jinling Hospital, Nanjing Medical University, Nanjing, 210002, Jiangsu, China
- Center of Reproductive Medicine, Clinical School of Medical College, Nanjing Jinling Hospital, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Xiaoqi Lin
- Center of Reproductive Medicine, Clinical School of Medical College, Nanjing Jinling Hospital, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Jinzhao Ma
- Center of Reproductive Medicine, Affiliated Jinling Hospital, Nanjing Medical University, Nanjing, 210002, Jiangsu, China.
- Center of Reproductive Medicine, Clinical School of Medical College, Nanjing Jinling Hospital, Nanjing University, Nanjing, 210002, Jiangsu, China.
| | - Bing Yao
- Center of Reproductive Medicine, Affiliated Jinling Hospital, Nanjing Medical University, Nanjing, 210002, Jiangsu, China.
- Center of Reproductive Medicine, Clinical School of Medical College, Nanjing Jinling Hospital, Nanjing University, Nanjing, 210002, Jiangsu, China.
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Bertrams W, Wilhelm J, Veeger PM, Hanko C, Brinke KAD, Klabunde B, Pott H, Weckler B, Greulich T, Vogelmeier CF, Schmeck B. A mRNA panel for differentiation between acute exacerbation or pneumonia in COPD patients. Front Med (Lausanne) 2024; 11:1234068. [PMID: 38585145 PMCID: PMC10995291 DOI: 10.3389/fmed.2024.1234068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 03/11/2024] [Indexed: 04/09/2024] Open
Abstract
Introduction Patients suffering from chronic obstructive pulmonary disease (COPD) are prone to acute exacerbations (AECOPD) or community acquired pneumonia (CAP), both posing severe risk of morbidity and mortality. There is no available biomarker that correctly separates AECOPD from COPD. However, because CAP and AECOPD differ in aetiology, treatment and prognosis, their discrimination would be important. Methods This study analysed the ability of selected candidate transcripts from peripheral blood mononuclear cells (PBMCs) to differentiate between patients with AECOPD, COPD & CAP, and CAP without pre-existing COPD. Results In a previous study, we identified differentially regulated genes between CAP and AECOPD in PBMCs. In the present new cohort, we tested the potential of selected candidate PBMC transcripts to differentiate at early time points AECOPD, CAP+COPD, and CAP without pre-existing COPD. Expression of YWHAG, E2F1 and TDRD9 held predictive power: This gene set predicted diseases markedly better (model accuracy up to 100%) than classical clinical markers like CRP, lymphocyte count and neutrophil count (model accuracy up to 82%). Discussion In summary, in our cohort expression levels of YWHAG, E2F1 and TDRD9 differentiated with high accuracy between COPD patients suffering from acute exacerbation or CAP.
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Affiliation(s)
- Wilhelm Bertrams
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany
- German Center for Lung Research (DZL) Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany
| | - Jochen Wilhelm
- German Center for Lung Research (DZL) Universities of Giessen and Marburg Lung Center (UGMLC), Justus-Liebig-University Giessen, Giessen, Germany
- Institute for Lung Health (ILH), Giessen, Germany
| | - Pia-Marie Veeger
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany
- German Center for Lung Research (DZL) Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany
| | - Carolina Hanko
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany
- German Center for Lung Research (DZL) Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany
| | - Kristina auf dem Brinke
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany
- German Center for Lung Research (DZL) Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany
| | - Björn Klabunde
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany
- German Center for Lung Research (DZL) Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany
| | - Hendrik Pott
- German Center for Lung Research (DZL) Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany
- Department of Medicine, Pulmonary and Critical Care Medicine, University Medical Center Marburg, Philipps-University, Marburg, Germany
| | - Barbara Weckler
- German Center for Lung Research (DZL) Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany
- Department of Medicine, Pulmonary and Critical Care Medicine, University Medical Center Marburg, Philipps-University, Marburg, Germany
| | - Timm Greulich
- German Center for Lung Research (DZL) Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany
- Department of Medicine, Pulmonary and Critical Care Medicine, University Medical Center Marburg, Philipps-University, Marburg, Germany
| | - Claus F. Vogelmeier
- German Center for Lung Research (DZL) Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany
- Department of Medicine, Pulmonary and Critical Care Medicine, University Medical Center Marburg, Philipps-University, Marburg, Germany
| | - Bernd Schmeck
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany
- German Center for Lung Research (DZL) Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany
- Institute for Lung Health (ILH), Giessen, Germany
- Department of Medicine, Pulmonary and Critical Care Medicine, University Medical Center Marburg, Philipps-University, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO) and German Center for Infectious Disease Research (DZIF), Philipps-University Marburg, Marburg, Germany
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Dapas M, Thompson EE, Wentworth-Sheilds W, Clay S, Visness CM, Calatroni A, Sordillo JE, Gold DR, Wood RA, Makhija M, Khurana Hershey GK, Sherenian MG, Gruchalla RS, Gill MA, Liu AH, Kim H, Kattan M, Bacharier LB, Rastogi D, Altman MC, Busse WW, Becker PM, Nicolae D, O’Connor GT, Gern JE, Jackson DJ, Ober C. Multi-omic association study identifies DNA methylation-mediated genotype and smoking exposure effects on lung function in children living in urban settings. PLoS Genet 2023; 19:e1010594. [PMID: 36638096 PMCID: PMC9879483 DOI: 10.1371/journal.pgen.1010594] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 01/26/2023] [Accepted: 12/23/2022] [Indexed: 01/14/2023] Open
Abstract
Impaired lung function in early life is associated with the subsequent development of chronic respiratory disease. Most genetic associations with lung function have been identified in adults of European descent and therefore may not represent those most relevant to pediatric populations and populations of different ancestries. In this study, we performed genome-wide association analyses of lung function in a multiethnic cohort of children (n = 1,035) living in low-income urban neighborhoods. We identified one novel locus at the TDRD9 gene in chromosome 14q32.33 associated with percent predicted forced expiratory volume in one second (FEV1) (p = 2.4x10-9; βz = -0.31, 95% CI = -0.41- -0.21). Mendelian randomization and mediation analyses revealed that this genetic effect on FEV1 was partially mediated by DNA methylation levels at this locus in airway epithelial cells, which were also associated with environmental tobacco smoke exposure (p = 0.015). Promoter-enhancer interactions in airway epithelial cells revealed chromatin interaction loops between FEV1-associated variants in TDRD9 and the promoter region of the PPP1R13B gene, a stimulator of p53-mediated apoptosis. Expression of PPP1R13B in airway epithelial cells was significantly associated the FEV1 risk alleles (p = 1.3x10-5; β = 0.12, 95% CI = 0.06-0.17). These combined results highlight a potential novel mechanism for reduced lung function in urban youth resulting from both genetics and smoking exposure.
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Affiliation(s)
- Matthew Dapas
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
| | - Emma E. Thompson
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
| | | | - Selene Clay
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
| | | | | | - Joanne E. Sordillo
- Department of Population Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Diane R. Gold
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert A. Wood
- Department of Pediatrics, Johns Hopkins University Medical Center, Baltimore, Maryland, United States of America
| | - Melanie Makhija
- Division of Allergy and Immunology, Ann & Robert H. Lurie Children’s Hospital, Chicago, Illinois, United States of America
| | - Gurjit K. Khurana Hershey
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Michael G. Sherenian
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Rebecca S. Gruchalla
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Michelle A. Gill
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Andrew H. Liu
- Department of Allergy and Immunology, Children’s Hospital Colorado, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Haejin Kim
- Department of Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Meyer Kattan
- Columbia University College of Physicians and Surgeons, New York, New York, United States of America
| | - Leonard B. Bacharier
- Monroe Carell Jr. Children’s Hospital at Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Deepa Rastogi
- Children’s National Health System, Washington, District of Columbia, United States of America
| | - Matthew C. Altman
- Department of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - William W. Busse
- Department of Pediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Patrice M. Becker
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Dan Nicolae
- Department of Statistics, University of Chicago, Chicago, Illinois, United States of America
| | - George T. O’Connor
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - James E. Gern
- Department of Pediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Daniel J. Jackson
- Department of Pediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
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Shi Z, Li X, Zhang L, Luo Y, Shrestha B, Hu X. Potential Novel Modules and Hub Genes as Prognostic Candidates of Thyroid Cancer by Weighted Gene Co-Expression Network Analysis. Int J Gen Med 2021; 14:9433-9444. [PMID: 34908870 PMCID: PMC8665846 DOI: 10.2147/ijgm.s329128] [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: 08/11/2021] [Accepted: 10/28/2021] [Indexed: 11/23/2022] Open
Abstract
Background Although thyroid cancer (THCA) is one of the most common type of endocrine malignancy, its highly complex molecular mechanisms of carcinogenesis are not completely known. Materials and Methods In this study, weighted gene co-expression network analysis (WGCNA) was utilized to construct gene co-expression networks and evaluate the relations between modules and clinical traits to identify potential prognostic biomarkers for THCA patients. RNA-seq data and clinical data were downloaded from The Cancer Genome Atlas (TCGA). Other independent datasets from the Gene Expression Omnibus (GEO) database and the Human Protein Atlas database were performed to validate findings. Results Finally, 11 co-expression modules were constructed and four hub genes, CCDC146, SLC4A4, TDRD9 and MUM1L1, were identified and validated statistically, which were considerably interrelated to worse survival of THCA patients. Conclusion This research study revealed four hub genes may be considered candidate prognostic biomarkers and potential therapeutic targets for THCA patients in the future.
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Affiliation(s)
- Zhiqiang Shi
- Department of Stomatology, University of Chinese Academy of Sciences - Shenzhen Hospital, Shenzhen, Guangdong, 518107, People's Republic of China
| | - Xinghui Li
- Department of Dermatology, University of Chinese Academy of Sciences - Shenzhen Hospital, Shenzhen, Guangdong, 518107, People's Republic of China
| | - Long Zhang
- Department of Stomatology, University of Chinese Academy of Sciences - Shenzhen Hospital, Shenzhen, Guangdong, 518107, People's Republic of China
| | - Yilang Luo
- Department of Stomatology, University of Chinese Academy of Sciences - Shenzhen Hospital, Shenzhen, Guangdong, 518107, People's Republic of China
| | - Bikal Shrestha
- Department of Conservative and Endodontics, Nepal Police Hospital, Kathmandu, 44600, Nepal
| | - Xuegang Hu
- Department of Stomatology, University of Chinese Academy of Sciences - Shenzhen Hospital, Shenzhen, Guangdong, 518107, People's Republic of China
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Rehman S, Gora AH, Siriyappagouder P, Brugman S, Fernandes JMO, Dias J, Kiron V. Zebrafish intestinal transcriptome highlights subdued inflammatory responses to dietary soya bean and efficacy of yeast β-glucan. JOURNAL OF FISH DISEASES 2021; 44:1619-1637. [PMID: 34237181 DOI: 10.1111/jfd.13484] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Anti-nutritional factors in dietary components can have a negative impact on the intestinal barrier. Here, we present soya bean-induced changes in the intestine of juvenile zebrafish and the effect of yeast β-glucan through a transcriptomic approach. The inclusion of soya bean meal affected the expression of several intestinal barrier function-related genes like arl4ca, rab25b, rhoub, muc5ac, muc5d, clcn2c and cltb in zebrafish. Several metabolic genes like cyp2x10.2, cyp2aa2, aldh3a2b, crata, elovl4, elovl6, slc51a, gpat2 and ATP-dependent peptidase activity (lonrf, clpxb) were altered in the intestinal tissue. The expression of immune-related genes like nlrc3, nlrp12, gimap8, prdm1 and tph1a, and genes related to cell cycle, DNA damage and DNA repair (e.g. spo11, rad21l1, nabp1b, spata22, tdrd9) were also affected in the soya bean fed group. Furthermore, our study suggests the plausible effect of yeast β-glucan through the modulation of several genes that regulate immune responses and barrier integrity. Our findings indicate a subdued inflammation in juvenile zebrafish fed soya bean meal and the efficacy of β-glucan to counter these subtle inflammatory responses.
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Affiliation(s)
- Saima Rehman
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Adnan H Gora
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | - Sylvia Brugman
- Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | | | | | - Viswanath Kiron
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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Integrated Analysis of the Roles of RNA Binding Proteins and Their Prognostic Value in Clear Cell Renal Cell Carcinoma. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:5568411. [PMID: 34306592 PMCID: PMC8263288 DOI: 10.1155/2021/5568411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/02/2021] [Accepted: 06/09/2021] [Indexed: 12/24/2022]
Abstract
Methods We downloaded the RNA sequencing data of ccRCC from the Cancer Genome Atlas (TCGA) database and identified differently expressed RBPs in different tissues. In this study, we used bioinformatics to analyze the expression and prognostic value of RBPs; then, we performed functional analysis and constructed a protein interaction network for them. We also screened out some RBPs related to the prognosis of ccRCC. Finally, based on the identified RBPs, we constructed a prognostic model that can predict patients' risk of illness and survival time. Also, the data in the HPA database were used for verification. Results In our experiment, we obtained 539 ccRCC samples and 72 normal controls. In the subsequent analysis, 87 upregulated RBPs and 38 downregulated RBPs were obtained. In addition, 9 genes related to the prognosis of patients were selected, namely, RPL36A, THOC6, RNASE2, NOVA2, TLR3, PPARGC1A, DARS, LARS2, and U2AF1L4. We further constructed a prognostic model based on these genes and plotted the ROC curve. This ROC curve performed well in judgement and evaluation. A nomogram that can judge the patient's life span is also made. Conclusion In conclusion, we have identified differentially expressed RBPs in ccRCC and carried out a series of in-depth research studies, the results of which may provide ideas for the diagnosis of ccRCC and the research of new targeted drugs.
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Lee E, Lokman NA, Oehler MK, Ricciardelli C, Grutzner F. A Comprehensive Molecular and Clinical Analysis of the piRNA Pathway Genes in Ovarian Cancer. Cancers (Basel) 2020; 13:cancers13010004. [PMID: 33374923 PMCID: PMC7792616 DOI: 10.3390/cancers13010004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/09/2020] [Accepted: 12/18/2020] [Indexed: 12/28/2022] Open
Abstract
Simple Summary Although ovarian cancer (OC) is one of the most lethal gynecological cancers, its development and progression remain poorly understood. The piRNA pathway is important for transposon defense and genome stability. piRNA maturation and function involve a number of genes known as the piRNA pathway genes. These genes have recently been implicated in cancer development and progression but information about their role in OC is limited. Our work aimed to provide a better understanding of the roles of piRNA pathway genes in OC. Through analyzing changes in the abundance of 10 piRNA pathway genes, we discovered gene expression differences in benign vs. cancer, chemosensitive vs. chemoresistant and post hormone treatment in OC samples and cells. Furthermore, we observed the differential effects of these genes on patient survival and OC cell invasion. Overall, this work supports a role of the piRNA pathway genes in OC progression and encourages further study of their clinical relevance. Abstract Ovarian cancer (OC) is one of the most lethal gynecological malignancies, yet molecular mechanisms underlying its origin and progression remain poorly understood. With increasing reports of piRNA pathway deregulation in various cancers, we aimed to better understand its role in OC through a comprehensive analysis of key genes: PIWIL1-4, DDX4, HENMT1, MAEL, PLD6, TDRD1,9 and mutants of PIWIL1 (P1∆17) and PIWIL2 (PL2L60). High-throughput qRT-PCR (n = 45) and CSIOVDB (n = 3431) showed differential gene expression when comparing benign ovarian tumors, low grade OC and high grade serous OC (HGSOC). Significant correlation of disparate piRNA pathway gene expression levels with better progression free, post-progression free and overall survival suggests a complex role of this pathway in OC. We discovered PIWIL3 expression in chemosensitive but not chemoresistant primary HGSOC cells, providing a potential target against chemoresistant disease. As a first, we revealed that follicle stimulating hormone increased PIWIL2 expression in OV-90 cells. PIWIL1, P1∆17, PIWIL2, PL2L60 and MAEL overexpression in vitro and in vivo decreased motility and invasion of OVCAR-3 and OV-90 cells. Interestingly, P1∆17 and PL2L60, induced increased motility and invasion compared to PIWIL1 and PIWIL2. Our results in HGSOC highlight the intricate role piRNA pathway genes play in the development of malignant neoplasms.
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Affiliation(s)
- Eunice Lee
- Department of Molecular and Biomedical Sciences, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia;
| | - Noor A. Lokman
- Discipline of Obstetrics and Gynaecology, Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5000, Australia; (N.A.L.); (M.K.O.)
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia
| | - Martin K. Oehler
- Discipline of Obstetrics and Gynaecology, Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5000, Australia; (N.A.L.); (M.K.O.)
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia
- Department of Gynaecological Oncology, Royal Adelaide Hospital, Adelaide, SA 5005, Australia
| | - Carmela Ricciardelli
- Discipline of Obstetrics and Gynaecology, Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5000, Australia; (N.A.L.); (M.K.O.)
- Correspondence: (C.R.); (F.G.); Tel.: +61-8-8313-8255 (C.R.); +61-8-8313-4812 (F.G.)
| | - Frank Grutzner
- Department of Molecular and Biomedical Sciences, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia;
- Correspondence: (C.R.); (F.G.); Tel.: +61-8-8313-8255 (C.R.); +61-8-8313-4812 (F.G.)
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Hosseinipour M, Shahbazi S, Roudbar-Mohammadi S, Khorasani M, Marjani M. Differential genes expression analysis of invasive aspergillosis: a bioinformatics study based on mRNA/microRNA. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2020; 9:173-180. [PMID: 33344664 PMCID: PMC7731968 DOI: 10.22099/mbrc.2020.37432.1509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Invasive aspergillosis is a severe opportunistic infection with high mortality in immunocompromised patients. Recently, the roles of microRNAs have been taken into consideration in the immune system and inflammatory responses. Using bioinformatics approaches, we aimed to study the microRNAs related to invasive aspergillosis to understand the molecular pathways involved in the disease pathogenesis. Data were extracted from the gene expression omnibus (GEO) database. We proposed 3 differentially expressed genes; S100B, TDRD9 and TMTC1 related to pathogenesis of invasive aspergillosis. Using miRWalk 2.0 predictive tool, microRNAs that targeted the selected genes were identified. The roles of microRNAs were investigated by microRNA target prediction and molecular pathways analysis. The significance of combined expression changes in selected genes was analyzed by ROC curves study. Thirty-three microRNAs were identified as the common regulator of S100B, TDRD9 and TMTC1 genes. Several of them were previously reported in the pathogenesis of fungal infections including miR-132. Predicted microRNAs were involved in innate immune response as well as toll-like receptor signaling. Most of the microRNAs were also linked to platelet activation. The ROC chart in the combination mode of S100B/TMTC1, showed the sensitivity of 95.65 percent and the specificity of 69.23 percent. New approaches are needed for rapid and accurate detection of invasive aspergillosis. Given the pivotal signaling pathways involved, predicted microRNAs can be considered as the potential candidates of the disease diagnosis. Further investigation of the microRNAs expression changes and related pathways would lead to identifying the effective biomarkers for IA detection.
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Affiliation(s)
- Maryam Hosseinipour
- Department of Medical Mycology, Faculty of Medical Science, Tarbiat Modares University, Tehran Iran
| | - Shirin Shahbazi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Shahla Roudbar-Mohammadi
- Department of Medical Mycology, Faculty of Medical Science, Tarbiat Modares University, Tehran Iran
| | - Maryam Khorasani
- Molecular Medicine Department, Pasteur Institute of Iran, Tehran, Iran
| | - Majid Marjani
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Fan X, Liu L, Shi Y, Guo F, Wang H, Zhao X, Zhong D, Li G. Integrated analysis of RNA-binding proteins in human colorectal cancer. World J Surg Oncol 2020; 18:222. [PMID: 32828126 PMCID: PMC7443297 DOI: 10.1186/s12957-020-01995-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 08/09/2020] [Indexed: 12/15/2022] Open
Abstract
Background Although RNA-binding proteins play an essential role in a variety of different tumours, there are still limited efforts made to systematically analyse the role of RNA-binding proteins (RBPs) in the survival of colorectal cancer (CRC) patients. Methods Analysis of CRC transcriptome data collected from the TCGA database was conducted, and RBPs were extracted from CRC. R software was applied to analyse the differentially expressed genes (DEGs) of RBPs. To identify related pathways and perform functional annotation of RBP DEGs, Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out using the database for annotation, visualization and integrated discovery. Protein-protein interactions (PPIs) of these DEGs were analysed based on the Search Tool for the Retrieval of Interacting Genes (STRING) database and visualized by Cytoscape software. Based on the Cox regression analysis of the prognostic value of RBPs (from the PPI network) with survival time, the RBPs related to survival were identified, and a prognostic model was constructed. To verify the model, the data stored in the TCGA database were designated as the training set, while the chip data obtained from the GEO database were treated as the test set. Then, both survival analysis and ROC curve verification were conducted. Finally, the risk curves and nomograms of the two groups were generated to predict the survival period. Results Among RBP DEGs, 314 genes were upregulated while 155 were downregulated, of which twelve RBPs (NOP14, MRPS23, MAK16, TDRD6, POP1, TDRD5, TDRD7, PPARGC1A, LIN28B, CELF4, LRRFIP2, MSI2) with prognostic value were obtained. Conclusions The twelve identified genes may be promising predictors of CRC and play an essential role in the pathogenesis of CRC. However, further investigation of the underlying mechanism is needed.
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Affiliation(s)
- Xuehui Fan
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Lili Liu
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Yue Shi
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Fanghan Guo
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Haining Wang
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Xiuli Zhao
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Di Zhong
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Guozhong Li
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China.
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10
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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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11
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DNA-PK in human malignant disorders: Mechanisms and implications for pharmacological interventions. Pharmacol Ther 2020; 215:107617. [PMID: 32610116 DOI: 10.1016/j.pharmthera.2020.107617] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/15/2020] [Indexed: 12/12/2022]
Abstract
The DNA-PK holoenzyme is a fundamental element of the DNA damage response machinery (DDR), which is responsible for cellular genomic stability. Consequently, and predictably, over the last decades since its identification and characterization, numerous pre-clinical and clinical studies reported observations correlating aberrant DNA-PK status and activity with cancer onset, progression and responses to therapeutic modalities. Notably, various studies have established in recent years the role of DNA-PK outside the DDR network, corroborating its role as a pleiotropic complex involved in transcriptional programs that operate biologic processes as epithelial to mesenchymal transition (EMT), hypoxia, metabolism, nuclear receptors signaling and inflammatory responses. In particular tumor entities as prostate cancer, immense research efforts assisted mapping and describing the overall signaling networks regulated by DNA-PK that control metastasis and tumor progression. Correspondingly, DNA-PK emerges as an obvious therapeutic target in cancer and data pertaining to various pharmacological approaches have been published, largely in context of combination with DNA-damaging agents (DDAs) that act by inflicting DNA double strand breaks (DSBs). Currently, new generation inhibitors are tested in clinical trials. Several excellent reviews have been published in recent years covering the biology of DNA-PK and its role in cancer. In the current article we are aiming to systematically describe the main findings on DNA-PK signaling in major cancer types, focusing on both preclinical and clinical reports and present a detailed current status of the DNA-PK inhibitors repertoire.
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12
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Tong DL, Kempsell KE, Szakmany T, Ball G. Development of a Bioinformatics Framework for Identification and Validation of Genomic Biomarkers and Key Immunopathology Processes and Controllers in Infectious and Non-infectious Severe Inflammatory Response Syndrome. Front Immunol 2020; 11:380. [PMID: 32318053 PMCID: PMC7147506 DOI: 10.3389/fimmu.2020.00380] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 02/17/2020] [Indexed: 12/12/2022] Open
Abstract
Sepsis is defined as dysregulated host response caused by systemic infection, leading to organ failure. It is a life-threatening condition, often requiring admission to an intensive care unit (ICU). The causative agents and processes involved are multifactorial but are characterized by an overarching inflammatory response, sharing elements in common with severe inflammatory response syndrome (SIRS) of non-infectious origin. Sepsis presents with a range of pathophysiological and genetic features which make clinical differentiation from SIRS very challenging. This may reflect a poor understanding of the key gene inter-activities and/or pathway associations underlying these disease processes. Improved understanding is critical for early differential recognition of sepsis and SIRS and to improve patient management and clinical outcomes. Judicious selection of gene biomarkers suitable for development of diagnostic tests/testing could make differentiation of sepsis and SIRS feasible. Here we describe a methodologic framework for the identification and validation of biomarkers in SIRS, sepsis and septic shock patients, using a 2-tier gene screening, artificial neural network (ANN) data mining technique, using previously published gene expression datasets. Eight key hub markers have been identified which may delineate distinct, core disease processes and which show potential for informing underlying immunological and pathological processes and thus patient stratification and treatment. These do not show sufficient fold change differences between the different disease states to be useful as primary diagnostic biomarkers, but are instrumental in identifying candidate pathways and other associated biomarkers for further exploration.
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Affiliation(s)
- Dong Ling Tong
- Artificial Intelligence Laboratory, Faculty of Engineering and Computing, First City University College, Petaling Jaya, Malaysia.,School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
| | - Karen E Kempsell
- Public Health England, National Infection Service, Porton Down, Salisbury, United Kingdom
| | - Tamas Szakmany
- Department of Anaesthesia Intensive Care and Pain Medicine, Division of Population Medicine, Cardiff University, Cardiff, United Kingdom
| | - Graham Ball
- School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
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13
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Mo HY, Choi EJ, Yoo NJ, Lee SH. Mutational alterations of TDRD 1, 4 and 9 genes in colorectal cancers. Pathol Oncol Res 2020; 26:2007-2008. [PMID: 32036563 DOI: 10.1007/s12253-020-00798-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 01/23/2020] [Indexed: 01/09/2023]
Affiliation(s)
- Ha Yoon Mo
- Department of Pathology, College of Medicine, The CatholicUniversity of Korea, 505 Banpo-dong, Socho-gu, 137-701, Seoul, Korea
| | - Eun Ji Choi
- Department of Pathology, College of Medicine, The CatholicUniversity of Korea, 505 Banpo-dong, Socho-gu, 137-701, Seoul, Korea
| | - Nam Jin Yoo
- Department of Pathology, College of Medicine, The CatholicUniversity of Korea, 505 Banpo-dong, Socho-gu, 137-701, Seoul, Korea
| | - Sug Hyung Lee
- Department of Pathology, College of Medicine, The CatholicUniversity of Korea, 505 Banpo-dong, Socho-gu, 137-701, Seoul, Korea. .,Cancer Research Institute, College of Medicine, The Catholic University of Korea, 137-701, Seoul, Korea.
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14
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Sun T, Han X. The disease-related biological functions of PIWI-interacting RNAs (piRNAs) and underlying molecular mechanisms. ACTA ACUST UNITED AC 2019. [DOI: 10.1186/s41544-019-0021-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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15
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Gan B, Chen S, Liu H, Min J, Liu K. Structure and function of eTudor domain containing TDRD proteins. Crit Rev Biochem Mol Biol 2019; 54:119-132. [DOI: 10.1080/10409238.2019.1603199] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Bing Gan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China
| | - Sizhuo Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China
| | - Huan Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China
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