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Chen X, Wu D. Comprehensive Analysis of Hub Genes Associated With Competing Endogenous RNA Networks in Stroke Using Bioinformatics Analysis. Front Genet 2022; 12:779923. [PMID: 35096003 PMCID: PMC8790239 DOI: 10.3389/fgene.2021.779923] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/23/2021] [Indexed: 12/13/2022] Open
Abstract
Background: Acute ischemic stroke (AIS) is the second leading cause of death and the third leading cause of disability worldwide. Long noncoding RNAs (lncRNAs) are promising biomarkers for the early diagnosis of AIS and closely participate in the mechanism of stroke onset. However, studies focusing on lncRNAs functioning as microRNA (miRNA) sponges to regulate the mRNA expression are rare and superficial. Methods: In this study, we systematically analyzed the expression profiles of lncRNA, mRNA (GSE58294), and miRNA (GSE110993) from the GEO database. Gene ontology (GO) analysis was performed to reveal the functions of differentially expressed genes (DEGs), and we used weighted gene co-expression network analysis (WGCNA) to investigate the relationships between clinical features and expression profiles and the co-expression of miRNA and lncRNA. Finally, we constructed a lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network with selected DEGs using bioinformatics methods and obtained ROC curves to assess the diagnostic efficacy of differentially expressed lncRNAs (DElncRNAs) and differentially expressed mRNAs (DEmRNAs) in our network. The GSE22255 dataset was used to confirm the diagnostic value of candidate genes. Results: In total, 199 DElncRNAs, 2068 DEmRNAs, and 96 differentially expressed miRNAs were detected. The GO analysis revealed that DEmRNAs primarily participate in neutrophil activation, neutrophil degranulation, vacuolar transport, and lysosomal transport. WGCNA screened out 16 lncRNAs and 195 mRNAs from DEGs, and only eight DElncRNAs maintained an area under the curve higher than 0.9. By investigating the relationships between lncRNAs and mRNAs, a ceRNA network containing three lncRNAs, three miRNAs, and seven mRNAs was constructed. GSE22255 confirmed that RP1-193H18.2 is more advantageous for diagnosing stroke, whereas no mRNA showed realistic diagnostic efficacy. Conclusion: The ceRNA network may broaden our understanding of AIS pathology, and the candidate lncRNA from the ceRNA network is assumed to be a promising therapeutic target and diagnostic biomarker for AIS.
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Affiliation(s)
- Xiuqi Chen
- Department of Neurology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Danhong Wu
- Department of Neurology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
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Varankar SS, More M, Abraham A, Pansare K, Kumar B, Narayanan NJ, Jolly MK, Mali AM, Bapat SA. Functional balance between Tcf21-Slug defines cellular plasticity and migratory modalities in high grade serous ovarian cancer cell lines. Carcinogenesis 2020; 41:515-526. [PMID: 31241128 DOI: 10.1093/carcin/bgz119] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/26/2019] [Accepted: 06/21/2019] [Indexed: 12/21/2022] Open
Abstract
Cellular plasticity and transitional phenotypes add to complexities of cancer metastasis that can be initiated by single cell epithelial to mesenchymal transition (EMT) or cooperative cell migration (CCM). Our study identifies novel regulatory cross-talks between Tcf21 and Slug in mediating phenotypic and migration plasticity in high-grade serous ovarian adenocarcinoma (HGSC). Differential expression and subcellular localization associate Tcf21, Slug with epithelial, mesenchymal phenotypes, respectively; however, gene manipulation approaches identify their association with additional intermediate phenotypic states, implying the existence of a multistep epithelial-mesenchymal transition program. Live imaging further associated distinct migratory modalities with the Tcf21/Slug status of cell systems and discerned proliferative/passive CCM, active CCM and EMT modes of migration. Tcf21-Slug balance identified across a phenotypic spectrum in HGSC cell lines, associated with microenvironment-induced transitions and the emergence of an epithelial phenotype following drug exposure. Phenotypic transitions and associated functionalities following drug exposure were affirmed to ensue from occupancy of Slug promoter E-box sequences by Tcf21. Our study effectively provides a framework for understanding the relevance of ovarian cancer plasticity as a function of two transcription factors.
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Affiliation(s)
- Sagar S Varankar
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, India
| | - Madhuri More
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, India
| | - Ancy Abraham
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, India
| | - Kshama Pansare
- Institute for Plasma Research & Tata Memorial Centre, Kharghar, Navi-Mumbai, India
| | - Brijesh Kumar
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, India
| | - Nivedhitha J Narayanan
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, India
| | - Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Avinash M Mali
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, India
| | - Sharmila A Bapat
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, India
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Barthelson K, Newman M, Lardelli M. Sorting Out the Role of the Sortilin-Related Receptor 1 in Alzheimer's Disease. J Alzheimers Dis Rep 2020; 4:123-140. [PMID: 32587946 PMCID: PMC7306921 DOI: 10.3233/adr-200177] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2020] [Indexed: 12/18/2022] Open
Abstract
Sortilin-related receptor 1 (SORL1) encodes a large, multi-domain containing, membrane-bound receptor involved in endosomal sorting of proteins between the trans-Golgi network, endosomes and the plasma membrane. It is genetically associated with Alzheimer's disease (AD), the most common form of dementia. SORL1 is a unique gene in AD, as it appears to show strong associations with the common, late-onset, sporadic form of AD and the rare, early-onset familial form of AD. Here, we review the genetics of SORL1 in AD and discuss potential roles it could play in AD pathogenesis.
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Affiliation(s)
- Karissa Barthelson
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Morgan Newman
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Michael Lardelli
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
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Chen J, Han G, Xu A, Cai H. Identification of Multidimensional Regulatory Modules Through Multi-Graph Matching With Network Constraints. IEEE Trans Biomed Eng 2020; 67:987-998. [DOI: 10.1109/tbme.2019.2927157] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Protective Effect of Ginsenoside Rg1 on Oxidative Damage Induced by Hydrogen Peroxide in Chicken Splenic Lymphocytes. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:8465030. [PMID: 31178974 PMCID: PMC6501224 DOI: 10.1155/2019/8465030] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/04/2019] [Indexed: 12/28/2022]
Abstract
Previous investigation showed that ginsenoside Rg1 (Rg1) extracted from Panax ginseng C.A. Mey has antioxidative effect on oxidative stress in chickens. The present study was designed to investigate the protective effects of Rg1 on chicken lymphocytes against hydrogen peroxide-induced oxidative stress and the potential mechanisms. Cell viability, apoptotic cells, malondialdehyde, activity of superoxide dismutase, mitochondrial membrane potential, and [Ca2+]i concentration were measured, and transcriptome analysis and quantitative real-time polymerase chain reaction were used to investigate the effect of Rg1 on gene expression of the cells. The results showed that treatment of lymphocytes with H2O2 induced oxidative stress and apoptosis. However, pretreatment of the cells with Rg1 dramatically enhanced cell viability, reduced apoptotic cells, and decreased oxidative stress induced by H2O2. In addition, Rg1 reduced these H2O2-dependent decreases in mitochondrial membrane potential and reversed [Ca2+]i overload. Transcriptome analysis showed that 323 genes were downregulated and 105 genes were upregulated in Rg1-treated cells. The differentially expressed genes were involved in Toll-like receptors, peroxisome proliferator-activated receptor signaling pathway, and cytokine-cytokine receptor interaction. The present study indicated that Rg1 may act as an antioxidative agent to protect cell damage caused by oxidative stress via regulating expression of genes such as RELT, EDA2R, and TLR4.
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Hapangama DK, Kamal A, Saretzki G. Implications of telomeres and telomerase in endometrial pathology. Hum Reprod Update 2017; 23:166-187. [PMID: 27979878 PMCID: PMC5850744 DOI: 10.1093/humupd/dmw044] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 12/02/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Eukaryotic chromosomal ends are linear and are protected by nucleoprotein complexes known as telomeres. The complex structural anatomy and the diverse functions of telomeres as well as the unique reverse transcriptase enzyme, telomerase that maintains telomeres are under intensive scientific scrutiny. Both are involved in many human diseases including cancer, but also in ageing and chronic disease such as diabetes. Their intricate involvement in many cellular processes and pathways is being dynamically deciphered in many organs including the endometrium. This review summarizes our current knowledge on the topic of telomeres and telomerase and their potential role in providing plausible explanations for endometrial aberrations related to common gynaecological pathologies. OBJECTIVE AND RATIONALE This review outlines the recent major findings in telomere and telomerase functions in the context of endometrial biology. It highlights the contemporary discoveries in hormonal regulation, normal endometrial regeneration, stem cells and common gynaecological diseases such as endometriosis, infertility, recurrent reproductive failure and endometrial cancer (EC). SEARCH METHODS The authors carried out systematic PubMed (Medline) and Ovid searches using the key words: telomerase, telomeres, telomere length, human telomerase reverse transcriptase, telomeric RNA component, with endometrium, hormonal regulation, endometrial stem/progenitor cells, endometrial regeneration, endometriosis, recurrent miscarriage, infertility, endometrial hyperplasia, EC and uterine cancer. Publications used in this review date from 1995 until 31st June 2016. OUTCOMES The human endometrium is a unique somatic organ, which displays dynamic telomerase activity (TA) related to the menstrual cycle. Telomerase is implicated in almost all endometrial pathologies and appears to be crucial to endometrial stem cells. In particular, it is vital for normal endometrial regeneration, providing a distinct route to formulate possible curative, non-hormonal therapies to treat chronic endometrial conditions. Furthermore, our current understanding of telomere maintenance in EC is incomplete. Data derived from other malignancies on the role of telomerase in carcinogenesis cannot be extrapolated to EC because unlike in other cancers, TA is already present in proliferating healthy endometrial cells. WIDER IMPLICATIONS Since telomerase is pivotal to endometrial regeneration, further studies elucidating the role of telomeres, telomerase, their associated proteins and their regulation in normal endometrial regeneration as well as their role in endometrial pathologies are essential. This approach may allow future development of novel treatment strategies that are not only non-hormonal but also potentially curative.
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Affiliation(s)
- D K Hapangama
- Department of Women's and Children's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, L8 7SS, UK.,Liverpool Women's Hospital NHS Foundation Trust, Crown Street, Liverpool L8 7SS, UK
| | - A Kamal
- Department of Women's and Children's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, L8 7SS, UK.,The National Center for Early Detection of Cancer, Oncology Teaching Hospital, Baghdad Medical City, Baghdad, Iraq
| | - G Saretzki
- Institute for Ageing and Institute for Cell and Molecular Biosciences, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, NE4 5PL, UK
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Virant-Klun I, Stimpfel M. Novel population of small tumour-initiating stem cells in the ovaries of women with borderline ovarian cancer. Sci Rep 2016; 6:34730. [PMID: 27703207 PMCID: PMC5050448 DOI: 10.1038/srep34730] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 09/15/2016] [Indexed: 12/12/2022] Open
Abstract
Small stem cells with diameters of up to 5 μm previously isolated from adult human ovaries indicated pluripotency and germinal lineage, especially primordial germ cells, and developed into primitive oocyte-like cells in vitro. Here, we show that a comparable population of small stem cells can be found in the ovarian tissue of women with borderline ovarian cancer, which, in contrast to small stem cells in "healthy" ovaries, formed spontaneous tumour-like structures and expressed some markers related to pluripotency and germinal lineage. The gene expression profile of these small putative cancer stem cells differed from similar cells sorted from "healthy" ovaries by 132 upregulated and 97 downregulated genes, including some important forkhead box and homeobox genes related to transcription regulation, developmental processes, embryogenesis, and ovarian cancer. These putative cancer stem cells are suggested to be a novel population of ovarian tumour-initiating cells in humans.
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Affiliation(s)
- Irma Virant-Klun
- Department of Obstetrics and Gynaecology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Martin Stimpfel
- Department of Obstetrics and Gynaecology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
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Kessous R, Walfisch A, Meirovitz M, Davidson E, Sergienko R, Sheiner E. Preterm delivery and future maternal risk of female malignancies. Arch Gynecol Obstet 2016; 295:205-210. [PMID: 27614746 DOI: 10.1007/s00404-016-4198-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 09/06/2016] [Indexed: 01/20/2023]
Abstract
PURPOSE To investigate whether an association exists between preterm delivery and a future risk for female malignancies. METHODS A population-based study compared the incidence of long-term female malignancies in a cohort of women with and without a history of PTD. Deliveries occurred between the years 1988-2013, with a mean follow-up duration of 12 years. We excluded women with known genetic predisposition or malignancies prior to the index pregnancy. Malignancies investigated included ovarian, uterine, breast and cervix. Cumulative incidence was assessed using a Kaplan-Meier survival curve. A Cox proportional hazards model was used to estimate the adjusted hazard ratios (HR) for female malignancy. RESULTS During the study period, 105,033 women met the inclusion criteria; 16.8 % (n = 17,596) of the patients delivered preterm. Patients with a history of PTD did not have an increased risk of later being diagnosed with female malignancies. The results remained insignificant in a sub-analysis based on malignancy type, early PTD, induced vs. spontaneous, and number of episodes per patient. Kaplan-Meier cumulative incidence was similar between the groups, and the adjusted HR was not significant (1.04, 95 % CI 0.88-1.22; p = 0.665). CONCLUSION A history of PTD does not appear to elevate the risk for subsequent long-term female malignancies.
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Affiliation(s)
- Roy Kessous
- Department of Obstetrics and Gynecology, Faculty of Health Sciences, Soroka University Medical Center, Ben-Gurion University of the Negev, POB 151, Beer Sheva, 84101, Israel
| | - Asnat Walfisch
- Department of Obstetrics and Gynecology, Faculty of Health Sciences, Soroka University Medical Center, Ben-Gurion University of the Negev, POB 151, Beer Sheva, 84101, Israel.
| | - Mihai Meirovitz
- Department of Obstetrics and Gynecology, Faculty of Health Sciences, Soroka University Medical Center, Ben-Gurion University of the Negev, POB 151, Beer Sheva, 84101, Israel
| | - Ehud Davidson
- Faculty of Health Sciences, Soroka University Medical Center, Clalit Health Services (Southern District), Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ruslan Sergienko
- Department of Public Health, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Eyal Sheiner
- Department of Obstetrics and Gynecology, Faculty of Health Sciences, Soroka University Medical Center, Ben-Gurion University of the Negev, POB 151, Beer Sheva, 84101, Israel
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