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Zou L, Meng L, Xu Y, Wang K, Zhang J. Revealing the diagnostic value and immune infiltration of senescence-related genes in endometriosis: a combined single-cell and machine learning analysis. Front Pharmacol 2023; 14:1259467. [PMID: 37860112 PMCID: PMC10583561 DOI: 10.3389/fphar.2023.1259467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 09/05/2023] [Indexed: 10/21/2023] Open
Abstract
Introduction: Endometriosis is a prevalent and recurrent medical condition associated with symptoms such as pelvic discomfort, dysmenorrhea, and reproductive challenges. Furthermore, it has the potential to progress into a malignant state, significantly impacting the quality of life for affected individuals. Despite its significance, there is currently a lack of precise and non-invasive diagnostic techniques for this condition. Methods: In this study, we leveraged microarray datasets and employed a multifaceted approach. We conducted differential gene analysis, implemented weighted gene co-expression network analysis (WGCNA), and utilized machine learning algorithms, including random forest, support vector machine, and LASSO analysis, to comprehensively explore senescence-related genes (SRGs) associated with endometriosis. Discussion: Our comprehensive analysis, which also encompassed profiling of immune cell infiltration and single-cell analysis, highlights the therapeutic potential of this gene assemblage as promising targets for alleviating endometriosis. Furthermore, the integration of these biomarkers into diagnostic protocols promises to enhance diagnostic precision, offering a more effective diagnostic journey for future endometriosis patients in clinical settings. Results: Our meticulous investigation led to the identification of a cluster of genes, namely BAK1, LMNA, and FLT1, which emerged as potential discerning biomarkers for endometriosis. These biomarkers were subsequently utilized to construct an artificial neural network classifier model and were graphically represented in the form of a Nomogram.
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Affiliation(s)
- Lian Zou
- Chongqing Emergency Medical Center, Department of Obstetrics and Gynecology in Chongging University Central Hospital, Chongqing, China
| | - Lou Meng
- Chongqing Emergency Medical Center, Department of Obstetrics and Gynecology in Chongging University Central Hospital, Chongqing, China
| | - Yan Xu
- Chongqing Emergency Medical Center, Department of Obstetrics and Gynecology in Chongging University Central Hospital, Chongqing, China
| | - Kana Wang
- Department of Gynecology, West China Second Hospital of Sichuan University, Chengdu, China
| | - Jiawen Zhang
- Department of Gynecology, West China Second Hospital of Sichuan University, Chengdu, China
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Liu ZP. Editorial: Insights in integrative bioinformatics-2021. Front Bioinform 2023; 3:1267370. [PMID: 37671243 PMCID: PMC10476083 DOI: 10.3389/fbinf.2023.1267370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/14/2023] [Indexed: 09/07/2023] Open
Affiliation(s)
- Zhi-Ping Liu
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong, China
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Wang FP, Zhang L, Lyu J, Liu Y, Xie YM. [Efficacy, safety, and mechanism of Huangkui Capsules in treating chronic kidney disease: Meta-analysis and integrative bioinformatics]. Zhongguo Zhong Yao Za Zhi 2023; 48:4493-4507. [PMID: 37802876 DOI: 10.19540/j.cnki.cjcmm.20230515.502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 10/08/2023]
Abstract
Meta-analysis and integrative bioinformatics were employed to comprehensively study the efficacy, safety, and mechanism of Huangkui Capsules in treating chronic kidney disease(CKD). CNKI, Wanfang, VIP, SinoMed, Cochrane Library, PubMed, EMbase, and Web of Science were searched for randomized controlled trial(RCT) of Huangkui Capsules for CKD from inception to January 3, 2023. The outcome indicators included urine protein, serum creatinine(Scr), and blood urea nitrogen(BUN) levels, and Cochrane Handbook 5.1 and RevMan 5.3 were employed to perform the Meta-analysis of the included RCT. The active ingredients of Huangkui Capsules were retrieved from CNKI, and the targets of CKD from GeneCards, OMIM, and TTD. Cytoscape 3.8.0 was used to build a "component-disease" network and a protein-protein interaction(PPI) network for the screening of core components and targets. Next, a differential analysis of the core targets of Huangkui Capsules for treating CKD was conducted with the clinical samples from GEO to identify the differentially expressed core targets, and correlation analysis and immune cell infiltration analysis were then performed for these targets. A total of 13 RCTs were included for the Meta-analysis, involving 2 372 patients(1 185 in the observation group and 1 187 in the control group). Meta-analysis showed that the Huangkui Capsules group and the losartan potassium group had no significant differences in reducing the urinary protein levels after 12(MD=19.60, 95%CI[-58.66, 97.86], P=0.62) and 24 weeks(MD=-66.00, 95%CI[-264.10, 132.11], P=0.51) of treatment. Huangkui Capsules in combination with conventional treatment was superior to conventional treatment alone(MD=-0.55, 95%CI[-0.86,-0.23], P=0.000 6). Huangkui Capsules combined with conventional treatment was superior to conventional treatment alone in recovering Scr(MD=-9.21, 95%CI[-15.85,-2.58], P=0.006) and BUN(MD=-1.02, 95%CI[-1.83,-0.21], P=0.01). Five patients showed clear adverse reactions, with abdominal or gastrointestinal discomfort. Huangkui Capsules had 43 active ingredients and 393 targets, and the core ingredients were myricetin, quercetin, gossypin, elaidic acid, dihydromyricetin, isochlorogenic acid B, and caffeic acid. CKD and Huangkui Capsules shared 247 common targets, including 25 core targets. The GEO differential analysis predicted 18 differentially expressed core targets, which were mainly positively correlated with immune cell expression and involved in immune inflammation, oxidative stress, pyroptosis, lipid metabolism, sex hormone metabolism, and cell repair. Conclusively, Huangkui Capsules combined with conventional treatment significantly reduced urine protein, Scr, and BUN. Huangkui Capsules alone and losartan potassium had no significant difference in reducing urine protein. This efficacy of Huangkui Capsules may be associated with the multi-component, multi-target, and multi-pathway responses to immune inflammation and oxidative stress. The included RCT had small sample sizes and general quality. More clinical trial protocols with large sample sizes and rigorous design and in line with international norms are needed to improve the evidence quality, and the results of bioinformatics analysis remain to be confirmed by further studies.
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Affiliation(s)
- Fu-Ping Wang
- Institute of Basic Research in Clinical Medicine,China Academy of Chinese Medical Sciences Beijing 100700,China
| | - Lei Zhang
- Institute of Basic Research in Clinical Medicine,China Academy of Chinese Medical Sciences Beijing 100700,China
| | - Jian Lyu
- Xiyuan Hospital,China Academy of Chinese Medical Sciences Beijing 100091,China
| | - Yi Liu
- Institute of Basic Research in Clinical Medicine,China Academy of Chinese Medical Sciences Beijing 100700,China
| | - Yan-Ming Xie
- Institute of Basic Research in Clinical Medicine,China Academy of Chinese Medical Sciences Beijing 100700,China
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Zeng T, Zhang C. Editorial: Expert opinions in integrative bioinformatics: 2022. Front Bioinform 2023; 3:1218466. [PMID: 37274753 PMCID: PMC10235704 DOI: 10.3389/fbinf.2023.1218466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 05/15/2023] [Indexed: 06/06/2023] Open
Affiliation(s)
- Tao Zeng
- Guangzhou Laboratory, Guangzhou, China
| | - Chuanchao Zhang
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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5
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Liu Y, Li Y, Zeng T. Multi-omics of extracellular vesicles: An integrative representation of functional mediators and perspectives on lung disease study. Front Bioinform 2023; 3:1117271. [PMID: 36844931 PMCID: PMC9947558 DOI: 10.3389/fbinf.2023.1117271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023] Open
Abstract
Extracellular vesicles are secreted by almost all cell types. EVs include a broader component known as exosomes that participate in cell-cell and tissue-tissue communication via carrying diverse biological signals from one cell type or tissue to another. EVs play roles as communication messengers of the intercellular network to mediate different physiological activities or pathological changes. In particular, most EVs are natural carriers of functional cargo such as DNA, RNA, and proteins, and thus they are relevant to advancing personalized targeted therapies in clinical practice. For the application of EVs, novel bioinformatic models and methods based on high-throughput technologies and multi-omics data are required to provide a deeper understanding of their biological and biomedical characteristics. These include qualitative and quantitative representation for identifying cargo markers, local cellular communication inference for tracing the origin and production of EVs, and distant organ communication reconstruction for targeting the influential microenvironment and transferable activators. Thus, this perspective paper introduces EVs in the context of multi-omics and provides an integrative bioinformatic viewpoint of the state of current research on EVs and their applications.
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Affiliation(s)
| | - Yixue Li
- *Correspondence: Yixue Li, ; Tao Zeng,
| | - Tao Zeng
- *Correspondence: Yixue Li, ; Tao Zeng,
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Ruskovska T, Budić-Leto I, Corral-Jara KF, Ajdžanović V, Arola-Arnal A, Bravo FI, Deligiannidou GE, Havlik J, Janeva M, Kistanova E, Kontogiorgis C, Krga I, Massaro M, Miler M, Milosevic V, Morand C, Scoditti E, Suárez M, Vauzour D, Milenkovic D. Systematic Bioinformatic Analyses of Nutrigenomic Modifications by Polyphenols Associated with Cardiometabolic Health in Humans-Evidence from Targeted Nutrigenomic Studies. Nutrients 2021; 13:nu13072326. [PMID: 34371836 PMCID: PMC8308901 DOI: 10.3390/nu13072326] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 12/14/2022] Open
Abstract
Cardiometabolic disorders are among the leading causes of mortality in the human population. Dietary polyphenols exert beneficial effects on cardiometabolic health in humans. Molecular mechanisms, however, are not completely understood. Aiming to conduct in-depth integrative bioinformatic analyses to elucidate molecular mechanisms underlying the protective effects of polyphenols on cardiometabolic health, we first conducted a systematic literature search to identify human intervention studies with polyphenols that demonstrate improvement of cardiometabolic risk factors in parallel with significant nutrigenomic effects. Applying the predefined inclusion criteria, we identified 58 differentially expressed genes at mRNA level and 5 miRNAs, analyzed in peripheral blood cells with RT-PCR methods. Subsequent integrative bioinformatic analyses demonstrated that polyphenols modulate genes that are mainly involved in the processes such as inflammation, lipid metabolism, and endothelial function. We also identified 37 transcription factors that are involved in the regulation of polyphenol modulated genes, including RELA/NFKB1, STAT1, JUN, or SIRT1. Integrative bioinformatic analysis of mRNA and miRNA-target pathways demonstrated several common enriched pathways that include MAPK signaling pathway, TNF signaling pathway, PI3K-Akt signaling pathway, focal adhesion, or PPAR signaling pathway. These bioinformatic analyses represent a valuable source of information for the identification of molecular mechanisms underlying the beneficial health effects of polyphenols and potential target genes for future nutrigenetic studies.
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Affiliation(s)
- Tatjana Ruskovska
- Faculty of Medical Sciences, Goce Delcev University, 2000 Stip, North Macedonia; (T.R.); (M.J.)
| | - Irena Budić-Leto
- Institute for Adriatic Crops and Karst Reclamation, 21000 Split, Croatia;
| | - Karla Fabiola Corral-Jara
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (I.K.); (C.M.)
| | - Vladimir Ajdžanović
- Institute for Biological Research “Siniša Stanković”—National Institute of Republic of Serbia, University of Belgrade, 11060 Belgrade, Serbia; (V.A.); (M.M.); (V.M.)
| | - Anna Arola-Arnal
- Nutrigenomics Research Group, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain; (A.A.-A.); (F.I.B.); (M.S.)
| | - Francisca Isabel Bravo
- Nutrigenomics Research Group, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain; (A.A.-A.); (F.I.B.); (M.S.)
| | - Georgia-Eirini Deligiannidou
- Department of Medicine, Democritus University of Thrace, Dragana, 68100 Alexandroupolis, Greece; (G.-E.D.); (C.K.)
| | - Jaroslav Havlik
- Department of Food Science, Czech University of Life Sciences, 16521 Prague, Czech Republic;
| | - Milkica Janeva
- Faculty of Medical Sciences, Goce Delcev University, 2000 Stip, North Macedonia; (T.R.); (M.J.)
| | - Elena Kistanova
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria;
| | - Christos Kontogiorgis
- Department of Medicine, Democritus University of Thrace, Dragana, 68100 Alexandroupolis, Greece; (G.-E.D.); (C.K.)
| | - Irena Krga
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (I.K.); (C.M.)
- Centre of Research Excellence in Nutrition and Metabolism, Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, 11060 Belgrade, Serbia
| | - Marika Massaro
- National Research Council (CNR) Institute of Clinical Physiology (IFC), 73100 Lecce, Italy; (M.M.); (E.S.)
| | - Marko Miler
- Institute for Biological Research “Siniša Stanković”—National Institute of Republic of Serbia, University of Belgrade, 11060 Belgrade, Serbia; (V.A.); (M.M.); (V.M.)
| | - Verica Milosevic
- Institute for Biological Research “Siniša Stanković”—National Institute of Republic of Serbia, University of Belgrade, 11060 Belgrade, Serbia; (V.A.); (M.M.); (V.M.)
| | - Christine Morand
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (I.K.); (C.M.)
| | - Egeria Scoditti
- National Research Council (CNR) Institute of Clinical Physiology (IFC), 73100 Lecce, Italy; (M.M.); (E.S.)
| | - Manuel Suárez
- Nutrigenomics Research Group, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain; (A.A.-A.); (F.I.B.); (M.S.)
| | - David Vauzour
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK;
| | - Dragan Milenkovic
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (I.K.); (C.M.)
- Department of Internal Medicine, Division of Cardiovascular Medicine, School of Medicine, University of California Davis, Davis, CA 95616, USA
- Correspondence:
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Willscher E, Hopp L, Kreuz M, Schmidt M, Hakobyan S, Arakelyan A, Hentschel B, Jones DTW, Pfister SM, Loeffler M, Loeffler-Wirth H, Binder H. High-Resolution Cartography of the Transcriptome and Methylome Landscapes of Diffuse Gliomas. Cancers (Basel) 2021; 13:3198. [PMID: 34206856 PMCID: PMC8268631 DOI: 10.3390/cancers13133198] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 02/01/2023] Open
Abstract
Molecular mechanisms of lower-grade (II-III) diffuse gliomas (LGG) are still poorly understood, mainly because of their heterogeneity. They split into astrocytoma- (IDH-A) and oligodendroglioma-like (IDH-O) tumors both carrying mutations(s) at the isocitrate dehydrogenase (IDH) gene and into IDH wild type (IDH-wt) gliomas of glioblastoma resemblance. We generated detailed maps of the transcriptomes and DNA methylomes, revealing that cell functions divided into three major archetypic hallmarks: (i) increased proliferation in IDH-wt and, to a lesser degree, IDH-O; (ii) increased inflammation in IDH-A and IDH-wt; and (iii) the loss of synaptic transmission in all subtypes. Immunogenic properties of IDH-A are diverse, partly resembling signatures observed in grade IV mesenchymal glioblastomas or in grade I pilocytic astrocytomas. We analyzed details of coregulation between gene expression and DNA methylation and of the immunogenic micro-environment presumably driving tumor development and treatment resistance. Our transcriptome and methylome maps support personalized, case-by-case views to decipher the heterogeneity of glioma states in terms of data portraits. Thereby, molecular cartography provides a graphical coordinate system that links gene-level information with glioma subtypes, their phenotypes, and clinical context.
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Affiliation(s)
- Edith Willscher
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
| | - Lydia Hopp
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
| | - Markus Kreuz
- IMISE, Institute for Medical Informatics, Statistics and Epidemiology, Universität of Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.K.); (B.H.); (M.L.)
| | - Maria Schmidt
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
| | - Siras Hakobyan
- Research Group of Bioinformatics, Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia, 7 Hasratyan Str., Yerevan 0014, Armenia; (S.H.); (A.A.)
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
| | - Arsen Arakelyan
- Research Group of Bioinformatics, Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia, 7 Hasratyan Str., Yerevan 0014, Armenia; (S.H.); (A.A.)
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
| | - Bettina Hentschel
- IMISE, Institute for Medical Informatics, Statistics and Epidemiology, Universität of Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.K.); (B.H.); (M.L.)
| | - David T. W. Jones
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Stefan M. Pfister
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Markus Loeffler
- IMISE, Institute for Medical Informatics, Statistics and Epidemiology, Universität of Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.K.); (B.H.); (M.L.)
| | - Henry Loeffler-Wirth
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
| | - Hans Binder
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
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Han K, Singh K, Rodman MJ, Hassanzadeh S, Baumer Y, Huffstutler RD, Chen J, Candia J, Cheung F, Stagliano KER, Pirooznia M, Powell-Wiley TM, Sack MN. Identification and Validation of Nutrient State-Dependent Serum Protein Mediators of Human CD4 + T Cell Responsiveness. Nutrients 2021; 13:nu13051492. [PMID: 33924911 PMCID: PMC8146063 DOI: 10.3390/nu13051492] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 02/07/2023] Open
Abstract
Intermittent fasting and fasting mimetic diets ameliorate inflammation. Similarly, serum extracted from fasted healthy and asthmatic subjects' blunt inflammation in vitro, implicating serum components in this immunomodulation. To identify the proteins orchestrating these effects, SOMAScan technology was employed to evaluate serum protein levels in healthy subjects following an overnight, 24-h fast and 3 h after refeeding. Partial least square discriminant analysis identified several serum proteins as potential candidates to confer feeding status immunomodulation. The characterization of recombinant IGFBP1 (elevated following 24 h of fasting) and PYY (elevated following refeeding) in primary human CD4+ T cells found that they blunted and induced immune activation, respectively. Furthermore, integrated univariate serum protein analysis compared to RNA-seq analysis from peripheral blood mononuclear cells identified the induction of IL1RL1 and MFGE8 levels in refeeding compared to the 24-h fasting in the same study. Subsequent quantitation of these candidate proteins in lean versus obese individuals identified an inverse regulation of serum levels in the fasted subjects compared to the obese subjects. In parallel, IL1RL1 and MFGE8 supplementation promoted increased CD4+ T responsiveness to T cell receptor activation. Together, these data show that caloric load-linked conditions evoke serological protein changes, which in turn confer biological effects on circulating CD4+ T cell immune responsiveness.
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Affiliation(s)
- Kim Han
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.H.); (M.J.R.); (S.H.)
| | - Komudi Singh
- Bioinformatics and Computational Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.S.); (M.P.)
| | - Matthew J. Rodman
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.H.); (M.J.R.); (S.H.)
| | - Shahin Hassanzadeh
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.H.); (M.J.R.); (S.H.)
| | - Yvonne Baumer
- Determinants of Obesity and Cardiovascular Risk, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; (Y.B.); (T.M.P.-W.)
| | - Rebecca D. Huffstutler
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Jinguo Chen
- Center of Human Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (J.C.); (J.C.); (F.C.); (K.E.R.S.)
| | - Julián Candia
- Center of Human Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (J.C.); (J.C.); (F.C.); (K.E.R.S.)
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Foo Cheung
- Center of Human Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (J.C.); (J.C.); (F.C.); (K.E.R.S.)
| | - Katherine E. R. Stagliano
- Center of Human Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (J.C.); (J.C.); (F.C.); (K.E.R.S.)
| | - Mehdi Pirooznia
- Bioinformatics and Computational Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.S.); (M.P.)
| | - Tiffany M. Powell-Wiley
- Determinants of Obesity and Cardiovascular Risk, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; (Y.B.); (T.M.P.-W.)
- National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael N. Sack
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.H.); (M.J.R.); (S.H.)
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA;
- Correspondence:
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Settino M, Cannataro M. MMRFBiolinks: an R-package for integrating and analyzing MMRF-CoMMpass data. Brief Bioinform 2021; 22:6209690. [PMID: 33821961 DOI: 10.1093/bib/bbab050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 01/18/2021] [Accepted: 02/03/2021] [Indexed: 01/05/2023] Open
Abstract
In order to understand the mechanisms underlying the onset and the drug responses in multiple myeloma (MM), the second most frequent hematological cancer, the use of appropriate bioinformatic tools for integrative analysis of publicly available genomic data is required. We present MMRFBiolinks, a new R package for integrating and analyzing datasets from the Multiple Myeloma Research Foundation (MMRF) CoMMpass (Clinical Outcomes in MM to Personal Assessment of Genetic Profile) study, available at MMRF Researcher Gateway (MMRF-RG), and from the National Cancer Institute Genomic Data Commons (NCI-GDC) Data Portal. The package provides several methods for integrative analysis (array-array intensity correlation, Kaplan-Meier survival analysis) and visualization (response to treatments plot) of MMRF data, for performing an easily comprehensible analysis workflow. MMRFBiolinks extends the TCGABiolinks package by providing 13 new functions to analyze MMRF-CoMMpass data: six dealing with MMRF-RG data and seven with NCI-GDC data. As validation of the tool, we present two cases studies for searching, downloading and analyzing MMRF data. The former presents a workflow for identifying genes involved in survival depending on treatment. The latter presents an analysis workflow for analyzing the Best Overall (BO) response through correlation plots between the BO Response with respect to treatments, time, duration of treatment and annotated variants, as well as through Kaplan-Meier survival curves. The case studies demonstrate how MMRFBiolinks is able of overcoming the limitations of the analysis tools available at NCI-GDC and MMRF-RG, facilitating and making more comprehensive the retrieval, downloading and analysis of MMRF data.
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Affiliation(s)
- Marzia Settino
- Data Analytics Research Center, Department of Medical and Surgical Sciences, University "Magna Graecia" of Catanzaro, Catanzaro, Italy
| | - Mario Cannataro
- Data Analytics Research Center, Department of Medical and Surgical Sciences, University "Magna Graecia" of Catanzaro, Catanzaro, Italy
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10
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Zong Z, Li H, Ning Z, Hu C, Tang F, Zhu X, Tian H, Zhou T, Wang H. Integrative bioinformatics analysis of prognostic alternative splicing signatures in gastric cancer. J Gastrointest Oncol 2020; 11:685-694. [PMID: 32953152 DOI: 10.21037/jgo-20-117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background The potential prognostic value of alternative splicing (AS) variants and regulatory splicing factors in gastric carcinogenesis is unclear. We aimed to exploit the aberrant AS signatures and splicing factors involved in gastric cancer (GC) and to determine their prognostic predictive values. Methods We performed detailed data acquisition using the Cancer Genome Atlas project and profiled genome-wide AS signatures in a cohort of 190 patients with stomach adenocarcinoma (STAD). Prognostic prediction models and splicing correlation networks were assessed using an integrative bioinformatics analysis approach. Results We detected 1,308 overall survival (OS)-related AS signatures in 993 genes, most of which were favorable prognostic factors. Six splicing factors have been suggested to be dysregulated in GC, i.e., DHX15, PPP4R2, PRPF38B, RBM9, RBM15, and ILF3. Another notable finding was that most favorable prognosis AS events were positively correlated with expression of splicing factors, while a majority of poor survival prognostic AS genes were negatively associated with the expression of splicing factors. Conclusions To our knowledge, the current study provided the first comprehensive profiling of global modifications in the RNA splicing to identify survival associated AS signatures of GC specific genes. Our findings contribute to a better understanding of aberrant AS signatures and splicing factors in STAD, which can potentially be used as prognostic biomarkers and therapeutic targets for GC.
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Affiliation(s)
- Zhen Zong
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hui Li
- Department of Rheumatology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhikun Ning
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Cegui Hu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Fuxin Tang
- Department of Gastroenterological Surgery and Hernia Center, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaojian Zhu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Huakai Tian
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Taicheng Zhou
- Department of Gastroenterological Surgery and Hernia Center, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - He Wang
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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11
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Singh N, Sahu DK, Tripathi RK, Mishra A, Shyam H, Shankar P, Jain M, Alam N, Kumar A, Mishra A, Chowdhry R, Singh A, Gupta S, Mehrotra D, Agarwal P, Goel MM, Chaturvedi A, Agarwal SP, Bajpai M, Gupta DK, Bhatt MLB, Kant R. Differentially expressed full-length, fusion and novel isoforms transcripts-based signature of well-differentiated keratinized oral squamous cell carcinoma. Oncotarget 2020; 11:3227-3243. [PMID: 32922662 PMCID: PMC7456611 DOI: 10.18632/oncotarget.27693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/14/2020] [Indexed: 12/20/2022] Open
Abstract
Highly keratinized oral squamous cell carcinoma (OSCC) exhibits an improved response to treatment and prognosis compared with weakly keratinized OSCC. Therefore, we aimed to develop gene transcript signature and to identify novel full-length isoforms, fusion transcript and non-coding RNA to differentiate well-differentiated (WD) with Moderately Differentiated (MD)/Poorly Differentiated (PD)/WD-lymphadenopathy OSCC through, HTA, Isoform sequencing, and NanoString. Additionally, specific copy number gain and loss were also identify in WD keratinized OSCC through Oncoscan array and validated through Real-time PCR in histopathologically characterized FFPE-WD keratinized OSCC. Three-hundred-thirty-eight (338) differentially expressed full-length (FL) transcript isoforms (317 upregulated and 21 down-regulated in OSCC) were identified through Isoform Sequencing using the PacBio platform. Thirty-four (34) highly upregulated differentially expressed transcripts from IsoSeq data were also correlated with HTA2.0 and validated in 42 OSCC samples. We were able to identify 18 differentially expressed transcripts, 12 fusion transcripts, and two long noncoding RNAs. These transcripts were involved in increased cell proliferation, dysregulated metabolic reprogramming, oxidative stress, and immune system markers with enhanced immune rearrangements, suggesting a cancerous nature. However, an increase in proteasomal activity and hemidesmosome proteins suggested an improved prognosis and tumor cell stability in keratinized OSCC and helped to characterize WD with MD/PD/WD with lymphadenopathy OSCC. Additionally, novel isoforms of IL37, NAA10, UCHL3, SPAG7, and RAB24 were identified while in silico functionally validated SPAG7 represented the premalignant phenotype of keratinized (K4) OSCC. Most importantly we found copy number gain and overexpression of EGFR suggest that TKIs may also be used as therapeutics in WD-OSCCs.
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Affiliation(s)
- Neetu Singh
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India.,These authors contributed equally to this work
| | - Dinesh Kumar Sahu
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India.,These authors contributed equally to this work
| | - Ratnesh Kumar Tripathi
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India.,These authors contributed equally to this work
| | - Archana Mishra
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India.,Department of Surgery, King George's Medical University, Lucknow, India
| | - Hari Shyam
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Pratap Shankar
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Mayank Jain
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Nawazish Alam
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Anil Kumar
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Abhishek Mishra
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Rebecca Chowdhry
- Department of Periodontology, All India Institute of Medical Sciences, Rishikesh, India
| | - Anjana Singh
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George's Medical University, Lucknow, India
| | - Divya Mehrotra
- Department of Oral and Maxillofacial Surgery, King George's Medical University, Lucknow, India
| | - Preeti Agarwal
- Department of Pathology, King George's Medical University, Lucknow, India
| | - Madhu Mati Goel
- Department of Pathology, King George's Medical University, Lucknow, India
| | - Arun Chaturvedi
- Department of Surgical Oncology, King George's Medical University, Lucknow, India
| | | | - Manish Bajpai
- Department of Physiology, King George's Medical University, Lucknow, India
| | - Devendra Kumar Gupta
- Department of Pediatric Surgery, Super Speciality Pediatric Hospital and Post Graduate Teaching Institute, Noida, India
| | | | - Ravi Kant
- Department of Surgical Oncology, All India Institute of Medical Sciences, Rishikesh, India
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12
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Fuchs M, Kreutzer FP, Kapsner LA, Mitzka S, Just A, Perbellini F, Terracciano CM, Xiao K, Geffers R, Bogdan C, Prokosch HU, Fiedler J, Thum T, Kunz M. Integrative Bioinformatic Analyses of Global Transcriptome Data Decipher Novel Molecular Insights into Cardiac Anti-Fibrotic Therapies. Int J Mol Sci 2020; 21:ijms21134727. [PMID: 32630753 PMCID: PMC7370212 DOI: 10.3390/ijms21134727] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/27/2020] [Accepted: 06/28/2020] [Indexed: 12/22/2022] Open
Abstract
Integrative bioinformatics is an emerging field in the big data era, offering a steadily increasing number of algorithms and analysis tools. However, for researchers in experimental life sciences it is often difficult to follow and properly apply the bioinformatical methods in order to unravel the complexity and systemic effects of omics data. Here, we present an integrative bioinformatics pipeline to decipher crucial biological insights from global transcriptome profiling data to validate innovative therapeutics. It is available as a web application for an interactive and simplified analysis without the need for programming skills or deep bioinformatics background. The approach was applied to an ex vivo cardiac model treated with natural anti-fibrotic compounds and we obtained new mechanistic insights into their anti-fibrotic action and molecular interplay with miRNAs in cardiac fibrosis. Several gene pathways associated with proliferation, extracellular matrix processes and wound healing were altered, and we could identify micro (mi) RNA-21-5p and miRNA-223-3p as key molecular components related to the anti-fibrotic treatment. Importantly, our pipeline is not restricted to a specific cell type or disease and can be broadly applied to better understand the unprecedented level of complexity in big data research.
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Affiliation(s)
- Maximilian Fuchs
- Chair of Medical Informatics, Friedrich-Alexander University (FAU) of Erlangen-Nürnberg, 91058 Erlangen, Germany; (M.F.); (H.-U.P.)
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, University of Würzburg, 97074 Würzburg, Germany
| | - Fabian Philipp Kreutzer
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, 30625 Hannover, Germany; (F.P.K.); (S.M.); (A.J.); (F.P.); (K.X.); (J.F.)
| | - Lorenz A. Kapsner
- Medical Center for Information and Communication Technology, Universitätsklinikum Erlangen, 91054 Erlangen, Germany;
| | - Saskia Mitzka
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, 30625 Hannover, Germany; (F.P.K.); (S.M.); (A.J.); (F.P.); (K.X.); (J.F.)
| | - Annette Just
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, 30625 Hannover, Germany; (F.P.K.); (S.M.); (A.J.); (F.P.); (K.X.); (J.F.)
| | - Filippo Perbellini
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, 30625 Hannover, Germany; (F.P.K.); (S.M.); (A.J.); (F.P.); (K.X.); (J.F.)
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London W12 0NN, UK;
| | - Cesare M. Terracciano
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London W12 0NN, UK;
| | - Ke Xiao
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, 30625 Hannover, Germany; (F.P.K.); (S.M.); (A.J.); (F.P.); (K.X.); (J.F.)
| | - Robert Geffers
- Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
| | - Christian Bogdan
- Mikrobiologisches Institut—Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen and Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany;
| | - Hans-Ulrich Prokosch
- Chair of Medical Informatics, Friedrich-Alexander University (FAU) of Erlangen-Nürnberg, 91058 Erlangen, Germany; (M.F.); (H.-U.P.)
| | - Jan Fiedler
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, 30625 Hannover, Germany; (F.P.K.); (S.M.); (A.J.); (F.P.); (K.X.); (J.F.)
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, 30625 Hannover, Germany; (F.P.K.); (S.M.); (A.J.); (F.P.); (K.X.); (J.F.)
- REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
- Correspondence: (T.T.); (M.K.); Tel.: +49-511-532-5272 (T.T.); +49-9131-85-26767 (M.K.); Fax: +49-511-532-5274 (T.T.); +49-9131-85-26754 (M.K.)
| | - Meik Kunz
- Chair of Medical Informatics, Friedrich-Alexander University (FAU) of Erlangen-Nürnberg, 91058 Erlangen, Germany; (M.F.); (H.-U.P.)
- Correspondence: (T.T.); (M.K.); Tel.: +49-511-532-5272 (T.T.); +49-9131-85-26767 (M.K.); Fax: +49-511-532-5274 (T.T.); +49-9131-85-26754 (M.K.)
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13
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Wang R, Zhou X, Wang H, Zhou B, Dong S, Ding Q, Peng M, Sheng X, Yao J, Huang R, Zeng Y, Long Y. Integrative analysis of gene expression profiles reveals distinct molecular characteristics in oral tongue squamous cell carcinoma. Oncol Lett 2018; 17:2377-2387. [PMID: 30675303 PMCID: PMC6341834 DOI: 10.3892/ol.2018.9866] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 11/29/2018] [Indexed: 12/17/2022] Open
Abstract
Oral tongue squamous cell carcinoma (OTSCC) is the most common type of oral cancer. Despite advances in knowledge regarding the genome-scale gene expression pattern of oral cancer, the molecular portrait of OTSCC biology has remained unclear over the last few decades. Furthermore, studies concerning OTSCC gene-expression profiles are limited or inconsistent owing to tissue heterogeneity in single-cohort studies. Consequently, the present study integrated the profile datasets of three cohorts in order to screen for differentially expressed genes (DEGs), and subsequently identified the potential candidate genes and pathways in OTSCC through gene enrichment analysis and protein-protein interaction (PPI) network construction. Using the selected Gene Expression Omnibus datasets GSE13601, GSE31056 and GSE78060, 206 DEGs (125 upregulated and 81 downregulated) were identified in OTSCC, principally associated with extracellular matrix (ECM) organization and the phosphoinositide 3-kinase/protein kinase B signaling pathway. Furthermore, 146/206 DEGs were filtered into the PPI network and 20 hub genes were sorted. Further results indicated that the two most significant modules filtered from the PPI network were associated with ECM organization and human papillomavirus infection, which are important factors affecting OTSCC pathology. Overall, a set of OTSCC-associated DEGs has been identified, including certain key candidate genes that may be of vital importance for diagnosis, therapy and prevention of this disease.
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Affiliation(s)
- Ranran Wang
- Translational Medicine Center, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China.,Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
| | - Xiao Zhou
- Translational Medicine Center, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China.,Department of Oncoplastic and Reconstructive Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
| | - Hui Wang
- Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
| | - Bo Zhou
- Department of Oncoplastic and Reconstructive Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
| | - Shanshan Dong
- Translational Medicine Center, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China.,Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
| | - Qi Ding
- Translational Medicine Center, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China.,Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
| | - Mingjing Peng
- Translational Medicine Center, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
| | - Xiaowu Sheng
- Translational Medicine Center, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
| | - Jianfeng Yao
- Reproductive Medicine Center, Quanzhou Maternal and Child Health Hospital, Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Rongfu Huang
- Clinical Laboratory, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Yong Zeng
- Translational Medicine Center, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China.,Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
| | - Ying Long
- Translational Medicine Center, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China.,Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
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14
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Hopp L, Löffler-Wirth H, Galle J, Binder H. Combined SOM-portrayal of gene expression and DNA methylation landscapes disentangles modes of epigenetic regulation in glioblastoma. Epigenomics 2018; 10:745-764. [PMID: 29888966 DOI: 10.2217/epi-2017-0140] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
AIM We present here a novel method that enables unraveling the interplay between gene expression and DNA methylation in complex diseases such as cancer. MATERIALS & METHODS The method is based on self-organizing maps and allows for analysis of data landscapes from 'governed by methylation' to 'governed by expression'. RESULTS We identified regulatory modules of coexpressed and comethylated genes in high-grade gliomas: two modes are governed by genes hypermethylated and underexpressed in IDH-mutated cases, while two other modes reflect immune and stromal signatures in the classical and mesenchymal subtypes. A fifth mode with proneural characteristics comprises genes of repressed and poised chromatin states active in healthy brain. Two additional modes enrich genes either in active or repressed chromatin states. CONCLUSION The method disentangles the interplay between gene expression and methylation. It has the potential to integrate also mutation and copy number data and to apply to large sample cohorts.
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Affiliation(s)
- Lydia Hopp
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Henry Löffler-Wirth
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Jörg Galle
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Hans Binder
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany
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15
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Reifenberger G, Weber RG, Riehmer V, Kaulich K, Willscher E, Wirth H, Gietzelt J, Hentschel B, Westphal M, Simon M, Schackert G, Schramm J, Matschke J, Sabel MC, Gramatzki D, Felsberg J, Hartmann C, Steinbach JP, Schlegel U, Wick W, Radlwimmer B, Pietsch T, Tonn JC, von Deimling A, Binder H, Weller M, Loeffler M. Molecular characterization of long-term survivors of glioblastoma using genome- and transcriptome-wide profiling. Int J Cancer 2014; 135:1822-31. [PMID: 24615357 DOI: 10.1002/ijc.28836] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 02/21/2014] [Indexed: 01/16/2023]
Abstract
The prognosis of glioblastoma, the most malignant type of glioma, is still poor, with only a minority of patients showing long-term survival of more than three years after diagnosis. To elucidate the molecular aberrations in glioblastomas of long-term survivors, we performed genome- and/or transcriptome-wide molecular profiling of glioblastoma samples from 94 patients, including 28 long-term survivors with >36 months overall survival (OS), 20 short-term survivors with <12 months OS and 46 patients with intermediate OS. Integrative bioinformatic analyses were used to characterize molecular aberrations in the distinct survival groups considering established molecular markers such as isocitrate dehydrogenase 1 or 2 (IDH1/2) mutations, and O(6) -methylguanine DNA methyltransferase (MGMT) promoter methylation. Patients with long-term survival were younger and more often had IDH1/2-mutant and MGMT-methylated tumors. Gene expression profiling revealed over-representation of a distinct (proneural-like) expression signature in long-term survivors that was linked to IDH1/2 mutation. However, IDH1/2-wildtype glioblastomas from long-term survivors did not show distinct gene expression profiles and included proneural, classical and mesenchymal glioblastoma subtypes. Genomic imbalances also differed between IDH1/2-mutant and IDH1/2-wildtype tumors, but not between survival groups of IDH1/2-wildtype patients. Thus, our data support an important role for MGMT promoter methylation and IDH1/2 mutation in glioblastoma long-term survival and corroborate the association of IDH1/2 mutation with distinct genomic and transcriptional profiles. Importantly, however, IDH1/2-wildtype glioblastomas in our cohort of long-term survivors lacked distinctive DNA copy number changes and gene expression signatures, indicating that other factors might have been responsible for long survival in this particular subgroup of patients.
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Affiliation(s)
- Guido Reifenberger
- Department of Neuropathology, Heinrich Heine University, Düsseldorf, and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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