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Bioinformatics Characterization of Candidate Genes Associated with Gene Network and miRNA Regulation in Esophageal Squamous Cell Carcinoma Patients. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The present study aimed to identify potential therapeutic targets for esophageal squamous cell carcinoma (ESCC). The gene expression profile GSE161533 contained 84 samples, in that 28 tumor tissues and 28 normal tissues encoded as ESCC patients were retrieved from the Gene Expression Omnibus database. The obtained data were validated and screened for differentially expressed genes (DEGs) between normal and tumor tissues with the GEO2R tool. Next, the protein–protein network (PPI) was constructed using the (STRING 2.0) and reconstructed with Cytoscape 3.8.2, and the top ten hub genes (HGsT10) were predicted using the Maximal Clique Centrality (MCC) algorithm of the CytoHubba plugin. The identified hub genes were mapped in GSE161533, and their expression was determined and compared with The Cancer Genome Atlas (TCGA.) ESCC patient’s samples. The overall survival rate for HGsT10 wild and mutated types was analyzed with the Gene Expression Profiling Interactive Analysis2 (GEPIA2) server and UCSC Xena database. The functional and pathway enrichment analysis was performed using the WebGestalt database with the reference gene from lumina human ref 8.v3.0 version. The promoter methylation for the HGsT10 was identified using the UALCAN server. Additionally, the miRNA-HGsT10 regulatory network was constructed to identify the top ten hub miRNAs (miRT10). Finally, we identified the top ten novel driving genes from the DEGs of GSE161533 ESCC patient’s sample using a multi-omics approach. It may provide new insights into the diagnosis and treatment for the ESCC affected patients early in the future.
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Burke SL, Maramaldi P. The Social Security Administration's Compassionate Allowances Initiative: Condition Spotlight on Rubinstein-Taybi Syndrome. HEALTH & SOCIAL WORK 2017; 42:e32-e43. [PMID: 28395077 DOI: 10.1093/hsw/hlw062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/25/2016] [Indexed: 06/07/2023]
Abstract
The Social Security Administration (SSA) Compassionate Allowances List (CAL) was created in 2008, generating a mechanism within SSA for identifying diseases and other medical conditions that by definition meet social security's standards for disability benefits. Currently, over 200 conditions are included in this expedited review program, though few of them are neurodevelopmental in nature. Exploration of a novel method for inclusion of additional conditions on CAL was undertaken using one condition as an exemplar. Peer-reviewed literature available in academic databases was reviewed and used as empirical evidence to demonstrate whether Rubinstein-Taybi syndrome (RTS) invariably met the three disability criteria set forth by SSA. After in-depth exploration of the empirical literature, RTS was found to meet SSA's definition, suggesting this condition should receive consideration as an addition to the Compassionate Allowances Initiative.
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Affiliation(s)
- Shanna L Burke
- School of Social Work, Robert Stempel College of Public Health and Social Work, Florida International University, 11200 SW 8th Street, Miami, FL, USA
| | - Peter Maramaldi
- Department of Social and Behavioral Sciences, Harvard T. H. Chan School of Public Health, Boston, USA
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Acevedo SF, Valencia C, Lutter M, McAdams CJ. Severity of eating disorder symptoms related to oxytocin receptor polymorphisms in anorexia nervosa. Psychiatry Res 2015; 228:641-8. [PMID: 26106053 PMCID: PMC4532594 DOI: 10.1016/j.psychres.2015.05.040] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 04/21/2015] [Accepted: 05/05/2015] [Indexed: 12/11/2022]
Abstract
Oxytocin is a peptide hormone important for social behavior and differences in psychological traits have been associated with variants of the oxytocin receptor gene in healthy people. We examined whether single nucleotide polymorphisms (SNPs) of the oxytocin receptor gene (OXTR) correlated with clinical symptoms in women with anorexia nervosa, bulimia nervosa, and healthy comparison (HC) women. Subjects completed clinical assessments and provided DNA for analysis. Subjects were divided into four groups: HC, subjects currently with anorexia nervosa (AN-C), subjects with a history of anorexia nervosa but in long-term weight recovery (AN-WR), and subjects with bulimia nervosa (BN). Five SNPs of the oxytocin receptor were examined. Minor allele carriers showed greater severity in most of the psychiatric symptoms. Importantly, the combination of having had anorexia and carrying either of the A alleles for two SNPS in the OXTR gene (rs53576, rs2254298) was associated with increased severity specifically for ED symptoms including cognitions and behaviors associated both with eating and appearance. A review of psychosocial data related to the OXTR polymorphisms examined is included in the discussion. OXTR polymorphisms may be a useful intermediate endophenotype to consider in the treatment of patients with anorexia nervosa.
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Affiliation(s)
- Summer F. Acevedo
- University of Texas at Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas TX 75390-8828
| | - Celeste Valencia
- University of Texas at Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas TX 75390-8828
| | - Michael Lutter
- Department of Psychiatry, University of Iowa, Carver College of Medicine, Iowa City, IA, USA. 52242
| | - Carrie J. McAdams
- University of Texas at Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas TX 75390-8828
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Costa D, Capuano M, Sommese L, Napoli C. Impact of epigenetic mechanisms on therapeutic approaches of hemoglobinopathies. Blood Cells Mol Dis 2015; 55:95-100. [DOI: 10.1016/j.bcmd.2015.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 05/08/2015] [Accepted: 05/10/2015] [Indexed: 11/24/2022]
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Elshimali YI, Khaddour H, Sarkissyan M, Wu Y, Vadgama JV. The clinical utilization of circulating cell free DNA (CCFDNA) in blood of cancer patients. Int J Mol Sci 2013; 14:18925-58. [PMID: 24065096 PMCID: PMC3794814 DOI: 10.3390/ijms140918925] [Citation(s) in RCA: 182] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 08/26/2013] [Accepted: 08/30/2013] [Indexed: 02/06/2023] Open
Abstract
Qualitative and quantitative testing of circulating cell free DNA (CCFDNA) can be applied for the management of malignant and benign neoplasms. Detecting circulating DNA in cancer patients may help develop a DNA profile for early stage diagnosis in malignancies. The technical issues of obtaining, using, and analyzing CCFDNA from blood will be discussed.
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Affiliation(s)
- Yahya I. Elshimali
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, 1720 East 120th Street, Los Angeles, CA 90059, USA; E-Mails: (M.S.); (Y.W.); (J.V.V.)
- Author to whom correspondence should be addressed; E-Mail: or ; Tel.: +1-818-515-7618; Fax: +1-818-994-9875
| | - Husseina Khaddour
- Laboratory Diagnostic Medicine, Faculty of Pharmacy, Mazzeh (17th April Street), Damascus University, Damascus, Syria; E-Mail:
| | - Marianna Sarkissyan
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, 1720 East 120th Street, Los Angeles, CA 90059, USA; E-Mails: (M.S.); (Y.W.); (J.V.V.)
| | - Yanyuan Wu
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, 1720 East 120th Street, Los Angeles, CA 90059, USA; E-Mails: (M.S.); (Y.W.); (J.V.V.)
- David Geffen School of Medicine at UCLA, UCLA’s Jonsson Comprehensive Cancer Center, 8-684 Factor Building, Box 951781, Los Angeles, CA 90095-1781, USA
| | - Jaydutt V. Vadgama
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, 1720 East 120th Street, Los Angeles, CA 90059, USA; E-Mails: (M.S.); (Y.W.); (J.V.V.)
- David Geffen School of Medicine at UCLA, UCLA’s Jonsson Comprehensive Cancer Center, 8-684 Factor Building, Box 951781, Los Angeles, CA 90095-1781, USA
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Lana E, Mégarbané A, Tourrière H, Sarda P, Lefranc G, Claustres M, De Sario A. DNA replication is altered in Immunodeficiency Centromeric instability Facial anomalies (ICF) cells carrying DNMT3B mutations. Eur J Hum Genet 2012; 20:1044-50. [PMID: 22378288 PMCID: PMC3449075 DOI: 10.1038/ejhg.2012.41] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 01/20/2012] [Accepted: 02/02/2012] [Indexed: 02/04/2023] Open
Abstract
ICF syndrome is a rare autosomal recessive disorder that is characterized by Immunodeficiency, Centromeric instability, and Facial anomalies. In all, 60% of ICF patients have mutations in the DNMT3B (DNA methyltransferase 3B) gene, encoding a de novo DNA methyltransferase. In ICF cells, constitutive heterochromatin is hypomethylated and decondensed, metaphase chromosomes undergo rearrangements (mainly involving juxtacentromeric regions), and more than 700 genes are aberrantly expressed. This work shows that DNA replication is also altered in ICF cells: (i) heterochromatic genes replicate earlier in the S-phase; (ii) global replication fork speed is higher; and (iii) S-phase is shorter. These replication defects may result from chromatin changes that modify DNA accessibility to the replication machinery and/or from changes in the expression level of genes involved in DNA replication. This work highlights the interest of using ICF cells as a model to investigate how DNA methylation regulates DNA replication in humans.
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Affiliation(s)
- Erica Lana
- INSERM U827, Montpellier, France
- Université Montpellier 1, Montpellier, France
| | - André Mégarbané
- Unité de Génétique Médicale and Laboratoire Associé INSERM à l'UMR S910, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
- Institut Jérôme Lejeune, Paris, France
| | | | | | - Gérard Lefranc
- CNRS UPR 1142, Montpellier, France
- Université Montpellier 2, Montpellier, France
| | - Mireille Claustres
- INSERM U827, Montpellier, France
- Université Montpellier 1, Montpellier, France
- CHRU, Montpellier, France
| | - Albertina De Sario
- INSERM U827, Montpellier, France
- Université Montpellier 1, Montpellier, France
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Butler JS, Koutelou E, Schibler AC, Dent SYR. Histone-modifying enzymes: regulators of developmental decisions and drivers of human disease. Epigenomics 2012; 4:163-77. [PMID: 22449188 DOI: 10.2217/epi.12.3] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Precise transcriptional networks drive the orchestration and execution of complex developmental processes. Transcription factors possessing sequence-specific DNA binding properties activate or repress target genes in a step-wise manner to control most cell lineage decisions. This regulation often requires the interaction between transcription factors and subunits of massive protein complexes that bear enzymatic activities towards histones. The functional coupling of transcription proteins and histone modifiers underscores the importance of transcriptional regulation through chromatin modification in developmental cell fate decisions and in disease pathogenesis.
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Affiliation(s)
- Jill S Butler
- Department of Molecular Carcinogenesis at The Virginia Harris Cockrell Cancer Research Center, University of Texas MD Anderson Cancer Center Science Park, PO Box 389, Smithville, TX 78957, USA
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Sarnico I, Branca C, Lanzillotta A, Porrini V, Benarese M, Spano PF, Pizzi M. NF-κB and epigenetic mechanisms as integrative regulators of brain resilience to anoxic stress. Brain Res 2012; 1476:203-10. [PMID: 22575713 DOI: 10.1016/j.brainres.2012.04.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 03/27/2012] [Accepted: 04/09/2012] [Indexed: 12/20/2022]
Abstract
Brain cells display an amazing ability to respond to several different types of environmental stimuli and integrate this response physiologically. Some of these responses can outlive the original stimulus by days, weeks or even longer. Long-lasting changes in both physiological and pathological conditions occurring in response to external stimuli are almost always mediated by changes in gene expression. To effect these changes, cells have developed an impressive repertoire of signaling systems designed to modulate the activity of numerous transcription factors and epigenetic mechanisms affecting the chromatin structure. Since its initial characterization in the nervous system, NF-κB has shown to respond to multiple signals and elicit pleiotropic activities suggesting that it may play a pivotal role in integration of different types of information within the brain. Ample evidence demonstrates that NF-κB factors are engaged in and necessary for neuronal development and synaptic plasticity, but they also regulate brain response to environmental noxae. By focusing on the complexity of NF-κB transcriptional activity in neuronal cell death, it emerged that the composition of NF-κB active dimers finely tunes the neuronal vulnerability to brain ischemia. Even though we are only beginning to understand the contribution of distinct NF-κB family members to the regulation of gene transcription in the brain, an additional level of regulation of NF-κB activity has emerged as operated by the epigenetic mechanisms modulating histone acetylation. We will discuss NF-κB and epigenetic mechanisms as integrative regulators of brain resilience to anoxic stress and useful drug targets for restoration of brain function. This article is part of a Special Issue entitled: Brain Integration.
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Affiliation(s)
- Ilenia Sarnico
- Department of Biomedical Sciences & Biotechnologies, University of Brescia and Istituto Nazionale di Neuroscienze, Italy
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Genes, Environment and Inheritance. Mol Med 2012. [DOI: 10.1016/b978-0-12-381451-7.00002-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] Open
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Hannibal MC, Buckingham KJ, Ng SB, Ming JE, Beck AE, McMillin MJ, Gildersleeve HI, Bigham AW, Tabor HK, Mefford HC, Cook J, Yoshiura KI, Matsumoto T, Matsumoto N, Miyake N, Tonoki H, Naritomi K, Kaname T, Nagai T, Ohashi H, Kurosawa K, Hou JW, Ohta T, Liang D, Sudo A, Morris CA, Banka S, Black GC, Clayton-Smith J, Nickerson DA, Zackai EH, Shaikh TH, Donnai D, Niikawa N, Shendure J, Bamshad MJ. Spectrum of MLL2 (ALR) mutations in 110 cases of Kabuki syndrome. Am J Med Genet A 2011; 155A:1511-6. [PMID: 21671394 DOI: 10.1002/ajmg.a.34074] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 03/30/2011] [Indexed: 12/24/2022]
Abstract
Kabuki syndrome is a rare, multiple malformation disorder characterized by a distinctive facial appearance, cardiac anomalies, skeletal abnormalities, and mild to moderate intellectual disability. Simplex cases make up the vast majority of the reported cases with Kabuki syndrome, but parent-to-child transmission in more than a half-dozen instances indicates that it is an autosomal dominant disorder. We recently reported that Kabuki syndrome is caused by mutations in MLL2, a gene that encodes a Trithorax-group histone methyltransferase, a protein important in the epigenetic control of active chromatin states. Here, we report on the screening of 110 families with Kabuki syndrome. MLL2 mutations were found in 81/110 (74%) of families. In simplex cases for which DNA was available from both parents, 25 mutations were confirmed to be de novo, while a transmitted MLL2 mutation was found in two of three familial cases. The majority of variants found to cause Kabuki syndrome were novel nonsense or frameshift mutations that are predicted to result in haploinsufficiency. The clinical characteristics of MLL2 mutation-positive cases did not differ significantly from MLL2 mutation-negative cases with the exception that renal anomalies were more common in MLL2 mutation-positive cases. These results are important for understanding the phenotypic consequences of MLL2 mutations for individuals and their families as well as for providing a basis for the identification of additional genes for Kabuki syndrome.
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Affiliation(s)
- Mark C Hannibal
- Department of Pediatrics, University of Washington, Seattle, 98195, USA
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Abstract
Epigenetics is one of the most rapidly expanding fields in biology. The recent characterization of a human DNA methylome at single nucleotide resolution, the discovery of the CpG island shores, the finding of new histone variants and modifications, and the unveiling of genome-wide nucleosome positioning maps highlight the accelerating speed of discovery over the past two years. Increasing interest in epigenetics has been accompanied by technological breakthroughs that now make it possible to undertake large-scale epigenomic studies. These allow the mapping of epigenetic marks, such as DNA methylation, histone modifications and nucleosome positioning, which are critical for regulating gene and noncoding RNA expression. In turn, we are learning how aberrant placement of these epigenetic marks and mutations in the epigenetic machinery is involved in disease. Thus, a comprehensive understanding of epigenetic mechanisms, their interactions and alterations in health and disease, has become a priority in biomedical research.
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Affiliation(s)
- Anna Portela
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, Barcelona, Catalonia, Spain
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Affiliation(s)
- Donna M Martin
- Department of Pediatrics, The University of Michigan, Ann Arbor, Michigan, United States of America.
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