Mrna and Mirna Expression Profiles in an Ectoderm-Biased Substate Of
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International Journal of Molecular Sciences Article Phenotypic Subtyping and Re-Analysis of Existing Methylation Data from Autistic Probands in Simplex Families Reveal ASD Subtype-Associated Differentially Methylated Genes and Biological Functions Elizabeth C. Lee y and Valerie W. Hu * Department of Biochemistry and Molecular Medicine, The George Washington University, School of Medicine and Health Sciences, Washington, DC 20037, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-202-994-8431 Current address: W. Harry Feinstone Department of Molecular Microbiology and Immunology, y Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA. Received: 25 August 2020; Accepted: 17 September 2020; Published: 19 September 2020 Abstract: Autism spectrum disorder (ASD) describes a group of neurodevelopmental disorders with core deficits in social communication and manifestation of restricted, repetitive, and stereotyped behaviors. Despite the core symptomatology, ASD is extremely heterogeneous with respect to the severity of symptoms and behaviors. This heterogeneity presents an inherent challenge to all large-scale genome-wide omics analyses. In the present study, we address this heterogeneity by stratifying ASD probands from simplex families according to the severity of behavioral scores on the Autism Diagnostic Interview-Revised diagnostic instrument, followed by re-analysis of existing DNA methylation data from individuals in three ASD subphenotypes in comparison to that of their respective unaffected siblings. We demonstrate that subphenotyping of cases enables the identification of over 1.6 times the number of statistically significant differentially methylated regions (DMR) and DMR-associated genes (DAGs) between cases and controls, compared to that identified when all cases are combined. Our analyses also reveal ASD-related neurological functions and comorbidities that are enriched among DAGs in each phenotypic subgroup but not in the combined case group. -
Small Cell Ovarian Carcinoma: Genomic Stability and Responsiveness to Therapeutics
Gamwell et al. Orphanet Journal of Rare Diseases 2013, 8:33 http://www.ojrd.com/content/8/1/33 RESEARCH Open Access Small cell ovarian carcinoma: genomic stability and responsiveness to therapeutics Lisa F Gamwell1,2, Karen Gambaro3, Maria Merziotis2, Colleen Crane2, Suzanna L Arcand4, Valerie Bourada1,2, Christopher Davis2, Jeremy A Squire6, David G Huntsman7,8, Patricia N Tonin3,4,5 and Barbara C Vanderhyden1,2* Abstract Background: The biology of small cell ovarian carcinoma of the hypercalcemic type (SCCOHT), which is a rare and aggressive form of ovarian cancer, is poorly understood. Tumourigenicity, in vitro growth characteristics, genetic and genomic anomalies, and sensitivity to standard and novel chemotherapeutic treatments were investigated in the unique SCCOHT cell line, BIN-67, to provide further insight in the biology of this rare type of ovarian cancer. Method: The tumourigenic potential of BIN-67 cells was determined and the tumours formed in a xenograft model was compared to human SCCOHT. DNA sequencing, spectral karyotyping and high density SNP array analysis was performed. The sensitivity of the BIN-67 cells to standard chemotherapeutic agents and to vesicular stomatitis virus (VSV) and the JX-594 vaccinia virus was tested. Results: BIN-67 cells were capable of forming spheroids in hanging drop cultures. When xenografted into immunodeficient mice, BIN-67 cells developed into tumours that reflected the hypercalcemia and histology of human SCCOHT, notably intense expression of WT-1 and vimentin, and lack of expression of inhibin. Somatic mutations in TP53 and the most common activating mutations in KRAS and BRAF were not found in BIN-67 cells by DNA sequencing. -
Molecular Genetic Delineation of 2Q37.3 Deletion in Autism and Osteodystrophy: Report of a Case and of New Markers for Deletion Screening by PCR
UC Irvine UC Irvine Previously Published Works Title Molecular genetic delineation of 2q37.3 deletion in autism and osteodystrophy: report of a case and of new markers for deletion screening by PCR. Permalink https://escholarship.org/uc/item/83f0x61r Journal Cytogenetics and cell genetics, 94(1-2) ISSN 0301-0171 Authors Smith, M Escamilla, JR Filipek, P et al. Publication Date 2001 DOI 10.1159/000048775 License https://creativecommons.org/licenses/by/4.0/ 4.0 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Original Article Cytogenet Cell Genet 94:15–22 (2001) Molecular genetic delineation of 2q37.3 deletion in autism and osteodystrophy: report of a case and of new markers for deletion screening by PCR M. Smith, J.R. Escamilla, P. Filipek, M.E. Bocian, C. Modahl, P. Flodman, and M.A. Spence Department of Pediatrics, University of California, Irvine CA (USA) Abstract. We recently studied a patient who meets criteria us to determine the parental origin of the deletion in our for autistic disorder and has a 2q37 deletion. Molecular cyto- patient. DNA from 8–13 unrelated individuals was used to genetic studies were carried out using DNA isolated from 22 determine heterozygosity estimates for these markers. We re- different 2q37 mapped BACs to more precisely define the view four genes deleted in our patient – genes whose known extent of the chromosome deletion. We also analyzed 2q37 functions and sites of expression in the brain and/or bone make mapped polymorphic markers. In addition DNA sequences of them candidates for involvement in autism and/or the osteo- BACs in the deletion region were scanned to identify microsa- dystrophy observed in patients with 2q37.3 deletions. -
Genetic and Genomic Analysis of Hyperlipidemia, Obesity and Diabetes Using (C57BL/6J × TALLYHO/Jngj) F2 Mice
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Nutrition Publications and Other Works Nutrition 12-19-2010 Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P. Stewart Marshall University Hyoung Y. Kim University of Tennessee - Knoxville, [email protected] Arnold M. Saxton University of Tennessee - Knoxville, [email protected] Jung H. Kim Marshall University Follow this and additional works at: https://trace.tennessee.edu/utk_nutrpubs Part of the Animal Sciences Commons, and the Nutrition Commons Recommended Citation BMC Genomics 2010, 11:713 doi:10.1186/1471-2164-11-713 This Article is brought to you for free and open access by the Nutrition at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Nutrition Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Stewart et al. BMC Genomics 2010, 11:713 http://www.biomedcentral.com/1471-2164/11/713 RESEARCH ARTICLE Open Access Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P Stewart1, Hyoung Yon Kim2, Arnold M Saxton3, Jung Han Kim1* Abstract Background: Type 2 diabetes (T2D) is the most common form of diabetes in humans and is closely associated with dyslipidemia and obesity that magnifies the mortality and morbidity related to T2D. The genetic contribution to human T2D and related metabolic disorders is evident, and mostly follows polygenic inheritance. The TALLYHO/ JngJ (TH) mice are a polygenic model for T2D characterized by obesity, hyperinsulinemia, impaired glucose uptake and tolerance, hyperlipidemia, and hyperglycemia. -
The Middle Temporal Gyrus Is Transcriptionally Altered in Patients with Alzheimer’S Disease
1 The middle temporal gyrus is transcriptionally altered in patients with Alzheimer’s Disease. 2 1 3 Shahan Mamoor 1Thomas Jefferson School of Law 4 East Islip, NY 11730 [email protected] 5 6 We sought to understand, at the systems level and in an unbiased fashion, how gene 7 expression was most different in the brains of patients with Alzheimer’s Disease (AD) by mining published microarray datasets (1, 2). Comparing global gene expression profiles between 8 patient and control revealed that a set of 84 genes were expressed at significantly different levels in the middle temporal gyrus (MTG) of patients with Alzheimer’s Disease (1, 2). We used 9 computational analyses to classify these genes into known pathways and existing gene sets, 10 and to describe the major differences in the epigenetic marks at the genomic loci of these genes. While a portion of these genes is computationally cognizable as part of a set of genes 11 up-regulated in the brains of patients with AD (3), many other genes in the gene set identified here have not previously been studied in association with AD. Transcriptional repression, both 12 pre- and post-transcription appears to be affected; nearly 40% of these genes are transcriptional 13 targets of MicroRNA-19A/B (miR-19A/B), the zinc finger protein 10 (ZNF10), or of the AP-1 repressor jun dimerization protein 2 (JDP2). 14 15 16 17 18 19 20 21 22 23 24 25 26 Keywords: Alzheimer’s Disease, systems biology of Alzheimer’s Disease, differential gene 27 expression, middle temporal gyrus. -
ZHX2 Promotes Hif1α Oncogenic Signaling in Triple-Negative Breast
bioRxiv preprint doi: https://doi.org/10.1101/2021.05.27.445959; this version posted May 28, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 ZHX2 Promotes HIF1 Oncogenic Signaling in Triple-Negative Breast Cancer 2 Wentong Fang,1,2* Chengheng Liao, 3* Rachel Shi, 3 Jeremy M. Simon, 2,4,5 Travis S. 3 Ptacek, 2,5 Giada Zurlo, 3 Youqiong Ye, 6,7 Leng Han, 7 Cheng Fan, 2 Christopher Llynard 4 Ortiz, 8,9,10 Hong-Rui Lin, 8 Ujjawal Manocha, 2 Weibo Luo, 3 William Y. Kim, 2 Lee-Wei Yang, 5 8,9,11 and Qing Zhang3* 6 7 1 Department of Pharmacy, The First Affiliated Hospital of Nanjing Medical University, 8 Nanjing, Jiangsu 210029, China 9 2 Lineberger Comprehensive Cancer Center, University of North Carolina School of 10 Medicine, Chapel Hill, NC 27599, USA 11 3 Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 12 75390, USA 13 4 Department of Genetics, Neuroscience Center, University of North Carolina, Chapel Hill, 14 NC 27599, USA 15 5 UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, University of 16 North Carolina, Chapel Hill, NC 27599, USA 17 6 Shanghai Institute of Immunology, Faculty of Basic Medicine, Shanghai Jiao Tong 18 University School of Medicine, Shanghai, 200025, China 19 7 Department of Biochemistry and Molecular Biology, The University of Texas Health 20 Science Center at Houston McGovern Medical School, Houston, TX, 77030, USA 21 8 Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 22 300, Taiwan bioRxiv preprint doi: https://doi.org/10.1101/2021.05.27.445959; this version posted May 28, 2021. -
Knowledge Management Enviroments for High Throughput Biology
Knowledge Management Enviroments for High Throughput Biology Abhey Shah A Thesis submitted for the degree of MPhil Biology Department University of York September 2007 Abstract With the growing complexity and scale of data sets in computational biology and chemoin- formatics, there is a need for novel knowledge processing tools and platforms. This thesis describes a newly developed knowledge processing platform that is different in its emphasis on architecture, flexibility, builtin facilities for datamining and easy cross platform usage. There exist thousands of bioinformatics and chemoinformatics databases, that are stored in many different forms with different access methods, this is a reflection of the range of data structures that make up complex biological and chemical data. Starting from a theoretical ba- sis, FCA (Formal Concept Analysis) an applied branch of lattice theory, is used in this thesis to develop a file system that automatically structures itself by it’s contents. The procedure of extracting concepts from data sets is examined. The system also finds appropriate labels for the discovered concepts by extracting data from ontological databases. A novel method for scaling non-binary data for use with the system is developed. Finally the future of integrative systems biology is discussed in the context of efficiently closed causal systems. Contents 1 Motivations and goals of the thesis 11 1.1 Conceptual frameworks . 11 1.2 Biological foundations . 12 1.2.1 Gene expression data . 13 1.2.2 Ontology . 14 1.3 Knowledge based computational environments . 15 1.3.1 Interfaces . 16 1.3.2 Databases and the character of biological data . -
ZHX3 Antibody Cat
ZHX3 Antibody Cat. No.: 56-766 ZHX3 Antibody Specifications HOST SPECIES: Rabbit SPECIES REACTIVITY: Human This ZHX3 antibody is generated from rabbits immunized with a KLH conjugated synthetic IMMUNOGEN: peptide between 645-674 amino acids from the C-terminal region of human ZHX3. TESTED APPLICATIONS: WB APPLICATIONS: For WB starting dilution is: 1:1000 PREDICTED MOLECULAR 105 kDa WEIGHT: Properties This antibody is purified through a protein A column, followed by peptide affinity PURIFICATION: purification. CLONALITY: Polyclonal ISOTYPE: Rabbit Ig CONJUGATE: Unconjugated PHYSICAL STATE: Liquid October 2, 2021 1 https://www.prosci-inc.com/zhx3-antibody-56-766.html BUFFER: Supplied in PBS with 0.09% (W/V) sodium azide. CONCENTRATION: batch dependent Store at 4˚C for three months and -20˚C, stable for up to one year. As with all antibodies STORAGE CONDITIONS: care should be taken to avoid repeated freeze thaw cycles. Antibodies should not be exposed to prolonged high temperatures. Additional Info OFFICIAL SYMBOL: ZHX3 Zinc fingers and homeoboxes protein 3, Triple homeobox protein 1, Zinc finger and ALTERNATE NAMES: homeodomain protein 3, ZHX3, KIAA0395, TIX1 ACCESSION NO.: Q9H4I2 PROTEIN GI NO.: 44889075 GENE ID: 23051 USER NOTE: Optimal dilutions for each application to be determined by the researcher. Background and References This gene encodes a member of the zinc fingers and homeoboxes (ZHX) gene family. The encoded protein contains two C2H2-type zinc fingers and five homeodomains and forms BACKGROUND: a dimer with itself or with zinc fingers and homeoboxes family member 1. In the nucleus, the dimerized protein interacts with the A subunit of the ubiquitous transcription factor nuclear factor-Y and may function as a transcriptional repressor. -
Agonists Regulate the Expression of Stemness and Differentiation Genes in Brain Tumour Stem Cells
British Journal of Cancer (2012) 106, 1702–1712 & 2012 Cancer Research UK All rights reserved 0007 – 0920/12 www.bjcancer.com PPARg agonists regulate the expression of stemness and differentiation genes in brain tumour stem cells E Pestereva1, S Kanakasabai1 and JJ Bright*,1,2 1 Neuroscience Research Laboratory, Methodist Research Institute, Indiana University Health, 1800 North Capitol Avenue, Noyes Building E504C, 2 Indianapolis, IN 46202, USA; Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA BACKGROUND: Brain tumour stem cells (BTSCs) are a small population of cancer cells that exhibit self-renewal, multi-drug resistance, and recurrence properties. We have shown earlier that peroxisome proliferator-activated receptor gamma (PPARg) agonists inhibit the expansion of BTSCs in T98G and U87MG glioma. In this study, we analysed the influence of PPARg agonists on the expression of stemness and differentiation genes in BTSCs. METHODS: The BTSCs were isolated from T98G and DB29 glioma cells, and cultured in neurobasal medium with epidermal growth factor þ basic fibroblast growth factor. Proliferation was measured by WST-1 (4-[3-(4-iodophenyl)-2-(4-nitrophenyl)-2 H-5- tetrazolio]-1,3-benzene disulphonate) and 3H thymidine uptake assays, and gene expression was analysed by quantitative reverse– transcription PCR and Taqman array. The expression of CD133, SRY box 2, and nanog homeobox (Nanog) was also evaluated by western blotting, immunostaining, and flow cytometry. 12,14 RESULTS: We found that PPARg agonists, ciglitazone and 15-deoxy-D -ProstaglandinJ2, inhibited cell viability and proliferation of þ T98G- and DB29-BTSCs. The PPARg agonists reduced the expansion of CD133 BTSCs and altered the expression of stemness and differentiation genes. -
Targeting SARS-Cov-2 Entry Title
Genomics-guided identication of potential modulators of SARS-CoV-2 entry proteases, TMPRSS2 and Cathepsins B/L Kartikay Prasad Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida Vijay Kumar ( [email protected] ) Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida https://orcid.org/0000- 0002-3621-5025 Research Article Keywords: COVID-19, TMPRSS2, Cathepsins, gene set enrichment, estradiol, retinoic acid Posted Date: January 1st, 2021 DOI: https://doi.org/10.21203/rs.3.rs-138273/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Running Title: Targeting SARS-CoV-2 entry Title: Genomics-guided identification of potential modulators of SARS-CoV-2 entry proteases, TMPRSS2 and Cathepsins B/L Kartikay Prasad1, and Vijay Kumar1* 1Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, UP- 201303, India *Address for Correspondence Vijay Kumar, Ph. D. Assistant Professor Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, UP- 201313, India E-mail: [email protected] ORCID: 0000-0002-3621-5025 1 Abstract The entry of SARS-CoV-2 into host cells requires the activation of its spike protein by host cell proteases. The serine protease, transmembrane serine protease 2 (TMPRSS2) and cysteine proteases, cathepsins B, L (CTSB/L) activate spike protein and enabling SARS-CoV-2 entry to the host cell through two completely different and independent pathways. Given that the uncertainty of how SARS-CoV-2 infects and kills, the need for a deep understanding of SARS- CoV-2 biology is imperative. Herein, we performed genomic-guided meta-analysis to identify upstream regulatory elements altering the expression of TMPRSS2 and CTSB/L genes. -
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Review Xatzipsalti Maria et al. Congenital Hypopituitarism: Various Genes, … Horm Metab Res 2018; 00: 00–00 Congenital Hypopituitarism: Various Genes, Various Phenotypes Authors Maria Xatzipsalti1, 2, Antonis Voutetakis1, Lela Stamoyannou2, George P. Chrousos1, Christina Kanaka-Gantenbein1 Affiliations ABSTRacT 1 Division of Endocrinology, Diabetes and Metabolism, The ontogenesis and development of the pituitary gland is a First Department of Pediatrics, Medical School, National highly complex process that depends on a cascade of transcrip- and Kapodistrian University of Athens, “Aghia Sofia” tion factors and signaling molecules. Spontaneous mutations Children's Hospital, Athens, Greece and transgenic murine models have demonstrated a role for 2 First Department of Pediatrics, “Aglaia Kyriakou” many of these factors, including HESX1, PROP1, PIT1, LHX3, Children's Hospital, Athens, Greece LHX4, SOX2, SOX3, OTX2, PAX6, FGFR1, SHH, GLI2, and FGF8 in the etiology of congenital hypopituitarism. Genetic muta- Key words tions in any of these factors can lead to congenital hypopitui- pituitary, combined pituitary hormone deficiency, congenital tarism, which is characterized by the deficiency in one or more hypopituitarism, transcription factors, syndromic hypopitui- pituitary hormones. The phenotype can be highly variable, tarism, non-syndromic hypopituitarism consisting of isolated hypopituitarism or more complex disor- ders. The same phenotype can be attributed to different gene received 27.03.2018 mutations; while a given gene mutation can -
FOS Rescues Neuronal Differentiation of Sox2-Deleted Neural Stem Cells by Genome-Wide Regulation of Common SOX2 and AP1(FOS-JUN) Target Genes
cells Article FOS Rescues Neuronal Differentiation of Sox2-Deleted Neural Stem Cells by Genome-Wide Regulation of Common SOX2 and AP1(FOS-JUN) Target Genes Miriam Pagin 1,† , Mattias Pernebrink 2,3,†, Mattia Pitasi 1, Federica Malighetti 1, Chew-Yee Ngan 4, Sergio Ottolenghi 1, Giulio Pavesi 5, Claudio Cantù 2,3,* and Silvia K. Nicolis 1,* 1 Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; [email protected] (M.P.); [email protected] (M.P.); [email protected] (F.M.); [email protected] (S.O.) 2 Wallenberg Centre for Molecular Medicine, Linköping University, SE-581 83 Linköping, Sweden; [email protected] 3 Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, SE-581 83 Linköping, Sweden 4 The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; [email protected] 5 Department of Biosciences, University of Milano, Via Celoria 26, 20134 Milano, Italy; [email protected] * Correspondence: [email protected] (C.C.); [email protected] (S.K.N.) † Joint first authors. Abstract: The transcription factor SOX2 is important for brain development and for neural stem Citation: Pagin, M.; Pernebrink, M.; cells (NSC) maintenance. Sox2-deleted (Sox2-del) NSC from neonatal mouse brain are lost after Pitasi, M.; Malighetti, F.; Ngan, C.-Y.; few passages in culture. Two highly expressed genes, Fos and Socs3, are strongly downregulated in Ottolenghi, S.; Pavesi, G.; Cantù, C.; Sox2-del NSC; we previously showed that Fos or Socs3 overexpression by lentiviral transduction fully Nicolis, S.K.