Systematic Survey of the Role of IGF in the Link Between Diabetes and Cancer
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Analysis of Gene Expression Data for Gene Ontology
ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION A Thesis Presented to The Graduate Faculty of The University of Akron In Partial Fulfillment of the Requirements for the Degree Master of Science Robert Daniel Macholan May 2011 ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION Robert Daniel Macholan Thesis Approved: Accepted: _______________________________ _______________________________ Advisor Department Chair Dr. Zhong-Hui Duan Dr. Chien-Chung Chan _______________________________ _______________________________ Committee Member Dean of the College Dr. Chien-Chung Chan Dr. Chand K. Midha _______________________________ _______________________________ Committee Member Dean of the Graduate School Dr. Yingcai Xiao Dr. George R. Newkome _______________________________ Date ii ABSTRACT A tremendous increase in genomic data has encouraged biologists to turn to bioinformatics in order to assist in its interpretation and processing. One of the present challenges that need to be overcome in order to understand this data more completely is the development of a reliable method to accurately predict the function of a protein from its genomic information. This study focuses on developing an effective algorithm for protein function prediction. The algorithm is based on proteins that have similar expression patterns. The similarity of the expression data is determined using a novel measure, the slope matrix. The slope matrix introduces a normalized method for the comparison of expression levels throughout a proteome. The algorithm is tested using real microarray gene expression data. Their functions are characterized using gene ontology annotations. The results of the case study indicate the protein function prediction algorithm developed is comparable to the prediction algorithms that are based on the annotations of homologous proteins. -
Irs2 and Irs4 Synergize in Non-Leprb Neurons to Control Energy Balance and Glucose Homeostasis#.” Molecular Metabolism 3 (1): 55-63
Irs2 and Irs4 synergize in non- LepRb neurons to control energy balance and glucose homeostasis# The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Sadagurski, Marianna, X. Charlie Dong, Martin G. Myers, and Morris F. White. 2013. “Irs2 and Irs4 synergize in non-LepRb neurons to control energy balance and glucose homeostasis#.” Molecular Metabolism 3 (1): 55-63. doi:10.1016/j.molmet.2013.10.004. http:// dx.doi.org/10.1016/j.molmet.2013.10.004. Published Version doi:10.1016/j.molmet.2013.10.004 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:11879880 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Original article Irs2 and Irs4 synergize in non-LepRb neurons to control energy balance and glucose homeostasis% Marianna Sadagurski 1,*,**, X. Charlie Dong 1,**,***, Martin G. Myers Jr.2,3, Morris F. White 1,**** ABSTRACT Insulin receptor substrates (Irs1, 2, 3 and Irs4) mediate the actions of insulin/IGF1 signaling. They have similar structure, but distinctly regulate development, growth, and metabolic homeostasis. Irs2 contributes to central metabolic sensing, partially by acting in leptin receptor (LepRb)- expressing neurons. Although Irs4 is largely restricted to the hypothalamus, its contribution to metabolic regulation is unclear because Irs4-null mice barely distinguishable from controls. We postulated that Irs2 and Irs4 synergize and complement each other in the brain. -
Targeting PH Domain Proteins for Cancer Therapy
The Texas Medical Center Library DigitalCommons@TMC The University of Texas MD Anderson Cancer Center UTHealth Graduate School of The University of Texas MD Anderson Cancer Biomedical Sciences Dissertations and Theses Center UTHealth Graduate School of (Open Access) Biomedical Sciences 12-2018 Targeting PH domain proteins for cancer therapy Zhi Tan Follow this and additional works at: https://digitalcommons.library.tmc.edu/utgsbs_dissertations Part of the Bioinformatics Commons, Medicinal Chemistry and Pharmaceutics Commons, Neoplasms Commons, and the Pharmacology Commons Recommended Citation Tan, Zhi, "Targeting PH domain proteins for cancer therapy" (2018). The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access). 910. https://digitalcommons.library.tmc.edu/utgsbs_dissertations/910 This Dissertation (PhD) is brought to you for free and open access by the The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences at DigitalCommons@TMC. It has been accepted for inclusion in The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access) by an authorized administrator of DigitalCommons@TMC. For more information, please contact [email protected]. TARGETING PH DOMAIN PROTEINS FOR CANCER THERAPY by Zhi Tan Approval page APPROVED: _____________________________________________ Advisory Professor, Shuxing Zhang, Ph.D. _____________________________________________ -
The Roma Paradigm
The Counteracting Effects of Demography on Functional Genomic Variation: The Roma Paradigm Neus Font-Porterias,1 Rocio Caro-Consuegra,1 Marcel Lucas-Sanchez,1 Marie Lopez,2 Aaron Gimenez,3 Annabel Carballo-Mesa,4 Elena Bosch,1,5 Francesc Calafell ,1 Lluıs Quintana-Murci,2,6 and David Comas *,1 Downloaded from https://academic.oup.com/mbe/article/38/7/2804/6169539 by Consejo Superior de Investigaciones Cientificas (CSIC) user on 31 August 2021 1Departament de Cie`ncies Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain 2Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Paris, France 3Facultat de Sociologia, Universitat Autonoma de Barcelona, Barcelona, Spain 4Facultat de Geografia i Historia, Universitat de Barcelona, Barcelona, Spain 5Centro de Investigacion Biomedica en Red de Salud Mental (CIBERSAM), Reus, Spain 6Human Genomics and Evolution, Colle`gedeFrance,Paris,France *Corresponding author: E-mail: [email protected]. Associate editor: Kelley Harris Abstract Demographic history plays a major role in shaping the distribution of genomic variation. Yet the interaction between different demographic forces and their effects in the genomesisnotfullyresolvedinhumanpopulations. Here, we focus on the Roma population, the largest transnational ethnic minority in Europe. They have a South Asian origin and their demographic history is characterized by recent dispersals, multiple founder events, and extensive gene flow from non- Roma groups. Through the analyses of new high-coverage whole exome sequences and genome-wide array data for 89 Iberian Roma individuals together with forward simulations, we show that founder effects have reduced their genetic diversity and proportion of rare variants, gene flow has counteracted the increase in mutational load, runs of homo- zygosity show ancestry-specific patterns of accumulation of deleterious homozygotes, and selection signals primarily derive from preadmixture adaptation in the Roma population sources. -
Mouse Irs4 Knockout Project (CRISPR/Cas9)
https://www.alphaknockout.com Mouse Irs4 Knockout Project (CRISPR/Cas9) Objective: To create a Irs4 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Irs4 gene (NCBI Reference Sequence: NM_010572 ; Ensembl: ENSMUSG00000054667 ) is located on Mouse chromosome X. 2 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 1 (Transcript: ENSMUST00000067841). Exon 1 will be selected as target site. Cas9 and gRNA will be co-injected into fertilized eggs for KO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Homozygotes for a targeted null mutation exhibit a 10% reduction in male adult size, slightly impaired oral glucose tolerance, and decreased reproductive ability. Exon 1 starts from about 0.03% of the coding region. Exon 1 covers 100.0% of the coding region. The size of effective KO region: ~3646 bp. The KO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 Legends Exon of mouse Irs4 Knockout region Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot (up) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section upstream of start codon is aligned with itself to determine if there are tandem repeats. Tandem repeats are found in the dot plot matrix. The gRNA site is selected outside of these tandem repeats. Overview of the Dot Plot (down) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section downstream of stop codon is aligned with itself to determine if there are tandem repeats. -
Breast Cancer Tumor Suppressors: a Special Emphasis on Novel Protein Nischarin Mazvita Maziveyi and Suresh K
Published OnlineFirst September 21, 2015; DOI: 10.1158/0008-5472.CAN-15-1395 Cancer Review Research Breast Cancer Tumor Suppressors: A Special Emphasis on Novel Protein Nischarin Mazvita Maziveyi and Suresh K. Alahari Abstract Tumor suppressor genes regulate cell growth and prevent vast number of cellular processes, including neuronal protection spontaneous proliferation that could lead to aberrant tissue and hypotension. The NISCH promoter experiences hypermethy- function. Deletions and mutations of these genes typically lead lation in several cancers, whereas some highly aggressive breast to progression through the cell-cycle checkpoints, as well as cancer cells exhibit genomic loss of the NISCH locus. Further- increased cell migration. Studies of these proteins are important more, we discuss data illustrating a novel role of Nischarin as as they may provide potential treatments for breast cancers. In this a tumor suppressor in breast cancer. Analysis of this new para- review, we discuss a comprehensive overview on Nischarin, a digm may shed light on various clinical questions. Finally, the novel protein discovered by our laboratory. Nischarin, or imida- therapeutic potential of Nischarin is discussed. Cancer Res; 75(20); zoline receptor antisera-selected protein, is a protein involved in a 4252–9. Ó2015 AACR. Introduction (6, 7). It also interacts with LIM kinase (LIMK) in order to prevent cytoskeletal reorganization (8). Typically, scaffold proteins such Breast cancer initiation and progression involve several genetic as Nischarin are characterized as caretaker genes because their events that can activate oncogenes and/or abrogate the function of effects on tumor growth are indirect. tumor suppressor genes. Tumor suppressor genes are commonly lost or deleted in cancers, facilitating the initiation and progres- sion of cancer through several biological events, including cell Discovery of Nischarin proliferation, cell death, cell migration, and cell invasion. -
Whole Exome Sequencing in Families at High Risk for Hodgkin Lymphoma: Identification of a Predisposing Mutation in the KDR Gene
Hodgkin Lymphoma SUPPLEMENTARY APPENDIX Whole exome sequencing in families at high risk for Hodgkin lymphoma: identification of a predisposing mutation in the KDR gene Melissa Rotunno, 1 Mary L. McMaster, 1 Joseph Boland, 2 Sara Bass, 2 Xijun Zhang, 2 Laurie Burdett, 2 Belynda Hicks, 2 Sarangan Ravichandran, 3 Brian T. Luke, 3 Meredith Yeager, 2 Laura Fontaine, 4 Paula L. Hyland, 1 Alisa M. Goldstein, 1 NCI DCEG Cancer Sequencing Working Group, NCI DCEG Cancer Genomics Research Laboratory, Stephen J. Chanock, 5 Neil E. Caporaso, 1 Margaret A. Tucker, 6 and Lynn R. Goldin 1 1Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 2Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 3Ad - vanced Biomedical Computing Center, Leidos Biomedical Research Inc.; Frederick National Laboratory for Cancer Research, Frederick, MD; 4Westat, Inc., Rockville MD; 5Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; and 6Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA ©2016 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol.2015.135475 Received: August 19, 2015. Accepted: January 7, 2016. Pre-published: June 13, 2016. Correspondence: [email protected] Supplemental Author Information: NCI DCEG Cancer Sequencing Working Group: Mark H. Greene, Allan Hildesheim, Nan Hu, Maria Theresa Landi, Jennifer Loud, Phuong Mai, Lisa Mirabello, Lindsay Morton, Dilys Parry, Anand Pathak, Douglas R. Stewart, Philip R. Taylor, Geoffrey S. Tobias, Xiaohong R. Yang, Guoqin Yu NCI DCEG Cancer Genomics Research Laboratory: Salma Chowdhury, Michael Cullen, Casey Dagnall, Herbert Higson, Amy A. -
Integrative Epigenomic and Genomic Analysis of Malignant Pheochromocytoma
EXPERIMENTAL and MOLECULAR MEDICINE, Vol. 42, No. 7, 484-502, July 2010 Integrative epigenomic and genomic analysis of malignant pheochromocytoma Johanna Sandgren1,2* Robin Andersson3*, pression examination in a malignant pheochromocy- Alvaro Rada-Iglesias3, Stefan Enroth3, toma sample. The integrated analysis of the tumor ex- Goran̈ Akerstro̊ m̈ 1, Jan P. Dumanski2, pression levels, in relation to normal adrenal medulla, Jan Komorowski3,4, Gunnar Westin1 and indicated that either histone modifications or chromo- somal alterations, or both, have great impact on the ex- Claes Wadelius2,5 pression of a substantial fraction of the genes in the in- vestigated sample. Candidate tumor suppressor 1Department of Surgical Sciences genes identified with decreased expression, a Uppsala University, Uppsala University Hospital H3K27me3 mark and/or in regions of deletion were for SE-75185 Uppsala, Sweden 2 instance TGIF1, DSC3, TNFRSF10B, RASSF2, HOXA9, Department of Genetics and Pathology Rudbeck Laboratory, Uppsala University PTPRE and CDH11. More genes were found with in- SE-75185 Uppsala, Sweden creased expression, a H3K4me3 mark, and/or in re- 3The Linnaeus Centre for Bioinformatics gions of gain. Potential oncogenes detected among Uppsala University those were GNAS, INSM1, DOK5, ETV1, RET, NTRK1, SE-751 24 Uppsala, Sweden IGF2, and the H3K27 trimethylase gene EZH2. Our ap- 4Interdisciplinary Centre for Mathematical and proach to associate histone methylations and DNA Computational Modelling copy number changes to gene expression revealed ap- Warsaw University parent impact on global gene transcription, and en- PL-02-106 Warszawa, Poland abled the identification of candidate tumor genes for 5Corresponding author: Tel, 46-18-471-40-76; further exploration. -
Open Data for Differential Network Analysis in Glioma
International Journal of Molecular Sciences Article Open Data for Differential Network Analysis in Glioma , Claire Jean-Quartier * y , Fleur Jeanquartier y and Andreas Holzinger Holzinger Group HCI-KDD, Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Auenbruggerplatz 2/V, 8036 Graz, Austria; [email protected] (F.J.); [email protected] (A.H.) * Correspondence: [email protected] These authors contributed equally to this work. y Received: 27 October 2019; Accepted: 3 January 2020; Published: 15 January 2020 Abstract: The complexity of cancer diseases demands bioinformatic techniques and translational research based on big data and personalized medicine. Open data enables researchers to accelerate cancer studies, save resources and foster collaboration. Several tools and programming approaches are available for analyzing data, including annotation, clustering, comparison and extrapolation, merging, enrichment, functional association and statistics. We exploit openly available data via cancer gene expression analysis, we apply refinement as well as enrichment analysis via gene ontology and conclude with graph-based visualization of involved protein interaction networks as a basis for signaling. The different databases allowed for the construction of huge networks or specified ones consisting of high-confidence interactions only. Several genes associated to glioma were isolated via a network analysis from top hub nodes as well as from an outlier analysis. The latter approach highlights a mitogen-activated protein kinase next to a member of histondeacetylases and a protein phosphatase as genes uncommonly associated with glioma. Cluster analysis from top hub nodes lists several identified glioma-associated gene products to function within protein complexes, including epidermal growth factors as well as cell cycle proteins or RAS proto-oncogenes. -
IRS4 (NM 003604) Human Tagged ORF Clone Lentiviral Particle – RC218385L4V | Origene
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for RC218385L4V IRS4 (NM_003604) Human Tagged ORF Clone Lentiviral Particle Product data: Product Type: Lentiviral Particles Product Name: IRS4 (NM_003604) Human Tagged ORF Clone Lentiviral Particle Symbol: IRS4 Synonyms: CHNG9; IRS-4; PY160 Vector: pLenti-C-mGFP-P2A-Puro (PS100093) ACCN: NM_003604 ORF Size: 3771 bp ORF Nucleotide The ORF insert of this clone is exactly the same as(RC218385). Sequence: OTI Disclaimer: The molecular sequence of this clone aligns with the gene accession number as a point of reference only. However, individual transcript sequences of the same gene can differ through naturally occurring variations (e.g. polymorphisms), each with its own valid existence. This clone is substantially in agreement with the reference, but a complete review of all prevailing variants is recommended prior to use. More info OTI Annotation: This clone was engineered to express the complete ORF with an expression tag. Expression varies depending on the nature of the gene. RefSeq: NM_003604.1 RefSeq Size: 3939 bp RefSeq ORF: 3774 bp Locus ID: 8471 UniProt ID: O14654 Protein Families: Druggable Genome Protein Pathways: Adipocytokine signaling pathway, Insulin signaling pathway, Neurotrophin signaling pathway, Type II diabetes mellitus MW: 133.6 kDa This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 2 IRS4 (NM_003604) Human Tagged ORF Clone Lentiviral Particle – RC218385L4V Gene Summary: IRS4 encodes the insulin receptor substrate 4, a cytoplasmic protein that contains many potential tyrosine and serine/threonine phosphorylation sites. -
Spatial and Temporal Aspects of Signalling 6 1
r r r Cell Signalling Biology Michael J. Berridge Module 6 Spatial and Temporal Aspects of Signalling 6 1 Module 6 Spatial and Temporal Aspects of Signalling Synopsis The function and efficiency of cell signalling pathways are very dependent on their organization both in space and time. With regard to spatial organization, signalling components are highly organized with respect to their cellular location and how they transmit information from one region of the cell to another. This spatial organization of signalling pathways depends on the molecular interactions that occur between signalling components that use signal transduction domains to construct signalling pathways. Very often, the components responsible for information transfer mechanisms are held in place by being attached to scaffolding proteins to form macromolecular signalling complexes. Sometimes these macromolecular complexes can be organized further by being localized to specific regions of the cell, as found in lipid rafts and caveolae or in the T-tubule regions of skeletal and cardiac cells. Another feature of the spatial aspects concerns the local Another important temporal aspect is timing and signal and global aspects of signalling. The spatial organization of integration, which relates to the way in which functional signalling molecules mentioned above can lead to highly interactions between signalling pathways are determined localized signalling events, but when the signalling mo- by both the order and the timing of their presentations. lecules are more evenly distributed, signals can spread The organization of signalling systems in both time and more globally throughout the cell. In addition, signals space greatly enhances both their efficiency and versatility. -
A Novel Transcript Is Upregulated by Fasting in the Hypothalamus and Enhances Insulin Signalling
Journal of Neuroendocrinology, 2013, 25, 292–301 ORIGINAL ARTICLE © 2012 British Society for Neuroendocrinology A novel Transcript is Up-Regulated by Fasting in the Hypothalamus and Enhances Insulin Signalling B. Chai, J.-Y. Li, D. Fritze, W. Zhang, Z. Xia and M. W. Mulholland Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA. Journal of A transcript of unknown function, regulated by fasting and feeding, was identified by micro- array analysis. The transcript is up-regulated in the fasting state. An 1168-bp cDNA was Neuroendocrinology cloned from rat hypothalamus and sequenced. This sequence is consistent with adipogenesis down-regulating transcript 3 (AGD3) (also known as human OCC-1) mRNA. A protein sequence identical to AGD3 was determined by mass spectrometry. In the rat brain, AGD3 mRNA is distributed in the arcuate nucleus, ventromedial hypothalamus, amygdaloid nuclei, hippocam- pus, and somatic cortex. Double in situ hybridisation showed that AGD3 mRNA is co-localised with pro-opiomelanocortin and neuropeptide Y in arcuate nucleus neurones. AGD3 binds with Correspondence to: insulin receptor substrate 4 and increases insulin-stimulated phospho-Akt and regulates AMP- Michael W. Mulholland, Department activated protein kinase and mammalian target of rapamycin downstream target S6 kinase of Surgery, University of Michigan phosphorylation. Medical School, 2101 Taubman Center, 1500 E. Medical Center Drive, Key words: adipogenesis down-regulating transcript 3, insulin, proopiomelanocortin, neuropeptide Y Ann Arbor, MI 48109-0346, USA (e-mail: [email protected]). doi: 10.1111/j.1365-2826.2012.02378.x Obesity and being overweight represent major public health prob- transcripts (8). When the functional roles have been unclear, these lems.