Influence of Genetic Variance on Biomarker Levels After
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Screening and Identification of Key Biomarkers in Clear Cell Renal Cell Carcinoma Based on Bioinformatics Analysis
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Screening and identification of key biomarkers in clear cell renal cell carcinoma based on bioinformatics analysis Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignancy of the urinary system. The pathogenesis and effective diagnosis of ccRCC have become popular topics for research in the previous decade. In the current study, an integrated bioinformatics analysis was performed to identify core genes associated in ccRCC. An expression dataset (GSE105261) was downloaded from the Gene Expression Omnibus database, and included 26 ccRCC and 9 normal kideny samples. Assessment of the microarray dataset led to the recognition of differentially expressed genes (DEGs), which was subsequently used for pathway and gene ontology (GO) enrichment analysis. -
ACVR1 Antibody Cat
ACVR1 Antibody Cat. No.: 4791 Western blot analysis of ACVR1 in A549 cell lysate with ACVR1 antibody at 1 μg/mL in (A) the absence and (B) the presence of blocking peptide. Specifications HOST SPECIES: Rabbit SPECIES REACTIVITY: Human, Mouse HOMOLOGY: Predicted species reactivity based on immunogen sequence: Bovine: (100%), Rat: (93%) ACVR1 antibody was raised against a 14 amino acid synthetic peptide near the amino terminus of the human ACVR1. IMMUNOGEN: The immunogen is located within the first 50 amino acids of ACVR1. TESTED APPLICATIONS: ELISA, WB ACVR1 antibody can be used for detection of ACVR1 by Western blot at 1 μg/mL. APPLICATIONS: Antibody validated: Western Blot in human samples. All other applications and species not yet tested. At least four isoforms of ACVR1 are known to exist. This antibody is predicted to have no SPECIFICITY: cross-reactivity to ACVR1B or ACVR1C. POSITIVE CONTROL: 1) Cat. No. 1203 - A549 Cell Lysate Properties October 1, 2021 1 https://www.prosci-inc.com/acvr1-antibody-4791.html PURIFICATION: ACVR1 Antibody is affinity chromatography purified via peptide column. CLONALITY: Polyclonal ISOTYPE: IgG CONJUGATE: Unconjugated PHYSICAL STATE: Liquid BUFFER: ACVR1 Antibody is supplied in PBS containing 0.02% sodium azide. CONCENTRATION: 1 mg/mL ACVR1 antibody can be stored at 4˚C for three months and -20˚C, stable for up to one STORAGE CONDITIONS: year. As with all antibodies care should be taken to avoid repeated freeze thaw cycles. Antibodies should not be exposed to prolonged high temperatures. Additional Info OFFICIAL SYMBOL: ACVR1 ACVR1 Antibody: FOP, ALK2, SKR1, TSRI, ACTRI, ACVR1A, ACVRLK2, Activin receptor type-1, ALTERNATE NAMES: Activin receptor type I, ACTR-I ACCESSION NO.: NP_001096 PROTEIN GI NO.: 4501895 GENE ID: 90 USER NOTE: Optimal dilutions for each application to be determined by the researcher. -
Primate Specific Retrotransposons, Svas, in the Evolution of Networks That Alter Brain Function
Title: Primate specific retrotransposons, SVAs, in the evolution of networks that alter brain function. Olga Vasieva1*, Sultan Cetiner1, Abigail Savage2, Gerald G. Schumann3, Vivien J Bubb2, John P Quinn2*, 1 Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, U.K 2 Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK 3 Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, D-63225 Germany *. Corresponding author Olga Vasieva: Institute of Integrative Biology, Department of Comparative genomics, University of Liverpool, Liverpool, L69 7ZB, [email protected] ; Tel: (+44) 151 795 4456; FAX:(+44) 151 795 4406 John Quinn: Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK, [email protected]; Tel: (+44) 151 794 5498. Key words: SVA, trans-mobilisation, behaviour, brain, evolution, psychiatric disorders 1 Abstract The hominid-specific non-LTR retrotransposon termed SINE–VNTR–Alu (SVA) is the youngest of the transposable elements in the human genome. The propagation of the most ancient SVA type A took place about 13.5 Myrs ago, and the youngest SVA types appeared in the human genome after the chimpanzee divergence. Functional enrichment analysis of genes associated with SVA insertions demonstrated their strong link to multiple ontological categories attributed to brain function and the disorders. SVA types that expanded their presence in the human genome at different stages of hominoid life history were also associated with progressively evolving behavioural features that indicated a potential impact of SVA propagation on a cognitive ability of a modern human. -
Saracatinib Is an Efficacious Clinical Candidate for Fibrodysplasia Ossificans Progressiva
RESEARCH ARTICLE Saracatinib is an efficacious clinical candidate for fibrodysplasia ossificans progressiva Eleanor Williams,1 Jana Bagarova,2 Georgina Kerr,1 Dong-Dong Xia,2 Elsie S. Place,3 Devaveena Dey,2 Yue Shen,2 Geoffrey A. Bocobo,2 Agustin H. Mohedas,2 Xiuli Huang,4 Philip E. Sanderson,4 Arthur Lee,4 Wei Zheng,4 Aris N. Economides,5 James C. Smith,3 Paul B. Yu,2 and Alex N. Bullock1 1Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom. 2Department of Medicine, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA. 3Developmental Biology Laboratory, Francis Crick Institute, London, United Kingdom. 4National Center for Advancing Translational Sciences, NIH, Bethesda, Maryland, USA. 5Regeneron Pharmaceuticals Inc., Tarrytown, New York, USA. Currently, no effective therapies exist for fibrodysplasia ossificans progressiva (FOP), a rare congenital syndrome in which heterotopic bone is formed in soft tissues owing to dysregulated activity of the bone morphogenetic protein (BMP) receptor kinase ALK2 (also known as ACVR1). From a screen of known biologically active compounds, we identified saracatinib as a potent ALK2 kinase inhibitor. In enzymatic and cell-based assays, saracatinib preferentially inhibited ALK2, compared with other receptors of the BMP/TGF-β signaling pathway, and induced dorsalization in zebrafish embryos consistent with BMP antagonism. We further tested the efficacy of saracatinib using an inducible ACVR1Q207D-transgenic mouse line, which provides a model of heterotopic ossification (HO), as well as an inducible ACVR1R206H-knockin mouse, which serves as a genetically and physiologically faithful FOP model. In both models, saracatinib was well tolerated and potently inhibited the development of HO, even when administered transiently following soft tissue injury. -
Supplementary Table 1: Adhesion Genes Data Set
Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like, -
High-Fidelity CRISPR/Cas9
ARTICLE DOI: 10.1038/s41467-018-05766-5 OPEN High-fidelity CRISPR/Cas9- based gene-specific hydroxymethylation rescues gene expression and attenuates renal fibrosis Xingbo Xu1,2, Xiaoying Tan2,3, Björn Tampe 3, Tim Wilhelmi1,2, Melanie S. Hulshoff1,2,4, Shoji Saito3, Tobias Moser 5, Raghu Kalluri6, Gerd Hasenfuss1,2, Elisabeth M. Zeisberg1,2 & Michael Zeisberg2,3 fi 1234567890():,; While suppression of speci c genes through aberrant promoter methylation contributes to different diseases including organ fibrosis, gene-specific reactivation technology is not yet available for therapy. TET enzymes catalyze hydroxymethylation of methylated DNA, reac- tivating gene expression. We here report generation of a high-fidelity CRISPR/Cas9-based gene-specific dioxygenase by fusing an endonuclease deactivated high-fidelity Cas9 (dHFCas9) to TET3 catalytic domain (TET3CD), targeted to specific genes by guiding RNAs (sgRNA). We demonstrate use of this technology in four different anti-fibrotic genes in different cell types in vitro, among them RASAL1 and Klotho, both hypermethylated in kidney fibrosis. Furthermore, in vivo lentiviral delivery of the Rasal1-targeted fusion protein to interstitial cells and of the Klotho-targeted fusion protein to tubular epithelial cells each results in specific gene reactivation and attenuation of fibrosis, providing gene-specific demethylating technology in a disease model. 1 Department of Cardiology and Pneumology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075 Göttingen, Germany. 2 German Center for Cardiovascular Research (DZHK) Partner Site, Göttingen, Germany. 3 Department of Nephrology and Rheumatology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075 Göttingen, Germany. 4 Department of Pathology and Medical Biology, University Medical Center Groningen, Hanzeplein 1, 9713 Groningen, GZ, Netherlands. -
Learning from Cadherin Structures and Sequences: Affinity Determinants and Protein Architecture
Learning from cadherin structures and sequences: affinity determinants and protein architecture Klára Fels ıvályi Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2014 Klara Felsovalyi All rights reserved ABSTRACT Learning from cadherin structures and sequences: affinity determinants and protein architecture Klara Felsovalyi Cadherins are a family of cell-surface proteins mediating adhesion that are important in development and maintenance of tissues. The family is defined by the repeating cadherin domain (EC) in their extracellular region, but they are diverse in terms of protein size, architecture and cellular function. The best-understood subfamily is the type I classical cadherins, which are found in vertebrates and have five EC domains. Among the five different type I classical cadherins, the binding interactions are highly specific in their homo- and heterophilic binding affinities, though their sequences are very similar. As previously shown, E- and N-cadherins, two prototypic members of the subfamily, differ in their homophilic K D by about an order of magnitude, while their heterophilic affinity is intermediate. To examine the source of the binding affinity differences among type I cadherins, we used crystal structures, analytical ultracentrifugation (AUC), surface plasmon resonance (SPR), and electron paramagnetic resonance (EPR) studies. Phylogenetic analysis and binding affinity behavior show that the type I cadherins can be further divided into two subgroups, with E- and N-cadherin representing each. In addition to the affinity differences in their wild-type binding through the strand-swapped interface, a second interface also shows an affinity difference between E- and N-cadherin. -
ACVR1C Antibody Cat
ACVR1C Antibody Cat. No.: 4795 ACVR1C Antibody Specifications HOST SPECIES: Rabbit SPECIES REACTIVITY: Human, Mouse, Rat ACVR1C antibody was raised against a 15 amino acid synthetic peptide near the amino terminus of the human ACVR1C. IMMUNOGEN: The immunogen is located within amino acids 130 - 180 of ACVR1C. TESTED APPLICATIONS: ELISA, WB ACVR1C antibody can be used for detection of ACVR1C by Western blot at 1 and 2 μg/mL. APPLICATIONS: Antibody validated: Western Blot in human samples. All other applications and species not yet tested. SPECIFICITY: This antibody is predicted to have no cross-reactivity to ACVR1 or ACVR1B. POSITIVE CONTROL: 1) Cat. No. 1309 - Human Placenta Tissue Lysate Properties PURIFICATION: ACVR1C Antibody is affinity chromatography purified via peptide column. CLONALITY: Polyclonal September 25, 2021 1 https://www.prosci-inc.com/acvr1c-antibody-4795.html ISOTYPE: IgG CONJUGATE: Unconjugated PHYSICAL STATE: Liquid BUFFER: ACVR1C Antibody is supplied in PBS containing 0.02% sodium azide. CONCENTRATION: 1 mg/mL ACVR1C antibody can be stored at 4˚C for three months and -20˚C, stable for up to one STORAGE CONDITIONS: year. As with all antibodies care should be taken to avoid repeated freeze thaw cycles. Antibodies should not be exposed to prolonged high temperatures. Additional Info OFFICIAL SYMBOL: ACVR1 ACVR1C Antibody: FOP, ALK2, SKR1, TSRI, ACTRI, ACVR1A, ACVRLK2, Activin receptor ALTERNATE NAMES: type-1, Activin receptor type I, ACTR-I ACCESSION NO.: Q8NER5 PROTEIN GI NO.: 4501895 GENE ID: 90 USER NOTE: Optimal dilutions for each application to be determined by the researcher. Background and References ACVR1C Antibody: Activins are dimeric growth and differentiation factors which belong to the transforming growth factor-beta (TGF-beta) superfamily of structurally related signaling proteins. -
Pan-Cancer Genomic Amplifications Underlie a WNT Hyperactivation Phenotype Associated with Stem Cell-Like Features Leading to Po
1 Pan-cancer genomic amplifications underlie a WNT hyperactivation phenotype 2 associated with stem cell-like features leading to poor prognosis 3 4 5 6 Running title: Prognosis of a 16-gene signature of WNT hyperactivation in six cancers 7 8 Wai Hoong Chang and Alvina G. Lai 9 10 11 Nuffield Department of Medicine, University of Oxford, 12 Old Road Campus, OX3 7FZ, United Kingdom 13 14 For correspondence: [email protected] 15 List of Abbreviations 16 TCGA The Cancer Genome Atlas KEGG Kyoto Encyclopedia of Genes and Genomes GO Gene Ontology ROC Receiver operating characteristic AUC Area under the curve HR Hazard ratio TNM Tumor, node and metastasis HIF Hypoxia inducible factor TF Transcription factor EMT Epithelial-to-mesenchymal transition 17 18 Abstract 19 20 Cancer stem cells pose significant obstacles to curative treatment contributing to tumor 21 relapse and poor prognosis. They share many signaling pathways with normal stem cells that 22 control cell proliferation, self-renewal and cell fate determination. One of these pathways 23 known as Wnt is frequently implicated in carcinogenesis where Wnt hyperactivation is seen in 24 cancer stem cells. Yet, the role of conserved genomic alterations in Wnt genes driving tumor 25 progression across multiple cancer types remains to be elucidated. In an integrated pan-cancer 26 study involving 21 cancers and 18,484 patients, we identified a core Wnt signature of 16 genes 27 that showed high frequency of somatic amplifications linked to increased transcript 28 expression. The signature successfully predicted overall survival rates in six cancer cohorts 29 (n=3,050): bladder (P=0.011), colon (P=0.013), head and neck (P=0.026), pan-kidney 30 (P<0.0001), clear cell renal cell (P<0.0001) and stomach (P=0.032). -
Human ALK-7 / ACVR1C Protein (ECD, Fc Tag)
Human ALK-7 / ACVR1C Protein (ECD, Fc Tag) Catalog Number: 10869-H02H General Information SDS-PAGE: Gene Name Synonym: ACVRLK7; ALK7 Protein Construction: A DNA sequence encoding the human ACVR1C (NP_660302.2) (Met1- Glu113) was expressed with the Fc region of human IgG1 at the C- terminus. Source: Human Expression Host: HEK293 Cells QC Testing Purity: > 95 % as determined by SDS-PAGE. Endotoxin: Protein Description < 1.0 EU per μg protein as determined by the LAL method. ALK-7, also known as ALK7 and ACVR1C, belongs to the ALK family. It is a type I receptor for the TGFB family of signaling molecules. TGF-β is the Stability: prototype of a protein superfamily which, in humans, contains at least 35 members, including activins, inhibins, bone morphogenetic proteins, Samples are stable for up to twelve months from date of receipt at -70 ℃ growth/differentiation factors, and Müllerian inhibiting substance. ALK-7 is a serine-threonine kinase that can cause the activation of one of the SMAD Predicted N terminal: Leu 22 signal transducers, SMAD2. ALK-7 has a ligand known as Nodal. Nodal Molecular Mass: stimulates the secretion of TIMP-1 and inhibits matrix metalloproteinases MMP-2 and MMP-9 activity. The overexpression of Nodal or constitutively The recombinant human ACVR1C consists 330 amino acids and predicts active ALK-7 decreases cell migration and invasion, whereas knock-down a molecular mass of 36.6 kDa. of Nodal and ALK-7 has the opposite effects. Formulation: References Lyophilized from sterile PBS, pH 7.4. 1.Lin YY, et al. (2012) Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. -
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229 3 <V>:<Iss> X ZHOU and others Gonadotrope-specific Bmpr1a 229229:3:3 331–341 Research knockout mice Normal gonadotropin production and fertility in gonadotrope- specific Bmpr1a knockout mice Xiang Zhou1,2, Ying Wang1,2, Luisina Ongaro1,2, Ulrich Boehm3, Vesa Kaartinen4, Yuji Mishina4 and Daniel J Bernard1,2 1Department of Pharmacology and Therapeutics, McGill University, Montreal, Québec, Canada 2Centre for Research in Reproduction and Development, McGill University, Montreal, Québec, Canada Correspondence 3Department of Pharmacology and Toxicology, University of Saarland School of Medicine, Homburg, Germany should be addressed 4Department of Biologic and Materials Sciences, School of Dentistry, University of Michigan, Ann Arbor, to D J Bernard Michigan, USA Email [email protected] Abstract Pituitary follicle-stimulating hormone (FSH) synthesis is regulated by transforming Key Words growth factor β superfamily ligands, most notably the activins and inhibins. Bone f pituitary morphogenetic proteins (BMPs) also regulate FSHβ subunit (Fshb) expression in f FSH immortalized murine gonadotrope-like LβT2 cells and in primary murine or ovine f bone morphogenetic Endocrinology primary pituitary cultures. BMP2 signals preferentially via the BMP type I receptor, protein of BMPR1A, to stimulate murine Fshb transcription in vitro. Here, we used a Cre–lox f activin receptor-like kinase approach to assess BMPR1A’s role in FSH synthesis in mice in vivo. Gonadotrope- Journal f Cre-lox specific Bmpr1a knockout animals developed normally and had reproductive organ weights comparable with those of controls. Knockouts were fertile, with normal serum gonadotropins and pituitary gonadotropin subunit mRNA expression. Cre-mediated recombination of the floxed Bmpr1a allele was efficient and specific, as indicated by PCR analysis of diverse tissues and isolated gonadotrope cells. -
Molecular Characteristics of Circulating Tumor Cells Resemble the Liver Metastasis More Closely Than the Primary Tumor in Metastatic Colorectal Cancer
www.impactjournals.com/oncotarget/ Oncotarget, Vol. 7, No. 37 Research Paper Molecular characteristics of circulating tumor cells resemble the liver metastasis more closely than the primary tumor in metastatic colorectal cancer Wendy Onstenk1, Anieta M. Sieuwerts1, Bianca Mostert1, Zarina Lalmahomed2, Joan B. Bolt-de Vries1, Anne van Galen1, Marcel Smid1, Jaco Kraan1, Mai Van1, Vanja de Weerd1, Raquel Ramírez-Moreno1, Katharina Biermann3, Cornelis Verhoef2, Dirk J. Grünhagen2, Jan N.M. IJzermans2, Jan W. Gratama1, John W.M. Martens1, John A. Foekens1, Stefan Sleijfer1 1Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Rotterdam, The Netherlands 2Department of Surgery, Erasmus University Medical Center, Rotterdam, The Netherlands 3Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands Correspondence to: Wendy Onstenk, email: [email protected] Keywords: circulating tumor cells, CTCs, CellSearch, colorectal cancer, gene expression profiling Received: April 06, 2016 Accepted: May 29, 2016 Published: June 20, 2016 ABSTRACT Background: CTCs are a promising alternative for metastatic tissue biopsies for use in precision medicine approaches. We investigated to what extent the molecular characteristics of circulating tumor cells (CTCs) resemble the liver metastasis and/ or the primary tumor from patients with metastatic colorectal cancer (mCRC). Results: The CTC profiles were concordant with the liver metastasis in 17/23 patients (74%) and with the primary tumor in 13 patients (57%). The CTCs better resembled the liver metastasis in 13 patients (57%), and the primary tumor in five patients (22%). The strength of the correlations was not associated with clinical parameters. Nine genes (CDH1, CDH17, CDX1, CEACAM5, FABP1, FCGBP, IGFBP3, IGFBP4, and MAPT) displayed significant differential expressions, all of which were downregulated, in CTCs compared to the tissues in the 23 patients.