Microrna Let-7I-5P Mediates the Relationship Between Muscle Fat
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Emerging Roles for Multifunctional Ion Channel Auxiliary Subunits in Cancer T ⁎ Alexander S
Cell Calcium 80 (2019) 125–140 Contents lists available at ScienceDirect Cell Calcium journal homepage: www.elsevier.com/locate/ceca Emerging roles for multifunctional ion channel auxiliary subunits in cancer T ⁎ Alexander S. Hawortha,b, William J. Brackenburya,b, a Department of Biology, University of York, Heslington, York, YO10 5DD, UK b York Biomedical Research Institute, University of York, Heslington, York, YO10 5DD, UK ARTICLE INFO ABSTRACT Keywords: Several superfamilies of plasma membrane channels which regulate transmembrane ion flux have also been Auxiliary subunit shown to regulate a multitude of cellular processes, including proliferation and migration. Ion channels are Cancer typically multimeric complexes consisting of conducting subunits and auxiliary, non-conducting subunits. Calcium channel Auxiliary subunits modulate the function of conducting subunits and have putative non-conducting roles, further Chloride channel expanding the repertoire of cellular processes governed by ion channel complexes to processes such as trans- Potassium channel cellular adhesion and gene transcription. Given this expansive influence of ion channels on cellular behaviour it Sodium channel is perhaps no surprise that aberrant ion channel expression is a common occurrence in cancer. This review will − focus on the conducting and non-conducting roles of the auxiliary subunits of various Ca2+,K+,Na+ and Cl channels and the burgeoning evidence linking such auxiliary subunits to cancer. Several subunits are upregu- lated (e.g. Cavβ,Cavγ) and downregulated (e.g. Kvβ) in cancer, while other subunits have been functionally implicated as oncogenes (e.g. Navβ1,Cavα2δ1) and tumour suppressor genes (e.g. CLCA2, KCNE2, BKγ1) based on in vivo studies. The strengthening link between ion channel auxiliary subunits and cancer has exposed these subunits as potential biomarkers and therapeutic targets. -
Transcriptomic Analysis of Native Versus Cultured Human and Mouse Dorsal Root Ganglia Focused on Pharmacological Targets Short
bioRxiv preprint doi: https://doi.org/10.1101/766865; this version posted September 12, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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-ND 4.0 International license. Transcriptomic analysis of native versus cultured human and mouse dorsal root ganglia focused on pharmacological targets Short title: Comparative transcriptomics of acutely dissected versus cultured DRGs Andi Wangzhou1, Lisa A. McIlvried2, Candler Paige1, Paulino Barragan-Iglesias1, Carolyn A. Guzman1, Gregory Dussor1, Pradipta R. Ray1,#, Robert W. Gereau IV2, # and Theodore J. Price1, # 1The University of Texas at Dallas, School of Behavioral and Brain Sciences and Center for Advanced Pain Studies, 800 W Campbell Rd. Richardson, TX, 75080, USA 2Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine # corresponding authors [email protected], [email protected] and [email protected] Funding: NIH grants T32DA007261 (LM); NS065926 and NS102161 (TJP); NS106953 and NS042595 (RWG). The authors declare no conflicts of interest Author Contributions Conceived of the Project: PRR, RWG IV and TJP Performed Experiments: AW, LAM, CP, PB-I Supervised Experiments: GD, RWG IV, TJP Analyzed Data: AW, LAM, CP, CAG, PRR Supervised Bioinformatics Analysis: PRR Drew Figures: AW, PRR Wrote and Edited Manuscript: AW, LAM, CP, GD, PRR, RWG IV, TJP All authors approved the final version of the manuscript. 1 bioRxiv preprint doi: https://doi.org/10.1101/766865; this version posted September 12, 2019. 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. -
Alternative Splicing in SCN1A: Biophysical
Alternative splicing in SCN1A: Biophysical consequences for NaV1.1 channels Emily Fletcher A thesis submitted to University College London for the degree of Doctor of Philosophy Department of Molecular Neuroscience Institute of Neurology Queen Square London WC1N 3BG 1 Declaration I, Emily Fletcher, confirm that the work presented in this thesis is my original research work. Where contributions of others are involved, this has been clearly indicated in the thesis. The copyright of this thesis rests with the author and no quotation from it or information derived from it may be published without the prior written consent of the author. 2 Acknowledgements I would like to thank my supervisor Stephanie Schorge for her continued support, patience and kindness towards me during my PhD and also to Dimitri Kullmann for the opportunity to work in his excellent lab. Most of all I‟d like to thank my family for their unconditional support and love. To my Dad for reading this gobbledygook through, to my Mum for her pep talks, to Ashleigh and my grandparents for making me laugh and to Claire especially, you‟re a fantastic big sister. Thank you. Lastly, I am truly grateful to have had opportunities for a good education. I am a very lucky person indeed. It's a new dawn It's a new day It's a new life For me And I'm feeling good Eunice Waymon, 1965 3 Abstract NaV1.1 is a voltage-gated sodium channel encoded by the gene SCN1A. Mutations in SCN1A cause dominantly inherited epilepsy syndromes in humans and NaV1.1 is an important target of several anti-epileptic drugs (AEDs). -
Genome-Wide Association and Transcriptome Studies Identify Candidate Genes and Pathways for Feed Conversion Ratio in Pigs
Miao et al. BMC Genomics (2021) 22:294 https://doi.org/10.1186/s12864-021-07570-w RESEARCH ARTICLE Open Access Genome-wide association and transcriptome studies identify candidate genes and pathways for feed conversion ratio in pigs Yuanxin Miao1,2,3, Quanshun Mei1,2, Chuanke Fu1,2, Mingxing Liao1,2,4, Yan Liu1,2, Xuewen Xu1,2, Xinyun Li1,2, Shuhong Zhao1,2 and Tao Xiang1,2* Abstract Background: The feed conversion ratio (FCR) is an important productive trait that greatly affects profits in the pig industry. Elucidating the genetic mechanisms underpinning FCR may promote more efficient improvement of FCR through artificial selection. In this study, we integrated a genome-wide association study (GWAS) with transcriptome analyses of different tissues in Yorkshire pigs (YY) with the aim of identifying key genes and signalling pathways associated with FCR. Results: A total of 61 significant single nucleotide polymorphisms (SNPs) were detected by GWAS in YY. All of these SNPs were located on porcine chromosome (SSC) 5, and the covered region was considered a quantitative trait locus (QTL) region for FCR. Some genes distributed around these significant SNPs were considered as candidates for regulating FCR, including TPH2, FAR2, IRAK3, YARS2, GRIP1, FRS2, CNOT2 and TRHDE. According to transcriptome analyses in the hypothalamus, TPH2 exhibits the potential to regulate intestinal motility through serotonergic synapse and oxytocin signalling pathways. In addition, GRIP1 may be involved in glutamatergic and GABAergic signalling pathways, which regulate FCR by affecting appetite in pigs. Moreover, GRIP1, FRS2, CNOT2,andTRHDE may regulate metabolism in various tissues through a thyroid hormone signalling pathway. -
Gene and Pathway-Based Second-Wave Analysis of Genome-Wide Association Studies
European Journal of Human Genetics (2010) 18, 111–117 & 2010 Macmillan Publishers Limited All rights reserved 1018-4813/10 $32.00 www.nature.com/ejhg ARTICLE Gene and pathway-based second-wave analysis of genome-wide association studies Gang Peng1, Li Luo2, Hoicheong Siu1, Yun Zhu1, Pengfei Hu1, Shengjun Hong1, Jinying Zhao3, Xiaodong Zhou4, John D Reveille4, Li Jin1, Christopher I Amos5 and Momiao Xiong*,2 Despite the great success of genome-wide association studies (GWAS) in identification of the common genetic variants associated with complex diseases, the current GWAS have focused on single-SNP analysis. However, single-SNP analysis often identifies only a few of the most significant SNPs that account for a small proportion of the genetic variants and offers only a limited understanding of complex diseases. To overcome these limitations, we propose gene and pathway-based association analysis as a new paradigm for GWAS. As a proof of concept, we performed a comprehensive gene and pathway-based association analysis of 13 published GWAS. Our results showed that the proposed new paradigm for GWAS not only identified the genes that include significant SNPs found by single-SNP analysis, but also detected new genes in which each single SNP conferred a small disease risk; however, their joint actions were implicated in the development of diseases. The results also showed that the new paradigm for GWAS was able to identify biologically meaningful pathways associated with the diseases, which were confirmed by a gene-set-rich analysis using gene expression -
An Advance About the Genetic Causes of Epilepsy
E3S Web of Conferences 271, 03068 (2021) https://doi.org/10.1051/e3sconf/202127103068 ICEPE 2021 An advance about the genetic causes of epilepsy Yu Sun1, a, *, †, Licheng Lu2, b, *, †, Lanxin Li3, c, *, †, Jingbo Wang4, d, *, † 1The School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801-3633, US 2High School Affiliated to Shanghai Jiao Tong University, Shanghai, 200441, China 3Applied Biology program, University of British Columbia, Vancouver, V6r3b1, Canada 4School of Chemical Machinery and Safety, Dalian University of Technology, Dalian, 116023, China †These authors contributed equally. Abstract: Human hereditary epilepsy has been found related to ion channel mutations in voltage-gated channels (Na+, K+, Ca2+, Cl-), ligand gated channels (GABA receptors), and G-protein coupled receptors, such as Mass1. In addition, some transmembrane proteins or receptor genes, including PRRT2 and nAChR, and glucose transporter genes, such as GLUT1 and SLC2A1, are also about the onset of epilepsy. The discovery of these genetic defects has contributed greatly to our understanding of the pathology of epilepsy. This review focuses on introducing and summarizing epilepsy-associated genes and related findings in recent decades, pointing out related mutant genes that need to be further studied in the future. 1 Introduction Epilepsy is a neurological disorder characterized by 2 Malfunction of Ion channel epileptic seizures caused by abnormal brain activity. 1 in Functional variation in voltage or ligand-gated ion 100 (50 million people) people are affected by symptoms channel mutations is a major cause of idiopathic epilepsy, of this disorder worldwide, with men, young children, and especially in rare genetic forms. -
Cav1.2 and Cav1.3 Voltage-Gated L-Type Ca2+ Channels in Rat White Fat Adipocytes
244 2 Journal of O A Fedorenko et al. Ca channels in white 244:2 369–381 Endocrinology adipocytes RESEARCH CaV1.2 and CaV1.3 voltage-gated L-type Ca2+ channels in rat white fat adipocytes Olena A Fedorenko1, Pawitra Pulbutr2, Elin Banke3, Nneoma E Akaniro-Ejim1, Donna C Bentley4, Charlotta S Olofsson3, Sue Chan1 and Paul A Smith1 1School of Life Sciences, University of Nottingham, Nottingham, UK 2Faculty of Pharmacy, Mahasarakham University, Mahasarakham, Thailand 3Department of Physiology/Metabolic Physiology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Göteborg, Sweden 4School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK Correspondence should be addressed to P A Smith: [email protected] Abstract L-type channel antagonists are of therapeutic benefit in the treatment of Key Words 2+ hyperlipidaemia and insulin resistance. Our aim was to identify L-type voltage-gated Ca f adipocyte 2+ channels in white fat adipocytes, and determine if they affect intracellular Ca , lipolysis f calcium channel and lipogenesis. We used a multidisciplinary approach of molecular biology, confocal f lipolysis 2+ microscopy, Ca imaging and metabolic assays to explore this problem using adipocytes f obesity isolated from adult rat epididymal fat pads. CaV1.2, CaV1.3 and CaV1.1 alpha1, beta and alpha2delta subunits were detected at the gene expression level. The CaV1.2 and CaV1.3 alpha1 subunits were identified in the plasma membrane at the protein level. Confocal microscopy with fluorescent antibodies labelled CaV1.2 in the plasma membrane. 2+ 2+ 2+ Ca imaging revealed that the intracellular Ca concentration, [Ca ]i was reversibly decreased by removal of extracellular Ca2+, an effect mimicked by verapamil, nifedipine and Co2+, all blockers of L-type channels, whereas the Ca2+ channel agonist BAY-K8644 2+ increased [Ca ]i. -
1 Molecular and Genetic Regulation of Pig Pancreatic Islet Cell Development 2 3 4 Seokho Kim1,9, Robert L
bioRxiv preprint doi: https://doi.org/10.1101/717090; this version posted January 24, 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. 1 Molecular and genetic regulation of pig pancreatic islet cell development 2 3 4 Seokho Kim1,9, Robert L. Whitener1,9, Heshan Peiris1, Xueying Gu1, Charles A. Chang1, 5 Jonathan Y. Lam1, Joan Camunas-Soler2, Insung Park3, Romina J. Bevacqua1, Krissie Tellez1, 6 Stephen R. Quake2,4, Jonathan R. T. Lakey5, Rita Bottino6, Pablo J. Ross3, Seung K. Kim1,7,8 7 8 1Department of Developmental Biology, Stanford University School of Medicine, 9 Stanford, CA, 94305 USA 10 2Department of Bioengineering, Stanford University, Stanford, CA, 94305 USA 11 3Department of Animal Science, University of California Davis, Davis, CA, 95616 USA 12 4Chan Zuckerberg Biohub, San Francisco, CA 94518, USA. 13 5Department of Surgery, University of California at Irvine, Irvine, CA, 92868 USA 14 6Institute of Cellular Therapeutics, Allegheny Health Network, Pittsburgh, PA, 15212 USA 15 7Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305 USA 16 8Stanford Diabetes Research Center, Stanford University School of Medicine, 17 Stanford, CA, 94305 USA 18 19 9These authors contributed equally 20 21 Correspondence and requests for materials should be addressed to S.K.K (email: 22 [email protected]) 23 24 Key Words: pancreas; metabolism; organogenesis; b-cell; a-cell; d-cell; diabetes mellitus 25 26 Summary Statement: This study reveals transcriptional, signaling and cellular programs 27 governing pig pancreatic islet development, including striking similarities to human islet 28 ontogeny, providing a novel resource for advancing human islet replacement strategies. -
Application of Microrna Database Mining in Biomarker Discovery and Identification of Therapeutic Targets for Complex Disease
Article Application of microRNA Database Mining in Biomarker Discovery and Identification of Therapeutic Targets for Complex Disease Jennifer L. Major, Rushita A. Bagchi * and Julie Pires da Silva * Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; [email protected] * Correspondence: [email protected] (R.A.B.); [email protected] (J.P.d.S.) Supplementary Tables Methods Protoc. 2021, 4, 5. https://doi.org/10.3390/mps4010005 www.mdpi.com/journal/mps Methods Protoc. 2021, 4, 5. https://doi.org/10.3390/mps4010005 2 of 25 Table 1. List of all hsa-miRs identified by Human microRNA Disease Database (HMDD; v3.2) analysis. hsa-miRs were identified using the term “genetics” and “circulating” as input in HMDD. Targets CAD hsa-miR-1 Targets IR injury hsa-miR-423 Targets Obesity hsa-miR-499 hsa-miR-146a Circulating Obesity Genetics CAD hsa-miR-423 hsa-miR-146a Circulating CAD hsa-miR-149 hsa-miR-499 Circulating IR Injury hsa-miR-146a Circulating Obesity hsa-miR-122 Genetics Stroke Circulating CAD hsa-miR-122 Circulating Stroke hsa-miR-122 Genetics Obesity Circulating Stroke hsa-miR-26b hsa-miR-17 hsa-miR-223 Targets CAD hsa-miR-340 hsa-miR-34a hsa-miR-92a hsa-miR-126 Circulating Obesity Targets IR injury hsa-miR-21 hsa-miR-423 hsa-miR-126 hsa-miR-143 Targets Obesity hsa-miR-21 hsa-miR-223 hsa-miR-34a hsa-miR-17 Targets CAD hsa-miR-223 hsa-miR-92a hsa-miR-126 Targets IR injury hsa-miR-155 hsa-miR-21 Circulating CAD hsa-miR-126 hsa-miR-145 hsa-miR-21 Targets Obesity hsa-mir-223 hsa-mir-499 hsa-mir-574 Targets IR injury hsa-mir-21 Circulating IR injury Targets Obesity hsa-mir-21 Targets CAD hsa-mir-22 hsa-mir-133a Targets IR injury hsa-mir-155 hsa-mir-21 Circulating Stroke hsa-mir-145 hsa-mir-146b Targets Obesity hsa-mir-21 hsa-mir-29b Methods Protoc. -
Pflugers Final
CORE Metadata, citation and similar papers at core.ac.uk Provided by Serveur académique lausannois A comprehensive analysis of gene expression profiles in distal parts of the mouse renal tubule. Sylvain Pradervand2, Annie Mercier Zuber1, Gabriel Centeno1, Olivier Bonny1,3,4 and Dmitri Firsov1,4 1 - Department of Pharmacology and Toxicology, University of Lausanne, 1005 Lausanne, Switzerland 2 - DNA Array Facility, University of Lausanne, 1015 Lausanne, Switzerland 3 - Service of Nephrology, Lausanne University Hospital, 1005 Lausanne, Switzerland 4 – these two authors have equally contributed to the study to whom correspondence should be addressed: Dmitri FIRSOV Department of Pharmacology and Toxicology, University of Lausanne, 27 rue du Bugnon, 1005 Lausanne, Switzerland Phone: ++ 41-216925406 Fax: ++ 41-216925355 e-mail: [email protected] and Olivier BONNY Department of Pharmacology and Toxicology, University of Lausanne, 27 rue du Bugnon, 1005 Lausanne, Switzerland Phone: ++ 41-216925417 Fax: ++ 41-216925355 e-mail: [email protected] 1 Abstract The distal parts of the renal tubule play a critical role in maintaining homeostasis of extracellular fluids. In this review, we present an in-depth analysis of microarray-based gene expression profiles available for microdissected mouse distal nephron segments, i.e., the distal convoluted tubule (DCT) and the connecting tubule (CNT), and for the cortical portion of the collecting duct (CCD) (Zuber et al., 2009). Classification of expressed transcripts in 14 major functional gene categories demonstrated that all principal proteins involved in maintaining of salt and water balance are represented by highly abundant transcripts. However, a significant number of transcripts belonging, for instance, to categories of G protein-coupled receptors (GPCR) or serine-threonine kinases exhibit high expression levels but remain unassigned to a specific renal function. -
Gene List of the Targeted NGS MCD and CCA Gene Panel AKT3,ALX1
Gene List of the targeted NGS MCD and CCA gene panel AKT3,ALX1,ALX3,ALX4,AMPD2,ARFGEF2,ARID1B,ARX,ASPM,ATR,ATRX,B3GALTL,BRPF1,c12orf57,C6orf70,CASK,CCND2,CDK5RAP2,CDON,C ENPJ,CEP170,CHMP1A,COL4A1,CREBBP,CYP11A1,DCHS1,DCLK1,DCX,DHCR24,DHCR7,DIS3L2,DISC1,DISP1,DLL1,DMRTA2,DYNC1H1,DYRK1 A,EARS2,EFNB1,EMX1,EOMES,EP300,ERBB4,ERMARD,EXOSC3,FAM36A,FGF8,FGFR1,FGFR2,FLNA,FOXC1,FOXG1,FOXH1,FZD10,GLI2,GLI3,GP R56,GPSM2,HCCS,HESX1,HNRNPU,IGBP1,IGFBP1,ISPD,ITPA,KAL1,KAT6B,KATNB1,KIAA1279,KIF14,KIF1A,KIF1B,KIF21A,KIF2A,KIF5C,KIF7,L1 CAM,LAMB1,LAMC3,LRP2,MCPH1,MED12,MID1,NDE1,NFIB,NPC1,NR2F1,NSD1,NTRK1,NTRK3,OCEL1,OPA1,OTX2,PAFAH1B1,PAX6,PEX1,PHF1 0,PIK3R2,POLR3A,POLR3B,POMT1,POMT2,PTCH1,PTPRS,PYCR1,RAB3GAP1,RARS2,RELN,RFX3,ROBO1,ROBO3,RPS6KA3,RTTN,SATB2,SEPSEC S,SHH,SIX3,SLC12A6,SOX2,SPOCK1,SRPX2,TBCD,TBCE,TCF4,TDGF1,TEAD1,THBS2,TMEM5,TSC1,TSC2,TSEN15,TSEN2,TSEN34,TSEN54,TUBA1 A,TUBA8,TUBB,TUBB2A,TUBB2B,TUBB3,TUBB4A,TUBG1,VAX1,VRK1,WDR47,WDR62,ZBTB18,ZEB2,ZIC2. Gene List of the targeted NGS epilepsy gene panel AARS, ADGRV1, ADRA2B, ADSL, ALDH4A1, ALDH7A1, ALG13, ALPL, ARHGEF15, ARHGEF9, ARX, ASAH1, ATP1A2, ATP1A3, BRD2, CACNA1A, CACNA1H, CACNA2D2, CACNB4, CBL, CDKL5, CERS1, CHD2, CHRNA2, CHRNA4, CHRNB2, CLCN2, CLCN4, CLN8, CLTC, CNKSR2, CNTNAP2, CPA6, CPLX1, CSNK1G1, CSNK2B, CTNND2, DEPDC5, DHDDS, DNM1, DOCK7, DYNC1H1, EEF1A2, EFHC1, EIF2S3, EMC1, EPM2A, FASN, FLNA, FOXG1, GABBR2, GABRA1, GABRA2, GABRA3, GABRB2, GABRB3, GABRD, GABRG2, GAL, GNAO1, GOSR2, GRIA1, GRIN1, GRIN2A, GRIN2B, HCN1, HCN4, HDAC4, HNRNPU, IDH3A, IQSEC2, JRK, KCNA1, KCNA2, KCNB1, -
Therapeutic Opportunities in Colon Cancer Focus on Phosphodiesterase Inhibitors
Life Sciences 230 (2019) 150–161 Contents lists available at ScienceDirect Life Sciences journal homepage: www.elsevier.com/locate/lifescie Review article Therapeutic opportunities in colon cancer: Focus on phosphodiesterase inhibitors T ⁎ Ankita Mehta, Bhoomika M. Patel Institute of Pharmacy, Nirma University, Ahmedabad, India ARTICLE INFO ABSTRACT Keywords: Despite novel technologies, colon cancer remains undiagnosed and 25% of patients are diagnosed with meta- Phosphodiesterases static colon cancer. Resistant to chemotherapeutic agents is one of the major problems associated with treating cAMP colon cancer which creates the need to develop novel agents targeting towards newer targets. A phosphodies- cGMP terase is a group of isoenzyme, which, hydrolyze cyclic nucleotides and thereby lowers intracellular levels of Adenylate cyclase cAMP and cGMP leading to tumorigenic effects. Many in vitro and in vivo studies have confirmed increased PDE Guanylate cyclase expression in different types of cancers including colon cancer. cAMP-specific PDE inhibitors increase in- Colon cancer tracellular cAMP that leads to activation of effector molecules-cAMP-dependent protein kinase A, exchange protein activated by cAMP and cAMP gated ion channels. These molecules regulate cellular responses and exert its anticancer role through different mechanisms including apoptosis, inhibition of angiogenesis, upregulating tumor suppressor genes and suppressing oncogenes. On the other hand, cGMP specific PDE inhibitors exhibit anticancer effects through cGMP dependent protein kinase and cGMP dependent cation channels. Elevation in cGMP works through activation of caspases, suppression of Wnt/b-catenin pathway and TCF transcription leading to inhibition of CDK and survivin. These studies point out towards the fact that PDE inhibition is as- sociated with anti-proliferative, anti-apoptotic and anti-angiogenic pathways involved in its anticancer effects in colon cancer.