DOCSLIB.ORG

DOCTOR of PHILOSOPHY Next Generation Sequencing And

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
DOCTOR of PHILOSOPHY Next Generation Sequencing And DOCTOR OF PHILOSOPHY Next Generation Sequencing and Genome-Wide Association Studies to Identify Mitochondrial Genomic Features Associated with Diabetic Kidney Disease Skelly, Ryan Award date: 2020 Awarding institution: Queen's University Belfast Link to publication Terms of use All those accessing thesis content in Queen’s University Belfast Research Portal are subject to the following terms and conditions of use • Copyright is subject to the Copyright, Designs and Patent Act 1988, or as modified by any successor legislation • Copyright and moral rights for thesis content are retained by the author and/or other copyright owners • A copy of a thesis may be downloaded for personal non-commercial research/study without the need for permission or charge • Distribution or reproduction of thesis content in any format is not permitted without the permission of the copyright holder • When citing this work, full bibliographic details should be supplied, including the author, title, awarding institution and date of thesis Take down policy A thesis can be removed from the Research Portal if there has been a breach of copyright, or a similarly robust reason. If you believe this document breaches copyright, or there is sufficient cause to take down, please contact us, citing details. Email: [email protected] Supplementary materials Where possible, we endeavour to provide supplementary materials to theses. This may include video, audio and other types of files. We endeavour to capture all content and upload as part of the Pure record for each thesis. Note, it may not be possible in all instances to convert analogue formats to usable digital formats for some supplementary materials. We exercise best efforts on our behalf and, in such instances, encourage the individual to consult the physical thesis for further information. Download date: 07. Oct. 2021 Next Generation Sequencing and Genome-Wide Association Studies to Identify Mitochondrial Genomic Features Associated with Diabetic Kidney Disease A thesis submitted to the School of Medicine, Dentistry and Biomedical Sciences of the Queen’s University of Belfast for the degree of: Doctor of Philosophy (PhD) 30th September 2019 Ryan Skelly B.Sc. (Hons) Human Biology (QUB, 2013) M.Sc. Bioinformatics and Computational Genomics (QUB, 2015) 1 Preface The research described in this thesis was carried out within the Nephrology Research Group at the Belfast City Hospital and the Centre of Public Health, Queen’s University Belfast between September 2016 and September 2019. Illumina sequencing was performed by the Genomics Core Technology Unit, Queen’s University Belfast. Funding was provided by the Department for the Economy. For any Tables and Figures reproduced or adapted from other sources suitable permissions have been requested and relevant references provided in the bibliography. 2 Acknowledgements I would like to thank my supervisors, Dr Amy Jayne McKnight and Professor Peter Maxwell, for their guidance and support throughout this project. Thank you for giving me the opportunity to carry out this research and your encouragement. I would also like to thank Jill Kilner and Christopher Wooster for providing support with lab work as well as Dr Laura Smyth and Dr Marisa Cañadas Garre for their help and guidance at various stages of the project. To everyone else within the NephRes group I offer my sincere thanks and gratitude and I am pleased to have been a part of this research team. I would also like to thank my family and friends for their support and understanding over the past three years. 3 Publications and Presentations from Work in this Thesis Genetic and epigenetic analysis in genes affecting mitochondrial function are associated with chronic kidney disease in an older population Cappa, R., Smyth, L., Cañadas-Garre, M., Polpo de Campos, C., Skelly, R., Cruise, S., Kee, F., McGuinness, B., Godson, C., Maxwell, A. & McKnight, A., 2018, (Submitted). Research output: Contribution to conference › Abstract Genetic susceptibility to chronic kidney disease – some more pieces for the heritability puzzle: Genetic predisposition to kidney disease Garre, M. C., Anderson, K., Cappa, R., Skelly, R., Smyth, L., McKnight, A. J. & Maxwell, A. P., 31 May 2019, In : Frontiers in Genetics. Research output: Contribution to journal › Review article Mitochondria and chronic kidney disease: a molecular update Skelly, R., Maxwell, A. & McKnight, A., 01 May 2019, In : SPG Biomed. Research output: Contribution to journal › Article Genetic risk factors in mitochondrial DNA associated with diabetic kidney disease – GWAS discovery and meta-analysis Skelly, R., Smyth, L., Cole, J., Maxwell, A., GENIE Consortium, DNCRI Consortium & McKnight, A., 2019, (Accepted). Research output: Contribution to conference › Poster 4 Abbreviations Used in this Thesis Abbreviation Long form 11βHSD1 11β-hydroxysteroid dehydrogenase 1 2-h PG one-off random plasma glucose concentration ACE angiotensin-converting enzyme ACE2 angiotensin-converting enzyme 2 ACR albumin to creatinine ratio AGEs advanced glycation end products AKI acute kidney injury AMPK 5' adenosine monophosphate-activated protein kinase AT1 angiotensin II receptor type 1 AT2 angiotensin II receptor type 2 ATP Adenosine Triphosphate AusDiane Austrian Diabetic Nephropathy Study BCH Belfast City Hospital BCL binary base call format BRTx Belfast renal transplant BST-DNA bisulfite-treated DNA CACTI Coronary Artery Calcification in Type 1 Diabetes cAMP cyclic adenosine monophosphate CD95L CD95 ligand CD-CV common disease/common variant CKD chronic kidney disease CVD cardiovascular disease DCCT/EDIC Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications DKD diabetic kidney disease D-loop displacement-loop DM diabetes mellitus DNA deoxyribonucleic acid DNMT DNA methyltransferase DNCRI Diabetic Nephropathy Collaborative Research Initiative DPP-4i dipeptidyl peptidase-4 inhibitors 5 ECM extra cellular matrix EDC Pittsburgh Epidemiology of Diabetes Complications Study eGFR estimated glomerular filtration rate EGFR epidermal growth factor receptor ESRD end-stage renal disease ET-1 endothelin-1 ETC electron transfer chain FFA free fatty acid FGF21 fibroblast growth factor 21 FIND Family Investigation of Nephropathy and Diabetes FinnDiane Finnish Diabetic Nephropathy Study FPG fasting plasma glucose GAD glutamic acid decarboxylase 65 GADPH glyceraldehyde-3-phosphate dehydrogenase GBM glomerular basement membrane GCTU Genomics Core Technology Unit GDM gestational diabetes mellitus GENEDIAB French and Belgian subjects from the Genetics of Diabetic Nephropathy GENIE Genetics of Nephropathy – an International Effort GFR glomerular filtration rate GLP1 glucagon-like peptide 1 GoKinD Genetics of Kidneys in Diabetes GoKinD Genetics of Kidneys in Diabetes US Study GSH reduced glutathione GWAS genome-wide association studies HapMap International Haplotype Map HbA1c haemoglobin A1c HGNC HUGO Gene Nomenclature Committee HLA human leucocyte antigens HSP heavy strand promoter H-Strand heavy strand iDCs immature dendritic cells 6 IDF International Diabetes Federation IFG impaired fasting glucose IFNγ interferon-γ IGT impaired glucose tolerance IR insulin resistance JAK2 janus kinase-2 JOSLIN Joslin Kidney Study LADA latent autoimmune diabetes of adults LatDiane Latvian Diabetic Nephropathy Study LD linkage disequilibrium LitDiane Lithuanian Diabetic Nephropathy Study lncRNA long ncRNA LSP Light Strand Promoter L-Strand Light Strand MAF minor allele frequency MHC major histocompatibility complex miRNA micro RNA mmol/L millimoles per litre MODY maturity onset diabetes of the young mRNA messenger RNA mtDNA mitochondrial DNA mtSSB mitochondrial single-stranded DNA-binding protein NADH reduced nicotinamide adenine dinucleotide NCR non-coding region ncRNA non-coding RNAs nDNA nuclear DNA NEMGs nuclear encoded mitochondrial genes NephRes QUB Nephrology Research Group NF-κB nuclear factor kappa-light-chain-enhancer of activated B cells NGS next-generation sequencing NICOLA Northern Ireland Cohort for the Longitudinal study of Ageing NOD non-obese diabetic 7 NP natriuretic peptide OH origin of replication for the H-strand OR odds ratio OXPHOS oxidative phosphorylation PCR polymerase chain reaction PIF1 petite integration frequency 1 piRNA piwi-interacting RNA PKC protein kinase C POLRMT mitochondrial RNA polymerase POLγ DNA polymerase γ POLγB DNA polymerase γ processivity factor PPARγ peroxisome proliferator-activated receptor gamma PTM post-translational modification QC quality control QUB Queen's University Belfast RAAS renin-angiotensin-aldosterone system RNA ribonucleic acid RNaseH1 ribonuclease H1 ROCK1 Rho-associated coiled coil-containing protein kinase 1 RomDiane Romanian Diabetic Nephropathy Study ROS reactive oxygen species rRNA Ribosomal RNA RRT renal replacement therapy SBS sequencing by synthesis SDM strand-displacement model SDRNT1BIO Scottish Diabetes Research Network Type 1 Bioresource SGLT2 sodium/glucose co-transporter 2 siRNA small interfering RNA SNP single nucleotide polymorphism snRNA small nuclear RNA SOD superoxide dismutase SOLiD Sequencing by Oligonucleotide Ligation and Detection 8 SPPARM selective peroxisome proliferator-activated receptor modulator SUMMIT Surrogate markers for Micro- and Macro-vascular har d endpoints for Innovative diabetes Tools SUV3 suppressor of Var1 3-Like Protein 1 T1DM type 1 diabetes mellitus T2DM type 2 diabetes mellitus TFAM mitochondrial transcription factor A TFBM mitochondrial transcription factor B TGF-β
Load more

Recommended publications
  • Viewed Under 23 (B) Or 203 (C) fi M M Male Cko Mice, and Largely Unaffected Magni Cation; Scale Bars, 500 M (B) and 50 M (C)
    BRIEF COMMUNICATION www.jasn.org Renal Fanconi Syndrome and Hypophosphatemic Rickets in the Absence of Xenotropic and Polytropic Retroviral Receptor in the Nephron Camille Ansermet,* Matthias B. Moor,* Gabriel Centeno,* Muriel Auberson,* † † ‡ Dorothy Zhang Hu, Roland Baron, Svetlana Nikolaeva,* Barbara Haenzi,* | Natalya Katanaeva,* Ivan Gautschi,* Vladimir Katanaev,*§ Samuel Rotman, Robert Koesters,¶ †† Laurent Schild,* Sylvain Pradervand,** Olivier Bonny,* and Dmitri Firsov* BRIEF COMMUNICATION *Department of Pharmacology and Toxicology and **Genomic Technologies Facility, University of Lausanne, Lausanne, Switzerland; †Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts; ‡Institute of Evolutionary Physiology and Biochemistry, St. Petersburg, Russia; §School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia; |Services of Pathology and ††Nephrology, Department of Medicine, University Hospital of Lausanne, Lausanne, Switzerland; and ¶Université Pierre et Marie Curie, Paris, France ABSTRACT Tight control of extracellular and intracellular inorganic phosphate (Pi) levels is crit- leaves.4 Most recently, Legati et al. have ical to most biochemical and physiologic processes. Urinary Pi is freely filtered at the shown an association between genetic kidney glomerulus and is reabsorbed in the renal tubule by the action of the apical polymorphisms in Xpr1 and primary fa- sodium-dependent phosphate transporters, NaPi-IIa/NaPi-IIc/Pit2. However, the milial brain calcification disorder.5 How- molecular identity of the protein(s) participating in the basolateral Pi efflux remains ever, the role of XPR1 in the maintenance unknown. Evidence has suggested that xenotropic and polytropic retroviral recep- of Pi homeostasis remains unknown. Here, tor 1 (XPR1) might be involved in this process. Here, we show that conditional in- we addressed this issue in mice deficient for activation of Xpr1 in the renal tubule in mice resulted in impaired renal Pi Xpr1 in the nephron.
    [Show full text]
  • Upregulation of Peroxisome Proliferator-Activated Receptor-Α And
    Upregulation of peroxisome proliferator-activated receptor-α and the lipid metabolism pathway promotes carcinogenesis of ampullary cancer Chih-Yang Wang, Ying-Jui Chao, Yi-Ling Chen, Tzu-Wen Wang, Nam Nhut Phan, Hui-Ping Hsu, Yan-Shen Shan, Ming-Derg Lai 1 Supplementary Table 1. Demographics and clinical outcomes of five patients with ampullary cancer Time of Tumor Time to Age Differentia survival/ Sex Staging size Morphology Recurrence recurrence Condition (years) tion expired (cm) (months) (months) T2N0, 51 F 211 Polypoid Unknown No -- Survived 193 stage Ib T2N0, 2.41.5 58 F Mixed Good Yes 14 Expired 17 stage Ib 0.6 T3N0, 4.53.5 68 M Polypoid Good No -- Survived 162 stage IIA 1.2 T3N0, 66 M 110.8 Ulcerative Good Yes 64 Expired 227 stage IIA T3N0, 60 M 21.81 Mixed Moderate Yes 5.6 Expired 16.7 stage IIA 2 Supplementary Table 2. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of an ampullary cancer microarray using the Database for Annotation, Visualization and Integrated Discovery (DAVID). This table contains only pathways with p values that ranged 0.0001~0.05. KEGG Pathway p value Genes Pentose and 1.50E-04 UGT1A6, CRYL1, UGT1A8, AKR1B1, UGT2B11, UGT2A3, glucuronate UGT2B10, UGT2B7, XYLB interconversions Drug metabolism 1.63E-04 CYP3A4, XDH, UGT1A6, CYP3A5, CES2, CYP3A7, UGT1A8, NAT2, UGT2B11, DPYD, UGT2A3, UGT2B10, UGT2B7 Maturity-onset 2.43E-04 HNF1A, HNF4A, SLC2A2, PKLR, NEUROD1, HNF4G, diabetes of the PDX1, NR5A2, NKX2-2 young Starch and sucrose 6.03E-04 GBA3, UGT1A6, G6PC, UGT1A8, ENPP3, MGAM, SI, metabolism
    [Show full text]
  • Table 2. Significant
    Table 2. Significant (Q < 0.05 and |d | > 0.5) transcripts from the meta-analysis Gene Chr Mb Gene Name Affy ProbeSet cDNA_IDs d HAP/LAP d HAP/LAP d d IS Average d Ztest P values Q-value Symbol ID (study #5) 1 2 STS B2m 2 122 beta-2 microglobulin 1452428_a_at AI848245 1.75334941 4 3.2 4 3.2316485 1.07398E-09 5.69E-08 Man2b1 8 84.4 mannosidase 2, alpha B1 1416340_a_at H4049B01 3.75722111 3.87309653 2.1 1.6 2.84852656 5.32443E-07 1.58E-05 1110032A03Rik 9 50.9 RIKEN cDNA 1110032A03 gene 1417211_a_at H4035E05 4 1.66015788 4 1.7 2.82772795 2.94266E-05 0.000527 NA 9 48.5 --- 1456111_at 3.43701477 1.85785922 4 2 2.8237185 9.97969E-08 3.48E-06 Scn4b 9 45.3 Sodium channel, type IV, beta 1434008_at AI844796 3.79536664 1.63774235 3.3 2.3 2.75319499 1.48057E-08 6.21E-07 polypeptide Gadd45gip1 8 84.1 RIKEN cDNA 2310040G17 gene 1417619_at 4 3.38875643 1.4 2 2.69163229 8.84279E-06 0.0001904 BC056474 15 12.1 Mus musculus cDNA clone 1424117_at H3030A06 3.95752801 2.42838452 1.9 2.2 2.62132809 1.3344E-08 5.66E-07 MGC:67360 IMAGE:6823629, complete cds NA 4 153 guanine nucleotide binding protein, 1454696_at -3.46081884 -4 -1.3 -1.6 -2.6026947 8.58458E-05 0.0012617 beta 1 Gnb1 4 153 guanine nucleotide binding protein, 1417432_a_at H3094D02 -3.13334396 -4 -1.6 -1.7 -2.5946297 1.04542E-05 0.0002202 beta 1 Gadd45gip1 8 84.1 RAD23a homolog (S.
    [Show full text]
  • Conflicting Nongenomic Effects of Progesterone in the Myometrium Of
    International Journal of Molecular Sciences Article Conflicting Nongenomic Effects of Progesterone in the Myometrium of Pregnant Rats Katsuhiko Yasuda *, Aya Yoshida and Hidetaka Okada Department of Obstetrics and Gynecology, Kansai Medical University, 2-5-1 Shinmachi, Hirakata, Osaka 573-1010, Japan; [email protected] (A.Y.); [email protected] (H.O.) * Correspondence: [email protected]; Tel.: +81-72-804-0101; Fax: +81-72-804-0122 Abstract: Recently, it has been suggested that progesterone affects the contractile activity of pregnant myometrium via nongenomic pathways; therefore, we aimed to clarify whether progesterone causes and/or inhibits pregnant myometrial contractions via nongenomic pathways. Our in vitro experi- ments using myometrial strips obtained from rats at 20 days of gestation revealed that progesterone caused myometrial contractions in a concentration- and time-dependent manner at concentrations up to 5 × 10−7 M; however, this effect decreased at concentrations higher than 5 × 10−5 M. Similarly, progesterone enhanced oxytocin-induced contractions up to 5 × 10−7 M and inhibited contractions at concentrations higher than 5 × 10−5 M. Conversely, progesterone did not enhance high-KCl- induced contractions but inhibited contractions in a concentration- and time-dependent manner at concentrations higher than 5 × 10−7 M. We also found that RU486 did not affect progesterone- induced contractions or the progesterone-induced inhibition of high-KCl-induced contractions; however, progesterone-induced contractions were blocked by calcium-free phosphate saline solu- tion, verapamil, and nifedipine. In addition, FPL64176, an activator of L-type voltage-dependent calcium channels, enhanced high-KCl-induced contractions and rescued the decrease in high-KCl- induced contractions caused by progesterone.
    [Show full text]
  • Structure and Function of Ion Channels Regulating Sperm Motility—An Overview
    International Journal of Molecular Sciences Review Structure and Function of Ion Channels Regulating Sperm Motility—An Overview Karolina Nowicka-Bauer 1,* and Monika Szymczak-Cendlak 2 1 Department of Chemical Physics, Faculty of Chemistry, Adam Mickiewicz University in Pozna´n, 61-614 Poznan, Poland 2 Department of Animal Physiology and Development, Faculty of Biology, Adam Mickiewicz University in Pozna´n,61-614 Poznan, Poland; [email protected] * Correspondence: [email protected] Abstract: Sperm motility is linked to the activation of signaling pathways that trigger movement. These pathways are mainly dependent on Ca2+, which acts as a secondary messenger. The mainte- nance of adequate Ca2+ concentrations is possible thanks to proper concentrations of other ions, such as K+ and Na+, among others, that modulate plasma membrane potential and the intracellular pH. Like in every cell, ion homeostasis in spermatozoa is ensured by a vast spectrum of ion channels supported by the work of ion pumps and transporters. To achieve success in fertilization, sperm ion channels have to be sensitive to various external and internal factors. This sensitivity is provided by specific channel structures. In addition, novel sperm-specific channels or isoforms have been found with compositions that increase the chance of fertilization. Notably, the most significant sperm ion channel is the cation channel of sperm (CatSper), which is a sperm-specific Ca2+ channel required for the hyperactivation of sperm motility. The role of other ion channels in the spermatozoa, such as voltage-gated Ca2+ channels (VGCCs), Ca2+-activated Cl-channels (CaCCs), SLO K+ channels or voltage-gated H+ channels (VGHCs), is to ensure the activation and modulation of CatSper.
    [Show full text]
  • The Role of Catsper1 and Catsper2 Ion Channels in Male Fertility and Infertility
    Available online at www.sciencedirect.com ScienceDirect Procedia Materials Science 10 ( 2015 ) 730 – 736 2nd International Conference on Nanomaterials and Technologies (CNT 2014) The role of CatSper1 and CatSper2 ion channels in male fertility and infertility Saikat Sahaa,b, Keka Talukdara, Amit K. Chakrabortya,b* a.Carbon Nanotechnology Group, Department of Physics, National Institute of Technology Durgapur-713209, West Bengal, India bCentre of Excellence in Advanced Materials, National Institute of Technology Durgapur-713209, West Bengal, India Abstract Ion channels in human body play multiple roles in many important biological processes. They regulate sperm maturation in the female reproductive tract and facilitates in hyperactivated motility, maturity through capacitation and acrosome reaction. The four sperm-associated cation channel, known as CatSpers and different ligand gated and voltage gated ion channels have been found to play crucial role for sperm physiology preparation for fertilization. The major function for maintaining Ca2+ concentration in flagellum is governed by CatSper channels in plasma membrane. Until now the role of these channels are not very clear. Here we have analysed the PDB structure (generated so far) of CatSper1 and CatSper2 channel proteins and found their ligand binding sites. The calculations are done by Charmm potential. Energies are calculated before and after ligand binding. We have also carried out Molecular Dynamics (MD) simulation for the protein model after filling up the simulation box with water and a number of K+ and Cl- ions. We see that the opening and closing of the channel pores depend on the binding of ligands. ©© 20152015 The The Authors. Authors. Published Published by Elsevierby Elsevier Ltd.
    [Show full text]
  • 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.
    [Show full text]
  • Epigenetic Mechanisms Are Involved in the Oncogenic Properties of ZNF518B in Colorectal Cancer
    Epigenetic mechanisms are involved in the oncogenic properties of ZNF518B in colorectal cancer Francisco Gimeno-Valiente, Ángela L. Riffo-Campos, Luis Torres, Noelia Tarazona, Valentina Gambardella, Andrés Cervantes, Gerardo López-Rodas, Luis Franco and Josefa Castillo SUPPLEMENTARY METHODS 1. Selection of genomic sequences for ChIP analysis To select the sequences for ChIP analysis in the five putative target genes, namely, PADI3, ZDHHC2, RGS4, EFNA5 and KAT2B, the genomic region corresponding to the gene was downloaded from Ensembl. Then, zoom was applied to see in detail the promoter, enhancers and regulatory sequences. The details for HCT116 cells were then recovered and the target sequences for factor binding examined. Obviously, there are not data for ZNF518B, but special attention was paid to the target sequences of other zinc-finger containing factors. Finally, the regions that may putatively bind ZNF518B were selected and primers defining amplicons spanning such sequences were searched out. Supplementary Figure S3 gives the location of the amplicons used in each gene. 2. Obtaining the raw data and generating the BAM files for in silico analysis of the effects of EHMT2 and EZH2 silencing The data of siEZH2 (SRR6384524), siG9a (SRR6384526) and siNon-target (SRR6384521) in HCT116 cell line, were downloaded from SRA (Bioproject PRJNA422822, https://www.ncbi. nlm.nih.gov/bioproject/), using SRA-tolkit (https://ncbi.github.io/sra-tools/). All data correspond to RNAseq single end. doBasics = TRUE doAll = FALSE $ fastq-dump -I --split-files SRR6384524 Data quality was checked using the software fastqc (https://www.bioinformatics.babraham. ac.uk /projects/fastqc/). The first low quality removing nucleotides were removed using FASTX- Toolkit (http://hannonlab.cshl.edu/fastxtoolkit/).
    [Show full text]
  • 1 1 2 3 Cell Type-Specific Transcriptomics of Hypothalamic
    1 2 3 4 Cell type-specific transcriptomics of hypothalamic energy-sensing neuron responses to 5 weight-loss 6 7 Fredrick E. Henry1,†, Ken Sugino1,†, Adam Tozer2, Tiago Branco2, Scott M. Sternson1,* 8 9 1Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 10 20147, USA. 11 2Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, 12 Cambridge CB2 0QH, UK 13 14 †Co-first author 15 *Correspondence to: [email protected] 16 Phone: 571-209-4103 17 18 Authors have no competing interests 19 1 20 Abstract 21 Molecular and cellular processes in neurons are critical for sensing and responding to energy 22 deficit states, such as during weight-loss. AGRP neurons are a key hypothalamic population 23 that is activated during energy deficit and increases appetite and weight-gain. Cell type-specific 24 transcriptomics can be used to identify pathways that counteract weight-loss, and here we 25 report high-quality gene expression profiles of AGRP neurons from well-fed and food-deprived 26 young adult mice. For comparison, we also analyzed POMC neurons, an intermingled 27 population that suppresses appetite and body weight. We find that AGRP neurons are 28 considerably more sensitive to energy deficit than POMC neurons. Furthermore, we identify cell 29 type-specific pathways involving endoplasmic reticulum-stress, circadian signaling, ion 30 channels, neuropeptides, and receptors. Combined with methods to validate and manipulate 31 these pathways, this resource greatly expands molecular insight into neuronal regulation of 32 body weight, and may be useful for devising therapeutic strategies for obesity and eating 33 disorders.
    [Show full text]
  • (C) Hit Agreement Between Seeding Densities
    (a) Morphological space (b) Identification of hits (c) Hit agreement between 1500 cells per well 1500 cells per well seeding densities DMSO 8 1.00 Pentamidine 1.00 Wiskostatin Hydroxychloroquine Imatinib 0.75 0.75 4 Gefitinib Compound DMSO Pentamidine 0.50 0.50 0 Vinblastine UMAP2 Wiskostatin Vinblastine 0.25 0.25 Vinblastine −4 Plate at 1500 cells/well Robust Hellinger Distance Wiskostatin Pentamidine 0.00 DMSO 0.00 −4 0 4 0.00 0.25 0.50 0.75 1.00 0.00 0.25 0.50 0.75 1.00 UMAP1 FDR−corrected p−value Plate at 750 cells/well Supp. Figure 1: BioProfiling.jl profiles of plates seeded at 750 and 1500 cells per well curated with are similar. (a) UMAP embedding preserving the cosine distance between the mor-phological profiles aggregated per field of view in the plate seeded with 1500 cells per well. Two out of four dimensions are represented. (b) Robust Hellinger distance and Ro-bust Morphological Perturbation Value (FDR-corrected p-value) of each compound in the plate seeded with 1500 cells per well compared to DMSO. Vertical dotted line indicates an FDR threshold of 0.1 and all compounds on its left are defined as morphological hits. (c) FDR-corrected p-value of the significance of morphological changes induced by each compound in both plates. Dotted lines indicate an FDR threshold of 0.1. CompoundName MOA Targets RMPV750 RMPV1500 (+)-Butaclamol hydrochloride 0.2479179 0 (+)-Cyclazocine 0.0288018 0.0012478 ["ABCC1", "ABCC2", "FPR1", (+/-)-Sulfinpyrazone ["Uricosuric blocker"] "SLC22A12"] 0.0019172 0.015413 (-)-JQ1 0.0003682 0 (-)-Perillic
    [Show full text]
  • The Relevance of Aquaporins for the Physiology, Pathology, and Aging of the Female Reproductive System in Mammals
    cells Review The Relevance of Aquaporins for the Physiology, Pathology, and Aging of the Female Reproductive System in Mammals Paweł Kordowitzki 1,2 , Wiesława Kranc 3, Rut Bryl 3, Bartosz Kempisty 3,4,5, Agnieszka Skowronska 6 and Mariusz T. Skowronski 1,* 1 Department of Basic and Preclinical Sciences, Institute for Veterinary Medicine, Nicolaus Copernicus University, 87-100 Torun, Poland; [email protected] 2 Institute of Animal Reproduction and Food Research of Polish Academy of Sciences, 10-243 Olsztyn, Poland 3 Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; [email protected] (W.K.); [email protected] (R.B.); [email protected] (B.K.) 4 Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland 5 Department of Veterinary Surgery, Institute for Veterinary Medicine, Nicolaus Copernicus University, 87-100 Torun, Poland 6 Department of Human Physiology and Pathophysiology, School of Medicine, Collegium Medicum, University of Warmia and Mazury, Warszawska Street 30, 10-082 Olsztyn, Poland; [email protected] * Correspondence: [email protected]; Tel.: +48-56-611-2231 Received: 27 October 2020; Accepted: 29 November 2020; Published: 1 December 2020 Abstract: Aquaporins constitute a group of water channel proteins located in numerous cell types. These are pore-forming transmembrane proteins, which mediate the specific passage of water molecules through membranes. It is well-known that water homeostasis plays a crucial role in different reproductive processes, e.g., oocyte transport, hormonal secretion, completion of successful fertilization, blastocyst formation, pregnancy, and birth. Further, aquaporins are involved in the process of spermatogenesis, and they have been reported to be involved during the storage of spermatozoa.
    [Show full text]
  • Theranostics Roles of Catsper Channels in the Pathogenesis Of
    Theranostics 2021, Vol. 11, Issue 6 2822 Ivyspring International Publisher Theranostics 2021; 11(6): 2822-2844. doi: 10.7150/thno.51869 Research Paper Roles of CatSper channels in the pathogenesis of asthenozoospermia and the therapeutic effects of acupuncture-like treatment on asthenozoospermia Zi-Run Jin1, Dong Fang1, Bo-Heng Liu1, Jie Cai1, Wen-Hao Tang3, Hui Jiang3, Guo-Gang Xing1,2 1. Neuroscience Research Institute, Peking University; Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center; Key Laboratory for Neuroscience, Ministry of Education of China & National Health Commission of China, Beijing 100191, China. 2. The Second Affiliated Hospital of Xinxiang Medical University, Henan, Xinxiang 453002, China. 3. Department of Urology, the Third Hospital, Peking University, Beijing 100191, China. Corresponding author: Guo-Gang Xing, Ph.D., Department of Neurobiology, School of Basic Medical Sciences and Neuroscience Research Institute, Peking University, Beijing 100191, China. Phone: +8610-8280-5842, E-mail: [email protected] © The author(s). This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/). See http://ivyspring.com/terms for full terms and conditions. Received: 2020.08.12; Accepted: 2020.12.13; Published: 2021.01.01 Abstract Rationale: Idiopathic asthenozoospermia (iAZS) is one of the major causes of male infertility and has no effective therapeutic treatment. Understanding the potential mechanisms that cause it may be helpful in seeking novel targets and treatment strategies for overcoming the problem of low sperm motility in iAZS individuals. Methods: Computer-assisted semen analysis (CASA) was utilized to assess the sperm motility.
    [Show full text]