Genetic Testing
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A Reciprocal Effort Towards Better Approaches for Drug Discovery
Acta Pharmacologica Sinica (2013) 34: 765–776 npg © 2013 CPS and SIMM All rights reserved 1671-4083/13 $32.00 www.nature.com/aps Review iPSCs and small molecules: a reciprocal effort towards better approaches for drug discovery Ru ZHANG1, Li-hong ZHANG2, Xin XIE1, 2, * 1Laboratory of Receptor-based Bio-medicine, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; 2CAS Key Laboratory of Receptor Research, the National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China The revolutionary induced pluripotent stem cell (iPSC) technology provides a new path for cell replacement therapies and drug screen- ing. Patient-specific iPSCs and subsequent differentiated cells manifesting disease phenotypes will finally position human disease pathology at the core of drug discovery. Cells used to test the toxic effects of drugs can also be generated from normal iPSCs and pro- vide a much more accurate and cost-effective system than many animal models. Here, we highlight the recent progress in iPSC-based cell therapy, disease modeling and drug evaluations. In addition, we discuss the use of small molecule drugs to improve the genera- tion of iPSCs and understand the reprogramming mechanism. It is foreseeable that the interplay between iPSC technology and small molecule compounds will push forward the applications of iPSC-based therapy and screening systems in the real world and eventually revolutionize the methods used to treat diseases. Keywords: induced pluripotent stem cells (iPSCs); disease modeling; drug screening; toxicity evaluation; cell replacement therapy; small molecules; drug development Acta Pharmacologica Sinica (2013) 34: 765–776; doi: 10.1038/aps.2013.21; published online 22 Apr 2013 Introduction his/her own iPSCs[1–3]. -
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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. -
1 Long-Read Genome Sequencing for the Diagnosis Of
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.02.185447; this version posted September 14, 2020. 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. Long-read genome sequencing for the diagnosis of neurodevelopmental disorders Susan M. Hiatt1, James M.J. Lawlor1, Lori H. Handley1, Ryne C. Ramaker1, Brianne B. Rogers1,2, E. Christopher Partridge1, Lori Beth Boston1, Melissa Williams1, Christopher B. Plott1, Jerry Jenkins1, David E. Gray1, James M. Holt1, Kevin M. Bowling1, E. Martina Bebin3, Jane Grimwood1, Jeremy Schmutz1, Gregory M. Cooper1* 1HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA, 35806 2Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA, 35924 3Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA, 35924 *[email protected], 256-327-9490 Conflicts of Interest The authors all declare no conflicts of interest. 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.02.185447; this version posted September 14, 2020. 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. Abstract Purpose Exome and genome sequencing have proven to be effective tools for the diagnosis of neurodevelopmental disorders (NDDs), but large fractions of NDDs cannot be attributed to currently detectable genetic variation. This is likely, at least in part, a result of the fact that many genetic variants are difficult or impossible to detect through typical short-read sequencing approaches. -
Identification of Novel Pathways That Promote Anoikis Through Genome-Wide Screens
University of Massachusetts Medical School eScholarship@UMMS GSBS Dissertations and Theses Graduate School of Biomedical Sciences 2016-10-14 Identification of Novel Pathways that Promote Anoikis through Genome-wide Screens Victoria E. Pedanou University of Massachusetts Medical School Let us know how access to this document benefits ou.y Follow this and additional works at: https://escholarship.umassmed.edu/gsbs_diss Part of the Biology Commons, and the Cancer Biology Commons Repository Citation Pedanou VE. (2016). Identification of Novel Pathways that Promote Anoikis through Genome-wide Screens. GSBS Dissertations and Theses. https://doi.org/10.13028/M27G6D. Retrieved from https://escholarship.umassmed.edu/gsbs_diss/889 This material is brought to you by eScholarship@UMMS. It has been accepted for inclusion in GSBS Dissertations and Theses by an authorized administrator of eScholarship@UMMS. For more information, please contact [email protected]. i TITLE PAGE IDENTIFICATION OF NOVEL PATHWAYS THAT PROMOTE ANOIKIS THROUGH GENOME-WIDE SCREENS A Dissertation Presented By VICTORIA ELIZABETH PEDANOU Submitted to the Faculty of the University of Massachusetts Graduate School of Biomedical Sciences, Worcester in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY OCTOBER 14TH, 2016 CANCER BIOLOGY ii SIGNATURE PAGE IDENTIFICATION OF NOVEL PATHWAYS THAT PROMOTE ANOIKIS THROUGH GENOME-WIDE SCREENS A Dissertation Presented By VICTORIA ELIZABETH PEDANOU This work was undertaken in the Graduate School of Biomedical Sciences Cancer Biology The signature of the Thesis Advisor signifies validation of Dissertation content ___________________________ Michael R. Green, Thesis Advisor The signatures of the Dissertation Defense Committee signify completion and approval as to style and content of the Dissertation __________________________________ Eric H. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
The Intracellular Ca2+ Release Channel TRPML1 Regulates Lower Urinary Tract Smooth Muscle Contractility
The intracellular Ca2+ release channel TRPML1 regulates lower urinary tract smooth muscle contractility Caoimhin S. Griffina, Michael G. Alvaradoa, Evan Yamasakia, Bernard T. Drummb,c, Vivek Krishnana, Sher Alia, Eleanor M. Naglea, Kenton M. Sandersb, and Scott Earleya,1 aDepartment of Pharmacology, Center for Molecular and Cellular Signaling in the Cardiovascular System, Reno School of Medicine, University of Nevada, Reno, NV 89557-0318; bDepartment of Physiology and Cell Biology, Reno School of Medicine, University of Nevada, Reno, NV 89557-0318; and cDepartment of Life & Health Sciences, Dundalk Institute of Technology, Louth, Ireland A91 K584 Edited by Mark T. Nelson, University of Vermont, Burlington, VT, and approved October 13, 2020 (received for review August 12, 2020) TRPML1 (transient receptor potential mucolipin 1) is a Ca2+-perme- including dense granulomembranous storage bodies in neurons, able, nonselective cation channel that is predominantly localized to elevated plasma gastrin, vacuolization in the gastric mucosa, and the membranes of late endosomes and lysosomes (LELs). Intracellular retinal degeneration (14). Interestingly, however, an anatomical release of Ca2+ through TRPML1 is thought to be pivotal for mainte- examination of these mice reveals dramatically distended bladders nance of intravesicular acidic pH as well as the maturation, fusion, and (14), leading us to question how TRPML1, an intracellular Ca2+- trafficking of LELs. Interestingly, genetic ablation of TRPML1 in mice release channel important in LEL function, affects bladder −/− (Mcoln1 ) induces a hyperdistended/hypertrophic bladder phenotype. physiology. Here, we investigated this phenomenon further by exploring an un- The lower urinary tract (LUT) is composed of the urinary conventional role for TRPML1 channels in the regulation of Ca2+-signal- bladder and urethra—structures that serve the simple, reciprocal ing activity and contractility in bladder and urethral smooth muscle cells functions of storing and voiding urine (15). -
Complete Loss of CASK Causes Severe Ataxia Through Cerebellar Degeneration
Complete loss of CASK causes severe ataxia through cerebellar degeneration Paras Patel Fralin Biomedical Research Institute at VTC Julia Hegert Orlando Health Corp Ingrid Cristian Orlando Health Corp Alicia Kerr National Eye Institute Leslie LaConte Fralin Biomedical Research Institute at VTC Michael Fox Fralin Biomedical Research Institute at VTC Sarika Srivastava Fralin Biomedical Research Institute at VTC Konark Mukherjee ( [email protected] ) Fralin Biomedical Research Institute at VTC https://orcid.org/0000-0002-6922-9554 Research article Keywords: CASK, MICPCH, neurodegeneration, X-linked, X-inactivation, cerebellum, ataxia Posted Date: May 4th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-456061/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/34 Abstract Background: Heterozygous loss of X-linked genes like CASK and MeCP2 (Rett syndrome) causes neurodevelopmental disorders (NDD) in girls, while in boys loss of the only allele of these genes leads to profound encephalopathy. The cellular basis for these disorders remains unknown. CASK is presumed to work through the Tbr1-reelin pathway in neuronal migration. Methods: Here we report clinical and histopathological analysis of a deceased 2-month-old boy with a CASK-null mutation. We rst analyze in vivo data from the subject including genetic characterization, magnetic resonance imaging (MRI) ndings, and spectral characteristics of the electroencephalogram (EEG). We next compare features of the cerebellum to an-age matched control. Based on this, we generate a murine model where CASK is completely deleted from post-migratory neurons in the cerebellum. Results: Although smaller, the CASK-null human brain exhibits normal lamination without defective neuronal differentiation, migration, or axonal guidance, excluding the role of reelin. -
Developing Biomarkers for Livestock Science
Developing biomarkers for livestock Science Ongoing research and future developments Marinus te Pas Outline . Introduction ● What are biomarkers ● Why do we need them . Examples ● omics levels . The future ● Big data ● Systems biology / Synthetic biology 2 Introduction: What are biomarkers? . Biological processes underlie all livestock (production) traits ● Measure the status of a biological process = know the trait! . Can be any molecule in a cell ● No need to know the causal factor for a trait . Well known example: blood glucose level for diabetes Introduction: Why do we need biomarkers? . The mission of WageningenUR: Sustainably produce enough high quality food for all people on the planet with an ecological footprint as low as possible 4 What can the industry do with biomarkers? . Diagnostic tool ● What is the biological mechanism underlying a trait? . Prediction tool ● What outcome can I expect from an intervention? . Monitoring tool ● What is the actual status of a process? . Speed up your process, improve your traits Some examples * Transcriptomics * Proteomics * Metabolomics Why Biomarkers for meat quality? . Meat quality has low heritability (h2=0.1-0.2) ● Predictive capacity of genetic markers low . High environmental influence ● Feed, animal handling (stress), management (housing), ... Meat quality can only be measured after 1-several days post slaughter . Need to differentiate between retail, processing industry, restaurants, .... Biomarkers can do all that and more faster, predictive, .. Example Transcriptomics biomarkers for meat quality . Pork production chain . Biomarkers for traits . High quality fresh pork . Meat colour N production chain ● A* 14 . German Pietrain ● L* 4 (microarray) ● Reflection 10 . Verification: Danish . Drip loss 2 Yorkshire (PCR) . Ultimate pH 6 . -
Leigh Syndrome: One Disorder, More Than 75 Monogenic Causes
Title: Leigh Syndrome: One disorder, more than 75 monogenic causes Running head: Leigh Syndrome: One disorder, many genes Author list: Nicole J. Lake, MSc,1,2 Alison G. Compton, PhD,1,2 Shamima Rahman, MD, PhD,3 and David R. Thorburn, PhD1,2,4 Affiliations: From the 1Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia; 2Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia; 3Mitochondrial Research Group, Genetics and Genomic Medicine, Institute of Child Health, University College London and Metabolic Unit, Great Ormond Street Hospital, London, United Kingdom; 4Victorian Clinical Genetic Services, Royal Children's Hospital, Melbourne, Victoria, Australia. Corresponding author: Prof. David Thorburn Email [email protected] Telephone +61 3 8341 6235 Fax +61 3 8341 6212 Address Murdoch Childrens Research Institute, The Royal Children’s Hospital, 50 Flemington Rd, Parkville, Victoria, 3052, Australia Number of characters in the title and running head: 51 and 35, respectively Number of words in the abstract (107), and the body of manuscript not including abstract (4877) Number of figures (3), colour figures (1/3), and tables (3) 1 Abstract Leigh syndrome is the most common pediatric presentation of mitochondrial disease. This neurodegenerative disorder is genetically heterogeneous, and to date pathogenic mutations in more than 75 genes have been identified, encoded by two genomes (mitochondrial and nuclear). More than a third of these disease genes have been characterized in the last 5 years alone, reflecting the significant advances made in understanding its etiological basis. We review the diverse biochemical and genetic etiology of Leigh syndrome and associated clinical, neuroradiological and metabolic features that can provide clues for diagnosis. -
Supplementary Table 1
SI Table S1. Broad protein kinase selectivity for PF-2771. Kinase, PF-2771 % Inhibition at 10 μM Service Kinase, PF-2771 % Inhibition at 1 μM Service rat RPS6KA1 (RSK1) 39 Dundee AURKA (AURA) 24 Invitrogen IKBKB (IKKb) 26 Dundee CDK2 /CyclinA 21 Invitrogen mouse LCK 25 Dundee rabbit MAP2K1 (MEK1) 19 Dundee AKT1 (AKT) 21 Dundee IKBKB (IKKb) 16 Dundee CAMK1 (CaMK1a) 19 Dundee PKN2 (PRK2) 14 Dundee RPS6KA5 (MSK1) 18 Dundee MAPKAPK5 14 Dundee PRKD1 (PKD1) 13 Dundee PIM3 12 Dundee MKNK2 (MNK2) 12 Dundee PRKD1 (PKD1) 12 Dundee MARK3 10 Dundee NTRK1 (TRKA) 12 Invitrogen SRPK1 9 Dundee MAPK12 (p38g) 11 Dundee MAPKAPK5 9 Dundee MAPK8 (JNK1a) 11 Dundee MAPK13 (p38d) 8 Dundee rat PRKAA2 (AMPKa2) 11 Dundee AURKB (AURB) 5 Dundee NEK2 11 Invitrogen CSK 5 Dundee CHEK2 (CHK2) 11 Invitrogen EEF2K (EEF-2 kinase) 4 Dundee MAPK9 (JNK2) 9 Dundee PRKCA (PKCa) 4 Dundee rat RPS6KA1 (RSK1) 8 Dundee rat PRKAA2 (AMPKa2) 4 Dundee DYRK2 7 Dundee rat CSNK1D (CKId) 3 Dundee AKT1 (AKT) 7 Dundee LYN 3 BioPrint PIM2 7 Invitrogen CSNK2A1 (CKIIa) 3 Dundee MAPK15 (ERK7) 6 Dundee CAMKK2 (CAMKKB) 1 Dundee mouse LCK 5 Dundee PIM3 1 Dundee PDPK1 (PDK1) (directed 5 Invitrogen rat DYRK1A (MNB) 1 Dundee RPS6KB1 (p70S6K) 5 Dundee PBK 0 Dundee CSNK2A1 (CKIIa) 4 Dundee PIM1 -1 Dundee CAMKK2 (CAMKKB) 4 Dundee DYRK2 -2 Dundee SRC 4 Invitrogen MAPK12 (p38g) -2 Dundee MYLK2 (MLCK_sk) 3 Invitrogen NEK6 -3 Dundee MKNK2 (MNK2) 2 Dundee RPS6KB1 (p70S6K) -3 Dundee SRPK1 2 Dundee AKT2 -3 Dundee MKNK1 (MNK1) 2 Dundee RPS6KA3 (RSK2) -3 Dundee CHEK1 (CHK1) 2 Invitrogen rabbit MAP2K1 (MEK1) -4 Dundee -
Development of the Stria Vascularis and Potassium Regulation in the Human Fetal Cochlea: Insights Into Hereditary Sensorineural Hearing Loss
Development of the Stria Vascularis and Potassium Regulation in the Human Fetal Cochlea: Insights into Hereditary Sensorineural Hearing Loss Heiko Locher,1,2 John C.M.J. de Groot,2 Liesbeth van Iperen,1 Margriet A. Huisman,2 Johan H.M. Frijns,2 Susana M. Chuva de Sousa Lopes1,3 1 Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, 2333 ZA, the Netherlands 2 Department of Otorhinolaryngology and Head and Neck Surgery, Leiden University Medical Center, Leiden, 2333 ZA, the Netherlands 3 Department for Reproductive Medicine, Ghent University Hospital, 9000 Ghent, Belgium Received 25 August 2014; revised 2 February 2015; accepted 2 February 2015 ABSTRACT: Sensorineural hearing loss (SNHL) is dynamics of key potassium-regulating proteins. At W12, one of the most common congenital disorders in humans, MITF1/SOX101/KIT1 neural-crest-derived melano- afflicting one in every thousand newborns. The majority cytes migrated into the cochlea and penetrated the base- is of heritable origin and can be divided in syndromic ment membrane of the lateral wall epithelium, and nonsyndromic forms. Knowledge of the expression developing into the intermediate cells of the stria vascula- profile of affected genes in the human fetal cochlea is lim- ris. These melanocytes tightly integrated with Na1/K1- ited, and as many of the gene mutations causing SNHL ATPase-positive marginal cells, which started to express likely affect the stria vascularis or cochlear potassium KCNQ1 in their apical membrane at W16. At W18, homeostasis (both essential to hearing), a better insight KCNJ10 and gap junction proteins GJB2/CX26 and into the embryological development of this organ is GJB6/CX30 were expressed in the cells in the outer sul- needed to understand SNHL etiologies. -
Nephrotoxicity of the BRAF-Kinase Inhibitor Vemurafenib Is Driven By
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.29.428783; this version posted January 31, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Nephrotoxicity of the BRAF-kinase inhibitor Vemurafenib is driven by off-target Ferrochelatase inhibition Yuntao Bai1, Ji Young Kim1, Laura A. Jayne1, Megha Gandhi1, Kevin M. Huang1, Josie A. Silvaroli1, Veronika Sander2, Jason Prosek3, Kenar D. Jhaveri4, Sharyn D. Baker1, Alex Sparreboom1, Amandeep Bajwa5, Navjot Singh Pabla1* 1Division of Pharmaceutics and Pharmacology, College of Pharmacy & Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA. 2Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand. 3The Ohio State University Wexner Medical Center, Columbus, OH, USA. 4Division of Kidney Diseases and Hypertension, Donald and Barbara Zucker School of Medicine at Hofstra-Northwell, Northwell Health, Great Neck, New York, USA. 5Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, USA. Running Title: Off-target mechanisms associated with vemurafenib nephrotoxicity. Correspondence should be addressed to: Navjot Pabla, Division of Pharmaceutics and Pharmacology, College of Pharmacy and Cancer Center, 460 W 12th Ave, Columbus, OH 43221, USA. Phone: 614-292-1063. E-mail: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.01.29.428783; this version posted January 31, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.