Reduction of Serum Free Fatty Acids and Triglycerides by Liver-Targeted Expression of Long Chain Acyl-Coa Synthetase 3
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bioRxiv preprint doi: https://doi.org/10.1101/2020.08.17.252007; this version posted November 3, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 4.0 International license. Oxylipin metabolism is controlled by mitochondrial b-oxidation during bacterial inflammation. Mariya Misheva1, Konstantinos Kotzamanis1*, Luke C Davies1*, Victoria J Tyrrell1, Patricia R S Rodrigues1, Gloria A Benavides2, Christine Hinz1, Robert C Murphy3, Paul Kennedy4, Philip R Taylor1,5, Marcela Rosas1, Simon A Jones1, Sumukh Deshpande1, Robert Andrews1, Magdalena A Czubala1, Mark Gurney1, Maceler Aldrovandi1, Sven W Meckelmann1, Peter Ghazal1, Victor Darley-Usmar2, Daniel White1, and Valerie B O’Donnell1 1Systems Immunity Research Institute and Division of Infection and Immunity, and School of Medicine, Cardiff University, UK, 2Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA, 3Department of Pharmacology, University of Colorado Denver, Aurora, CO 80045, USA, 4Cayman Chemical 1180 E Ellsworth Rd, Ann Arbor, MI 48108, United States, 5UK Dementia Research Institute at Cardiff, Cardiff University, UK Address correspondence: Valerie O’Donnell, [email protected] or Daniel White, [email protected], Systems Immunity Research Institute, Cardiff University *Both authors contributed equally to the study 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.17.252007; this version posted November 3, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
Inborn Errors of Metabolism Test Requisition
LABORATORY OF GENETICS AND GENOMICS Mailing Address: For local courier service and/or inquiries, please contact 513-636-4474 • Fax: 513-636-4373 3333 Burnet Avenue, Room R1042 www.cincinnatichildrens.org/moleculargenetics • Email: [email protected] Cincinnati, OH 45229 INBORN ERRORS OF METABOLISM TEST REQUISITION All Information Must Be Completed Before Sample Can Be Processed PATIENT INFORMATION ETHNIC/RACIAL BACKGROUND (Choose All) Patient Name: ___________________ , ___________________ , ________ European American (White) African-American (Black) Last First MI Native American or Alaskan Asian-American Address: ____________________________________________________ Pacific Islander Ashkenazi Jewish ancestry ____________________________________________________ Latino-Hispanic _____________________________________________ Home Phone: ________________________________________________ (specify country/region of origin) MR# __________________ Date of Birth ________ / ________ / _______ Other ____________________________________________________ (specify country/region of origin) Gender: Male Female BILLING INFORMATION (Choose ONE method of payment) o REFERRING INSTITUTION o COMMERCIAL INSURANCE* Insurance can only be billed if requested at the time of service. Institution: ____________________________________________________ Policy Holder Name: _____________________________________________ Address: _____________________________________________________ Gender: ________________ Date of Birth ________ / ________ / _______ -
Loss of Fam60a, a Sin3a Subunit, Results in Embryonic Lethality and Is Associated with Aberrant Methylation at a Subset of Gene
RESEARCH ARTICLE Loss of Fam60a, a Sin3a subunit, results in embryonic lethality and is associated with aberrant methylation at a subset of gene promoters Ryo Nabeshima1,2, Osamu Nishimura3,4, Takako Maeda1, Natsumi Shimizu2, Takahiro Ide2, Kenta Yashiro1†, Yasuo Sakai1, Chikara Meno1, Mitsutaka Kadota3,4, Hidetaka Shiratori1†, Shigehiro Kuraku3,4*, Hiroshi Hamada1,2* 1Developmental Genetics Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan; 2Laboratory for Organismal Patterning, RIKEN Center for Developmental Biology, Kobe, Japan; 3Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe, Japan; 4Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan Abstract We have examined the role of Fam60a, a gene highly expressed in embryonic stem cells, in mouse development. Fam60a interacts with components of the Sin3a-Hdac transcriptional corepressor complex, and most Fam60a–/– embryos manifest hypoplasia of visceral organs and die in utero. Fam60a is recruited to the promoter regions of a subset of genes, with the expression of these genes being either up- or down-regulated in Fam60a–/– embryos. The DNA methylation level of the Fam60a target gene Adhfe1 is maintained at embryonic day (E) 7.5 but markedly reduced at –/– *For correspondence: E9.5 in Fam60a embryos, suggesting that DNA demethylation is enhanced in the mutant. [email protected] (SK); Examination of genome-wide DNA methylation identified several differentially methylated regions, [email protected] (HH) which were preferentially hypomethylated, in Fam60a–/– embryos. Our data suggest that Fam60a is †These authors contributed required for proper embryogenesis, at least in part as a result of its regulation of DNA methylation equally to this work at specific gene promoters. -
Mergeomics: Multidimensional Data Integration to Identify Pathogenic Perturbations to Biological Systems
Shu et al. BMC Genomics (2016) 17:874 DOI 10.1186/s12864-016-3198-9 METHODOLOGY ARTICLE Open Access Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems Le Shu1, Yuqi Zhao1, Zeyneb Kurt1, Sean Geoffrey Byars2,3, Taru Tukiainen4, Johannes Kettunen4, Luz D. Orozco5, Matteo Pellegrini5, Aldons J. Lusis6, Samuli Ripatti4, Bin Zhang7, Michael Inouye2,3,8, Ville-Petteri Mäkinen1,9,10,11* and Xia Yang1,12* Abstract Background: Complex diseases are characterized by multiple subtle perturbations to biological processes. New omics platforms can detect these perturbations, but translating the diverse molecular and statistical information into testable mechanistic hypotheses is challenging. Therefore, we set out to create a public tool that integrates these data across multiple datasets, platforms, study designs and species in order to detect the most promising targets for further mechanistic studies. Results: We developed Mergeomics, a computational pipeline consisting of independent modules that 1) leverage multi-omics association data to identify biological processes that are perturbed in disease, and 2) overlay the disease- associated processes onto molecular interaction networks to pinpoint hubs as potential key regulators. Unlike existing tools that are mostly dedicated to specific data type or settings, the Mergeomics pipeline accepts and integrates datasets across platforms, data types and species. We optimized and evaluated the performance of Mergeomics using simulation and multiple independent datasets, and benchmarked the results against alternative methods. We also demonstrate the versatility of Mergeomics in two case studies that include genome-wide, epigenome-wide and transcriptome-wide datasets from human and mouse studies of total cholesterol and fasting glucose. -
A Unique Retrogene Within a Gene That Has Acquired Multiple Promoters and a Specific Function in Spermatogenesis
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Developmental Biology 304 (2007) 848–859 www.elsevier.com/locate/ydbio Genomes & Developmental Control Utp14b: A unique retrogene within a gene that has acquired multiple promoters and a specific function in spermatogenesis Ming Zhao a,1, Jan Rohozinski b,1, Manju Sharma c, Jun Ju a, Robert E. Braun c, ⁎ Colin E. Bishop b,d, Marvin L. Meistrich a, a Department of Experimental Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Box 066, 1515 Holcombe Blvd, Houston, TX 77030, USA b Department of Obstetrics and Gynecology, Baylor College of Medicine, 1709 Dryden Road, Houston, TX 77030, USA c Department of Genome Sciences, University of Washington School of Medicine, Box 357730, 1705 N.E. Pacific Street, Seattle, WA 98195, USA d Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA Received for publication 28 September 2006; revised 9 December 2006; accepted 3 January 2007 Available online 9 January 2007 Abstract The mouse retrogene Utp14b is essential for male fertility, and a mutation in its sequence results in the sterile juvenile spermatogonial depletion (jsd) phenotype. It is a retrotransposed copy of the Utp14a gene, which is located on the X chromosome, and is inserted within an intron of the autosomal acyl-CoA synthetase long-chain family member 3 (Acsl3) gene. To elucidate the roles of the Utp14 genes in normal spermatogenic cell development as a basis for understanding the defects that result in the jsd phenotype, we analyzed the various mRNAs produced from the Utp14b retrogene and their expression in different cell types. -
Elucidating Biological Roles of Novel Murine Genes in Hearing Impairment in Africa
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 19 September 2019 doi:10.20944/preprints201909.0222.v1 Review Elucidating Biological Roles of Novel Murine Genes in Hearing Impairment in Africa Oluwafemi Gabriel Oluwole,1* Abdoulaye Yal 1,2, Edmond Wonkam1, Noluthando Manyisa1, Jack Morrice1, Gaston K. Mazanda1 and Ambroise Wonkam1* 1Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa. 2Department of Neurology, Point G Teaching Hospital, University of Sciences, Techniques and Technology, Bamako, Mali. *Correspondence to: [email protected]; [email protected] Abstract: The prevalence of congenital hearing impairment (HI) is highest in Africa. Estimates evaluated genetic causes to account for 31% of HI cases in Africa, but the identification of associated causative genes mutations have been challenging. In this study, we reviewed the potential roles, in humans, of 38 novel genes identified in a murine study. We gathered information from various genomic annotation databases and performed functional enrichment analysis using online resources i.e. genemania and g.proflier. Results revealed that 27/38 genes are express mostly in the brain, suggesting additional cognitive roles. Indeed, HERC1- R3250X had been associated with intellectual disability in a Moroccan family. A homozygous 216-bp deletion in KLC2 was found in two siblings of Egyptian descent with spastic paraplegia. Up to 27/38 murine genes have link to at least a disease, and the commonest mode of inheritance is autosomal recessive (n=8). Network analysis indicates that 20 other genes have intermediate and biological links to the novel genes, suggesting their possible roles in HI. -
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European Review for Medical and Pharmacological Sciences 2019; 23: 1710-1721 Next-generation sequencing identifies a homozygous mutation in ACADVL associated with pediatric familial dilated cardiomyopathy S.J. CARLUS1, I.S. ALMUZAINI2, M. KARTHIKEYAN3, L. LOGANATHAN3, G.S. AL-HARBI1, A.M. ABDALLAH4, K.M. AL-HARBI1 1Pediatrics Department, Cardiogenetics Unit, College of Medicine, Taibah University, Al-Madinah, Kingdom of Saudi Arabia 2Department of Pediatric Cardiology, Al-Madinah Maternity and Children Hospital (MMCH), Al-Madinah, Kingdom of Saudi Arabia 3Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India 4West Midlands Regional Genetics Laboratory, Birmingham Women’s NHS Foundation Trust, Birmingham, United Kingdom Abstract. – OBJECTIVE: Pediatric familial di- Key Words lated cardiomyopathy (DCM) is a rare and se- Pediatric familial dilated cardiomyopathy, Targeted vere heart disease. The genetics of familial DCM gene sequencing, ACADVL, Saudi Arabia, Consanguinity, are complex and include over 100 known dis- Molecular docking, Molecular dynamics. ease-causing genes, but many causative genes are unknown. We aimed to identify the causative gene for DCM in a consanguineous Saudi Ara- bian family with affected family members and a history of sudden death. Introduction PATIENTS AND METHODS: Affected (two chil- dren) and unaffected (one sibling and the mother) Dilated cardiomyopathy (DCM) is a heart family members were screened by next-gener- ation sequencing (NGS) for 181 candidate DCM disease characterized by ventricular dilation and genes and underwent metabolic screening. Fif- impaired myocardial contractility. DCM affects ty-seven clinically annotated controls and 46 DCM 1 in 2500 of the general population and is one of cases were then tested for the identified mutation. -
ACSL3–PAI-1 Signaling Axis Mediates Tumor-Stroma Cross-Talk Promoting Pancreatic Cancer Progression
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Bern Open Repository and Information System (BORIS) SCIENCE ADVANCES | RESEARCH ARTICLE CANCER Copyright © 2020 The Authors, some rights reserved; ACSL3–PAI-1 signaling axis mediates tumor-stroma exclusive licensee American Association cross-talk promoting pancreatic cancer progression for the Advancement Matteo Rossi Sebastiano1, Chiara Pozzato1, Maria Saliakoura1, Zhang Yang2, of Science. No claim to 2 3 1 1,4 original U.S. Government Ren-Wang Peng , Mirco Galiè , Kevin Oberson , Hans-Uwe Simon , Works. Distributed 5 1 Evanthia Karamitopoulou , Georgia Konstantinidou * under a Creative Commons Attribution Pancreatic ductal adenocarcinoma (PDAC) is characterized by marked fibrosis and low immunogenicity, features License 4.0 (CC BY). that are linked to treatment resistance and poor clinical outcomes. Therefore, understanding how PDAC regulates the desmoplastic and immune stromal components is of great clinical importance. We found that acyl-CoA synthetase long-chain 3 (ACSL3) is up-regulated in PDAC and correlates with increased fibrosis. Our in vivo results show that Acsl3 knockout hinders PDAC progression, markedly reduces tumor fibrosis and tumor-infiltrating immunosuppressive cells, and increases cytotoxic T cell infiltration. This effect is, at least in part, due to decreased plasminogen activator inhibitor–1 (PAI-1) secretion from tumor cells. Accordingly, PAI-1 expression in PDAC positively correlates with markers of fibrosis and immunosuppression and predicts poor patient survival. We found that PAI-1 pharmacological inhibition strongly enhances chemo- and immunotherapeutic response against PDAC, increasing survival of mice. Thus, our results unveil ACSL3–PAI-1 signaling as a requirement for PDAC progression with druggable attributes. -
A Metabolic Modeling Approach Reveals Promising Therapeutic Targets and Antiviral Drugs to Combat COVID-19
www.nature.com/scientificreports OPEN A metabolic modeling approach reveals promising therapeutic targets and antiviral drugs to combat COVID‑19 Fernando Santos‑Beneit 1, Vytautas Raškevičius2, Vytenis A. Skeberdis2 & Sergio Bordel 1,2* In this study we have developed a method based on Flux Balance Analysis to identify human metabolic enzymes which can be targeted for therapeutic intervention against COVID‑19. A literature search was carried out in order to identify suitable inhibitors of these enzymes, which were confrmed by docking calculations. In total, 10 targets and 12 bioactive molecules have been predicted. Among the most promising molecules we identifed Triacsin C, which inhibits ACSL3, and which has been shown to be very efective against diferent viruses, including positive‑sense single‑stranded RNA viruses. Similarly, we also identifed the drug Celgosivir, which has been successfully tested in cells infected with diferent types of viruses such as Dengue, Zika, Hepatitis C and Infuenza. Finally, other drugs targeting enzymes of lipid metabolism, carbohydrate metabolism or protein palmitoylation (such as Propylthiouracil, 2‑Bromopalmitate, Lipofermata, Tunicamycin, Benzyl Isothiocyanate, Tipifarnib and Lonafarnib) are also proposed. Te COVID-19 pandemic, caused by the virus SARS-CoV-2, has resulted in a substantial increase in mortality and serious economic and social disruption worldwide1. In this context, the rapid identifcation of therapeutic molecules against SARS-CoV-2 is essential. To this aim an extensive collaboration and teamwork among research- ers of all academic disciplines is required2. Computational methods and systems biology approaches, as the one presented here, can play a signifcant role in this process of identifcation of suitable drugs. -
The Endogenous Subcellular Localisations of the Long Chain Fatty Acid-Activating Enzymes ACSL3 and ACSL4 in Sarcoma and Breast C
Molecular and Cellular Biochemistry https://doi.org/10.1007/s11010-018-3332-x The endogenous subcellular localisations of the long chain fatty acid- activating enzymes ACSL3 and ACSL4 in sarcoma and breast cancer cells Yassmeen Radif1 · Haarith Ndiaye1 · Vasiliki Kalantzi1 · Ruth Jacobs1 · Andrew Hall2 · Shane Minogue1 · Mark G. Waugh1 Received: 18 August 2017 / Accepted: 9 February 2018 © The Author(s) 2018. This article is an open access publication Abstract Fatty acid uptake and metabolism are often dysregulated in cancer cells. Fatty acid activation is a critical step that allows these biomolecules to enter cellular metabolic pathways such as mitochondrial β-oxidation for ATP generation or the lipogenic routes that generate bioactive lipids such as the inositol phospholipids. Fatty acid activation by the addition of coenzyme A is catalysed by a family of enzymes called the acyl CoA synthetase ligases (ACSL). Furthermore, enhanced expression of particular ACSL isoforms, such as ACSL4, is a feature of some more aggressive cancers and may contribute to the oncogenic phenotype. This study focuses on ACSL3 and ACSL4, closely related structural homologues that preferentially activate palmitate and arachidonate fatty acids, respectively. In this study, immunohistochemical screening of multiple soft tissue tumour arrays revealed that ACSL3 and ACSL4 were highly, but differentially, expressed in a subset of leiomyosarcomas, fibrosarcomas and rhabdomyosarcomas, with consistent cytoplasmic and granular stainings of tumour cells. The intracellular localisations of endogenously expressed ACSL3 and ACSL4 were further investigated by detailed subcellular fractionation analyses of HT1080 fibrosarcoma and MCF-7 breast cancer cells. ACSL3 distribution closely overlapped with proteins involved in trafficking from the trans-Golgi network and endosomes. -
Joint Profiling of Chromatin Accessibility and CAR-T Integration Site Analysis at Population and Single-Cell Levels
Joint profiling of chromatin accessibility and CAR-T integration site analysis at population and single-cell levels Wenliang Wanga,b,c,d, Maria Fasolinoa,b,c,d, Benjamin Cattaua,b,c,d, Naomi Goldmana,b,c,d, Weimin Konge,f,g, Megan A. Fredericka,b,c,d, Sam J. McCrighta,b,c,d, Karun Kiania,b,c,d, Joseph A. Fraiettae,f,g,h, and Golnaz Vahedia,b,c,d,f,1 aDepartment of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104; bInstitute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104; cEpigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104; dInstitute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104; eDepartment of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104; fAbramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104; gCenter for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104; and hParker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 Edited by Anjana Rao, La Jolla Institute for Allergy and Immunology, La Jolla, CA, and approved January 30, 2020 (received for review November 3, 2019) Chimeric antigen receptor (CAR)-T immunotherapy has yielded tumor killing. To determine the extent to which these two sce- impressive results in several B cell malignancies, establishing itself narios occur in vivo, it is essential to simultaneously determine as a powerful means to redirect the natural properties of T lym- T cell fate and map where CAR-T vectors integrate into the phocytes. -
Ab118182 – Fatty Acid Oxidation Human In-Cell ELISA
ab118182 – Fatty Acid Oxidation Human In-Cell ELISA Kit (ACADVL, ACADM, HADHA) Instructions for Use For measuring in high throughput very long chain specific acyl-CoA dehydrogenase, medium-chain specific acyl-CoA dehydrogenase and long-chain 3-hydroxyl-CoA dehydrogenase This product is for research use only and is not intended for diagnostic use. 1 Table of Contents 1. Introduction 3 2. Assay Summary 6 3. Kit Contents 7 4. Storage and Handling 7 5. Additional Materials Required 8 6. Preparation of Reagents 8 7. Sample Preparation 9 8. Assay Procedure 11 9. Data Analysis 14 10. Assay Performance and Specificity 14 11. Frequently Asked Questions 18 12. Troubleshooting 21 2 1. Introduction Principle: ab118182 uses quantitative immunocytochemistry to measure protein levels or post-translational modifications in cultured cells. Cells are fixed in a microplate and targets of interest are detected with highly specific, well-characterized monoclonal antibodies, and levels are quantified with IRDye®-labeled Secondary Antibodies. IR imaging and quantitation is performed using a LI- COR® Odyssey® or Aerius® system. Background: The Fatty acid B-oxidation (FAO) pathway is a key metabolic pathway that plays an important role in energy homeostasis particularly in organs such as the liver, heart and skeletal muscle. Oxidation of fatty acids occurs inside the mitochondria where acyl-CoA esters (activated fatty acids) of various lengths are shortened into units of acetyl-CoA each time a cycle is fully completed. Each unit of acetyl-CoA is then oxidized by the mitochondria into CO 2 and H 2O via the citric acid cycle and the mitochondria respiratory chain.