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Millo T, Rivera A, Obolensky A, Marks-Ohana D, Xu M, Li Y, Wilhelm E, Gopalakrishnan P, Gross M, Rosin B, Hanany M, Webster A, Tracewska AM, Koenekoop RK, Chen R, Arno G, Schueler-Furman O, Roosing S, Banin E, Sharon D. Identification of autosomal recessive novel genes and retinal phenotypes in members of the solute carrier (SLC) superfamily. Genet Med 2022; 24:1523-1535. [PMID: 35486108 DOI: 10.1016/j.gim.2022.03.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 03/20/2022] [Accepted: 03/28/2022] [Indexed: 12/01/2022] Open
Abstract
PURPOSE This study aimed to investigate the clinical and genetic aspects of solute carrier (SLC) genes in inherited retinal diseases (IRDs). METHODS Exome sequencing data were filtered to identify pathogenic variants in SLC genes. Analysis of transcript and protein expression was performed on fibroblast cell lines and retinal sections. RESULTS Comprehensive analysis of 433 SLC genes in 913 exome sequencing IRD samples revealed homozygous pathogenic variants in 6 SLC genes, including 2 candidate novel genes, which were 2 variants in SLC66A1, causing autosomal recessive retinitis pigmentosa (ARRP), and a variant in SLC39A12, causing autosomal recessive mild widespread retinal degeneration with marked macular involvement. In addition, we present 4 families with ARRP and homozygous null variants in SLC37A3 that were previously suggested to cause retinitis pigmentosa, 2 of which cause exon skipping. The recently reported SLC4A7- c.2007dup variant was found in 2 patients with ARRP resulting in the absence of protein. Finally, variants in SLC24A1 were found in 4 individuals with either ARRP or congenital stationary night blindness. CONCLUSION We report on SLC66A1 and SLC39A12 as candidate novel IRD genes, establish SLC37A3 pathogenicity, and provide further evidence of SLC4A7 as IRD genes. We extend the phenotypic spectrum of SLC24A1 and suggest that its ARRP phenotype may be more common than previously reported.
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Affiliation(s)
- Talya Millo
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Antonio Rivera
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alexey Obolensky
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Devora Marks-Ohana
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mingchu Xu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Yumei Li
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Enosh Wilhelm
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Prakadeeswari Gopalakrishnan
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Menachem Gross
- Department of Otolaryngology/Head and Neck Surgery, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Boris Rosin
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mor Hanany
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Andrew Webster
- University College London, Institute of Ophthalmology, London, United Kingdom; Moorfields Eye Hospital, NHS Foundation Trust, London, United Kingdom
| | - Anna Maria Tracewska
- Łukasiewicz Research Network - PORT Polish Center for Technology Development, Stabłowicka, Wrocław, Poland
| | - Robert K Koenekoop
- Department of Paediatric surgery, Human Genetics and Ophthalmology, Montreal Children's Hospital, McGill University Health Centre, Montreal, Quebec, Canada
| | - Rui Chen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Gavin Arno
- University College London, Institute of Ophthalmology, London, United Kingdom; Moorfields Eye Hospital, NHS Foundation Trust, London, United Kingdom
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Israel
| | - Susanne Roosing
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Eyal Banin
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Dror Sharon
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
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Pantaleo E, Monaco A, Amoroso N, Lombardi A, Bellantuono L, Urso D, Lo Giudice C, Picardi E, Tafuri B, Nigro S, Pesole G, Tangaro S, Logroscino G, Bellotti R. A Machine Learning Approach to Parkinson’s Disease Blood Transcriptomics. Genes (Basel) 2022; 13:genes13050727. [PMID: 35627112 PMCID: PMC9141063 DOI: 10.3390/genes13050727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 12/23/2022] Open
Abstract
The increased incidence and the significant health burden associated with Parkinson’s disease (PD) have stimulated substantial research efforts towards the identification of effective treatments and diagnostic procedures. Despite technological advancements, a cure is still not available and PD is often diagnosed a long time after onset when irreversible damage has already occurred. Blood transcriptomics represents a potentially disruptive technology for the early diagnosis of PD. We used transcriptome data from the PPMI study, a large cohort study with early PD subjects and age matched controls (HC), to perform the classification of PD vs. HC in around 550 samples. Using a nested feature selection procedure based on Random Forests and XGBoost we reached an AUC of 72% and found 493 candidate genes. We further discussed the importance of the selected genes through a functional analysis based on GOs and KEGG pathways.
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Affiliation(s)
- Ester Pantaleo
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Via A. Orabona 4, 70125 Bari, Italy; (E.P.); (A.M.); (N.A.); (L.B.); (S.T.); (R.B.)
- Dipartimento di Scienze Mediche di Base, Neuroscienze e Organi di Senso, Università degli Studi di Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy;
- Dipartimento Interateneo di Fisica M. Merlin, Università degli Studi di Bari Aldo Moro, Via G. Amendola 173, 70125 Bari, Italy
| | - Alfonso Monaco
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Via A. Orabona 4, 70125 Bari, Italy; (E.P.); (A.M.); (N.A.); (L.B.); (S.T.); (R.B.)
| | - Nicola Amoroso
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Via A. Orabona 4, 70125 Bari, Italy; (E.P.); (A.M.); (N.A.); (L.B.); (S.T.); (R.B.)
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, Via A. Orabona 4, 70125 Bari, Italy
| | - Angela Lombardi
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Via A. Orabona 4, 70125 Bari, Italy; (E.P.); (A.M.); (N.A.); (L.B.); (S.T.); (R.B.)
- Dipartimento Interateneo di Fisica M. Merlin, Università degli Studi di Bari Aldo Moro, Via G. Amendola 173, 70125 Bari, Italy
- Correspondence:
| | - Loredana Bellantuono
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Via A. Orabona 4, 70125 Bari, Italy; (E.P.); (A.M.); (N.A.); (L.B.); (S.T.); (R.B.)
- Dipartimento di Scienze Mediche di Base, Neuroscienze e Organi di Senso, Università degli Studi di Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy;
| | - Daniele Urso
- Centro per le Malattie Neurodegenerative e l’Invecchiamento Cerebrale, Dipartimento di Ricerca Clinica in Neurologia, Università degli Studi di Bari Aldo Moro, Pia Fondazione Cardinale G. Panico, 73039 Tricase, Italy; (D.U.); (B.T.); (S.N.)
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, De Crespigny Park, London SE5 8AF, UK
| | - Claudio Lo Giudice
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo Moro, Via A. Orabona 4, 70125 Bari, Italy; (C.L.G.); (E.P.); (G.P.)
| | - Ernesto Picardi
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo Moro, Via A. Orabona 4, 70125 Bari, Italy; (C.L.G.); (E.P.); (G.P.)
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/O, 70126 Bari, Italy
| | - Benedetta Tafuri
- Centro per le Malattie Neurodegenerative e l’Invecchiamento Cerebrale, Dipartimento di Ricerca Clinica in Neurologia, Università degli Studi di Bari Aldo Moro, Pia Fondazione Cardinale G. Panico, 73039 Tricase, Italy; (D.U.); (B.T.); (S.N.)
| | - Salvatore Nigro
- Centro per le Malattie Neurodegenerative e l’Invecchiamento Cerebrale, Dipartimento di Ricerca Clinica in Neurologia, Università degli Studi di Bari Aldo Moro, Pia Fondazione Cardinale G. Panico, 73039 Tricase, Italy; (D.U.); (B.T.); (S.N.)
- Istituto di Nanotecnologia (NANOTEC), Consiglio Nazionale delle Ricerche, Via Monteroni, 73100 Lecce, Italy
| | - Graziano Pesole
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo Moro, Via A. Orabona 4, 70125 Bari, Italy; (C.L.G.); (E.P.); (G.P.)
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/O, 70126 Bari, Italy
| | - Sabina Tangaro
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Via A. Orabona 4, 70125 Bari, Italy; (E.P.); (A.M.); (N.A.); (L.B.); (S.T.); (R.B.)
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Via A. Orabona 4, 70125 Bari, Italy
| | - Giancarlo Logroscino
- Dipartimento di Scienze Mediche di Base, Neuroscienze e Organi di Senso, Università degli Studi di Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy;
- Centro per le Malattie Neurodegenerative e l’Invecchiamento Cerebrale, Dipartimento di Ricerca Clinica in Neurologia, Università degli Studi di Bari Aldo Moro, Pia Fondazione Cardinale G. Panico, 73039 Tricase, Italy; (D.U.); (B.T.); (S.N.)
| | - Roberto Bellotti
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Via A. Orabona 4, 70125 Bari, Italy; (E.P.); (A.M.); (N.A.); (L.B.); (S.T.); (R.B.)
- Dipartimento Interateneo di Fisica M. Merlin, Università degli Studi di Bari Aldo Moro, Via G. Amendola 173, 70125 Bari, Italy
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Markowicz-Piasecka M, Markiewicz A, Darłak P, Sikora J, Adla SK, Bagina S, Huttunen KM. Current Chemical, Biological, and Physiological Views in the Development of Successful Brain-Targeted Pharmaceutics. Neurotherapeutics 2022; 19:942-976. [PMID: 35391662 PMCID: PMC9294128 DOI: 10.1007/s13311-022-01228-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2022] [Indexed: 12/13/2022] Open
Abstract
One of the greatest challenges with successful pharmaceutical treatments of central nervous system (CNS) diseases is the delivery of drugs into their target sites with appropriate concentrations. For example, the physically tight blood-brain barrier (BBB) effectively blocks compounds from penetrating into the brain, also by the action of metabolizing enzymes and efflux transport mechanisms. However, many endogenous compounds, including both smaller compounds and macromolecules, like amino acids, sugars, vitamins, nucleosides, hormones, steroids, and electrolytes, have their peculiar internalization routes across the BBB. These delivery mechanisms, namely carrier-mediated transport and receptor-mediated transcytosis have been utilized to some extent in brain-targeted drug development. The incomplete knowledge of the BBB and the smaller than a desirable number of chemical tools have hindered the development of successful brain-targeted pharmaceutics. This review discusses the recent advancements achieved in the field from the point of medicinal chemistry view and discusses how brain drug delivery can be improved in the future.
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Affiliation(s)
- Magdalena Markowicz-Piasecka
- Laboratory of Bioanalysis, Department of Pharmaceutical Chemistry, Drug Analysis and Radiopharmacy, Medical University of Lodz, ul. Muszyńskiego1, 90-151 Lodz, Poland
| | - Agata Markiewicz
- Students Research Group, Laboratory of Bioanalysis, Department of Pharmaceutical Chemistry, Drug Analysis and Radiopharmacy, Medical University of Lodz, ul. Muszyńskiego 1, 90-151 Lodz, Poland
| | - Patrycja Darłak
- Students Research Group, Laboratory of Bioanalysis, Department of Pharmaceutical Chemistry, Drug Analysis and Radiopharmacy, Medical University of Lodz, ul. Muszyńskiego 1, 90-151 Lodz, Poland
| | - Joanna Sikora
- Department of Bioinorganic Chemistry, Medical University of Lodz, Medical University of Lodz, ul. Muszyńskiego1, 90-151 Lodz, Poland
| | - Santosh Kumar Adla
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Yliopistonranta 1C, POB 1627, 70211 Kuopio, Finland
- Institute of Organic Chemistry and Biochemistry (IOCB), Czech Academy of Sciences, Flemingovo Namesti 542/2, 160 00 Prague, Czech Republic
| | - Sreelatha Bagina
- Charles River Discovery Research Services Finland Oy, Neulaniementie 4, 70210 Kuopio, Finland
| | - Kristiina M. Huttunen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Yliopistonranta 1C, POB 1627, 70211 Kuopio, Finland
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Trujillo-Del Río C, Tortajada-Pérez J, Gómez-Escribano AP, Casterá F, Peiró C, Millán JM, Herrero MJ, Vázquez-Manrique RP. Metformin to treat Huntington disease: a pleiotropic drug against a multi-system disorder. Mech Ageing Dev 2022; 204:111670. [DOI: 10.1016/j.mad.2022.111670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 12/17/2022]
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Roblek M, Bicher J, van Gogh M, György A, Seeböck R, Szulc B, Damme M, Olczak M, Borsig L, Siekhaus DE. The Solute Carrier MFSD1 Decreases the Activation Status of β1 Integrin and Thus Tumor Metastasis. Front Oncol 2022; 12:777634. [PMID: 35211397 PMCID: PMC8861502 DOI: 10.3389/fonc.2022.777634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/13/2022] [Indexed: 11/17/2022] Open
Abstract
Solute carriers are increasingly recognized as participating in a plethora of pathologies, including cancer. We describe here the involvement of the orphan solute carrier Major Facilitator Superfamily Domain-containing protein 1 (MFSD1) in the regulation of tumor cell migration. Loss of MFSD1 enabled higher levels of metastasis in experimental and spontaneous metastasis mouse models. We identified an increased migratory potential in MFSD1−/− tumor cells which was mediated by increased focal adhesion turnover, reduced stability of mature inactive β1 integrin, and the resulting increased integrin activation index. We show that MFSD1 promoted recycling to the cell surface of endocytosed inactive β1 integrin and thereby protected β1 integrin from proteolytic degradation; this led to dampening of the integrin activation index. Furthermore, downregulation of MFSD1 expression was observed during the early steps of tumorigenesis, and higher MFSD1 expression levels correlate with a better cancer patient prognosis. In sum, we describe a requirement for endolysosomal MFSD1 in efficient β1 integrin recycling to suppress tumor cell dissemination.
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Affiliation(s)
- Marko Roblek
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Julia Bicher
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Merel van Gogh
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Attila György
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Rita Seeböck
- Institute of Clinical Pathology, University Hospital St. Polten, St. Polten, Austria
| | - Bozena Szulc
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Markus Damme
- Institute of Biochemistry, University of Kiel, Kiel, Germany
| | - Mariusz Olczak
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Lubor Borsig
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Daria E Siekhaus
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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Gyawali A, Latif S, Choi SH, Hyeon SJ, Ryu H, Kang YS. Monocarboxylate transporter functions and neuroprotective effects of valproic acid in experimental models of amyotrophic lateral sclerosis. J Biomed Sci 2022; 29:2. [PMID: 35012534 PMCID: PMC8744235 DOI: 10.1186/s12929-022-00785-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/04/2022] [Indexed: 12/11/2022] Open
Abstract
Background Amyotrophic lateral sclerosis (ALS) is a devasting neurodegenerative disorder for which no successful therapeutics are available. Valproic acid (VPA), a monocarboxylate derivative, is a known antiepileptic drug and a histone deacetylase inhibitor.
Methods To investigate whether monocarboxylate transporter 1 (MCT1) and sodium-coupled MCT1 (SMCT1) are altered in ALS cell and mouse models, a cellular uptake study, quantitative real time polymerase chain reaction and western blot parameters were used. Similarly, whether VPA provides a neuroprotective effect in the wild-type (WT; hSOD1WT) and ALS mutant-type (MT; hSOD1G93A) NSC-34 motor neuron-like cell lines was determined through the cell viability assay.
Results [3H]VPA uptake was dependent on time, pH, sodium and concentration, and the uptake rate was significantly lower in the MT cell line than the WT cell line. Interestingly, two VPA transport systems were expressed, and the VPA uptake was modulated by SMCT substrates/inhibitors in both cell lines. Furthermore, MCT1 and SMCT1 expression was significantly lower in motor neurons of ALS (G93A) model mice than in those of WT mice. Notably, VPA ameliorated glutamate- and hydrogen peroxide-induced neurotoxicity in both the WT and MT ALS cell lines. Conclusions Together, the current findings demonstrate that VPA exhibits a neuroprotective effect regardless of the dysfunction of an MCT in ALS, which could help develop useful therapeutic strategies for ALS.
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Affiliation(s)
- Asmita Gyawali
- College of Pharmacy and Drug Information Research Institute, Sookmyung Women's University, Cheongpa-ro 47-gil 100 (Cheongpa-dong 2ga), Yongsan-gu, Seoul, 04310, Republic of Korea
| | - Sana Latif
- College of Pharmacy and Drug Information Research Institute, Sookmyung Women's University, Cheongpa-ro 47-gil 100 (Cheongpa-dong 2ga), Yongsan-gu, Seoul, 04310, Republic of Korea
| | - Seung-Hye Choi
- Brain Science Institute, Korea Institute of Science and Technology, Seoul, 02792, South Korea
| | - Seung Jae Hyeon
- Brain Science Institute, Korea Institute of Science and Technology, Seoul, 02792, South Korea
| | - Hoon Ryu
- Brain Science Institute, Korea Institute of Science and Technology, Seoul, 02792, South Korea
| | - Young-Sook Kang
- College of Pharmacy and Drug Information Research Institute, Sookmyung Women's University, Cheongpa-ro 47-gil 100 (Cheongpa-dong 2ga), Yongsan-gu, Seoul, 04310, Republic of Korea.
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Catta-Preta R, Zdilar I, Jenner B, Doisy ET, Tercovich K, Nord AS, Gurkoff GG. Transcriptional Pathology Evolves over Time in Rat Hippocampus after Lateral Fluid Percussion Traumatic Brain Injury. Neurotrauma Rep 2021; 2:512-525. [PMID: 34909768 PMCID: PMC8667199 DOI: 10.1089/neur.2021.0021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Traumatic brain injury (TBI) causes acute and lasting impacts on the brain, driving pathology along anatomical, cellular, and behavioral dimensions. Rodent models offer an opportunity to study the temporal progression of disease from injury to recovery. Transcriptomic and epigenomic analysis were applied to evaluate gene expression in ipsilateral hippocampus at 1 and 14 days after sham (n = 2 and 4, respectively per time point) and moderate lateral fluid percussion injury (n = 4 per time point). This enabled the identification of dynamic changes and differential gene expression (differentially expressed genes; DEGs) modules linked to underlying epigenetic response. We observed acute signatures associated with cell death, astrocytosis, and neurotransmission that largely recovered by 2 weeks. Inflammation and immune signatures segregated into upregulated modules with distinct expression trajectories and functions. Whereas most down-regulated genes recovered by 14 days, two modules with delayed and persistent changes were associated with cholesterol metabolism, amyloid beta clearance, and neurodegeneration. Differential expression was paralleled by changes in histone H3 lysine residue 4 trimethylation at the promoters of DEGs at 1 day post-TBI, with the strongest changes observed for inflammation and immune response genes. These results demonstrate how integrated genomics analysis in the pre-clinical setting has the potential to identify stage-specific biomarkers for injury and/or recovery. Though limited in scope here, our general strategy has the potential to capture pathological signatures over time and evaluate treatment efficacy at the systems level.
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Affiliation(s)
- Rinaldo Catta-Preta
- Department of Neurobiology, Physiology, and Behavior, University of California Davis, Davis, California, USA
- Center for Neuroscience, University of California Davis, Davis, California, USA
| | - Iva Zdilar
- Department of Neurobiology, Physiology, and Behavior, University of California Davis, Davis, California, USA
- Center for Neuroscience, University of California Davis, Davis, California, USA
| | - Bradley Jenner
- Department of Neurobiology, Physiology, and Behavior, University of California Davis, Davis, California, USA
- Center for Neuroscience, University of California Davis, Davis, California, USA
| | - Emily T. Doisy
- Department of Neurological Surgery, University of California Davis, Davis, California, USA
| | - Kayleen Tercovich
- Department of Neurological Surgery, University of California Davis, Davis, California, USA
- Center for Neuroscience, University of California Davis, Davis, California, USA
| | - Alex S. Nord
- Department of Neurobiology, Physiology, and Behavior, University of California Davis, Davis, California, USA
- Center for Neuroscience, University of California Davis, Davis, California, USA
| | - Gene G. Gurkoff
- Department of Neurological Surgery, University of California Davis, Davis, California, USA
- Center for Neuroscience, University of California Davis, Davis, California, USA
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Mir A, Almudhry M, Alghamdi F, Albaradie R, Ibrahim M, Aldurayhim F, Alhedaithy A, Alamr M, Bawazir M, Mohammad S, Abdelhay S, Bashir S, Housawi Y. SLC gene mutations and pediatric neurological disorders: diverse clinical phenotypes in a Saudi Arabian population. Hum Genet 2021; 141:81-99. [PMID: 34797406 DOI: 10.1007/s00439-021-02404-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 11/12/2021] [Indexed: 12/12/2022]
Abstract
The uptake and efflux of solutes across a plasma membrane is controlled by transporters. There are two main superfamilies of transporters, adenosine 5'-triphosphate (ATP) binding cassettes (ABCs) and solute carriers (SLCs). In the brain, SLC transporters are involved in transporting various solutes across the blood-brain barrier, blood-cerebrospinal fluid barrier, astrocytes, neurons, and other brain cell types including oligodendrocytes and microglial cells. SLCs play an important role in maintaining normal brain function. Hence, mutations in the genes that encode SLC transporters can cause a variety of neurological disorders. We identified the following SLC gene variants in 25 patients in our cohort: SLC1A2, SLC2A1, SLC5A1, SLC6A3, SLC6A5, SLC6A8, SLC9A6, SLC9A9, SLC12A6, SLC13A5, SLC16A1, SLC17A5, SLC19A3, SLC25A12, SLC25A15, SLC27A4, SLC45A1, SLC46A1, and SLC52A3. Eight patients harbored pathogenic or likely pathogenic mutations (SLC5A1, SLC9A6, SLC12A6, SLC16A1, SLC19A3, and SLC52A3), and 12 patients were found to have variants of unknown clinical significance (VOUS); these variants occurred in 11 genes (SLC1A2, SLC2A1, SLC6A3, SLC6A5, SLC6A8, SLC9A6, SLC9A9, SLC13A5, SLC25A12, SLC27A4, and SLC45A1). Five patients were excluded as they were carriers. In the remaining 20 patients with SLC gene variants, we identified 16 possible distinct neurological disorders. Based on the clinical presentation, we categorized them into genes causing intellectual delay (ID) or autism spectrum disorder (ASD), those causing epilepsy, those causing vitamin-related disorders, and those causing other neurological diseases. Several variants were detected that indicated possible personalized therapies: SLC2A1 led to dystonia or epilepsy, which can be treated with a ketogenic diet; SLC6A3 led to infantile parkinsonism-dystonia 1, which can be treated with levodopa; SLC6A5 led to hyperekplexia 3, for which unnecessary treatment with antiepileptic drugs should be avoided; SLC6A8 led to creatine deficiency syndrome type 1, which can be treated with creatine monohydrate; SLC16A1 led to monocarboxylate transporter 1 deficiency, which causes seizures that should not be treated with a ketogenic diet; SLC19A3 led to biotin-thiamine-responsive basal ganglia disease, which can be treated with biotin and thiamine; and SLC52A3 led to Brown-Vialetto-Van-Laere syndrome 1, which can be treated with riboflavin. The present study examines the prevalence of SLC gene mutations in our cohort of children with epilepsy and other neurological disorders. It highlights the diverse phenotypes associated with mutations in this large family of SLC transporter proteins, and an opportunity for personalized genomics and personalized therapeutics.
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Affiliation(s)
- Ali Mir
- Department of Pediatric Neurology, Neuroscience Center, King Fahad Specialist Hospital, Ammar Bin Thabit Street, Dammam, 31444, Kingdom of Saudi Arabia.
| | - Montaha Almudhry
- Department of Pediatric Neurology, Neuroscience Center, King Fahad Specialist Hospital, Ammar Bin Thabit Street, Dammam, 31444, Kingdom of Saudi Arabia
| | - Fouad Alghamdi
- Department of Pediatric Neurology, Neuroscience Center, King Fahad Specialist Hospital, Ammar Bin Thabit Street, Dammam, 31444, Kingdom of Saudi Arabia
| | - Raidah Albaradie
- Department of Pediatric Neurology, Neuroscience Center, King Fahad Specialist Hospital, Ammar Bin Thabit Street, Dammam, 31444, Kingdom of Saudi Arabia
| | - Mona Ibrahim
- Department of Pediatric Neurology, Neuroscience Center, King Fahad Specialist Hospital, Ammar Bin Thabit Street, Dammam, 31444, Kingdom of Saudi Arabia
| | - Fatimah Aldurayhim
- Department of Pediatric Neurology, Neuroscience Center, King Fahad Specialist Hospital, Ammar Bin Thabit Street, Dammam, 31444, Kingdom of Saudi Arabia
| | - Abdullah Alhedaithy
- Department of Pediatric Neurology, Neuroscience Center, King Fahad Specialist Hospital, Ammar Bin Thabit Street, Dammam, 31444, Kingdom of Saudi Arabia
| | - Mushari Alamr
- Genetic and Metabolic Department, King Fahad Specialist Hospital, Dammam, Kingdom of Saudi Arabia
| | - Maryam Bawazir
- Genetic and Metabolic Department, King Fahad Specialist Hospital, Dammam, Kingdom of Saudi Arabia
| | - Sahar Mohammad
- Department of Pediatric, King Fahad Specialist Hospital, Dammam, Kingdom of Saudi Arabia
| | - Salma Abdelhay
- Department of Pediatric, King Fahad Specialist Hospital, Dammam, Kingdom of Saudi Arabia
| | - Shahid Bashir
- Department of Pediatric Neurology, Neuroscience Center, King Fahad Specialist Hospital, Ammar Bin Thabit Street, Dammam, 31444, Kingdom of Saudi Arabia
| | - Yousef Housawi
- Genetic and Metabolic Department, King Fahad Specialist Hospital, Dammam, Kingdom of Saudi Arabia
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Brain age estimation at tract group level and its association with daily life measures, cardiac risk factors and genetic variants. Sci Rep 2021; 11:20563. [PMID: 34663856 PMCID: PMC8523533 DOI: 10.1038/s41598-021-99153-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/14/2021] [Indexed: 11/08/2022] Open
Abstract
Brain age can be estimated using different Magnetic Resonance Imaging (MRI) modalities including diffusion MRI. Recent studies demonstrated that white matter (WM) tracts that share the same function might experience similar alterations. Therefore, in this work, we sought to investigate such issue focusing on five WM bundles holding that feature that is Association, Brainstem, Commissural, Limbic and Projection fibers, respectively. For each tract group, we estimated brain age for 15,335 healthy participants from United Kingdom Biobank relying on diffusion MRI data derived endophenotypes, Bayesian ridge regression modeling and 10 fold-cross validation. Furthermore, we estimated brain age for an Ensemble model that gathers all the considered WM bundles. Association analysis was subsequently performed between the estimated brain age delta as resulting from the six models, that is for each tract group as well as for the Ensemble model, and 38 daily life style measures, 14 cardiac risk factors and cardiovascular magnetic resonance imaging features and genetic variants. The Ensemble model that used all tracts from all fiber groups (FG) performed better than other models to estimate brain age. Limbic tracts based model reached the highest accuracy with a Mean Absolute Error (MAE) of 5.08, followed by the Commissural ([Formula: see text]), Association ([Formula: see text]), and Projection ([Formula: see text]) ones. The Brainstem tracts based model was the less accurate achieving a MAE of 5.86. Accordingly, our study suggests that the Limbic tracts experience less brain aging or allows for more accurate estimates compared to other tract groups. Moreover, the results suggest that Limbic tract leads to the largest number of significant associations with daily lifestyle factors than the other tract groups. Lastly, two SNPs were significantly (p value [Formula: see text]) associated with brain age delta in the Projection fibers. Those SNPs are mapped to HIST1H1A and SLC17A3 genes.
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60
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Valdebenito-Maturana B, Arancibia E, Riadi G, Tapia JC, Carrasco M. Locus-specific analysis of Transposable Elements during the progression of ALS in the SOD1G93A mouse model. PLoS One 2021; 16:e0258291. [PMID: 34614020 PMCID: PMC8494334 DOI: 10.1371/journal.pone.0258291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/24/2021] [Indexed: 11/19/2022] Open
Abstract
Transposable Elements (TEs) are ubiquitous genetic elements with the ability to move within a genome. TEs contribute to a large fraction of the repetitive elements of a genome, and because of their nature, they are not routinely analyzed in RNA-Seq gene expression studies. Amyotrophic Lateral Sclerosis (ALS) is a lethal neurodegenerative disease, and a well-accepted model for its study is the mouse harboring the human SOD1G93A mutant. In this model, landmark stages of the disease can be recapitulated at specific time points, making possible to understand changes in gene expression across time. While there are several works reporting TE activity in ALS models, they have not explored their activity through the disease progression. Moreover, they have done it at the expense of losing their locus of expression. Depending on their genomic location, TEs can regulate genes in cis and in trans, making locus-specific analysis of TEs of importance in order to understand their role in modulating gene expression. Particularly, the locus-specific role of TEs in ALS has not been fully elucidated. In this work, we analyzed publicly available RNA-Seq datasets of the SOD1G93A mouse model, to understand the locus-specific role of TEs. We show that TEs become up-regulated at the early stages of the disease, and via statistical associations, we speculate that they can regulate several genes, which in turn might be contributing to the genetic dysfunction observed in ALS.
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Affiliation(s)
| | - Esteban Arancibia
- Centre for Bioinformatics, Simulation and Modelling, CBSM, Department of Bioinformatics, Faculty of Engineering, University of Talca, Talca, Chile
| | - Gonzalo Riadi
- ANID – Millennium Science Initiative Program Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Centre for Bioinformatics, Simulation and Modelling, CBSM, Department of Bioinformatics, Faculty of Engineering, University of Talca, Talca, Chile
| | - Juan Carlos Tapia
- School of Medicine, Universidad de Talca, Talca, Chile
- * E-mail: (JCT); (MC)
| | - Mónica Carrasco
- School of Medicine, Universidad de Talca, Talca, Chile
- * E-mail: (JCT); (MC)
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61
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Rajendran R, Menon KN, Nair SC. Nanotechnology Approaches for Enhanced CNS Drug Delivery in the Management of Schizophrenia. Adv Pharm Bull 2021; 12:490-508. [PMID: 35935056 PMCID: PMC9348538 DOI: 10.34172/apb.2022.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 06/02/2021] [Accepted: 09/27/2021] [Indexed: 11/09/2022] Open
Abstract
Schizophrenia is a neuropsychiatric disorder mainly affecting the central nervous system, presented with auditory and visual hallucinations, delusion and withdrawal from society. Abnormal dopamine levels mainly characterise the disease; various theories of neurotransmitters explain the pathophysiology of the disease. The current therapeutic approach deals with the systemic administration of drugs other than the enteral route, altering the neurotransmitter levels within the brain and providing symptomatic relief. Fluid biomarkers help in the early detection of the disease, which would improve the therapeutic efficacy. However, the major challenge faced in CNS drug delivery is the blood-brain barrier. Nanotherapeutic approaches may overcome these limitations, which will improve safety, efficacy, and targeted drug delivery. This review article addresses the main challenges faced in CNS drug delivery and the significance of current therapeutic strategies and nanotherapeutic approaches for a better understanding and enhanced drug delivery to the brain, which improve the quality of life of schizophrenia patients.
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Affiliation(s)
| | - Krishnakumar Neelakandha Menon
- Amrita Centre for Nanosciences and Molecular Medicine, Amrita Institute of Medical Science and Research Centre, Amrita Vishwa Vidyapeetham, Kochi-682041, Kerala, India
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62
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Meng X, Yuan H, Li W, Xiong Z, Dong W, Xiao W, Zhang X. Solute carrier family 16 member 5 downregulation and its methylation might serve as a prognostic indicator of prostate cancer. IUBMB Life 2021; 73:1363-1377. [PMID: 34549875 DOI: 10.1002/iub.2560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/04/2021] [Accepted: 09/13/2021] [Indexed: 02/06/2023]
Abstract
Prostate cancer (PCa), characterized by high invasion, metastasis, and recurrence, is the most prevalent malignant tumor in men worldwide. A clear understanding of the underlying molecular mechanisms and their role during PCa tumorigenesis can help develop prognostic and targeted therapies. We analyzed datasets from public databases, including the Cancer Genome Atlas (TCGA) and Oncomine and Gene Expression Profiling Interactive Analysis for differential expression of solute carrier family 16 member 5 (SLC16A5). We further investigated its relationship with clinical stage, pathological grade, and prognosis of PCa. The promoter methylation level of SLC16A5 in PCa was also investigated by UALCAN. We also utilized datasets from UCSC Xena to explore the prognostic role of SLC16A5 methylation levels and CpG site. Correlations between SLC16A5 and immune infiltration were discovered through TIMER. We observed significantly lower levels of SLC16A5 mRNA in PCa relative to normal tissues across six datasets from Oncomine database (p < .001) and 498 cases from TCGA database (p < .0001). SLC16A5 is strongly negatively regulated by its DNA methylation, with a Spearman of -0.81 and Pearson of -0.80 (p < .001). The aberrant SLC16A5 expression resulted in a significant relationship with clinical stage, pathological grade, and lower SLC16A5 mRNA expression, and its hypermethylation was related to a poorer PCa prognosis. SLC16A5 acted as an important factor for PCa diagnosis, with an AUC of 0.9038 (95% CI: 0.8597-0.9479; p < .0001). Besides, the aberrant SLC16A5 expression revealed close correlations with multiple immune cells. Overall, these results indicate that decreased SLC16A5 expression might be a potential biomarker for determining prognosis and immune infiltration in PCa. The positive SLC16A5 modulation might be a promising therapeutic target for PCa.
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Affiliation(s)
- Xiangui Meng
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China.,Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongwei Yuan
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China.,Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weiquan Li
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China.,Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhiyong Xiong
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China.,Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Dong
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China.,Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wen Xiao
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China.,Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoping Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China.,Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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63
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Sürmen MG, Sürmen S, Cansız D, Ünal İ, Üstündağ ÜV, Alturfan AA, Emekli-Alturfan E. Quantitative phosphoproteomics to resolve the cellular responses to octanoic acid in rotenone exposed zebrafish. J Food Biochem 2021; 45:e13923. [PMID: 34494670 DOI: 10.1111/jfbc.13923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/29/2021] [Accepted: 08/20/2021] [Indexed: 01/02/2023]
Abstract
Ketosis is a potentially beneficial metabolic state for health especially in neurological conditions including Parkinson's disease (PD). Medium-chain-triglycerides (MCT) have specific metabolic properties and they are described as ketogenic even without restriction of carbohydrate. Octanoic acid (C8) is the main MCT showing this effect. Rotenone is a neurotoxin that is used to induce experimental PD model. Rotenone inhibits mitochondrial respiratory complex 1 (MRC1) and causes reactive oxygen species formation. Mass spectrometry (MS)-based phosphoproteomic methods enable discovering specific signaling events in special molecular pathways through identification and quantification of phosphoproteins. Signaling networks involved in rotenone-mediated biological processes and beneficial effects of MCTs on neurodegenerative diseases are not well understood. We aimed to gain comprehensive molecular perspective on the global phosphoproteome differences in rotenone-exposed zebrafish treated with octanoic acid. Raw files obtained from MS analysis were processed and searched against the Danio rerio protein database using SEQUEST-HT algorithm to identify and quantify phosphopeptides with 2,569 unique phosphoproteins and 4,161 unique phosphopeptides corresponding to 2005 proteins. Microtubule-associated protein (MAP) family members were significantly lower in rotenone group. Phosphoproteins involved in ion binding (calcium, magnesium, zinc ion), oxygen binding, microtubule binding, ATP- and GTP-binding were among differentially expressed 347 proteins in rotenone group and they were reversed after octanoic acid treatments. Phosphoproteins and phosphorylation sites were identified for future exploration of signaling pathways involved in rotenone toxicity. We believe our findings might help in the formulation of effective therapeutic strategies for the treatment of PD using ketogenic formulations involving MCTs. PRACTICAL APPLICATIONS: Ketosis is a potentially beneficial metabolic state for health especially in neurological conditions including Parkinson's disease (PD). Medium-chain-triglycerides (MCT) (C6-C12) have specific metabolic properties making them described as ketogenic even without restriction of carbohydrate. Octanoic acid (caprylic acid, C8) is the main MCT showing this effect. Our findings might help in the formulation of effective therapeutic strategies for the treatment of Parkinson's disease using ketogenic formulations involving Medium-chain-triglycerides.
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Affiliation(s)
- Mustafa Gani Sürmen
- Department of Molecular Medicine, Hamidiye Institute of Health Sciences, University of Health Sciences, Istanbul, Turkey
| | - Saime Sürmen
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University-Çapa, Istanbul, Turkey
| | - Derya Cansız
- Department of Biochemistry, Faculty of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - İsmail Ünal
- Department of Biochemistry, Institute of Health Sciences, Marmara University, Istanbul, Turkey
| | - Ünsal Veli Üstündağ
- Medical Biochemistry, Faculty of Medicine, Department Medipol University, Istanbul, Turkey
| | - Ahmet Ata Alturfan
- Department of Biochemistry, Faculty of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Ebru Emekli-Alturfan
- Department of Basic Medical Sciences, Faculty of Dentistry, Marmara University, Istanbul, Turkey
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64
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Minor Allele Frequencies and Molecular Pathways Differences for SNPs Associated with Amyotrophic Lateral Sclerosis in Subjects Participating in the UKBB and 1000 Genomes Project. J Clin Med 2021; 10:jcm10153394. [PMID: 34362180 PMCID: PMC8348602 DOI: 10.3390/jcm10153394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/12/2021] [Accepted: 07/28/2021] [Indexed: 12/25/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a complex disease with a late onset and is characterized by the progressive loss of muscular and respiratory functions. Although recent studies have partially elucidated ALS's mechanisms, many questions remain such as what the most important molecular pathways involved in ALS are and why there is such a large difference in ALS onset among different populations. In this study, we addressed this issue with a bioinformatics approach, using the United Kingdom Biobank (UKBB) and the European 1000 Genomes Project (1KG) in order to analyze the most ALS-representative single nucleotide polymorphisms (SNPs) that differ for minor allele frequency (MAF) between the United Kingdom population and some European populations including Finnish in Finland, Iberian population in Spain, and Tuscans in Italy. We found 84 SNPs associated with 46 genes that are involved in different pathways including: "Ca2+ activated K+ channels", "cGMP effects", "Nitric oxide stimulates guanylate cyclase", "Proton/oligopeptide cotransporters", and "Signaling by MAPK mutants". In addition, we revealed that 83% of the 84 SNPs can alter transcription factor-motives binding sites of 224 genes implicated in "Regulation of beta-cell development", "Transcription-al regulation by RUNX3", "Transcriptional regulation of pluripotent stem cells", and "FOXO-mediated transcription of cell death genes". In conclusion, the genes and pathways analyzed could explain the cause of the difference of ALS onset.
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65
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Ayala-Lopez N, Watts SW. Physiology and Pharmacology of Neurotransmitter Transporters. Compr Physiol 2021; 11:2279-2295. [PMID: 34190339 DOI: 10.1002/cphy.c200035] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Regulation of the ability of a neurotransmitter [our focus: serotonin, norepinephrine, dopamine, acetylcholine, glycine, and gamma-aminobutyric acid (GABA)] to reach its receptor targets is regulated in part by controlling the access the neurotransmitter has to receptors. Transporters, located at both the cellular plasma membrane and in subcellular vesicles, carry a myriad of responsibilities that include enabling neurotransmitter release and controlling uptake of neurotransmitter back into a cell or vesicle. Driven largely by electrochemical gradients, these transporters move neurotransmitters. The regulation of the transporters themselves through changes in expression and/or posttranslational modification allows for fine-tuning of this system. Transporters have been best recognized as targets for psychoactive stimulants and remain a mainstay target of primarily central nervous system (CNS) acting drugs for treatment of debilitating diseases such as depression and anxiety. Studies reveal, however, that transporters are found and functional in tissues outside the CNS (gastrointestinal and cardiovascular tissues, for example). The importance of neurotransmitter transporters is underscored with discoveries that dysfunction of transporters can cause life-changing disease. This article provides a high-level review of major classes of both plasma membrane transporters and vesicular transporters. © 2021 American Physiological Society. Compr Physiol 11:2279-2295, 2021.
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Affiliation(s)
- Nadia Ayala-Lopez
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Stephanie W Watts
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
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66
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Mohammadnejad A, Li W, Lund JB, Li S, Larsen MJ, Mengel-From J, Michel TM, Christiansen L, Christensen K, Hjelmborg J, Baumbach J, Tan Q. Global Gene Expression Profiling and Transcription Factor Network Analysis of Cognitive Aging in Monozygotic Twins. Front Genet 2021; 12:675587. [PMID: 34194475 PMCID: PMC8236849 DOI: 10.3389/fgene.2021.675587] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/26/2021] [Indexed: 12/15/2022] Open
Abstract
Cognitive aging is one of the major problems worldwide, especially as people get older. This study aimed to perform global gene expression profiling of cognitive function to identify associated genes and pathways and a novel transcriptional regulatory network analysis to identify important regulons. We performed single transcript analysis on 400 monozygotic twins using an assumption-free generalized correlation coefficient (GCC), linear mixed-effect model (LME) and kinship model and identified six probes (one significant at the standard FDR < 0.05 while the other results were suggestive with 0.18 ≤ FDR ≤ 0.28). We combined the GCC and linear model results to cover diverse patterns of relationships, and meaningful and novel genes like APOBEC3G, H6PD, SLC45A1, GRIN3B, and PDE4D were detected. Our exploratory study showed the downregulation of all these genes with increasing cognitive function or vice versa except the SLC45A1 gene, which was upregulated with increasing cognitive function. Linear models found only H6PD and SLC45A1, the other genes were captured by GCC. Significant functional pathways (FDR < 3.95e-10) such as focal adhesion, ribosome, cysteine and methionine metabolism, Huntington's disease, eukaryotic translation elongation, nervous system development, influenza infection, metabolism of RNA, and cell cycle were identified. A total of five regulons (FDR< 1.3e-4) were enriched in a transcriptional regulatory analysis in which CTCF and REST were activated and SP3, SRF, and XBP1 were repressed regulons. The genome-wide transcription analysis using both assumption-free GCC and linear models identified important genes and biological pathways implicated in cognitive performance, cognitive aging, and neurological diseases. Also, the regulatory network analysis revealed significant activated and repressed regulons on cognitive function.
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Affiliation(s)
- Afsaneh Mohammadnejad
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Weilong Li
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark.,Population Research Unit, Faculty of Social Sciences, University of Helsinki, Helsinki, Finland
| | - Jesper Beltoft Lund
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark.,Digital Health & Machine Learning Research Group, Hasso Plattner Institute for Digital Engineering, Potsdam, Germany
| | - Shuxia Li
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Martin J Larsen
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Jonas Mengel-From
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark.,Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Tanja Maria Michel
- Department of Psychiatry, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Psychiatry in the Region of Southern Denmark, Odense University Hospital, Odense, Denmark.,Brain Research-Inter-Disciplinary Guided Excellence, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Lene Christiansen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark.,Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Kaare Christensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark.,Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jacob Hjelmborg
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Jan Baumbach
- Computational Biomedicine, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark.,Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Qihua Tan
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark.,Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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67
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Tripathi R, Aggarwal T, Fredriksson R. SLC38A10 Transporter Plays a Role in Cell Survival Under Oxidative Stress and Glutamate Toxicity. Front Mol Biosci 2021; 8:671865. [PMID: 34026845 PMCID: PMC8133219 DOI: 10.3389/fmolb.2021.671865] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/09/2021] [Indexed: 11/13/2022] Open
Abstract
Solute carrier (SLC) transporters regulate amino acids, glucose, ions, and metabolites that flow across cell membranes. In the brain, SLCs are the key regulators of neurotransmission, in particular, the glutamate/GABA-glutamine (GGG) cycle. Genetic mutations in SLCs are associated with various neurodevelopmental and neurodegenerative diseases. In this study, we have investigated the role of SLC38A10 under acute oxidative and glutamate stress in mouse primary cortical cells from SLC38A10 knockout (KO) mice. The ER/golgi localized transporter, SLC38A10, transports glutamate, glutamine, and alanine in brain cells, and the aim of this study was to determine the possible effects of removal of SLC38A10 in primary cortical cells under glutamate and oxidative challenges. Primary cortical neuronal cultures of wild-type (WT) cell and SLC38A10 KO mice were subjected to different concentrations of glutamate and hydrogen peroxide. There was no morphological change observed between KO and WT cortical neurons in culture. Interestingly, KO cells showed significantly lower cell viability and higher cell death compared to WT cells under both glutamate and hydrogen peroxide exposure. Further, we evaluated the possible role of p53 in neuronal cell apoptosis in KO cells. We found decreased intracellular p53 protein levels under glutamate and hydrogen peroxide treatment in KO cortical cells. In contrast, caspase 3/7 activity remains unaltered under all conditions. These results demonstrate an indirect relationship between the expression of SLC38A10 and p53 and a role in the cell defense mechanism against neurotoxicity.
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Affiliation(s)
- Rekha Tripathi
- Molecular Neuropharmacology, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Tanya Aggarwal
- Molecular Neuropharmacology, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Robert Fredriksson
- Molecular Neuropharmacology, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
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68
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Wang H, Han Q, Chen Y, Hu G, Xing H. Novel insights into cytochrome P450 enzyme and solute carrier families in cadmium-induced liver injury of pigs. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 211:111910. [PMID: 33444879 DOI: 10.1016/j.ecoenv.2021.111910] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/01/2021] [Accepted: 01/05/2021] [Indexed: 06/12/2023]
Abstract
Cadmium (Cd) is a typical pollutant and carcinogen in environment. Exposure assessment of contaminants is an important component of occupational and environmental epidemiological studies. Early studies of Cd have focused on aquatic animals, chickens and rats. However, toxicological evaluation of Cd in pigs has not been reported. Therefore, twelve pigs were randomly divided into two groups (n = 6): the control group and the Cd group (Cd content: 15 ± 0.242 mg/kg feed) in this study, the experimental period was 30 d, and the toxic effects of Cd on the liver of weanling piglets were examined by antioxidant function, liver function, Cd content, histological examination and transcriptomics. The results showed that the changes of antioxidant function, liver function and Cd content were significant in the liver. Transcriptional profiling results showed that 399 differentially expressed genes (DEGs) were significantly up-regulated while 369 DEGs were remarkably down-regulated in Cd group, and which were concentrated in three ontologies: molecular function, cellular component and biological processes. Interestingly, significant changes in some genes of the cytochrome P450 enzyme (CYP450) and solute carrier (SLC) families have been observed and were consistent with qRT-PCR results. In conclusion, Cd could cause liver injury in weanling piglets and change the transcriptomic characteristics of liver. CYP450 and SLC families play an indispensable role in Cd-mediated hepatotoxicity. Importantly, changes in mRNA levels of CYP2B22, CYP7A1, CYP8B1, SLC26A8, SLC11A1, SLC27A2 and SLC22A7 induced by Cd have been reported for the first time. Our findings will provide a new insight for better assessing the mechanism of Cd toxicity to the liver.
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Affiliation(s)
- Huan Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Qi Han
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Yongjie Chen
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Guanghui Hu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, People's Republic of China.
| | - Houjuan Xing
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, People's Republic of China.
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Alvarenga AB, Oliveira HR, Chen SY, Miller SP, Marchant-Forde JN, Grigoletto L, Brito LF. A Systematic Review of Genomic Regions and Candidate Genes Underlying Behavioral Traits in Farmed Mammals and Their Link with Human Disorders. Animals (Basel) 2021; 11:ani11030715. [PMID: 33800722 PMCID: PMC7999279 DOI: 10.3390/ani11030715] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/21/2021] [Accepted: 02/27/2021] [Indexed: 12/25/2022] Open
Abstract
Simple Summary This study is a comprehensive review of genomic regions associated with animal behavior in farmed mammals (beef and dairy cattle, pigs, and sheep) which contributes to a better understanding of the biological mechanisms influencing the target indicator trait and to gene expression studies by suggesting genes likely controlling the trait, and it will be useful in optimizing genomic predictions of breeding values incorporating biological information. Behavioral mechanisms are complex traits, genetically controlled by multiple genes spread across the whole genome. The majority of the genes identified in cattle, pigs, and sheep in association with a plethora of behavioral measurements (e.g., temperament, terrain use, milking speed, tail biting, and sucking reflex) are likely controlling stimuli reception (e.g., olfactory), internal recognition of stimuli (e.g., neuroactive ligand–receptor interaction), and body response to a stimulus (e.g., blood pressure, fatty acidy metabolism, hormone signaling, and inflammatory pathways). Six genes were commonly identified between cattle and pigs. About half of the genes for behavior identified in farmed mammals were also identified in humans for behavioral, mental, and neuronal disorders. Our findings indicate that the majority of the genes identified are likely controlling animal behavioral outcomes because their biological functions as well as potentially differing allele frequencies between two breed groups (subjectively) clustered based on their temperament characteristics. Abstract The main objectives of this study were to perform a systematic review of genomic regions associated with various behavioral traits in the main farmed mammals and identify key candidate genes and potential causal mutations by contrasting the frequency of polymorphisms in cattle breeds with divergent behavioral traits (based on a subjective clustering approach). A total of 687 (cattle), 1391 (pigs), and 148 (sheep) genomic regions associated with 37 (cattle), 55 (pigs), and 22 (sheep) behavioral traits were identified in the literature. In total, 383, 317, and 15 genes overlap with genomic regions identified for cattle, pigs, and sheep, respectively. Six common genes (e.g., NR3C2, PITPNM3, RERG, SPNS3, U6, and ZFAT) were found for cattle and pigs. A combined gene-set of 634 human genes was produced through identified homologous genes. A total of 313 out of 634 genes have previously been associated with behavioral, mental, and neurologic disorders (e.g., anxiety and schizophrenia) in humans. Additionally, a total of 491 candidate genes had at least one statistically significant polymorphism (p-value < 0.05). Out of those, 110 genes were defined as having polymorphic regions differing in greater than 50% of exon regions. Therefore, conserved genomic regions controlling behavior were found across farmed mammal species and humans.
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Affiliation(s)
- Amanda B. Alvarenga
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.); (S.-Y.C.); (L.G.)
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.); (S.-Y.C.); (L.G.)
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Shi-Yi Chen
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.); (S.-Y.C.); (L.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 625014, China
| | | | - Jeremy N. Marchant-Forde
- Livestock Behavior Research Unit, United States Department of Agriculture—Agricultural Research Service (USDA–ARS), West Lafayette, IN 47907, USA;
| | - Lais Grigoletto
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.); (S.-Y.C.); (L.G.)
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga 05508, São Paulo, Brazil
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.); (S.-Y.C.); (L.G.)
- Correspondence:
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Xia C, Zhang X, Zhang Y, Li J, Xing H. Ammonia exposure causes the disruption of the solute carrier family gene network in pigs. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 210:111870. [PMID: 33440271 DOI: 10.1016/j.ecoenv.2020.111870] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/22/2020] [Accepted: 12/25/2020] [Indexed: 06/12/2023]
Abstract
Ammonia is the main harmful gas in livestock houses. However, the toxic mechanism of ammonia is still unclear. Therefore, we examined the effects of ammonia exposure on different tissues of fattening pigs by histological analysis and transcriptome techniques in this study. The results showed that there were varying degrees of pathological changes in liver, kidney, hypothalamus, jejunum, lungs, spleen, heart and trachea of fattening pigs under ammonia exposure. Notably, the extent of damage in liver, kidney, jejunum, lungs, hypothalamus and trachea was more severe than that in heart and spleen. Transcriptome results showed that ammonia exposure caused changes in 349, 335, 340, 229, 120, 578, 407 and 115 differentially expressed genes in liver, kidney, spleen, lung, trachea, hypothalamus, jejunum and heart, respectively. Interestingly, the changes in solute vector (SLC) family genes were found in all 8 tissues, and the verified gene results (SLC11A1, SLC17A7, SLC17A6, SLC6A4, SLC22A7, SLC25A3, SLC28A3, SLC7A2, SLC6A6, SLC38A5, SLC22A12, SLC34A1, SLC26A1, SLC26A6, SLC27A5, SLC22A8 and SLC44A4) were consistent with qRT-PCR results. In conclusion, ammonia exposure can cause pathological changes in many tissues and organs of fattening pigs and changes in the SCL family gene network. Importantly, the SCL family is involved in the toxic mechanism of ammonia. Our findings will provide a new insight for better assessing the mechanism of ammonia toxicity.
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Affiliation(s)
- Chunli Xia
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Xinxin Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Yu Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, People's Republic of China; Heilongjiang Agricultural and Rural Department, 4-1 Wenfu Street, Harbin 150060, People's Republic of China
| | - Jichang Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, People's Republic of China.
| | - Houjuan Xing
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, People's Republic of China.
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Bernstein HG, Keilhoff G, Dobrowolny H, Steiner J. SLC Solute Carrier Transporters and Neurodegenerative Disorders: Drawing Attention to Cationic Amino Acid Transporters 1 and 2. CLINICAL PSYCHOPHARMACOLOGY AND NEUROSCIENCE 2020; 18:467-468. [PMID: 32702228 PMCID: PMC7383006 DOI: 10.9758/cpn.2020.18.3.467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 05/07/2020] [Indexed: 01/22/2023]
Affiliation(s)
- Hans-Gert Bernstein
- Department of Psychiatry, Faculty of Medicine, Otto-von-Guericke University, Magdeburg, Germany
| | - Gerburg Keilhoff
- Institute of Biochemistry and Cell Biology, Faculty of Medicine, Otto-von-Guericke University, Magdeburg, Germany
| | - Henrik Dobrowolny
- Department of Psychiatry, Faculty of Medicine, Otto-von-Guericke University, Magdeburg, Germany
| | - Johann Steiner
- Department of Psychiatry, Faculty of Medicine, Otto-von-Guericke University, Magdeburg, Germany
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