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Balachandran S, Prada-Medina CA, Mensah MA, Glaser J, Kakar N, Nagel I, Pozojevic J, Audain E, Hitz MP, Kircher M, Sreenivasan VK, Spielmann M. STIGMA: Single-cell tissue-specific gene prioritization using machine learning. Am J Hum Genet 2024; 111:618. [PMID: 38458167 PMCID: PMC10940010 DOI: 10.1016/j.ajhg.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2024] Open
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Balachandran S, Prada-Medina CA, Mensah MA, Kakar N, Nagel I, Pozojevic J, Audain E, Hitz MP, Kircher M, Sreenivasan VKA, Spielmann M. STIGMA: Single-cell tissue-specific gene prioritization using machine learning. Am J Hum Genet 2024; 111:338-349. [PMID: 38228144 PMCID: PMC10870135 DOI: 10.1016/j.ajhg.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 01/18/2024] Open
Abstract
Clinical exome and genome sequencing have revolutionized the understanding of human disease genetics. Yet many genes remain functionally uncharacterized, complicating the establishment of causal disease links for genetic variants. While several scoring methods have been devised to prioritize these candidate genes, these methods fall short of capturing the expression heterogeneity across cell subpopulations within tissues. Here, we introduce single-cell tissue-specific gene prioritization using machine learning (STIGMA), an approach that leverages single-cell RNA-seq (scRNA-seq) data to prioritize candidate genes associated with rare congenital diseases. STIGMA prioritizes genes by learning the temporal dynamics of gene expression across cell types during healthy organogenesis. To assess the efficacy of our framework, we applied STIGMA to mouse limb and human fetal heart scRNA-seq datasets. In a cohort of individuals with congenital limb malformation, STIGMA prioritized 469 variants in 345 genes, with UBA2 as a notable example. For congenital heart defects, we detected 34 genes harboring nonsynonymous de novo variants (nsDNVs) in two or more individuals from a set of 7,958 individuals, including the ortholog of Prdm1, which is associated with hypoplastic left ventricle and hypoplastic aortic arch. Overall, our findings demonstrate that STIGMA effectively prioritizes tissue-specific candidate genes by utilizing single-cell transcriptome data. The ability to capture the heterogeneity of gene expression across cell populations makes STIGMA a powerful tool for the discovery of disease-associated genes and facilitates the identification of causal variants underlying human genetic disorders.
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Affiliation(s)
- Saranya Balachandran
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Cesar A Prada-Medina
- Human Molecular Genetics Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Martin A Mensah
- Institut für Medizinische Genetik und Humangenetik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; BIH Charité Digital Clinician Scientist Program, BIH Biomedical Innovation Academy, Anna-Louisa-Karsch-Strasse 2, 10178 Berlin, Germany; RG Development & Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Naseebullah Kakar
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany; Department of Biotechnology, BUITEMS, Quetta, Pakistan
| | - Inga Nagel
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Jelena Pozojevic
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Enrique Audain
- Institute of Medical Genetics, Carl von Ossietzky University, 26129 Oldenburg, Germany; DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck; Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, 24105 Kiel, Germany
| | - Marc-Phillip Hitz
- Institute of Medical Genetics, Carl von Ossietzky University, 26129 Oldenburg, Germany; DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck; Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, 24105 Kiel, Germany
| | - Martin Kircher
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Varun K A Sreenivasan
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany.
| | - Malte Spielmann
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany; Human Molecular Genetics Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck.
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Monfeuga T, Norlin J, Bugge A, Gaalsgaard ED, Prada-Medina CA, Latta M, Veidal SS, Petersen PS, Feigh M, Holst D. Evaluation of long acting GLP1R/GCGR agonist in a DIO and biopsy-confirmed mouse model of NASH suggest a beneficial role of GLP-1/glucagon agonism in NASH patients. Mol Metab 2024; 79:101850. [PMID: 38065435 PMCID: PMC10772820 DOI: 10.1016/j.molmet.2023.101850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/28/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
OBJECTIVE The metabolic benefits of GLP-1 receptor (GLP-1R) agonists on glycemic and weight control are well established as therapy for type 2 diabetes and obesity. Glucagon's ability to increase energy expenditure is well described, and the combination of these mechanisms-of-actions has the potential to further lower hepatic steatosis in metabolic disorders and could therefore be attractive for the treatment for non-alcoholic steatohepatitis (NASH). Here, we have investigated the effects of a dual GLP-1/glucagon receptor agonist NN1177 on hepatic steatosis, fibrosis, and inflammation in a preclinical mouse model of NASH. Having observed strong effects on body weight loss in a pilot study with NN1177, we hypothesized that direct engagement of the hepatic glucagon receptor (GCGR) would result in a superior effect on steatosis and other liver related parameters as compared to the GLP-1R agonist semaglutide at equal body weight. METHODS Male C57Bl/6 mice were fed a diet high in trans-fat, fructose, and cholesterol (Diet-Induced Obese (DIO)-NASH) for 36 weeks. Following randomization based on the degree of fibrosis at baseline, mice were treated once daily with subcutaneous administration of a vehicle or three different doses of NN1177 or semaglutide for 8 weeks. Hepatic steatosis, inflammation and fibrosis were assessed by immunohistochemistry and morphometric analyses. Plasma levels of lipids and liver enzymes were determined, and hepatic gene expression was analyzed by RNA sequencing. RESULTS NN1177 dose-dependently reduced body weight up to 22% compared to vehicle treatment. Plasma levels of ALT, a measure of liver injury, were reduced in all treatment groups with body weight loss. The dual agonist reduced hepatic steatosis to a greater extent than semaglutide at equal body weight loss, as demonstrated by three independent methods. Both the co-agonist and semaglutide significantly decreased histological markers of inflammation such as CD11b and Galectin-3, in addition to markers of hepatic stellate activation (αSMA) and fibrosis (Collagen I). Interestingly, the maximal beneficial effects on above mentioned clinically relevant endpoints of NN1177 treatment on hepatic health appear to be achieved with the middle dose tested. Administering the highest dose resulted in a further reduction of liver fat and accompanied by a massive induction in genes involved in oxidative phosphorylation and resulted in exaggerated body weight loss and a downregulation of a module of co-expressed genes involved in steroid hormone biology, bile secretion, and retinol and linoleic acid metabolism that are also downregulated due to NASH itself. CONCLUSIONS These results indicate that, in a setting of overnutrition, the liver health benefits of activating the fasting-related metabolic pathways controlled by the glucagon receptor displays a bell-shaped curve. This observation is of interest to the scientific community, due to the high number of ongoing clinical trials attempting to leverage the positive effects of glucagon biology to improve metabolic health.
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Affiliation(s)
- Thomas Monfeuga
- AI & Digital Research, Research & Early Development, Novo Nordisk Research Centre Oxford, UK
| | - Jenny Norlin
- Novo Nordisk A/S, Novo Park, DK-2750 Maaloev, Denmark
| | - Anne Bugge
- Novo Nordisk A/S, Novo Park, DK-2750 Maaloev, Denmark
| | | | - Cesar A Prada-Medina
- AI & Digital Research, Research & Early Development, Novo Nordisk Research Centre Oxford, UK
| | - Markus Latta
- Novo Nordisk A/S, Novo Park, DK-2750 Maaloev, Denmark
| | - Sanne S Veidal
- Gubra A/S, Hørsholm Kongevej 11, B, DK-2970 Hørsholm, Denmark
| | - Pia S Petersen
- Gubra A/S, Hørsholm Kongevej 11, B, DK-2970 Hørsholm, Denmark
| | - Michael Feigh
- Gubra A/S, Hørsholm Kongevej 11, B, DK-2970 Hørsholm, Denmark
| | - Dorte Holst
- Novo Nordisk A/S, Novo Park, DK-2750 Maaloev, Denmark.
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Melo US, Jatzlau J, Prada-Medina CA, Flex E, Hartmann S, Ali S, Schöpflin R, Bernardini L, Ciolfi A, Moeinzadeh MH, Klever MK, Altay A, Vallecillo-García P, Carpentieri G, Delledonne M, Ort MJ, Schwestka M, Ferrero GB, Tartaglia M, Brusco A, Gossen M, Strunk D, Geißler S, Mundlos S, Stricker S, Knaus P, Giorgio E, Spielmann M. Author Correction: Enhancer hijacking at the ARHGAP36 locus is associated with connective tissue to bone transformation. Nat Commun 2023; 14:6301. [PMID: 37813867 PMCID: PMC10562428 DOI: 10.1038/s41467-023-42123-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023] Open
Affiliation(s)
- Uirá Souto Melo
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany.
- Institute for Medical Genetics and Human Genetics, Charité University Medicine Berlin, 13353, Berlin, Germany.
| | - Jerome Jatzlau
- Freie Universität Berlin, Institute for Chemistry and Biochemistry, 14195, Berlin, Germany
| | - Cesar A Prada-Medina
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany
| | - Elisabetta Flex
- Istituto Superiore di Sanità, Department of Oncology and Molecular Medicine, 00161, Rome, Italy
| | - Sunhild Hartmann
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany
| | - Salaheddine Ali
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany
| | - Robert Schöpflin
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany
| | - Laura Bernardini
- Cytogenetics Unit, Casa Sollievo della Sofferenza Foundation, IRCCS, 71013, San Giovanni Rotondo, Foggia, Italy
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - M-Hossein Moeinzadeh
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, 14195, Berlin, Germany
| | - Marius-Konstantin Klever
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany
- Institute for Medical Genetics and Human Genetics, Charité University Medicine Berlin, 13353, Berlin, Germany
| | - Aybuge Altay
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, 14195, Berlin, Germany
| | | | - Giovanna Carpentieri
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | | | - Melanie-Jasmin Ort
- Freie Universität Berlin, Institute for Chemistry and Biochemistry, 14195, Berlin, Germany
- Julius Wolff Institute (JWI), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Marko Schwestka
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513, Teltow, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353, Berlin, Germany
| | | | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, 10126, Torino, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Torino, 10126, Italy
| | - Manfred Gossen
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513, Teltow, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353, Berlin, Germany
| | - Dirk Strunk
- Cell Therapy Institute, Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University (PMU), 5020, Salzburg, Austria
| | - Sven Geißler
- Julius Wolff Institute (JWI), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353, Berlin, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany
- Institute for Medical Genetics and Human Genetics, Charité University Medicine Berlin, 13353, Berlin, Germany
| | - Sigmar Stricker
- Freie Universität Berlin, Institute for Chemistry and Biochemistry, 14195, Berlin, Germany
| | - Petra Knaus
- Freie Universität Berlin, Institute for Chemistry and Biochemistry, 14195, Berlin, Germany
| | - Elisa Giorgio
- Department of Molecular Medicine, University of Pavia, 27100, Pavia, Italy.
- Medical Genetics Unit, IRCCS Mondino Foundation, 27100, Pavia, Italy.
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany.
- Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and University of Kiel, Lübeck, 23562, Germany.
- DZHK (German Centre for Cardiovascular Research) Germany, partner site Hamburg, Lübeck, Kiel, Lübeck, 23562, Germany.
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Melo US, Jatzlau J, Prada-Medina CA, Flex E, Hartmann S, Ali S, Schöpflin R, Bernardini L, Ciolfi A, Moeinzadeh MH, Klever MK, Altay A, Vallecillo-García P, Carpentieri G, Delledonne M, Ort MJ, Schwestka M, Ferrero GB, Tartaglia M, Brusco A, Gossen M, Strunk D, Geißler S, Mundlos S, Stricker S, Knaus P, Giorgio E, Spielmann M. Enhancer hijacking at the ARHGAP36 locus is associated with connective tissue to bone transformation. Nat Commun 2023; 14:2034. [PMID: 37041138 PMCID: PMC10090176 DOI: 10.1038/s41467-023-37585-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 03/21/2023] [Indexed: 04/13/2023] Open
Abstract
Heterotopic ossification is a disorder caused by abnormal mineralization of soft tissues in which signaling pathways such as BMP, TGFβ and WNT are known key players in driving ectopic bone formation. Identifying novel genes and pathways related to the mineralization process are important steps for future gene therapy in bone disorders. In this study, we detect an inter-chromosomal insertional duplication in a female proband disrupting a topologically associating domain and causing an ultra-rare progressive form of heterotopic ossification. This structural variant lead to enhancer hijacking and misexpression of ARHGAP36 in fibroblasts, validated here by orthogonal in vitro studies. In addition, ARHGAP36 overexpression inhibits TGFβ, and activates hedgehog signaling and genes/proteins related to extracellular matrix production. Our work on the genetic cause of this heterotopic ossification case has revealed that ARHGAP36 plays a role in bone formation and metabolism, outlining first details of this gene contributing to bone-formation and -disease.
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Affiliation(s)
- Uirá Souto Melo
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany.
- Institute for Medical Genetics and Human Genetics, Charité University Medicine Berlin, 13353, Berlin, Germany.
| | - Jerome Jatzlau
- Freie Universität Berlin, Institute for Chemistry and Biochemistry, 14195, Berlin, Germany
| | - Cesar A Prada-Medina
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany
| | - Elisabetta Flex
- Istituto Superiore di Sanità, Department of Oncology and Molecular Medicine, 00161, Rome, Italy
| | - Sunhild Hartmann
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany
| | - Salaheddine Ali
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany
| | - Robert Schöpflin
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany
| | - Laura Bernardini
- Cytogenetics Unit, Casa Sollievo della Sofferenza Foundation, IRCCS, 71013, San Giovanni Rotondo, Foggia, Italy
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - M-Hossein Moeinzadeh
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, 14195, Berlin, Germany
| | - Marius-Konstantin Klever
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany
- Institute for Medical Genetics and Human Genetics, Charité University Medicine Berlin, 13353, Berlin, Germany
| | - Aybuge Altay
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, 14195, Berlin, Germany
| | | | - Giovanna Carpentieri
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | | | - Melanie-Jasmin Ort
- Freie Universität Berlin, Institute for Chemistry and Biochemistry, 14195, Berlin, Germany
- Julius Wolff Institute (JWI), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Marko Schwestka
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513, Teltow, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353, Berlin, Germany
| | | | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, 10126, Torino, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Torino, 10126, Italy
| | - Manfred Gossen
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513, Teltow, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353, Berlin, Germany
| | - Dirk Strunk
- Cell Therapy Institute, Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University (PMU), 5020, Salzburg, Austria
| | - Sven Geißler
- Julius Wolff Institute (JWI), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353, Berlin, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany
- Institute for Medical Genetics and Human Genetics, Charité University Medicine Berlin, 13353, Berlin, Germany
| | - Sigmar Stricker
- Freie Universität Berlin, Institute for Chemistry and Biochemistry, 14195, Berlin, Germany
| | - Petra Knaus
- Freie Universität Berlin, Institute for Chemistry and Biochemistry, 14195, Berlin, Germany
| | - Elisa Giorgio
- Department of Molecular Medicine, University of Pavia, 27100, Pavia, Italy.
- Medical Genetics Unit, IRCCS Mondino Foundation, 27100, Pavia, Italy.
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, Development and Disease Group, 14195, Berlin, Germany.
- Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and University of Kiel, Lübeck, 23562, Germany.
- DZHK (German Centre for Cardiovascular Research) Germany, partner site Hamburg, Lübeck, Kiel, Lübeck, 23562, Germany.
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Boschann F, Cogulu MÖ, Pehlivan D, Balachandran S, Vallecillo-Garcia P, Grochowski CM, Hansmeier NR, Coban Akdemir ZH, Prada-Medina CA, Aykut A, Fischer-Zirnsak B, Badura S, Durmaz B, Ozkinay F, Hägerling R, Posey JE, Stricker S, Gillessen-Kaesbach G, Spielmann M, Horn D, Brockmann K, Lupski JR, Kornak U, Schmidt J. Biallelic variants in ADAMTS15 cause a novel form of distal arthrogryposis. Genet Med 2023; 25:100799. [PMID: 36853234 DOI: 10.1016/j.gim.2023.100799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Affiliation(s)
- Felix Boschann
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Muhsin Ö Cogulu
- Department of Pediatric Genetics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Saranya Balachandran
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany; Institute of Human Genetics, Kiel University, Kiel, Germany
| | | | | | - Nils R Hansmeier
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany; BIH Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Zeynep H Coban Akdemir
- Department of Epidemiology, Human Genetics and Environmental Science, UTHealth School of Public Health, The University of Texas Houston, TX
| | - Cesar A Prada-Medina
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ayca Aykut
- Department of Medical Genetics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Björn Fischer-Zirnsak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Simon Badura
- Interdisciplinary Pediatric Center for Children With Developmental Disabilities and Severe Chronic Disorders, Department of Pediatrics and Adolescent Medicine, University Medical Center Göttingen, Göttingen, Germany
| | - Burak Durmaz
- Department of Pediatric Genetics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Ferda Ozkinay
- Department of Medical Genetics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - René Hägerling
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany; BIH Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Sigmar Stricker
- Institute of Biochemistry, Freie University Berlin, Berlin, Germany
| | | | - Malte Spielmann
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany; Institute of Human Genetics, Kiel University, Kiel, Germany
| | - Denise Horn
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Knut Brockmann
- Interdisciplinary Pediatric Center for Children With Developmental Disabilities and Severe Chronic Disorders, Department of Pediatrics and Adolescent Medicine, University Medical Center Göttingen, Göttingen, Germany
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - Uwe Kornak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Julia Schmidt
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany; Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
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7
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Boschann F, Cogulu MÖ, Pehlivan D, Balachandran S, Vallecillo-Garcia P, Grochowski CM, Hansmeier NR, Coban Akdemir ZH, Prada-Medina CA, Aykut A, Fischer-Zirnsak B, Badura S, Durmaz B, Ozkinay F, Hägerling R, Posey JE, Stricker S, Gillessen-Kaesbach G, Spielmann M, Horn D, Brockmann K, Lupski JR, Kornak U, Schmidt J. Biallelic variants in ADAMTS15 cause a novel form of distal arthrogryposis. Genet Med 2022; 24:2187-2193. [PMID: 35962790 PMCID: PMC9982667 DOI: 10.1016/j.gim.2022.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 10/15/2022] Open
Abstract
PURPOSE We aimed to identify the underlying genetic cause for a novel form of distal arthrogryposis. METHODS Rare variant family-based genomics, exome sequencing, and disease-specific panel sequencing were used to detect ADAMTS15 variants in affected individuals. Adamts15 expression was analyzed at the single-cell level during murine embryogenesis. Expression patterns were characterized using in situ hybridization and RNAscope. RESULTS We identified homozygous rare variant alleles of ADAMTS15 in 5 affected individuals from 4 unrelated consanguineous families presenting with congenital flexion contractures of the interphalangeal joints and hypoplastic or absent palmar creases. Radiographic investigations showed physiological interphalangeal joint morphology. Additional features included knee, Achilles tendon, and toe contractures, spinal stiffness, scoliosis, and orthodontic abnormalities. Analysis of mouse whole-embryo single-cell sequencing data revealed a tightly regulated Adamts15 expression in the limb mesenchyme between embryonic stages E11.5 and E15.0. A perimuscular and peritendinous expression was evident in in situ hybridization in the developing mouse limb. In accordance, RNAscope analysis detected a significant coexpression with Osr1, but not with markers for skeletal muscle or joint formation. CONCLUSION In aggregate, our findings provide evidence that rare biallelic recessive trait variants in ADAMTS15 cause a novel autosomal recessive connective tissue disorder, resulting in a distal arthrogryposis syndrome.
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Affiliation(s)
- Felix Boschann
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Muhsin Ö Cogulu
- Department of Pediatric Genetics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Saranya Balachandran
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany; Institute of Human Genetics, Kiel University, Kiel, Germany
| | | | | | - Nils R Hansmeier
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany; BIH Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Zeynep H Coban Akdemir
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health, The University of Texas, Houston, TX
| | - Cesar A Prada-Medina
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ayca Aykut
- Department of Medical Genetics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Björn Fischer-Zirnsak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Simon Badura
- Interdisciplinary Pediatric Center for Children With Developmental Disabilities and Severe Chronic Disorders, Department of Pediatrics and Adolescent Medicine, University Medical Center Göttingen, Göttingen, Germany
| | - Burak Durmaz
- Department of Pediatric Genetics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Ferda Ozkinay
- Department of Medical Genetics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - René Hägerling
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany; BIH Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Sigmar Stricker
- Institute of Biochemistry, Freie University Berlin, Berlin, Germany
| | | | - Malte Spielmann
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany; Institute of Human Genetics, Kiel University, Kiel, Germany
| | - Denise Horn
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Knut Brockmann
- Interdisciplinary Pediatric Center for Children With Developmental Disabilities and Severe Chronic Disorders, Department of Pediatrics and Adolescent Medicine, University Medical Center Göttingen, Göttingen, Germany
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - Uwe Kornak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany.
| | - Julia Schmidt
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany; Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
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8
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Ringel AR, Szabo Q, Chiariello AM, Chudzik K, Schöpflin R, Rothe P, Mattei AL, Zehnder T, Harnett D, Laupert V, Bianco S, Hetzel S, Glaser J, Phan MHQ, Schindler M, Ibrahim DM, Paliou C, Esposito A, Prada-Medina CA, Haas SA, Giere P, Vingron M, Wittler L, Meissner A, Nicodemi M, Cavalli G, Bantignies F, Mundlos S, Robson MI. Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes. Cell 2022; 185:3689-3704.e21. [PMID: 36179666 PMCID: PMC9567273 DOI: 10.1016/j.cell.2022.09.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 06/03/2022] [Accepted: 08/30/2022] [Indexed: 01/26/2023]
Abstract
Regulatory landscapes drive complex developmental gene expression, but it remains unclear how their integrity is maintained when incorporating novel genes and functions during evolution. Here, we investigated how a placental mammal-specific gene, Zfp42, emerged in an ancient vertebrate topologically associated domain (TAD) without adopting or disrupting the conserved expression of its gene, Fat1. In ESCs, physical TAD partitioning separates Zfp42 and Fat1 with distinct local enhancers that drive their independent expression. This separation is driven by chromatin activity and not CTCF/cohesin. In contrast, in embryonic limbs, inactive Zfp42 shares Fat1's intact TAD without responding to active Fat1 enhancers. However, neither Fat1 enhancer-incompatibility nor nuclear envelope-attachment account for Zfp42's unresponsiveness. Rather, Zfp42's promoter is rendered inert to enhancers by context-dependent DNA methylation. Thus, diverse mechanisms enabled the integration of independent Zfp42 regulation in the Fat1 locus. Critically, such regulatory complexity appears common in evolution as, genome wide, most TADs contain multiple independently expressed genes.
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Affiliation(s)
- Alessa R Ringel
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Quentin Szabo
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Andrea M Chiariello
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Konrad Chudzik
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Robert Schöpflin
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Patricia Rothe
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexandra L Mattei
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Tobias Zehnder
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Dermot Harnett
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Verena Laupert
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Simona Bianco
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Sara Hetzel
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Juliane Glaser
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Mai H Q Phan
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Magdalena Schindler
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Daniel M Ibrahim
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany; Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Christina Paliou
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - Andrea Esposito
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Cesar A Prada-Medina
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Stefan A Haas
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Peter Giere
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lars Wittler
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexander Meissner
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Giacomo Cavalli
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Frédéric Bantignies
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany; Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany.
| | - Michael I Robson
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany; Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
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9
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Smajić S, Prada-Medina CA, Landoulsi Z, Ghelfi J, Delcambre S, Dietrich C, Jarazo J, Henck J, Balachandran S, Pachchek S, Morris CM, Antony P, Timmermann B, Sauer S, Pereira SL, Schwamborn JC, May P, Grünewald A, Spielmann M. Single-cell sequencing of human midbrain reveals glial activation and a Parkinson-specific neuronal state. Brain 2022; 145:964-978. [PMID: 34919646 PMCID: PMC9050543 DOI: 10.1093/brain/awab446] [Citation(s) in RCA: 145] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/21/2021] [Accepted: 11/18/2021] [Indexed: 11/29/2022] Open
Abstract
Idiopathic Parkinson's disease is characterized by a progressive loss of dopaminergic neurons, but the exact disease aetiology remains largely unknown. To date, Parkinson's disease research has mainly focused on nigral dopaminergic neurons, although recent studies suggest disease-related changes also in non-neuronal cells and in midbrain regions beyond the substantia nigra. While there is some evidence for glial involvement in Parkinson's disease, the molecular mechanisms remain poorly understood. The aim of this study was to characterize the contribution of all cell types of the midbrain to Parkinson's disease pathology by single-nuclei RNA sequencing and to assess the cell type-specific risk for Parkinson's disease using the latest genome-wide association study. We profiled >41 000 single-nuclei transcriptomes of post-mortem midbrain from six idiopathic Parkinson's disease patients and five age-/sex-matched controls. To validate our findings in a spatial context, we utilized immunolabelling of the same tissues. Moreover, we analysed Parkinson's disease-associated risk enrichment in genes with cell type-specific expression patterns. We discovered a neuronal cell cluster characterized by CADPS2 overexpression and low TH levels, which was exclusively present in idiopathic Parkinson's disease midbrains. Validation analyses in laser-microdissected neurons suggest that this cluster represents dysfunctional dopaminergic neurons. With regard to glial cells, we observed an increase in nigral microglia in Parkinson's disease patients. Moreover, nigral idiopathic Parkinson's disease microglia were more amoeboid, indicating an activated state. We also discovered a reduction in idiopathic Parkinson's disease oligodendrocyte numbers with the remaining cells being characterized by a stress-induced upregulation of S100B. Parkinson's disease risk variants were associated with glia- and neuron-specific gene expression patterns in idiopathic Parkinson's disease cases. Furthermore, astrocytes and microglia presented idiopathic Parkinson's disease-specific cell proliferation and dysregulation of genes related to unfolded protein response and cytokine signalling. While reactive patient astrocytes showed CD44 overexpression, idiopathic Parkinson's disease microglia revealed a pro-inflammatory trajectory characterized by elevated levels of IL1B, GPNMB and HSP90AA1. Taken together, we generated the first single-nuclei RNA sequencing dataset from the idiopathic Parkinson's disease midbrain, which highlights a disease-specific neuronal cell cluster as well as 'pan-glial' activation as a central mechanism in the pathology of the movement disorder. This finding warrants further research into inflammatory signalling and immunomodulatory treatments in Parkinson's disease.
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Affiliation(s)
- Semra Smajić
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | | | - Zied Landoulsi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Jenny Ghelfi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Sylvie Delcambre
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Carola Dietrich
- Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
| | - Javier Jarazo
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
- OrganoTherapeutics SARL-S, L-4362 Esch-sur-Alzette, Luxembourg
| | - Jana Henck
- Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
| | | | - Sinthuja Pachchek
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Christopher M. Morris
- Newcastle Brain Tissue Resource, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, NE1 7RU Newcastle upon Tyne, UK
| | - Paul Antony
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
| | - Sascha Sauer
- Max-Delbrück-Centrum für Molekulare Medizin, Genomics Group, D-13125 Berlin, Germany
| | - Sandro L. Pereira
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Jens C. Schwamborn
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
- OrganoTherapeutics SARL-S, L-4362 Esch-sur-Alzette, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Anne Grünewald
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
- Institute of Neurogenetics, University of Lübeck, D-23562 Lübeck, Germany
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
- Institute of Human Genetics, Kiel University, D-42118 Kiel, Germany
- Institute of Human Genetics, University of Lübeck, D-23562 Lübeck, Germany
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10
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Wasner K, Smajic S, Ghelfi J, Delcambre S, Prada-Medina CA, Knappe E, Arena G, Mulica P, Agyeah G, Rakovic A, Boussaad I, Badanjak K, Ohnmacht J, Gérardy JJ, Takanashi M, Trinh J, Mittelbronn M, Hattori N, Klein C, Antony P, Seibler P, Spielmann M, Pereira SL, Grünewald A. Parkin Deficiency Impairs Mitochondrial DNA Dynamics and Propagates Inflammation. Mov Disord 2022; 37:1405-1415. [PMID: 35460111 DOI: 10.1002/mds.29025] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/07/2022] [Accepted: 03/27/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Mutations in the E3 ubiquitin ligase parkin cause autosomal recessive Parkinson's disease (PD). Together with PTEN-induced kinase 1 (PINK1), parkin regulates the clearance of dysfunctional mitochondria. New mitochondria are generated through an interplay of nuclear- and mitochondrial-encoded proteins, and recent studies suggest that parkin influences this process at both levels. In addition, parkin was shown to prevent mitochondrial membrane permeability, impeding mitochondrial DNA (mtDNA) escape and subsequent neuroinflammation. However, parkin's regulatory roles independent of mitophagy are not well described in patient-derived neurons. OBJECTIVES We sought to investigate parkin's role in preventing neuronal mtDNA dyshomeostasis, release, and glial activation at the endogenous level. METHODS We generated induced pluripotent stem cell (iPSC)-derived midbrain neurons from PD patients with parkin (PRKN) mutations and healthy controls. Live-cell imaging, proteomic, mtDNA integrity, and gene expression analyses were employed to investigate mitochondrial biogenesis and genome maintenance. To assess neuroinflammation, we performed single-nuclei RNA sequencing in postmortem tissue and quantified interleukin expression in mtDNA/lipopolysaccharides (LPS)-treated iPSC-derived neuron-microglia co-cultures. RESULTS Neurons from patients with PRKN mutations revealed deficits in the mitochondrial biogenesis pathway, resulting in mtDNA dyshomeostasis. Moreover, the energy sensor sirtuin 1, which controls mitochondrial biogenesis and clearance, was downregulated in parkin-deficient cells. Linking mtDNA disintegration to neuroinflammation, in postmortem midbrain with PRKN mutations, we confirmed mtDNA dyshomeostasis and detected an upregulation of microglia overexpressing proinflammatory cytokines. Finally, parkin-deficient neuron-microglia co-cultures elicited an enhanced immune response when exposed to mtDNA/LPS. CONCLUSIONS Our findings suggest that parkin coregulates mitophagy, mitochondrial biogenesis, and mtDNA maintenance pathways, thereby protecting midbrain neurons from neuroinflammation and degeneration. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Kobi Wasner
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette
| | - Semra Smajic
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette
| | - Jenny Ghelfi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette
| | - Sylvie Delcambre
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette
| | | | - Evelyn Knappe
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Giuseppe Arena
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette
| | - Patrycja Mulica
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette
| | - Gideon Agyeah
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette
| | | | - Ibrahim Boussaad
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette.,Disease Modeling and Screening Platform, Luxembourg Centre of Systems Biomedicine, University of Luxembourg & Luxembourg Institute of Health, Luxembourg
| | - Katja Badanjak
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette
| | - Jochen Ohnmacht
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette.,Department of Life Science and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jean-Jacques Gérardy
- National Center of Pathology, Laboratoire National de Santé, Dudelange, Luxembourg
| | | | - Joanne Trinh
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Michel Mittelbronn
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette.,National Center of Pathology, Laboratoire National de Santé, Dudelange, Luxembourg.,Luxembourg Center of Neuropathology, Dudelange, Luxembourg.,Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | | | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Paul Antony
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette.,Disease Modeling and Screening Platform, Luxembourg Centre of Systems Biomedicine, University of Luxembourg & Luxembourg Institute of Health, Luxembourg
| | - Philip Seibler
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Sandro L Pereira
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette.,Department of Neurology, Juntendo University, Tokyo, Japan
| | - Anne Grünewald
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette.,Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
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11
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Allou L, Balzano S, Magg A, Quinodoz M, Royer-Bertrand B, Schöpflin R, Chan WL, Speck-Martins CE, Carvalho DR, Farage L, Lourenço CM, Albuquerque R, Rajagopal S, Nampoothiri S, Campos-Xavier B, Chiesa C, Niel-Bütschi F, Wittler L, Timmermann B, Spielmann M, Robson MI, Ringel A, Heinrich V, Cova G, Andrey G, Prada-Medina CA, Pescini-Gobert R, Unger S, Bonafé L, Grote P, Rivolta C, Mundlos S, Superti-Furga A. Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator. Nature 2021; 592:93-98. [DOI: 10.1038/s41586-021-03208-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 01/07/2021] [Indexed: 11/09/2022]
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12
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Prada-Medina CA, Fukutani KF, Pavan Kumar N, Gil-Santana L, Babu S, Lichtenstein F, West K, Sivakumar S, Menon PA, Viswanathan V, Andrade BB, Nakaya HI, Kornfeld H. Systems Immunology of Diabetes-Tuberculosis Comorbidity Reveals Signatures of Disease Complications. Sci Rep 2017; 7:1999. [PMID: 28515464 PMCID: PMC5435727 DOI: 10.1038/s41598-017-01767-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 04/10/2017] [Indexed: 12/13/2022] Open
Abstract
Comorbid diabetes mellitus (DM) increases tuberculosis (TB) risk and adverse outcomes but the pathological interactions between DM and TB remain incompletely understood. We performed an integrative analysis of whole blood gene expression and plasma analytes, comparing South Indian TB patients with and without DM to diabetic and non-diabetic controls without TB. Luminex assay of plasma cytokines and growth factors delineated a distinct biosignature in comorbid TBDM in this cohort. Transcriptional profiling revealed elements in common with published TB signatures from cohorts that excluded DM. Neutrophil count correlated with the molecular degree of perturbation, especially in TBDM patients. Body mass index and HDL cholesterol were negatively correlated with molecular degree of perturbation. Diabetic complication pathways including several pathways linked to epigenetic reprogramming were activated in TBDM above levels observed with DM alone. Our data provide a rationale for trials of host-directed therapies in TBDM, targeting neutrophilic inflammation and diabetic complication pathways to address the greater morbidity and mortality associated with this increasingly prevalent dual burden of communicable and non-communicable diseases.
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Affiliation(s)
- Cesar A Prada-Medina
- Department of Pathophysiology and Toxicology, School of Pharmaceutical Sciences, University of São Paulo, 05508, São Paulo, Brazil
| | - Kiyoshi F Fukutani
- Laboratório de Imunoparasitologia, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Nathella Pavan Kumar
- National Institutes of Health- NIRT - International Center for Excellence in Research, Chennai, India
| | - Leonardo Gil-Santana
- Unidade de Medicina Investigativa, Laboratório Integrado de Microbiologia e Imunorregulação, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil.,Multinational Organization Network Sponsoring Translational and Epidemiological Research, Instituto Brasileiro para a Investigação da Tuberculose, Fundação José Silveira, Salvador, Brazil.,Curso de Medicina, Faculdade de Tecnologia e Ciências, Salvador, Brazil
| | - Subash Babu
- National Institutes of Health- NIRT - International Center for Excellence in Research, Chennai, India
| | - Flávio Lichtenstein
- Department of Pathophysiology and Toxicology, School of Pharmaceutical Sciences, University of São Paulo, 05508, São Paulo, Brazil
| | - Kim West
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | | | - Pradeep A Menon
- National Institute for Research in Tuberculosis, Chennai, India
| | | | - Bruno B Andrade
- Unidade de Medicina Investigativa, Laboratório Integrado de Microbiologia e Imunorregulação, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil.,Multinational Organization Network Sponsoring Translational and Epidemiological Research, Instituto Brasileiro para a Investigação da Tuberculose, Fundação José Silveira, Salvador, Brazil.,Curso de Medicina, Faculdade de Tecnologia e Ciências, Salvador, Brazil.,Universidade Salvador (UNIFACS), Laureate Universities, Salvador, Brazil.,Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, USA
| | - Helder I Nakaya
- Department of Pathophysiology and Toxicology, School of Pharmaceutical Sciences, University of São Paulo, 05508, São Paulo, Brazil.
| | - Hardy Kornfeld
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America.
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