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Gierten J, Welz B, Fitzgerald T, Thumberger T, Hummel O, Leger A, Weber P, Hassel D, Hübner N, Birney E, Wittbrodt J. Natural genetic variation quantitatively regulates heart rate and dimension. bioRxiv 2023:2023.09.01.555906. [PMID: 37693611 PMCID: PMC10491305 DOI: 10.1101/2023.09.01.555906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The polygenic contribution to heart development and function along the health-disease continuum remains unresolved. To gain insight into the genetic basis of quantitative cardiac phenotypes, we utilize highly inbred Japanese rice fish models, Oryzias latipes, and Oryzias sakaizumii. Employing automated quantification of embryonic heart rates as core metric, we profiled phenotype variability across five inbred strains. We observed maximal phenotypic contrast between individuals of the HO5 and the HdrR strain. HO5 showed elevated heart rates associated with embryonic ventricular hypoplasia and impaired adult cardiac function. This contrast served as the basis for genome-wide mapping. In a segregation population of 1192 HO5 x HdrR F2 embryos, we mapped 59 loci (173 genes) associated with heart rate. Experimental validation of the top 12 candidate genes in loss-of-function models revealed their causal and distinct impact on heart rate, development, ventricle size, and arrhythmia. Our study uncovers new diagnostic and therapeutic targets for developmental and electrophysiological cardiac diseases and provides a novel scalable approach to investigate the intricate genetic architecture of the vertebrate heart.
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Affiliation(s)
- Jakob Gierten
- Centre for Organismal Studies (COS), Heidelberg University; Heidelberg, 69120, Germany
- Department of Pediatric Cardiology, Heidelberg University Hospital; Heidelberg, 69120, Germany
- German Centre for Cardiovascular Research (DZHK); Partner Site Heidelberg/Mannheim, Germany
| | - Bettina Welz
- Centre for Organismal Studies (COS), Heidelberg University; Heidelberg, 69120, Germany
- German Centre for Cardiovascular Research (DZHK); Partner Site Heidelberg/Mannheim, Germany
- Heidelberg Biosciences International Graduate School (HBIGS), Heidelberg University; Heidelberg, 69120, Germany
| | - Tomas Fitzgerald
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI); Cambridge, CB10 1SD, UK
| | - Thomas Thumberger
- Centre for Organismal Studies (COS), Heidelberg University; Heidelberg, 69120, Germany
| | - Oliver Hummel
- Max Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC); Berlin, 13125, Germany
| | - Adrien Leger
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI); Cambridge, CB10 1SD, UK
| | - Philipp Weber
- Department of Cardiology, Heidelberg University Hospital; Heidelberg, 69120, Germany
| | - David Hassel
- German Centre for Cardiovascular Research (DZHK); Partner Site Heidelberg/Mannheim, Germany
- Department of Cardiology, Heidelberg University Hospital; Heidelberg, 69120, Germany
| | - Norbert Hübner
- Max Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC); Berlin, 13125, Germany
- Charité-Universitätsmedizin Berlin; Berlin, 10117, Germany
- German Centre for Cardiovascular Research (DZHK); Partner Site Berlin, Germany
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI); Cambridge, CB10 1SD, UK
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS), Heidelberg University; Heidelberg, 69120, Germany
- German Centre for Cardiovascular Research (DZHK); Partner Site Heidelberg/Mannheim, Germany
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Tan H, Gerchen MF, Bach P, Lee AM, Hummel O, Sommer W, Kirsch P, Kiefer F, Vollstädt-Klein S. Decoding fMRI alcohol cue reactivity and its association with drinking behaviour. BMJ Ment Health 2023; 26:e300639. [PMID: 36822819 PMCID: PMC10035780 DOI: 10.1136/bmjment-2022-300639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/10/2023] [Indexed: 02/25/2023]
Abstract
BACKGROUND Cue reactivity, the enhanced sensitivity to conditioned cues, is associated with habitual and compulsive alcohol consumption. However, most previous studies in alcohol use disorder (AUD) compared brain activity between alcohol and neutral conditions, solely as cue-triggered neural reactivity. OBJECTIVE This study aims to find the neural subprocesses during the processing of visual alcohol cues in AUD individuals, and how these neural patterns are predictive for relapse. METHODS Using cue reactivity and rating tasks, we separately modelled the patterns decoding the processes of visual object recognition and reward appraisal of alcohol cues with representational similarity analysis, and compared the decoding involvements (ie, distance between neural responses and hypothesised decoding models) between AUD and healthy individuals. We further explored connectivity between the identified neural systems and the whole brain and predicted relapse within 6 months using decoding involvements of the neural patterns. FINDINGS AUD individuals, compared with healthy individuals, showed higher involvement of motor-related brain regions in decoding visual features, and their reward, habit and executive networks were more engaged in appraising reward values. Connectivity analyses showed the involved neural systems were widely connected with higher cognitive networks during alcohol cue processing in AUD individuals, and decoding involvements of frontal eye fields and dorsolateral prefrontal cortex could contribute to relapse prediction. CONCLUSIONS These findings provide insight into how AUD individuals differently decode alcohol cues compared with healthy participants, from the componential processes of visual object recognition and reward appraisal. CLINICAL IMPLICATIONS The identified patterns are suggested as biomarkers and potential therapeutic targets in AUD.
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Affiliation(s)
- Haoye Tan
- Department of Addictive Behaviour and Addiction Medicine, Central Institute of Mental Health, Medical Faculty of Mannheim, Heidelberg University, Mannheim, Germany
| | - Martin Fungisai Gerchen
- Department of Clinical Psychology, Central Institute of Mental Health, Medical Faculty of Mannheim, Heidelberg University, Mannheim, Germany
- Bernstein Center for Computational Neuroscience Heidelberg/Mannheim, Mannheim, Germany
- Department of Psychology, Heidelberg University, Heidelberg, Germany
| | - Patrick Bach
- Department of Addictive Behaviour and Addiction Medicine, Central Institute of Mental Health, Medical Faculty of Mannheim, Heidelberg University, Mannheim, Germany
| | - Alycia M Lee
- Department of Addictive Behaviour and Addiction Medicine, Central Institute of Mental Health, Medical Faculty of Mannheim, Heidelberg University, Mannheim, Germany
| | - Oliver Hummel
- Faculty of Computer Science, Hochschule Mannheim, Mannheim, Germany
| | - Wolfgang Sommer
- Department of Addictive Behaviour and Addiction Medicine, Central Institute of Mental Health, Medical Faculty of Mannheim, Heidelberg University, Mannheim, Germany
- Institute of Psychopharmacology, Central Institute of Mental Health, Heidelberg University, Mannheim, Germany
- Bethanian Hospital for Psychiatry, Psychosomatics and Psychotherapy, Greifswald, Germany
| | - Peter Kirsch
- Department of Clinical Psychology, Central Institute of Mental Health, Medical Faculty of Mannheim, Heidelberg University, Mannheim, Germany
- Bernstein Center for Computational Neuroscience Heidelberg/Mannheim, Mannheim, Germany
- Department of Psychology, Heidelberg University, Heidelberg, Germany
| | - Falk Kiefer
- Department of Addictive Behaviour and Addiction Medicine, Central Institute of Mental Health, Medical Faculty of Mannheim, Heidelberg University, Mannheim, Germany
- Mannheim Center for Translational Neurosciences (MCTN), Medical Faculty of Mannheim, Heidelberg University, Mannheim, Germany
- Feuerlein Center on Translational Addiction Medicine, Heidelberg University, Heidelberg, Germany
| | - Sabine Vollstädt-Klein
- Department of Addictive Behaviour and Addiction Medicine, Central Institute of Mental Health, Medical Faculty of Mannheim, Heidelberg University, Mannheim, Germany
- Mannheim Center for Translational Neurosciences (MCTN), Medical Faculty of Mannheim, Heidelberg University, Mannheim, Germany
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Aoki M, Gamayun I, Wyatt A, Grünewald R, Simon-Thomas M, Philipp SE, Hummel O, Wagenpfeil S, Kattler K, Gasparoni G, Walter J, Qiao S, Grattan DR, Boehm U. Prolactin-sensitive olfactory sensory neurons regulate male preference in female mice by modulating responses to chemosensory cues. Sci Adv 2021; 7:eabg4074. [PMID: 34623921 PMCID: PMC8500514 DOI: 10.1126/sciadv.abg4074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 08/19/2021] [Indexed: 06/10/2023]
Abstract
Chemosensory cues detected in the nose need to be integrated with the hormonal status to trigger appropriate behaviors, but the neural circuits linking the olfactory and the endocrine system are insufficiently understood. Here, we characterize olfactory sensory neurons in the murine nose that respond to the pituitary hormone prolactin. Deletion of prolactin receptor in these cells results in impaired detection of social odors and blunts male preference in females. The prolactin-responsive olfactory sensory neurons exhibit a distinctive projection pattern to the brain that is similar across different individuals and express a limited subset of chemosensory receptors. Prolactin modulates the responses within these neurons to discrete chemosensory cues contained in male urine, providing a mechanism by which the hormonal status can be directly linked with distinct olfactory cues to generate appropriate behavioral responses.
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Affiliation(s)
- Mari Aoki
- Department of Pharmacology, Center for Molecular Signaling (PZMS), Saarland University School of Medicine, Homburg, Germany
| | - Igor Gamayun
- Department of Pharmacology, Center for Molecular Signaling (PZMS), Saarland University School of Medicine, Homburg, Germany
| | - Amanda Wyatt
- Department of Pharmacology, Center for Molecular Signaling (PZMS), Saarland University School of Medicine, Homburg, Germany
| | - Ramona Grünewald
- Department of Pharmacology, Center for Molecular Signaling (PZMS), Saarland University School of Medicine, Homburg, Germany
| | - Martin Simon-Thomas
- Department of Pharmacology, Center for Molecular Signaling (PZMS), Saarland University School of Medicine, Homburg, Germany
| | - Stephan E. Philipp
- Department of Pharmacology, Center for Molecular Signaling (PZMS), Saarland University School of Medicine, Homburg, Germany
| | - Oliver Hummel
- Faculty of Computer Science, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Stefan Wagenpfeil
- Institute for Medical Biometry, Epidemiology and Medical Informatics, Saarland University School of Medicine, Homburg, Germany
| | - Kathrin Kattler
- Department of Genetics, Saarland University, Saarbrücken, Germany
| | - Gilles Gasparoni
- Department of Genetics, Saarland University, Saarbrücken, Germany
| | - Jörn Walter
- Department of Genetics, Saarland University, Saarbrücken, Germany
| | - Sen Qiao
- Department of Pharmacology, Center for Molecular Signaling (PZMS), Saarland University School of Medicine, Homburg, Germany
| | - David R. Grattan
- Centre for Neuroendocrinology and Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Ulrich Boehm
- Department of Pharmacology, Center for Molecular Signaling (PZMS), Saarland University School of Medicine, Homburg, Germany
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Witte F, Ruiz-Orera J, Mattioli CC, Blachut S, Adami E, Schulz JF, Schneider-Lunitz V, Hummel O, Patone G, Mücke MB, Šilhavý J, Heinig M, Bottolo L, Sanchis D, Vingron M, Chekulaeva M, Pravenec M, Hubner N, van Heesch S. A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion. Genome Biol 2021; 22:191. [PMID: 34183069 PMCID: PMC8240307 DOI: 10.1186/s13059-021-02397-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 07/17/2020] [Accepted: 06/02/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Little is known about the impact of trans-acting genetic variation on the rates with which proteins are synthesized by ribosomes. Here, we investigate the influence of such distant genetic loci on the efficiency of mRNA translation and define their contribution to the development of complex disease phenotypes within a panel of rat recombinant inbred lines. RESULTS We identify several tissue-specific master regulatory hotspots that each control the translation rates of multiple proteins. One of these loci is restricted to hypertrophic hearts, where it drives a translatome-wide and protein length-dependent change in translational efficiency, altering the stoichiometric translation rates of sarcomere proteins. Mechanistic dissection of this locus across multiple congenic lines points to a translation machinery defect, characterized by marked differences in polysome profiles and misregulation of the small nucleolar RNA SNORA48. Strikingly, from yeast to humans, we observe reproducible protein length-dependent shifts in translational efficiency as a conserved hallmark of translation machinery mutants, including those that cause ribosomopathies. Depending on the factor mutated, a pre-existing negative correlation between protein length and translation rates could either be enhanced or reduced, which we propose to result from mRNA-specific imbalances in canonical translation initiation and reinitiation rates. CONCLUSIONS We show that distant genetic control of mRNA translation is abundant in mammalian tissues, exemplified by a single genomic locus that triggers a translation-driven molecular mechanism. Our work illustrates the complexity through which genetic variation can drive phenotypic variability between individuals and thereby contribute to complex disease.
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Affiliation(s)
- Franziska Witte
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- Present Address: NUVISAN ICB GmbH, Lead Discovery-Structrual Biology, 13353, Berlin, Germany
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Camilla Ciolli Mattioli
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany
- Present Address: Department of Biological Regulation, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Susanne Blachut
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Eleonora Adami
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- Present Address: Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
| | - Jana Felicitas Schulz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Valentin Schneider-Lunitz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Oliver Hummel
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Michael Benedikt Mücke
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347, Berlin, Germany
- Charité-Universitätsmedizin, 10117, Berlin, Germany
| | - Jan Šilhavý
- Institute of Physiology of the Czech Academy of Sciences, 4, 142 20, Praha, Czech Republic
| | - Matthias Heinig
- Institute of Computational Biology (ICB), HMGU, Ingolstaedter Landstr. 1, 85764 Neuherberg, Munich, Germany
- Department of Informatics, Technische Universitaet Muenchen (TUM), Boltzmannstr. 3, 85748 Garching, Munich, Germany
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- The Alan Turing Institute, London, NW1 2DB, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Daniel Sanchis
- Institut de Recerca Biomedica de Lleida (IRBLLEIDA), Universitat de Lleida, Edifici Biomedicina-I. Av. Rovira Roure, 80, 25198, Lleida, Spain
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Marina Chekulaeva
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany
| | - Michal Pravenec
- Institute of Physiology of the Czech Academy of Sciences, 4, 142 20, Praha, Czech Republic
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347, Berlin, Germany.
- Charité-Universitätsmedizin, 10117, Berlin, Germany.
| | - Sebastiaan van Heesch
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany.
- Present Address: The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
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Su X, Feng Y, Rahman SA, Wu S, Li G, Rüschendorf F, Zhao L, Cui H, Liang J, Fang L, Hu H, Froehler S, Yu Y, Patone G, Hummel O, Chen Q, Raile K, Luft FC, Bähring S, Hussain K, Chen W, Zhang J, Gong M. Phosphatidylinositol 4-kinase β mutations cause nonsyndromic sensorineural deafness and inner ear malformation. J Genet Genomics 2020; 47:618-626. [PMID: 33358777 DOI: 10.1016/j.jgg.2020.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 03/05/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 10/23/2022]
Abstract
Congenital hearing loss is a common disorder worldwide. Heterogeneous gene variation accounts for approximately 20-25% of such patients. We investigated a five-generation Chinese family with autosomal-dominant nonsyndromic sensorineural hearing loss (SNHL). No wave was detected in the pure-tone audiometry, and the auditory brainstem response was absent in all patients. Computed tomography of the patients, as well as of two sporadic SNHL cases, showed bilateral inner ear anomaly, cochlear maldevelopment, absence of the osseous spiral lamina, and an enlarged vestibular aqueduct. Such findings were absent in nonaffected persons. We used linkage analysis and exome sequencing and uncovered a heterozygous missense mutation in the PI4KB gene (p.Gln121Arg) encoding phosphatidylinositol 4-kinase β (PI4KB) from the patients in this family. In addition, 3 missense PI4KB (p.Val434Gly, p.Glu667Lys, and p.Met739Arg) mutations were identified in five patients with nonsyndromic SNHL from 57 sporadic cases. No such mutations were present within 600 Chinese controls, the 1000 genome project, gnomAD, or similar databases. Depleting pi4kb mRNA expression in zebrafish caused inner ear abnormalities and audiosensory impairment, mimicking the patient phenotypes. Moreover, overexpression of 4 human missense PI4KB mutant mRNAs in zebrafish embryos resulted in impaired hearing function, suggesting dominant-negative effects. Taken together, our results reveal that PI4KB mutations can cause SNHL and inner ear malformation. PI4KB should be included in neonatal deafness screening.
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Affiliation(s)
- Xiulan Su
- Clinical Medicine Research Center, Affiliated Hospital of Inner Mongolia Medical University, Huhhot, 010050, China
| | - Yufei Feng
- Affiliated Hospital of Guangdong Medical University & Key Laboratory of Zebrafish Model for Development and Disease of Guangdong Medical University, Zhanjiang, 524001, China; Marine Medical Research Institute of Guangdong Zhanjiang, Zhanjiang, 524023, China
| | - Sofia A Rahman
- Genomic Medicine Programme, UCL Institute of Child Health and Great Ormond Street Hospital for Children, 30 Guilford Street, London, WC1N 1EH, UK
| | - Shuilong Wu
- Affiliated Hospital of Guangdong Medical University & Key Laboratory of Zebrafish Model for Development and Disease of Guangdong Medical University, Zhanjiang, 524001, China; Marine Medical Research Institute of Guangdong Zhanjiang, Zhanjiang, 524023, China
| | - Guoan Li
- Affiliated Hospital of Guangdong Medical University & Key Laboratory of Zebrafish Model for Development and Disease of Guangdong Medical University, Zhanjiang, 524001, China; Marine Medical Research Institute of Guangdong Zhanjiang, Zhanjiang, 524023, China
| | - Franz Rüschendorf
- Max-Delbrueck-Center for Molecular Medicine (MDC), Robert-Roessle-Str.10, Berlin, 13125, Germany
| | - Lei Zhao
- Department of Radiology, Affiliated Hospital of Inner Mongolia Medical University, Huhhot, 010050, China
| | - Hongwei Cui
- Clinical Medicine Research Center, Affiliated Hospital of Inner Mongolia Medical University, Huhhot, 010050, China
| | - Junqing Liang
- Affiliated People Hospital of Inner Mongolia Medical University, Huhhot, 010050, China
| | - Liang Fang
- Max-Delbrueck-Center for Molecular Medicine (MDC), Robert-Roessle-Str.10, Berlin, 13125, Germany; Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Hao Hu
- Guangzhou Women and Children's Medical Center, Guangzhou, 510623, China
| | - Sebastian Froehler
- Max-Delbrueck-Center for Molecular Medicine (MDC), Robert-Roessle-Str.10, Berlin, 13125, Germany
| | - Yong Yu
- Max-Delbrueck-Center for Molecular Medicine (MDC), Robert-Roessle-Str.10, Berlin, 13125, Germany
| | - Giannino Patone
- Max-Delbrueck-Center for Molecular Medicine (MDC), Robert-Roessle-Str.10, Berlin, 13125, Germany
| | - Oliver Hummel
- Max-Delbrueck-Center for Molecular Medicine (MDC), Robert-Roessle-Str.10, Berlin, 13125, Germany
| | - Qinghua Chen
- Department of Radiology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
| | - Klemens Raile
- Experimental and Clinical Research Center (ECRC), A Joint Cooperation Between the Charité Medical Faculty and the Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Lindenberger Weg.80, Berlin, 13125, Germany
| | - Friedrich C Luft
- Experimental and Clinical Research Center (ECRC), A Joint Cooperation Between the Charité Medical Faculty and the Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Lindenberger Weg.80, Berlin, 13125, Germany
| | - Sylvia Bähring
- Experimental and Clinical Research Center (ECRC), A Joint Cooperation Between the Charité Medical Faculty and the Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Lindenberger Weg.80, Berlin, 13125, Germany
| | - Khalid Hussain
- Department of Paediatric Medicine Division of Endocrinology, Sidra Medical & Research Center, OPC, Doha, C6-337, Qatar
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China; Medi-X Institute, SUSTec Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jingjing Zhang
- Affiliated Hospital of Guangdong Medical University & Key Laboratory of Zebrafish Model for Development and Disease of Guangdong Medical University, Zhanjiang, 524001, China; Marine Medical Research Institute of Guangdong Zhanjiang, Zhanjiang, 524023, China.
| | - Maolian Gong
- Experimental and Clinical Research Center (ECRC), A Joint Cooperation Between the Charité Medical Faculty and the Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Lindenberger Weg.80, Berlin, 13125, Germany.
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Kim HG, Rosenfeld JA, Scott DA, Bénédicte G, Labonne JD, Brown J, McGuire M, Mahida S, Naidu S, Gutierrez J, Lesca G, des Portes V, Bruel AL, Sorlin A, Xia F, Capri Y, Muller E, McKnight D, Torti E, Rüschendorf F, Hummel O, Islam Z, Kolatkar PR, Layman LC, Ryu D, Kong IK, Madan-Khetarpal S, Kim CH. Disruption of PHF21A causes syndromic intellectual disability with craniofacial anomalies, epilepsy, hypotonia, and neurobehavioral problems including autism. Mol Autism 2019; 10:35. [PMID: 31649809 PMCID: PMC6805429 DOI: 10.1186/s13229-019-0286-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/01/2019] [Indexed: 02/02/2023] Open
Abstract
Background PHF21A has been associated with intellectual disability and craniofacial anomalies based on its deletion in the Potocki-Shaffer syndrome region at 11p11.2 and its disruption in three patients with balanced translocations. In addition, three patients with de novo truncating mutations in PHF21A were reported recently. Here, we analyze genomic data from seven unrelated individuals with mutations in PHF21A and provide detailed clinical descriptions, further expanding the phenotype associated with PHF21A haploinsufficiency. Methods Diagnostic trio whole exome sequencing, Sanger sequencing, use of GeneMatcher, targeted gene panel sequencing, and MiSeq sequencing techniques were used to identify and confirm variants. RT-qPCR was used to measure the normal expression pattern of PHF21A in multiple human tissues including 13 different brain tissues. Protein-DNA modeling was performed to substantiate the pathogenicity of the missense mutation. Results We have identified seven heterozygous coding mutations, among which six are de novo (not maternal in one). Mutations include four frameshifts, one nonsense mutation in two patients, and one heterozygous missense mutation in the AT Hook domain, predicted to be deleterious and likely to cause loss of PHF21A function. We also found a new C-terminal domain composed of an intrinsically disordered region. This domain is truncated in six patients and thus likely to play an important role in the function of PHF21A, suggesting that haploinsufficiency is the likely underlying mechanism in the phenotype of seven patients. Our results extend the phenotypic spectrum of PHF21A mutations by adding autism spectrum disorder, epilepsy, hypotonia, and neurobehavioral problems. Furthermore, PHF21A is highly expressed in the human fetal brain, which is consistent with the neurodevelopmental phenotype. Conclusion Deleterious nonsense, frameshift, and missense mutations disrupting the AT Hook domain and/or an intrinsically disordered region in PHF21A were found to be associated with autism spectrum disorder, epilepsy, hypotonia, neurobehavioral problems, tapering fingers, clinodactyly, and syndactyly, in addition to intellectual disability and craniofacial anomalies. This suggests that PHF21A is involved in autism spectrum disorder and intellectual disability, and its haploinsufficiency causes a diverse neurological phenotype. Electronic supplementary material The online version of this article (10.1186/s13229-019-0286-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hyung-Goo Kim
- 1Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Jill A Rosenfeld
- 2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Daryl A Scott
- 2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA.,3Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX USA
| | - Gerard Bénédicte
- 4Laboratoires de Diagnostic Génétique, Unité de génétique moléculaire, Nouvel Hôpital Civil, Strasbourg Cedex, France
| | - Jonathan D Labonne
- 5Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA USA
| | - Jason Brown
- 5Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA USA
| | | | | | | | - Jacqueline Gutierrez
- 3Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX USA
| | - Gaetan Lesca
- 8Department of Medical Genetics, Lyon University Hospital, Lyon, France
| | - Vincent des Portes
- 9Department of Pediatric Neurology, Lyon University Hospital, Lyon, France
| | - Ange-Line Bruel
- 10Équipe Génétique des Anomalies du Développement (GAD), INSERM, Dijon, France
| | - Arthur Sorlin
- Centre de Génétique, CHU Dijon Bourgogne, Dijon, France
| | - Fan Xia
- 2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Yline Capri
- Service de Génétique Clinique, CHU Robert Debré, Paris, France
| | - Eric Muller
- 13Clinical Genetics, Stanford Children's Health at CPMC, San Francisco, CA USA
| | | | | | | | - Oliver Hummel
- 15Max Delbrück Center (MDC) for Molecular Medicine, Berlin, Germany
| | - Zeyaul Islam
- 16Diabetes Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Prasanna R Kolatkar
- 16Diabetes Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Lawrence C Layman
- 5Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA USA.,17Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, GA USA
| | - Duchwan Ryu
- 18Department of Statistics and Actuarial Science, Northern Illinois University, DeKalb, IL USA
| | - Il-Keun Kong
- 19Department of Animal Science, Division of Applied Life Science (BK21plus), Gyeongsang National University, Jinju, Korea
| | | | - Cheol-Hee Kim
- 21Department of Biology, Chungnam National University, Daejeon, Korea
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7
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Coan PM, Hummel O, Garcia Diaz A, Barrier M, Alfazema N, Norsworthy PJ, Pravenec M, Petretto E, Hübner N, Aitman TJ. Genetic, physiological and comparative genomic studies of hypertension and insulin resistance in the spontaneously hypertensive rat. Dis Model Mech 2017; 10:297-306. [PMID: 28130354 PMCID: PMC5374317 DOI: 10.1242/dmm.026716] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 01/23/2017] [Indexed: 12/18/2022] Open
Abstract
We previously mapped hypertension-related insulin resistance quantitative trait loci (QTLs) to rat chromosomes 4, 12 and 16 using adipocytes from F2 crosses between spontaneously hypertensive (SHR) and Wistar Kyoto (WKY) rats, and subsequently identified Cd36 as the gene underlying the chromosome 4 locus. The identity of the chromosome 12 and 16 genes remains unknown. To identify whole-body phenotypes associated with the chromosome 12 and 16 linkage regions, we generated and characterised new congenic strains, with WKY donor segments introgressed onto an SHR genetic background, for the chromosome 12 and 16 linkage regions. We found a >50% increase in insulin sensitivity in both the chromosome 12 and 16 strains. Blood pressure and left ventricular mass were reduced in the two congenic strains consistent with the congenic segments harbouring SHR genes for insulin resistance, hypertension and cardiac hypertrophy. Integrated genomic analysis, using physiological and whole-genome sequence data across 42 rat strains, identified variants within the congenic regions in Upk3bl, RGD1565131 and AABR06087018.1 that were associated with blood pressure, cardiac mass and insulin sensitivity. Quantitative trait transcript analysis across 29 recombinant inbred strains showed correlation between expression of Hspb1, Zkscan5 and Pdgfrl with adipocyte volume, systolic blood pressure and cardiac mass, respectively. Comparative genome analysis showed a marked enrichment of orthologues for human GWAS-associated genes for insulin resistance within the syntenic regions of both the chromosome 12 and 16 congenic intervals. Our study defines whole-body phenotypes associated with the SHR chromosome 12 and 16 insulin-resistance QTLs, identifies candidate genes for these SHR QTLs and finds human orthologues of rat genes in these regions that associate with related human traits. Further study of these genes in the congenic strains will lead to robust identification of the underlying genes and cellular mechanisms. Summary: Comparative genome analyses identify candidate genes for hypertension and insulin resistance on rat chromosomes 12 and 16, and marked enrichment of insulin resistance genes in the syntenic regions of the human genome.
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Affiliation(s)
- Philip M Coan
- Centre for Genomic and Experimental Medicine & Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Oliver Hummel
- Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Ana Garcia Diaz
- Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Marjorie Barrier
- Centre for Genomic and Experimental Medicine & Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Neza Alfazema
- Centre for Genomic and Experimental Medicine & Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Penny J Norsworthy
- MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK
| | - Michal Pravenec
- Department of Model Diseases, Institute of Physiology, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Enrico Petretto
- MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK.,Duke-NUS Medical School, Singapore 169857, Republic of Singapore
| | - Norbert Hübner
- Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, 13316 Berlin, Germany.,Charité-Universitätsmedizin, 10117 Berlin, Germany
| | - Timothy J Aitman
- Centre for Genomic and Experimental Medicine & Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH4 2XU, UK.,Department of Medicine, Imperial College London, London SW7 2AZ, UK
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8
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Rubattu S, Di Castro S, Schulz H, Geurts AM, Cotugno M, Bianchi F, Maatz H, Hummel O, Falak S, Stanzione R, Marchitti S, Scarpino S, Giusti B, Kura A, Gensini GF, Peyvandi F, Mannucci PM, Rasura M, Sciarretta S, Dwinell MR, Hubner N, Volpe M. Ndufc2 Gene Inhibition Is Associated With Mitochondrial Dysfunction and Increased Stroke Susceptibility in an Animal Model of Complex Human Disease. J Am Heart Assoc 2016; 5:JAHA.115.002701. [PMID: 26888427 PMCID: PMC4802485 DOI: 10.1161/jaha.115.002701] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Background The genetic basis of stroke susceptibility remains to be elucidated. STR1 quantitative trait locus (STR1/QTL) was identified on rat chromosome 1 of stroke‐prone spontaneously hypertensive rat (SHRSP) upon Japanese‐style stroke‐permissive diet (JD), and it contributes to 20% of the stroke phenotype variance. Methods and Results Nine hundred eighty‐six probe sets mapping on STR1 were selected from the Rat RAE230A array and screened through a microarray differential expression analysis in brains of SHRSP and stroke‐resistant SHR (SHRSR) fed with either regular diet or JD. The gene encoding Ndufc2 (NADH dehydrogenase [ubiquinone] 1 subunit), mapping 8 Mb apart from STR1/QTL Lod score peak, was found significantly down‐regulated under JD in SHRSP compared to SHRSR. Ndufc2 disruption altered complex I assembly and activity, reduced mitochondrial membrane potential and ATP levels, and increased reactive oxygen species production and inflammation both in vitro and in vivo. SHRSR carrying heterozygous Ndufc2 deletion showed renal abnormalities and stroke occurrence under JD, similarly to SHRSP. In humans, T allele variant at NDUFC2/rs11237379 was associated with significant reduction in gene expression and with increased occurrence of early‐onset ischemic stroke by recessive mode of transmission (odds ratio [OR], 1.39; CI, 1.07–1.80; P=0.012). Subjects carrying TT/rs11237379 and A allele variant at NDUFC2/rs641836 had further increased risk of stroke (OR=1.56; CI, 1.14–2.13; P=0.006). Conclusions A significant reduction of Ndufc2 expression causes complex I dysfunction and contributes to stroke susceptibility in SHRSP. Moreover, our current evidence may suggest that Ndufc2 can contribute to an increased occurrence of early‐onset ischemic stroke in humans.
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Affiliation(s)
- Speranza Rubattu
- IRCCS Neuromed, Pozzilli (Isernia), Italy Department of Clinical and Molecular Medicine, School of Medicine and Psychology, Sapienza University of Rome, Ospedale S. Andrea, Rome, Italy
| | | | | | - Aron M Geurts
- Department of Physiology and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI
| | | | | | | | | | | | | | | | - Stefania Scarpino
- Department of Cytology and Histology, School of Medicine and Psychology, University Sapienza of Rome, Ospedale S. Andrea, Rome, Itlay
| | - Betti Giusti
- Department of Experimental and Clinical Medicine, University of Florence, Italy Atherothrombotic Disease Center, AOU Careggi, Florence, Italy
| | - Ada Kura
- Department of Experimental and Clinical Medicine, University of Florence, Italy Atherothrombotic Disease Center, AOU Careggi, Florence, Italy
| | - Gian Franco Gensini
- Department of Experimental and Clinical Medicine, University of Florence, Italy Department of Cardiothoracovascular Medicine, AOU Careggi, Florence, Italy Don Carlo Gnocchi Foundation, Florence, Italy
| | - Flora Peyvandi
- IRCCS Ca' Granda Maggiore Policlinico Hospital Foundation, Milan, Italy
| | | | - Maurizia Rasura
- Stroke Unit, School of Medicine and Psychology, Sapienza University of Rome, Ospedale S. Andrea, Rome, Italy
| | - Sebastiano Sciarretta
- IRCCS Neuromed, Pozzilli (Isernia), Italy Department of Medical-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
| | - Melinda R Dwinell
- Department of Physiology and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI
| | | | - Massimo Volpe
- IRCCS Neuromed, Pozzilli (Isernia), Italy Department of Clinical and Molecular Medicine, School of Medicine and Psychology, Sapienza University of Rome, Ospedale S. Andrea, Rome, Italy
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9
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Rintisch C, Heinig M, Bauerfeind A, Schafer S, Mieth C, Patone G, Hummel O, Chen W, Cook S, Cuppen E, Colomé-Tatché M, Johannes F, Jansen RC, Neil H, Werner M, Pravenec M, Vingron M, Hubner N. Natural variation of histone modification and its impact on gene expression in the rat genome. Genome Res 2014; 24:942-53. [PMID: 24793478 PMCID: PMC4032858 DOI: 10.1101/gr.169029.113] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [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] [Indexed: 11/25/2022]
Abstract
Histone modifications are epigenetic marks that play fundamental roles in many biological processes including the control of chromatin-mediated regulation of gene expression. Little is known about interindividual variability of histone modification levels across the genome and to what extent they are influenced by genetic variation. We annotated the rat genome with histone modification maps, identified differences in histone trimethyl-lysine levels among strains, and described their underlying genetic basis at the genome-wide scale using ChIP-seq in heart and liver tissues in a panel of rat recombinant inbred and their progenitor strains. We identified extensive variation of histone methylation levels among individuals and mapped hundreds of underlying cis- and trans-acting loci throughout the genome that regulate histone methylation levels in an allele-specific manner. Interestingly, most histone methylation level variation was trans-linked and the most prominent QTL identified influenced H3K4me3 levels at 899 putative promoters throughout the genome in the heart. Cis- acting variation was enriched in binding sites of distinct transcription factors in heart and liver. The integrated analysis of DNA variation together with histone methylation and gene expression levels showed that histoneQTLs are an important predictor of gene expression and that a joint analysis significantly enhanced the prediction of gene expression traits (eQTLs). Our data suggest that genetic variation has a widespread impact on histone trimethylation marks that may help to uncover novel genotype-phenotype relationships.
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Affiliation(s)
- Carola Rintisch
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Matthias Heinig
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany; Department of Computational Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Anja Bauerfeind
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Sebastian Schafer
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Christin Mieth
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Giannino Patone
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Oliver Hummel
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Wei Chen
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Stuart Cook
- National Heart and Lung Institute, Cardiovascular Genetics and Genomics, London, SW3 6NP, United Kingdom; Duke-NUS Graduate Medical School, 169857 Singapore; National Heart Center Singapore, 169609 Singapore
| | - Edwin Cuppen
- Center for Molecular Medicine, University Medical Center Utrecht, Hubrecht Institute KNAW, 3584 CT Utrecht, The Netherlands
| | - Maria Colomé-Tatché
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, NL-9713 AV Groningen, The Netherlands
| | - Frank Johannes
- Groningen Bioinformatics Centre (GBIC), Groningen Biomolecular Sciences and Biotechnology Institute (GBB), 9747AG Groningen, The Netherlands
| | - Ritsert C Jansen
- Groningen Bioinformatics Centre (GBIC), Groningen Biomolecular Sciences and Biotechnology Institute (GBB), 9747AG Groningen, The Netherlands
| | - Helen Neil
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), iBiTec-S, Université Paris-Sud, CNRS FRE3377, F-91191 Gif-sur-Yvette cedex, France
| | - Michel Werner
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), iBiTec-S, Université Paris-Sud, CNRS FRE3377, F-91191 Gif-sur-Yvette cedex, France
| | - Michal Pravenec
- Institut of Physiology, Academy of Sciences of the Czech Republic, Videnska 1083, CZ-14220 Prague 4, Czech Republic
| | - Martin Vingron
- Department of Computational Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Norbert Hubner
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner site Berlin, 13125 Berlin, Germany
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10
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Falak S, Schafer S, Baud A, Hummel O, Schulz H, Gauguier D, Hubner N, Osborne-Pellegrin M. Protease inhibitor 15, a candidate gene for abdominal aortic internal elastic lamina ruptures in the rat. Physiol Genomics 2014; 46:418-28. [PMID: 24790086 PMCID: PMC4060037 DOI: 10.1152/physiolgenomics.00004.2014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The inbred Brown Norway (BN) rat develops spontaneous ruptures of the internal elastic lamina (RIEL) of the abdominal aorta (AA) and iliac arteries. Prior studies with crosses of the BN/Orl RJ (susceptible) and LOU/M (resistant) showed the presence of a significant QTL on chromosome 5 and the production of congenic rats proved the involvement of this locus. In this study, we further dissected the above-mentioned QTL by creating a new panel of LOU.BN(chr5) congenic and subcongenic lines and reduced the locus to 5.2 Mb. Then we studied 1,002 heterogeneous stock (HS) rats, whose phenotyping revealed a low prevalence and high variability for RIEL. High-resolution mapping in the HS panel detected the major locus on chromosome 5 (log P > 35) and refined it to 1.4 Mb. Subsequently, RNA-seq analysis on AA of BN, congenics, and LOU revealed expression differences for only protease inhibitor 15 (Pi15) gene and a putative long intergenic noncoding RNA (lincRNA) within the linkage region. The high abundance of lincRNA with respect to reduced Pi15 expression, in conjunction with exertion of longitudinal strain, may be related to RIEL, indicating the potential importance of proteases in biological processes related to defective aortic internal elastic lamina structure. Similar mechanisms may be involved in aneurysm initiation in the human AA.
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Affiliation(s)
- Samreen Falak
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | - Amelie Baud
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Oliver Hummel
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Herbert Schulz
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Dominique Gauguier
- Institute of Cardiometabolism and Nutrition, University Pierre & Marie Curie, Hospital Pitié Salpetrière, Paris, France; and
| | - Norbert Hubner
- Max Delbrück Center for Molecular Medicine, Berlin, Germany;
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11
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Aksoy I, Giudice V, Delahaye E, Wianny F, Aubry M, Mure M, Chen J, Jauch R, Bogu GK, Nolden T, Himmelbauer H, Xavier Doss M, Sachinidis A, Schulz H, Hummel O, Martinelli P, Hübner N, Stanton LW, Real FX, Bourillot PY, Savatier P. Klf4 and Klf5 differentially inhibit mesoderm and endoderm differentiation in embryonic stem cells. Nat Commun 2014; 5:3719. [PMID: 24770696 DOI: 10.1038/ncomms4719] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 03/24/2014] [Indexed: 01/04/2023] Open
Abstract
Krüppel-like factors (Klf) 4 and 5 are two closely related members of the Klf family, known to play key roles in cell cycle regulation, somatic cell reprogramming and pluripotency. Here we focus on the functional divergence between Klf4 and Klf5 in the inhibition of mouse embryonic stem (ES) cell differentiation. Using microarrays and chromatin immunoprecipitation coupled to ultra-high-throughput DNA sequencing, we show that Klf4 negatively regulates the expression of endodermal markers in the undifferentiated ES cells, including transcription factors involved in the commitment of pluripotent stem cells to endoderm differentiation. Knockdown of Klf4 enhances differentiation towards visceral and definitive endoderm. In contrast, Klf5 negatively regulates the expression of mesodermal markers, some of which control commitment to the mesoderm lineage, and knockdown of Klf5 specifically enhances differentiation towards mesoderm. We conclude that Klf4 and Klf5 differentially inhibit mesoderm and endoderm differentiation in murine ES cells.
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Affiliation(s)
- Irène Aksoy
- 1] Inserm, U846, 18 Avenue Doyen Lepine, Bron 69500, France [2] Stem Cell and Brain Research Institute, Bron 69500, France [3] Université de Lyon, Université Lyon 1, Lyon 69003, France [4] Genome Institute of Singapore, 60 Biopolis street, Singapore 138672, Singapore [5]
| | - Vincent Giudice
- 1] Inserm, U846, 18 Avenue Doyen Lepine, Bron 69500, France [2] Stem Cell and Brain Research Institute, Bron 69500, France [3] Université de Lyon, Université Lyon 1, Lyon 69003, France [4]
| | - Edwige Delahaye
- 1] Inserm, U846, 18 Avenue Doyen Lepine, Bron 69500, France [2] Stem Cell and Brain Research Institute, Bron 69500, France [3] Université de Lyon, Université Lyon 1, Lyon 69003, France
| | - Florence Wianny
- 1] Inserm, U846, 18 Avenue Doyen Lepine, Bron 69500, France [2] Stem Cell and Brain Research Institute, Bron 69500, France [3] Université de Lyon, Université Lyon 1, Lyon 69003, France
| | - Maxime Aubry
- 1] Inserm, U846, 18 Avenue Doyen Lepine, Bron 69500, France [2] Stem Cell and Brain Research Institute, Bron 69500, France [3] Université de Lyon, Université Lyon 1, Lyon 69003, France
| | - Magali Mure
- 1] Inserm, U846, 18 Avenue Doyen Lepine, Bron 69500, France [2] Stem Cell and Brain Research Institute, Bron 69500, France [3] Université de Lyon, Université Lyon 1, Lyon 69003, France
| | - Jiaxuan Chen
- Genome Institute of Singapore, 60 Biopolis street, Singapore 138672, Singapore
| | - Ralf Jauch
- 1] Genome Institute of Singapore, 60 Biopolis street, Singapore 138672, Singapore [2] Genome Regulation Laboratory, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Gireesh K Bogu
- Genome Institute of Singapore, 60 Biopolis street, Singapore 138672, Singapore
| | - Tobias Nolden
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Heinz Himmelbauer
- 1] Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany [2] Center for Genomic Regulation (CRG), C. Dr. Aiguader 88, Barcelona 08003, Spain [3] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, Barcelona 08003, Spain
| | - Michael Xavier Doss
- 1] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, Barcelona 08003, Spain [2]
| | - Agapios Sachinidis
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, Robert-Koch-Strasse. 39, Cologne 50931, Germany
| | - Herbert Schulz
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, Berlin 13125, Germany
| | - Oliver Hummel
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, Berlin 13125, Germany
| | - Paola Martinelli
- Centro Nacional de Investigaciones Oncológicas, Melchor Fernández Almagro 3, Madrid 28029, Spain
| | - Norbert Hübner
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, Berlin 13125, Germany
| | - Lawrence W Stanton
- Genome Institute of Singapore, 60 Biopolis street, Singapore 138672, Singapore
| | - Francisco X Real
- 1] Centro Nacional de Investigaciones Oncológicas, Melchor Fernández Almagro 3, Madrid 28029, Spain [2] Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08002, Spain
| | - Pierre-Yves Bourillot
- 1] Inserm, U846, 18 Avenue Doyen Lepine, Bron 69500, France [2] Stem Cell and Brain Research Institute, Bron 69500, France [3] Université de Lyon, Université Lyon 1, Lyon 69003, France
| | - Pierre Savatier
- 1] Inserm, U846, 18 Avenue Doyen Lepine, Bron 69500, France [2] Stem Cell and Brain Research Institute, Bron 69500, France [3] Université de Lyon, Université Lyon 1, Lyon 69003, France
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12
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Baud A, Guryev V, Hummel O, Johannesson M, Flint J. Erratum: Genomes and phenomes of a population of outbred rats and its progenitors. Sci Data 2014; 1:140016. [PMID: 25982460 PMCID: PMC4387707 DOI: 10.1038/sdata.2014.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
[This corrects the article DOI: 10.1038/sdata.2014.11.].
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13
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Atanur SS, Diaz AG, Maratou K, Sarkis A, Rotival M, Game L, Tschannen MR, Kaisaki PJ, Otto GW, Ma MCJ, Keane TM, Hummel O, Saar K, Chen W, Guryev V, Gopalakrishnan K, Garrett MR, Joe B, Citterio L, Bianchi G, McBride M, Dominiczak A, Adams DJ, Serikawa T, Flicek P, Cuppen E, Hubner N, Petretto E, Gauguier D, Kwitek A, Jacob H, Aitman TJ. Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat. Cell 2013; 154:691-703. [PMID: 23890820 PMCID: PMC3732391 DOI: 10.1016/j.cell.2013.06.040] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 04/30/2013] [Accepted: 06/21/2013] [Indexed: 12/24/2022]
Abstract
Large numbers of inbred laboratory rat strains have been developed for a range of complex disease phenotypes. To gain insights into the evolutionary pressures underlying selection for these phenotypes, we sequenced the genomes of 27 rat strains, including 11 models of hypertension, diabetes, and insulin resistance, along with their respective control strains. Altogether, we identified more than 13 million single-nucleotide variants, indels, and structural variants across these rat strains. Analysis of strain-specific selective sweeps and gene clusters implicated genes and pathways involved in cation transport, angiotensin production, and regulators of oxidative stress in the development of cardiovascular disease phenotypes in rats. Many of the rat loci that we identified overlap with previously mapped loci for related traits in humans, indicating the presence of shared pathways underlying these phenotypes in rats and humans. These data represent a step change in resources available for evolutionary analysis of complex traits in disease models. PaperClip
Genomes of 27 rat strains were sequenced; >13 million sequence variants identified Selective sweeps and coevolved gene clusters were detected in 11 disease models Previously identified and new disease genes and pathways were identified This is first evolutionary analysis of artificial selection for disease phenotypes
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Affiliation(s)
- Santosh S Atanur
- Physiological Genomic and Medicine Group, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK
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14
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Yang C, Stingo FC, Ahn KW, Liu P, Vannucci M, Laud PW, Skelton M, O'Connor P, Kurth T, Ryan RP, Moreno C, Tsaih SW, Patone G, Hummel O, Jacob HJ, Liang M, Cowley AW. Increased proliferative cells in the medullary thick ascending limb of the loop of Henle in the Dahl salt-sensitive rat. Hypertension 2012. [PMID: 23184381 DOI: 10.1161/hypertensionaha.112.199380] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Studies of transcriptome profiles have provided new insights into mechanisms underlying the development of hypertension. Cell type heterogeneity in tissue samples, however, has been a significant hindrance in these studies. We performed a transcriptome analysis in medullary thick ascending limbs of the loop of Henle isolated from Dahl salt-sensitive rats. Genes differentially expressed between Dahl salt-sensitive rats and salt-insensitive consomic SS.13(BN) rats on either 0.4% or 7 days of 8.0% NaCl diet (n=4) were highly enriched for genes located on chromosome 13, the chromosome substituted in the SS.13(BN) rat. A pathway involving cell proliferation and cell cycle regulation was identified as one of the most highly ranked pathways based on differentially expressed genes and by a Bayesian model analysis. Immunofluorescent analysis indicated that just 1 week of a high-salt diet resulted in a severalfold increase in proliferative medullary thick ascending limb cells in both rat strains, and that Dahl salt-sensitive rats exhibited a significantly greater proportion of medullary thick ascending limb cells in a proliferative state than in SS.13(BN) rats (15.0±1.4% versus 10.1±0.6%; n=7-9; P<0.05). The total number of cells per medullary thick ascending limb section analyzed was not different between the 2 strains. The study revealed alterations in regulatory pathways in Dahl salt-sensitive rats in tissues highly enriched for a single cell type, leading to the unexpected finding of a greater increase in the number of proliferative medullary thick ascending limb cells in Dahl salt-sensitive rats on a high-salt diet.
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Affiliation(s)
- Chun Yang
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
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15
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Jackson M, Axton RA, Taylor AH, Wilson JA, Gordon-Keylock SAM, Kokkaliaris KD, Brickman JM, Schulz H, Hummel O, Hubner N, Forrester LM. HOXB4 can enhance the differentiation of embryonic stem cells by modulating the hematopoietic niche. Stem Cells 2012; 30:150-60. [PMID: 22084016 DOI: 10.1002/stem.782] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Hematopoietic differentiation of embryonic stem cells (ESCs) in vitro has been used as a model to study early hematopoietic development, and it is well documented that hematopoietic differentiation can be enhanced by overexpression of HOXB4. HOXB4 is expressed in hematopoietic progenitor cells (HPCs) where it promotes self-renewal, but it is also expressed in the primitive streak of the gastrulating embryo. This led us to hypothesize that HOXB4 might modulate gene expression in prehematopoietic mesoderm and that this property might contribute to its prohematopoietic effect in differentiating ESCs. To test our hypothesis, we developed a conditionally activated HOXB4 expression system using the mutant estrogen receptor (ER(T2)) and showed that a pulse of HOXB4 prior to HPC emergence in differentiating ESCs led to an increase in hematopoietic differentiation. Expression profiling revealed an increase in the expression of genes associated with paraxial mesoderm that gives rise to the hematopoietic niche. Therefore, we considered that HOXB4 might modulate the formation of the hematopoietic niche as well as the production of hematopoietic cells per se. Cell mixing experiments supported this hypothesis demonstrating that HOXB4 activation can generate a paracrine as well as a cell autonomous effect on hematopoietic differentiation. We provide evidence to demonstrate that this activity is partly mediated by the secreted protein FRZB.
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Affiliation(s)
- Melany Jackson
- MRC Centre for Regenerative Medicine, Scottish Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
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Stodola TJ, de Resende MM, Sarkis AB, Didier DN, Jacob HJ, Huebner N, Hummel O, Saar K, Moreno C, Greene AS. Characterization of the genomic structure and function of regions influencing renin and angiogenesis in the SS rat. Physiol Genomics 2011; 43:808-17. [PMID: 21521778 DOI: 10.1152/physiolgenomics.00171.2010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Impaired regulation of renin in Dahl salt-sensitive rats (SS/JRHsdMcwi, SS) contributes to attenuated angiogenesis in this strain. This study examined angiogenic function and genomic structure of regions surrounding the renin gene using subcongenic strains of the SS and BN/NHsdMcwi (BN) rat to identify important genomic variations between SS and BN involved in angiogenesis. Three candidate regions on Chr 13 were studied: two congenic strains containing 0.89 and 2.62 Mb portions of BN Chr 13 that excluded the BN renin allele and a third strain that contained a 2.02 Mb overlapping region that included the BN renin allele. Angiogenesis induced by electrical stimulation of the tibialis anterior muscle was attenuated in the SS compared with the BN. Congenics carrying the SS renin allele had impaired angiogenesis, while strains carrying the BN renin allele had angiogenesis restored. The exception was a congenic including a region of BN genome 0.4 Mb distal to renin that restored both renin regulation and angiogenesis. This suggests that there is a distant regulatory element in the BN capable of restoring normal regulation of the SS renin allele. The importance of ANG II in the restored angiogenic response was demonstrated by blocking with losartan. Sequencing of the 4.05 Mb candidate region in SS and BN revealed a total of 8,850 SNPs and other sequence variants. An analysis of the genes and their variants in the region suggested a number of pathways that may explain the impaired regulation of renin and angiogenesis in the SS rat.
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Affiliation(s)
- Timothy J Stodola
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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Atanur SS, Birol I, Guryev V, Hirst M, Hummel O, Morrissey C, Behmoaras J, Fernandez-Suarez XM, Johnson MD, McLaren WM, Patone G, Petretto E, Plessy C, Rockland KS, Rockland C, Saar K, Zhao Y, Carninci P, Flicek P, Kurtz T, Cuppen E, Pravenec M, Hubner N, Jones SJM, Birney E, Aitman TJ. The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. Genome Res 2010; 20:791-803. [PMID: 20430781 DOI: 10.1101/gr.103499.109] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The spontaneously hypertensive rat (SHR) is the most widely studied animal model of hypertension. Scores of SHR quantitative loci (QTLs) have been mapped for hypertension and other phenotypes. We have sequenced the SHR/OlaIpcv genome at 10.7-fold coverage by paired-end sequencing on the Illumina platform. We identified 3.6 million high-quality single nucleotide polymorphisms (SNPs) between the SHR/OlaIpcv and Brown Norway (BN) reference genome, with a high rate of validation (sensitivity 96.3%-98.0% and specificity 99%-100%). We also identified 343,243 short indels between the SHR/OlaIpcv and reference genomes. These SNPs and indels resulted in 161 gain or loss of stop codons and 629 frameshifts compared with the BN reference sequence. We also identified 13,438 larger deletions that result in complete or partial absence of 107 genes in the SHR/OlaIpcv genome compared with the BN reference and 588 copy number variants (CNVs) that overlap with the gene regions of 688 genes. Genomic regions containing genes whose expression had been previously mapped as cis-regulated expression quantitative trait loci (eQTLs) were significantly enriched with SNPs, short indels, and larger deletions, suggesting that some of these variants have functional effects on gene expression. Genes that were affected by major alterations in their coding sequence were highly enriched for genes related to ion transport, transport, and plasma membrane localization, providing insights into the likely molecular and cellular basis of hypertension and other phenotypes specific to the SHR strain. This near complete catalog of genomic differences between two extensively studied rat strains provides the starting point for complete elucidation, at the molecular level, of the physiological and pathophysiological phenotypic differences between individuals from these strains.
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Affiliation(s)
- Santosh S Atanur
- Physiological Genomics and Medicine Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, United Kingdom
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Rolletschek A, Schroeder IS, Schulz H, Hummel O, Huebner N, Wobus AM. Characterization of mouse embryonic stem cell differentiation into the pancreatic lineage in vitro by transcriptional profiling, quantitative RT-PCR and immunocytochemistry. Int J Dev Biol 2010; 54:41-54. [PMID: 19876843 DOI: 10.1387/ijdb.082694ar] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
We have previously shown that mouse embryonic stem (ES) cells differentiate into insulin-positive cells via multi-lineage progenitors. Here, we used Affymetrix chips and quantitative RT-PCR analysis to determine transcriptional profiles of undifferentiated wildtype (wt) and Pax4 expressing (Pax4+) ES cells and differentiated cells of committed progenitor and advanced stages. From undifferentiated to the committed stage, 237 (wt) and 263 (Pax4+) transcripts were 5- or more-fold up-regulated, whereas from the committed to the advanced stage, 28 (wt) and 5 (Pax4+) transcripts, respectively, were two- or more-fold up-regulated. Transcripts were classified into main subclasses including transcriptional regulation, signalling/growth factors, adhesion/extracellular matrix, membrane/transport, metabolism and organogenesis. Remarkably, endoderm-specific Sox17 and early pancreas-specific Isl1 transcripts were up-regulated at an earlier stage of multi-lineage progenitors, whereas highly up-regulated probe sets and transcripts of genes involved in endoderm, pancreatic, hepatic, angiogenic and neural differentiation were detected at the committed progenitor stage. Pax4+ cells showed specific differences in transcript up-regulation and a lower amount of up-regulated neural-specific transcripts in comparison to wt cells, but no enhanced gene expression complexity. Immunocytochemical analysis of selected proteins involved in endoderm and pancreatic differentiation, such as chromogranin B, transthyretin, Foxa1 and neuronatin revealed co-expression with insulin- or C-peptide-positive cells. The comparison of transcript profiles of ES cells differentiating in vitro with those of the embryonic and adult pancreas in vivo suggested that in vitro differentiated cells resemble an embryonal stage of development, supporting the view that ES-derived pancreatic cells are unable to complete pancreatic differentiation in vitro.
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Affiliation(s)
- Alexandra Rolletschek
- In vitro Differentiation Group, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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Wenzel K, Wallukat G, Qadri F, Hubner N, Schulz H, Hummel O, Herse F, Heuser A, Fischer R, Heidecke H, Luft FC, Muller DN, Dietz R, Dechend R. Alpha1A-adrenergic receptor-directed autoimmunity induces left ventricular damage and diastolic dysfunction in rats. PLoS One 2010; 5:e9409. [PMID: 20195525 PMCID: PMC2827566 DOI: 10.1371/journal.pone.0009409] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 01/16/2010] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Agonistic autoantibodies to the alpha(1)-adrenergic receptor occur in nearly half of patients with refractory hypertension; however, their relevance is uncertain. METHODS/PRINCIPAL FINDINGS We immunized Lewis rats with the second extracellular-loop peptides of the human alpha(1A)-adrenergic receptor and maintained them for one year. Alpha(1A)-adrenergic antibodies (alpha(1A)-AR-AB) were monitored with a neonatal cardiomyocyte contraction assay by ELISA, and by ERK1/2 phosphorylation in human alpha(1A)-adrenergic receptor transfected Chinese hamster ovary cells. The rats were followed with radiotelemetric blood pressure measurements and echocardiography. At 12 months, the left ventricles of immunized rats had greater wall thickness than control rats. The fractional shortening and dp/dt(max) demonstrated preserved systolic function. A decreased E/A ratio in immunized rats indicated a diastolic dysfunction. Invasive hemodynamics revealed increased left ventricular end-diastolic pressures and decreased dp/dt(min). Mean diameter of cardiomyocytes showed hypertrophy in immunized rats. Long-term blood pressure values and heart rates were not different. Genes encoding sarcomeric proteins, collagens, extracellular matrix proteins, calcium regulating proteins, and proteins of energy metabolism in immunized rat hearts were upregulated, compared to controls. Furthermore, fibrosis was present in immunized hearts, but not in control hearts. A subset of immunized and control rats was infused with angiotensin (Ang) II. The stressor raised blood pressure to a greater degree and led to more cardiac fibrosis in immunized, than in control rats. CONCLUSIONS/SIGNIFICANCE We show that alpha(1A)-AR-AB cause diastolic dysfunction independent of hypertension, and can increase the sensitivity to Ang II. We suggest that alpha(1A)-AR-AB could contribute to cardiovascular endorgan damage.
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Bourillot PY, Aksoy I, Schreiber V, Wianny F, Schulz H, Hummel O, Hubner N, Savatier P. Novel STAT3 target genes exert distinct roles in the inhibition of mesoderm and endoderm differentiation in cooperation with Nanog. Stem Cells 2010; 27:1760-71. [PMID: 19544440 DOI: 10.1002/stem.110] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Leukemia inhibitory factor (LIF) activates the transcription factor signal transducer and activator of transcription 3 (STAT3), which results in the maintenance of mouse embryonic stem cells in the pluripotent state by inhibiting both mesodermal and endodermal differentiation. How the LIF/STAT3 pathway inhibits commitment to both mesoderm and endoderm lineages is presently unknown. Using a hormone-dependent STAT3 and with microarray analysis, we identified 58 targets of STAT3 including 20 unknown genes. Functional analysis showed that 22 among the 23 STAT3 target genes analyzed contribute to the maintenance of the undifferentiated state, as evidenced by an increase in the frequency of differentiated colonies in a self-renewal assay and a concomitant elevation of early differentiation markers upon knockdown. Fourteen of them, including Dact1, Klf4, Klf5, Rgs16, Smad7, Ccrn4l, Cnnm1, Ocln, Ier3, Pim1, Cyr61, and Sgk, were also regulated by Nanog. Analysis of lineage-specific markers showed that the STAT3 target genes fell into three distinct categories, depending on their capacity to inhibit either mesoderm or endoderm differentiation or both. The identification of genes that harness self-renewal and are downstream targets of both STAT3 and Nanog shed light on the mechanisms underlying functional redundancy between STAT3 and Nanog in mouse embryonic stem cells.
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Storm MP, Kumpfmueller B, Thompson B, Kolde R, Vilo J, Hummel O, Schulz H, Welham MJ. Characterization of the phosphoinositide 3-kinase-dependent transcriptome in murine embryonic stem cells: identification of novel regulators of pluripotency. Stem Cells 2009; 27:764-75. [PMID: 19350676 DOI: 10.1002/stem.3] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Phosphoinositide 3-kinase (PI3K)-dependent signaling has been implicated in the regulation of embryonic stem (ES) cell fate. To gain further insight into the mechanisms regulated by PI3Ks in murine ES cells, we have performed expression profiling using Affymetrix GeneChips to characterize the transcriptional changes that arise as a result of inhibition of PI3K-dependent signaling. Using filtering of greater than 1.5-fold change in expression and an analysis of variance significance level of p < .05, we have defined a dataset comprising 646 probe sets that detect changes in transcript expression (469 down and 177 up) on inhibition of PI3Ks. Changes in expression of selected genes have been validated by quantitative reverse transcription polymerase chain reaction. Gene ontology analyses reveal significant over-representation of transcriptional regulators within our dataset. In addition, several known regulators of ES cell pluripotency, for example, Nanog, Esrrb, Tbx3, and Tcl-1, are among the downregulated genes. To evaluate the functional involvement of selected genes in regulation of ES cell self-renewal, we have used short interfering RNA-mediated knockdown. These studies identify genes not previously associated with control of ES cell fate that are involved in regulating ES cell pluripotency, including the protein tyrosine phosphatase Shp-1 and the Zscan4 family of zinc finger proteins. Further gain-of-function analyses demonstrate the importance of Zscan4c in regulation of ES cell pluripotency.
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Affiliation(s)
- Michael P Storm
- Department of Pharmacy and Pharmacology, Centre for Regenerative Medicine, University of Bath, Bath, United Kingdom
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22
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Trouillas M, Saucourt C, Guillotin B, Gauthereau X, Ding L, Buchholz F, Doss MX, Sachinidis A, Hescheler J, Hummel O, Huebner N, Kolde R, Vilo J, Schulz H, Boeuf H. Three LIF-dependent signatures and gene clusters with atypical expression profiles, identified by transcriptome studies in mouse ES cells and early derivatives. BMC Genomics 2009; 10:73. [PMID: 19203379 PMCID: PMC2674464 DOI: 10.1186/1471-2164-10-73] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [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: 09/17/2008] [Accepted: 02/09/2009] [Indexed: 12/29/2022] Open
Abstract
Background Mouse embryonic stem (ES) cells remain pluripotent in vitro when grown in the presence of the cytokine Leukaemia Inhibitory Factor (LIF). Identification of LIF targets and of genes regulating the transition between pluripotent and early differentiated cells is a critical step for understanding the control of ES cell pluripotency. Results By gene profiling studies carried out with mRNAs from ES cells and their early derivatives treated or not with LIF, we have identified i) LIF-dependent genes, highly expressed in pluripotent cells, whose expression level decreases sharply upon LIF withdrawal [Pluri genes], ii) LIF induced genes [Lifind genes] whose expression is differentially regulated depending upon cell context and iii) genes specific to the reversible or irreversible committed states. In addition, by hierarchical gene clustering, we have identified, among eight independent gene clusters, two atypical groups of genes, whose expression level was highly modulated in committed cells only. Computer based analyses led to the characterization of different sub-types of Pluri and Lifind genes, and revealed their differential modulation by Oct4 or Nanog master genes. Individual knock down of a selection of Pluri and Lifind genes leads to weak changes in the expression of early differentiation markers, in cell growth conditions in which these master genes are still expressed. Conclusion We have identified different sets of LIF-regulated genes depending upon the cell state (reversible or irreversible commitment), which allowed us to present a novel global view of LIF responses. We are also reporting on the identification of genes whose expression is strictly regulated during the commitment step. Furthermore, our studies identify sub-networks of genes with a restricted expression in pluripotent ES cells, whose down regulation occurs while the master knot (composed of OCT4, SOX2 and NANOG) is still expressed and which might be down-regulated together for driving cells towards differentiation.
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Doss MX, Chen S, Winkler J, Hippler-Altenburg R, Odenthal M, Wickenhauser C, Balaraman S, Schulz H, Hummel O, Hübner N, Ghosh-Choudhury N, Sotiriadou I, Hescheler J, Sachinidis A. Transcriptomic and phenotypic analysis of murine embryonic stem cell derived BMP2+ lineage cells: an insight into mesodermal patterning. Genome Biol 2008; 8:R184. [PMID: 17784959 PMCID: PMC2375022 DOI: 10.1186/gb-2007-8-9-r184] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Revised: 05/30/2007] [Accepted: 09/04/2007] [Indexed: 01/08/2023] Open
Abstract
Transcriptome analysis of BMP2+ cells in comparison to the undifferentiated BMP2 ES cells and the control population from 7-day old embryoid bodies led to the identification of 479 specifically upregulated and 193 downregulated transcripts. Background Bone morphogenetic protein (BMP)2 is a late mesodermal marker expressed during vertebrate development and plays a crucial role in early embryonic development. The nature of the BMP2-expressing cells during the early stages of embryonic development, their transcriptome and cell phenotypes developed from these cells have not yet been characterized. Results We generated a transgenic BMP2 embryonic stem (ES) cell lineage expressing both puromycin acetyltransferase and enhanced green fluorescent protein (EGFP) driven by the BMP2 promoter. Puromycin resistant and EGFP positive BMP2+ cells with a purity of over 93% were isolated. Complete transcriptome analysis of BMP2+ cells in comparison to the undifferentiated ES cells and the control population from seven-day-old embryoid bodies (EBs; intersection of genes differentially expressed between undifferentiated ES cells and BMP2+ EBs as well as differentially expressed between seven-day-old control EBs and BMP2+ EBs by t-test, p < 0.01, fold change >2) by microarray analysis led to identification of 479 specifically upregulated and 193 downregulated transcripts. Transcription factors, apoptosis promoting factors and other signaling molecules involved in early embryonic development are mainly upregulated in BMP2+ cells. Long-term differentiation of the BMP2+ cells resulted in neural crest stem cells (NCSCs), smooth muscle cells, epithelial-like cells, neuronal-like cells, osteoblasts and monocytes. Interestingly, development of cardiomyocytes from the BMP2+ cells requires secondary EB formation. Conclusion This is the first study to identify the complete transcriptome of BMP2+ cells and cell phenotypes from a mesodermal origin, thus offering an insight into the role of BMP2+ cells during embryonic developmental processes in vivo.
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Affiliation(s)
- Michael Xavier Doss
- Institute of Neurophysiology, University of Cologne, Robert-Koch Str. 39, 50931 Cologne, Germany
| | - Shuhua Chen
- Institute of Neurophysiology, University of Cologne, Robert-Koch Str. 39, 50931 Cologne, Germany
| | - Johannes Winkler
- Institute of Neurophysiology, University of Cologne, Robert-Koch Str. 39, 50931 Cologne, Germany
| | - Rita Hippler-Altenburg
- Institute of Neurophysiology, University of Cologne, Robert-Koch Str. 39, 50931 Cologne, Germany
| | - Margareta Odenthal
- Institute of Pathology, University of Cologne, Joseph-Stelzmann-Str. 9, 50931 Cologne, Germany
| | - Claudia Wickenhauser
- Institute of Pathology, University of Cologne, Joseph-Stelzmann-Str. 9, 50931 Cologne, Germany
| | - Sridevi Balaraman
- Institute of Pathology, University of Cologne, Joseph-Stelzmann-Str. 9, 50931 Cologne, Germany
| | - Herbert Schulz
- Max-Delbrueck-Center for Molecular Medicine - MDC, Robert-Rössle Str. 10, 13092 Berlin, Germany
| | - Oliver Hummel
- Max-Delbrueck-Center for Molecular Medicine - MDC, Robert-Rössle Str. 10, 13092 Berlin, Germany
| | - Norbert Hübner
- Max-Delbrueck-Center for Molecular Medicine - MDC, Robert-Rössle Str. 10, 13092 Berlin, Germany
| | - Nandini Ghosh-Choudhury
- Department of Pathology, The University of Texas Health Science Center at San Antonio, TX 78229, USA
| | - Isaia Sotiriadou
- Institute of Neurophysiology, University of Cologne, Robert-Koch Str. 39, 50931 Cologne, Germany
| | - Jürgen Hescheler
- Institute of Neurophysiology, University of Cologne, Robert-Koch Str. 39, 50931 Cologne, Germany
| | - Agapios Sachinidis
- Institute of Neurophysiology, University of Cologne, Robert-Koch Str. 39, 50931 Cologne, Germany
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Karantzali E, Schulz H, Hummel O, Hubner N, Hatzopoulos A, Kretsovali A. Histone deacetylase inhibition accelerates the early events of stem cell differentiation: transcriptomic and epigenetic analysis. Genome Biol 2008; 9:R65. [PMID: 18394158 PMCID: PMC2643936 DOI: 10.1186/gb-2008-9-4-r65] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [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: 10/17/2007] [Revised: 01/14/2008] [Accepted: 04/04/2008] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Epigenetic mechanisms regulate gene expression patterns affecting cell function and differentiation. In this report, we examine the role of histone acetylation in gene expression regulation in mouse embryonic stem cells employing transcriptomic and epigenetic analysis. RESULTS Embryonic stem cells treated with the histone deacetylase inhibitor Trichostatin A (TSA), undergo morphological and gene expression changes indicative of differentiation. Gene profiling utilizing Affymetrix microarrays revealed the suppression of important pluripotency factors, including Nanog, a master regulator of stem cell identity, and the activation of differentiation-related genes. Transcriptional and epigenetic changes induced after 6-12 hours of TSA treatment mimic those that appear during embryoid body differentiation. We show here that the early steps of stem cell differentiation are marked by the enhancement of bulk activatory histone modifications. At the individual gene level, we found that transcriptional reprogramming triggered by histone deacetylase inhibition correlates with rapid changes in activating K4 trimethylation and repressive K27 trimethylation of histone H3. The establishment of H3K27 trimethylation is required for stable gene suppression whereas in its absence, genes can be reactivated upon TSA removal. CONCLUSION Our data suggest that inhibition of histone deacetylases accelerates the early events of differentiation by regulating the expression of pluripotency- and differentiation-associated genes in an opposite manner. This analysis provides information about genes that are important for embryonic stem cell function and the epigenetic mechanisms that regulate their expression.
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Affiliation(s)
- Efthimia Karantzali
- Institute of Molecular Biology and Biotehnology, FORTH, Heraklion 71110 Greece
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Hubner N, Monti J, Fischer J, Paskas S, Heinig M, Schulz H, Goesele C, Heuser A, Fischer R, Schmidt C, Schirdewan A, Gross V, Hummel O, Maatz H, Patone G, Saar K, Vingron M, Weldon SM, Hammock BD, Rohde K, Dietz R, Cook SA, Schunck W, Luft FC. Soluble epoxide hydrolase (Ephx2) is a susceptibility gene for heart failure in a rat model of human disease 3044. FASEB J 2008. [DOI: 10.1096/fasebj.22.1_supplement.479.10] [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: 11/11/2022]
Affiliation(s)
| | - Jan Monti
- Department of Clinical and Molecular CardiologyFranz‐Volhard ClinicHelios Clinics GmbHCharité Universitaetsmedizin BerlinBerlinGermany
| | | | | | | | | | | | - Arnd Heuser
- Max‐Delbruck‐Center for Molecular MedicineBerlinGermany
| | | | | | - Alexander Schirdewan
- Department of Clinical and Molecular CardiologyFranz‐Volhard ClinicHelios Clinics GmbHCharité Universitaetsmedizin BerlinBerlinGermany
| | - Volkmar Gross
- Max‐Delbruck‐Center for Molecular MedicineBerlinGermany
| | - Oliver Hummel
- Max‐Delbruck‐Center for Molecular MedicineBerlinGermany
| | - Henrike Maatz
- Max‐Delbruck‐Center for Molecular MedicineBerlinGermany
| | | | - Kathrin Saar
- Max‐Delbruck‐Center for Molecular MedicineBerlinGermany
| | - Martin Vingron
- Department of BioinformaticsMax‐Planck‐Institute for Molecular GeneticsBerlinGermany
| | | | - Bruce D. Hammock
- Departments of Entomology and Nutrition and Cancer Research CenterUC DavisSacramentoCA
| | - Klaus Rohde
- Max‐Delbruck‐Center for Molecular MedicineBerlinGermany
| | - Rainer Dietz
- Max‐Delbruck‐Center for Molecular MedicineBerlinGermany
| | - Stuart A. Cook
- MRC Clinical Sciences Centre Faculty of MedicineImperial CollegeLondonUnited Kingdom
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Doss MX, Winkler J, Chen S, Hippler-Altenburg R, Sotiriadou I, Halbach M, Pfannkuche K, Liang H, Schulz H, Hummel O, Hübner N, Rottscheidt R, Hescheler J, Sachinidis A. Global transcriptome analysis of murine embryonic stem cell-derived cardiomyocytes. Genome Biol 2007; 8:R56. [PMID: 17428332 PMCID: PMC1896009 DOI: 10.1186/gb-2007-8-4-r56] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Revised: 02/16/2007] [Accepted: 04/11/2007] [Indexed: 12/12/2022] Open
Abstract
Microarray analysis reveals that the specific pattern of gene expression in cardiomyocytes derived from embryonic stem cells reflects the biological, physiological and functional processes occurring in mature cardiomyocytes. Background Characterization of gene expression signatures for cardiomyocytes derived from embryonic stem cells will help to define their early biologic processes. Results A transgenic α-myosin heavy chain (MHC) embryonic stem cell lineage was generated, exhibiting puromycin resistance and expressing enhanced green fluorescent protein (EGFP) under the control of the α-MHC promoter. A puromycin-resistant, EGFP-positive, α-MHC-positive cardiomyocyte population was isolated with over 92% purity. RNA was isolated after electrophysiological characterization of the cardiomyocytes. Comprehensive transcriptome analysis of α-MHC-positive cardiomyocytes in comparison with undifferentiated α-MHC embryonic stem cells and the control population from 15-day-old embryoid bodies led to identification of 884 upregulated probe sets and 951 downregulated probe sets in α-MHC-positive cardiomyocytes. A subset of upregulated genes encodes cytoskeletal and voltage-dependent channel proteins, and proteins that participate in aerobic energy metabolism. Interestingly, mitosis, apoptosis, and Wnt signaling-associated genes were downregulated in the cardiomyocytes. In contrast, annotations for genes upregulated in the α-MHC-positive cardiomyocytes are enriched for the following Gene Ontology (GO) categories: enzyme-linked receptor protein signaling pathway (GO:0007167), protein kinase activity (GO:0004672), negative regulation of Wnt receptor signaling pathway (GO:0030178), and regulation of cell size (O:0008361). They were also enriched for the Biocarta p38 mitogen-activated protein kinase signaling pathway and Kyoto Encyclopedia of Genes and Genomes (KEGG) calcium signaling pathway. Conclusion The specific pattern of gene expression in the cardiomyocytes derived from embryonic stem cells reflects the biologic, physiologic, and functional processes that take place in mature cardiomyocytes. Identification of cardiomyocyte-specific gene expression patterns and signaling pathways will contribute toward elucidating their roles in intact cardiac function.
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Affiliation(s)
- Michael Xavier Doss
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Robert Koch Str., 50931 Cologne, Germany
| | - Johannes Winkler
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Robert Koch Str., 50931 Cologne, Germany
| | - Shuhua Chen
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Robert Koch Str., 50931 Cologne, Germany
| | - Rita Hippler-Altenburg
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Robert Koch Str., 50931 Cologne, Germany
| | - Isaia Sotiriadou
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Robert Koch Str., 50931 Cologne, Germany
| | - Marcel Halbach
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Robert Koch Str., 50931 Cologne, Germany
| | - Kurt Pfannkuche
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Robert Koch Str., 50931 Cologne, Germany
| | - Huamin Liang
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Robert Koch Str., 50931 Cologne, Germany
| | - Herbert Schulz
- Max-Delbrueck-Center for Molecular Medicine - MDC, Robert-Rössle Str., 13092 Berlin, Germany
| | - Oliver Hummel
- Max-Delbrueck-Center for Molecular Medicine - MDC, Robert-Rössle Str., 13092 Berlin, Germany
| | - Norbert Hübner
- Max-Delbrueck-Center for Molecular Medicine - MDC, Robert-Rössle Str., 13092 Berlin, Germany
| | - Ruth Rottscheidt
- Institute for Genetics, Department of Evolutionary Genetics, University of Cologne, Zülpicher Str., 50674 Cologne, Germany
| | - Jürgen Hescheler
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Robert Koch Str., 50931 Cologne, Germany
| | - Agapios Sachinidis
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Robert Koch Str., 50931 Cologne, Germany
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Lee-Kirsch MA, Gong M, Chowdhury D, Senenko L, Engel K, Lee YA, de Silva U, Bailey SL, Witte T, Vyse TJ, Kere J, Pfeiffer C, Harvey S, Wong A, Koskenmies S, Hummel O, Rohde K, Schmidt RE, Dominiczak AF, Gahr M, Hollis T, Perrino FW, Lieberman J, Hübner N. Mutations in the gene encoding the 3'-5' DNA exonuclease TREX1 are associated with systemic lupus erythematosus. Nat Genet 2007; 39:1065-7. [PMID: 17660818 DOI: 10.1038/ng2091] [Citation(s) in RCA: 499] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Accepted: 05/29/2007] [Indexed: 11/08/2022]
Abstract
TREX1 acts in concert with the SET complex in granzyme A-mediated apoptosis, and mutations in TREX1 cause Aicardi-Goutières syndrome and familial chilblain lupus. Here, we report monoallelic frameshift or missense mutations and one 3' UTR variant of TREX1 present in 9/417 individuals with systemic lupus erythematosus but absent in 1,712 controls (P = 4.1 x 10(-7)). We demonstrate that two mutant TREX1 alleles alter subcellular targeting. Our findings implicate TREX1 in the pathogenesis of SLE.
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Affiliation(s)
- Min Ae Lee-Kirsch
- Klinik für Kinder- und Jugendmedizin, Technische Universität Dresden, 01307 Dresden, Germany.
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28
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Doss M, Winkler J, Chen S, Hippler-Altenburg R, Sotiriadou I, Halbach M, Pfannkuche K, Liang H, Schulz H, Hummel O, Hubner N, Rottscheidt R, Hescheler J, Sachinidis A. Global transcriptomic analysis of murine embryonic stem cell-derived cardiomyocytes. J Stem Cells Regen Med 2007; 2:96-97. [PMID: 24692927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- Mx Doss
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne , Robert Koch Str., 50931 Cologne, Germany
| | - J Winkler
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne , Robert Koch Str., 50931 Cologne, Germany
| | - S Chen
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne , Robert Koch Str., 50931 Cologne, Germany
| | - R Hippler-Altenburg
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne , Robert Koch Str., 50931 Cologne, Germany
| | - I Sotiriadou
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne , Robert Koch Str., 50931 Cologne, Germany
| | - M Halbach
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne , Robert Koch Str., 50931 Cologne, Germany
| | - K Pfannkuche
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne , Robert Koch Str., 50931 Cologne, Germany
| | - H Liang
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne , Robert Koch Str., 50931 Cologne, Germany
| | - H Schulz
- Max-Delbrueck-Center for Molecular Medicine - MDC , Robert-Rossle Str., 13092 Berlin, Germany
| | - O Hummel
- Max-Delbrueck-Center for Molecular Medicine - MDC , Robert-Rossle Str., 13092 Berlin, Germany
| | - N Hubner
- Max-Delbrueck-Center for Molecular Medicine - MDC , Robert-Rossle Str., 13092 Berlin, Germany
| | - R Rottscheidt
- Institute for Genetics, Department of Evolutionary Genetics, University of Cologne , Zulpicher Str., 50674 Cologne, Germany
| | - J Hescheler
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne , Robert Koch Str., 50931 Cologne, Germany
| | - A Sachinidis
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne , Robert Koch Str., 50931 Cologne, Germany
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29
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Wenzel K, Zabojszcza J, Carl M, Taubert S, Lass A, Harris CL, Ho M, Schulz H, Hummel O, Hubner N, Osterziel KJ, Spuler S. Increased Susceptibility to Complement Attack due to Down-Regulation of Decay-Accelerating Factor/CD55 in Dysferlin-Deficient Muscular Dystrophy. J Immunol 2005; 175:6219-25. [PMID: 16237120 DOI: 10.4049/jimmunol.175.9.6219] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Dysferlin is expressed in skeletal and cardiac muscles. However, dysferlin deficiency results in skeletal muscle weakness, but spares the heart. We compared intraindividual mRNA expression profiles of cardiac and skeletal muscle in dysferlin-deficient SJL/J mice and found down-regulation of the complement inhibitor, decay-accelerating factor/CD55, in skeletal muscle only. This finding was confirmed on mRNA and protein levels in two additional dysferlin-deficient mouse strains, A/J mice and Dysf-/- mice, as well as in patients with dysferlin-deficient muscular dystrophy. In vitro, the absence of CD55 led to an increased susceptibility of human myotubes to complement attack. Evidence is provided that decay-accelerating factor/CD55 is regulated via the myostatin-SMAD pathway. In conclusion, a novel mechanism of muscle fiber injury in dysferlin-deficient muscular dystrophy is demonstrated, possibly opening therapeutic avenues in this to date untreatable disorder.
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Affiliation(s)
- Katrin Wenzel
- Myology Research Group, Department of Neurology, Charité University Hospital, Berlin, Germany
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30
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Salih F, Khatami R, Steinheimer S, Hummel O, Kühn A, Grosse P. Inhibitory and excitatory intracortical circuits across the human sleep-wake cycle using paired-pulse transcranial magnetic stimulation. J Physiol 2005; 565:695-701. [PMID: 15802295 PMCID: PMC1464540 DOI: 10.1113/jphysiol.2004.082040] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 12/22/2004] [Accepted: 03/30/2005] [Indexed: 11/08/2022] Open
Abstract
Studies using single-pulse transcranial magnetic stimulation (TMS) have shown that excitability of the corticospinal system is systematically reduced in natural human sleep as compared to wakefulness with significant differences between sleep stages. However, the underlying excitatory and inhibitory interactions on the corticospinal system across the sleep-wake cycle are poorly understood. Here, we specifically asked whether in the motor cortex short intracortical inhibition (SICI) and facilitation (ICF) can be elicited at all in sleep using the paired-pulse TMS protocol, and if so, how SICI and ICF vary across sleep stages. We studied 28 healthy subjects at interstimulus intervals of 3 ms (SICI) and 10 ms (ICF), respectively. Magnetic stimulation was performed over the hand area of the motor cortex using a focal coil and evoked motor potentials were recorded from the contralateral first dorsal interosseus muscle (1DI). Relevant data was obtained from 13 subjects (NREM 2: n=7; NREM 3/4: n=7; REM: n=7). Results show that both SICI and ICF were present in NREM sleep. SICI was significantly enhanced in NREM 3/4 as compared to wakefulness and all other sleep stages whereas in NREM 2 neither SICI nor ICF differed from wakefulness. In REM sleep SICI was in the same range as in wakefulness, but ICF was entirely absent. These results in humans support the hypothesis derived from animal experiments which suggests that intracortical inhibitory mechanisms are involved in the control of neocortical pyramidal cells in NREM and REM sleep, but along different intraneuronal circuits. Further, our findings suggest that cortical mechanisms may additionally contribute to the inhibition of spinal motoneurones in REM sleep.
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Affiliation(s)
- F Salih
- Neurologische Klinik und Poliklinik, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.
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31
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Hubner N, Wallace CA, Zimdahl H, Petretto E, Schulz H, Maciver F, Mueller M, Hummel O, Monti J, Zidek V, Musilova A, Kren V, Causton H, Game L, Born G, Schmidt S, Müller A, Cook SA, Kurtz TW, Whittaker J, Pravenec M, Aitman TJ. Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nat Genet 2005; 37:243-53. [PMID: 15711544 DOI: 10.1038/ng1522] [Citation(s) in RCA: 384] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2004] [Accepted: 01/26/2005] [Indexed: 11/08/2022]
Abstract
Integration of genome-wide expression profiling with linkage analysis is a new approach to identifying genes underlying complex traits. We applied this approach to the regulation of gene expression in the BXH/HXB panel of rat recombinant inbred strains, one of the largest available rodent recombinant inbred panels and a leading resource for genetic analysis of the highly prevalent metabolic syndrome. In two tissues important to the pathogenesis of the metabolic syndrome, we mapped cis- and trans-regulatory control elements for expression of thousands of genes across the genome. Many of the most highly linked expression quantitative trait loci are regulated in cis, are inherited essentially as monogenic traits and are good candidate genes for previously mapped physiological quantitative trait loci in the rat. By comparative mapping we generated a data set of 73 candidate genes for hypertension that merit testing in human populations. Mining of this publicly available data set is expected to lead to new insights into the genes and regulatory pathways underlying the extensive range of metabolic and cardiovascular disease phenotypes that segregate in these recombinant inbred strains.
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Affiliation(s)
- Norbert Hubner
- Max-Delbrück-Center for Molecular Medicine, Berlin-Buch 13125, Germany
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32
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Krzywinski M, Wallis J, Gösele C, Bosdet I, Chiu R, Graves T, Hummel O, Layman D, Mathewson C, Wye N, Zhu B, Albracht D, Asano J, Barber S, Brown-John M, Chan S, Chand S, Cloutier A, Davito J, Fjell C, Gaige T, Ganten D, Girn N, Guggenheimer K, Himmelbauer H, Kreitler T, Leach S, Lee D, Lehrach H, Mayo M, Mead K, Olson T, Pandoh P, Prabhu AL, Shin H, Tänzer S, Thompson J, Tsai M, Walker J, Yang G, Sekhon M, Hillier L, Zimdahl H, Marziali A, Osoegawa K, Zhao S, Siddiqui A, de Jong PJ, Warren W, Mardis E, McPherson JD, Wilson R, Hübner N, Jones S, Marra M, Schein J. Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome. Genome Res 2004; 14:766-79. [PMID: 15060021 PMCID: PMC383324 DOI: 10.1101/gr.2336604] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC library. These BAC clones provide approximately 13-fold redundant coverage of the genome and have been assembled into 376 fingerprint contigs. A yeast artificial chromosome (YAC) map was also constructed and aligned with the BAC map via fingerprinted BAC and P1 artificial chromosome clones (PACs) sharing interspersed repetitive sequence markers with the YAC-based physical map. We have annotated 95% of the fingerprint map clones in contigs with coordinates on the version 3.1 rat genome sequence assembly, using BAC-end sequences and in silico mapping methods. These coordinates have allowed anchoring 358 of the 376 fingerprint map contigs onto the sequence assembly. Of these, 324 contigs are anchored to rat genome sequences localized to chromosomes, and 34 contigs are anchored to unlocalized portions of the rat sequence assembly. The remaining 18 contigs, containing 54 clones, still require placement. The fingerprint map is a high-resolution integrative data resource that provides genome-ordered associations among BAC, YAC, and PAC clones and the assembled sequence of the rat genome.
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Affiliation(s)
- Martin Krzywinski
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada V5Z 4E6
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33
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Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Simons R, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 2004; 428:493-521. [PMID: 15057822 DOI: 10.1038/nature02426] [Citation(s) in RCA: 1512] [Impact Index Per Article: 75.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2003] [Accepted: 02/20/2004] [Indexed: 01/16/2023]
Abstract
The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.
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Affiliation(s)
- Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA. http://www.hgsc.bcm.tmc.edu
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34
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Zimdahl H, Nyakatura G, Brandt P, Schulz H, Hummel O, Fartmann B, Brett D, Droege M, Monti J, Lee YA, Sun Y, Zhao S, Winter EE, Ponting CP, Chen Y, Kasprzyk A, Birney E, Ganten D, Hubner N. A SNP Map of the Rat Genome Generated from cDNA Sequences. Science 2004; 303:807. [PMID: 14764869 DOI: 10.1126/science.1092427] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Heike Zimdahl
- Max-Delbruck-Center for Molecular Medicine (MDC), Robert-Rossle-Str. 10, 13092 Berlin-Buch, Germany
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35
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Uckert W, Walther W, Hummel O. Influence of retrovirally transduced human tumor-necrosis-factor-alpha on the expression of C-myc, k-ras, C-jun, p53, tgf-alpha, and cea in human colon-carcinoma cell-lines. Int J Oncol 1995; 6:1027-31. [PMID: 21556635 DOI: 10.3892/ijo.6.5.1027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Northern slot blot hybridization and immunohistochemical staining were applied for the characterization of tumor necrosis factor alpha (TNF)-transduced human colon carcinoma cell lines. A significant decrease in the CEA-specific mRNA and protein was observed in TNF-transduced tumor cells LS174T and LoVo while other probes (c-myc, K-ras, c-jun, p53, TGF alpha) as well as anti-K-ras- and anti-p53-antibodies failed to detect differences between cytokine-transduced and parental tumor cells.
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