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Khani S, Topel H, Kardinal R, Tavanez AR, Josephrajan A, Larsen BDM, Gaudry MJ, Leyendecker P, Egedal NM, Güller AS, Stanic N, Ruppert PMM, Gaziano I, Hansmeier NR, Schmidt E, Klemm P, Vagliano LM, Stahl R, Duthie F, Krause JH, Bici A, Engelhard CA, Gohlke S, Frommolt P, Gnad T, Rada-Iglesias A, Pradas-Juni M, Schulz TJ, Wunderlich FT, Pfeifer A, Bartelt A, Jastroch M, Wachten D, Kornfeld JW. Cold-induced expression of a truncated adenylyl cyclase 3 acts as rheostat to brown fat function. Nat Metab 2024; 6:1053-1075. [PMID: 38684889 DOI: 10.1038/s42255-024-01033-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 03/25/2024] [Indexed: 05/02/2024]
Abstract
Promoting brown adipose tissue (BAT) activity innovatively targets obesity and metabolic disease. While thermogenic activation of BAT is well understood, the rheostatic regulation of BAT to avoid excessive energy dissipation remains ill-defined. Here, we demonstrate that adenylyl cyclase 3 (AC3) is key for BAT function. We identified a cold-inducible promoter that generates a 5' truncated AC3 mRNA isoform (Adcy3-at), whose expression is driven by a cold-induced, truncated isoform of PPARGC1A (PPARGC1A-AT). Male mice lacking Adcy3-at display increased energy expenditure and are resistant to obesity and ensuing metabolic imbalances. Mouse and human AC3-AT are retained in the endoplasmic reticulum, unable to translocate to the plasma membrane and lack enzymatic activity. AC3-AT interacts with AC3 and sequesters it in the endoplasmic reticulum, reducing the pool of adenylyl cyclases available for G-protein-mediated cAMP synthesis. Thus, AC3-AT acts as a cold-induced rheostat in BAT, limiting adverse consequences of cAMP activity during chronic BAT activation.
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Affiliation(s)
- Sajjad Khani
- Institute for Genetics, University of Cologne, Cologne, Germany
- Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Hande Topel
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Novo Nordisk Foundation Center for Adipocyte Signaling (Adiposign), University of Southern Denmark, Odense, Denmark
| | - Ronja Kardinal
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Ana Rita Tavanez
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Novo Nordisk Foundation Center for Adipocyte Signaling (Adiposign), University of Southern Denmark, Odense, Denmark
| | - Ajeetha Josephrajan
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Novo Nordisk Foundation Center for Adipocyte Signaling (Adiposign), University of Southern Denmark, Odense, Denmark
| | | | - Michael James Gaudry
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Philipp Leyendecker
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Nadia Meincke Egedal
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Novo Nordisk Foundation Center for Adipocyte Signaling (Adiposign), University of Southern Denmark, Odense, Denmark
| | - Aylin Seren Güller
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Natasa Stanic
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Novo Nordisk Foundation Center for Adipocyte Signaling (Adiposign), University of Southern Denmark, Odense, Denmark
| | - Phillip M M Ruppert
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | | | | | - Elena Schmidt
- Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Paul Klemm
- Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Lara-Marie Vagliano
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Rainer Stahl
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Fraser Duthie
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Jens-Henning Krause
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Ana Bici
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University, Munich, Germany
| | - Christoph Andreas Engelhard
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Centre for Physical Activity Research, Department of Infectious Diseases, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sabrina Gohlke
- Department of Adipocyte Development and Nutrition, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany
| | - Peter Frommolt
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thorsten Gnad
- Institute of Pharmacology and Toxicology, University Hospital, University of Bonn, Bonn, Germany
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria, Santander, Spain
| | - Marta Pradas-Juni
- Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), Copenhagen, Denmark
| | - Tim Julius Schulz
- Department of Adipocyte Development and Nutrition, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | | | - Alexander Pfeifer
- Institute of Pharmacology and Toxicology, University Hospital, University of Bonn, Bonn, Germany
| | - Alexander Bartelt
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University, Munich, Germany
- Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
- Department of Molecular Metabolism and Sabri Ülker Center for Metabolic Research, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Martin Jastroch
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Dagmar Wachten
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany.
| | - Jan-Wilhelm Kornfeld
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
- Novo Nordisk Foundation Center for Adipocyte Signaling (Adiposign), University of Southern Denmark, Odense, Denmark.
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Yuan N, Shen L, Peng Q, Sha R, Wang Z, Xie Z, You X, Feng Y. SRSF1 Is Required for Mitochondrial Homeostasis and Thermogenic Function in Brown Adipocytes Through its Control of Ndufs3 Splicing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306871. [PMID: 38569495 PMCID: PMC11151030 DOI: 10.1002/advs.202306871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 02/04/2024] [Indexed: 04/05/2024]
Abstract
RNA splicing dysregulation and the involvement of specific splicing factors are emerging as common factors in both obesity and metabolic disorders. The study provides compelling evidence that the absence of the splicing factor SRSF1 in mature adipocytes results in whitening of brown adipocyte tissue (BAT) and impaired thermogenesis, along with the inhibition of white adipose tissue browning in mice. Combining single-nucleus RNA sequencing with transmission electron microscopy, it is observed that the transformation of BAT cell types is associated with dysfunctional mitochondria, and SRSF1 deficiency leads to degenerated and fragmented mitochondria within BAT. The results demonstrate that SRSF1 effectively binds to constitutive exon 6 of Ndufs3 pre-mRNA and promotes its inclusion. Conversely, the deficiency of SRSF1 results in impaired splicing of Ndufs3, leading to reduced levels of functional proteins that are essential for mitochondrial complex I assembly and activity. Consequently, this deficiency disrupts mitochondrial integrity, ultimately compromising the thermogenic capacity of BAT. These findings illuminate a novel role for SRSF1 in influencing mitochondrial function and BAT thermogenesis through its regulation of Ndufs3 splicing within BAT.
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Affiliation(s)
- Ningyang Yuan
- CAS Key Laboratory of Nutrition, Metabolism and Food SafetyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
- Lin He's Academician Workstation of New Medicine and Clinical Translation in Jining Medical UniversityJining Medical UniversityJining272067China
| | - Lei Shen
- Department of General SurgeryZhongshan HospitalFudan UniversityShanghai200032China
| | - Qian Peng
- CAS Key Laboratory of Nutrition, Metabolism and Food SafetyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
| | - Rula Sha
- CAS Key Laboratory of Nutrition, Metabolism and Food SafetyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
| | - Zhenzhen Wang
- CAS Key Laboratory of Nutrition, Metabolism and Food SafetyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
| | - Zhiqi Xie
- CAS Key Laboratory of Nutrition, Metabolism and Food SafetyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
| | - Xue You
- Lin He's Academician Workstation of New Medicine and Clinical Translation in Jining Medical UniversityJining Medical UniversityJining272067China
| | - Ying Feng
- CAS Key Laboratory of Nutrition, Metabolism and Food SafetyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
- Lin He's Academician Workstation of New Medicine and Clinical Translation in Jining Medical UniversityJining Medical UniversityJining272067China
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3
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Hazell Pickering S, Abdelhalim M, Collas P, Briand N. Alternative isoform expression of key thermogenic genes in human beige adipocytes. Front Endocrinol (Lausanne) 2024; 15:1395750. [PMID: 38859907 PMCID: PMC11163967 DOI: 10.3389/fendo.2024.1395750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/07/2024] [Indexed: 06/12/2024] Open
Abstract
Background The beneficial effect of thermogenic adipocytes in maintaining body weight and protecting against metabolic disorders has raised interest in understanding the regulatory mechanisms defining white and beige adipocyte identity. Although alternative splicing has been shown to propagate adipose browning signals in mice, this has yet to be thoroughly investigated in human adipocytes. Methods We performed parallel white and beige adipogenic differentiation using primary adipose stem cells from 6 unrelated healthy subjects and assessed differential gene and isoform expression in mature adipocytes by RNA sequencing. Results We find 777 exon junctions with robust differential usage between white and beige adipocytes in all 6 subjects, mapping to 562 genes. Importantly, only 10% of these differentially spliced genes are also differentially expressed, indicating that alternative splicing constitutes an additional layer of gene expression regulation during beige adipocyte differentiation. Functional classification of alternative isoforms points to a gain of function for key thermogenic transcription factors such as PPARG and CITED1, and enzymes such as PEMT, or LPIN1. We find that a large majority of the splice variants arise from differential TSS usage, with beige-specific TSSs being enriched for PPARγ and MED1 binding compared to white-specific TSSs. Finally, we validate beige specific isoform expression at the protein level for two thermogenic regulators, PPARγ and PEMT. Discussion These results suggest that differential isoform expression through alternative TSS usage is an important regulatory mechanism for human adipocyte thermogenic specification.
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Affiliation(s)
- Sarah Hazell Pickering
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Mohamed Abdelhalim
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - Nolwenn Briand
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
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4
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Taylor BC, Steinthal LH, Dias M, Yalamanchili HK, Ochsner SA, Zapata GE, Mehta NR, McKenna NJ, Young NL, Nuotio-Antar AM. Histone proteoform analysis reveals epigenetic changes in adult mouse brown adipose tissue in response to cold stress. Epigenetics Chromatin 2024; 17:12. [PMID: 38678237 PMCID: PMC11055387 DOI: 10.1186/s13072-024-00536-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/09/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Regulation of the thermogenic response by brown adipose tissue (BAT) is an important component of energy homeostasis with implications for the treatment of obesity and diabetes. Our preliminary analyses of RNA-Seq data uncovered many nodes representing epigenetic modifiers that are altered in BAT in response to chronic thermogenic activation. Thus, we hypothesized that chronic thermogenic activation broadly alters epigenetic modifications of DNA and histones in BAT. RESULTS Motivated to understand how BAT function is regulated epigenetically, we developed a novel method for the first-ever unbiased top-down proteomic quantitation of histone modifications in BAT and validated our results with a multi-omic approach. To test our hypothesis, wildtype male C57BL/6J mice were housed under chronic conditions of thermoneutral temperature (TN, 28°C), mild cold/room temperature (RT, 22°C), or severe cold (SC, 8°C) and BAT was analyzed for DNA methylation and histone modifications. Methylation of promoters and intragenic regions in genomic DNA decrease in response to chronic cold exposure. Integration of DNA methylation and RNA expression datasets suggest a role for epigenetic modification of DNA in regulation of gene expression in response to cold. In response to cold housing, we observe increased bulk acetylation of histones H3.2 and H4, increased histone H3.2 proteoforms with di- and trimethylation of lysine 9 (K9me2 and K9me3), and increased histone H4 proteoforms with acetylation of lysine 16 (K16ac) in BAT. CONCLUSIONS Our results reveal global epigenetically-regulated transcriptional "on" and "off" signals in murine BAT in response to varying degrees of chronic cold stimuli and establish a novel methodology to quantitatively study histones in BAT, allowing for direct comparisons to decipher mechanistic changes during the thermogenic response. Additionally, we make histone PTM and proteoform quantitation, RNA splicing, RRBS, and transcriptional footprint datasets available as a resource for future research.
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Affiliation(s)
- Bethany C Taylor
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Loic H Steinthal
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA
| | - Michelle Dias
- Department of Pediatrics, Division of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Hari Krishna Yalamanchili
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Division of Neurology, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Scott A Ochsner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Gladys E Zapata
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA
| | - Nitesh R Mehta
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA
| | - Neil J McKenna
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Nicolas L Young
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA.
| | - Alli M Nuotio-Antar
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA.
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5
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Nakamura M. Lipotoxicity as a therapeutic target in obesity and diabetic cardiomyopathy. JOURNAL OF PHARMACY & PHARMACEUTICAL SCIENCES : A PUBLICATION OF THE CANADIAN SOCIETY FOR PHARMACEUTICAL SCIENCES, SOCIETE CANADIENNE DES SCIENCES PHARMACEUTIQUES 2024; 27:12568. [PMID: 38706718 PMCID: PMC11066298 DOI: 10.3389/jpps.2024.12568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/09/2024] [Indexed: 05/07/2024]
Abstract
Unhealthy sources of fats, ultra-processed foods with added sugars, and a sedentary lifestyle make humans more susceptible to developing overweight and obesity. While lipids constitute an integral component of the organism, excessive and abnormal lipid accumulation that exceeds the storage capacity of lipid droplets disrupts the intracellular composition of fatty acids and results in the release of deleterious lipid species, thereby giving rise to a pathological state termed lipotoxicity. This condition induces endoplasmic reticulum stress, mitochondrial dysfunction, inflammatory responses, and cell death. Recent advances in omics technologies and analytical methodologies and clinical research have provided novel insights into the mechanisms of lipotoxicity, including gut dysbiosis, epigenetic and epitranscriptomic modifications, dysfunction of lipid droplets, post-translational modifications, and altered membrane lipid composition. In this review, we discuss the recent knowledge on the mechanisms underlying the development of lipotoxicity and lipotoxic cardiometabolic disease in obesity, with a particular focus on lipotoxic and diabetic cardiomyopathy.
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Affiliation(s)
- Michinari Nakamura
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, United States
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6
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Ciampi L, Serrano L, Irimia M. Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States. Mol Syst Biol 2024; 20:296-310. [PMID: 38438733 PMCID: PMC10987577 DOI: 10.1038/s44320-024-00020-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/04/2024] [Accepted: 01/12/2024] [Indexed: 03/06/2024] Open
Abstract
Alternative Splicing (AS) programs serve as instructive signals of cell type specificity, particularly within the brain, which comprises dozens of molecularly and functionally distinct cell types. Among them, retinal photoreceptors stand out due to their unique transcriptome, making them a particularly well-suited system for studying how AS shapes cell type-specific molecular functions. Here, we use the Splicing Regulatory State (SRS) as a novel framework to discuss the splicing factors governing the unique AS pattern of photoreceptors, and how this pattern may aid in the specification of their highly specialized sensory cilia. In addition, we discuss how other sensory cells with ciliated structures, for which data is much scarcer, also rely on specific SRSs to implement a proteome specialized in the detection of sensory stimuli. By reviewing the general rules of cell type- and tissue-specific AS programs, firstly in the brain and subsequently in specialized sensory neurons, we propose a novel paradigm on how SRSs are established and how they can diversify. Finally, we illustrate how SRSs shape the outcome of mutations in splicing factors to produce cell type-specific phenotypes that can lead to various human diseases.
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Affiliation(s)
- Ludovica Ciampi
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Luis Serrano
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Manuel Irimia
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
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7
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Farris KM, Senior AM, Sobreira DR, Mitchell RM, Weber ZT, Ingerslev LR, Barrès R, Simpson SJ, Crean AJ, Nobrega MA. Dietary macronutrient composition impacts gene regulation in adipose tissue. Commun Biol 2024; 7:194. [PMID: 38365885 PMCID: PMC10873408 DOI: 10.1038/s42003-024-05876-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 01/30/2024] [Indexed: 02/18/2024] Open
Abstract
Diet is a key lifestyle component that influences metabolic health through several factors, including total energy intake and macronutrient composition. While the impact of caloric intake on gene expression and physiological phenomena in various tissues is well described, the influence of dietary macronutrient composition on these parameters is less well studied. Here, we use the Nutritional Geometry framework to investigate the role of macronutrient composition on metabolic function and gene regulation in adipose tissue. Using ten isocaloric diets that vary systematically in their proportion of energy from fat, protein, and carbohydrates, we find that gene expression and splicing are highly responsive to macronutrient composition, with distinct sets of genes regulated by different macronutrient interactions. Specifically, the expression of many genes associated with Bardet-Biedl syndrome is responsive to dietary fat content. Splicing and expression changes occur in largely separate gene sets, highlighting distinct mechanisms by which dietary composition influences the transcriptome and emphasizing the importance of considering splicing changes to more fully capture the gene regulation response to environmental changes such as diet. Our study provides insight into the gene regulation plasticity of adipose tissue in response to macronutrient composition, beyond the already well-characterized response to caloric intake.
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Affiliation(s)
- Kathryn M Farris
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
| | - Alistair M Senior
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Débora R Sobreira
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Robert M Mitchell
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Zachary T Weber
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Lars R Ingerslev
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, DK-2200, Copenhagen, Denmark.
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur & Centre National pour la Recherche Scientifique (CNRS), Valbonne, 06560, France.
| | - Stephen J Simpson
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Angela J Crean
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.
| | - Marcelo A Nobrega
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
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8
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Castellá M, Mestres-Arenas A, Gavaldà-Navarro A, Blasco-Roset A, Quesada-López T, Romero-Carramiñana I, Giralt M, Villarroya F, Cereijo R. The splicing factor SF3B1 is involved in brown adipocyte thermogenic activation. Biochem Pharmacol 2024; 220:116014. [PMID: 38158020 DOI: 10.1016/j.bcp.2023.116014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
The ability of alternative splicing mechanisms to control gene expression is increasingly being recognized as relevant for adipose tissue function. The expression of SF3B1, a key component of the SF3B complex directly involved in spliceosome formation, was previously reported to be significantly induced in brown adipose tissue under cold-induced thermogenic activation. Here, we identify that noradrenergic cAMP-mediated thermogenic stimulation increases SF3B1 expression in brown and beige adipocytes. We further show that pladienolide-B, a drug that binds SF3B1 to inhibit pre-mRNA splicing by targeting the SF3B complex, down-regulates key components of the thermogenic machinery (e.g., UCP1 gene expression), differentially alters the expression of alternative splicing-regulated transcripts encoding molecular actors involved in the oxidative metabolism of brown adipocytes (e.g., peroxisome proliferator-activated receptor-gamma co-activator-alpha [PGC-1α] and cytochrome oxidase subunit 7a genes), and impairs the respiratory activity of brown adipocytes. Similar alterations were found in brown adipocytes with siRNA-mediated knockdown of SF3B1 protein levels. Our findings collectively indicate that SF3B1 is a key factor in the appropriate thermogenic activation of differentiated brown adipocytes. This work exemplifies the importance of splicing processes in adaptive thermogenesis and suggests that pharmacological tools, such as pladienolide-B, may be used to modulate brown adipocyte thermogenic activity.
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Affiliation(s)
- Moisés Castellá
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain; CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Alberto Mestres-Arenas
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain; CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Aleix Gavaldà-Navarro
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain; CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Albert Blasco-Roset
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain; CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Tania Quesada-López
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain; CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain; Institut d'Investigació Biomèdica Sant Pau (IIB-SANT PAU), and Department of Infectious Diseases, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain
| | - Inés Romero-Carramiñana
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain; Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM); Instituto de Investigación Hospital 12 de Octubre, Universidad Autónoma de Madrid; and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) ISCIII, 28049 Madrid, Spain
| | - Marta Giralt
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain; CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Francesc Villarroya
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain; CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain.
| | - Rubén Cereijo
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain; CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain.
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9
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Taylor BC, Steinthal LH, Dias M, Yalamanchili HK, Ochsner SA, Zapata GE, Mehta NR, McKenna NJ, Young NL, Nuotio-Antar AM. Histone proteoform analysis reveals epigenetic changes in adult mouse brown adipose tissue in response to cold stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.30.551059. [PMID: 38328142 PMCID: PMC10849524 DOI: 10.1101/2023.07.30.551059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Regulation of the thermogenic response by brown adipose tissue (BAT) is an important component of energy homeostasis with implications for the treatment of obesity and diabetes. Our preliminary analyses uncovered many nodes representing epigenetic modifiers that are altered in BAT in response to chronic thermogenic activation. Thus, we hypothesized that chronic thermogenic activation broadly alters epigenetic modifications of DNA and histones in BAT. Motivated to understand how BAT function is regulated epigenetically, we developed a novel method for the first-ever unbiased top-down proteomic quantitation of histone modifications in BAT and validated our results with a multi-omic approach. To test our hypothesis, wildtype male C57BL/6J mice were housed under chronic conditions of thermoneutral temperature (TN, 28.8°C), mild cold/room temperature (RT, 22°C), or severe cold (SC, 8°C) and BAT was analyzed for DNA methylation and histone modifications. Methylation of promoters and intragenic regions in genomic DNA decrease in response to chronic cold exposure. Integration of DNA methylation and RNA expression data suggest a role for epigenetic modification of DNA in gene regulation in response to cold. In response to cold housing, we observe increased bulk acetylation of histones H3.2 and H4, increased histone H3.2 proteoforms with di- and trimethylation of lysine 9 (K9me2 and K9me3), and increased histone H4 proteoforms with acetylation of lysine 16 (K16ac) in BAT. Taken together, our results reveal global epigenetically-regulated transcriptional "on" and "off" signals in murine BAT in response to varying degrees of chronic cold stimuli and establish a novel methodology to quantitatively study histones in BAT, allowing for direct comparisons to decipher mechanistic changes during the thermogenic response. Additionally, we make histone PTM and proteoform quantitation, RNA splicing, RRBS, and transcriptional footprint datasets available as a resource for future research.
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Affiliation(s)
- Bethany C. Taylor
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX
| | - Loic H. Steinthal
- Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX
| | - Michelle Dias
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX
| | - Hari K. Yalamanchili
- Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX
| | - Scott A. Ochsner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Gladys E. Zapata
- Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX
| | - Nitesh R. Mehta
- Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX
| | - Neil J. McKenna
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Nicolas L. Young
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
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10
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Jobbins AM, Yu S, Paterson HAB, Maude H, Kefala-Stavridi A, Speck C, Cebola I, Vernia S. Pre-RNA splicing in metabolic homeostasis and liver disease. Trends Endocrinol Metab 2023; 34:823-837. [PMID: 37673766 DOI: 10.1016/j.tem.2023.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023]
Abstract
The liver plays a key role in sensing nutritional and hormonal inputs to maintain metabolic homeostasis. Recent studies into pre-mRNA splicing and alternative splicing (AS) and their effects on gene expression have revealed considerable transcriptional complexity in the liver, both in health and disease. While the contribution of these mechanisms to cell and tissue identity is widely accepted, their role in physiological and pathological contexts within tissues is just beginning to be appreciated. In this review, we showcase recent studies on the splicing and AS of key genes in metabolic pathways in the liver, the effect of metabolic signals on the spliceosome, and therapeutic intervention points based on RNA splicing.
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Affiliation(s)
- Andrew M Jobbins
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Sijia Yu
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Helen A B Paterson
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Hannah Maude
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Antonia Kefala-Stavridi
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Christian Speck
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Santiago Vernia
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
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11
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Nobrega M, Farris K, Andersen E, Donkin I, Versteyhe S, Kristiansen VB, Simpson S, Barres R. Splicing across adipocyte differentiation is highly dynamic and impacted by metabolic phenotype. RESEARCH SQUARE 2023:rs.3.rs-3487148. [PMID: 37961160 PMCID: PMC10635361 DOI: 10.21203/rs.3.rs-3487148/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Adipose tissue dysfunction underlies many of the metabolic complications associated with obesity. A better understanding of the gene regulation differences present in metabolically unhealthy adipose tissue can provide insights into the mechanisms underlying adipose tissue dysfunction. Here, we used RNA-seq data collected from a differentiation time course of lean, obese, and obese with type 2 diabetes (T2D) individuals to characterize the role of alterative splicing in adipocyte differentiation and function. We found that splicing was highly dynamic across adipocyte differentiation in all three cohorts, and that the dynamics of splicing were significantly impacted by metabolic phenotype. We also found that there was very little overlap between genes that were differentially spliced in adipocyte differentiation and those that were differentially expressed, positioning alternative splicing as a largely independent gene regulatory mechanism whose impact would be missed when looking at gene expression changes alone. To assess the impact of alternative splicing across adipocyte differentiation on genetic risk for metabolic diseases, we integrated the differential splicing results generated here with genome-wide association study results for body mass index and T2D, and found that variants associated with T2D were enriched in regions that were differentially spliced in early differentiation. These findings provide insight into the role of alternative splicing in adipocyte differentiation and can serve as a resource to guide future variant-to-function studies.
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Affiliation(s)
| | | | | | | | | | | | | | - Romain Barres
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark
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12
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Engelhard CA, Khani S, Derdak S, Bilban M, Kornfeld JW. Nanopore sequencing unveils the complexity of the cold-activated murine brown adipose tissue transcriptome. iScience 2023; 26:107190. [PMID: 37564700 PMCID: PMC10410515 DOI: 10.1016/j.isci.2023.107190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/28/2023] [Accepted: 06/16/2023] [Indexed: 08/12/2023] Open
Abstract
Alternative transcription increases transcriptome complexity by expression of multiple transcripts per gene. Annotation and quantification of transcripts using short-read sequencing is non-trivial. Long-read sequencing aims at overcoming these problems by sequencing full-length transcripts. Activation of brown adipose tissue (BAT) thermogenesis involves major transcriptomic remodeling and positively affects metabolism via increased energy expenditure. We benchmark Oxford Nanopore Technology (ONT) long-read sequencing protocols to Illumina short-read sequencing assessing alignment characteristics, gene and transcript detection and quantification, differential gene and transcript expression, transcriptome reannotation, and differential transcript usage (DTU). We find ONT sequencing is superior to Illumina for transcriptome reassembly, reducing the risk of false-positive events by unambiguously mapping reads to transcripts. We identified novel isoforms of genes undergoing DTU in cold-activated BAT including Cars2, Adtrp, Acsl5, Scp2, Aldoa, and Pde4d, validated by real-time PCR. The reannotated murine BAT transcriptome established here provides a framework for future investigations into the regulation of BAT.
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Affiliation(s)
- Christoph Andreas Engelhard
- Department for Biochemistry and Molecular Biology (BMB), University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Sajjad Khani
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Sophia Derdak
- Core Facilities, Medical University of Vienna, Lazarettgasse 14, 1090 Vienna, Austria
| | - Martin Bilban
- Department of Laboratory Medicine & Core Facilities, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Jan-Wilhelm Kornfeld
- Department for Biochemistry and Molecular Biology (BMB), University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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13
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Snyman M, Xu S. The effects of mutations on gene expression and alternative splicing. Proc Biol Sci 2023; 290:20230565. [PMID: 37403507 PMCID: PMC10320348 DOI: 10.1098/rspb.2023.0565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
Understanding the relationship between mutations and their genomic and phenotypic consequences has been a longstanding goal of evolutionary biology. However, few studies have investigated the impact of mutations on gene expression and alternative splicing on the genome-wide scale. In this study, we aim to bridge this knowledge gap by utilizing whole-genome sequencing data and RNA sequencing data from 16 obligately parthenogenetic Daphnia mutant lines to investigate the effects of ethyl methanesulfonate-induced mutations on gene expression and alternative splicing. Using rigorous analyses of mutations, expression changes and alternative splicing, we show that trans-effects are the major contributor to the variance in gene expression and alternative splicing between the wild-type and mutant lines, whereas cis mutations only affected a limited number of genes and do not always alter gene expression. Moreover, we show that there is a significant association between differentially expressed genes and exonic mutations, indicating that exonic mutations are an important driver of altered gene expression.
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Affiliation(s)
- Marelize Snyman
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Sen Xu
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
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14
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Castellá M, Blasco-Roset A, Peyrou M, Gavaldà-Navarro A, Villarroya J, Quesada-López T, Lorente-Poch L, Sancho J, Szymczak F, Piron A, Rodríguez-Fernández S, Carobbio S, Goday A, Domingo P, Vidal-Puig A, Giralt M, Eizirik DL, Villarroya F, Cereijo R. Adipose tissue plasticity in pheochromocytoma patients suggests a role of the splicing machinery in human adipose browning. iScience 2023; 26:106847. [PMID: 37250773 PMCID: PMC10209542 DOI: 10.1016/j.isci.2023.106847] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/31/2023] [Accepted: 05/04/2023] [Indexed: 05/31/2023] Open
Abstract
Adipose tissue from pheochromocytoma patients acquires brown fat features, making it a valuable model for studying the mechanisms that control thermogenic adipose plasticity in humans. Transcriptomic analyses revealed a massive downregulation of splicing machinery components and splicing regulatory factors in browned adipose tissue from patients, with upregulation of a few genes encoding RNA-binding proteins potentially involved in splicing regulation. These changes were also observed in cell culture models of human brown adipocyte differentiation, confirming a potential involvement of splicing in the cell-autonomous control of adipose browning. The coordinated changes in splicing are associated with a profound modification in the expression levels of splicing-driven transcript isoforms for genes involved in the specialized metabolism of brown adipocytes and those encoding master transcriptional regulators of adipose browning. Splicing control appears to be a relevant component of the coordinated gene expression changes that allow human adipose tissue to acquire a brown phenotype.
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Affiliation(s)
- Moisés Castellá
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Albert Blasco-Roset
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Marion Peyrou
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Aleix Gavaldà-Navarro
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Joan Villarroya
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Tania Quesada-López
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
- Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Hospital de la Santa Creu i Sant Pau, and Department of Infectious Diseases, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain
| | | | - Juan Sancho
- Endocrine Surgery Unit, Hospital del Mar, 08003 Barcelona, Spain
| | - Florian Szymczak
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), 1070 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Anthony Piron
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), 1070 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Sonia Rodríguez-Fernández
- University of Cambridge Metabolic Research Laboratories, Wellcome-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge 289, UK
| | - Stefania Carobbio
- Bases Moleculares de Patologías Humanas, Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain
| | - Albert Goday
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
- Endocrinology Service, Hospital del Mar, IMIM, 08003 Barcelona, Spain
- Department of Medicine, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Pere Domingo
- Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Hospital de la Santa Creu i Sant Pau, and Department of Infectious Diseases, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain
- Department of Medicine, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Antonio Vidal-Puig
- University of Cambridge Metabolic Research Laboratories, Wellcome-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge 289, UK
| | - Marta Giralt
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Décio L. Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), 1070 Brussels, Belgium
| | - Francesc Villarroya
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Rubén Cereijo
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
- Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Hospital de la Santa Creu i Sant Pau, and Department of Infectious Diseases, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain
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15
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Naing YT, Sun L. The Role of Splicing Factors in Adipogenesis and Thermogenesis. Mol Cells 2023; 46:268-277. [PMID: 37170770 PMCID: PMC10183792 DOI: 10.14348/molcells.2023.2195] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/27/2023] [Accepted: 03/03/2023] [Indexed: 05/13/2023] Open
Abstract
Obesity is a significant global health risk that can cause a range of serious metabolic problems, such as type 2 diabetes and cardiovascular diseases. Adipose tissue plays a pivotal role in regulating energy and lipid storage. New research has underlined the crucial role of splicing factors in the physiological and functional regulation of adipose tissue. By generating multiple transcripts from a single gene, alternative splicing allows for a greater diversity of the proteome and transcriptome, which subsequently influence adipocyte development and metabolism. In this review, we provide an outlook on the part of splicing factors in adipogenesis and thermogenesis, and investigate how the different spliced isoforms can affect the development and function of adipose tissue.
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Affiliation(s)
- Yadanar Than Naing
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore 169857
| | - Lei Sun
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore 169857
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16
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Marasco LE, Kornblihtt AR. The physiology of alternative splicing. Nat Rev Mol Cell Biol 2023; 24:242-254. [PMID: 36229538 DOI: 10.1038/s41580-022-00545-z] [Citation(s) in RCA: 116] [Impact Index Per Article: 116.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2022] [Indexed: 11/09/2022]
Abstract
Alternative splicing is a substantial contributor to the high complexity of transcriptomes of multicellular eukaryotes. In this Review, we discuss the accumulated evidence that most of this complexity is reflected at the protein level and fundamentally shapes the physiology and pathology of organisms. This notion is supported not only by genome-wide analyses but, mainly, by detailed studies showing that global and gene-specific modulations of alternative splicing regulate highly diverse processes such as tissue-specific and species-specific cell differentiation, thermal regulation, neuron self-avoidance, infrared sensing, the Warburg effect, maintenance of telomere length, cancer and autism spectrum disorders (ASD). We also discuss how mastering the control of alternative splicing paved the way to clinically approved therapies for hereditary diseases.
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Affiliation(s)
- Luciano E Marasco
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Moleculary Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Alberto R Kornblihtt
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Moleculary Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina.
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17
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Phosphorylation of RXRα mediates the effect of JNK to suppress hepatic FGF21 expression and promote metabolic syndrome. Proc Natl Acad Sci U S A 2022; 119:e2210434119. [PMID: 36282921 PMCID: PMC9636906 DOI: 10.1073/pnas.2210434119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cJun NH2-terminal kinase (JNK) signaling pathway in the liver promotes systemic changes in metabolism by regulating peroxisome proliferator-activated receptor α (PPARα)-dependent expression of the hepatokine fibroblast growth factor 21 (FGF21). Hepatocyte-specific gene ablation studies demonstrated that the Mapk9 gene (encoding JNK2) plays a key mechanistic role. Mutually exclusive inclusion of exons 7a and 7b yields expression of the isoforms JNK2α and JNK2β. Here we demonstrate that Fgf21 gene expression and metabolic regulation are primarily regulated by the JNK2α isoform. To identify relevant substrates of JNK2α, we performed a quantitative phosphoproteomic study of livers isolated from control mice, mice with JNK deficiency in hepatocytes, and mice that express only JNK2α or JNK2β in hepatocytes. We identified the JNK substrate retinoid X receptor α (RXRα) as a protein that exhibited JNK2α-promoted phosphorylation in vivo. RXRα functions as a heterodimeric partner of PPARα and may therefore mediate the effects of JNK2α signaling on Fgf21 expression. To test this hypothesis, we established mice with hepatocyte-specific expression of wild-type or mutated RXRα proteins. We found that the RXRα phosphorylation site Ser260 was required for suppression of Fgf21 gene expression. Collectively, these data establish a JNK-mediated signaling pathway that regulates hepatic Fgf21 expression.
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18
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Nova1 or Bim Deficiency in Pancreatic β-Cells Does Not Alter Multiple Low-Dose Streptozotocin-Induced Diabetes and Diet-Induced Obesity in Mice. Nutrients 2022; 14:nu14183866. [PMID: 36145242 PMCID: PMC9500891 DOI: 10.3390/nu14183866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 11/17/2022] Open
Abstract
The loss of functional pancreatic β-cell mass is an important hallmark of both type 1 and type 2 diabetes. The RNA-binding protein NOVA1 is expressed in human and rodent pancreatic β-cells. Previous in vitro studies indicated that NOVA1 is necessary for glucose-stimulated insulin secretion and its deficiency-enhanced cytokine-induced apoptosis. Moreover, Bim, a proapoptotic protein, is differentially spliced and potentiates apoptosis in NOVA1-deficient β-cells in culture. We generated two novel mouse models by Cre-Lox technology lacking Nova1 (βNova1-/-) or Bim (βBim-/-) in β-cells. To test the impact of Nova1 or Bim deletion on β-cell function, mice were subjected to multiple low-dose streptozotocin (MLD-STZ)-induced diabetes or high-fat diet-induced insulin resistance. β-cell-specific Nova1 or Bim deficiency failed to affect diabetes development in response to MLD-STZ-induced β-cell dysfunction and death evidenced by unaltered blood glucose levels and pancreatic insulin content. In addition, body composition, glucose and insulin tolerance test, and pancreatic insulin content were indistinguishable between control and βNova1-/- or βBim-/- mice on a high fat diet. Thus, Nova1 or Bim deletion in β-cells does not impact on glucose homeostasis or diabetes development in mice. Together, these data argue against an in vivo role for the Nova1-Bim axis in β-cells.
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19
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Therapeutic RNA-silencing oligonucleotides in metabolic diseases. Nat Rev Drug Discov 2022; 21:417-439. [PMID: 35210608 DOI: 10.1038/s41573-022-00407-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2022] [Indexed: 12/14/2022]
Abstract
Recent years have seen unprecedented activity in the development of RNA-silencing oligonucleotide therapeutics for metabolic diseases. Improved oligonucleotide design and optimization of synthetic nucleic acid chemistry, in combination with the development of highly selective and efficient conjugate delivery technology platforms, have established and validated oligonucleotides as a new class of drugs. To date, there are five marketed oligonucleotide therapies, with many more in clinical studies, for both rare and common liver-driven metabolic diseases. Here, we provide an overview of recent developments in the field of oligonucleotide therapeutics in metabolism, review past and current clinical trials, and discuss ongoing challenges and possible future developments.
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20
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Gohr A, Mantica F, Hermoso-Pulido A, Tapial J, Márquez Y, Irimia M. Computational Analysis of Alternative Splicing Using VAST-TOOLS and the VastDB Framework. Methods Mol Biol 2022; 2537:97-128. [PMID: 35895261 DOI: 10.1007/978-1-0716-2521-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Alternative splicing (AS) can vastly expand animal transcriptomes and proteomes. Two main open questions in the field are how AS is regulated across cell/tissue types and disease, and what roles different AS events play. To facilitate AS research, we have created the computational VastDB framework, which comprises a series of complementary software and resources that we describe in this chapter. The VastDB framework is especially designed to aid biomedical researchers without a strong computational background. It offers tools and resources to: (a) quantify AS and identify differentially spliced AS events using RNA-seq data (vast-tools), (b) perform multiple genomic and sequence analyses for investigating AS events (Matt), (c) identify AS events with genomic and regulatory conservation among species (ExOrthist), and (d) help with the biological interpretation of the results, and, ultimately, with the identification of interesting AS events to design wet-lab experiments (VastDB and PastDB).
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Affiliation(s)
- André Gohr
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Federica Mantica
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Antonio Hermoso-Pulido
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Javier Tapial
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Yamile Márquez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
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21
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Smith AO, Jonassen JA, Preval KM, Davis RJ, Pazour GJ. c-Jun N-terminal kinase (JNK) signaling contributes to cystic burden in polycystic kidney disease. PLoS Genet 2021; 17:e1009711. [PMID: 34962918 PMCID: PMC8746764 DOI: 10.1371/journal.pgen.1009711] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 01/10/2022] [Accepted: 12/11/2021] [Indexed: 11/18/2022] Open
Abstract
Polycystic kidney disease is an inherited degenerative disease in which the uriniferous tubules are replaced by expanding fluid-filled cysts that ultimately destroy organ function. Autosomal dominant polycystic kidney disease (ADPKD) is the most common form, afflicting approximately 1 in 1,000 people. It primarily is caused by mutations in the transmembrane proteins polycystin-1 (Pkd1) and polycystin-2 (Pkd2). The most proximal effects of Pkd mutations leading to cyst formation are not known, but pro-proliferative signaling must be involved for the tubule epithelial cells to increase in number over time. The c-Jun N-terminal kinase (JNK) pathway promotes proliferation and is activated in acute and chronic kidney diseases. Using a mouse model of cystic kidney disease caused by Pkd2 loss, we observe JNK activation in cystic kidneys and observe increased nuclear phospho c-Jun in cystic epithelium. Genetic removal of Jnk1 and Jnk2 suppresses the nuclear accumulation of phospho c-Jun, reduces proliferation and reduces the severity of cystic disease. While Jnk1 and Jnk2 are thought to have largely overlapping functions, we find that Jnk1 loss is nearly as effective as the double loss of Jnk1 and Jnk2. Jnk pathway inhibitors are in development for neurodegeneration, cancer, and fibrotic diseases. Our work suggests that the JNK pathway should be explored as a therapeutic target for ADPKD. Autosomal dominant polycystic kidney disease is a leading cause of end stage renal disease requiring dialysis or kidney transplant. During disease development, the cells lining the kidney tubules proliferate. This proliferation transforms normally small diameter tubules into fluid-filled cysts that enlarge with time, eventually destroying all kidney function. Despite decades of research, polycystic kidney disease remains incurable. Furthermore, the precise signaling events involved in cyst initiation and growth remain unclear. The c-Jun N-terminal kinase (JNK), is a major pathway regulating cellular proliferation and differentiation but its importance to polycystic kidney disease was not known. We show that JNK activity is elevated in cystic kidneys and that reducing JNK activity decreases cyst growth pointing to JNK inhibition as a therapeutic strategy for treating polycystic kidney disease.
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Affiliation(s)
- Abigail O. Smith
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Biotech II, Worcester, Massachusetts, United States of America
| | - Julie A. Jonassen
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester Massachusetts, United States of America
| | - Kenley M. Preval
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Biotech II, Worcester, Massachusetts, United States of America
| | - Roger J. Davis
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Biotech II, Worcester, Massachusetts, United States of America
| | - Gregory J. Pazour
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Biotech II, Worcester, Massachusetts, United States of America
- * E-mail:
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22
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Cataldi S, Aprile M, Melillo D, Mucel I, Giorgetti-Peraldi S, Cormont M, Italiani P, Blüher M, Tanti JF, Ciccodicola A, Costa V. TNFα Mediates Inflammation-Induced Effects on PPARG Splicing in Adipose Tissue and Mesenchymal Precursor Cells. Cells 2021; 11:cells11010042. [PMID: 35011604 PMCID: PMC8750445 DOI: 10.3390/cells11010042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 01/18/2023] Open
Abstract
Low-grade chronic inflammation and reduced differentiation capacity are hallmarks of hypertrophic adipose tissue (AT) and key contributors of insulin resistance. We identified PPARGΔ5 as a dominant-negative splicing isoform overexpressed in the AT of obese/diabetic patients able to impair adipocyte differentiation and PPARγ activity in hypertrophic adipocytes. Herein, we investigate the impact of macrophage-secreted pro-inflammatory factors on PPARG splicing, focusing on PPARGΔ5. We report that the epididymal AT of LPS-treated mice displays increased PpargΔ5/cPparg ratio and reduced expression of Pparg-regulated genes. Interestingly, pro-inflammatory factors secreted from murine and human pro-inflammatory macrophages enhance the PPARGΔ5/cPPARG ratio in exposed adipogenic precursors. TNFα is identified herein as factor able to alter PPARG splicing—increasing PPARGΔ5/cPPARG ratio—through PI3K/Akt signaling and SRp40 splicing factor. In line with in vitro data, TNFA expression is higher in the SAT of obese (vs. lean) patients and positively correlates with PPARGΔ5 levels. In conclusion, our results indicate that inflammatory factors secreted by metabolically-activated macrophages are potent stimuli that modulate the expression and splicing of PPARG. The resulting imbalance between canonical and dominant negative isoforms may crucially contribute to impair PPARγ activity in hypertrophic AT, exacerbating the defective adipogenic capacity of precursor cells.
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Affiliation(s)
- Simona Cataldi
- Institute of Genetics and Biophysics ‘‘Adriano Buzzati-Traverso’’, CNR, Via P. Castellino 111, 80131 Naples, Italy; (S.C.); (M.A.); (A.C.)
| | - Marianna Aprile
- Institute of Genetics and Biophysics ‘‘Adriano Buzzati-Traverso’’, CNR, Via P. Castellino 111, 80131 Naples, Italy; (S.C.); (M.A.); (A.C.)
| | - Daniela Melillo
- Institute of Biochemistry and Cell Biology, CNR, Via P. Castellino 111, 80131 Naples, Italy; (D.M.); (P.I.)
| | - Inès Mucel
- Université Côte d’Azur, Inserm UMR1065, C3M, Team Cellular and Molecular Pathophysiology of Obesity, 06204 Nice, France; (I.M.); (S.G.-P.); (M.C.); (J.-F.T.)
| | - Sophie Giorgetti-Peraldi
- Université Côte d’Azur, Inserm UMR1065, C3M, Team Cellular and Molecular Pathophysiology of Obesity, 06204 Nice, France; (I.M.); (S.G.-P.); (M.C.); (J.-F.T.)
| | - Mireille Cormont
- Université Côte d’Azur, Inserm UMR1065, C3M, Team Cellular and Molecular Pathophysiology of Obesity, 06204 Nice, France; (I.M.); (S.G.-P.); (M.C.); (J.-F.T.)
| | - Paola Italiani
- Institute of Biochemistry and Cell Biology, CNR, Via P. Castellino 111, 80131 Naples, Italy; (D.M.); (P.I.)
| | - Matthias Blüher
- Medical Department III-Endocrinology, Nephrology and Rheumatology, University of Leipzig, 04103 Leipzig, Germany;
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Philipp-Rosenthal-Str. 27, 04103 Leipzig, Germany
| | - Jean-François Tanti
- Université Côte d’Azur, Inserm UMR1065, C3M, Team Cellular and Molecular Pathophysiology of Obesity, 06204 Nice, France; (I.M.); (S.G.-P.); (M.C.); (J.-F.T.)
| | - Alfredo Ciccodicola
- Institute of Genetics and Biophysics ‘‘Adriano Buzzati-Traverso’’, CNR, Via P. Castellino 111, 80131 Naples, Italy; (S.C.); (M.A.); (A.C.)
- Department of Science and Technology, University of Naples ‘‘Parthenope’’, 80143 Naples, Italy
| | - Valerio Costa
- Institute of Genetics and Biophysics ‘‘Adriano Buzzati-Traverso’’, CNR, Via P. Castellino 111, 80131 Naples, Italy; (S.C.); (M.A.); (A.C.)
- Correspondence: ; Tel.: +39-0816132617
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23
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Liu K, Su Q, Kang K, Chen M, Wang WX, Zhang WQ, Pang R. Genome-wide Analysis of Alternative Gene Splicing Associated with Virulence in the Brown Planthopper Nilaparvata lugens (Hemiptera: Delphacidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2021; 114:2512-2523. [PMID: 34568947 DOI: 10.1093/jee/toab186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Indexed: 06/13/2023]
Abstract
Alternative splicing of protein coding genes plays a profound role in phenotypic variation for many eukaryotic organisms. The development of high-throughput sequencing and bioinformatics algorithms provides the possibility of genome-wide identification of alternative splicing events in eukaryotes. However, for the brown planthopper Nilaparvata lugens, a destructive pest of rice crops, whole-genome distribution of alternative splicing events and the role of alternative splicing in the phenotypic plasticity of virulence have not previously been estimated. Here, we developed an analysis pipeline to identify alternative splicing events in the genome of N. lugens. Differential expression analysis and functional annotation were performed on datasets related to different virulence phenotypes. In total, 27,880 alternative splicing events corresponding to 9,787 multi-exon genes were detected in N. lugens. Among them, specifically expressed alternative splicing transcripts in the virulent Mudgo population were enriched in metabolic process categories, while transcripts in the avirulent TN1 population were enriched in regulator activity categories. In addition, genes encoding odorant receptor, secreted saliva protein and xenobiotic metabolic P450 monooxygenase showed different splicing patterns between Mudgo population and TN1 population. Host change experiment also revealed that an isoform of a P450 gene could be specially induced by the stimulation of resistant rice variety Mudgo. This research pioneered a genome-wide study of alternative gene splicing in the rice brown planthopper. Differences in alternative splicing between virulent and avirulent populations indicated that alternative splicing might play an important role in the formation of virulence phenotypes in N. lugens.
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Affiliation(s)
- Kai Liu
- Innovative Institute for Plant Health, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Qin Su
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Kui Kang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Meng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wei-Xia Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Wen-Qing Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Rui Pang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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24
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Suchý T, Kaczmarek I, Maricic T, Zieschang C, Schöneberg T, Thor D, Liebscher I. Evaluating the feasibility of Cas9 overexpression in 3T3-L1 cells for generation of genetic knock-out adipocyte cell lines. Adipocyte 2021; 10:631-645. [PMID: 34915813 PMCID: PMC8735834 DOI: 10.1080/21623945.2021.1990480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Cell lines recapitulating physiological processes can represent alternatives to animal or human studies. The 3T3-L1 cell line is used to mimic adipocyte function and differentiation. Since transfection of 3T3-L1 cells is difficult, we used a modified 3T3-L1 cell line overexpressing Cas9 for a straightforward generation of gene knock-outs. As an example, we intended to generate 3T3-L1 cell lines deficient for adhesion G protein-coupled receptors Gpr64/Adgr2 and Gpr126/Adgr6 using the CRISPR/Cas approach. Surprisingly, all the generated knock-out as well as scramble control cell lines were unresponsive to isoprenaline in respect to adiponectin secretion and lipolysis in contrast to the wild type 3T3-L1 cells. We, therefore, analysed the properties of these stable Cas9-overexpressing 3T3-L1 cells. We demonstrate that this commercially available cell line exhibits dysfunction in cAMP signalling pathways as well as reduced insulin sensitivity independent of gRNA transfection. We tried transient transfection of plasmids harbouring Cas9 as well as direct introduction of the Cas9 protein as alternate approaches to the stable expression of this enzyme. We find that transfection of the Cas9 protein is not only feasible but also does not impair adipogenesis and, therefore, represents a preferable alternative to achieve genetic knock-out.
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Affiliation(s)
- Tomás Suchý
- Department of Molecular Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Isabell Kaczmarek
- Department of Molecular Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Tomislav Maricic
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Christian Zieschang
- Department of Molecular Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Torsten Schöneberg
- Department of Molecular Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Doreen Thor
- Department of Molecular Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Ines Liebscher
- Department of Molecular Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
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25
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Kaczmarek I, Suchý T, Prömel S, Schöneberg T, Liebscher I, Thor D. The relevance of adhesion G protein-coupled receptors in metabolic functions. Biol Chem 2021; 403:195-209. [PMID: 34218541 DOI: 10.1515/hsz-2021-0146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 06/08/2021] [Indexed: 01/06/2023]
Abstract
G protein-coupled receptors (GPCRs) modulate a variety of physiological functions and have been proven to be outstanding drug targets. However, approximately one-third of all non-olfactory GPCRs are still orphans in respect to their signal transduction and physiological functions. Receptors of the class of Adhesion GPCRs (aGPCRs) are among these orphan receptors. They are characterized by unique features in their structure and tissue-specific expression, which yields them interesting candidates for deorphanization and testing as potential therapeutic targets. Capable of G-protein coupling and non-G protein-mediated function, aGPCRs may extend our repertoire of influencing physiological function. Besides their described significance in the immune and central nervous systems, growing evidence indicates a high importance of these receptors in metabolic tissue. RNAseq analyses revealed high expression of several aGPCRs in pancreatic islets, adipose tissue, liver, and intestine but also in neurons governing food intake. In this review, we focus on aGPCRs and their function in regulating metabolic pathways. Based on current knowledge, this receptor class represents high potential for future pharmacological approaches addressing obesity and other metabolic diseases.
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Affiliation(s)
- Isabell Kaczmarek
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Johannisallee 30, D-04103 Leipzig, Germany
| | - Tomáš Suchý
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Johannisallee 30, D-04103 Leipzig, Germany
| | - Simone Prömel
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Johannisallee 30, D-04103 Leipzig, Germany
- Institute of Cell Biology, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Johannisallee 30, D-04103 Leipzig, Germany
| | - Ines Liebscher
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Johannisallee 30, D-04103 Leipzig, Germany
| | - Doreen Thor
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Johannisallee 30, D-04103 Leipzig, Germany
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26
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Bast-Habersbrunner A, Kiefer C, Weber P, Fromme T, Schießl A, Schwalie PC, Deplancke B, Li Y, Klingenspor M. LncRNA Ctcflos orchestrates transcription and alternative splicing in thermogenic adipogenesis. EMBO Rep 2021; 22:e51289. [PMID: 34056831 PMCID: PMC8256291 DOI: 10.15252/embr.202051289] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/12/2022] Open
Abstract
The recruitment of thermogenic brite adipocytes within white adipose tissue attenuates obesity and metabolic comorbidities, arousing interest in understanding the underlying regulatory mechanisms. The molecular network of brite adipogenesis, however, remains largely unresolved. In this light, long noncoding RNAs (lncRNAs) emerged as a versatile class of modulators that control many steps within the differentiation machinery. Leveraging the naturally varying propensities of different inbred mouse strains for white adipose tissue browning, we identify the nuclear lncRNA Ctcflos as a pivotal orchestrator of thermogenic gene expression during brite adipocyte differentiation. Mechanistically, Ctcflos acts as a pleiotropic regulator, being essential for the transcriptional recruitment of the early core thermogenic regulatory program and the modulation of alternative splicing to drive brite adipogenesis. This is showcased by Ctcflos‐regulated gene transcription and splicing of the key browning factor Prdm16 toward the isoform that is specific for the thermogenic gene program. Conclusively, our findings emphasize the mechanistic versatility of lncRNAs acting at several independent levels of gene expression for effective regulation of key differentiation factors to direct cell fate and function.
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Affiliation(s)
- Andrea Bast-Habersbrunner
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.,EKFZ - Else Kröner-Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany
| | - Christoph Kiefer
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Peter Weber
- Research Unit Radiation Cytogenetics, Helmholtz Center Munich Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Tobias Fromme
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Anna Schießl
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Petra C Schwalie
- School of Life Sciences, EPFL and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Bart Deplancke
- School of Life Sciences, EPFL and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Yongguo Li
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.,EKFZ - Else Kröner-Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany
| | - Martin Klingenspor
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.,EKFZ - Else Kröner-Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany
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27
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Tan W, Jiang P, Zhang W, Hu Z, Lin S, Chen L, Li Y, Peng C, Li Z, Sun A, Chen Y, Zhu W, Xue Y, Yao Y, Li X, Song Q, He F, Qin W, Pei H. Posttranscriptional regulation of de novo lipogenesis by glucose-induced O-GlcNAcylation. Mol Cell 2021; 81:1890-1904.e7. [PMID: 33657401 DOI: 10.1016/j.molcel.2021.02.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/21/2020] [Accepted: 02/03/2021] [Indexed: 02/07/2023]
Abstract
O-linked β-N-acetyl glucosamine (O-GlcNAc) is attached to proteins under glucose-replete conditions; this posttranslational modification results in molecular and physiological changes that affect cell fate. Here we show that posttranslational modification of serine/arginine-rich protein kinase 2 (SRPK2) by O-GlcNAc regulates de novo lipogenesis by regulating pre-mRNA splicing. We found that O-GlcNAc transferase O-GlcNAcylated SRPK2 at a nuclear localization signal (NLS), which triggers binding of SRPK2 to importin α. Consequently, O-GlcNAcylated SRPK2 was imported into the nucleus, where it phosphorylated serine/arginine-rich proteins and promoted splicing of lipogenic pre-mRNAs. We determined that protein nuclear import by O-GlcNAcylation-dependent binding of cargo protein to importin α might be a general mechanism in cells. This work reveals a role of O-GlcNAc in posttranscriptional regulation of de novo lipogenesis, and our findings indicate that importin α is a "reader" of an O-GlcNAcylated NLS.
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Affiliation(s)
- Wei Tan
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Science, 2300 Eye Street, N.W., Washington, DC 20037, USA
| | - Pei Jiang
- State Key Laboratory of Proteomics, National Center for Protein Sciences - Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China; Cancer Center, Renmin Hospital of Wuhan University, Wuhan 430062, China
| | - Wanjun Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences - Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Zhaohua Hu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan 430062, China
| | - Shaofeng Lin
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Lulu Chen
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan 430062, China; GW Cancer Center, George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
| | - Yingge Li
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan 430062, China; GW Cancer Center, George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
| | - Changmin Peng
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Science, 2300 Eye Street, N.W., Washington, DC 20037, USA; GW Cancer Center, George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
| | - Zhuqing Li
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Science, 2300 Eye Street, N.W., Washington, DC 20037, USA; GW Cancer Center, George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
| | - Aihua Sun
- State Key Laboratory of Proteomics, National Center for Protein Sciences - Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yali Chen
- State Key Laboratory of Proteomics, National Center for Protein Sciences - Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Wenge Zhu
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Science, 2300 Eye Street, N.W., Washington, DC 20037, USA; GW Cancer Center, George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
| | - Yu Xue
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yi Yao
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan 430062, China
| | - Xiangpan Li
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan 430062, China
| | - Qibin Song
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan 430062, China
| | - Fuchu He
- State Key Laboratory of Proteomics, National Center for Protein Sciences - Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China.
| | - Weijie Qin
- State Key Laboratory of Proteomics, National Center for Protein Sciences - Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China.
| | - Huadong Pei
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Science, 2300 Eye Street, N.W., Washington, DC 20037, USA; GW Cancer Center, George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA.
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28
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Chao Y, Jiang Y, Zhong M, Wei K, Hu C, Qin Y, Zuo Y, Yang L, Shen Z, Zou C. Regulatory roles and mechanisms of alternative RNA splicing in adipogenesis and human metabolic health. Cell Biosci 2021; 11:66. [PMID: 33795017 PMCID: PMC8017860 DOI: 10.1186/s13578-021-00581-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/24/2021] [Indexed: 12/15/2022] Open
Abstract
Alternative splicing (AS) regulates gene expression patterns at the post-transcriptional level and generates a striking expansion of coding capacities of genomes and cellular protein diversity. RNA splicing could undergo modulation and close interaction with genetic and epigenetic machinery. Notably, during the adipogenesis processes of white, brown and beige adipocytes, AS tightly interplays with the differentiation gene program networks. Here, we integrate the available findings on specific splicing events and distinct functions of different splicing regulators as examples to highlight the directive biological contribution of AS mechanism in adipogenesis and adipocyte biology. Furthermore, accumulating evidence has suggested that mutations and/or altered expression in splicing regulators and aberrant splicing alterations in the obesity-associated genes are often linked to humans’ diet-induced obesity and metabolic dysregulation phenotypes. Therefore, significant attempts have been finally made to overview novel detailed discussion on the prospects of splicing machinery with obesity and metabolic disorders to supply featured potential management mechanisms in clinical applicability for obesity treatment strategies.
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Affiliation(s)
- Yunqi Chao
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Yonghui Jiang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Mianling Zhong
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Kaiyan Wei
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Chenxi Hu
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Yifang Qin
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Yiming Zuo
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Lili Yang
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Zheng Shen
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Chaochun Zou
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China.
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29
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Garg R, Kumariya S, Katekar R, Verma S, Goand UK, Gayen JR. JNK signaling pathway in metabolic disorders: An emerging therapeutic target. Eur J Pharmacol 2021; 901:174079. [PMID: 33812885 DOI: 10.1016/j.ejphar.2021.174079] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/18/2021] [Accepted: 03/25/2021] [Indexed: 02/08/2023]
Abstract
Metabolic Syndrome is a multifactorial disease associated with increased risk of cardiovascular disorders, type 2 diabetes mellitus, fatty liver disease, etc. Various stress stimuli such as reactive oxygen species, endoplasmic reticulum stress, mitochondrial dysfunction, increased cytokines, or free fatty acids are known to aggravate progressive development of hyperglycemia and hyperlipidemia. Although the exact mechanism contributing to altered metabolism is unclear. Evidence suggests stress kinase role to be a crucial one in metabolic syndrome. Stress kinase, c-jun N-terminal kinase activation (JNK) is involved in various metabolic manifestations including obesity, insulin resistance, fatty liver disease as well as cardiometabolic disorders. It emerged as a foremost mediator in regulating metabolism in the liver, skeletal muscle, adipose tissue as well as pancreatic β cells. It has three isoforms each having a unique and tissue-specific role in altered metabolism. Current findings based on genetic manipulation or chemical inhibition studies identified JNK isoforms to play a central role in the regulation of whole-body metabolism, suggesting it to be a novel therapeutic target. Hence, it is imperative to elucidate its role in metabolic syndrome onset and progression. The purpose of this review is to elucidate in vitro and in vivo implications of JNK signaling along with the therapeutic strategy to inhibit specific isoform. Since metabolic syndrome is an array of diseases and complex pathway, carefully examining each tissue will be important for specific treatment strategies.
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Affiliation(s)
- Richa Garg
- Pharmaceutics & Pharmacokinetics, CSIR-Central Drug Research Institute, Jankipuram Extension, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sanjana Kumariya
- Pharmaceutics & Pharmacokinetics, CSIR-Central Drug Research Institute, Jankipuram Extension, Lucknow, 226031, India
| | - Roshan Katekar
- Pharmaceutics & Pharmacokinetics, CSIR-Central Drug Research Institute, Jankipuram Extension, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Saurabh Verma
- Pharmaceutics & Pharmacokinetics, CSIR-Central Drug Research Institute, Jankipuram Extension, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Umesh K Goand
- Pharmaceutics & Pharmacokinetics, CSIR-Central Drug Research Institute, Jankipuram Extension, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jiaur R Gayen
- Pharmaceutics & Pharmacokinetics, CSIR-Central Drug Research Institute, Jankipuram Extension, Lucknow, 226031, India; Pharmacology Division, CSIR-Central Drug Research Institute, Jankipuram Extension, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Multilevel Regulation of Protein Kinase CδI Alternative Splicing by Lithium Chloride. Mol Cell Biol 2021; 41:e0033820. [PMID: 33288642 PMCID: PMC8088272 DOI: 10.1128/mcb.00338-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Lithium chloride (LiCl) is commonly used in treatment of mood disorders; however, its usage leads to weight gain, which promotes metabolic disorders. Protein kinase C delta (PKCδ), a serine/threonine kinase, is alternatively spliced to PKCδI and PKCδII in 3T3-L1 cells. We previously demonstrated that PKCδI is the predominantly expressed isoform in 3T3-L1 preadipocytes. Here, we demonstrate that LiCl treatment decreases PKCδI levels, increases formation of lipid droplets, and increases oxidative stress. Hence, we investigated the molecular mechanisms underlying the regulation of PKCδI alternative splicing by LiCl. We previously demonstrated that the splice factor SFRS10 is essential for PKCδI splicing. Our results demonstrate that glycogen synthase kinase 3 beta (GSK3β) phosphorylates SFRS10, and SFRS10 is in a complex with long noncoding RNA NEAT1 to promote PKCδI splicing. Using PKCδ splicing minigene and RNA immunoprecipitation assays, our results demonstrate that upon LiCl treatment, NEAT1 levels are reduced, GSK3β activity is inhibited, and SFRS10 phosphorylation is decreased, which leads to decreased expression of PKCδI. Integration of the GSK3β signaling pathway with the ribonucleoprotein complex of long noncoding RNA (lncRNA) NEAT1 and SFRS10 enables fine-tuning of PKCδI expression during adipogenesis. Knowledge of the molecular pathways impacted by LiCl provides an understanding of the ascent of obesity as a comorbidity in disease management.
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Abstract
Obesity, which has long since reached epidemic proportions worldwide, is associated with long-term stress to a variety of organs and results in diseases including type 2 diabetes. In the brain, overnutrition induces hypothalamic stress associated with the activation of several signalling pathways, together with central insulin and leptin resistance. This central action of nutrient overload appears very rapidly, suggesting that nutrition-induced hypothalamic stress is a major upstream initiator of obesity and associated diseases. The cellular response to nutrient overload includes the activation of the stress-activated c-Jun N-terminal kinases (JNKs) JNK1, JNK2 and JNK3, which are widely expressed in the brain. Here, we review recent findings on the regulation and effects of these kinases, with particular focus on the hypothalamus, a key brain region in the control of energy and glucose homeostasis. JNK1 blocks the hypothalamic-pituitary-thyroid axis, reducing energy expenditure and promoting obesity. Recently, opposing roles have been identified for JNK1 and JNK3 in hypothalamic agouti gene-related protein (AgRP) neurons: while JNK1 activation in AgRP neurons induces feeding and weight gain and impairs insulin and leptin signalling, JNK3 (also known as MAPK10) deletion in the same neuronal population produces very similar effects. The opposing roles of these kinases, and the unknown role of hypothalamic JNK2, reflect the complexity of JNK biology. Future studies should address the specific function of each kinase, not only in different neuronal subsets, but also in non-neuronal cells in the central nervous system. Decoding the puzzle of brain stress kinases will help to define the central stimuli and mechanisms implicated in the control of energy balance. Graphical abstract.
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Affiliation(s)
- Rubén Nogueiras
- Department of Physiology, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), University of Santiago de Compostela-Instituto de Investigación Sanitaria, Santiago de Compostela, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Santiago de Compostela, Spain
- Galician Agency of Innovation (GAIN), Xunta de Galicia, Santiago de Compostela, Spain
| | - Guadalupe Sabio
- Department of Myocardial Pathophysiology, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.
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Teitsma XM, Devenport J, Jacobs JWG, Pethö-Schramm A, Borm MEA, Budde P, Bijlsma JWJ, Lafeber FPJG. Comprehensive exploratory autoantibody profiling in patients with early rheumatoid arthritis treated with methotrexate or tocilizumab. PLoS One 2020; 15:e0241189. [PMID: 33301475 PMCID: PMC7728181 DOI: 10.1371/journal.pone.0241189] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/14/2020] [Indexed: 12/18/2022] Open
Abstract
Background We sought to identify immunoglobin G autoantibodies predictive of early treatment response to methotrexate, the recommended first-line therapy for patients with newly diagnosed rheumatoid arthritis, and to the interleukin-6 receptor inhibitor biologic tocilizumab, initiated as the first disease-modifying anti-rheumatic drug. Materials and methods In baseline sera of a subset of patients with newly diagnosed rheumatoid arthritis in the U-Act-Early study, selected based on specific responder/non-responder criteria using the Disease Activity Score assessing 28 joints (DAS28) within the first 20 weeks, we measured immunoglobin G antibody reactivity against 463 protein antigens and performed supervised cluster analysis to identify predictive autoantibodies for treatment response. The analysis subset comprised 56 patients in the methotrexate arm (22 responders, 34 non-responders) and 50 patients in the tocilizumab arm (34 responders, 16 non-responders). For comparison, these analyses were also performed in 50 age- and gender-matched healthy controls. Results Increased reactivity in responders versus non-responders was found in the methotrexate arm against two antigens—DOT1-like histone lysine methyltransferase (p = 0.009) and tropomyosin (p = 0.003)—and in the tocilizumab arm against one antigen—neuro-oncological ventral antigen 2 (p = 0.039). Decreased reactivity was detected against two antigens in the methotrexate arm—G1 to S phase transition 2 (p = 0.023) and the zinc finger protein ZPR1 (p = 0.021). Reactivity against the identified antigens was not statistically significant in either treatment arm for patients with rheumatoid factor–positive versus–negative or anti-cyclic citrullinated test–positive versus test–negative rheumatoid arthritis (p ≥ 0.06). Conclusions Comprehensive profiling of baseline sera revealed several novel immunoglobin G autoantibodies associated with early treatment response to methotrexate and to tocilizumab in disease-modifying anti-rheumatic drug-naive patients with rheumatoid arthritis. These findings could eventually yield clinically relevant predictive markers, if corroborated in different patient cohorts, and may facilitate future benefit in personalised healthcare.
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Affiliation(s)
- Xavier M. Teitsma
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Department of Rheumatology & Clinical Immunology, Utrecht University, Utrecht, Netherlands
- * E-mail:
| | - Jenny Devenport
- Pharmaceuticals Division, F. Hoffmann-La Roche, Basel, Switzerland
| | - Johannes W. G. Jacobs
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Department of Rheumatology & Clinical Immunology, Utrecht University, Utrecht, Netherlands
| | | | | | - Petra Budde
- Department of Medical Research, Oncimmune Germany GmbH, Dortmund, Germany
| | - Johannes W. J. Bijlsma
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Department of Rheumatology & Clinical Immunology, Utrecht University, Utrecht, Netherlands
| | - Floris P. J. G. Lafeber
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Department of Rheumatology & Clinical Immunology, Utrecht University, Utrecht, Netherlands
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del Río-Moreno M, Luque RM, Rangel-Zúñiga OA, Alors-Pérez E, Alcalá-Diaz JF, Roncero-Ramos I, Camargo A, Gahete MD, López-Miranda J, Castaño JP. Dietary Intervention Modulates the Expression of Splicing Machinery in Cardiovascular Patients at High Risk of Type 2 Diabetes Development: From the CORDIOPREV Study. Nutrients 2020; 12:E3528. [PMID: 33212780 PMCID: PMC7696699 DOI: 10.3390/nu12113528] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/03/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
Type-2 diabetes mellitus (T2DM) has become a major health problem worldwide. T2DM risk can be reduced with healthy dietary interventions, but the precise molecular underpinnings behind this association are still incompletely understood. We recently discovered that the expression profile of the splicing machinery is associated with the risk of T2DM development. Thus, the aim of this work was to evaluate the influence of 3-year dietary intervention in the expression pattern of the splicing machinery components in peripheral blood mononuclear cells (PBMCs) from patients within the CORDIOPREV study. Expression of splicing machinery components was determined in PBMCs, at baseline and after 3 years of follow-up, from all patients who developed T2DM (Incident-T2DM, n = 107) and 108 randomly selected non-T2DM subjects, who were randomly enrolled in two healthy dietary patterns (Mediterranean or low-fat diets). Dietary intervention modulated the expression of key splicing machinery components (i.e., up-regulation of SPFQ/RMB45/RNU6, etc., down-regulation of RNU2/SRSF6) after three years, independently of the type of healthy diet. Some of these changes (SPFQ/RMB45/SRSF6) were associated with key clinical features and were differentially induced in Incident-T2DM patients and non-T2DM subjects. This study reveals that splicing machinery can be modulated by long-term dietary intervention, and could become a valuable tool to screen the progression of T2DM.
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Grants
- PIE14/00005 Instituto de Salud Carlos III
- PIE14/00031 Instituto de Salud Carlos III
- PI16/00264 Instituto de Salud Carlos III
- CP15/00156 Instituto de Salud Carlos III
- PI17/002287 Instituto de Salud Carlos III
- BFU2016-80360-R Ministerio de Economía, Industria y Competitividad, Gobierno de España
- TIN2017-83445-P Ministerio de Economía, Industria y Competitividad, Gobierno de España
- PI13/00023 Ministerio de Economía, Industria y Competitividad, Gobierno de España
- AGL2012/39615 Ministerio de Economía, Industria y Competitividad, Gobierno de España
- AGL2015-67896-P Ministerio de Economía, Industria y Competitividad, Gobierno de España
- BIO-0139 Junta de Andalucía
- CTS-1406 Junta de Andalucía
- CTS-525 Junta de Andalucía
- PI-0541-2013 Junta de Andalucía
- CVI-7450 Junta de Andalucía
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Affiliation(s)
- Mercedes del Río-Moreno
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain; (M.d.R.-M.); (O.A.R.-Z.); (E.A.-P.); (J.F.A.-D.); (I.R.-R.); (A.C.)
- Department of Cell Biology, University of Córdoba, 14004 Córdoba, Spain
- Reina Sofia University Hospital, 14004 Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 14004 Córdoba, Spain
| | - Raúl M. Luque
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain; (M.d.R.-M.); (O.A.R.-Z.); (E.A.-P.); (J.F.A.-D.); (I.R.-R.); (A.C.)
- Department of Cell Biology, University of Córdoba, 14004 Córdoba, Spain
- Reina Sofia University Hospital, 14004 Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 14004 Córdoba, Spain
| | - Oriol A. Rangel-Zúñiga
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain; (M.d.R.-M.); (O.A.R.-Z.); (E.A.-P.); (J.F.A.-D.); (I.R.-R.); (A.C.)
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 14004 Córdoba, Spain
- Lipid and Atherosclerosis Unit, Department of Medicine, Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain
| | - Emilia Alors-Pérez
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain; (M.d.R.-M.); (O.A.R.-Z.); (E.A.-P.); (J.F.A.-D.); (I.R.-R.); (A.C.)
- Department of Cell Biology, University of Córdoba, 14004 Córdoba, Spain
- Reina Sofia University Hospital, 14004 Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 14004 Córdoba, Spain
| | - Juan F. Alcalá-Diaz
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain; (M.d.R.-M.); (O.A.R.-Z.); (E.A.-P.); (J.F.A.-D.); (I.R.-R.); (A.C.)
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 14004 Córdoba, Spain
- Lipid and Atherosclerosis Unit, Department of Medicine, Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain
| | - Irene Roncero-Ramos
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain; (M.d.R.-M.); (O.A.R.-Z.); (E.A.-P.); (J.F.A.-D.); (I.R.-R.); (A.C.)
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 14004 Córdoba, Spain
- Lipid and Atherosclerosis Unit, Department of Medicine, Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain
| | - Antonio Camargo
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain; (M.d.R.-M.); (O.A.R.-Z.); (E.A.-P.); (J.F.A.-D.); (I.R.-R.); (A.C.)
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 14004 Córdoba, Spain
- Lipid and Atherosclerosis Unit, Department of Medicine, Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain
| | - Manuel D. Gahete
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain; (M.d.R.-M.); (O.A.R.-Z.); (E.A.-P.); (J.F.A.-D.); (I.R.-R.); (A.C.)
- Department of Cell Biology, University of Córdoba, 14004 Córdoba, Spain
- Reina Sofia University Hospital, 14004 Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 14004 Córdoba, Spain
| | - José López-Miranda
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain; (M.d.R.-M.); (O.A.R.-Z.); (E.A.-P.); (J.F.A.-D.); (I.R.-R.); (A.C.)
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 14004 Córdoba, Spain
- Lipid and Atherosclerosis Unit, Department of Medicine, Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain
| | - Justo P. Castaño
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain; (M.d.R.-M.); (O.A.R.-Z.); (E.A.-P.); (J.F.A.-D.); (I.R.-R.); (A.C.)
- Department of Cell Biology, University of Córdoba, 14004 Córdoba, Spain
- Reina Sofia University Hospital, 14004 Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 14004 Córdoba, Spain
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Batista TM, Jayavelu AK, Wewer Albrechtsen NJ, Iovino S, Lebastchi J, Pan H, Dreyfuss JM, Krook A, Zierath JR, Mann M, Kahn CR. A Cell-Autonomous Signature of Dysregulated Protein Phosphorylation Underlies Muscle Insulin Resistance in Type 2 Diabetes. Cell Metab 2020; 32:844-859.e5. [PMID: 32888406 PMCID: PMC7875546 DOI: 10.1016/j.cmet.2020.08.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/26/2020] [Accepted: 08/11/2020] [Indexed: 02/06/2023]
Abstract
Skeletal muscle insulin resistance is the earliest defect in type 2 diabetes (T2D), preceding and predicting disease development. To what extent this reflects a primary defect or is secondary to tissue cross talk due to changes in hormones or circulating metabolites is unknown. To address this question, we have developed an in vitro disease-in-a-dish model using iPS cells from T2D patients differentiated into myoblasts (iMyos). We find that T2D iMyos in culture exhibit multiple defects mirroring human disease, including an altered insulin signaling, decreased insulin-stimulated glucose uptake, and reduced mitochondrial oxidation. More strikingly, global phosphoproteomic analysis reveals a multidimensional network of signaling defects in T2D iMyos going beyond the canonical insulin-signaling cascade, including proteins involved in regulation of Rho GTPases, mRNA splicing and/or processing, vesicular trafficking, gene transcription, and chromatin remodeling. These cell-autonomous defects and the dysregulated network of protein phosphorylation reveal a new dimension in the cellular mechanisms underlying the fundamental defects in T2D.
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Affiliation(s)
- Thiago M Batista
- Section of Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Ashok Kumar Jayavelu
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Nicolai J Wewer Albrechtsen
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark; Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen, Copenhagen 2100, Denmark
| | - Salvatore Iovino
- Section of Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jasmin Lebastchi
- Section of Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Hui Pan
- Bioinformatics and Biostatistics Core, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jonathan M Dreyfuss
- Bioinformatics and Biostatistics Core, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Anna Krook
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Juleen R Zierath
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark; Section of Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm 171 76, Sweden
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - C Ronald Kahn
- Section of Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA.
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Nikolaou KC, Vatandaslar H, Meyer C, Schmid MW, Tuschl T, Stoffel M. The RNA-Binding Protein A1CF Regulates Hepatic Fructose and Glycerol Metabolism via Alternative RNA Splicing. Cell Rep 2020; 29:283-300.e8. [PMID: 31597092 DOI: 10.1016/j.celrep.2019.08.100] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/09/2019] [Accepted: 08/29/2019] [Indexed: 01/11/2023] Open
Abstract
The regulation of hepatic gene expression has been extensively studied at the transcriptional level; however, the control of metabolism through posttranscriptional gene regulation by RNA-binding proteins in physiological and disease states is less understood. Here, we report a major role for the hormone-sensitive RNA-binding protein (RBP) APOBEC1 complementation factor (A1CF) in the generation of hepatocyte-specific and alternatively spliced transcripts. Among these transcripts are isoforms for the dominant and high-affinity fructose-metabolizing ketohexokinase C and glycerol kinase, two key metabolic enzymes that are linked to hepatic gluconeogenesis and found to be markedly reduced upon hepatic ablation of A1cf. Consequently, mice lacking A1CF exhibit improved glucose tolerance and are protected from fructose-induced hyperglycemia, hepatic steatosis, and development of obesity. Our results identify a previously unreported function of A1CF as a regulator of alternative splicing of a subset of genes influencing hepatic glucose production through fructose and glycerol metabolism.
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Affiliation(s)
- Kostas C Nikolaou
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093 Zürich, Switzerland
| | - Hasan Vatandaslar
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093 Zürich, Switzerland
| | - Cindy Meyer
- Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
| | - Marc W Schmid
- MWSchmid GmbH, Möhrlistrasse 25, 8006 Zurich, Switzerland
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
| | - Markus Stoffel
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093 Zürich, Switzerland; Medical Faculty, University of Zurich, 8091 Zurich, Switzerland.
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Yu P, Li J, Deng SP, Zhang F, Grozdanov PN, Chin EWM, Martin SD, Vergnes L, Islam MS, Sun D, LaSalle JM, McGee SL, Goh E, MacDonald CC, Jin P. Integrated analysis of a compendium of RNA-Seq datasets for splicing factors. Sci Data 2020; 7:178. [PMID: 32546682 PMCID: PMC7297722 DOI: 10.1038/s41597-020-0514-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/13/2020] [Indexed: 02/05/2023] Open
Abstract
A vast amount of public RNA-sequencing datasets have been generated and used widely to study transcriptome mechanisms. These data offer precious opportunity for advancing biological research in transcriptome studies such as alternative splicing. We report the first large-scale integrated analysis of RNA-Seq data of splicing factors for systematically identifying key factors in diseases and biological processes. We analyzed 1,321 RNA-Seq libraries of various mouse tissues and cell lines, comprising more than 6.6 TB sequences from 75 independent studies that experimentally manipulated 56 splicing factors. Using these data, RNA splicing signatures and gene expression signatures were computed, and signature comparison analysis identified a list of key splicing factors in Rett syndrome and cold-induced thermogenesis. We show that cold-induced RNA-binding proteins rescue the neurite outgrowth defects in Rett syndrome using neuronal morphology analysis, and we also reveal that SRSF1 and PTBP1 are required for energy expenditure in adipocytes using metabolic flux analysis. Our study provides an integrated analysis for identifying key factors in diseases and biological processes and highlights the importance of public data resources for identifying hypotheses for experimental testing.
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Affiliation(s)
- Peng Yu
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China.
- Medical Big Data Center, Sichuan University, Chengdu, China.
| | - Jin Li
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - Su-Ping Deng
- School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, Jiangsu, 215009, China
| | - Feiran Zhang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Petar N Grozdanov
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, 79430, USA
| | - Eunice W M Chin
- Neuroscience Academic Clinical Programme, Duke-NUS Medical School, NA, Singapore
| | - Sheree D Martin
- Metabolic Reprogramming Laboratory, Metabolic Research Unit, School of Medicine and Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria, Australia
| | - Laurent Vergnes
- Department of Human Genetics, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - M Saharul Islam
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California Davis, Davis, CA, USA
| | - Deqiang Sun
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California Davis, Davis, CA, USA
| | - Sean L McGee
- Metabolic Reprogramming Laboratory, Metabolic Research Unit, School of Medicine and Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria, Australia
| | - Eyleen Goh
- Neuroscience Academic Clinical Programme, Duke-NUS Medical School, NA, Singapore
| | - Clinton C MacDonald
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, 79430, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
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Meldolesi J. Alternative Splicing by NOVA Factors: From Gene Expression to Cell Physiology and Pathology. Int J Mol Sci 2020; 21:ijms21113941. [PMID: 32486302 PMCID: PMC7312376 DOI: 10.3390/ijms21113941] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 12/24/2022] Open
Abstract
NOVA1 and NOVA2, the two members of the NOVA family of alternative splicing factors, bind YCAY clusters of pre-mRNAs and assemble spliceosomes to induce the maintenance/removal of introns and exons, thus governing the development of mRNAs. Members of other splicing families operate analogously. Activity of NOVAs accounts for up to 700 alternative splicing events per cell, taking place both in the nucleus (co-transcription of mRNAs) and in the cytoplasm. Brain neurons express high levels of NOVAs, with NOVA1 predominant in cerebellum and spinal cord, NOVA2 in the cortex. Among brain physiological processes NOVAs play critical roles in axon pathfinding and spreading, structure and function of synapses, as well as the regulation of surface receptors and voltage-gated channels. In pathology, NOVAs contribute to neurodegenerative diseases and epilepsy. In vessel endothelial cells, NOVA2 is essential for angiogenesis, while in adipocytes, NOVA1 contributes to regulation of thermogenesis and obesity. In many cancers NOVA1 and also NOVA2, by interacting with specific miRNAs and by additional mechanisms, activate oncogenic roles promoting cell proliferation, colony formation, migration, and invasion. In conclusion, NOVAs regulate cell functions of physiological and pathological nature. Single cell identification and distinction, and new therapies addressed to NOVA targets might be developed in the near future.
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Affiliation(s)
- Jacopo Meldolesi
- Department of Neuroscience, San Raffaele Institute and San Raffaele University, via Olgettina 58, 20132 Milan, Italy
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Suchý T, Zieschang C, Popkova Y, Kaczmarek I, Weiner J, Liebing AD, Çakir MV, Landgraf K, Gericke M, Pospisilik JA, Körner A, Heiker JT, Dannenberger D, Schiller J, Schöneberg T, Liebscher I, Thor D. The repertoire of Adhesion G protein-coupled receptors in adipocytes and their functional relevance. Int J Obes (Lond) 2020; 44:2124-2136. [PMID: 32203115 PMCID: PMC7508673 DOI: 10.1038/s41366-020-0570-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/25/2020] [Accepted: 03/04/2020] [Indexed: 01/30/2023]
Abstract
BACKGROUND G protein-coupled receptors (GPCR) are well-characterized regulators of a plethora of physiological functions among them the modulation of adipogenesis and adipocyte function. The class of Adhesion GPCR (aGPCR) and their role in adipose tissue, however, is poorly studied. With respect to the demand for novel targets in obesity treatment, we present a comprehensive study on the expression and function of this enigmatic GPCR class during adipogenesis and in mature adipocytes. METHODS The expression of all aGPCR representatives was determined by reanalyzing RNA-Seq data and by performing qPCR in different mouse and human adipose tissues under low- and high-fat conditions. The impact of aGPCR expression on adipocyte differentiation and lipid accumulation was studied by siRNA-mediated knockdown of all expressed members of this receptor class. The biological characteristics and function of mature adipocytes lacking selected aGPCR were analyzed by mass spectrometry and biochemical methods (lipolysis, glucose uptake, adiponectin secretion). RESULTS More than ten aGPCR are significantly expressed in visceral and subcutaneous adipose tissues and several aGPCR are differentially regulated under high-caloric conditions in human and mouse. Receptor knockdown of six receptors resulted in an impaired adipogenesis indicating their expression is essential for proper adipogenesis. The altered lipid composition was studied in more detail for two representatives, ADGRG2/GPR64 and ADGRG6/GPR126. While GPR126 is mainly involved in adipocyte differentiation, GPR64 has an additional role in mature adipocytes by regulating metabolic processes. CONCLUSIONS Adhesion GPCR are significantly involved in qualitative and quantitative adipocyte lipid accumulation and can control lipolysis. Factors driving adipocyte formation and function are governed by signaling pathways induced by aGPCR yielding these receptors potential targets for treating obesity.
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Affiliation(s)
- Tomáš Suchý
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Christian Zieschang
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Yulia Popkova
- Institute for Medical Physics and Biophysics, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Isabell Kaczmarek
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Juliane Weiner
- Department of Endocrinology, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Aenne-Dorothea Liebing
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Mehmet Volkan Çakir
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Kathrin Landgraf
- Center for Pediatric Research Leipzig, Hospital for Children & Adolescents, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Martin Gericke
- Institute for Anatomy and Cell biology, Medical Faculty, Halle University, Halle (Saale), Germany
| | | | - Antje Körner
- Center for Pediatric Research Leipzig, Hospital for Children & Adolescents, Medical Faculty, Leipzig University, Leipzig, Germany
| | - John T Heiker
- IFB Adiposity Diseases, Leipzig University, Leipzig, Germany.,Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Dirk Dannenberger
- Leibniz Institute for Farm Animal Biology, Institute of Muscle Biology and Growth, Dummerstorf, Germany
| | - Jürgen Schiller
- Institute for Medical Physics and Biophysics, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Ines Liebscher
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany.
| | - Doreen Thor
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany.
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Baek S, Oh TG, Secker G, Sutton DL, Okuda KS, Paterson S, Bower NI, Toubia J, Koltowska K, Capon SJ, Baillie GJ, Simons C, Muscat GEO, Lagendijk AK, Smith KA, Harvey NL, Hogan BM. The Alternative Splicing Regulator Nova2 Constrains Vascular Erk Signaling to Limit Specification of the Lymphatic Lineage. Dev Cell 2020; 49:279-292.e5. [PMID: 31014480 DOI: 10.1016/j.devcel.2019.03.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/30/2019] [Accepted: 03/19/2019] [Indexed: 02/06/2023]
Abstract
The correct assignment of cell fate within fields of multipotent progenitors is essential for accurate tissue diversification. The first lymphatic vessels arise from pre-existing veins after venous endothelial cells become specified as lymphatic progenitors. Prox1 specifies lymphatic fate and labels these progenitors; however, the mechanisms restricting Prox1 expression and limiting the progenitor pool remain unknown. We identified a zebrafish mutant that displayed premature, expanded, and prolonged lymphatic specification. The gene responsible encodes the regulator of alternative splicing, Nova2. In zebrafish and human endothelial cells, Nova2 selectively regulates pre-mRNA splicing for components of signaling pathways and phosphoproteins. Nova2-deficient endothelial cells display increased Mapk/Erk signaling, and Prox1 expression is dynamically controlled by Erk signaling. We identify a mechanism whereby Nova2-regulated splicing constrains Erk signaling, thus limiting lymphatic progenitor cell specification. This identifies the capacity of a factor that tunes mRNA splicing to control assignment of cell fate during vascular differentiation.
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Affiliation(s)
- Sungmin Baek
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4073, Australia
| | - Tae Gyu Oh
- Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4073, Australia
| | - Genevieve Secker
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Drew L Sutton
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Kazuhide S Okuda
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4073, Australia
| | - Scott Paterson
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4073, Australia
| | - Neil I Bower
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4073, Australia
| | - John Toubia
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia; Australian Cancer Research, Centre for Cancer Biology, Foundation Cancer Genomics Facility, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia
| | - Katarzyna Koltowska
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4073, Australia
| | - Samuel J Capon
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4073, Australia
| | - Gregory J Baillie
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4073, Australia
| | - Cas Simons
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4073, Australia
| | - George E O Muscat
- Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4073, Australia
| | - Anne K Lagendijk
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4073, Australia
| | - Kelly A Smith
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4073, Australia
| | - Natasha L Harvey
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Benjamin M Hogan
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4073, Australia.
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Belloni E, Di Matteo A, Pradella D, Vacca M, Wyatt CDR, Alfieri R, Maffia A, Sabbioneda S, Ghigna C. Gene Expression Profiles Controlled by the Alternative Splicing Factor Nova2 in Endothelial Cells. Cells 2019; 8:cells8121498. [PMID: 31771184 PMCID: PMC6953062 DOI: 10.3390/cells8121498] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/11/2019] [Accepted: 11/20/2019] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing (AS) plays an important role in expanding the complexity of the human genome through the production of specialized proteins regulating organ development and physiological functions, as well as contributing to several pathological conditions. How AS programs impact on the signaling pathways controlling endothelial cell (EC) functions and vascular development is largely unknown. Here we identified, through RNA-seq, changes in mRNA steady-state levels in ECs caused by the neuro-oncological ventral antigen 2 (Nova2), a key AS regulator of the vascular morphogenesis. Bioinformatics analyses identified significant enrichment for genes regulated by peroxisome proliferator-activated receptor-gamma (Ppar-γ) and E2F1 transcription factors. We also showed that Nova2 in ECs controlled the AS profiles of Ppar-γ and E2F dimerization partner 2 (Tfdp2), thus generating different protein isoforms with distinct function (Ppar-γ) or subcellular localization (Tfdp2). Collectively, our results supported a mechanism whereby Nova2 integrated splicing decisions in order to regulate Ppar-γ and E2F1 activities. Our data added a layer to the sequential series of events controlled by Nova2 in ECs to orchestrate vascular biology.
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Affiliation(s)
- Elisa Belloni
- Istituto di Genetica Molecolare, “Luigi Luca Cavalli-Sforza”, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100 Pavia, Italy; (E.B.); (A.D.M.); (D.P.); (M.V.); (R.A.); (A.M.); (S.S.)
| | - Anna Di Matteo
- Istituto di Genetica Molecolare, “Luigi Luca Cavalli-Sforza”, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100 Pavia, Italy; (E.B.); (A.D.M.); (D.P.); (M.V.); (R.A.); (A.M.); (S.S.)
| | - Davide Pradella
- Istituto di Genetica Molecolare, “Luigi Luca Cavalli-Sforza”, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100 Pavia, Italy; (E.B.); (A.D.M.); (D.P.); (M.V.); (R.A.); (A.M.); (S.S.)
| | - Margherita Vacca
- Istituto di Genetica Molecolare, “Luigi Luca Cavalli-Sforza”, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100 Pavia, Italy; (E.B.); (A.D.M.); (D.P.); (M.V.); (R.A.); (A.M.); (S.S.)
| | - Christopher D. R. Wyatt
- Centre for Biodiversity and Environment Research, University College London, Gower Street, London WC1E 6BT, UK
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra, Plaça de la Mercè, 10-12, 08002 Barcelona, Spain
| | - Roberta Alfieri
- Istituto di Genetica Molecolare, “Luigi Luca Cavalli-Sforza”, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100 Pavia, Italy; (E.B.); (A.D.M.); (D.P.); (M.V.); (R.A.); (A.M.); (S.S.)
| | - Antonio Maffia
- Istituto di Genetica Molecolare, “Luigi Luca Cavalli-Sforza”, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100 Pavia, Italy; (E.B.); (A.D.M.); (D.P.); (M.V.); (R.A.); (A.M.); (S.S.)
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare, “Luigi Luca Cavalli-Sforza”, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100 Pavia, Italy; (E.B.); (A.D.M.); (D.P.); (M.V.); (R.A.); (A.M.); (S.S.)
| | - Claudia Ghigna
- Istituto di Genetica Molecolare, “Luigi Luca Cavalli-Sforza”, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100 Pavia, Italy; (E.B.); (A.D.M.); (D.P.); (M.V.); (R.A.); (A.M.); (S.S.)
- Correspondence:
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JNK and cardiometabolic dysfunction. Biosci Rep 2019; 39:BSR20190267. [PMID: 31270248 PMCID: PMC6639461 DOI: 10.1042/bsr20190267] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/28/2019] [Accepted: 07/02/2019] [Indexed: 02/06/2023] Open
Abstract
Cardiometabolic syndrome (CMS) describes the cluster of metabolic and cardiovascular diseases that are generally characterized by impaired glucose tolerance, intra-abdominal adiposity, dyslipidemia, and hypertension. CMS currently affects more than 25% of the world’s population and the rates of diseases are rapidly rising. These CMS conditions represent critical risk factors for cardiovascular diseases including atherosclerosis, heart failure, myocardial infarction, and peripheral artery disease (PAD). Therefore, it is imperative to elucidate the underlying signaling involved in disease onset and progression. The c-Jun N-terminal Kinases (JNKs) are a family of stress signaling kinases that have been recently indicated in CMS. The purpose of this review is to examine the in vivo implications of JNK as a potential therapeutic target for CMS. As the constellation of diseases associated with CMS are complex and involve multiple tissues and environmental triggers, carefully examining what is known about the JNK pathway will be important for specificity in treatment strategies.
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Li J, Deng SP, Wei G, Yu P. CITGeneDB: a comprehensive database of human and mouse genes enhancing or suppressing cold-induced thermogenesis validated by perturbation experiments in mice. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:4953403. [PMID: 29688375 PMCID: PMC5868181 DOI: 10.1093/database/bay012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/18/2018] [Indexed: 11/14/2022]
Abstract
Abstract Cold-induced thermogenesis increases energy expenditure and can reduce body weight in mammals, so the genes involved in it are thought to be potential therapeutic targets for treating obesity and diabetes. In the quest for more effective therapies, a great deal of research has been conducted to elucidate the regulatory mechanism of cold-induced thermogenesis. Over the last decade, a large number of genes that can enhance or suppress cold-induced thermogenesis have been discovered, but a comprehensive list of these genes is lacking. To fill this gap, we examined all of the annotated human and mouse genes and curated those demonstrated to enhance or suppress cold-induced thermogenesis by in vivo or ex vivo experiments in mice. The results of this highly accurate and comprehensive annotation are hosted on a database called CITGeneDB, which includes a searchable web interface to facilitate broad public use. The database will be updated as new genes are found to enhance or suppress cold-induced thermogenesis. It is expected that CITGeneDB will be a valuable resource in future explorations of the molecular mechanism of cold-induced thermogenesis, helping pave the way for new obesity and diabetes treatments.
Database URL: http://citgenedb.yubiolab.org.
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Affiliation(s)
- Jin Li
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA.,TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Su-Ping Deng
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA.,TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Gang Wei
- Shanghai Key Laboratory of Diabetes, Shanghai Institute for Diabetes, Shanghai Clinical Medical Centre of Diabetes, Shanghai Key Clinical Centre of Metabolic Diseases, Department of Endocrinology and Metabolism, Shanghai Jiao-Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Peng Yu
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA.,TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX 77843, USA
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Mao S, Zhang S, Zhou Z, Shi X, Huang T, Feng W, Yao C, Gu X, Yu B. Alternative RNA splicing associated with axon regeneration after rat peripheral nerve injury. Exp Neurol 2018; 308:80-89. [DOI: 10.1016/j.expneurol.2018.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/11/2018] [Accepted: 07/03/2018] [Indexed: 10/28/2022]
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44
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Gallo S, Arcidiacono MV, Tisato V, Piva R, Penolazzi L, Bosi C, Feo CV, Gafà R, Secchiero P. Upregulation of the alternative splicing factor NOVA2 in colorectal cancer vasculature. Onco Targets Ther 2018; 11:6049-6056. [PMID: 30275709 PMCID: PMC6157992 DOI: 10.2147/ott.s171678] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Tumor-specific isoforms generated by alternative splicing (AS) are demonstrated to contribute to tumor progression and can represent potential biomarkers. NOVA2 is an AS factor that in physiological conditions regulates endothelial cells' (ECs) polarity and vessel lumen maturation, likely by mediating AS of apical-basal polarity regulators. However, NOVA2 expression in tumor ECs and its regulation have never been investigated. Methods To elucidate this, 40 colorectal cancer patients were enrolled and NOVA2 expression was investigated by immunohistochemistry in samples bearing both the normal mucosa and the tumor tissue. Results NOVA2 was found expressed in ECs of tumor vasculature and, importantly, it was upregulated in tumor ECs with respect to normal mucosa ECs in all cases (P<0.001). The same samples analyzed by immunohistochemistry for the expression HIF1α, a marker of hypoxia, showed a positive and significant association with NOVA2 levels (P=0.045). Of note, NOVA2 was upregulated by hypoxia also in an in vitro ECs model. Conclusion Our results provide, for the first time, evidence of NOVA2 expression and upregulation in tumor ECs and highlight hypoxia as a potential regulatory factor. These findings open a completely new perspective to study tumor vasculature and to uncover NOVA2 as a potential source of biomarkers and therapeutic targets based on AS isoforms.
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Affiliation(s)
- Stefania Gallo
- Department of Morphology, Surgery, Experimental Medicine and LTTA Center, University of Ferrara, Ferrara, Italy,
| | | | - Veronica Tisato
- Department of Morphology, Surgery, Experimental Medicine and LTTA Center, University of Ferrara, Ferrara, Italy,
| | - Roberta Piva
- Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, Ferrara, Italy
| | - Letizia Penolazzi
- Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, Ferrara, Italy
| | - Cristina Bosi
- Department of Morphology, Surgery, Experimental Medicine and LTTA Center, University of Ferrara, Ferrara, Italy,
| | - Carlo V Feo
- Department of Morphology, Surgery, Experimental Medicine and LTTA Center, University of Ferrara, Ferrara, Italy,
| | - Roberta Gafà
- Department of Morphology, Surgery, Experimental Medicine and LTTA Center, University of Ferrara, Ferrara, Italy,
| | - Paola Secchiero
- Department of Morphology, Surgery, Experimental Medicine and LTTA Center, University of Ferrara, Ferrara, Italy,
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Anton I, Húth B, Füller I, Rózsa L, Holló G, Zsolnai A. Effect of single nucleotide polymorphisms on intramuscular fat content in Hungarian Simmental cattle. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018. [PMID: 29531185 PMCID: PMC6127569 DOI: 10.5713/ajas.17.0773] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Objective To estimate effect of single nucleotide polymorphisms on the intramuscular fat content (IMF) of Hungarian Simmental bulls. Methods Genotypes were determined on high-density Illumina Bovine DNA Chip. After slaughtering of animals, chemical percentage of intramuscular fat was determined from longissimus dorsi muscle. A multi-locus mixed-model was applied for statistical analyses. Results Analyses revealed four loci (rs43284251, rs109210955, rs41630030, and rs41642251) to be highly associated (−log10P>12) with IMF located on chromosome 1, 6, 13, and 17, respectively. The frequency of their minor alleles was 0.426, 0.221, 0.162, and 0.106. Conclusion The loci above can be useful in selection programs and gives the possibility to assist selection by molecular tools.
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Affiliation(s)
- István Anton
- NARIC-Research Institute for Animal Breeding Nutrition and Meat Science, Gesztenyes u. 1., Herceghalom, 2053, Hungary
| | - Balázs Húth
- Department of Animal Husbandry and Management, Institute of Animal Science, Faculty of Agricultural and Environmental Sciences, University of Kaposvár, Kaposvár, Guba S. u. 40., 7400, Hungary.,Association of Hungarian Simmental Cattle Breeders, Zrinyi u. 3., Bonyhád, 7150, Hungary
| | - Imre Füller
- Association of Hungarian Simmental Cattle Breeders, Zrinyi u. 3., Bonyhád, 7150, Hungary
| | - László Rózsa
- NARIC-Research Institute for Animal Breeding Nutrition and Meat Science, Gesztenyes u. 1., Herceghalom, 2053, Hungary
| | - Gabriella Holló
- Department of Animal Husbandry and Management, Institute of Animal Science, Faculty of Agricultural and Environmental Sciences, University of Kaposvár, Kaposvár, Guba S. u. 40., 7400, Hungary
| | - Attila Zsolnai
- NARIC-Research Institute for Animal Breeding Nutrition and Meat Science, Gesztenyes u. 1., Herceghalom, 2053, Hungary.,Department of Animal Husbandry and Management, Institute of Animal Science, Faculty of Agricultural and Environmental Sciences, University of Kaposvár, Kaposvár, Guba S. u. 40., 7400, Hungary
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46
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Mugabo Y, Sadeghi M, Fang NN, Mayor T, Lim GE. Elucidation of the 14-3-3ζ interactome reveals critical roles of RNA-splicing factors during adipogenesis. J Biol Chem 2018. [PMID: 29530978 DOI: 10.1074/jbc.m117.816272] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Adipogenesis involves a complex signaling network requiring strict temporal and spatial organization of effector molecules. Molecular scaffolds, such as 14-3-3 proteins, facilitate such organization, and we have previously identified 14-3-3ζ as an essential scaffold in adipocyte differentiation. The interactome of 14-3-3ζ is large and diverse, and it is possible that novel adipogenic factors may be present within it, but this possibility has not yet been tested. Herein, we generated mouse embryonic fibroblasts from mice overexpressing a tandem affinity purification (TAP) epitope-tagged 14-3-3ζ molecule. After inducing adipogenesis, TAP-14-3-3ζ complexes were purified, followed by MS analysis to determine the 14-3-3ζ interactome. We observed more than 100 proteins that were unique to adipocyte differentiation, 56 of which were novel interacting partners. Among these, we were able to identify previously established regulators of adipogenesis (i.e. Ptrf/Cavin1) within the 14-3-3ζ interactome, confirming the utility of this approach to detect adipogenic factors. We found that proteins related to RNA metabolism, processing, and splicing were enriched in the interactome. Analysis of transcriptomic data revealed that 14-3-3ζ depletion in 3T3-L1 cells affected alternative splicing of mRNA during adipocyte differentiation. siRNA-mediated depletion of RNA-splicing factors within the 14-3-3ζ interactome, that is, of Hnrpf, Hnrpk, Ddx6, and Sfpq, revealed that they have essential roles in adipogenesis and in the alternative splicing of Pparg and the adipogenesis-associated gene Lpin1 In summary, we have identified novel adipogenic factors within the 14-3-3ζ interactome. Further characterization of additional proteins within the 14-3-3ζ interactome may help identify novel targets to block obesity-associated expansion of adipose tissues.
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Affiliation(s)
- Yves Mugabo
- From the Centre Hospitalier de l'Université de Montréal, Montréal, Québec H2X 029, Canada.,the Department of Medicine, Université de Montréal, Montréal, Québec H3T 1J4, Canada, and
| | - Mina Sadeghi
- From the Centre Hospitalier de l'Université de Montréal, Montréal, Québec H2X 029, Canada.,the Department of Medicine, Université de Montréal, Montréal, Québec H3T 1J4, Canada, and
| | - Nancy N Fang
- the Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Thibault Mayor
- the Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Gareth E Lim
- From the Centre Hospitalier de l'Université de Montréal, Montréal, Québec H2X 029, Canada, .,the Department of Medicine, Université de Montréal, Montréal, Québec H3T 1J4, Canada, and
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47
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Alternative mRNA Splicing in the Pathogenesis of Obesity. Int J Mol Sci 2018; 19:ijms19020632. [PMID: 29473878 PMCID: PMC5855854 DOI: 10.3390/ijms19020632] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/21/2018] [Accepted: 02/21/2018] [Indexed: 12/22/2022] Open
Abstract
Alternative mRNA splicing is an important mechanism in expansion of proteome diversity by production of multiple protein isoforms. However, emerging evidence indicates that only a limited number of annotated protein isoforms by alternative splicing are detected, and the coding sequence of alternative splice variants usually is only slightly different from that of the canonical sequence. Nevertheless, mis-splicing is associated with a large array of human diseases. Previous reviews mainly focused on hereditary and somatic mutations in cis-acting RNA sequence elements and trans-acting splicing factors. The importance of environmental perturbations contributed to mis-splicing is not assessed. As significant changes in exon skipping and splicing factors expression levels are observed with diet-induced obesity, this review focuses on several well-known alternatively spliced metabolic factors and discusses recent advances in the regulation of the expressions of splice variants under the pathophysiological conditions of obesity. The potential of targeting the alternative mRNA mis-splicing for obesity-associated diseases therapies will also be discussed.
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Fazakerley DJ, Chaudhuri R, Yang P, Maghzal GJ, Thomas KC, Krycer JR, Humphrey SJ, Parker BL, Fisher-Wellman KH, Meoli CC, Hoffman NJ, Diskin C, Burchfield JG, Cowley MJ, Kaplan W, Modrusan Z, Kolumam G, Yang JY, Chen DL, Samocha-Bonet D, Greenfield JR, Hoehn KL, Stocker R, James DE. Mitochondrial CoQ deficiency is a common driver of mitochondrial oxidants and insulin resistance. eLife 2018; 7:32111. [PMID: 29402381 PMCID: PMC5800848 DOI: 10.7554/elife.32111] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 01/02/2018] [Indexed: 12/11/2022] Open
Abstract
Insulin resistance in muscle, adipocytes and liver is a gateway to a number of metabolic diseases. Here, we show a selective deficiency in mitochondrial coenzyme Q (CoQ) in insulin-resistant adipose and muscle tissue. This defect was observed in a range of in vitro insulin resistance models and adipose tissue from insulin-resistant humans and was concomitant with lower expression of mevalonate/CoQ biosynthesis pathway proteins in most models. Pharmacologic or genetic manipulations that decreased mitochondrial CoQ triggered mitochondrial oxidants and insulin resistance while CoQ supplementation in either insulin-resistant cell models or mice restored normal insulin sensitivity. Specifically, lowering of mitochondrial CoQ caused insulin resistance in adipocytes as a result of increased superoxide/hydrogen peroxide production via complex II. These data suggest that mitochondrial CoQ is a proximal driver of mitochondrial oxidants and insulin resistance, and that mechanisms that restore mitochondrial CoQ may be effective therapeutic targets for treating insulin resistance. After we eat, our blood sugar levels increase. To counteract this, the pancreas releases a hormone called insulin. Part of insulin’s effect is to promote the uptake of sugar from the blood into muscle and fat tissue for storage. Under certain conditions, such as obesity, this process can become defective, leading to a condition known as insulin resistance. This condition makes a number of human diseases more likely to develop, including type 2 diabetes. Working out how insulin resistance develops could therefore unveil new treatment strategies for these diseases. Mitochondria – structures that produce most of a cell’s energy supply – appear to play a role in the development of insulin resistance. Mitochondria convert nutrients such as fats and sugars into molecules called ATP that fuel the many processes required for life. However, ATP production can also generate potentially harmful intermediates often referred to as ‘reactive oxygen species’ or ‘oxidants’. Previous studies have suggested that an increase in the amount of oxidants produced in mitochondria can cause insulin resistance. Fazakerley et al. therefore set out to identify the reason for increased oxidants in mitochondria, and did so by analysing the levels of proteins and oxidants found in cells grown in the laboratory, and mouse and human tissue samples. This led them to find that concentrations of a molecule called coenzyme Q (CoQ), an essential component of mitochondria that helps to produce ATP, were lower in mitochondria from insulin-resistant fat and muscle tissue. Further experiments suggested a link between the lower levels of CoQ and the higher levels of oxidants in the mitochondria. Replenishing the mitochondria of the lab-grown cells and insulin-resistant mice with CoQ restored ‘normal’ oxidant levels and prevented the development of insulin resistance. Strategies that aim to increase mitochondria CoQ levels may therefore prevent or reverse insulin resistance. Although CoQ supplements are readily available, swallowing CoQ does not efficiently deliver CoQ to mitochondria in humans, so alternative treatment methods must be found. It is also of interest that statins, common drugs taken by millions of people around the world to lower cholesterol, also lower CoQ and have been reported to increase the risk of developing type 2 diabetes. Further research is therefore needed to investigate whether CoQ might provide the link between statins and type 2 diabetes.
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Affiliation(s)
- Daniel J Fazakerley
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Rima Chaudhuri
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Pengyi Yang
- School of Mathematics and Statistics, University of Sydney, Camperdown, Australia
| | - Ghassan J Maghzal
- Vascular Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Kristen C Thomas
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - James R Krycer
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Sean J Humphrey
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Benjamin L Parker
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Kelsey H Fisher-Wellman
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, United States
| | - Christopher C Meoli
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Nolan J Hoffman
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Ciana Diskin
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - James G Burchfield
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Mark J Cowley
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Warren Kaplan
- Peter Wills Bioinformatics Centre, Garvan Institute of Medical Research, Darlinghurst, Australia
| | | | | | - Jean Yh Yang
- School of Mathematics and Statistics, University of Sydney, Camperdown, Australia
| | - Daniel L Chen
- Garvan Institute of Medical Research, Darlinghurst, Australia
| | | | | | - Kyle L Hoehn
- School of Biotechnology and Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Roland Stocker
- Vascular Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, Australia
| | - David E James
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia.,Charles Perkins Centre, Sydney Medical School, University of Sydney, Camperdown NSW, Australia
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Bush SJ, Chen L, Tovar-Corona JM, Urrutia AO. Alternative splicing and the evolution of phenotypic novelty. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0474. [PMID: 27994117 DOI: 10.1098/rstb.2015.0474] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2016] [Indexed: 12/21/2022] Open
Abstract
Alternative splicing, a mechanism of post-transcriptional RNA processing whereby a single gene can encode multiple distinct transcripts, has been proposed to underlie morphological innovations in multicellular organisms. Genes with developmental functions are enriched for alternative splicing events, suggestive of a contribution of alternative splicing to developmental programmes. The role of alternative splicing as a source of transcript diversification has previously been compared to that of gene duplication, with the relationship between the two extensively explored. Alternative splicing is reduced following gene duplication with the retention of duplicate copies higher for genes which were alternatively spliced prior to duplication. Furthermore, and unlike the case for overall gene number, the proportion of alternatively spliced genes has also increased in line with the evolutionary diversification of cell types, suggesting alternative splicing may contribute to the complexity of developmental programmes. Together these observations suggest a prominent role for alternative splicing as a source of functional innovation. However, it is unknown whether the proliferation of alternative splicing events indeed reflects a functional expansion of the transcriptome or instead results from weaker selection acting on larger species, which tend to have a higher number of cell types and lower population sizes.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Stephen J Bush
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Lu Chen
- West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, People's Republic of China
| | | | - Araxi O Urrutia
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK .,Milner Centre for Evolution, University of Bath, Bath BA2 7AY, UK
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Brinegar AE, Xia Z, Loehr JA, Li W, Rodney GG, Cooper TA. Extensive alternative splicing transitions during postnatal skeletal muscle development are required for calcium handling functions. eLife 2017; 6:27192. [PMID: 28826478 PMCID: PMC5577920 DOI: 10.7554/elife.27192] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 08/04/2017] [Indexed: 01/08/2023] Open
Abstract
Postnatal development of skeletal muscle is a highly dynamic period of tissue remodeling. Here, we used RNA-seq to identify transcriptome changes from late embryonic to adult mouse muscle and demonstrate that alternative splicing developmental transitions impact muscle physiology. The first 2 weeks after birth are particularly dynamic for differential gene expression and alternative splicing transitions, and calcium-handling functions are significantly enriched among genes that undergo alternative splicing. We focused on the postnatal splicing transitions of the three calcineurin A genes, calcium-dependent phosphatases that regulate multiple aspects of muscle biology. Redirected splicing of calcineurin A to the fetal isoforms in adult muscle and in differentiated C2C12 slows the timing of muscle relaxation, promotes nuclear localization of calcineurin target Nfatc3, and/or affects expression of Nfatc transcription targets. The results demonstrate a previously unknown specificity of calcineurin isoforms as well as the broader impact of alternative splicing during muscle postnatal development.
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Affiliation(s)
- Amy E Brinegar
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, United States.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, United States
| | - Zheng Xia
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, United States.,Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, United States
| | - James Anthony Loehr
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, United States
| | - Wei Li
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, United States.,Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, United States
| | - George Gerald Rodney
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, United States
| | - Thomas A Cooper
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, United States.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, United States.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, United States
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