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Meurant S, Mauclet L, Dieu M, Arnould T, Eyckerman S, Renard P. Endogenous TOM20 Proximity Labeling: A Swiss-Knife for the Study of Mitochondrial Proteins in Human Cells. Int J Mol Sci 2023; 24:ijms24119604. [PMID: 37298552 DOI: 10.3390/ijms24119604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Biotin-based proximity labeling approaches, such as BioID, have demonstrated their use for the study of mitochondria proteomes in living cells. The use of genetically engineered BioID cell lines enables the detailed characterization of poorly characterized processes such as mitochondrial co-translational import. In this process, translation is coupled to the translocation of the mitochondrial proteins, alleviating the energy cost typically associated with the post-translational import relying on chaperone systems. However, the mechanisms are still unclear with only few actors identified but none that have been described in mammals yet. We thus profiled the TOM20 proxisome using BioID, assuming that some of the identified proteins could be molecular actors of the co-translational import in human cells. The obtained results showed a high enrichment of RNA binding proteins close to the TOM complex. However, for the few selected candidates, we could not demonstrate a role in the mitochondrial co-translational import process. Nonetheless, we were able to demonstrate additional uses of our BioID cell line. Indeed, the experimental approach used in this study is thus proposed for the identification of mitochondrial co-translational import effectors and for the monitoring of protein entry inside mitochondria with a potential application in the prediction of mitochondrial protein half-life.
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Affiliation(s)
- Sébastien Meurant
- URBC, Namur Research Institute for Life Sciences (Narilis), University of Namur (UNamur), 5000 Namur, Belgium
| | - Lorris Mauclet
- URBC, Namur Research Institute for Life Sciences (Narilis), University of Namur (UNamur), 5000 Namur, Belgium
| | - Marc Dieu
- Mass Spectrometry Platform (MaSUN), Namur Research Institute for Life Sciences (Narilis), University of Namur (UNamur), 5000 Namur, Belgium
| | - Thierry Arnould
- URBC, Namur Research Institute for Life Sciences (Narilis), University of Namur (UNamur), 5000 Namur, Belgium
| | - Sven Eyckerman
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Patricia Renard
- URBC, Namur Research Institute for Life Sciences (Narilis), University of Namur (UNamur), 5000 Namur, Belgium
- Mass Spectrometry Platform (MaSUN), Namur Research Institute for Life Sciences (Narilis), University of Namur (UNamur), 5000 Namur, Belgium
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2
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Vomhof-DeKrey EE, Singhal S, Singhal SK, Stover AD, Rajpathy O, Preszler E, Garcia L, Basson MD. RNA Sequencing of Intestinal Enterocytes Pre- and Post-Roux-en-Y Gastric Bypass Reveals Alteration in Gene Expression Related to Enterocyte Differentiation, Restitution, and Obesity with Regulation by Schlafen 12. Cells 2022; 11:3283. [PMID: 36291149 PMCID: PMC9601224 DOI: 10.3390/cells11203283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/10/2022] [Accepted: 10/14/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The intestinal lining renews itself in a programmed fashion that can be affected by adaptation to surgical procedures such as gastric bypass. METHODS To assess adaptive mechanisms in the human intestine after Roux-en-Y gastric bypass (RYGB), we biopsied proximal jejunum at the anastomotic site during surgery to establish a baseline and endoscopically re-biopsied the same area 6-9 months after bypass for comparison. Laser microdissection was performed on pre- and post-RYGB biopsies to isolate enterocytes for RNA sequencing. RESULTS RNA sequencing suggested significant decreases in gene expression associated with G2/M DNA damage checkpoint regulation of the cell cycle pathway, and significant increases in gene expression associated with the CDP-diacylglycerol biosynthesis pathway TCA cycle II pathway, and pyrimidine ribonucleotide salvage pathway after RYGB. Since Schlafen 12 (SLFN12) is reported to influence enterocytic differentiation, we stained mucosa for SLFN12 and observed increased SLFN12 immunoreactivity. We investigated SLFN12 overexpression in HIEC-6 and FHs 74 Int intestinal epithelial cells and observed similar increased expression of the following genes that were also increased after RYGB: HES2, CARD9, SLC19A2, FBXW7, STXBP4, SPARCL1, and UTS. CONCLUSIONS Our data suggest that RYGB promotes SLFN12 protein expression, cellular mechanism and replication pathways, and genes associated with differentiation and restitution (HES2, CARD9, SLC19A2), as well as obesity-related genes (FBXW7, STXBP4, SPARCL1, UTS).
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Affiliation(s)
- Emilie E. Vomhof-DeKrey
- Department of Surgery, School of Medicine and the Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
- Department of Biomedical Sciences, School of Medicine and the Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Sonalika Singhal
- Department of Pathology, School of Medicine and the Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Sandeep K. Singhal
- Department of Pathology, School of Medicine and the Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Allie D. Stover
- Department of Biomedical Sciences, School of Medicine and the Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Odele Rajpathy
- Department of Biomedical Sciences, School of Medicine and the Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Elizabeth Preszler
- Department of Biomedical Sciences, School of Medicine and the Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Luis Garcia
- Sanford Health Clinic, Sioux Falls, ND 57117, USA
| | - Marc D. Basson
- Department of Surgery, School of Medicine and the Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
- Department of Biomedical Sciences, School of Medicine and the Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
- Department of Pathology, School of Medicine and the Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
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Molecular Mechanisms Contributing to the Etiology of Congenital Diaphragmatic Hernia: A Review and Novel Cases. J Pediatr 2022; 246:251-265.e2. [PMID: 35314152 DOI: 10.1016/j.jpeds.2022.03.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/01/2022] [Accepted: 03/15/2022] [Indexed: 12/25/2022]
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Venigalla S, Straub J, Idigo O, Rinderle C, Stephens JM, Newman JJ. MED12 Regulates Human Adipose-Derived Stem Cell Adipogenesis and Mediator Kinase Subunit Expression in Murine Adipose Depots. Stem Cells Dev 2022; 31:119-131. [PMID: 35018809 PMCID: PMC9206493 DOI: 10.1089/scd.2021.0302] [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: 11/13/2022] Open
Abstract
The mediator kinase module plays a critical role in the regulation of transcription during metabolic processes. Here we demonstrate that in human adipose-derived stem cells (hASCs), kinase module subunits have distinct mRNA and protein expression profiles during different stages of adipogenesis. In addition, siRNA-mediated loss of MED12 results in decreased adipogenesis as evident through decreased lipid accumulation and decreased expression of PPARγ, a master regulator of adipogenesis. Moreover, the decrease in adipogenesis and reduced PPARγ expression are observed only during the early stages of MED12 knockdown. At later stages, knockdown of MED12 did not have any significant effects on adipogenesis or PPARγ expression. We also observed that MED12 was present in a protein complex with PPARγ and C/EBPα during all stages of adipogenesis in hASCs. In 3T3-L1 preadipocytes and adipocytes, MED12 is present in protein complexes with PPARγ1, C/EBPα, and STAT5A. CDK8, another member of the kinase module, was only found to interact with C/EBPα. We found that the expression of all kinase module subunits decreased in inguinal, gonadal, and retroperitoneal white adipose tissue (WAT) depots in the fed state after an overnight fast, whereas the expression of kinase module subunits remained consistent in mesenteric WAT (mWAT) and brown adipose tissue. These data demonstrate that the kinase module undergoes physiologic regulation during fasting and feeding in specific mouse adipose tissue depots, and that MED12 likely plays a specific role in initiating and maintaining adipogenesis.
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Affiliation(s)
- Sree Venigalla
- School of Biological Sciences, Louisiana Tech University, Ruston, Louisiana, USA
| | - Joseph Straub
- School of Biological Sciences, Louisiana Tech University, Ruston, Louisiana, USA
| | - Onyekachi Idigo
- School of Biological Sciences, Louisiana Tech University, Ruston, Louisiana, USA
| | - Caroline Rinderle
- School of Biological Sciences, Louisiana Tech University, Ruston, Louisiana, USA
| | | | - Jamie J. Newman
- School of Biological Sciences, Louisiana Tech University, Ruston, Louisiana, USA.,Address correspondence to: Dr. Jamie J. Newman, School of Biological Sciences, Louisiana Tech University, Ruston, LA 71272, USA
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Lu A, Hsieh F, Sharma BR, Vaughn SR, Enrich C, Pfeffer SR. CRISPR screens for lipid regulators reveal a role for ER-bound SNX13 in lysosomal cholesterol export. J Cell Biol 2022; 221:212937. [PMID: 34936700 PMCID: PMC8704955 DOI: 10.1083/jcb.202105060] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 11/02/2021] [Accepted: 11/29/2021] [Indexed: 11/22/2022] Open
Abstract
We report here two genome-wide CRISPR screens performed to identify genes that, when knocked out, alter levels of lysosomal cholesterol or bis(monoacylglycero)phosphate. In addition, these screens were also performed under conditions of NPC1 inhibition to identify modifiers of NPC1 function in lysosomal cholesterol export. The screens confirm tight coregulation of cholesterol and bis(monoacylglycero)phosphate in cells and reveal an unexpected role for the ER-localized SNX13 protein as a negative regulator of lysosomal cholesterol export and contributor to ER–lysosome membrane contact sites. In the absence of NPC1 function, SNX13 knockdown redistributes lysosomal cholesterol and is accompanied by triacylglycerol-rich lipid droplet accumulation and increased lysosomal bis(monoacylglycero)phosphate. These experiments provide unexpected insight into the regulation of lysosomal lipids and modification of these processes by novel gene products.
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Affiliation(s)
- Albert Lu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA.,Departament de Biomedicina, Unitat de Biologia Cel·lular, Facultat de Medicina i Ciències de la Salut, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain
| | | | - Bikal R Sharma
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA
| | - Sydney R Vaughn
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA
| | - Carlos Enrich
- Departament de Biomedicina, Unitat de Biologia Cel·lular, Facultat de Medicina i Ciències de la Salut, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain
| | - Suzanne R Pfeffer
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA
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6
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Hollomon JM, Liu Z, Rusin SF, Jenkins NP, Smith AK, Koeppen K, Kettenbach AN, Myers LC, Hogan DA. The Candida albicans Cdk8-dependent phosphoproteome reveals repression of hyphal growth through a Flo8-dependent pathway. PLoS Genet 2022; 18:e1009622. [PMID: 34982775 PMCID: PMC8769334 DOI: 10.1371/journal.pgen.1009622] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 01/19/2022] [Accepted: 12/06/2021] [Indexed: 12/26/2022] Open
Abstract
Ssn3, also known as Cdk8, is a member of the four protein Cdk8 submodule within the multi-subunit Mediator complex involved in the co-regulation of transcription. In Candida albicans, the loss of Ssn3 kinase activity affects multiple phenotypes including cellular morphology, metabolism, nutrient acquisition, immune cell interactions, and drug resistance. In these studies, we generated a strain in which Ssn3 was replaced with a functional variant of Ssn3 that can be rapidly and selectively inhibited by the ATP analog 3-MB-PP1. Consistent with ssn3 null mutant and kinase dead phenotypes, inhibition of Ssn3 kinase activity promoted hypha formation. Furthermore, the increased expression of hypha-specific genes was the strongest transcriptional signal upon inhibition of Ssn3 in transcriptomics analyses. Rapid inactivation of Ssn3 was used for phosphoproteomic studies performed to identify Ssn3 kinase substrates associated with filamentation potential. Both previously validated and novel Ssn3 targets were identified. Protein phosphorylation sites that were reduced specifically upon Ssn3 inhibition included two sites in Flo8 which is a transcription factor known to positively regulate C. albicans morphology. Mutation of the two Flo8 phosphosites (threonine 589 and serine 620) was sufficient to increase Flo8-HA levels and Flo8 dependent transcriptional and morphological changes, suggesting that Ssn3 kinase activity negatively regulates Flo8.Under embedded conditions, when ssn3Δ/Δ and efg1Δ/Δ mutants were hyperfilamentous, FLO8 was essential for hypha formation. Previous work has also shown that loss of Ssn3 activity leads to increased alkalinization of medium with amino acids. Here, we show that the ssn3Δ/Δ medium alkalinization phenotype, which is dependent on STP2, a transcription factor involved in amino acid utilization, also requires FLO8 and EFG1. Together, these data show that Ssn3 activity can modulate Flo8 and its direct and indirect interactions in different ways, and underscores the potential importance of considering Ssn3 function in the control of transcription factor activities. In Candida albicans, Ssn3 kinase activity co-regulates the transcription of numerous genes involved in hyphal growth, metabolism and nutrient acquisition, immune cell interactions, and drug resistance. Using a strain in which Ssn3 could be rapidly and selectively inhibited, we identified both known and novel Ssn3 targets. We identified two phosphosites in Flo8, a regulator of morphology and virulence, that were shown to negatively regulate Flo8 levels and activity. The data and tools presented here will enable a better understanding of how Ssn3 impacts transcriptional and post-transcriptional regulation in order to coordinate processes during physiological and morphological transitions as well as during steady state growth.
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Affiliation(s)
- Jeffrey M. Hollomon
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Zhongle Liu
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Scott F. Rusin
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- Norris Cotton Cancer Center, Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center at Dartmouth, Lebanon, New Hampshire, United States of America
| | - Nicole P. Jenkins
- Norris Cotton Cancer Center, Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center at Dartmouth, Lebanon, New Hampshire, United States of America
| | - Allia K. Smith
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Katja Koeppen
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Arminja N. Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- Norris Cotton Cancer Center, Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center at Dartmouth, Lebanon, New Hampshire, United States of America
| | - Lawrence C. Myers
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- Department of Medical Education, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- * E-mail: (LCM); (DAH)
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- * E-mail: (LCM); (DAH)
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7
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Zhang X, Ma Z, Song E, Xu T. Islet organoid as a promising model for diabetes. Protein Cell 2021; 13:239-257. [PMID: 33751396 PMCID: PMC7943334 DOI: 10.1007/s13238-021-00831-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/22/2021] [Indexed: 02/06/2023] Open
Abstract
Studies on diabetes have long been hampered by a lack of authentic disease models that, ideally, should be unlimited and able to recapitulate the abnormalities involved in the development, structure, and function of human pancreatic islets under pathological conditions. Stem cell-based islet organoids faithfully recapitulate islet development in vitro and provide large amounts of three-dimensional functional islet biomimetic materials with a morphological structure and cellular composition similar to those of native islets. Thus, islet organoids hold great promise for modeling islet development and function, deciphering the mechanisms underlying the onset of diabetes, providing an in vitro human organ model for infection of viruses such as SARS-CoV-2, and contributing to drug screening and autologous islet transplantation. However, the currently established islet organoids are generally immature compared with native islets, and further efforts should be made to improve the heterogeneity and functionality of islet organoids, making it an authentic and informative disease model for diabetes. Here, we review the advances and challenges in the generation of islet organoids, focusing on human pluripotent stem cell-derived islet organoids, and the potential applications of islet organoids as disease models and regenerative therapies for diabetes.
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Affiliation(s)
- Xiaofei Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Zhuo Ma
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Eli Song
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Tao Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China. .,Guangzhou Regenerative Medicine and Health Guangdong Laboratory (Bioland Laboratory), Guangzhou, 510005, China.
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8
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Binenbaum I, Atamni HAT, Fotakis G, Kontogianni G, Koutsandreas T, Pilalis E, Mott R, Himmelbauer H, Iraqi FA, Chatziioannou AA. Container-aided integrative QTL and RNA-seq analysis of Collaborative Cross mice supports distinct sex-oriented molecular modes of response in obesity. BMC Genomics 2020; 21:761. [PMID: 33143653 PMCID: PMC7640698 DOI: 10.1186/s12864-020-07173-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/21/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The Collaborative Cross (CC) mouse population is a valuable resource to study the genetic basis of complex traits, such as obesity. Although the development of obesity is influenced by environmental factors, underlying genetic mechanisms play a crucial role in the response to these factors. The interplay between the genetic background and the gene expression pattern can provide further insight into this response, but we lack robust and easily reproducible workflows to integrate genomic and transcriptomic information in the CC mouse population. RESULTS We established an automated and reproducible integrative workflow to analyse complex traits in the CC mouse genetic reference panel at the genomic and transcriptomic levels. We implemented the analytical workflow to assess the underlying genetic mechanisms of host susceptibility to diet induced obesity and integrated these results with diet induced changes in the hepatic gene expression of susceptible and resistant mice. Hepatic gene expression differs significantly between obese and non-obese mice, with a significant sex effect, where male and female mice exhibit different responses and coping mechanisms. CONCLUSION Integration of the data showed that different genes but similar pathways are involved in the genetic susceptibility and disturbed in diet induced obesity. Genetic mechanisms underlying susceptibility to high-fat diet induced obesity are different in female and male mice. The clear distinction we observed in the systemic response to the high-fat diet challenge and to obesity between male and female mice points to the need for further research into distinct sex-related mechanisms in metabolic disease.
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Affiliation(s)
- Ilona Binenbaum
- Division of Pediatric Hematology-Oncology, First Department of Pediatrics, National and Kapodistrian University of Athens, Athens, Greece
- Department of Biology, University of Patras, Patras, Greece
| | - Hanifa Abu-Toamih Atamni
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Georgios Fotakis
- Division of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
- e-NIOS PC, Kallithea, Athens, Greece
| | - Georgia Kontogianni
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Theodoros Koutsandreas
- e-NIOS PC, Kallithea, Athens, Greece
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Eleftherios Pilalis
- e-NIOS PC, Kallithea, Athens, Greece
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Richard Mott
- Department of Genetics, University College of London, London, UK
| | - Heinz Himmelbauer
- Institute of Computational Biology, Department of Biotechnology, University of Life Sciences and Natural Resources, Vienna (BOKU), Vienna, Austria
- Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Fuad A Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.
| | - Aristotelis A Chatziioannou
- e-NIOS PC, Kallithea, Athens, Greece.
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
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9
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Zhang T, Xin G, Jia M, Zhuang T, Zhu S, Zhang B, Wang G, Jiang Q, Zhang C. The Plk1 kinase negatively regulates the Hedgehog signaling pathway by phosphorylating Gli1. J Cell Sci 2019; 132:jcs220384. [PMID: 30578313 DOI: 10.1242/jcs.220384] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 12/17/2018] [Indexed: 12/12/2022] Open
Abstract
Hedgehog (Hh) signaling is a highly conserved cell signaling pathway important for cell life, development and tumorigenesis. Increasing evidence suggests that the Hh signaling pathway functions in certain phases of the cell cycle. However, the coordination between Hh signaling and cell cycle control remains poorly understood. Here, we show that polo-like kinase-1 (Plk1), a critical protein kinase regulating many processes during the cell cycle, also regulates Hh signaling by phosphorylating and inhibiting Gli1, a downstream transcription factor of the Hh signaling pathway. Gli1 expression increases along with Hh signaling activation, leading to upregulation of Hh target genes, including cyclin E, during the G1 and S phases. Gli1 is phosphorylated at S481 by Plk1, and this phosphorylation facilitates the nuclear export and binding of Gli1 with its negative regulator Sufu, leading to a reduction in Hh signaling activity. Inhibition of Plk1 kinase activity led to Gli1 maintaining is role in promoting downstream gene expression. Collectively, our data reveal a novel mechanism regarding the crosstalk between Hh signaling and cell cycle control.
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Affiliation(s)
- Tingting Zhang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Guangwei Xin
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Mingkang Jia
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Tenghan Zhuang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Shicong Zhu
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Boyan Zhang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Gang Wang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Qing Jiang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Chuanmao Zhang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
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10
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Li Z, Liu H, Niu Z, Zhong W, Xue M, Wang J, Yang F, Zhou Y, Zhou Y, Xu T, Hou J. Temporal Proteomic Analysis of Pancreatic β-Cells in Response to Lipotoxicity and Glucolipotoxicity. Mol Cell Proteomics 2018; 17:2119-2131. [PMID: 30082485 DOI: 10.1074/mcp.ra118.000698] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 08/03/2018] [Indexed: 12/12/2022] Open
Abstract
Chronic hyperlipidemia causes the dysfunction of pancreatic β-cells, such as apoptosis and impaired insulin secretion, which are aggravated in the presence of hyperglycemia. The underlying mechanisms, such as endoplasmic reticulum (ER) stress, oxidative stress and metabolic disorders, have been reported before; however, the time sequence of these molecular events is not fully understood. Here, using isobaric labeling-based mass spectrometry, we investigated the dynamic proteomes of INS-1 cells exposed to high palmitate in the absence and presence of high glucose. Using bioinformatics analysis of differentially expressed proteins, including the time-course expression pattern, protein-protein interaction, gene set enrichment and KEGG pathway analysis, we analyzed the dynamic features of previously reported and newly identified lipotoxicity- and glucolipotoxicity-related molecular events in more detail. Our temporal data highlight cholesterol metabolism occurring at 4 h, earlier than fatty acid metabolism that started at 8 h and likely acting as an early toxic event highly associated with ER stress induced by palmitate. Interestingly, we found that the proliferation of INS-1 cells was significantly increased at 48 h by combined treatment of palmitate and glucose. Moreover, benefit from the time-course quantitative data, we identified and validated two new molecular targets: Setd8 for cell replication and Rhob for apoptosis, demonstrating that our temporal dataset serves as a valuable resource to identify potential candidates for mechanistic studies of lipotoxicity and glucolipotoxicity in pancreatic β-cells.
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Affiliation(s)
- Zonghong Li
- From the ‡National Laboratory of Biomacramolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,§Jilin Province Key Laboratory on Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun, 130024, China
| | - Hongyang Liu
- From the ‡National Laboratory of Biomacramolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,‖Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhangjing Niu
- From the ‡National Laboratory of Biomacramolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,‖Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen Zhong
- ***College of Life Science and Technology, HuaZhong University of Science and Technology, Wuhan 430074, China
| | - Miaomiao Xue
- From the ‡National Laboratory of Biomacramolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,¶College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jifeng Wang
- ‡‡Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fuquan Yang
- ‡‡Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,¶College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Zhou
- §§ThermoFisher Scientific, Building 6, No. 27, Xin Jinqiao Rd, Pudong, Shanghai, 201206, China
| | - Yifa Zhou
- §Jilin Province Key Laboratory on Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun, 130024, China;
| | - Tao Xu
- From the ‡National Laboratory of Biomacramolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; .,¶College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junjie Hou
- From the ‡National Laboratory of Biomacramolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China;
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Putlyaev EV, Ibragimov AN, Lebedeva LA, Georgiev PG, Shidlovskii YV. Structure and Functions of the Mediator Complex. BIOCHEMISTRY (MOSCOW) 2018; 83:423-436. [PMID: 29626929 DOI: 10.1134/s0006297918040132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mediator is a key factor in the regulation of expression of RNA polymerase II-transcribed genes. Recent studies have shown that Mediator acts as a coordinator of transcription activation and participates in maintaining chromatin architecture in the cell nucleus. In this review, we present current concepts on the structure and functions of Mediator.
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Affiliation(s)
- E V Putlyaev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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