1
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Li X, Liu J, Lu L, Huang T, Hou W, Wang F, Yu L, Wu F, Qi J, Chen X, Meng Z, Zhu M. Sirt7 associates with ELK1 to participate in hyperglycemia memory and diabetic nephropathy via modulation of DAPK3 expression and endothelial inflammation. Transl Res 2022; 247:99-116. [PMID: 35470010 DOI: 10.1016/j.trsl.2022.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 04/01/2022] [Accepted: 04/18/2022] [Indexed: 02/08/2023]
Abstract
Diabetic nephropathy (DN) is one of the most serious complications of advanced diabetes, and increases patient mortality. Recently, epigenetics-mediated hyperglycemic memory in pathological process of DN has received attention. The purpose of this study was to determine the underlying mechanism by which sirt7 modulates hyperglycemic memory in DN. In glomerular endothelial cells (GECs) cultured in high glucose and glomeruli of DN patients and rats, an increase in p65 phosphorylation and endothelial adhesion molecule levels persisted after glucose normalization but was reversed by glucose normalization associated with death-associated protein kinase-3 (DAPK3) knockout or DAPK3 inhibitor. High glucose-mediated decrease in sirt7, the deacetylase modulating H3K18-acetylation (H3K18ac), was sustained after normoglycemia. Sirt7 overexpression accompanied by glucose normalization suppressed DAPK3 expression and inflammation in GECs. Moreover, sh-sirt7-induced inflammation was inhibited by si-DAPK3. Furthermore, sirt7 and H3K18ac were located at the DAPK3 promoter region. ELK1 was found to combine with sirt7. si-ELK1 supplemented with normoglycemia inhibited high glucose-induced DAPK3 expression and inflammation in GECs. ELK1 overexpression-mediated inflammation was inhibited by si-DAPK3. In addition, ELK1 and sirt7 were located at the same promoter region of DAPK3. ELK1 overexpression enhanced DAPK3 promoter activity, which disappeared after specific binding site mutation. In vivo, sirt7 overexpression decreased inflammation and improved renal function during insulin treatment of DN rats, whereas insulin alone did not work. Our data demonstrated high glucose-mediated mutual inhibition between sirt7 and ELK1 induced DAPK3 transcription and inflammation despite normoglycemia in GECs, thus forming a vicious cycle and participating in the occurrence of hyperglycemic memory in DN.
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Affiliation(s)
- Xue Li
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jing Liu
- Department of Anaesthesiology, Huzhou Maternal & Child Health Care Hospital, Huzhou, Zhejiang, China
| | - Lihong Lu
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ting Huang
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenting Hou
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fei Wang
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lang Yu
- Department of Anaesthesiology, Huzhou Central Hospital, Affiliated Central Hospital of HuZhou University, No.1558 Sanhuan North Road, Huzhou, Zhejiang, China
| | - Fengfeng Wu
- Department of Orthopedics and Rehabilitation, Huzhou Central Hospital, Affiliated Central Hospital of HuZhou University, No.1558 Sanhuan North Road, Huzhou, Zhejiang, China
| | - Jie Qi
- Department of Anesthesiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiangyuan Chen
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Zhipeng Meng
- Department of Anaesthesiology, Huzhou Central Hospital, Affiliated Central Hospital of HuZhou University, No.1558 Sanhuan North Road, Huzhou, Zhejiang, China.
| | - Minmin Zhu
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Department of Anesthesiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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2
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Jin H, Goossens P, Juhasz P, Eijgelaar W, Manca M, Karel JMH, Smirnov E, Sikkink CJJM, Mees BME, Waring O, van Kuijk K, Fazzi GE, Gijbels MJJ, Kutmon M, Evelo CTA, Hedin U, Daemen MJAP, Sluimer JC, Matic L, Biessen EAL. Integrative multiomics analysis of human atherosclerosis reveals a serum response factor-driven network associated with intraplaque hemorrhage. Clin Transl Med 2021; 11:e458. [PMID: 34185408 PMCID: PMC8236116 DOI: 10.1002/ctm2.458] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND While single-omics analyses on human atherosclerotic plaque have been very useful to map stage- or disease-related differences in expression, they only partly capture the array of changes in this tissue and suffer from scale-intrinsic limitations. In order to better identify processes associated with intraplaque hemorrhage and plaque instability, we therefore combined multiple omics into an integrated model. METHODS In this study, we compared protein and gene makeup of low- versus high-risk atherosclerotic lesion segments from carotid endarterectomy patients, as judged from the absence or presence of intraplaque hemorrhage, respectively. Transcriptomic, proteomic, and peptidomic data of this plaque cohort were aggregated and analyzed by DIABLO, an integrative multivariate classification and feature selection method. RESULTS We identified a protein-gene associated multiomics model able to segregate stable, nonhemorrhaged from vulnerable, hemorrhaged lesions at high predictive performance (AUC >0.95). The dominant component of this model correlated with αSMA- PDGFRα+ fibroblast-like cell content (p = 2.4E-05) and Arg1+ macrophage content (p = 2.2E-04) and was driven by serum response factor (SRF), possibly in a megakaryoblastic leukemia-1/2 (MKL1/2) dependent manner. Gene set overrepresentation analysis on the selected key features of this model pointed to a clear cardiovascular disease signature, with overrepresentation of extracellular matrix synthesis and organization, focal adhesion, and cholesterol metabolism terms, suggestive of the model's relevance for the plaque vulnerability. Finally, we were able to corroborate the predictive power of the selected features in several independent mRNA and proteomic plaque cohorts. CONCLUSIONS In conclusion, our integrative omics study has identified an intraplaque hemorrhage-associated cardiovascular signature that provides excellent stratification of low- from high-risk carotid artery plaques in several independent cohorts. Further study revealed suppression of an SRF-regulated disease network, controlling lesion stability, in vulnerable plaque, which can serve as a scaffold for the design of targeted intervention in plaque destabilization.
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Affiliation(s)
- Han Jin
- Department of PathologySchool for Cardiovascular Diseases (CARIM)Maastricht UMC+MaastrichtThe Netherlands
| | - Pieter Goossens
- Department of PathologySchool for Cardiovascular Diseases (CARIM)Maastricht UMC+MaastrichtThe Netherlands
| | | | - Wouter Eijgelaar
- Department of PathologySchool for Cardiovascular Diseases (CARIM)Maastricht UMC+MaastrichtThe Netherlands
| | - Marco Manca
- Department of PathologySchool for Cardiovascular Diseases (CARIM)Maastricht UMC+MaastrichtThe Netherlands
| | - Joël M. H. Karel
- Department of Data Science and Knowledge EngineeringMaastricht UniversityMaastrichtThe Netherlands
| | - Evgueni Smirnov
- Department of Data Science and Knowledge EngineeringMaastricht UniversityMaastrichtThe Netherlands
| | | | | | - Olivia Waring
- Department of PathologySchool for Cardiovascular Diseases (CARIM)Maastricht UMC+MaastrichtThe Netherlands
| | - Kim van Kuijk
- Department of PathologySchool for Cardiovascular Diseases (CARIM)Maastricht UMC+MaastrichtThe Netherlands
| | - Gregorio E. Fazzi
- Department of PathologySchool for Cardiovascular Diseases (CARIM)Maastricht UMC+MaastrichtThe Netherlands
| | - Marion J. J. Gijbels
- Department of PathologySchool for Cardiovascular Diseases (CARIM)Maastricht UMC+MaastrichtThe Netherlands
- Department of Medical BiochemistryExperimental Vascular BiologyAmsterdam UMCAmsterdamThe Netherlands
- School for Oncology and Developmental Biology (GROW)Maastricht UniversityMaastrichtThe Netherlands
| | - Martina Kutmon
- Department of Bioinformatics (BiGCaT)Maastricht Centre for Systems Biology (MaCSBio)Maastricht UniversityMaastrichtThe Netherlands
| | - Chris T. A. Evelo
- Department of Bioinformatics (BiGCaT)Maastricht Centre for Systems Biology (MaCSBio)Maastricht UniversityMaastrichtThe Netherlands
| | - Ulf Hedin
- Department of Molecular Medicine and SurgeryKarolinska InstituteSolnaSweden
| | - Mat J. A. P. Daemen
- Department of PathologyAmsterdam Cardiovascular SciencesAmsterdam UMCAmsterdamThe Netherlands
| | - Judith C. Sluimer
- Department of PathologySchool for Cardiovascular Diseases (CARIM)Maastricht UMC+MaastrichtThe Netherlands
- BHF Centre for Cardiovascular Science (CVS)University of EdinburghEdinburghScotland
| | - Ljubica Matic
- Department of Molecular Medicine and SurgeryKarolinska InstituteSolnaSweden
| | - Erik A. L. Biessen
- Department of PathologySchool for Cardiovascular Diseases (CARIM)Maastricht UMC+MaastrichtThe Netherlands
- Institute for Molecular Cardiovascular ResearchRWTH Aachen UniversityAachenGermany
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3
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Cartland SP, Lin RCY, Genner S, Patil MS, Martínez GJ, Barraclough JY, Gloss B, Misra A, Patel S, Kavurma MM. Vascular transcriptome landscape of Trail -/- mice: Implications and therapeutic strategies for diabetic vascular disease. FASEB J 2020; 34:9547-9562. [PMID: 32501591 DOI: 10.1096/fj.201902785r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 04/30/2020] [Accepted: 05/08/2020] [Indexed: 12/20/2022]
Abstract
Circulating plasma TRAIL levels are suppressed in patients with cardiovascular and diabetic diseases. To identify novel targets in vascular metabolic diseases, genome-wide transcriptome of aortic tissue from Trail-/- versus Trail+/+ mice were interrogated. We found 861 genes differentially expressed with TRAIL deletion. Gene enrichment analyses showed many of these genes were related to inflammation, cell-to-cell cytoskeletal interactions, and transcriptional modulation. We identified vascular protective and pathological gene clusters, with Ifi205 as the most significantly reduced vascular protective gene, whereas Glut1, the most significantly increased pathological gene with TRAIL deletion. We hypothesized that therapeutic targets could be devised from such integrated analysis and validated our findings from vascular tissues of diabetic mice. From the differentially expressed gene targets, enriched transcription factor (TF) and microRNA binding motifs were identified. The top two TFs were Elk1 and Sp1, with enrichment to eight gene targets common to both. miR-520d-3p and miR-377-3p were the top enriched microRNAs with TRAIL deletion; with four overlapping genes enriched for both microRNAs. Our findings offer an alternate in silico approach for therapeutic target identification and present a deeper understanding of gene signatures and pathways altered with TRAIL suppression in the vasculature.
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Affiliation(s)
- Siân P Cartland
- Heart Research Institute, Sydney, NSW, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Ruby C Y Lin
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Scott Genner
- Heart Research Institute, Sydney, NSW, Australia
| | - Manisha S Patil
- Heart Research Institute, Sydney, NSW, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Gonzalo J Martínez
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Sydney, NSW, Australia.,División de Enfermedades Cardiovasculares, Pontificia Universidad Católica de Chile, Santiago, Chile.,Millennium Nucleus for Cardiovascular Magnetic Resonance, Santiago, Chile
| | - Jennifer Y Barraclough
- Heart Research Institute, Sydney, NSW, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Brian Gloss
- Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Ashish Misra
- Heart Research Institute, Sydney, NSW, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Sanjay Patel
- Heart Research Institute, Sydney, NSW, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Mary M Kavurma
- Heart Research Institute, Sydney, NSW, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
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4
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Hicks JA, Porter TE, Sunny NE, Liu HC. Delayed Feeding Alters Transcriptional and Post-Transcriptional Regulation of Hepatic Metabolic Pathways in Peri-Hatch Broiler Chicks. Genes (Basel) 2019; 10:genes10040272. [PMID: 30987204 PMCID: PMC6523616 DOI: 10.3390/genes10040272] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/19/2019] [Accepted: 04/01/2019] [Indexed: 12/14/2022] Open
Abstract
Hepatic fatty acid oxidation of yolk lipoproteins provides the main energy source for chick embryos. Post-hatching these yolk lipids are rapidly exhausted and metabolism switches to a carbohydrate-based energy source. We recently demonstrated that many microRNAs (miRNAs) are key regulators of hepatic metabolic pathways during this metabolic switching. MiRNAs are small non-coding RNAs that post-transcriptionally regulate gene expression in most eukaryotes. To further elucidate the roles of miRNAs in the metabolic switch, we used delayed feeding for 48 h to impede the hepatic metabolic switch. We found that hepatic expression of several miRNAs including miR-33, miR-20b, miR-34a, and miR-454 was affected by delaying feed consumption for 48 h. For example, we found that delayed feeding resulted in increased miR-20b expression and conversely reduced expression of its target FADS1, an enzyme involved in fatty acid synthesis. Interestingly, the expression of a previously identified miR-20b regulator FOXO3 was also higher in delayed fed chicks. FOXO3 also functions in protection of cells from oxidative stress. Delayed fed chicks also had much higher levels of plasma ketone bodies than their normal fed counterparts. This suggests that delayed fed chicks rely almost exclusively on lipid oxidation for energy production and are likely under higher oxidative stress. Thus, it is possible that FOXO3 may function to both limit lipogenesis as well as to help protect against oxidative stress in peri-hatch chicks until the initiation of feed consumption. This is further supported by evidence that the FOXO3-regulated histone deacetylase (HDAC2) was found to recognize the FASN (involved in fatty acid synthesis) chicken promoter in a yeast one-hybrid assay. Expression of FASN mRNA was lower in delayed fed chicks until feed consumption. The present study demonstrated that many transcriptional and post-transcriptional mechanisms, including miRNA, form a complex interconnected regulatory network that is involved in controlling lipid and glucose molecular pathways during the metabolic transition in peri-hatch chicks.
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Affiliation(s)
- Julie A Hicks
- Department of Animal Science, North Carolina State University, Raleigh, NC 27607, USA.
| | - Tom E Porter
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA.
| | - Nishanth E Sunny
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA.
| | - Hsiao-Ching Liu
- Department of Animal Science, North Carolina State University, Raleigh, NC 27607, USA.
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5
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Apazoglou K, Farley S, Gorgievski V, Belzeaux R, Lopez JP, Grenier J, Ibrahim EC, El Khoury MA, Tse YC, Mongredien R, Barbé A, de Macedo CEA, Jaworski W, Bochereau A, Orrico A, Isingrini E, Guinaudie C, Mikasova L, Louis F, Gautron S, Groc L, Massaad C, Yildirim F, Vialou V, Dumas S, Marti F, Mechawar N, Morice E, Wong TP, Caboche J, Turecki G, Giros B, Tzavara ET. Antidepressive effects of targeting ELK-1 signal transduction. Nat Med 2018; 24:591-597. [DOI: 10.1038/s41591-018-0011-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 02/12/2018] [Indexed: 12/28/2022]
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6
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Castellano-Castillo D, Denechaud PD, Moreno-Indias I, Tinahones F, Fajas L, Queipo-Ortuño MI, Cardona F. Chromatin immunoprecipitation improvements for the processing of small frozen pieces of adipose tissue. PLoS One 2018; 13:e0192314. [PMID: 29444131 PMCID: PMC5812632 DOI: 10.1371/journal.pone.0192314] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/22/2018] [Indexed: 02/06/2023] Open
Abstract
Chromatin immunoprecipitation (ChIP) has gained importance to identify links between the genome and the proteome. Adipose tissue has emerged as an active tissue, which secretes a wide range of molecules that have been related to metabolic and obesity-related disorders, such as diabetes, cardiovascular failure, metabolic syndrome, or cancer. In turn, epigenetics has raised the importance in discerning the possible relationship between metabolic disorders, lifestyle and environment. However, ChIP application in human adipose tissue is limited by several factors, such as sample size, frozen sample availability, high lipid content and cellular composition of the tissue. Here, we optimize the standard protocol of ChIP for small pieces of frozen human adipose tissue. In addition, we test ChIP for the histone mark H3K4m3, which is related to active promoters, and validate the performance of the ChIP by analyzing gene promoters for factors usually studied in adipose tissue using qPCR. Our improvements result in a higher performance in chromatin shearing and DNA recovery of adipocytes from the tissue, which may be useful for ChIP-qPCR or ChIP-seq analysis.
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Affiliation(s)
- Daniel Castellano-Castillo
- Unidad de Gestión Clínica de Endocrinología y Nutrición del Hospital Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Universidad de Málaga, Málaga, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición, CIBERobn, Madrid, Spain
| | - Pierre-Damien Denechaud
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Department of Physiology, University of Lausanne, Lausanne, Switzerland
- Institut des Maladies Métaboliques et Cardiovasculaires, Inserm UMR 1048, Toulouse, France
| | - Isabel Moreno-Indias
- Unidad de Gestión Clínica de Endocrinología y Nutrición del Hospital Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Universidad de Málaga, Málaga, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición, CIBERobn, Madrid, Spain
| | - Francisco Tinahones
- Unidad de Gestión Clínica de Endocrinología y Nutrición del Hospital Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Universidad de Málaga, Málaga, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición, CIBERobn, Madrid, Spain
| | - Lluis Fajas
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - María Isabel Queipo-Ortuño
- Unidad de Gestión Clínica de Endocrinología y Nutrición del Hospital Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Universidad de Málaga, Málaga, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición, CIBERobn, Madrid, Spain
| | - Fernando Cardona
- Unidad de Gestión Clínica de Endocrinología y Nutrición del Hospital Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Universidad de Málaga, Málaga, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición, CIBERobn, Madrid, Spain
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7
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Tao YF, Qiang J, Yin GJ, Xu P, Shi Q, Bao JW. Identification and characterization of lipid metabolism-related microRNAs in the liver of genetically improved farmed tilapia (GIFT, Oreochromis niloticus) by deep sequencing. FISH & SHELLFISH IMMUNOLOGY 2017; 69:227-235. [PMID: 28838655 DOI: 10.1016/j.fsi.2017.08.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 06/26/2017] [Accepted: 08/21/2017] [Indexed: 06/07/2023]
Abstract
MicroRNAs (miRNAs) play vital roles in modulating diverse metabolic processes in the liver, including lipid metabolism. Genetically improved farmed tilapia (GIFT, Oreochromis niloticus), an important aquaculture species in China, is susceptible to hepatic steatosis when reared in intensive culture systems. To investigate the miRNAs involved in GIFT lipid metabolism, two hepatic small RNA libraries from high-fat diet-fed and normal-fat diet-fed GIFT were constructed and sequenced using high-throughput sequencing technology. A total of 204 known and 56 novel miRNAs were identified by aligning the sequencing data with known Danio rerio miRNAs listed in miRBase 21.0. Six known miRNAs (miR-30a-5p, miR-34a, miR-145-5p, miR-29a, miR-205-5p, and miR-23a-3p) that were differentially expressed between the high-fat diet and normal-fat diet groups were validated by quantitative real-time PCR. Bioinformatics tools were used to predict the potential target genes of these differentially expressed miRNAs, and Gene Ontology enrichment analysis indicated that these miRNAs may play important roles in diet-induced hepatic steatosis in GIFT. Our results provide a foundation for further studies of the role of miRNAs in tilapia lipid homeostasis regulation, and may help to identify novel targets for therapeutic interventions to reduce the occurrence of fatty liver disease in farmed tilapia.
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Affiliation(s)
- Yi-Fan Tao
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jun Qiang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Guo-Jun Yin
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
| | - Pao Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen 518083, China
| | - Jing-Wen Bao
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
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8
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Interactome-transcriptome analysis discovers signatures complementary to GWAS Loci of Type 2 Diabetes. Sci Rep 2016; 6:35228. [PMID: 27752041 PMCID: PMC5067504 DOI: 10.1038/srep35228] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 09/26/2016] [Indexed: 01/13/2023] Open
Abstract
Protein interactions play significant roles in complex diseases. We analyzed peripheral blood mononuclear cells (PBMC) transcriptome using a multi-method strategy. We constructed a tissue-specific interactome (T2Di) and identified 420 molecular signatures associated with T2D-related comorbidity and symptoms, mainly implicated in inflammation, adipogenesis, protein phosphorylation and hormonal secretion. Apart from explaining the residual associations within the DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) study, the T2Di signatures were enriched in pathogenic cell type-specific regulatory elements related to fetal development, immunity and expression quantitative trait loci (eQTL). The T2Di revealed a novel locus near a well-established GWAS loci AChE, in which SRRT interacts with JAZF1, a T2D-GWAS gene implicated in pancreatic function. The T2Di also included known anti-diabetic drug targets (e.g. PPARD, MAOB) and identified possible druggable targets (e.g. NCOR2, PDGFR). These T2Di signatures were validated by an independent computational method, and by expression data of pancreatic islet, muscle and liver with some of the signatures (CEBPB, SREBF1, MLST8, SRF, SRRT and SLC12A9) confirmed in PBMC from an independent cohort of 66 T2D and 66 control subjects. By combining prior knowledge and transcriptome analysis, we have constructed an interactome to explain the multi-layered regulatory pathways in T2D.
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9
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Chang CF, Yang J, Li XF, Zhao WM, Chen SS, Wang GP, Xu CS. SPINK3: A novel growth factor that promotes rat liver regeneration. Mol Biol 2016. [DOI: 10.1134/s0026893316030055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Chen C, Wang Y, Yang S, Li H, Zhao G, Wang F, Yang L, Wang DW. MiR-320a contributes to atherogenesis by augmenting multiple risk factors and down-regulating SRF. J Cell Mol Med 2015; 19:970-85. [PMID: 25728840 PMCID: PMC4420600 DOI: 10.1111/jcmm.12483] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/07/2014] [Indexed: 01/29/2023] Open
Abstract
Atherosclerosis progress is regulated by a variety of factors. Here, we show that miR-320a, an intergenic miRNA, is markedly elevated in the peripheral blood of coronary heart disease patients and high-risk patients. Microarray analysis and qRT-PCR assays showed that circulating miRNA-320a was highly expressed in coronary artery disease patients. In vivo study showed that overexpression of miR-320a resulted in significant increase in levels of plasma lipid (total cholesterol, Triglyceride and low-density lipoprotein) and serum inflammatory cytokines (IL-6, MCP-1, sICAM, pSelectin, TNF-α and fibrinogen). In ApoE(-/-) mice, miR-320a expression attenuates endothelium cell function and promotes atherogenesis. Bioinformatics analysis identified serum response factor as a potential target for miR-320a, which was validated by luciferase reporter activity assay and western-blot in vitro and in vivo. Moreover, miR-320a expression inhibits human-derived endothelium cell proliferation and induces apoptosis. We also found that SP1 transcriptionally up-regulates hsa-miR-320a expression. Our observations indicate that miR-320a is a key regulator contributing to multiple aspects of atherogenesis.
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Affiliation(s)
- Chen Chen
- Department of Internal Medicine and Gene Therapy Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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11
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Uchiumi F, Miyazaki S, Tanuma SI. [Biological functions of the duplicated GGAA-motifs in various human promoter regions]. YAKUGAKU ZASSHI 2011; 131:1787-800. [PMID: 22129877 DOI: 10.1248/yakushi.131.1787] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Transcription is one of the most fundamental cellular functions and is an enzyme-complex mediated reaction that converts DNA sequences into mRNA. TATA-box is known to be an important motif for transcription. However, there are majority of promoters that have no TATA-box. They are called as TATA-less promoters and possess other elements that determine the transcription start site (TSS) of the genes. Multiple protein factors including ETS family proteins are known to recognize and bind to the GGAA containing sequences. In addition, it has been reported that the ETS binding motifs play important roles in regulation of various promoters. Here, we propose that the duplication and multiplication of the GGAA motifs are responsible for the initiation of transcription from TATA-less promoters.
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Affiliation(s)
- Fumiaki Uchiumi
- Department of Gene Regulation, Tokyo University of Science, Noda, Chiba, Japan.
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Zhang X, Azhar G, Helms S, Burton B, Huang C, Zhong Y, Gu X, Fang H, Tong W, Wei JY. Identification of New SRF Binding Sites in Genes Modulated by SRF Over-Expression in Mouse Hearts. GENE REGULATION AND SYSTEMS BIOLOGY 2011; 5:41-59. [PMID: 21792293 PMCID: PMC3140411 DOI: 10.4137/grsb.s7457] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Background: To identify in vivo new cardiac binding sites of serum response factor (SRF) in genes and to study the response of these genes to mild over-expression of SRF, we employed a cardiac-specific, transgenic mouse model, with mild over-expression of SRF (Mild-O SRF Tg). Methodology: Microarray experiments were performed on hearts of Mild-O-SRF Tg at 6 months of age. We identified 207 genes that are important for cardiac function that were differentially expressed in vivo. Among them the promoter region of 192 genes had SRF binding motifs, the classic CArG or CArG-like (CArG-L) elements. Fifty-one of the 56 genes with classic SRF binding sites had not been previously reported. These SRF-modulated genes were grouped into 12 categories based on their function. It was observed that genes associated with cardiac energy metabolism shifted toward that of carbohydrate metabolism and away from that of fatty acid metabolism. The expression of genes that are involved in transcription and ion regulation were decreased, but expression of cytoskeletal genes was significantly increased. Using public databases of mouse models of hemodynamic stress (GEO database), we also found that similar altered expression of the SRF-modulated genes occurred in these hearts with cardiac ischemia or aortic constriction as well. Conclusion and significance: SRF-modulated genes are actively regulated under various physiological and pathological conditions. We have discovered that a large number of cardiac genes have classic SRF binding sites and were significantly modulated in the Mild-O-SRF Tg mouse hearts. Hence, the mild elevation of SRF protein in the heart that is observed during typical adult aging may have a major impact on many SRF-modulated genes, thereby affecting cardiac structure and performance. The results from our study could help to enhance our understanding of SRF regulation of cellular processes in the aged heart.
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Affiliation(s)
- Xiaomin Zhang
- Donald W. Reynolds Department of Geriatrics, The University of Arkansas for Medical Sciences and Geriatric Research, Education, and Clinical Center, Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
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Sarkar A, Zhang M, Liu SH, Sarkar S, Brunicardi FC, Berger DH, Belaguli NS. Serum response factor expression is enriched in pancreatic β cells and regulates insulin gene expression. FASEB J 2011; 25:2592-603. [PMID: 21525490 DOI: 10.1096/fj.10-173757] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Serum response factor (SRF) is an essential regulator of myogenic and neurogenic genes and the ubiquitously expressed immediate-early genes. The purpose of this study is to determine SRF expression pattern in murine pancreas and examine the role of SRF in pancreatic gene expression. Immunohistochemical analysis of wild-type pancreas and LacZ staining of pancreas from SRF LacZ knock-in animals showed that SRF expression is restricted to β cells. SRF bound to the rat insulin promoter II (RIP II) serum response element, an element conserved in both rat I and murine I and II insulin promoters. SRF activated RIP II, and SRF binding to RIP II and the exon 5-encoded 64-aa subdomain of SRF was required for this activation. Transient or stable knockdown of SRF leads to down-regulation of insulin gene expression, suggesting that SRF is required for insulin gene expression. Further, SRF physically interacted with the pancreas and duodenum homeobox-1 (Pdx-1) and synergistically activated RIP II. Elevated glucose concentration down-regulated SRF binding to RIP II SRE, and this down-regulation was associated with decreased RIP II activity and increased SRF phosphorylation on serine 103. Together, our results demonstrate that SRF is a glucose concentration-sensitive regulator of insulin gene expression.
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Affiliation(s)
- Aloke Sarkar
- Michael E. DeBakey VA Medical Center, 2002 Holcombe Blvd., Houston, TX 77030, USA
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Canbaz D, Kırımtay K, Karaca E, Karabay A. SPG4 gene promoter regulation via Elk1 transcription factor. J Neurochem 2011; 117:724-34. [PMID: 21395583 DOI: 10.1111/j.1471-4159.2011.07243.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The most common cause of autosomal dominant hereditary spastic paraplegia, that is characterized with axonal degeneration in corticospinal tracts and posterior columns, is known to be caused by mutations in the SPG4 gene which encodes spastin, a microtubule severing ATPase belonging to AAA family. Spastin promotes the formation of microtubule networks that are essential for axon growth and branching which are important for neuronal plasticity. Mutations observed in SPG4 gene of hereditary spastic paraplegia patients have been shown to cause reduced spastin levels. In addition to mutations, transcriptional regulation of spastin gene expression may also affect spastin level. ETS (E Twenty Six-specific)-domain transcription factor, Elk1, has been shown to be important for synaptic plasticity and interact with microtubules. In this study, we aimed to identify the critical promoter regions of SPG4 gene and effects of Elk on SPG4 gene expression. We identified 700 bp TATA-less promoter including a critical CpG island as an optimal promoter, and deletion of the CpG island gradually decreased the SPG4 promoter activity. In addition, we identified the binding sites of Elk1 on the SPG4 promoter by EMSA. Over-expression of Elk1 showed that it repressed the SPG4 promoter and also decreased spastin protein level in SHSY-5Y cells.
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Affiliation(s)
- Derya Canbaz
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
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15
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The possible functions of duplicated ets (GGAA) motifs located near transcription start sites of various human genes. Cell Mol Life Sci 2011; 68:2039-51. [PMID: 21461879 PMCID: PMC3101357 DOI: 10.1007/s00018-011-0674-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 02/28/2011] [Accepted: 03/17/2011] [Indexed: 12/19/2022]
Abstract
Transcription is one of the most fundamental nuclear functions and is an enzyme complex-mediated reaction that converts DNA sequences into mRNA. Analyzing DNA sequences of 5′-flanking regions of several human genes that respond to 12-O-tetradecanoyl-phorbol-13-acetate (TPA) in HL-60 cells, we have identified that the ets (GGAA) motifs are duplicated, overlapped, or clustered within a 500-bp distance from the most 5′-upstream region of the cDNA. Multiple protein factors including Ets family proteins are known to recognize and bind to the GGAA containing sequences. In addition, it has been reported that the ets motifs play important roles in regulation of various promoters. Here, we propose a molecular mechanism, defined by the presence of duplication and multiplication of the GGAA motifs, that is responsible for the initiation of transcription of several genes and for the recruitment of binding proteins to the transcription start site (TSS) of TATA-less promoters.
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Fernández-Alvarez A, Soledad Alvarez M, Cucarella C, Casado M. Characterization of the human insulin-induced gene 2 (INSIG2) promoter: the role of Ets-binding motifs. J Biol Chem 2010; 285:11765-74. [PMID: 20145255 DOI: 10.1074/jbc.m109.067447] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Insulin-induced gene 2 (INSIG2) and its homolog INSIG1 encode closely related endoplasmic reticulum proteins that regulate the proteolytic activation of sterol regulatory element-binding proteins, transcription factors that activate the synthesis of cholesterol and fatty acids in animal cells. Several studies have been carried out to identify INSIG2 genetic variants associated with metabolic diseases. However, few data have been published regarding the regulation of INSIG2 gene expression. Two Insig2 transcripts have been described in rodents through the use of different promoters that produce different noncoding first exons that splice into a common second exon. Herein we report the cloning and characterization of the human INSIG2 promoter and the detection of an INSIG2-specific transcript homologous to the Insig2b mouse variant in human liver. Deletion analyses on 3 kb of 5'-flanking DNA of the human INSIG2 gene revealed the functional importance of a 350-bp region upstream of the transcription start site. Mutated analyses, chromatin immunoprecipitation assays, and RNA interference analyses unveiled the significance of an Ets-consensus motif in the proximal region and the interaction of the Ets family member SAP1a (serum response factor (SRF) accessory protein-1a) with this region of the human INSIG2 promoter. Moreover, our findings suggest that insulin activated the human INSIG2 promoter in a process mediated by phosphorylated SAP1a. Overall, these results map the functional elements in the human INSIG2 promoter sequence and suggest an unexpected regulation of INSIG2 gene expression in human liver.
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Affiliation(s)
- Ana Fernández-Alvarez
- Instituto de Biomedicina de Valencia (Consejo Superior de Investigaciones Científicas), Valencia, Spain
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Yang LX, Razzaghi H, Hokanson JE, Kamboh MI. Identification and characterization of a novel 5 bp deletion in a putative insulin response element in the lipoprotein lipase gene. Biochim Biophys Acta Mol Cell Biol Lipids 2009; 1791:1057-65. [PMID: 19563912 DOI: 10.1016/j.bbalip.2009.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Revised: 06/18/2009] [Accepted: 06/22/2009] [Indexed: 11/17/2022]
Abstract
Our aim was to identify an insulin response element (IRE) in the lipoprotein lipase (LPL) gene. We identified a 19 bp sequence as a putative IRE in LPL non-coding exon 10 using bioinformatics. Upon sequencing the IRE region, a novel 5 bp deletion was identified in Hispanics (N=406) with a carrier frequency of 4.2% but not in non-Hispanic whites (N=604) or Africans. Electrophoretic mobility shift assay revealed binding sites for regulatory factor(s) in muscle cell nuclear extracts with putative IRE sequence. Antibody supershift assay using human aorta smooth muscle cell nuclear extract revealed that Elk-1 specifically binds to putative IRE. TaqMan real-time RT-PCR of the 5 bp deletion, the mutant and wild type cDNA expressed in COS-1 and human muscle cells revealed that the 5 bp deletion was associated with modest reduction in LPL expression. There was also a slight reduction in LPL translation in the deletion mutant. Our data suggest the presence of an IRE in the 3'UTR of the LPL gene.
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Affiliation(s)
- Li-Xia Yang
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA
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Dahlman I, Nilsson M, Gu HF, Lecoeur C, Efendic S, Ostenson CG, Brismar K, Gustafsson JA, Froguel P, Vaxillaire M, Dahlman-Wright K, Steffensen KR. Functional and genetic analysis in type 2 diabetes of liver X receptor alleles--a cohort study. BMC MEDICAL GENETICS 2009; 10:27. [PMID: 19292929 PMCID: PMC2664799 DOI: 10.1186/1471-2350-10-27] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Accepted: 03/17/2009] [Indexed: 12/20/2022]
Abstract
BACKGROUND Liver X receptor alpha (LXRA) and beta (LXRB) regulate glucose and lipid homeostasis in model systems but their importance in human physiology is poorly understood. This project aimed to determine whether common genetic variations in LXRA and LXRB associate with type 2 diabetes (T2D) and quantitative measures of glucose homeostasis, and, if so, reveal the underlying mechanisms. METHODS Eight common single nucleotide polymorphisms in LXRA and LXRB were analyzed for association with T2D in one French cohort (N = 988 cases and 941 controls), and for association with quantitative measures reflecting glucose homeostasis in two non-diabetic population-based samples comprising N = 697 and N = 1344 adults. Investigated quantitative phenotypes included fasting plasma glucose, serum insulin, and HOMAIR as measure of overall insulin resistance. An oral glucose tolerance test was performed in N = 1344 of adults. The two alleles of the proximal LXRB promoter, differing only at the SNP rs17373080, were cloned into reporter vectors and transiently transfected, whereupon allele-specific luciferase activity was measured. rs17373080 overlapped, according to in silico analysis, with a binding site for Nuclear factor 1 (NF1). Promoter alleles were tested for interaction with NF1 using direct DNA binding and transactivation assays. RESULTS Genotypes at two LXRB promoter SNPs, rs35463555 and rs17373080, associated nominally with T2D (P values 0.047 and 0.026). No LXRA or LXRB SNP associated with quantitative measures reflecting glucose homeostasis. The rs17373080 C allele displayed higher basal transcription activity (P value < 0.05). The DNA-mobility shift assay indicated that oligonucleotides corresponding to either rs17373080 allele bound NF1 transcription factors in whole cell extracts to the same extent. Different NF1 family members showed different capacity to transactivate the LXRB gene promoter, but there was no difference between promoter alleles in NF1 induced transactivation activity. CONCLUSION Variations in the LXRB gene promoter may be part of the aetiology of T2D. However, the association between LXRB rs35463555 and rs17373080, and T2D are preliminary and needs to be investigated in additional larger cohorts. Common genetic variation in LXRA is unlikely to affect the risk of developing T2D or quantitative phenotypes related to glucose homeostasis.
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Affiliation(s)
- Ingrid Dahlman
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.
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