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Chen M, Lv J, Guo N, Ji T, Fang Y, Wang Z, He X. Crtc1 deficiency protects against sepsis-associated acute lung injury through activating akt signaling pathway. J Inflamm (Lond) 2024; 21:12. [PMID: 38644501 PMCID: PMC11034098 DOI: 10.1186/s12950-024-00385-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/08/2024] [Indexed: 04/23/2024] Open
Abstract
BACKGROUND Interplay between systemic inflammation and programmed cell death contributes to the pathogenesis of acute lung injury (ALI). cAMP-regulated transcriptional coactivator 1 (CRTC1) has been involved in the normal function of the pulmonary system, but its role in ALI remains unclear. METHODS AND RESULTS We generated a Crtc1 knockout (KO; Crtc1-/-) mouse line. Sepsis-induced ALI was established by cecal ligation and puncture (CLP) for 24 h. The data showed that Ctrc1 KO substantially ameliorated CLP-induced ALI phenotypes, including improved lung structure destruction, reduced pulmonary vascular permeability, diminished levels of proinflammatory cytokines and chemokines, compared with the wildtype mice. Consistently, in lipopolysaccharide (LPS)-treated RAW264.7 cells, Crtc1 knockdown significantly inhibited the expression of inflammatory effectors, including TNF-α, IL-1β, IL-6 and CXCL1, whereas their expressions were significantly enhanced by Crtc1 overexpression. Moreover, both Crtc1 KO in mice and its knockdown in RAW264.7 cells dramatically reduced TUNEL-positive cells and the expression of pro-apoptotic proteins. In contrast, Crtc1 overexpression led to an increase in the pro-apoptotic proteins and LPS-induced TUNEL-positive cells. Mechanically, we found that the phosphorylation of Akt was significantly enhanced by Crtc1 knockout or knockdown, but suppressed by Crtc1 overexpression. Administration of Triciribine, an Akt inhibitor, substantially blocked the protection of Crtc1 knockdown on LPS-induced inflammation and cell death in RAW264.7 cells. CONCLUSIONS Our study demonstrates that CRTC1 contribute to the pathological processes of inflammation and apoptosis in sepsis-induced ALI, and provides mechanistic insights into the molecular function of CRTC1 in the lung. Targeting CRTC1 would be a promising strategy to treat sepsis-induced ALI in clinic.
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Affiliation(s)
- Meng Chen
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, 430071, Wuhan, Hubei, China
- Department of Anesthesiology, Maternal and Child Health Hospital of Hubei Province, 745 Wuluo Road, 430070, Wuhan, Hubei, China
| | - Jian Lv
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, 518057, Shenzhen, China
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 100037, Beijing, China
| | - Ningning Guo
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, 518057, Shenzhen, China
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 100037, Beijing, China
| | - Tuo Ji
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, 430071, Wuhan, Hubei, China
- Department of Anesthesiology, School and Hospital of Stomatology, Wuhan University, 430079, Wuhan, China
| | - Yu Fang
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, 518057, Shenzhen, China
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 100037, Beijing, China
| | - Zhihua Wang
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, 518057, Shenzhen, China.
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 100037, Beijing, China.
| | - Xianghu He
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, 430071, Wuhan, Hubei, China.
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Zhao X, Khan R, Hongfang G, Abbas Raza SH, Ayari-Akkari A, Othman G, Alshammari AM, Aloufi BH, Alabbosh KF, Alshammari WB, Linsen Z. Genetic variants of TORC1 gene promoter and their association with carcass quality and body measurement traits in Qinchuan beef cattle. Anim Biotechnol 2023; 34:2537-2545. [PMID: 35916659 DOI: 10.1080/10495398.2022.2105226] [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: 11/01/2022]
Abstract
In the present study, sequencing of TORC1 prompter region explored three SNPs at loci g.80G>T, g.93A>T, and g.1253G>A. The SNP1 produced GG, GT and TT, SNP2 AA, AT and TT, and SNP3 produced GG, GA and AA genotypes. Allelic and genotypic frequencies analysis exhibited that SNP1 is within Hardy-Weinberg equilibrium (HWE). All three SNPs were found highly polymorphic as PIC value (0.25 < PIC < 0.50). At loci g.80G>T the cattle with genotype GG showed significantly (P <0.01) larger body length (BL), Wither height (WH), Hip height (HH), Rump length (RL), Hip width (HW), Chest depth (CD), and Chest circumference (CC). The genotype AA at g.93A>T showed significantly (P< 0.01 and 0.05) Larger body length (BL), Wither height (WH), Hip height, Rump length (RL), Hip width (HW), Chest depth (CD), and Chest circumference (CC). Interestingly, the carcass quality parameters such as Ultrasound loin area (ULA) and Intramuscular fat percentage (IF%) was highest in genotype GG at loci g.1253G>A. These findings conclude that genotype GG at loci g.80 G>T and AA at loci g.93A>T could be used as genetic markers for body measurement and genotype GG at loci g.1253G>A for carcass quality traits of TORC1 gene in Qinchuan beef cattle.
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Affiliation(s)
- Xianlin Zhao
- College of Pharmacy, Heze University, Heze, China
| | - Rajwali Khan
- Department of Livestock Management, Breeding and Genetic, The University of Agriculture Peshawar, Peshawar, Pakistan
| | - Guo Hongfang
- Medical College, Xuchang University, Xuchang, China
| | | | - Amel Ayari-Akkari
- Biology Department, College of Science, King Khalid University, Abha, Saudi Arabia
- Laboratory of Diversity, Management and Conservation of Biological Systems, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Gehan Othman
- Biology Department, College of Science, King Khalid University, Abha, Saudi Arabia
| | | | - Bandar Hamad Aloufi
- Department of Biology, College of Science, University of Hail, Ha'il, Saudi Arabia
| | | | - Wasimah B Alshammari
- Department of Biology, College of Science, University of Hail, Ha'il, Saudi Arabia
| | - Zan Linsen
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Zhu Z, Chen X, Zhang S, Yu R, Qi C, Cheng L, Zhang X. Leveraging molecular quantitative trait loci to comprehend complex diseases/traits from the omics perspective. Hum Genet 2023; 142:1543-1560. [PMID: 37755483 DOI: 10.1007/s00439-023-02602-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023]
Abstract
Comprehending the molecular basis of quantitative genetic variation is a principal goal for complex diseases or traits. Molecular quantitative trait loci (molQTLs) have made it possible to investigate the effects of genetic variants hiding behind large-scale omics data. A deeper understanding of molQTL is urgently required in light of the multi-dimensionalization of omics data to more fully elucidate the pertinent biological mechanisms. Herein, we reviewed molQTLs with the corresponding resource from the omics perspective and further discussed the integrative strategy of GWAS-molQTL to infer their causal effects. Subsequently, we described the opportunities and challenges encountered by molQTL. The case studies showed that molQTL is essential for complex diseases and traits, whether single- or multi-omics QTLs. Overall, we highlighted the functional significance of genetic variants to employ the discovery of molQTL in complex diseases and traits.
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Affiliation(s)
- Zijun Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xinyu Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Sainan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Rui Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Changlu Qi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Liang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
- NHC Key Laboratory of Molecular Probe and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150028, Heilongjiang, China.
| | - Xue Zhang
- NHC Key Laboratory of Molecular Probe and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150028, Heilongjiang, China
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
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4
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Rossetti C, Cherix A, Guiraud LF, Cardinaux JR. New Insights Into the Pivotal Role of CREB-Regulated Transcription Coactivator 1 in Depression and Comorbid Obesity. Front Mol Neurosci 2022; 15:810641. [PMID: 35242012 PMCID: PMC8886117 DOI: 10.3389/fnmol.2022.810641] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Depression and obesity are major public health concerns, and there is mounting evidence that they share etiopathophysiological mechanisms. The neurobiological pathways involved in both mood and energy balance regulation are complex, multifactorial and still incompletely understood. As a coactivator of the pleiotropic transcription factor cAMP response element-binding protein (CREB), CREB-regulated transcription coactivator 1 (CRTC1) has recently emerged as a novel regulator of neuronal plasticity and brain functions, while CRTC1 dysfunction has been associated with neurodegenerative and psychiatric diseases. This review focuses on recent evidence emphasizing the critical role of CRTC1 in the neurobiology of depression and comorbid obesity. We discuss the role of CRTC1 downregulation in mediating chronic stress-induced depressive-like behaviors, and antidepressant response in the light of the previously characterized Crtc1 knockout mouse model of depression. The putative role of CRTC1 in the alteration of brain energy homeostasis observed in depression is also discussed. Finally, we highlight rodent and human studies supporting the critical involvement of CRTC1 in depression-associated obesity.
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Affiliation(s)
- Clara Rossetti
- Center for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital, University of Lausanne, Prilly, Switzerland
- Service of Child and Adolescent Psychiatry, Department of Psychiatry, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Antoine Cherix
- Center for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital, University of Lausanne, Prilly, Switzerland
- Laboratory for Functional and Metabolic Imaging (LIFMET), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Laetitia F. Guiraud
- Center for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital, University of Lausanne, Prilly, Switzerland
- Service of Child and Adolescent Psychiatry, Department of Psychiatry, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Jean-René Cardinaux
- Center for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital, University of Lausanne, Prilly, Switzerland
- Service of Child and Adolescent Psychiatry, Department of Psychiatry, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
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5
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Clark KC, Kwitek AE. Multi-Omic Approaches to Identify Genetic Factors in Metabolic Syndrome. Compr Physiol 2021; 12:3045-3084. [PMID: 34964118 PMCID: PMC9373910 DOI: 10.1002/cphy.c210010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Metabolic syndrome (MetS) is a highly heritable disease and a major public health burden worldwide. MetS diagnosis criteria are met by the simultaneous presence of any three of the following: high triglycerides, low HDL/high LDL cholesterol, insulin resistance, hypertension, and central obesity. These diseases act synergistically in people suffering from MetS and dramatically increase risk of morbidity and mortality due to stroke and cardiovascular disease, as well as certain cancers. Each of these component features is itself a complex disease, as is MetS. As a genetically complex disease, genetic risk factors for MetS are numerous, but not very powerful individually, often requiring specific environmental stressors for the disease to manifest. When taken together, all sequence variants that contribute to MetS disease risk explain only a fraction of the heritable variance, suggesting additional, novel loci have yet to be discovered. In this article, we will give a brief overview on the genetic concepts needed to interpret genome-wide association studies (GWAS) and quantitative trait locus (QTL) data, summarize the state of the field of MetS physiological genomics, and to introduce tools and resources that can be used by the physiologist to integrate genomics into their own research on MetS and any of its component features. There is a wealth of phenotypic and molecular data in animal models and humans that can be leveraged as outlined in this article. Integrating these multi-omic QTL data for complex diseases such as MetS provides a means to unravel the pathways and mechanisms leading to complex disease and promise for novel treatments. © 2022 American Physiological Society. Compr Physiol 12:1-40, 2022.
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Affiliation(s)
- Karen C Clark
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Anne E Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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6
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Abstract
Obesity is a chronic and complex psychosomatic disease that is becoming increasingly prevalent worldwide. This study aimed to analyze whole methylation profiles to uncover the epigenetic mechanisms associated with obesity. DNA methylation profiles in blood samples from patients with obesity and normal controls were studied using the Illumina 850 K methylation microarray. The diagnostic value of the differentially methylated genes was determined using receiver operating characteristic (ROC) analysis. The expression of selected candidate genes was verified using reverse transcription quantitative polymerase chain reaction (RT-qPCR) and pyrosequencing. A total of 9,371 significantly differentially methylated sites (7,974 hypermethylated sites and 1,397 hypomethylated sites) were identified in 4,571 genes. A difference in the distribution of differentially methylated sites (hypermethylated and hypomethylated) in both gene structures and CpG islands was observed. A total of 114 key differentially methylated sites were identified in the CpG islands. ROC results indicated that Inhibin Subunit Beta B (INHBB), Homeobox A9 (HOXA9), Troponin T3 (TNNT3), Cyclic adenosine monophosphate (cAMP)-responsive element binding protein (CREB)-regulated transcription coactivator 1 (CRTC1) and Zinc finger and BTB domain-containing 7 B (ZBTB7B) could discriminate patients with obesity from normal controls. RT-qPCR results of CRTC1 and ZBTB7B were consistent with our methylation profile results. The pyrosequencing results showed that the methylation levels of CRTC1 CpG sites (CpG1 and CpG2-cg11660071) and INHBB CpG sites (CpG2) were significantly changed in patients with obesity compared with normal controls, which was consistent with our DNA methylation profile results. Our study provides new insights into the pathological mechanism of obesity.
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Affiliation(s)
- Chunhu Wang
- 17th Department of Plastic Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Meng Wang
- 17th Department of Plastic Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiguang Ma
- 17th Department of Plastic Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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7
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Matsumura S, Ishikawa F, Sasaki T, Terkelsen MK, Ravnskjaer K, Jinno T, Tanaka J, Goto T, Inoue K. Loss of CREB Coactivator CRTC1 in SF1 Cells Leads to Hyperphagia and Obesity by High-fat Diet But Not Normal Chow Diet. Endocrinology 2021; 162:6224280. [PMID: 33846709 PMCID: PMC8682520 DOI: 10.1210/endocr/bqab076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 12/19/2022]
Abstract
Cyclic adenosine monophosphate responsive element-binding protein-1-regulated transcription coactivator-1 (CRTC1) is a cytoplasmic coactivator that translocates to the nucleus in response to cyclic adenosine monophosphate. Whole-body knockdown of Crtc1 causes obesity, resulting in increased food intake and reduced energy expenditure. CRTC1 is highly expressed in the brain; therefore, it might play an important role in energy metabolism via the neuronal pathway. However, the precise mechanism by which CRTC1 regulates energy metabolism remains unknown. Here, we showed that mice lacking CRTC1, specifically in steroidogenic factor-1 expressing cells (SF1 cells), were sensitive to high-fat diet (HFD)-induced obesity, exhibiting hyperphagia and increased body weight gain. The loss of CRTC1 in SF1 cells impaired glucose metabolism. Unlike whole-body CRTC1 knockout mice, SF1 cell-specific CRTC1 deletion did not affect body weight gain or food intake in normal chow feeding. Thus, CRTC1 in SF1 cells is required for normal appetite regulation in HFD-fed mice. CRTC1 is primarily expressed in the brain. Within the hypothalamus, which plays an important role for appetite regulation, SF1 cells are only found in ventromedial hypothalamus. RNA sequencing analysis of microdissected ventromedial hypothalamus samples revealed that the loss of CRTC1 significantly changed the expression levels of certain genes. Our results revealed the important protective role of CRTC1 in SF1 cells against dietary metabolic imbalance.
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Affiliation(s)
- Shigenobu Matsumura
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Kyoto, 611-0011, Japan
- Graduate School of Comprehensive Rehabilitation, Osaka Prefecture University, Osaka, 583-8555, Japan
- Correspondence: Shigenobu Matsumura, Graduate School of Comprehensive Rehabilitation, Osaka Prefecture University, Habikino, Osaka, 583-8555, Japan. E-mail:
| | - Fuka Ishikawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Kyoto, 611-0011, Japan
| | - Tsutomu Sasaki
- Department of Neurology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Mike Krogh Terkelsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Kim Ravnskjaer
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Tomoki Jinno
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Kyoto, 611-0011, Japan
| | - Jin Tanaka
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Kyoto, 611-0011, Japan
| | - Tsuyoshi Goto
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Kyoto, 611-0011, Japan
| | - Kazuo Inoue
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Kyoto, 611-0011, Japan
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8
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Hu Y, Lv J, Fang Y, Luo Q, He Y, Li L, Fan M, Wang Z. Crtc1 Deficiency Causes Obesity Potentially via Regulating PPARγ Pathway in White Adipose. Front Cell Dev Biol 2021; 9:602529. [PMID: 33912553 PMCID: PMC8075410 DOI: 10.3389/fcell.2021.602529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/23/2021] [Indexed: 11/13/2022] Open
Abstract
Obesity is characterized by excessive fat accumulation and associated with glucose and lipid metabolism disorders. Crtc1, a transcription cofactor regulating CREB activity, has been involved in the pathogenesis of metabolic syndrome; however, the underlying mechanism remains under debate. Here we generated a Crtc1-/- mouse line using the CRISPR/Cas9 system. Under normal feeding conditions, Crtc1-/- mice exhibited an obese phenotype resultant from the abnormal expansion of the white adipocytes. The development of obesity in Crtc1-/- mice is independent of alterations in food intake or energy expenditure. Moreover, Crtc1-/- mice were more prone to insulin resistance and dyslipidemia, as evidenced by higher levels of plasma glucose, insulin and FABP4 than wildtype mice. Transcriptome analysis in liver and epididymal white adipose tissue (eWAT) showed that the fat accumulation caused by Crtc1 deletion was mainly related to lipid metabolism in adipose tissue, but not in liver. GSEA and KEGG analysis identified PPAR pathway to be of the highest impact on lipid metabolism in eWAT. This regulation was independent of a direct interaction between CRTC1 and PPARγ. Our findings demonstrate a crucial role of Crtc1 in regulating lipid metabolism in adipose during development, and provide novel insights into obesity prevention and therapeutics.
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Affiliation(s)
- Yimeng Hu
- Department of Endocrinology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jian Lv
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yu Fang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qiang Luo
- Department of Endocrinology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yuan He
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lili Li
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Mingxia Fan
- Animal Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhihua Wang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China.,Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, China
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9
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Naji MM, Utsunomiya YT, Sölkner J, Rosen BD, Mészáros G. Investigation of ancestral alleles in the Bovinae subfamily. BMC Genomics 2021; 22:108. [PMID: 33557747 PMCID: PMC7871596 DOI: 10.1186/s12864-021-07412-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/27/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND In evolutionary theory, divergence and speciation can arise from long periods of reproductive isolation, genetic mutation, selection and environmental adaptation. After divergence, alleles can either persist in their initial state (ancestral allele - AA), co-exist or be replaced by a mutated state (derived alleles -DA). In this study, we aligned whole genome sequences of individuals from the Bovinae subfamily to the cattle reference genome (ARS.UCD-1.2) for defining ancestral alleles necessary for selection signatures study. RESULTS Accommodating independent divergent of each lineage from the initial ancestral state, AA were defined based on fixed alleles on at least two groups of yak, bison and gayal-gaur-banteng resulting in ~ 32.4 million variants. Using non-overlapping scanning windows of 10 Kb, we counted the AA observed within taurine and zebu cattle. We focused on the extreme points, regions with top 0. 1% (high count) and regions without any occurrence of AA (null count). High count regions preserved gene functions from ancestral states that are still beneficial in the current condition, while null counts regions were linked to mutated ones. For both cattle, high count regions were associated with basal lipid metabolism, essential for survival of various environmental pressures. Mutated regions were associated to productive traits in taurine, i.e. higher metabolism, cell development and behaviors and in immune response domain for zebu. CONCLUSIONS Our findings suggest that retaining and losing AA in some regions are varied and made it species-specific with possibility of overlapping as it depends on the selective pressure they had to experience.
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Affiliation(s)
- Maulana M. Naji
- University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Yuri T. Utsunomiya
- São Paulo State University (Unesp), School of Veterinary Medicine, Department of Production and Animal Health, Araçatuba, São Paulo Brazil
- International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, São Paulo Brazil
- AgroPartners Consulting. R. Floriano Peixoto, 120-Sala 43A-Centro, Araçatuba, SP 16010-220 Brazil
- Personal-PEC. R. Sebastiao Lima, 1336-Centro, Campo Grande, MS 79004-600 Brazil
| | - Johann Sölkner
- University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | | | - Gábor Mészáros
- University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
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10
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Rønningen T, Dahl MB, Valderhaug TG, Cayir A, Keller M, Tönjes A, Blüher M, Böttcher Y. m6A Regulators in Human Adipose Tissue - Depot-Specificity and Correlation With Obesity. Front Endocrinol (Lausanne) 2021; 12:778875. [PMID: 34950106 PMCID: PMC8689137 DOI: 10.3389/fendo.2021.778875] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/15/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) is one of the most abundant post-transcriptional modifications on mRNA influencing mRNA metabolism. There is emerging evidence for its implication in metabolic disease. No comprehensive analyses on gene expression of m6A regulators in human adipose tissue, especially in paired adipose tissue depots, and its correlation with clinical variables were reported so far. We hypothesized that inter-depot specific gene expression of m6A regulators may differentially correlate with clinical variables related to obesity and fat distribution. METHODS We extracted intra-individually paired gene expression data (omental visceral adipose tissue (OVAT) N=48; subcutaneous adipose tissue (SAT) N=56) of m6A regulators from an existing microarray dataset. We also measured gene expression in another sample set of paired OVAT and SAT (N=46) using RT-qPCR. Finally, we extracted existing gene expression data from peripheral mononuclear blood cells (PBMCs) and single nucleotide polymorphisms (SNPs) in METTL3 and YTHDF3 from genome wide data from the Sorbs population (N=1049). The data were analysed for differential gene expression between OVAT and SAT; and for association with obesity and clinical variables. We further tested for association of SNP markers with gene expression and clinical traits. RESULTS In adipose tissue we observed that several m6A regulators (WTAP, VIRMA, YTHDC1 and ALKBH5) correlate with obesity and clinical variables. Moreover, we found adipose tissue depot specific gene expression for METTL3, WTAP, VIRMA, FTO and YTHDC1. In PBMCs, we identified ALKBH5 and YTHDF3 correlated with obesity. Genetic markers in METTL3 associate with BMI whilst SNPs in YTHDF3 are associated with its gene expression. CONCLUSIONS Our data show that expression of m6A regulators correlates with obesity, is adipose tissue depot-specific and related to clinical traits. Genetic variation in m6A regulators adds an additional layer of variability to the functional consequences.
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Affiliation(s)
- Torunn Rønningen
- Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus Universitetssykehus, Lørenskog, Norway
| | - Mai Britt Dahl
- Department of Clinical Molecular Biology (EpiGen), Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Akin Cayir
- Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus Universitetssykehus, Lørenskog, Norway
- Vocational Health College, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | - Maria Keller
- Department of Medicine, University of Leipzig, 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, Germany
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Matthias Blüher
- Department of Medicine, University of Leipzig, 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, Germany
| | - Yvonne Böttcher
- Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus Universitetssykehus, Lørenskog, Norway
- Department of Clinical Molecular Biology (EpiGen), Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital, Leipzig, Germany
- *Correspondence: Yvonne Böttcher,
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Khan R, Raza SHA, Schreurs N, Xiaoyu W, Hongbao W, Ullah I, Rahman A, Suhail SM, Khan S, Linsen Z. Bioinformatics analysis and transcriptional regulation of TORC1 gene through transcription factors NRF1 and Smad3 in bovine preadipocytes. Genomics 2020; 112:1575-1587. [DOI: 10.1016/j.ygeno.2019.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/23/2019] [Accepted: 09/11/2019] [Indexed: 12/25/2022]
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Rohde K, Rønningen T, la Cour Poulsen L, Keller M, Blüher M, Böttcher Y. Role of the DNA repair genes H2AX and HMGB1 in human fat distribution and lipid profiles. BMJ Open Diabetes Res Care 2020; 8:8/1/e000831. [PMID: 32114485 PMCID: PMC7050360 DOI: 10.1136/bmjdrc-2019-000831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/25/2019] [Accepted: 01/15/2020] [Indexed: 11/05/2022] Open
Abstract
INTRODUCTION Regional fat distribution strongly relates to metabolic comorbidities. We identified the DNA repair genes H2AX and HMGB1 to be differentially expressed between human subcutaneous (SAT) and omental visceral adipose tissue (OVAT) depots. As increased DNA damage is linked to metabolic disease, we here sought to analyze whether depot-specific H2AX and HMGB1 expression is related to anthropometric and metabolic profiles of obesity. We further tested for different H2AX mRNA regulatory mechanisms by analyzing promoter DNA methylation and genotyped rs7350 in the H2AX locus. RESEARCH DESIGN AND METHODS Gene expression (OVAT n=48; SAT n=55) and DNA promoter methylation data (OVAT and SAT n=77) were extracted from an existing dataset as described elsewhere. Genotype data for the 3'untranslated region (3'UTR) H2AX variant rs7350 were generated by using the TaqMan genotyping system in 243 subjects of the same cohort. Statistical analyses were done using SPSS statistics software 24 and GraphPad Prism 6. RESULTS We identified H2AX being higher (p=0.002) and HMGB1 being less expressed (p=0.0001) in OVAT compared with SAT. Further, we observed positive interdepot correlations of OVAT and SAT for both HMGB1 (p=1×10-6) and H2AX mRNA levels (p=0.024). Depot-specific associations were observed for both genes' methylation levels with either high density lipoprotein cholesterol, low density lipoprotein cholesterol, triglycerides and/or with OVAT/SAT-ratio (all p<0.05). A significantly lower level of total cholesterol in minor A-Allele carriers of rs7350 compared with AG and GG carriers (p=0.001) was observed. Additionally, subjects carrying the A-allele showed lower SAT HMGB1 expression level (p=0.030). CONCLUSION Our results suggest a fat depot-specific regulation of H2AX and HMGB1 potentially mediated by both DNA methylation and genetic variation. Rs7350, DNA methylation and/or mRNA levels of H2AX and HMGB1 are related to lipid parameters. Further studies are warranted to evaluate the functional role of the DNA repair genes H2AX and HMGB1 in obesity and fat distribution.
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Affiliation(s)
- Kerstin Rohde
- Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
| | - Torunn Rønningen
- Department of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
| | - Lars la Cour Poulsen
- Department of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
| | - Maria Keller
- Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
| | - Matthias Blüher
- Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Medical Department, University of Leipzig, Leipzig, Germany
| | - Yvonne Böttcher
- Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
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Booij L. Genetic and epigenetic regulation of CRTC1 in human eating behaviour and fat distribution: Methodological and clinical insights and considerations. EBioMedicine 2019; 45:15-16. [PMID: 31227440 PMCID: PMC6642252 DOI: 10.1016/j.ebiom.2019.06.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 12/12/2022] Open
Affiliation(s)
- Linda Booij
- Department of Psychology, Concordia University; CHU Sainte-Justine Research Centre, Montreal, Canada.
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