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Li Z, Melograna F, Hoskens H, Duroux D, Marazita ML, Walsh S, Weinberg SM, Shriver MD, Müller-Myhsok B, Claes P, Van Steen K. netMUG: a novel network-guided multi-view clustering workflow for dissecting genetic and facial heterogeneity. Front Genet 2023; 14:1286800. [PMID: 38125750 PMCID: PMC10731261 DOI: 10.3389/fgene.2023.1286800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction: Multi-view data offer advantages over single-view data for characterizing individuals, which is crucial in precision medicine toward personalized prevention, diagnosis, or treatment follow-up. Methods: Here, we develop a network-guided multi-view clustering framework named netMUG to identify actionable subgroups of individuals. This pipeline first adopts sparse multiple canonical correlation analysis to select multi-view features possibly informed by extraneous data, which are then used to construct individual-specific networks (ISNs). Finally, the individual subtypes are automatically derived by hierarchical clustering on these network representations. Results: We applied netMUG to a dataset containing genomic data and facial images to obtain BMI-informed multi-view strata and showed how it could be used for a refined obesity characterization. Benchmark analysis of netMUG on synthetic data with known strata of individuals indicated its superior performance compared with both baseline and benchmark methods for multi-view clustering. The clustering derived from netMUG achieved an adjusted Rand index of 1 with respect to the synthesized true labels. In addition, the real-data analysis revealed subgroups strongly linked to BMI and genetic and facial determinants of these subgroups. Discussion: netMUG provides a powerful strategy, exploiting individual-specific networks to identify meaningful and actionable strata. Moreover, the implementation is easy to generalize to accommodate heterogeneous data sources or highlight data structures.
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Affiliation(s)
- Zuqi Li
- BIO3 - Laboratory for Systems Medicine, Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Federico Melograna
- BIO3 - Laboratory for Systems Medicine, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Hanne Hoskens
- BIO3 - Laboratory for Systems Medicine, Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Diane Duroux
- BIO3 - Laboratory for Systems Genetics, GIGA-R Medical Genomics, University of Liège, Liège, Belgium
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Susan Walsh
- Department of Biology, Indiana University Indianapolis, Indianapolis, IN, United States
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Mark D. Shriver
- Department of Anthropology, Pennsylvania State University, State College, PA, United States
| | | | - Peter Claes
- BIO3 - Laboratory for Systems Medicine, Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, KU Leuven, Leuven, Belgium
- Murdoch Children’s Research Institute, Melbourne, VIC, Australia
| | - Kristel Van Steen
- BIO3 - Laboratory for Systems Medicine, Department of Human Genetics, KU Leuven, Leuven, Belgium
- BIO3 - Laboratory for Systems Genetics, GIGA-R Medical Genomics, University of Liège, Liège, Belgium
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Li Z, Melograna F, Hoskens H, Duroux D, Marazita ML, Walsh S, Weinberg SM, Shriver MD, Müller-Myhsok B, Claes P, Van Steen K. netMUG: a novel network-guided multi-view clustering workflow for dissecting genetic and facial heterogeneity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.04.539350. [PMID: 37205363 PMCID: PMC10187283 DOI: 10.1101/2023.05.04.539350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Multi-view data offer advantages over single-view data for characterizing individuals, which is crucial in precision medicine toward personalized prevention, diagnosis, or treatment follow-up. Here, we develop a network-guided multi-view clustering framework named netMUG to identify actionable subgroups of individuals. This pipeline first adopts sparse multiple canonical correlation analysis to select multi-view features possibly informed by extraneous data, which are then used to construct individual-specific networks (ISNs). Finally, the individual subtypes are automatically derived by hierarchical clustering on these network representations. We applied netMUG to a dataset containing genomic data and facial images to obtain BMI-informed multi-view strata and showed how it could be used for a refined obesity characterization. Benchmark analysis of netMUG on synthetic data with known strata of individuals indicated its superior performance compared with both baseline and benchmark methods for multi-view clustering. In addition, the real-data analysis revealed subgroups strongly linked to BMI and genetic and facial determinants of these classes. NetMUG provides a powerful strategy, exploiting individual-specific networks to identify meaningful and actionable strata. Moreover, the implementation is easy to generalize to accommodate heterogeneous data sources or highlight data structures.
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Affiliation(s)
- Zuqi Li
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | | | - Hanne Hoskens
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Diane Duroux
- GIGA-R Medical Genomics, University of Liège, Liège, Belgium
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Susan Walsh
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Mark D. Shriver
- Department of Anthropology, Pennsylvania State University, State College, PA 16801, USA
| | | | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Kristel Van Steen
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- GIGA-R Medical Genomics, University of Liège, Liège, Belgium
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Kim D, Justice AE, Chittoor G, Blanco E, Burrows R, Graff M, Howard AG, Wang Y, Rohde R, Buchanan VL, Voruganti VS, Almeida M, Peralta J, Lehman DM, Curran JE, Comuzzie AG, Duggirala R, Blangero J, Albala C, Santos JL, Angel B, Lozoff B, Gahagan S, North KE. Genetic determinants of metabolic biomarkers and their associations with cardiometabolic traits in Hispanic/Latino adolescents. Pediatr Res 2022; 92:563-571. [PMID: 34645953 PMCID: PMC9005573 DOI: 10.1038/s41390-021-01729-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 06/08/2021] [Accepted: 08/17/2021] [Indexed: 01/05/2023]
Abstract
BACKGROUND Metabolic regulation plays a significant role in energy homeostasis, and adolescence is a crucial life stage for the development of cardiometabolic disease (CMD). This study aims to investigate the genetic determinants of metabolic biomarkers-adiponectin, leptin, ghrelin, and orexin-and their associations with CMD risk factors. METHODS We characterized the genetic determinants of the biomarkers among Hispanic/Latino adolescents of the Santiago Longitudinal Study (SLS) and identified the cumulative effects of genetic variants on adiponectin and leptin using biomarker polygenic risk scores (PRS). We further investigated the direct and indirect effect of the biomarker PRS on downstream body fat percent (BF%) and glycemic traits using structural equation modeling. RESULTS We identified putatively novel genetic variants associated with the metabolic biomarkers. A substantial amount of biomarker variance was explained by SLS-specific PRS, and the prediction was improved by including the putatively novel loci. Fasting blood insulin and insulin resistance were associated with PRS for adiponectin, leptin, and ghrelin, and BF% was associated with PRS for adiponectin and leptin. We found evidence of substantial mediation of these associations by the biomarker levels. CONCLUSIONS The genetic underpinnings of metabolic biomarkers can affect the early development of CMD, partly mediated by the biomarkers. IMPACT This study characterized the genetic underpinnings of four metabolic hormones and investigated their potential influence on adiposity and insulin biology among Hispanic/Latino adolescents. Fasting blood insulin and insulin resistance were associated with polygenic risk score (PRS) for adiponectin, leptin, and ghrelin, with evidence of some degree of mediation by the biomarker levels. Body fat percent (BF%) was also associated with PRS for adiponectin and leptin. This provides important insight on biological mechanisms underlying early metabolic dysfunction and reveals candidates for prevention efforts. Our findings also highlight the importance of ancestrally diverse populations to facilitate valid studies of the genetic architecture of metabolic biomarker levels.
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Affiliation(s)
- Daeeun Kim
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Anne E. Justice
- Department of Population Health Sciences, Geisinger, Danville, PA
| | - Geetha Chittoor
- Department of Population Health Sciences, Geisinger, Danville, PA
| | - Estela Blanco
- Division of Academic General Pediatrics, Child Development and Community Health at the Center for Community Health, University of California at San Diego, San Diego, CA,Department of Public Health, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Raquel Burrows
- Department of Public Health Nutrition, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Annie Green Howard
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Yujie Wang
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Rebecca Rohde
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Victoria L. Buchanan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - V. Saroja Voruganti
- Department of Nutrition and Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis NC
| | - Marcio Almeida
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX
| | - Juan Peralta
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX
| | - Donna M. Lehman
- Departments of Medicine and Epidemiology and Biostatistics, University of Texas Health San Antonio, San Antonio, TX
| | - Joanne E. Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX
| | | | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX
| | - Cecilia Albala
- Department of Public Health Nutrition, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - José L. Santos
- Department of Nutrition, Diabetes and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Bárbara Angel
- Department of Public Health Nutrition, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - Betsy Lozoff
- Department of Pediatrics, University of Michigan, Ann Arbor, MI
| | - Sheila Gahagan
- Division of Academic General Pediatrics, Child Development and Community Health at the Center for Community Health, University of California at San Diego, San Diego, CA
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
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Causal associations of circulating adiponectin with cardiometabolic diseases and osteoporotic fracture. Sci Rep 2022; 12:6689. [PMID: 35461346 PMCID: PMC9035157 DOI: 10.1038/s41598-022-10586-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 04/07/2022] [Indexed: 02/05/2023] Open
Abstract
Circulating adiponectin shows some relationships with the occurrence of cardiometabolic diseases and osteoporotic fracture, but little is known about their causal associations. This two-sample Mendelian randomization (MR) study aims to explore the causal roles of circulating adiponectin in cardiometabolic diseases and osteoporotic fracture. We used 15 single nucleotide polymorphisms associated with circulating adiponectin as the instrumental variables. Inverse variance weighted, weighted median and MR-Egger regression methods were applied to study the causal associations. The results found that high circulating adiponectin was causally associated with reduced risk of type 2 diabetes (beta-estimate: -0.030, 95% CI: -0.048 to -0.011, SE: 0.009, P-value = 0.002) and may be the risk factor of coronary artery disease (beta-estimate: 0.012, 95% CI: 0.001 to 0.023, SE: 0.006, P-value = 0.030). No causal associations were seen between circulating adiponectin and other outcomes including heart failure, atrial fibrillation, cerebral ischemia, intracerebral hemorrhage or osteoporotic fracture. This study found the potential causal roles of high circulating adiponectin in reduced risk of type 2 diabetes and increased risk of coronary artery disease, which may help prevent and treat these two diseases.
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Guo J, Wu J, Wei D, Wang T, Hu Y, Lin Y, Chen M, Yang L, Wen Y, Cai Y, Xu X, Li H, Wu S, Xie X. Association between greenness and dyslipidemia in patients with coronary heart disease: A proteomic approach. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 231:113199. [PMID: 35042090 DOI: 10.1016/j.ecoenv.2022.113199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/27/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Residential surrounding greenness may be protective of dyslipidemia are often theorized but remain poorly quantified. In particular, the underlying biological mechanisms of blood lipid changes with green spaces remain unclear. METHODS Our observational epidemiology study included a residentially stable sample of 1035 coronary heart disease patients, and proteomics study included 16 participants. Normalized Difference Vegetation Index (NDVI) was used to evaluate residential greenness exposures. Proteomics technology was used to identify plasma greenness-related proteome disturbance, and the pathway analysis was employed to evaluate the potential biological mechanisms of greenness decreasing dyslipidemia risk. RESULT Higher residential surrounding greenness in the 500-m area was associated with lower risks of dyslipidemia (odds ratio (OR) = 0.871, 95% confidence interval (CI): 0.763, 0.994 for per one-quartile NDVI increase). Lymphocytes mediated 18.7% of the association between greenness and dyslipidemia. Greenness related proteins (including PLXDC1, IGFBP2 and LY6D) may regulate the biological functions of lipid metabolism and transport-related proteins (including ADIPOQ and CES1) through a series of biological processes. CONCLUSION People in greener surroundings have a lower risk of dyslipidemia, which may be due to their lower inflammation, stronger lipid transporter activity, and normal cholesterol metabolism.
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Affiliation(s)
- Jianhui Guo
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Jieyu Wu
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Donghong Wei
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Tinggui Wang
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Yuduan Hu
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Yawen Lin
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Mingjun Chen
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Le Yang
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Yeyin Wen
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Yingying Cai
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Xingyan Xu
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Huanyuan Li
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
| | - Siying Wu
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
| | - Xiaoxu Xie
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
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He B, Zhao J, Zhang M, Yin L, Quan Z, Ou Y, Huang W. Causal roles of circulating adiponectin in osteoporosis and cancers. Bone 2022; 155:116266. [PMID: 34844025 DOI: 10.1016/j.bone.2021.116266] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/07/2021] [Accepted: 11/22/2021] [Indexed: 01/04/2023]
Abstract
Circulating adiponectin has some association with the risk of osteoporosis and cancers, but their causal relationships remains elusive. Mendelian randomization (MR) study was used to explore the causal roles of circulating adiponectin in osteoporosis and cancers by using genome-wide association studies (GWASs) associated with circulating adiponectin, osteoporosis and cancers. Fifteen single nucleotide polymorphisms (SNPs) were used as instrumental variables for circulating adiponectin. Genetic predisposition to high circulating adiponectin was strongly associated with low femoral neck bone mineral density (FN-BMD, beta-estimate: -0.015, 95% CI: -0.023 to -0.006, SE: 0.004, P-value = 0.001), low forearm BMD (FA-BMD, beta-estimate: -0.027, 95% CI: -0.050 to -0.004, SE: 0.012, P-value = 0.023) and increased risk of breast cancer (beta-estimate: 0.011, 95% CI: 0.001 to 0.022, SE: 0.005, P-value = 0.031). There was limited evidence of the associations between circulating adiponectin and other outcomes (i.e. lumbar spine BMD [LS-BMD], colorectal cancer, liver cancer, lung cancer, bone cancer and prostate cancer). This study provides robust evidence that high circulating adiponectin is causally associated with low FN-BMD, low FA-BMD and increased risk of breast cancer, which may provide new insight to prevent and treat osteoporosis and breast cancer.
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Affiliation(s)
- Bin He
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Jinqiu Zhao
- Department of Infectious diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Muzi Zhang
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Lifeng Yin
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Zhengxue Quan
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yunsheng Ou
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Wei Huang
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
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Zhang X, Li TY, Xiao HM, Ehrlich KC, Shen H, Deng HW, Ehrlich M. Epigenomic and Transcriptomic Prioritization of Candidate Obesity-Risk Regulatory GWAS SNPs. Int J Mol Sci 2022; 23:1271. [PMID: 35163195 PMCID: PMC8836216 DOI: 10.3390/ijms23031271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 02/06/2023] Open
Abstract
Concern about rising rates of obesity has prompted searches for obesity-related single nucleotide polymorphisms (SNPs) in genome-wide association studies (GWAS). Identifying plausible regulatory SNPs is very difficult partially because of linkage disequilibrium. We used an unusual epigenomic and transcriptomic analysis of obesity GWAS-derived SNPs in adipose versus heterologous tissues. From 50 GWAS and 121,064 expanded SNPs, we prioritized 47 potential causal regulatory SNPs (Tier-1 SNPs) for 14 gene loci. A detailed examination of seven loci revealed that four (CABLES1, PC, PEMT, and FAM13A) had Tier-1 SNPs positioned so that they could regulate use of alternative transcription start sites, resulting in different polypeptides being generated or different amounts of an intronic microRNA gene being expressed. HOXA11 and long noncoding RNA gene RP11-392O17.1 had Tier-1 SNPs in their 3' or promoter region, respectively, and strong preferences for expression in subcutaneous versus visceral adipose tissue. ZBED3-AS1 had two intragenic Tier-1 SNPs, each of which could contribute to mediating obesity risk through modulating long-distance chromatin interactions. Our approach not only revealed especially credible novel regulatory SNPs, but also helped evaluate previously highlighted obesity GWAS SNPs that were candidates for transcription regulation.
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Affiliation(s)
- Xiao Zhang
- Tulane Center for Biomedical Informatics and Genomics, Division of Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (X.Z.); (K.C.E.); (H.S.)
| | - Tian-Ying Li
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha 410013, China; (T.-Y.L.); (H.-M.X.)
| | - Hong-Mei Xiao
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha 410013, China; (T.-Y.L.); (H.-M.X.)
| | - Kenneth C. Ehrlich
- Tulane Center for Biomedical Informatics and Genomics, Division of Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (X.Z.); (K.C.E.); (H.S.)
| | - Hui Shen
- Tulane Center for Biomedical Informatics and Genomics, Division of Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (X.Z.); (K.C.E.); (H.S.)
| | - Hong-Wen Deng
- Tulane Center for Biomedical Informatics and Genomics, Division of Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (X.Z.); (K.C.E.); (H.S.)
| | - Melanie Ehrlich
- Tulane Center for Biomedical Informatics and Genomics, Division of Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (X.Z.); (K.C.E.); (H.S.)
- Tulane Cancer Center and Hayward Genetics Center, Tulane University, New Orleans, LA 70112, USA
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Xie S, Jiang X, Qin R, Song S, Lu Y, Wang L, Chen Y, Lu D. miR-1307 promotes hepatocarcinogenesis by CALR-OSTC-endoplasmic reticulum protein folding pathway. iScience 2021; 24:103271. [PMID: 34761190 PMCID: PMC8567365 DOI: 10.1016/j.isci.2021.103271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/27/2021] [Accepted: 10/12/2021] [Indexed: 12/20/2022] Open
Abstract
miR-1307 is highly expressed in liver cancer and inhibits methyltransferase protein8. Thereby, miR-1307 inhibits the expression of KDM3A and KDM3B and increases the methylation modification of histone H3 lysine 9, which enhances the expression of endoplasmic-reticulum-related gene CALR. Of note, miR-1307 weakens the binding ability of OSTC to CDK2, CDK4, CyclinD1, and cyclinE and enhances the binding ability of CALR to CDK2, CDK4, CyclinD1, and cyclinE, decreasing of p21WAF1/CIP1, GADD45, pRB, and p18, and decreasing of ppRB. Furthermore, miR-1307 increases the activity of H-Ras, PKM2, and PLK1. Strikingly, miR-1307 reduces the binding ability of OSTC to ATG4 and enhances the binding ability of CALR to ATG4. Therefore, miR-1307 reduces the occurrence of autophagy based on ATG4-LC3-ATG3-ATG7-ATG5-ATG16L1-ATG12-ATG9- Beclin1. In particular, miR-1307 enhances the expression of PAK2, PLK1, PRKAR2A, MYBL1, and Trim44 and inhibits the expression of Sash1 and Smad5 via autophagy. Our observations suggest that miR-1307 promotes hepatocarcinogenesis by CALR-OSTC-endoplasmic reticulum protein folding pathway.
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Affiliation(s)
- Sijie Xie
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
| | - Xiaoxue Jiang
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
| | - Rushi Qin
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
| | - Shuting Song
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
| | - Yanan Lu
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
| | - Liyan Wang
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
| | - Yingjie Chen
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
| | - Dongdong Lu
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
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9
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Liu Y, Yang H, Liu X, Gu H, Li Y, Sun C. Protein acetylation: a novel modus of obesity regulation. J Mol Med (Berl) 2021; 99:1221-1235. [PMID: 34061242 DOI: 10.1007/s00109-021-02082-2] [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: 09/28/2020] [Revised: 03/09/2021] [Accepted: 04/21/2021] [Indexed: 11/27/2022]
Abstract
Obesity is a chronic epidemic disease worldwide which has become one of the important public health issues. It is a process that excessive accumulation of adipose tissue caused by long-term energy intake exceeding energy expenditure. So far, the prevention and treatment strategies of obesity on individuals and population have not been successful in the long term. Acetylation is one of the most common ways of protein post-translational modification (PTM). It exists on thousands of non-histone proteins in almost every cell chamber. It has many influences on protein levels and metabolome levels, which is involved in a variety of metabolic reactions, including sugar metabolism, tricarboxylic acid cycle, and fatty acid metabolism, which are closely related to biological activities. Studies have shown that protein acetylation levels are dynamically regulated by lysine acetyltransferases (KATs) and lysine deacetylases (KDACs). Protein acetylation modifies protein-protein and protein-DNA interactions and regulates the activity of enzymes or cytokines which is related to obesity in order to participate in the occurrence and treatment of obesity-related metabolic diseases. Therefore, we speculated that acetylation was likely to become effective means of controlling obesity in the future. In consequence, this review focuses on the mechanisms of protein acetylation controlled obesity, to provide theoretical basis for controlling obesity and curing obesity-related diseases, which is a significance for regulating obesity in the future. This review will focus on the role of protein acetylation in controlling obesity.
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Affiliation(s)
- Yuexia Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hong Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xuanchen Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Huihui Gu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yizhou Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chao Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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10
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Dimou NL, Papadimitriou N, Mariosa D, Johansson M, Brennan P, Peters U, Chanock SJ, Purdue M, Bishop DT, Gago‐Dominquez M, Giles GG, Moreno V, Platz EA, Tangen CM, Wolk A, Zheng W, Wu X, Campbell PT, Giovannucci E, Lin Y, Gunter MJ, Murphy N. Circulating adipokine concentrations and risk of five obesity-related cancers: A Mendelian randomization study. Int J Cancer 2021; 148:1625-1636. [PMID: 33038280 PMCID: PMC7894468 DOI: 10.1002/ijc.33338] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/27/2020] [Accepted: 09/17/2020] [Indexed: 12/20/2022]
Abstract
Obesity is considered a chronic inflammatory state characterized by continued secretion of adipokines and cytokines. Experimental and epidemiological evidence indicates that circulating adipokines may be associated with the development of obesity-related cancers, but it is unclear if these associations are causal or confounded. We examined potential causal associations of specific adipokines (adiponectin, leptin, soluble leptin receptor [sOB-R] and plasminogen activator inhibitor-1 [PAI-1]) with five obesity-related cancers (colorectal, pancreatic, renal cell carcinoma [RCC], ovarian and endometrial) using Mendelian randomization (MR) methods. We used summary-level data from large genetic consortia for 114 530 cancer cases and 245 284 controls. We constructed genetic instruments using 18 genetic variants for adiponectin, 2 for leptin and 4 for both sOB-R and PAI-1 (P value for inclusion<5 × 10-8 ). Causal estimates were obtained using two-sample MR methods. In the inverse-variance weighted models, we found an inverse association between adiponectin and risk of colorectal cancer (odds ratio per 1 μg/mL increment in adiponectin concentration: 0.90 [95% confidence interval = 0.84-0.97]; P = .01); but, evidence of horizontal pleiotropy was detected and the association was not present when this was taken into consideration. No association was found for adiponectin and risks of pancreatic cancer, RCC, ovarian cancer and endometrial cancer. Leptin, sOB-R and PAI-1 were also similarly unrelated to risk of obesity-related cancers. Despite the large sample size, our MR analyses do not support causal effects of circulating adiponectin, leptin, sOB-R and PAI-1 concentrations on the development of five obesity-related cancers.
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Affiliation(s)
- Niki L. Dimou
- Section of Nutrition and Metabolism, International Agency for Research on CancerLyonFrance
| | - Nikos Papadimitriou
- Section of Nutrition and Metabolism, International Agency for Research on CancerLyonFrance
| | - Daniela Mariosa
- Section of Genetics, International Agency for Research on CancerLyonFrance
| | - Mattias Johansson
- Section of Genetics, International Agency for Research on CancerLyonFrance
| | - Paul Brennan
- Section of Genetics, International Agency for Research on CancerLyonFrance
| | - Ulrike Peters
- Fred Hutchinson Cancer Research CenterSeattleWashingtonUSA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer InstituteNational Institutes of HealthBethesdaMarylandUSA
| | - Mark Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer InstituteNational Institutes of HealthBethesdaMarylandUSA
| | | | - Manuela Gago‐Dominquez
- Fundación Gallega de Medicina Genómica, Grupo de Genéticadel CáncerInstituto de Investigación Sanitaria de Santiago IDISComplejo Hospitalario Univ. Santiago‐CHUS, SERGAS, Santiago de CompostelaSpain
- Moores Cancer CenterUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Graham G. Giles
- Cancer Epidemiology DivisionCancer Council VictoriaMelbourneVictoriaAustralia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global HealthThe University of MelbourneMelbourneVictoriaAustralia
- Precision MedicineSchool of Clinical Sciences at Monash Health, Monash UniversityClaytonVictoriaAustralia
| | - Victor Moreno
- Oncology Data Analytics ProgramCatalan Institute of Oncology‐IDIBELL, L'Hospitalet de LlobregatBarcelonaSpain
- CIBER Epidemiología y SaludPública (CIBERESP)MadridSpain
- Department of Clinical Sciences, Faculty of MedicineUniversity of BarcelonaBarcelonaSpain
- ONCOBEL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de LlobregatBarcelonaSpain
| | - Elizabeth A. Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public HealthBaltimoreMarylandUSA
| | - Catherine M. Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research CenterSeattleWashingtonUSA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska InstitutetStockholmSweden
- Department of Surgical SciencesUppsala UniversityUppsalaSweden
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt‐Ingram Cancer CenterVanderbilt UniversityNashvilleTennesseeUSA
| | - Xifeng Wu
- Department of EpidemiologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
- Department of Precision Health and Data Science, School of Public Health and the Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Peter T. Campbell
- Behavioral and Epidemiology Research Group, American Cancer SocietyAtlantaGeorgiaUSA
| | - Edward Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public HealthHarvard UniversityBostonMassachusettsUSA
- Department of NutritionT.H. Chan School of Public HealthBostonMassachusettsUSA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical SchoolBostonMassachusettsUSA
| | - Yi Lin
- Public Health Sciences Division, Fred Hutchinson Cancer Research CenterSeattleWashingtonUSA
| | | | - Marc J. Gunter
- Section of Nutrition and Metabolism, International Agency for Research on CancerLyonFrance
| | - Neil Murphy
- Section of Nutrition and Metabolism, International Agency for Research on CancerLyonFrance
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11
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Brancolini C, Di Giorgio E, Formisano L, Gagliano T. Quis Custodiet Ipsos Custodes (Who Controls the Controllers)? Two Decades of Studies on HDAC9. Life (Basel) 2021; 11:life11020090. [PMID: 33513699 PMCID: PMC7912504 DOI: 10.3390/life11020090] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 01/20/2021] [Accepted: 01/24/2021] [Indexed: 12/21/2022] Open
Abstract
Understanding how an epigenetic regulator drives different cellular responses can be a tricky task. Very often, their activities are modulated by large multiprotein complexes, the composition of which is context- and time-dependent. As a consequence, experiments aimed to unveil the functions of an epigenetic regulator can provide different outcomes and conclusions, depending on the circumstances. HDAC9 (histone deacetylase), an epigenetic regulator that influences different differentiating and adaptive responses, makes no exception. Since its discovery, different phenotypes and/or dysfunctions have been observed after the artificial manipulation of its expression. The cells and the microenvironment use multiple strategies to control and monitor HDAC9 activities. To date, some of the genes under HDAC9 control have been identified. However, the exact mechanisms through which HDAC9 can achieve all the different tasks so far described, remain mysterious. Whether it can assemble into different multiprotein complexes and how the cells modulate these complexes is not clearly defined. In summary, despite several cellular responses are known to be affected by HDAC9, many aspects of its network of interactions still remain to be defined.
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Affiliation(s)
- Claudio Brancolini
- Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy; (E.D.G.); (T.G.)
- Correspondence:
| | - Eros Di Giorgio
- Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy; (E.D.G.); (T.G.)
| | - Luigi Formisano
- Department of Neuroscience, School of Medicine, “Federico II” University of Naples, Via Pansini, 5, 80131 Naples, Italy;
| | - Teresa Gagliano
- Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy; (E.D.G.); (T.G.)
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12
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Wan L, Lu J, Huang J, Huo Y, Jiang S, Guo C. Association Between Peripheral Adiponectin and Lipids Levels and the Therapeutic Response to Donepezil Treatment in Han Chinese Patients With Alzheimer's Disease. Front Aging Neurosci 2020; 12:532386. [PMID: 33061904 PMCID: PMC7518373 DOI: 10.3389/fnagi.2020.532386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 08/12/2020] [Indexed: 01/11/2023] Open
Abstract
Acetylcholinesterase inhibitors (AChEIs) including donepezil (DNP) are considered to be the most promising therapeutic possibilities of Alzheimer's disease (AD). The response to DNP in AD patients varies and it is valuable to identify the potential markers that can predict the efficacy. Moreover, DNP has been found to affect bone function, but the exact mechanism is still unclear. Lipids and adipokine may link to AD and DNP directly or indirectly and might be potential biomarkers or therapeutic drug targets. The goal of this study was to investigate the relationships among adiponectin (APN), lipids levels, and the response to DNP, and to identify whether the effect of DNP in AD treatment is related to its effect on the level of APN in systemic circulation. The study recruited 85 AD patients with DNP treatment, of whom 47 were DNP responders and 38 were DNP nonresponders. The Mini-Mental State Examination was performed to evaluate the memory impairment. Plasma APN was measured with ELISA. The genotypes of single nucleotide polymorphisms rs1501299 and rs22417661 in APN for each patient were identified. Plasma lipids were quantified with gas chromatography coupled with mass spectrometry. Correlations among APN, lipid metabolomics, and DNP responded were evaluated. APN was significantly decreased in DNP responders. Methyl stearate and glycerol-3-phosphate, used for characterizing adipogenic differentiation, were significantly decreased in DNP responders compared to DNP nonresponders. APN and small-molecule lipids can be used as potential biomarkers to evaluate the efficacy of DNP. The results of metabolomics indicated that there was no change in the metabolic pathway of fatty acid metabolism and glucose metabolism in DNP responders, suggesting that APN-related biological function did not decrease in DNP responders. Our result suggests that more attention should be pay to the sources and biological functions of APN in AD with DNP treatment.
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Affiliation(s)
- Lili Wan
- Department of Pharmacy, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Jin Lu
- Department of Pharmacy, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Jinlu Huang
- Department of Pharmacy, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Yan Huo
- Department of Pharmacy, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Shan Jiang
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Icahn Institute for Data Science and Genomic Technology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Cheng Guo
- Department of Pharmacy, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
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13
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Adiponectin and leptin gene variants and their effects on body weight trajectories in children from birth to 6 years of age: the PREDI Study. Br J Nutr 2020; 125:241-250. [PMID: 32693844 DOI: 10.1017/s0007114520002780] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Excess body weight confers a high risk to human health. Body weight variation between subjects can be partially explained by genetic differences. The aim of the present study was to investigate the association of genetic variants in the ADIPOQ (rs2241766) and LEP (rs7799039) genes with body weight trajectories in children from birth to 6 years of age. This was a prospective cohort (PREDI Study). Socio-economic, biological and anthropometric data were collected at four time points: at birth in the maternity unit; 1-2, 4-5 and 6 years old at the participants' homes. Genotyping was performed by PCR-restriction fragment length polymorphism. Poisson regression and linear mixed-effect regression models were used to address the association of ADIPOQ and LEP genotypes with BMI. Excessive body weight at pre-pregnancy (β = 0·339, P = 0·01) and excessive gestational weight gain (β = 0·51, P < 0·001) were associated with children's BMI trajectory from birth to 6 years. The ADIPOQ-rs2241766 TG or GG genotype was associated with a higher risk of excess body weight in the first 6 years of life (both sexes relative risk 1·25, 95 % CI 1·01, 1·56; female relative risk 1·67, 95 % CI 1·20, 2·31). BMI increased over the years according to the presence of the TG or GG genotype (β = 0·01, 95 % CI 0·01, 0·02), particularly in females (β = 0·02, 95 % CI 0·01, 0·04). The ADIPOQ-rs2241766 TG and GG genotypes increased the risk of excess body weight in children from birth to 6 years of age and had a positive effect on body weight trajectories in girls. The LEP-rs7799039 genetic variant was not associated with body weight trajectory in children.
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14
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Genetic variation, adipokines, and cardiometabolic disease. Curr Opin Pharmacol 2020; 52:33-39. [PMID: 32480034 DOI: 10.1016/j.coph.2020.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 11/24/2022]
Abstract
Adipokines are adipocyte-secreted cell signalling proteins that travel to distant target organs and tissues, where they regulate a variety of biological actions implicated in cardiometabolic health. In the past decade, genome-wide association studies have identified multiple genetic variants associated with circulating levels of adipokines, providing new instruments for examining the role of adipokines in cardiometabolic pathologies. Currently, there is limited genetic evidence of causal relationships between adipokines and cardiometabolic disease, which is consistent with findings from randomized clinical trials that have thus far shown limited success for adipokine-based treatments in improving cardiometabolic health. Incorporating human genetic data in early phases of target selection is essential for enhancing the success of adipokine-based therapies for cardiometabolic disease.
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15
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Criscitiello MF, Kraev I, Lange S. Deiminated proteins in extracellular vesicles and serum of llama (Lama glama)-Novel insights into camelid immunity. Mol Immunol 2020; 117:37-53. [PMID: 31733447 PMCID: PMC7112542 DOI: 10.1016/j.molimm.2019.10.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/05/2019] [Accepted: 10/23/2019] [Indexed: 02/07/2023]
Abstract
Peptidylarginine deiminases (PADs) are phylogenetically conserved calcium-dependent enzymes which post-translationally convert arginine into citrulline in target proteins in an irreversible manner, causing functional and structural changes in target proteins. Protein deimination causes generation of neo-epitopes, affects gene regulation and also allows for protein moonlighting. Furthermore, PADs have been found to be a phylogenetically conserved regulator for extracellular vesicle (EVs) release. EVs are found in most body fluids and participate in cellular communication via transfer of cargo proteins and genetic material. In this study, post-translationally deiminated proteins in serum and serum-EVs are described for the first time in camelids, using the llama (Lama glama L. 1758) as a model animal. We report a poly-dispersed population of llama serum EVs, positive for phylogenetically conserved EV-specific markers and characterised by TEM. In serum, 103 deiminated proteins were overall identified, including key immune and metabolic mediators including complement components, immunoglobulin-based nanobodies, adiponectin and heat shock proteins. In serum, 60 deiminated proteins were identified that were not in EVs, and 25 deiminated proteins were found to be unique to EVs, with 43 shared deiminated protein hits between both serum and EVs. Deiminated histone H3, a marker of neutrophil extracellular trap formation, was also detected in llama serum. PAD homologues were identified in llama serum by Western blotting, via cross reaction with human PAD antibodies, and detected at an expected 70 kDa size. This is the first report of deiminated proteins in serum and EVs of a camelid species, highlighting a hitherto unrecognized post-translational modification in key immune and metabolic proteins in camelids, which may be translatable to and inform a range of human metabolic and inflammatory pathologies.
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Affiliation(s)
- Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA; Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station, TX, 77843, USA.
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes, MK7 6AA, UK.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK.
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16
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Pamenter ME, Uysal-Onganer P, Huynh KW, Kraev I, Lange S. Post-Translational Deimination of Immunological and Metabolic Protein Markers in Plasma and Extracellular Vesicles of Naked Mole-Rat ( Heterocephalus glaber). Int J Mol Sci 2019; 20:E5378. [PMID: 31671738 PMCID: PMC6862702 DOI: 10.3390/ijms20215378] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/17/2019] [Accepted: 10/28/2019] [Indexed: 12/16/2022] Open
Abstract
Naked mole-rats are long-lived animals that show unusual resistance to hypoxia, cancer and ageing. Protein deimination is an irreversible post-translational modification caused by the peptidylarginine deiminase (PAD) family of enzymes, which convert arginine into citrulline in target proteins. Protein deimination can cause structural and functional protein changes, facilitating protein moonlighting, but also leading to neo-epitope generation and effects on gene regulation. Furthermore, PADs have been found to regulate cellular release of extracellular vesicles (EVs), which are lipid-vesicles released from cells as part of cellular communication. EVs carry protein and genetic cargo and are indicative biomarkers that can be isolated from most body fluids. This study was aimed at profiling deiminated proteins in plasma and EVs of naked mole-rat. Key immune and metabolic proteins were identified to be post-translationally deiminated, with 65 proteins specific for plasma, while 42 proteins were identified to be deiminated in EVs only. Using protein-protein interaction network analysis, deiminated plasma proteins were found to belong to KEEG (Kyoto Encyclopedia of Genes and Genomes) pathways of immunity, infection, cholesterol and drug metabolism, while deiminated proteins in EVs were also linked to KEEG pathways of HIF-1 signalling and glycolysis. The mole-rat EV profiles showed a poly-dispersed population of 50-300 nm, similar to observations of human plasma. Furthermore, the EVs were assessed for three key microRNAs involved in cancer, inflammation and hypoxia. The identification of post-translational deimination of critical immunological and metabolic markers contributes to the current understanding of protein moonlighting functions, via post-translational changes, in the longevity and cancer resistance of naked mole-rats.
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Affiliation(s)
- Matthew E Pamenter
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
- Brain and Mind Research Institute, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
| | - Pinar Uysal-Onganer
- Cancer Research Group, School of Life Sciences, College of Liberal Arts and Sciences, University of Westminster, London W1W 6 UW, UK.
| | - Kenny W Huynh
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
- Brain and Mind Research Institute, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Walton Hall, Milton Keynes MK7 6AA, UK.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, College of Liberal Arts and Sciences, University of Westminster, London W1W 6 UW, UK.
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