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Gu S, Huang Q, Jie Y, Sun C, Wen C, Yang N. Transcriptomic and epigenomic landscapes of muscle growth during the postnatal period of broilers. J Anim Sci Biotechnol 2024; 15:91. [PMID: 38961455 PMCID: PMC11223452 DOI: 10.1186/s40104-024-01049-w] [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: 02/04/2024] [Accepted: 05/12/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND Broilers stand out as one of the fastest-growing livestock globally, making a substantial contribution to animal meat production. However, the molecular and epigenetic mechanisms underlying the rapid growth and development of broiler chickens are still unclear. This study aims to explore muscle development patterns and regulatory networks during the postnatal rapid growth phase of fast-growing broilers. We measured the growth performance of Cornish (CC) and White Plymouth Rock (RR) over a 42-d period. Pectoral muscle samples from both CC and RR were randomly collected at day 21 after hatching (D21) and D42 for RNA-seq and ATAC-seq library construction. RESULTS The consistent increase in body weight and pectoral muscle weight across both breeds was observed as they matured, with CC outpacing RR in terms of weight at each stage of development. Differential expression analysis identified 398 and 1,129 genes in the two dimensions of breeds and ages, respectively. A total of 75,149 ATAC-seq peaks were annotated in promoter, exon, intron and intergenic regions, with a higher number of peaks in the promoter and intronic regions. The age-biased genes and breed-biased genes of RNA-seq were combined with the ATAC-seq data for subsequent analysis. The results spotlighted the upregulation of ACTC1 and FDPS at D21, which were primarily associated with muscle structure development by gene cluster enrichment. Additionally, a noteworthy upregulation of MUSTN1, FOS and TGFB3 was spotted in broiler chickens at D42, which were involved in cell differentiation and muscle regeneration after injury, suggesting a regulatory role of muscle growth and repair. CONCLUSIONS This work provided a regulatory network of postnatal broiler chickens and revealed ACTC1 and MUSTN1 as the key responsible for muscle development and regeneration. Our findings highlight that rapid growth in broiler chickens triggers ongoing muscle damage and subsequent regeneration. These findings provide a foundation for future research to investigate the functional aspects of muscle development.
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Affiliation(s)
- Shuang Gu
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology China Agricultural University, Beijing, 100193, China
| | - Qiang Huang
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology China Agricultural University, Beijing, 100193, China
| | - Yuchen Jie
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology China Agricultural University, Beijing, 100193, China
| | - Congjiao Sun
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Hainan, 572025, China
| | - Chaoliang Wen
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Hainan, 572025, China
| | - Ning Yang
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China.
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Hainan, 572025, China.
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Pastika L, Sau A, Patlatzoglou K, Sieliwonczyk E, Ribeiro AH, McGurk KA, Khan S, Mandic D, Scott WR, Ware JS, Peters NS, Ribeiro ALP, Kramer DB, Waks JW, Ng FS. Artificial intelligence-enhanced electrocardiography derived body mass index as a predictor of future cardiometabolic disease. NPJ Digit Med 2024; 7:167. [PMID: 38918595 PMCID: PMC11199586 DOI: 10.1038/s41746-024-01170-0] [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: 01/24/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
The electrocardiogram (ECG) can capture obesity-related cardiac changes. Artificial intelligence-enhanced ECG (AI-ECG) can identify subclinical disease. We trained an AI-ECG model to predict body mass index (BMI) from the ECG alone. Developed from 512,950 12-lead ECGs from the Beth Israel Deaconess Medical Center (BIDMC), a secondary care cohort, and validated on UK Biobank (UKB) (n = 42,386), the model achieved a Pearson correlation coefficient (r) of 0.65 and 0.62, and an R2 of 0.43 and 0.39 in the BIDMC cohort and UK Biobank, respectively for AI-ECG BMI vs. measured BMI. We found delta-BMI, the difference between measured BMI and AI-ECG-predicted BMI (AI-ECG-BMI), to be a biomarker of cardiometabolic health. The top tertile of delta-BMI showed increased risk of future cardiometabolic disease (BIDMC: HR 1.15, p < 0.001; UKB: HR 1.58, p < 0.001) and diabetes mellitus (BIDMC: HR 1.25, p < 0.001; UKB: HR 2.28, p < 0.001) after adjusting for covariates including measured BMI. Significant enhancements in model fit, reclassification and improvements in discriminatory power were observed with the inclusion of delta-BMI in both cohorts. Phenotypic profiling highlighted associations between delta-BMI and cardiometabolic diseases, anthropometric measures of truncal obesity, and pericardial fat mass. Metabolic and proteomic profiling associates delta-BMI positively with valine, lipids in small HDL, syntaxin-3, and carnosine dipeptidase 1, and inversely with glutamine, glycine, colipase, and adiponectin. A genome-wide association study revealed associations with regulators of cardiovascular/metabolic traits, including SCN10A, SCN5A, EXOG and RXRG. In summary, our AI-ECG-BMI model accurately predicts BMI and introduces delta-BMI as a non-invasive biomarker for cardiometabolic risk stratification.
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Affiliation(s)
- Libor Pastika
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Arunashis Sau
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Department of Cardiology, Imperial College Healthcare NHS Trust, London, United Kingdom
| | | | - Ewa Sieliwonczyk
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- MRC Laboratory of Medical Sciences, Imperial College London, London, United Kingdom
| | - Antônio H Ribeiro
- Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Kathryn A McGurk
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- MRC Laboratory of Medical Sciences, Imperial College London, London, United Kingdom
| | - Sadia Khan
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Chelsea and Westminster NHS Foundation Trust, London, United Kingdom
| | - Danilo Mandic
- Department of Electrical and Electronic Engineering, Imperial College London, London, United Kingdom
| | - William R Scott
- MRC Laboratory of Medical Sciences, Imperial College London, London, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - James S Ware
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- MRC Laboratory of Medical Sciences, Imperial College London, London, United Kingdom
| | - Nicholas S Peters
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Department of Cardiology, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Antonio Luiz P Ribeiro
- Department of Internal Medicine, Faculdade de Medicina, and Telehealth Center and Cardiology Service, Hospital das Clínicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Daniel B Kramer
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Richard A. and Susan F. Smith Center for Outcomes Research in Cardiology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jonathan W Waks
- Harvard-Thorndike Electrophysiology Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Fu Siong Ng
- National Heart and Lung Institute, Imperial College London, London, United Kingdom.
- Department of Cardiology, Imperial College Healthcare NHS Trust, London, United Kingdom.
- Chelsea and Westminster NHS Foundation Trust, London, United Kingdom.
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Lekkos K, Bhuiyan AA, Albloshi AMK, Brooks PM, Coate TM, Lionikas A. Validation of positional candidates Rps6ka6 and Pou3f4 for a locus associated with skeletal muscle mass variability. G3 (BETHESDA, MD.) 2024; 14:jkae046. [PMID: 38577978 PMCID: PMC11075558 DOI: 10.1093/g3journal/jkae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/17/2024] [Indexed: 04/06/2024]
Abstract
Genetic variability significantly contributes to individual differences in skeletal muscle mass; however, the specific genes involved in that process remain elusive. In this study, we examined the role of positional candidates, Rps6ka6 and Pou3f4, of a chromosome X locus, implicated in muscle mass variability in CFW laboratory mice. Histology of hindlimb muscles was studied in CFW male mice carrying the muscle "increasing" allele C (n = 15) or "decreasing" allele T (n = 15) at the peak marker of the locus, rs31308852, and in the Pou3f4y/- and their wild-type male littermates. To study the role of the Rps6ka6 gene, we deleted exon 7 (Rps6ka6-ΔE7) using clustered regularly interspaced palindromic repeats-Cas9 based method in H2Kb myogenic cells creating a severely truncated RSK4 protein. We then tested whether that mutation affected myoblast proliferation, migration, and/or differentiation. The extensor digitorum longus muscle was 7% larger (P < 0.0001) due to 10% more muscle fibers (P = 0.0176) in the carriers of the "increasing" compared with the "decreasing" CFW allele. The number of fibers was reduced by 15% (P = 0.0268) in the slow-twitch soleus but not in the fast-twitch extensor digitorum longus (P = 0.2947) of Pou3f4y/- mice. The proliferation and migration did not differ between the Rps6ka6-ΔE7 and wild-type H2Kb myoblasts. However, indices of differentiation (myosin expression, P < 0.0001; size of myosin-expressing cells, P < 0.0001; and fusion index, P = 0.0013) were significantly reduced in Rps6ka6-ΔE7 cells. This study suggests that the effect of the X chromosome locus on muscle fiber numbers in the fast-twitch extensor digitorum longus is mediated by the Rps6ka6 gene, whereas the Pou3f4 gene affects fiber number in slow-twitch soleus.
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Affiliation(s)
- Konstantinos Lekkos
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Afra A Bhuiyan
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Abdullah M K Albloshi
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK
- Department of Anatomy and Histology, School of Medicine, University of Albaha, Alaqiq 65779, Saudi Arabia
| | - Paige M Brooks
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | - Thomas M Coate
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | - Arimantas Lionikas
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK
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Cao X, Zhang S, Sha Q. A novel method for multiple phenotype association studies based on genotype and phenotype network. PLoS Genet 2024; 20:e1011245. [PMID: 38728360 PMCID: PMC11111089 DOI: 10.1371/journal.pgen.1011245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 05/22/2024] [Accepted: 03/29/2024] [Indexed: 05/12/2024] Open
Abstract
Joint analysis of multiple correlated phenotypes for genome-wide association studies (GWAS) can identify and interpret pleiotropic loci which are essential to understand pleiotropy in diseases and complex traits. Meanwhile, constructing a network based on associations between phenotypes and genotypes provides a new insight to analyze multiple phenotypes, which can explore whether phenotypes and genotypes might be related to each other at a higher level of cellular and organismal organization. In this paper, we first develop a bipartite signed network by linking phenotypes and genotypes into a Genotype and Phenotype Network (GPN). The GPN can be constructed by a mixture of quantitative and qualitative phenotypes and is applicable to binary phenotypes with extremely unbalanced case-control ratios in large-scale biobank datasets. We then apply a powerful community detection method to partition phenotypes into disjoint network modules based on GPN. Finally, we jointly test the association between multiple phenotypes in a network module and a single nucleotide polymorphism (SNP). Simulations and analyses of 72 complex traits in the UK Biobank show that multiple phenotype association tests based on network modules detected by GPN are much more powerful than those without considering network modules. The newly proposed GPN provides a new insight to investigate the genetic architecture among different types of phenotypes. Multiple phenotypes association studies based on GPN are improved by incorporating the genetic information into the phenotype clustering. Notably, it might broaden the understanding of genetic architecture that exists between diagnoses, genes, and pleiotropy.
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Affiliation(s)
- Xuewei Cao
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Shuanglin Zhang
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Qiuying Sha
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
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5
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Novakov V, Novakova O, Churnosova M, Aristova I, Ponomarenko M, Reshetnikova Y, Churnosov V, Sorokina I, Ponomarenko I, Efremova O, Orlova V, Batlutskaya I, Polonikov A, Reshetnikov E, Churnosov M. Polymorphism rs143384 GDF5 reduces the risk of knee osteoarthritis development in obese individuals and increases the disease risk in non-obese population. ARTHROPLASTY 2024; 6:12. [PMID: 38424630 PMCID: PMC10905832 DOI: 10.1186/s42836-023-00229-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/26/2023] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND We investigated the effect of obesity on the association of genome-wide associative studies (GWAS)-significant genes with the risk of knee osteoarthritis (KOA). METHODS All study participants (n = 1,100) were divided into 2 groups in terms of body mass index (BMI): BMI ≥ 30 (255 KOA patients and 167 controls) and BMI < 30 (245 KOA and 433 controls). The eight GWAS-significant KOA single nucleotide polymorphisms (SNP) of six candidate genes, such as LYPLAL1 (rs2820436, rs2820443), SBNO1 (rs1060105, rs56116847), WWP2 (rs34195470), NFAT5 (rs6499244), TGFA (rs3771501), GDF5 (rs143384), were genotyped. Logistic regression analysis (gPLINK online program) was used for SNPs associations study with the risk of developing KOA into 2 groups (BMI ≥ 30 and BMI < 30) separately. The functional effects of KOA risk loci were evaluated using in silico bioinformatic analysis. RESULTS Multidirectional relationships of the rs143384 GDF5 with KOA in BMI-different groups were found: This SNP was KOA protective locus among individuals with BMI ≥ 30 (OR 0.41 [95%CI 0.20-0.94] recessive model) and was disorder risk locus among individuals with BMI < 30 (OR 1.32 [95%CI 1.05-1.65] allele model, OR 1.44 [95%CI 1.10-1.86] additive model, OR 1.67 [95%CI 1.10-2.52] dominant model). Polymorphism rs143384 GDF5 manifested its regulatory effects in relation to nine genes (GDF5, CPNE1, EDEM2, ERGIC3, GDF5OS, PROCR, RBM39, RPL36P4, UQCC1) in adipose tissue, which were involved in the regulation of pathways of apoptosis of striated muscle cells. CONCLUSIONS In summary, the effect of obesity on the association of the rs143384 GDF5 with KOA was shown: the "protective" value of this polymorphism in the BMI ≥ 30 group and the "risk" meaning in BMI < 30 cohort.
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Affiliation(s)
- Vitaly Novakov
- Department of Medical Biological Disciplines, Belgorod State National Research University, Belgorod, 308015, Russia
| | - Olga Novakova
- Department of Medical Biological Disciplines, Belgorod State National Research University, Belgorod, 308015, Russia
| | - Maria Churnosova
- Department of Medical Biological Disciplines, Belgorod State National Research University, Belgorod, 308015, Russia
| | - Inna Aristova
- Department of Medical Biological Disciplines, Belgorod State National Research University, Belgorod, 308015, Russia
| | - Marina Ponomarenko
- Department of Medical Biological Disciplines, Belgorod State National Research University, Belgorod, 308015, Russia
| | - Yuliya Reshetnikova
- Department of Medical Biological Disciplines, Belgorod State National Research University, Belgorod, 308015, Russia
| | - Vladimir Churnosov
- Department of Medical Biological Disciplines, Belgorod State National Research University, Belgorod, 308015, Russia
| | - Inna Sorokina
- Department of Medical Biological Disciplines, Belgorod State National Research University, Belgorod, 308015, Russia
| | - Irina Ponomarenko
- Department of Medical Biological Disciplines, Belgorod State National Research University, Belgorod, 308015, Russia
| | - Olga Efremova
- Department of Medical Biological Disciplines, Belgorod State National Research University, Belgorod, 308015, Russia
| | - Valentina Orlova
- Department of Medical Biological Disciplines, Belgorod State National Research University, Belgorod, 308015, Russia
| | - Irina Batlutskaya
- Department of Medical Biological Disciplines, Belgorod State National Research University, Belgorod, 308015, Russia
| | - Alexey Polonikov
- Department of Medical Biological Disciplines, Belgorod State National Research University, Belgorod, 308015, Russia
- Department of Biology, Medical Genetics and Ecology and Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, Kursk, 305041, Russia
| | - Evgeny Reshetnikov
- Department of Medical Biological Disciplines, Belgorod State National Research University, Belgorod, 308015, Russia
| | - Mikhail Churnosov
- Department of Medical Biological Disciplines, Belgorod State National Research University, Belgorod, 308015, Russia.
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Qie S, Xiong H, Liu Y, Yan C, Wang Y, Tian L, Wang C, Sang N. Stanniocalcin 2 governs cancer cell adaptation to nutrient insufficiency through alleviation of oxidative stress. RESEARCH SQUARE 2024:rs.3.rs-3904465. [PMID: 38464261 PMCID: PMC10925426 DOI: 10.21203/rs.3.rs-3904465/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Solid tumours often endure nutrient insufficiency during progression. How tumour cells adapt to temporal and spatial nutrient insufficiency remains unclear. We previously identified STC2 as one of the most upregulated genes in cells exposed to nutrient insufficiency by transcriptome screening, indicating the potential of STC2 in cellular adaptation to nutrient insufficiency. However, the molecular mechanisms underlying STC2 induction by nutrient insufficiency and subsequent adaptation remain elusive. Here, we report that STC2 protein is dramatically increased and secreted into the culture media by Gln-/Glc-deprivation. STC2 promoter contains cis-elements that are activated by ATF4 and p65/RelA, two transcription factors activated by a variety of cellular stress. Biologically, STC2 induction and secretion promote cell survival but attenuate cell proliferation during nutrient insufficiency, thus switching the priority of cancer cells from proliferation to survival. Loss of STC2 impairs tumour growth by inducing both apoptosis and necrosis in mouse xenografts. Mechanistically, under nutrient insufficient conditions, cells have increased levels of reactive oxygen species (ROS), and lack of STC2 further elevates ROS levels that lead to increased apoptosis. RNA-Seq analyses reveal STC2 induction suppresses the expression of monoamine oxidase B (MAOB), a mitochondrial membrane enzyme that produces ROS. Moreover, a negative correlation between STC2 and MAOB levels is also identified in human tumour samples. Importantly, the administration of recombinant STC2 to the culture media effectively suppresses MAOB expression as well as apoptosis, suggesting STC2 functions in an autocrine/paracrine manner. Taken together, our findings indicate that nutrient insufficiency induces STC2 expression, which in turn governs the adaptation of cancer cells to nutrient insufficiency through the maintenance of redox homeostasis, highlighting the potential of STC2 as a therapeutic target for cancer treatment.
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Affiliation(s)
- Shuo Qie
- Tianjin Medical University Cancer Institute and Hospital
| | - Haijuan Xiong
- Tianjin Medical University Cancer Institute and Hospital
| | - Yaqi Liu
- Tianjin Medical University Cancer Institute and Hospital
| | - Chenhui Yan
- Tianjin Medical University Cancer Institute and Hospital
| | | | - Lifeng Tian
- Kimmel Cancer Center, Thomas Jefferson University
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Cao Y, Jia Q, Xing Y, Ma C, Guan H, Tian W, Kang X, Tian Y, Liu X, Li H. STC2 Inhibits Hepatic Lipid Synthesis and Correlates with Intramuscular Fatty Acid Composition, Body Weight and Carcass Traits in Chickens. Animals (Basel) 2024; 14:383. [PMID: 38338026 PMCID: PMC10854843 DOI: 10.3390/ani14030383] [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: 10/26/2023] [Revised: 12/18/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Stanniocalcin 2 (STC2) is a secreted glycoprotein involved in multiple biological processes. To systemically study the biological role of STC2 in chickens, phylogenetic tree analysis and conservation analysis were conducted. Association analysis between variations in the STC2 gene and the economic traits of Gushi-Anka F2 was conducted. The tissue expression patterns of STC2 expression in different chicken tissues and liver at different stages were detected. The biological role of STC2 in chicken liver was investigated through overexpression and interfering methods in the LMH cell line. Correlation analyses between STC2 expression and lipid components were conducted. (1) The phylogenetic tree displayed that chicken STC2 is most closely related with Japanese quail and most distantly related with Xenopus tropicalis. STC2 has the same identical conserved motifs as other species. (2) rs9949205 (T > C) found in STC2 intron was highly significantly correlated with chicken body weight at 0, 2, 4, 6, 8, 10 and 12 weeks (p < 0.01). Extremely significant correlations of rs9949205 with semi-evisceration weight (SEW), evisceration weight (EW), breast muscle weight (BMW), leg muscle weight (LMW), liver weight and abdominal fat weight (AFW) were revealed (p < 0.01). Significant associations between rs9949205 and abdominal fat percentage, liver weight rate, breast muscle weight rate and leg muscle weight rate were also found (p < 0.05). Individuals with TT or TC genotypes had significantly lower abdominal fat percentage and liver weight rate compared to those with the CC genotype, while their body weight and other carcass traits were higher. (3) STC2 showed a high expression level in chicken liver tissue, which significantly increased with the progression of age (p < 0.05). STC2 was observed to inhibit the content of lipid droplets, triglycerides (TG) and cholesterol (TC), as well the expression level of genes related to lipid metabolism in LMH cells. (4) Correlation analysis showed that the STC2 gene was significantly correlated with 176 lipids in the breast muscle (p < 0.05) and mainly enriched in omega-3 and omega-6 unsaturated fatty acids. In conclusion, the STC2 gene in chicken might potentially play a crucial role in chicken growth and development, as well as liver lipid metabolism and muscle lipid deposition. This study provides a scientific foundation for further investigation into the regulatory mechanism of the STC2 gene on lipid metabolism and deposition in chicken liver.
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Affiliation(s)
- Yuzhu Cao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Q.J.); (Y.X.); (C.M.); (H.G.); (W.T.); (X.K.); (Y.T.); (X.L.)
| | - Qihui Jia
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Q.J.); (Y.X.); (C.M.); (H.G.); (W.T.); (X.K.); (Y.T.); (X.L.)
| | - Yuxin Xing
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Q.J.); (Y.X.); (C.M.); (H.G.); (W.T.); (X.K.); (Y.T.); (X.L.)
| | - Chenglin Ma
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Q.J.); (Y.X.); (C.M.); (H.G.); (W.T.); (X.K.); (Y.T.); (X.L.)
| | - Hongbo Guan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Q.J.); (Y.X.); (C.M.); (H.G.); (W.T.); (X.K.); (Y.T.); (X.L.)
| | - Weihua Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Q.J.); (Y.X.); (C.M.); (H.G.); (W.T.); (X.K.); (Y.T.); (X.L.)
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Q.J.); (Y.X.); (C.M.); (H.G.); (W.T.); (X.K.); (Y.T.); (X.L.)
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Q.J.); (Y.X.); (C.M.); (H.G.); (W.T.); (X.K.); (Y.T.); (X.L.)
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Q.J.); (Y.X.); (C.M.); (H.G.); (W.T.); (X.K.); (Y.T.); (X.L.)
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Hong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Q.J.); (Y.X.); (C.M.); (H.G.); (W.T.); (X.K.); (Y.T.); (X.L.)
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
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Fattahi M, Rezaee D, Fakhari F, Najafi S, Aghaei-Zarch SM, Beyranvand P, Rashidi MA, Bagheri-Mohammadi S, Zamani-Rarani F, Bakhtiari M, Bakhtiari A, Falahi S, Kenarkoohi A, Majidpoor J, Nguyen PU. microRNA-184 in the landscape of human malignancies: a review to roles and clinical significance. Cell Death Discov 2023; 9:423. [PMID: 38001121 PMCID: PMC10673883 DOI: 10.1038/s41420-023-01718-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 11/05/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of non-coding RNAs (ncRNAs) with a short length of 19-22 nucleotides. miRNAs are posttranscriptional regulators of gene expression involved in various biological processes like cell growth, apoptosis, and angiogenesis. miR-184 is a well-studied miRNA, for which most studies report its downregulation in cancer cells and tissues and experiments support its role as a tumor suppressor inhibiting malignant biological behaviors of cancer cells in vitro and in vivo. To exert its functions, miR-184 affects some signaling pathways involved in tumorigenesis like Wnt and β-catenin, and AKT/mTORC1 pathway, oncogenic factors (e.g., c-Myc) or apoptotic proteins, such as Bcl-2. Interestingly, clinical investigations have shown miR-184 with good performance as a prognostic/diagnostic biomarker for various cancers. Additionally, exogenous miR-184 in cell and xenograft animal studies suggest it as a therapeutic anticancer target. In this review, we outline the studies that evaluated the roles of miR-184 in tumorigenesis as well as its clinical significance.
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Affiliation(s)
- Mehdi Fattahi
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam
- School of Engineering & Technology, Duy Tan University, Da Nang, Vietnam
| | - Delsuz Rezaee
- School of Allied Medical Sciences, Ilam University of Medical Sciences, Ilam, Iran
| | - Fatemeh Fakhari
- Department of Toxicology and Pharmacology, School of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Seyed Mohsen Aghaei-Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parisa Beyranvand
- Department of Molecular Genetics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Mohammad Amin Rashidi
- Student Research Committee, Department of Occupational Health and Safety, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeid Bagheri-Mohammadi
- Department of Physiology and Neurophysiology Research Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fahimeh Zamani-Rarani
- Department of Anatomical Sciences, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Abbas Bakhtiari
- Anatomical Sciences Department, Medical Faculty, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Shahab Falahi
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Azra Kenarkoohi
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
- Department of Microbiology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Jamal Majidpoor
- Department of Anatomy, Faculty of Medicine, Infectious Disease Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - P U Nguyen
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam
- School of Engineering & Technology, Duy Tan University, Da Nang, Vietnam
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9
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Szrok-Jurga S, Czumaj A, Turyn J, Hebanowska A, Swierczynski J, Sledzinski T, Stelmanska E. The Physiological and Pathological Role of Acyl-CoA Oxidation. Int J Mol Sci 2023; 24:14857. [PMID: 37834305 PMCID: PMC10573383 DOI: 10.3390/ijms241914857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/27/2023] [Accepted: 09/30/2023] [Indexed: 10/15/2023] Open
Abstract
Fatty acid metabolism, including β-oxidation (βOX), plays an important role in human physiology and pathology. βOX is an essential process in the energy metabolism of most human cells. Moreover, βOX is also the source of acetyl-CoA, the substrate for (a) ketone bodies synthesis, (b) cholesterol synthesis, (c) phase II detoxication, (d) protein acetylation, and (d) the synthesis of many other compounds, including N-acetylglutamate-an important regulator of urea synthesis. This review describes the current knowledge on the importance of the mitochondrial and peroxisomal βOX in various organs, including the liver, heart, kidney, lung, gastrointestinal tract, peripheral white blood cells, and other cells. In addition, the diseases associated with a disturbance of fatty acid oxidation (FAO) in the liver, heart, kidney, lung, alimentary tract, and other organs or cells are presented. Special attention was paid to abnormalities of FAO in cancer cells and the diseases caused by mutations in gene-encoding enzymes involved in FAO. Finally, issues related to α- and ω- fatty acid oxidation are discussed.
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Affiliation(s)
- Sylwia Szrok-Jurga
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (S.S.-J.); (J.T.); (A.H.)
| | - Aleksandra Czumaj
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Medical University of Gdansk, 80-211 Gdansk, Poland;
| | - Jacek Turyn
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (S.S.-J.); (J.T.); (A.H.)
| | - Areta Hebanowska
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (S.S.-J.); (J.T.); (A.H.)
| | - Julian Swierczynski
- Institue of Nursing and Medical Rescue, State University of Applied Sciences in Koszalin, 75-582 Koszalin, Poland;
| | - Tomasz Sledzinski
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Medical University of Gdansk, 80-211 Gdansk, Poland;
| | - Ewa Stelmanska
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (S.S.-J.); (J.T.); (A.H.)
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10
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Kavousi M, Bos MM, Barnes HJ, Lino Cardenas CL, Wong D, Lu H, Hodonsky CJ, Landsmeer LPL, Turner AW, Kho M, Hasbani NR, de Vries PS, Bowden DW, Chopade S, Deelen J, Benavente ED, Guo X, Hofer E, Hwang SJ, Lutz SM, Lyytikäinen LP, Slenders L, Smith AV, Stanislawski MA, van Setten J, Wong Q, Yanek LR, Becker DM, Beekman M, Budoff MJ, Feitosa MF, Finan C, Hilliard AT, Kardia SLR, Kovacic JC, Kral BG, Langefeld CD, Launer LJ, Malik S, Hoesein FAAM, Mokry M, Schmidt R, Smith JA, Taylor KD, Terry JG, van der Grond J, van Meurs J, Vliegenthart R, Xu J, Young KA, Zilhão NR, Zweiker R, Assimes TL, Becker LC, Bos D, Carr JJ, Cupples LA, de Kleijn DPV, de Winther M, den Ruijter HM, Fornage M, Freedman BI, Gudnason V, Hingorani AD, Hokanson JE, Ikram MA, Išgum I, Jacobs DR, Kähönen M, Lange LA, Lehtimäki T, Pasterkamp G, Raitakari OT, Schmidt H, Slagboom PE, Uitterlinden AG, Vernooij MW, Bis JC, Franceschini N, Psaty BM, Post WS, Rotter JI, Björkegren JLM, O'Donnell CJ, Bielak LF, Peyser PA, Malhotra R, van der Laan SW, Miller CL. Multi-ancestry genome-wide study identifies effector genes and druggable pathways for coronary artery calcification. Nat Genet 2023; 55:1651-1664. [PMID: 37770635 PMCID: PMC10601987 DOI: 10.1038/s41588-023-01518-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 08/29/2023] [Indexed: 09/30/2023]
Abstract
Coronary artery calcification (CAC), a measure of subclinical atherosclerosis, predicts future symptomatic coronary artery disease (CAD). Identifying genetic risk factors for CAC may point to new therapeutic avenues for prevention. Currently, there are only four known risk loci for CAC identified from genome-wide association studies (GWAS) in the general population. Here we conducted the largest multi-ancestry GWAS meta-analysis of CAC to date, which comprised 26,909 individuals of European ancestry and 8,867 individuals of African ancestry. We identified 11 independent risk loci, of which eight were new for CAC and five had not been reported for CAD. These new CAC loci are related to bone mineralization, phosphate catabolism and hormone metabolic pathways. Several new loci harbor candidate causal genes supported by multiple lines of functional evidence and are regulators of smooth muscle cell-mediated calcification ex vivo and in vitro. Together, these findings help refine the genetic architecture of CAC and extend our understanding of the biological and potential druggable pathways underlying CAC.
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Affiliation(s)
- Maryam Kavousi
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Maxime M Bos
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Hanna J Barnes
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Christian L Lino Cardenas
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Doris Wong
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Haojie Lu
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Chani J Hodonsky
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Lennart P L Landsmeer
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Adam W Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Minjung Kho
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Graduate School of Data Science, Seoul National University, Seoul, Republic of Korea
| | - Natalie R Hasbani
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Center at Houston, Houston, TX, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Center at Houston, Houston, TX, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Sandesh Chopade
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
- University College London British Heart Foundation Research Accelerator Centre, London, UK
| | - Joris Deelen
- Biomedical Data Sciences, Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Max Planck Institute for Biology of Aging, Cologne, Germany
| | - Ernest Diez Benavente
- Laboratory of Experimental Cardiology, Division of Heart and Lungs, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Edith Hofer
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University of Graz, Graz, Austria
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | | | - Sharon M Lutz
- Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, MA, USA
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Lotte Slenders
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Albert V Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Icelandic Heart Association, Kopavogur, Iceland
| | - Maggie A Stanislawski
- Department of Biomedical Informatics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Jessica van Setten
- Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Quenna Wong
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Lisa R Yanek
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Diane M Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marian Beekman
- Biomedical Data Sciences, Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Matthew J Budoff
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Mary F Feitosa
- Department of Genetics, Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO, USA
| | - Chris Finan
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
- University College London British Heart Foundation Research Accelerator Centre, London, UK
- Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | | | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jason C Kovacic
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
- St Vincent's Clinical School, University of NSW, Sydney, New South Wales, Australia
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Brian G Kral
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences and Data Science, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Shaista Malik
- Susan Samueli Integrative Health Institute, Department of Medicine, University of California Irvine, Irvine, CA, USA
| | | | - Michal Mokry
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Laboratory of Experimental Cardiology, Division of Heart and Lungs, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Reinhold Schmidt
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University of Graz, Graz, Austria
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - James G Terry
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeroen van der Grond
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Joyce van Meurs
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rozemarijn Vliegenthart
- Department of Radiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jianzhao Xu
- Department of Biochemistry, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Kendra A Young
- Department of Epidemiology, University of Colorado, Anschutz Medical Campus, Denver, CO, USA
| | | | - Robert Zweiker
- Department of Internal Medicine, Division of Cardiology, Medical University of Graz, Graz, Austria
| | - Themistocles L Assimes
- VA Palo Alto Healthcare System, Palo Alto, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Lewis C Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel Bos
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - J Jeffrey Carr
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - L Adrienne Cupples
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Dominique P V de Kleijn
- Department of Vascular Surgery, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Menno de Winther
- Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam Cardiovascular Sciences: Atherosclerosis and Ischemic syndromes, Amsterdam Infection and Immunity: Inflammatory diseases, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Hester M den Ruijter
- Laboratory of Experimental Cardiology, Division of Heart and Lungs, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Myriam Fornage
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Barry I Freedman
- Department of Internal Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, School of Public Health, University of Iceland, Reykjavik, Iceland
| | - Aroon D Hingorani
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
- University College London British Heart Foundation Research Accelerator Centre, London, UK
| | - John E Hokanson
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ivana Išgum
- Image Sciences Institute, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Biomedical Engineering and Physics, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - David R Jacobs
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Leslie A Lange
- Department of Biomedical Informatics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Gerard Pasterkamp
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Olli T Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Helena Schmidt
- Gottfried Schatz Research Center (for Cell Signaling, Metabolism and Aging), Medical University of Graz, Graz, Austria
| | - P Eline Slagboom
- Biomedical Data Sciences, Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Meike W Vernooij
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Vascular Surgery, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Departments of Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Wendy S Post
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Medicine, Integrated Cardio Metabolic Centre, Karolinska Institutet, Huddinge, Sweden
| | - Christopher J O'Donnell
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Cardiology Section, Department of Medicine, Veterans Affairs Boston Healthcare System, Boston, MA, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Rajeev Malhotra
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sander W van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Clint L Miller
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA.
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11
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Arruda AL, Hartley A, Katsoula G, Smith GD, Morris AP, Zeggini E. Genetic underpinning of the comorbidity between type 2 diabetes and osteoarthritis. Am J Hum Genet 2023; 110:1304-1318. [PMID: 37433298 PMCID: PMC10432145 DOI: 10.1016/j.ajhg.2023.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/13/2023] Open
Abstract
Multimorbidity is a rising public health challenge with important implications for health management and policy. The most common multimorbidity pattern is the combination of cardiometabolic and osteoarticular diseases. Here, we study the genetic underpinning of the comorbidity between type 2 diabetes and osteoarthritis. We find genome-wide genetic correlation between the two diseases and robust evidence for association-signal colocalization at 18 genomic regions. We integrate multi-omics and functional information to resolve the colocalizing signals and identify high-confidence effector genes, including FTO and IRX3, which provide proof-of-concept insights into the epidemiologic link between obesity and both diseases. We find enrichment for lipid metabolism and skeletal formation pathways for signals underpinning the knee and hip osteoarthritis comorbidities with type 2 diabetes, respectively. Causal inference analysis identifies complex effects of tissue-specific gene expression on comorbidity outcomes. Our findings provide insights into the biological basis for the type 2 diabetes-osteoarthritis disease co-occurrence.
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Affiliation(s)
- Ana Luiza Arruda
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany; Munich School of Data Science, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany; Technical University of Munich (TUM), School of Medicine, Graduate School of Experimental Medicine, 81675 Munich, Germany
| | - April Hartley
- MRC Integrative Epidemiology Unit, University of Bristol, BS8 2BN Bristol, UK
| | - Georgia Katsoula
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany; Technical University of Munich (TUM), School of Medicine, Graduate School of Experimental Medicine, 81675 Munich, Germany
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, BS8 2BN Bristol, UK
| | - Andrew P Morris
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany; Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, M13 9PT Manchester, UK
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany; TUM School of Medicine, Technical University Munich and Klinikum Rechts der Isar, 81675 Munich, Germany.
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12
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Lionikas A, Hernandez Cordero AI, Kilikevicius A, Carroll AM, Bewick GS, Bunger L, Ratkevicius A, Heisler LK, Harboe M, Oxvig C. Stanniocalcin-2 inhibits skeletal muscle growth and is upregulated in functional overload-induced hypertrophy. Physiol Rep 2023; 11:e15793. [PMID: 37568262 PMCID: PMC10510475 DOI: 10.14814/phy2.15793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
AIMS Stanniocalcin-2 (STC2) has recently been implicated in human muscle mass variability by genetic analysis. Biochemically, STC2 inhibits the proteolytic activity of the metalloproteinase PAPP-A, which promotes muscle growth by upregulating the insulin-like growth factor (IGF) axis. The aim was to examine if STC2 affects skeletal muscle mass and to assess how the IGF axis mediates muscle hypertrophy induced by functional overload. METHODS We compared muscle mass and muscle fiber morphology between Stc2-/- (n = 21) and wild-type (n = 15) mice. We then quantified IGF1, IGF2, IGF binding proteins -4 and -5 (IGFBP-4, IGFBP-5), PAPP-A and STC2 in plantaris muscles of wild-type mice subjected to 4-week unilateral overload (n = 14). RESULTS Stc2-/- mice showed up to 10% larger muscle mass compared with wild-type mice. This increase was mediated by greater cross-sectional area of muscle fibers. Overload increased plantaris mass and components of the IGF axis, including quantities of IGF1 (by 2.41-fold, p = 0.0117), IGF2 (1.70-fold, p = 0.0461), IGFBP-4 (1.48-fold, p = 0.0268), PAPP-A (1.30-fold, p = 0.0154) and STC2 (1.28-fold, p = 0.019). CONCLUSION Here we provide evidence that STC2 is an inhibitor of muscle growth upregulated, along with other components of the IGF axis, during overload-induced muscle hypertrophy.
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Affiliation(s)
- Arimantas Lionikas
- School of Medicine, Medical Sciences and NutritionUniversity of AberdeenAberdeenUK
| | - Ana I. Hernandez Cordero
- Centre for Heart Lung InnovationUniversity of British Columbia, St. Paul's HospitalVancouverCanada
| | - Audrius Kilikevicius
- Department of Health Promotion and RehabilitationLithuanian Sports UniversityKaunasLithuania
| | - Andrew M. Carroll
- The New Zealand Institute for Plant & Food Research LimitedPalmerston NorthNew Zealand
| | - Guy S. Bewick
- School of Medicine, Medical Sciences and NutritionUniversity of AberdeenAberdeenUK
| | - Lutz Bunger
- Animal Genetics Company (AnGeCo)EdinburghScotland
| | - Aivaras Ratkevicius
- Department of Health Promotion and RehabilitationLithuanian Sports UniversityKaunasLithuania
| | - Lora K. Heisler
- School of Medicine, Medical Sciences and NutritionUniversity of AberdeenAberdeenUK
| | - Mette Harboe
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Claus Oxvig
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
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13
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Grahnemo L, Nethander M, Coward E, Gabrielsen ME, Sree S, Billod JM, Sjögren K, Engstrand L, Dekkers KF, Fall T, Langhammer A, Hveem K, Ohlsson C. Identification of three bacterial species associated with increased appendicular lean mass: the HUNT study. Nat Commun 2023; 14:2250. [PMID: 37080991 PMCID: PMC10119287 DOI: 10.1038/s41467-023-37978-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 04/05/2023] [Indexed: 04/22/2023] Open
Abstract
Appendicular lean mass (ALM) associates with mobility and bone mineral density (BMD). While associations between gut microbiota composition and ALM have been reported, previous studies rely on relatively small sample sizes. Here, we determine the associations between prevalent gut microbes and ALM in large discovery and replication cohorts with information on relevant confounders within the population-based Norwegian HUNT cohort (n = 5196, including women and men). We show that the presence of three bacterial species - Coprococcus comes, Dorea longicatena, and Eubacterium ventriosum - are reproducibly associated with higher ALM. When combined into an anabolic species count, participants with all three anabolic species have 0.80 kg higher ALM than those without any. In an exploratory analysis, the anabolic species count is positively associated with femoral neck and total hip BMD. We conclude that the anabolic species count may be used as a marker of ALM and BMD. The therapeutic potential of these anabolic species to prevent sarcopenia and osteoporosis needs to be determined.
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Affiliation(s)
- Louise Grahnemo
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
| | - Maria Nethander
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Eivind Coward
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Maiken Elvestad Gabrielsen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Satya Sree
- Bio-Me, Oslo Science Park, Gaustadalléen 21, N-0349, Oslo, Norway
| | - Jean-Marc Billod
- Bio-Me, Oslo Science Park, Gaustadalléen 21, N-0349, Oslo, Norway
| | - Klara Sjögren
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Karolinska Hospital, Biomedicum A8, Solnavägen 9, 171 65, Stockholm, Sweden
| | - Koen F Dekkers
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tove Fall
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Arnulf Langhammer
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Claes Ohlsson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Drug Treatment, Gothenburg, Sweden
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14
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Henrot P, Dupin I, Schilfarth P, Esteves P, Blervaque L, Zysman M, Gouzi F, Hayot M, Pomiès P, Berger P. Main Pathogenic Mechanisms and Recent Advances in COPD Peripheral Skeletal Muscle Wasting. Int J Mol Sci 2023; 24:ijms24076454. [PMID: 37047427 PMCID: PMC10095391 DOI: 10.3390/ijms24076454] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a worldwide prevalent respiratory disease mainly caused by tobacco smoke exposure. COPD is now considered as a systemic disease with several comorbidities. Among them, skeletal muscle dysfunction affects around 20% of COPD patients and is associated with higher morbidity and mortality. Although the histological alterations are well characterized, including myofiber atrophy, a decreased proportion of slow-twitch myofibers, and a decreased capillarization and oxidative phosphorylation capacity, the molecular basis for muscle atrophy is complex and remains partly unknown. Major difficulties lie in patient heterogeneity, accessing patients' samples, and complex multifactorial process including extrinsic mechanisms, such as tobacco smoke or disuse, and intrinsic mechanisms, such as oxidative stress, hypoxia, or systemic inflammation. Muscle wasting is also a highly dynamic process whose investigation is hampered by the differential protein regulation according to the stage of atrophy. In this review, we report and discuss recent data regarding the molecular alterations in COPD leading to impaired muscle mass, including inflammation, hypoxia and hypercapnia, mitochondrial dysfunction, diverse metabolic changes such as oxidative and nitrosative stress and genetic and epigenetic modifications, all leading to an impaired anabolic/catabolic balance in the myocyte. We recapitulate data concerning skeletal muscle dysfunction obtained in the different rodent models of COPD. Finally, we propose several pathways that should be investigated in COPD skeletal muscle dysfunction in the future.
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Affiliation(s)
- Pauline Henrot
- Centre de Recherche Cardio-Thoracique de Bordeaux, Univ. Bordeaux, U1045, F-33604 Pessac, France
- INSERM, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, CIC 1401, F-33604 Pessac, France
- CHU de Bordeaux, Service d'Exploration Fonctionnelle Respiratoire, CIC 1401, Service de Pneumologie, F-33604 Pessac, France
| | - Isabelle Dupin
- Centre de Recherche Cardio-Thoracique de Bordeaux, Univ. Bordeaux, U1045, F-33604 Pessac, France
- INSERM, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, CIC 1401, F-33604 Pessac, France
| | - Pierre Schilfarth
- Centre de Recherche Cardio-Thoracique de Bordeaux, Univ. Bordeaux, U1045, F-33604 Pessac, France
- INSERM, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, CIC 1401, F-33604 Pessac, France
- CHU de Bordeaux, Service d'Exploration Fonctionnelle Respiratoire, CIC 1401, Service de Pneumologie, F-33604 Pessac, France
| | - Pauline Esteves
- Centre de Recherche Cardio-Thoracique de Bordeaux, Univ. Bordeaux, U1045, F-33604 Pessac, France
- INSERM, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, CIC 1401, F-33604 Pessac, France
| | - Léo Blervaque
- PhyMedExp, INSERM-CNRS-Montpellier University, F-34090 Montpellier, France
| | - Maéva Zysman
- Centre de Recherche Cardio-Thoracique de Bordeaux, Univ. Bordeaux, U1045, F-33604 Pessac, France
- INSERM, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, CIC 1401, F-33604 Pessac, France
- CHU de Bordeaux, Service d'Exploration Fonctionnelle Respiratoire, CIC 1401, Service de Pneumologie, F-33604 Pessac, France
| | - Fares Gouzi
- PhyMedExp, INSERM-CNRS-Montpellier University, CHRU Montpellier, F-34090 Montpellier, France
| | - Maurice Hayot
- PhyMedExp, INSERM-CNRS-Montpellier University, CHRU Montpellier, F-34090 Montpellier, France
| | - Pascal Pomiès
- PhyMedExp, INSERM-CNRS-Montpellier University, F-34090 Montpellier, France
| | - Patrick Berger
- Centre de Recherche Cardio-Thoracique de Bordeaux, Univ. Bordeaux, U1045, F-33604 Pessac, France
- INSERM, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, CIC 1401, F-33604 Pessac, France
- CHU de Bordeaux, Service d'Exploration Fonctionnelle Respiratoire, CIC 1401, Service de Pneumologie, F-33604 Pessac, France
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15
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CPNE1 regulates myogenesis through the PERK-eIF2α pathway mediated by endoplasmic reticulum stress. Cell Tissue Res 2023; 391:545-560. [PMID: 36525128 PMCID: PMC9974702 DOI: 10.1007/s00441-022-03720-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022]
Abstract
Sarcopenia is characterized by a progressive reduction in muscle mass or muscle physiological function associated with aging, but the relevant molecular mechanisms are not clear. Here, we identify the role of the myogenesis modifier CPNE1 in sarcopenia. CPNE1 is upregulated in aged skeletal muscles and young skeletal muscle satellite cells with palmitate-induced atrophy. The overexpression of CPNE1 hinders proliferation and differentiation and increases muscle atrophy characteristics in young skeletal muscle-derived satellite cells. In addition, CPNE1 overexpression disrupts the balance of mitochondrial fusion and division and causes endoplasmic reticulum stress. We found that the effects of CPNE1 on mitochondrial function are dependent on the PERK/eIF2α/ATF4 pathway. The overexpression of CPNE1 in young muscles alters membrane lipid composition, reduces skeletal muscle fibrosis regeneration, and exercise capacity in mice. These effects were reversed by PERK inhibitor GSK2606414. Moreover, immunoprecipitation indicates that CPNE1 overexpression greatly increased the acetylation of PERK. Therefore, CPNE1 is an important modifier that drives mitochondrial homeostasis to regulate myogenic cell proliferation and differentiation via the PERK-eIF2α pathway, which could be a valuable target for age-related sarcopenia.
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16
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Identification and Characterization of Genomic Predictors of Sarcopenia and Sarcopenic Obesity Using UK Biobank Data. Nutrients 2023; 15:nu15030758. [PMID: 36771461 PMCID: PMC9920138 DOI: 10.3390/nu15030758] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/28/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The substantial decline in skeletal muscle mass, strength, and gait speed is a sign of severe sarcopenia, which may partly depend on genetic risk factors. So far, hundreds of genome-wide significant single nucleotide polymorphisms (SNPs) associated with handgrip strength, lean mass and walking pace have been identified in the UK Biobank cohort; however, their pleiotropic effects on all three phenotypes have not been investigated. By combining summary statistics of genome-wide association studies (GWAS) of handgrip strength, lean mass and walking pace, we have identified 78 independent SNPs (from 73 loci) associated with all three traits with consistent effect directions. Of the 78 SNPs, 55 polymorphisms were also associated with body fat percentage and 25 polymorphisms with type 2 diabetes (T2D), indicating that sarcopenia, obesity and T2D share many common risk alleles. Follow-up bioinformatic analysis revealed that sarcopenia risk alleles were associated with tiredness, falls in the last year, neuroticism, alcohol intake frequency, smoking, time spent watching television, higher salt, white bread, and processed meat intake; whereas protective alleles were positively associated with bone mineral density, serum testosterone, IGF1, and 25-hydroxyvitamin D levels, height, intelligence, cognitive performance, educational attainment, income, physical activity, ground coffee drinking and healthier diet (muesli, cereal, wholemeal or wholegrain bread, potassium, magnesium, cheese, oily fish, protein, water, fruit, and vegetable intake). Furthermore, the literature data suggest that single-bout resistance exercise may induce significant changes in the expression of 26 of the 73 implicated genes in m. vastus lateralis, which may partly explain beneficial effects of strength training in the prevention and treatment of sarcopenia. In conclusion, we have identified and characterized 78 SNPs associated with sarcopenia and 55 SNPs with sarcopenic obesity in European-ancestry individuals from the UK Biobank.
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17
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Venckunas T, Degens H. Genetic polymorphisms of muscular fitness in young healthy men. PLoS One 2022; 17:e0275179. [PMID: 36166425 PMCID: PMC9514622 DOI: 10.1371/journal.pone.0275179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022] Open
Abstract
The effects of genetic polymorphisms on muscle structure and function remain elusive. The present study tested for possible associations of 16 polymorphisms (across ten candidate genes) with fittness and skeletal muscle phenotypes in 17- to 37-year-old healthy Caucasian male endurance (n = 86), power/strength (n = 75) and team athletes (n = 60), and non-athletes (n = 218). Skeletal muscle function was measured with eight performance tests covering multiple aspects of muscular fitness. Along with body mass and height, the upper arm and limb girths, and maximal oxygen uptake were measured. Genotyping was conducted on DNA extracted from blood. Of the 16 polymorphisms studied, nine (spanning seven candidate genes and four gene families/signalling pathways) were independently associated with at least one skeletal muscle fitness measure (size or function, or both) measure and explained up to 4.1% of its variation. Five of the studied polymorphisms (activin- and adreno-receptors, as well as myosine light chain kinase 1) in a group of one to three combined with body height, age and/or group explained up to 20.4% of the variation of muscle function. ACVR1B (rs2854464) contributed 2.0–3.6% to explain up to 14.6% of limb proximal girths. The G allele (genotypes AG and GG) of the ACVR1B (rs2854464) polymorphism was significantly overrepresented among team (60.4%) and power (62.0%) athletes compared to controls (52.3%) and endurance athletes (39.2%), and G allele was also most consistently/frequently associated with muscle size and power. Overall, the investigated polymorphisms determined up to 4.1% of the variability of muscular fitness in healthy young humans.
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Affiliation(s)
- Tomas Venckunas
- Institute of Sport Science and Innovations, Lithuanian Sports University, Kaunas, Lithuania
- * E-mail:
| | - Hans Degens
- Institute of Sport Science and Innovations, Lithuanian Sports University, Kaunas, Lithuania
- Department of Life Sciences, Musculoskeletal Science and Sports Medicine Research Centre, Institute of Sport, Manchester Metropolitan University, Manchester, United Kingdom
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18
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Polygenic Models Partially Predict Muscle Size and Strength but Not Low Muscle Mass in Older Women. Genes (Basel) 2022; 13:genes13060982. [PMID: 35741744 PMCID: PMC9223182 DOI: 10.3390/genes13060982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/17/2022] [Accepted: 05/21/2022] [Indexed: 01/01/2023] Open
Abstract
Background: Heritability explains 45-82% of muscle mass and strength variation, yet polygenic models for muscle phenotypes in older women are scarce. Therefore, the objective of the present study was to (1) assess if total genotype predisposition score (GPSTOTAL) for a set of polymorphisms differed between older women with low and high muscle mass, and (2) utilise a data-driven GPS (GPSDD) to predict the variance in muscle size and strength-related phenotypes. Methods: In three-hundred 60- to 91-year-old Caucasian women (70.7 ± 5.7 years), skeletal muscle mass, biceps brachii thickness, vastus lateralis anatomical cross-sectional area (VLACSA), hand grip strength (HGS), and elbow flexion (MVCEF) and knee extension (MVCKE) maximum voluntary contraction were measured. Participants were classified as having low muscle mass if the skeletal muscle index (SMI) < 6.76 kg/m2 or relative skeletal muscle mass (%SMMr) < 22.1%. Genotyping was completed for 24 single-nucleotide polymorphisms (SNPs). GPSTOTAL was calculated from 23 SNPs and compared between the low and high muscle mass groups. A GPSDD was performed to identify the association of SNPs with other skeletal muscle phenotypes. Results: There was no significant difference in GPSTOTAL between low and high muscle mass groups, irrespective of classification based on SMI or %SMMr. The GPSDD model, using 23 selected SNPs, revealed that 13 SNPs were associated with at least one skeletal muscle phenotype: HIF1A rs11549465 was associated with four phenotypes and, in descending number of phenotype associations, ACE rs4341 with three; PTK2 rs7460 and CNTFR rs2070802 with two; and MTHFR rs17421511, ACVR1B rs10783485, CNTF rs1800169, MTHFR rs1801131, MTHFR rs1537516, TRHR rs7832552, MSTN rs1805086, COL1A1 rs1800012, and FTO rs9939609 with one phenotype. The GPSDD with age included as a predictor variable explained 1.7% variance of biceps brachii thickness, 12.5% of VLACSA, 19.0% of HGS, 8.2% of MVCEF, and 9.6% of MVCKE. Conclusions: In older women, GPSTOTAL did not differ between low and high muscle mass groups. However, GPSDD was associated with muscle size and strength phenotypes. Further advancement of polygenic models to understand skeletal muscle function during ageing might become useful in targeting interventions towards older adults most likely to lose physical independence.
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19
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St Pierre CL, Macias-Velasco JF, Wayhart JP, Yin L, Semenkovich CF, Lawson HA. Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression. Genome Res 2022; 32:1042-1057. [PMID: 35501130 PMCID: PMC9248887 DOI: 10.1101/gr.276193.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 04/14/2022] [Indexed: 12/03/2022]
Abstract
Allele-specific expression (ASE) is a phenomenon in which one allele is preferentially expressed over the other. Genetic and epigenetic factors cause ASE by altering the final composition of a gene's product, leading to expression imbalances that can have functional consequences on phenotypes. Environmental signals also impact allele-specific expression, but how they contribute to this cross talk remains understudied. Here, we explored how genotype, parent-of-origin, tissue, sex, and dietary fat simultaneously influence ASE biases. Male and female mice from a F1 reciprocal cross of the LG/J and SM/J strains were fed a high or low fat diet. We harnessed strain-specific variants to distinguish between two ASE classes: parent-of-origin-dependent (unequal expression based on parental origin) and sequence-dependent (unequal expression based on nucleotide identity). We present a comprehensive map of ASE patterns in 2853 genes across three tissues and nine environmental contexts. We found that both ASE classes are highly dependent on tissue and environmental context. They vary across metabolically relevant tissues, between males and females, and in response to dietary fat. We also found 45 genes with inconsistent ASE biases that switched direction across tissues and/or environments. Finally, we integrated ASE and QTL data from published intercrosses of the LG/J and SM/J strains. Our ASE genes are often enriched in QTLs for metabolic and musculoskeletal traits, highlighting how this orthogonal approach can prioritize candidate genes. Together, our results provide novel insights into how genetic, epigenetic, and environmental mechanisms govern allele-specific expression, which is an essential step toward deciphering the genotype-to-phenotype map.
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Affiliation(s)
| | | | | | - Li Yin
- Washington University in Saint Louis
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20
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Multi-omics research in sarcopenia: Current progress and future prospects. Ageing Res Rev 2022; 76:101576. [PMID: 35104630 DOI: 10.1016/j.arr.2022.101576] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 12/13/2021] [Accepted: 01/26/2022] [Indexed: 12/17/2022]
Abstract
Sarcopenia is a systemic disease with progressive and generalized skeletal muscle dysfunction defined by age-related low muscle mass, high content of muscle slow fibers, and low muscle function. Muscle phenotypes and sarcopenia risk are heritable; however, the genetic architecture and molecular mechanisms underlying sarcopenia remain largely unclear. In recent years, significant progress has been made in determining susceptibility loci using genome-wide association studies. In addition, recent advances in omics techniques, including genomics, epigenomics, transcriptomics, proteomics, and metabolomics, offer new opportunities to identify novel targets to help us understand the pathophysiology of sarcopenia. However, each individual technology cannot capture the entire view of the biological complexity of this disorder, while integrative multi-omics analyses may be able to reveal new insights. Here, we review the latest findings of multi-omics studies for sarcopenia and provide an in-depth summary of our current understanding of sarcopenia pathogenesis. Leveraging multi-omics data could give us a holistic understanding of sarcopenia etiology that may lead to new clinical applications. This review offers guidance and recommendations for fundamental research, innovative perspectives, and preventative and therapeutic interventions for sarcopenia.
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21
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Abstract
Sports genomics is the scientific discipline that focuses on the organization and function of the genome in elite athletes, and aims to develop molecular methods for talent identification, personalized exercise training, nutritional need and prevention of exercise-related diseases. It postulates that both genetic and environmental factors play a key role in athletic performance and related phenotypes. This update on the panel of genetic markers (DNA polymorphisms) associated with athlete status and soft-tissue injuries covers advances in research reported in recent years, including one whole genome sequencing (WGS) and four genome-wide association (GWAS) studies, as well as findings from collaborative projects and meta-analyses. At end of 2020, the total number of DNA polymorphisms associated with athlete status was 220, of which 97 markers have been found significant in at least two studies (35 endurance-related, 24 power-related, and 38 strength-related). Furthermore, 29 genetic markers have been linked to soft-tissue injuries in at least two studies. The most promising genetic markers include HFE rs1799945, MYBPC3 rs1052373, NFIA-AS2 rs1572312, PPARA rs4253778, and PPARGC1A rs8192678 for endurance; ACTN3 rs1815739, AMPD1 rs17602729, CPNE5 rs3213537, CKM rs8111989, and NOS3 rs2070744 for power; LRPPRC rs10186876, MMS22L rs9320823, PHACTR1 rs6905419, and PPARG rs1801282 for strength; and COL1A1 rs1800012, COL5A1 rs12722, COL12A1 rs970547, MMP1 rs1799750, MMP3 rs679620, and TIMP2 rs4789932 for soft-tissue injuries. It should be appreciated, however, that hundreds and even thousands of DNA polymorphisms are needed for the prediction of athletic performance and injury risk.
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22
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Alcina A, Fedetz M, Vidal-Cobo I, Andrés-León E, García-Sánchez MI, Barroso-Del-Jesus A, Eichau S, Gil-Varea E, Villar LM, Saiz A, Leyva L, Vandenbroeck K, Otaegui D, Izquierdo G, Comabella M, Urcelay E, Matesanz F. Identification of the genetic mechanism that associates L3MBTL3 to multiple sclerosis. Hum Mol Genet 2022; 31:2155-2163. [PMID: 35088080 PMCID: PMC9262392 DOI: 10.1093/hmg/ddac009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/19/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
Multiple sclerosis (MS) is a complex and demyelinating disease of the central nervous system. One of the challenges of the post-GWAS era is to understand the molecular basis of statistical associations to reveal gene networks and potential therapeutic targets. The L3MBTL3 locus has been associated with MS risk by GWAS. To identify the causal variant of the locus, we performed fine mapping in a cohort of 3440 MS patients and 1688 healthy controls. The variant that best explained the association was rs6569648 (P = 4.13E-10, OR = 0.71, 95% CI = 0.64-0.79), which tagged rs7740107, located in intron 7 of L3MBTL3. The rs7740107 (A/T) variant has been reported to be the best expression and splice quantitative trait locus (eQTL and sQTL) of the region in up to 35 human GTEx tissues. By sequencing RNA from blood of 17 MS patients and quantification by digital qPCR, we determined that this eQTL/sQTL originated from the expression of a novel short transcript starting in intron 7 near rs7740107. The short transcript was translated into three proteins starting at different translation initiation codons. These N-terminal truncated proteins lacked the region where L3MBTL3 interacts with the transcriptional regulator RBPJ (Recombination Signal Binding Protein for Immunoglobulin Kappa J Region) which, in turn, regulates the Notch signaling pathway. Our data and other functional studies suggest that the genetic mechanism underlying the MS association of rs7740107 affects not only the expression of L3MBTL3 isoforms, but might also involve the Notch signaling pathway.
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Affiliation(s)
- Antonio Alcina
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas (IPBLN-CSIC) 18016 Granada, Spain
| | - Maria Fedetz
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas (IPBLN-CSIC) 18016 Granada, Spain
| | - Isabel Vidal-Cobo
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas (IPBLN-CSIC) 18016 Granada, Spain
| | - Eduardo Andrés-León
- Bioinformatic Unit, Instituto de Parasitología y Biomedicina López Neyra (IPBLN-CSIC), Granada, Spain
| | - Maria-Isabel García-Sánchez
- UGC Neurología. Nodo Hospital Universitario Virgen Macarena, Biobanco del Sistema Sanitario Público de Andalucía, Sevilla, (Spain)
| | - Alicia Barroso-Del-Jesus
- Genomics Unit, Instituto de Parasitología y Biomedicina López Neyra (IPBLN-CSIC), Granada, Spain
| | - Sara Eichau
- UGC Neurología. Hospital Universitario Virgen Macarena, Sevilla, Spain
| | - Elia Gil-Varea
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat). Institut de Recerca Vall d'Hebron (VHIR). Hospital Universitari Vall d'Hebron. Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Luisa-Maria Villar
- Departments of Immunology, Hospital Ramon y Cajal, (IRYCIS), Madrid, Spain
| | - Albert Saiz
- Servicio de Neurología, Hospital Clinic and Institut d'Investigació Biomèdica Pi i Sunyer (IDIBAPS), Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
| | - Laura Leyva
- Instituto de Investigación Biomédica de Málaga-IBIMA, UGC Neurología, Hospital Regional Universitario de Málaga, 29010 Málaga, Spain
| | - Koen Vandenbroeck
- Inflammation & Biomarkers Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain.,IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - David Otaegui
- Neurosciences Area, Biodonostia Health Research Institute, 20014 San Sebastián, Spain
| | - Guillermo Izquierdo
- Multiple Sclerosis Unit, Neurology Service, Vithas Nisa Hospital, 41950 Seville, Spain
| | - Manuel Comabella
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat). Institut de Recerca Vall d'Hebron (VHIR). Hospital Universitari Vall d'Hebron. Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Elena Urcelay
- Lab. of Genetics of Complex Diseases, Hospital Clinico San Carlos, Instituto de Investigacion Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain
| | - Fuencisla Matesanz
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas (IPBLN-CSIC) 18016 Granada, Spain
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23
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Guo M, Xiang L, Yao J, Zhang J, Zhu S, Wang D, Liu C, Li G, Wang J, Gao Y, Xie C, Ma X, Xu L, Zhou J. Comprehensive Transcriptome Profiling of NAFLD- and NASH-Induced Skeletal Muscle Dysfunction. Front Endocrinol (Lausanne) 2022; 13:851520. [PMID: 35265044 PMCID: PMC8899658 DOI: 10.3389/fendo.2022.851520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD), characterized by extensive triglyceride accumulation in hepatocytes, may progress to nonalcoholic steatohepatitis (NASH) with liver fibrosis and inflammation and increase the risk of cirrhosis, cancer, and death. It has been reported that physical exercise is effective in ameliorating NAFLD and NASH, while skeletal muscle dysfunctions, including lipid deposition and weakness, are accompanied with NAFLD and NASH. However, the molecular characteristics and alterations in skeletal muscle in the progress of NAFLD and NASH remain unclear. In the present study, we provide a comprehensive analysis on the similarity and heterogeneity of quadriceps muscle in NAFLD and NASH mice models by RNA sequencing. Importantly, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway functional enrichment analysis revealed that NAFLD and NASH led to impaired glucose and lipid metabolism and deteriorated functionality in skeletal muscle. Besides this, we identified that myokines possibly mediate the crosstalk between muscles and other metabolic organs in pathological conditions. Overall, our analysis revealed a comprehensive understanding of the molecular signature of skeletal muscles in NAFLD and NASH, thus providing a basis for physical exercise as an intervention against liver diseases.
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Affiliation(s)
- Mingwei Guo
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Liping Xiang
- Department of Endocrinology and Metabolism, Shanghai Clinical Center for Diabetes, Shanghai Diabetes Institute, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Jing Yao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jun Zhang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Shuangshuang Zhu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Dongmei Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Caizhi Liu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Guoqiang Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jiawen Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yuqing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Cen Xie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xinran Ma
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
- *Correspondence: Xinran Ma, ; Lingyan Xu, ; Jian Zhou,
| | - Lingyan Xu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
- *Correspondence: Xinran Ma, ; Lingyan Xu, ; Jian Zhou,
| | - Jian Zhou
- Department of Endocrinology and Metabolism, Shanghai Clinical Center for Diabetes, Shanghai Diabetes Institute, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
- *Correspondence: Xinran Ma, ; Lingyan Xu, ; Jian Zhou,
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24
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Tang H, Pang P, Qin Z, Zhao Z, Wu Q, Song S, Li F. The CPNE Family and Their Role in Cancers. Front Genet 2021; 12:689097. [PMID: 34367247 PMCID: PMC8345009 DOI: 10.3389/fgene.2021.689097] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/21/2021] [Indexed: 12/13/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. Despite significant advances in cancer research and treatment, the overall prognosis of lung cancer patients remains poor. Therefore, the identification for novel therapeutic targets is critical for the diagnosis and treatment of lung cancer. CPNEs (copines) are a family of membrane-bound proteins that are highly conserved, soluble, ubiquitous, calcium dependent in a variety of eukaryotes. Emerging evidences have also indicated CPNE family members are involved in cancer development and progression as well. However, the expression patterns and clinical roles in cancer have not yet been well understood. In this review, we summarize recent advances concerning CPNE family members and provide insights into new potential mechanism involved in cancer development.
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Affiliation(s)
- Haicheng Tang
- Department of Respiratory and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Pei Pang
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhu Qin
- Department of Respiratory and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Zhangyan Zhao
- Department of Respiratory and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Qingguo Wu
- Department of Respiratory and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Shu Song
- Department of Pathology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Feng Li
- Department of Respiratory and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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25
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Arora D, Srikanth K, Lee J, Lee D, Park N, Wy S, Kim H, Park JE, Chai HH, Lim D, Cho IC, Kim J, Park W. Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon. Sci Rep 2021; 11:7219. [PMID: 33785872 PMCID: PMC8009959 DOI: 10.1038/s41598-021-86683-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/12/2021] [Indexed: 02/01/2023] Open
Abstract
Pig as a food source serves daily dietary demand to a wide population around the world. Preference of meat depends on various factors with muscle play the central role. In this regards, selective breeding abled us to develop "Nanchukmacdon" a pig breeds with an enhanced variety of meat and high fertility rate. To identify genomic regions under selection we performed whole-genome resequencing, transcriptome, and whole-genome bisulfite sequencing from Nanchukmacdon muscles samples and used published data for three other breeds such as Landrace, Duroc, Jeju native pig and analyzed the functional characterization of candidate genes. In this study, we present a comprehensive approach to identify candidate genes by using multi-omics approaches. We performed two different methods XP-EHH, XP-CLR to identify traces of artificial selection for traits of economic importance. Moreover, RNAseq analysis was done to identify differentially expressed genes in the crossed breed population. Several genes (UGT8, ZGRF1, NDUFA10, EBF3, ELN, UBE2L6, NCALD, MELK, SERP2, GDPD5, and FHL2) were identified as selective sweep and differentially expressed in muscles related pathways. Furthermore, nucleotide diversity analysis revealed low genetic diversity in Nanchukmacdon for identified genes in comparison to related breeds and whole-genome bisulfite sequencing data shows the critical role of DNA methylation pattern in identified genes that leads to enhanced variety of meat. This work demonstrates a way to identify the molecular signature and lays a foundation for future genomic enabled pig breeding.
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Affiliation(s)
- Devender Arora
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea
| | - Krishnamoorthy Srikanth
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea ,grid.5386.8000000041936877XDepartment of Animal Science, Cornell University, Ithaca, NY 14853 USA
| | - Jongin Lee
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Daehwan Lee
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Nayoung Park
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Suyeon Wy
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Hyeonji Kim
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Jong-Eun Park
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea
| | - Han-Ha Chai
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea
| | - Dajeong Lim
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea
| | - In-Cheol Cho
- grid.484502.f0000 0004 5935 1171Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju, 63242 Korea
| | - Jaebum Kim
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Woncheoul Park
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea
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26
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Aguirre M, Tanigawa Y, Venkataraman GR, Tibshirani R, Hastie T, Rivas MA. Polygenic risk modeling with latent trait-related genetic components. Eur J Hum Genet 2021; 29:1071-1081. [PMID: 33558700 DOI: 10.1038/s41431-021-00813-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 12/26/2020] [Accepted: 01/14/2021] [Indexed: 02/06/2023] Open
Abstract
Polygenic risk models have led to significant advances in understanding complex diseases and their clinical presentation. While polygenic risk scores (PRS) can effectively predict outcomes, they do not generally account for disease subtypes or pathways which underlie within-trait diversity. Here, we introduce a latent factor model of genetic risk based on components from Decomposition of Genetic Associations (DeGAs), which we call the DeGAs polygenic risk score (dPRS). We compute DeGAs using genetic associations for 977 traits and find that dPRS performs comparably to standard PRS while offering greater interpretability. We show how to decompose an individual's genetic risk for a trait across DeGAs components, with examples for body mass index (BMI) and myocardial infarction (heart attack) in 337,151 white British individuals in the UK Biobank, with replication in a further set of 25,486 non-British white individuals. We find that BMI polygenic risk factorizes into components related to fat-free mass, fat mass, and overall health indicators like physical activity. Most individuals with high dPRS for BMI have strong contributions from both a fat-mass component and a fat-free mass component, whereas a few "outlier" individuals have strong contributions from only one of the two components. Overall, our method enables fine-scale interpretation of the drivers of genetic risk for complex traits.
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Affiliation(s)
- Matthew Aguirre
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, CA, USA.,Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Yosuke Tanigawa
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, CA, USA
| | - Guhan Ram Venkataraman
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, CA, USA
| | - Rob Tibshirani
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, CA, USA.,Department of Statistics, Stanford University, Stanford, CA, USA
| | - Trevor Hastie
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, CA, USA.,Department of Statistics, Stanford University, Stanford, CA, USA
| | - Manuel A Rivas
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, CA, USA.
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27
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Ahisar Y, Thanassoulis G, Huang KN, Ohayon SM, Afilalo J. Intersecting Genetics of Frailty and Cardiovascular Disease. J Nutr Health Aging 2021; 25:1023-1027. [PMID: 34545923 DOI: 10.1007/s12603-021-1673-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVES To determine the genetic correlates of physical frailty and sarcopenia, focusing on single nucleotide polymorphisms (SNPs) in genome-wide association studies (GWAS), and to explore the genetic overlap of frailty with cardiovascular disease (CVD) and its risk factors. METHODS PubMed was systematically searched for GWAS studies investigating the association between SNPs and objective measures of physical frailty or sarcopenia. SNPs were retained if they were associated with one of the phenotypes of interest by a p-value of 5.0x10-8 or less. RESULTS Ten studies were included, with a total of 237 SNPs in 181 genes being associated with physical frailty or sarcopenia; as measured by handgrip strength or lean (muscle) mass. These genes were cross-referenced in the GWAS Catalog, and many of them were found to be associated with CVD or metabolic syndrome. CONCLUSIONS Evidence from GWAS has shown that frailty is associated with common genetic polymorphisms. Many of these polymorphisms have been implicated in CVD, supporting the hypothesis of a shared pathophysiology between these entities. Future studies are eagerly anticipated to map out the mechanistic links and discover therapeutic targets and novel biomarkers for frailty.
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Affiliation(s)
- Y Ahisar
- Jonathan Afilalo, MD, MSc, FACC, FRCPC, Associate Professor, McGill University, Director, Geriatric Cardiology Fellowship Program, Jewish General Hospital, 3755 Cote Ste Catherine Rd, E-222, Montreal, QC H3T 1E2, Phone: (514) 340-7540 | Fax: (514) 340-7534,
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28
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Yaghootkar H, Zhang Y, Spracklen CN, Karaderi T, Huang LO, Bradfield J, Schurmann C, Fine RS, Preuss MH, Kutalik Z, Wittemans LBL, Lu Y, Metz S, Willems SM, Li-Gao R, Grarup N, Wang S, Molnos S, Sandoval-Zárate AA, Nalls MA, Lange LA, Haesser J, Guo X, Lyytikäinen LP, Feitosa MF, Sitlani CM, Venturini C, Mahajan A, Kacprowski T, Wang CA, Chasman DI, Amin N, Broer L, Robertson N, Young KL, Allison M, Auer PL, Blüher M, Borja JB, Bork-Jensen J, Carrasquilla GD, Christofidou P, Demirkan A, Doege CA, Garcia ME, Graff M, Guo K, Hakonarson H, Hong J, Ida Chen YD, Jackson R, Jakupović H, Jousilahti P, Justice AE, Kähönen M, Kizer JR, Kriebel J, LeDuc CA, Li J, Lind L, Luan J, Mackey DA, Mangino M, Männistö S, Martin Carli JF, Medina-Gomez C, Mook-Kanamori DO, Morris AP, de Mutsert R, Nauck M, Prokic I, Pennell CE, Pradhan AD, Psaty BM, Raitakari OT, Scott RA, Skaaby T, Strauch K, Taylor KD, Teumer A, Uitterlinden AG, Wu Y, Yao J, Walker M, North KE, Kovacs P, Ikram MA, van Duijn CM, Ridker PM, Lye S, Homuth G, Ingelsson E, Spector TD, McKnight B, Province MA, Lehtimäki T, Adair LS, Rotter JI, Reiner AP, Wilson JG, Harris TB, Ripatti S, Grallert H, Meigs JB, Salomaa V, Hansen T, Willems van Dijk K, Wareham NJ, Grant SFA, Langenberg C, Frayling TM, Lindgren CM, Mohlke KL, Leibel RL, Loos RJF, Kilpeläinen TO. Genetic Studies of Leptin Concentrations Implicate Leptin in the Regulation of Early Adiposity. Diabetes 2020; 69:2806-2818. [PMID: 32917775 PMCID: PMC7679778 DOI: 10.2337/db20-0070] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 09/09/2020] [Indexed: 02/02/2023]
Abstract
Leptin influences food intake by informing the brain about the status of body fat stores. Rare LEP mutations associated with congenital leptin deficiency cause severe early-onset obesity that can be mitigated by administering leptin. However, the role of genetic regulation of leptin in polygenic obesity remains poorly understood. We performed an exome-based analysis in up to 57,232 individuals of diverse ancestries to identify genetic variants that influence adiposity-adjusted leptin concentrations. We identify five novel variants, including four missense variants, in LEP, ZNF800, KLHL31, and ACTL9, and one intergenic variant near KLF14. The missense variant Val94Met (rs17151919) in LEP was common in individuals of African ancestry only, and its association with lower leptin concentrations was specific to this ancestry (P = 2 × 10-16, n = 3,901). Using in vitro analyses, we show that the Met94 allele decreases leptin secretion. We also show that the Met94 allele is associated with higher BMI in young African-ancestry children but not in adults, suggesting that leptin regulates early adiposity.
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Affiliation(s)
- Hanieh Yaghootkar
- Genetics of Complex Traits, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, U.K.
- Division of Medical Sciences, Department of Health Sciences, Luleå University of Technology, Luleå, Sweden
- Research Centre for Optimal Health, School of Life Sciences, University of Westminster, London, U.K
| | - Yiying Zhang
- Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, NY
| | - Cassandra N Spracklen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst, Amherst, MA
| | - Tugce Karaderi
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Department of Biological Sciences, Faculty of Arts and Sciences, Eastern Mediterranean University, Famagusta, Cyprus
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- DTU Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Lam Opal Huang
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan Bradfield
- Center for Applied Genomics, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA
- Quantinuum Research LLC, San Diego, CA
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Rebecca S Fine
- Department of Genetics, Harvard Medical School, Boston, MA
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Zoltan Kutalik
- Genetics of Complex Traits, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, U.K
- Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Laura B L Wittemans
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- MRC Epidemiology Unit, University of Cambridge, Cambridge, U.K
| | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, and Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Sophia Metz
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sara M Willems
- MRC Epidemiology Unit, University of Cambridge, Cambridge, U.K
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Shuai Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Sophie Molnos
- German Center for Diabetes Research, München-Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, München-Neuherberg, Germany
| | | | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD
- Data Tecnica International, Glen Echo, MD
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado-Denver, Denver, CO
| | - Jeffrey Haesser
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Colleen M Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
| | - Cristina Venturini
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, U.K
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, U.K
| | - Tim Kacprowski
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Carol A Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Linda Broer
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Neil Robertson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, U.K
| | - Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Matthew Allison
- Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, CA
| | - Paul L Auer
- Joseph J. Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI
| | - Matthias Blüher
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Judith B Borja
- Office of Population Studies Foundation, Inc., Cebu City, Philippines
- Department of Nutrition and Dietetics, University of San Carlos, Cebu City, Philippines
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Germán D Carrasquilla
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Ayse Demirkan
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Claudia A Doege
- Department of Pathology and Cell Biology, Columbia University, New York, NY
| | - Melissa E Garcia
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Bethesda, MD
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Carolina Center for Genome Sciences, Chapel Hill, NC
| | - Kaiying Guo
- Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, NY
| | - Hakon Hakonarson
- Center for Applied Genomics, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jaeyoung Hong
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Rebecca Jackson
- Division of Endocrinology, Diabetes, and Metabolism, Ohio State University, Columbus, OH
| | - Hermina Jakupović
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pekka Jousilahti
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Anne E Justice
- Center for Biomedical and Translational Informatics, Geisinger, Danville, PA
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
- Department of Clinical Physiology, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jorge R Kizer
- Cardiology Section, San Francisco Veterans Affairs Health Care System, University of California San Francisco, San Francisco, CA
- Departments of Medicine and Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA
| | - Jennifer Kriebel
- German Center for Diabetes Research, München-Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, München-Neuherberg, Germany
| | - Charles A LeDuc
- Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, NY
| | - Jin Li
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Palo Alto, CA
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge, Cambridge, U.K
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, The University of Western Australia, Perth, West Australia, Australia
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, U.K
- NIHR Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, U.K
| | - Satu Männistö
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Jayne F Martin Carli
- Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, NY
| | - Carolina Medina-Gomez
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, the Netherlands
| | - Andrew P Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Department of Biostatistics, University of Liverpool, Liverpool, U.K
- Division of Musculoskeletal and Dermatological Sciences, University of Manchester, Manchester, U.K
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Matthias Nauck
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Ivana Prokic
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Craig E Pennell
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Arund D Pradhan
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Epidemiology, Medicine, and Health Services, University of Washington, Seattle, WA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA
| | - Olli T Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, Turku University Hospital, Turku, Finland
| | - Robert A Scott
- MRC Epidemiology Unit, University of Cambridge, Cambridge, U.K
| | - Tea Skaaby
- Center for Clinical Research and Disease Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Chair of Genetic Epidemiology, Insitute of Medical Information Processing, Biometry, and Epidemiology (IBE), Faculty of Medicine, Ludwig Maximilian University Munich, München, Germany
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Alexander Teumer
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Andre G Uitterlinden
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Ying Wu
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Mark Walker
- Institute of Cellular Medicine (Diabetes), Newcastle University, Newcastle upon Tyne, U.K
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Stephen Lye
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Erik Ingelsson
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Palo Alto, CA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Palo Alto, CA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA
- Molecular Epidemiology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, U.K
| | - Barbara McKnight
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Michael A Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Linda S Adair
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Alexander P Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS
| | - Tamara B Harris
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Bethesda, MD
| | - Samuli Ripatti
- Broad Institute of MIT and Harvard, Cambridge, MA
- Institute for Molecular Medicine Finland, Helsinki, Finland
- Public Health, University of Helsinki, Helsinki, Finland
| | - Harald Grallert
- German Center for Diabetes Research, München-Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, München-Neuherberg, Germany
| | - James B Meigs
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Program in Population and Medical Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Veikko Salomaa
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ko Willems van Dijk
- Division of Endocrinology, Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden, the Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Struan F A Grant
- Center for Applied Genomics, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Center for Spatial and Functional Genomics, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA
- Division of Endocrinology and Diabetes, The Children's Hospital of Philadelphia, Philadelphia, PA
- Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | | | - Timothy M Frayling
- Genetics of Complex Traits, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, U.K
| | - Cecilia M Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Broad Institute of MIT and Harvard, Cambridge, MA
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Rudolph L Leibel
- Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, NY
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Tuomas O Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY
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29
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Timmins IR, Zaccardi F, Nelson CP, Franks PW, Yates T, Dudbridge F. Genome-wide association study of self-reported walking pace suggests beneficial effects of brisk walking on health and survival. Commun Biol 2020; 3:634. [PMID: 33128006 PMCID: PMC7599247 DOI: 10.1038/s42003-020-01357-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/01/2020] [Indexed: 12/19/2022] Open
Abstract
Walking is a simple form of exercise, widely promoted for its health benefits. Self-reported walking pace has been associated with a range of cardiorespiratory and cancer outcomes, and is a strong predictor of mortality. Here we perform a genome-wide association study of self-reported walking pace in 450,967 European ancestry UK Biobank participants. We identify 70 independent associated loci (P < 5 × 10-8), 11 of which are novel. We estimate the SNP-based heritability as 13.2% (s.e. = 0.21%), reducing to 8.9% (s.e. = 0.17%) with adjustment for body mass index. Significant genetic correlations are observed with cardiometabolic, respiratory and psychiatric traits, educational attainment and all-cause mortality. Mendelian randomization analyses suggest a potential causal link of increasing walking pace with a lower cardiometabolic risk profile. Given its low heritability and simple measurement, these findings suggest that self-reported walking pace is a pragmatic target for interventions aiming for general benefits on health.
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Affiliation(s)
- Iain R Timmins
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Christopher P Nelson
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK.,NIHR Leicester Biomedical Research Centre, University Hospitals of Leicester NHS Trust & University of Leicester, Leicester, UK
| | - Paul W Franks
- Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Thomas Yates
- Diabetes Research Centre, University of Leicester, Leicester, UK.,NIHR Leicester Biomedical Research Centre, University Hospitals of Leicester NHS Trust & University of Leicester, Leicester, UK
| | - Frank Dudbridge
- Department of Health Sciences, University of Leicester, Leicester, UK.
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30
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Pei YF, Liu YZ, Yang XL, Zhang H, Feng GJ, Wei XT, Zhang L. The genetic architecture of appendicular lean mass characterized by association analysis in the UK Biobank study. Commun Biol 2020; 3:608. [PMID: 33097823 PMCID: PMC7585446 DOI: 10.1038/s42003-020-01334-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 09/30/2020] [Indexed: 01/19/2023] Open
Abstract
Appendicular lean mass (ALM) is a heritable trait associated with loss of lean muscle mass and strength, or sarcopenia, but its genetic determinants are largely unknown. Here we conducted a genome-wide association study (GWAS) with 450,243 UK Biobank participants to uncover its genetic architecture. A total of 1059 conditionally independent variants from 799 loci were identified at the genome-wide significance level (p < 5 × 10-9), all of which were also significant at p < 5 × 10-5 in both sexes. These variants explained ~15.5% of the phenotypic variance, accounting for more than one quarter of the total ~50% GWAS-attributable heritability. There was no difference in genetic effect between sexes or among different age strata. Heritability was enriched in certain functional categories, such as conserved and coding regions, and in tissues related to the musculoskeletal system. Polygenic risk score prediction well distinguished participants with high and low ALM. The findings are important not only for lean mass but also for other complex diseases, such as type 2 diabetes, as ALM is shown to be a protective factor for type 2 diabetes.
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Affiliation(s)
- Yu-Fang Pei
- Department of Epidemiology and Health Statistics, School of Public Health, Medical College of Soochow University, Soochow, Jiangsu, PR China.
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College of Soochow University, Soochow, Jiangsu, PR China.
| | - Yao-Zhong Liu
- Department of Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Xiao-Lin Yang
- Department of Research, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Hong Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College of Soochow University, Soochow, Jiangsu, PR China
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Soochow, Jiangsu, PR China
| | - Gui-Juan Feng
- Department of Epidemiology and Health Statistics, School of Public Health, Medical College of Soochow University, Soochow, Jiangsu, PR China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College of Soochow University, Soochow, Jiangsu, PR China
| | - Xin-Tong Wei
- Department of Epidemiology and Health Statistics, School of Public Health, Medical College of Soochow University, Soochow, Jiangsu, PR China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College of Soochow University, Soochow, Jiangsu, PR China
| | - Lei Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College of Soochow University, Soochow, Jiangsu, PR China.
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Soochow, Jiangsu, PR China.
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31
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Chitre AS, Polesskaya O, Holl K, Gao J, Cheng R, Bimschleger H, Garcia Martinez A, George T, Gileta AF, Han W, Horvath A, Hughson A, Ishiwari K, King CP, Lamparelli A, Versaggi CL, Martin C, St Pierre CL, Tripi JA, Wang T, Chen H, Flagel SB, Meyer P, Richards J, Robinson TE, Palmer AA, Solberg Woods LC. Genome-Wide Association Study in 3,173 Outbred Rats Identifies Multiple Loci for Body Weight, Adiposity, and Fasting Glucose. Obesity (Silver Spring) 2020; 28:1964-1973. [PMID: 32860487 PMCID: PMC7511439 DOI: 10.1002/oby.22927] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 05/03/2020] [Accepted: 05/04/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Obesity is influenced by genetic and environmental factors. Despite the success of human genome-wide association studies, the specific genes that confer obesity remain largely unknown. The objective of this study was to use outbred rats to identify the genetic loci underlying obesity and related morphometric and metabolic traits. METHODS This study measured obesity-relevant traits, including body weight, body length, BMI, fasting glucose, and retroperitoneal, epididymal, and parametrial fat pad weight in 3,173 male and female adult N/NIH heterogeneous stock (HS) rats across three institutions, providing data for the largest rat genome-wide association study to date. Genetic loci were identified using a linear mixed model to account for the complex family relationships of the HS and using covariates to account for differences among the three phenotyping centers. RESULTS This study identified 32 independent loci, several of which contained only a single gene (e.g., Epha5, Nrg1, Klhl14) or obvious candidate genes (e.g., Adcy3, Prlhr). There were strong phenotypic and genetic correlations among obesity-related traits, and there was extensive pleiotropy at individual loci. CONCLUSIONS This study demonstrates the utility of HS rats for investigating the genetics of obesity-related traits across institutions and identify several candidate genes for future functional testing.
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Affiliation(s)
- Apurva S Chitre
- Department of Psychiatry, University of California, San Diego, La Jolla, California, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California, San Diego, La Jolla, California, USA
| | - Katie Holl
- Human and Molecular Genetic Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jianjun Gao
- Department of Psychiatry, University of California, San Diego, La Jolla, California, USA
| | - Riyan Cheng
- Department of Psychiatry, University of California, San Diego, La Jolla, California, USA
| | - Hannah Bimschleger
- Department of Psychiatry, University of California, San Diego, La Jolla, California, USA
| | - Angel Garcia Martinez
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Tony George
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, New York, USA
| | - Alexander F Gileta
- Department of Psychiatry, University of California, San Diego, La Jolla, California, USA
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Wenyan Han
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Aidan Horvath
- Department of Psychiatry, University of Michigan, Ann Arbor, Michigan, USA
| | - Alesa Hughson
- Department of Psychiatry, University of Michigan, Ann Arbor, Michigan, USA
| | - Keita Ishiwari
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, New York, USA
| | | | | | | | - Connor Martin
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, New York, USA
| | | | - Jordan A Tripi
- Department of Psychology, University at Buffalo, Buffalo, New York, USA
| | - Tengfei Wang
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Hao Chen
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Shelly B Flagel
- Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Paul Meyer
- Department of Psychology, University at Buffalo, Buffalo, New York, USA
| | - Jerry Richards
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, New York, USA
| | - Terry E Robinson
- Department of Psychology, University of Michigan, Ann Arbor, Michigan, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California, San Diego, La Jolla, California, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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32
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The Genetic Effect on Muscular Changes in an Older Population: A Follow-Up Study after One-Year Cessation of Structured Training. Genes (Basel) 2020; 11:genes11090968. [PMID: 32825595 PMCID: PMC7564970 DOI: 10.3390/genes11090968] [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: 07/30/2020] [Revised: 08/14/2020] [Accepted: 08/19/2020] [Indexed: 12/25/2022] Open
Abstract
Older adults lose muscle mass and strength at different speeds after the cessation of physical exercise, which might be genotype related. This study aimed to explore the genetic association with changes in muscle mass and strength one year after the cessation of structured training in an older population. Participants (n = 113, aged between 61 and 81 years) who performed one-year of combined fitness (n = 44) or whole-body vibration (n = 69) training were assessed one year after the cessation of the training. Whole-body skeletal muscle mass and knee strength were measured. Data-driven genetic predisposition scores (GPSs) were calculated and analysed in a general linear model with sex, age, body mass index and post-training values of skeletal muscle mass or muscle strength as covariates. Forty-six single nucleotide polymorphisms (SNPs) from an initial 170 muscle-related SNPs were identified as being significantly linked to muscular changes after cessation. Data-driven GPSs and over time muscular changes were significantly related (p < 0.01). Participants with higher GPSs had less muscular declines during the cessation period while data-driven GPSs accounted for 26–37% of the phenotypic variances. Our findings indicate that the loss of training benefits in older adults is partially genotype related.
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33
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Johnson EC, Chang Y, Agrawal A. An update on the role of common genetic variation underlying substance use disorders. CURRENT GENETIC MEDICINE REPORTS 2020; 8:35-46. [PMID: 33457110 PMCID: PMC7810203 DOI: 10.1007/s40142-020-00184-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
PURPOSE OF THE REVIEW Sample size increases have resulted in novel and replicable loci for substance use disorders (SUDs). We summarize some of the latest insights into SUD genetics and discuss some next steps in addiction genetics. RECENT FINDINGS Genome-wide association studies have substantiated the role of previously known variants (e.g., rs1229984 in ADH1B for alcohol) and identified several novel loci for alcohol, tobacco, cannabis, opioid and cocaine use disorders. SUDs are genetically correlated with psychiatric outcomes, while liability to substance use is inconsistently associated with these outcomes and more closely associated with lifestyle factors. Specific variant associations appear to differ somewhat across populations, although similar genes and systems are implicated. SUMMARY The next decade of human genetic studies of addiction should focus on expanding to non-European populations, consider pleiotropy across SUD and with other psychiatric disorders, and leverage human and cross-species functional data to elucidate the biological mechanisms underlying SUDs.
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Affiliation(s)
- Emma C Johnson
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO
| | - Yoonhoo Chang
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, Saint Louis, MO
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO
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34
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Zhou X, St Pierre CL, Gonzales NM, Zou J, Cheng R, Chitre AS, Sokoloff G, Palmer AA. Genome-Wide Association Study in Two Cohorts from a Multi-generational Mouse Advanced Intercross Line Highlights the Difficulty of Replication Due to Study-Specific Heterogeneity. G3 (BETHESDA, MD.) 2020; 10:951-965. [PMID: 31974095 PMCID: PMC7056977 DOI: 10.1534/g3.119.400763] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 10/17/2019] [Indexed: 12/12/2022]
Abstract
There has been extensive discussion of the "Replication Crisis" in many fields, including genome-wide association studies (GWAS). We explored replication in a mouse model using an advanced intercross line (AIL), which is a multigenerational intercross between two inbred strains. We re-genotyped a previously published cohort of LG/J x SM/J AIL mice (F34; n = 428) using a denser marker set and genotyped a new cohort of AIL mice (F39-43; n = 600) for the first time. We identified 36 novel genome-wide significant loci in the F34 and 25 novel loci in the F39-43 cohort. The subset of traits that were measured in both cohorts (locomotor activity, body weight, and coat color) showed high genetic correlations, although the SNP heritabilities were slightly lower in the F39-43 cohort. For this subset of traits, we attempted to replicate loci identified in either F34 or F39-43 in the other cohort. Coat color was robustly replicated; locomotor activity and body weight were only partially replicated, which was inconsistent with our power simulations. We used a random effects model to show that the partial replications could not be explained by Winner's Curse but could be explained by study-specific heterogeneity. Despite this heterogeneity, we performed a mega-analysis by combining F34 and F39-43 cohorts (n = 1,028), which identified four novel loci associated with locomotor activity and body weight. These results illustrate that even with the high degree of genetic and environmental control possible in our experimental system, replication was hindered by study-specific heterogeneity, which has broad implications for ongoing concerns about reproducibility.
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Affiliation(s)
- Xinzhu Zhou
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, 92092
| | - Celine L St Pierre
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110
| | | | - Jennifer Zou
- Department of Computer Science, University of California, Los Angeles, CA, 90095
| | | | | | - Greta Sokoloff
- Department of Psychological & Brain Sciences, University of Iowa, Iowa City, IO, 52242
| | - Abraham A Palmer
- Department of Psychiatry,
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92037 and
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35
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Pratt J, Boreham C, Ennis S, Ryan AW, De Vito G. Genetic Associations with Aging Muscle: A Systematic Review. Cells 2019; 9:E12. [PMID: 31861518 PMCID: PMC7016601 DOI: 10.3390/cells9010012] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 12/24/2022] Open
Abstract
The age-related decline in skeletal muscle mass, strength and function known as 'sarcopenia' is associated with multiple adverse health outcomes, including cardiovascular disease, stroke, functional disability and mortality. While skeletal muscle properties are known to be highly heritable, evidence regarding the specific genes underpinning this heritability is currently inconclusive. This review aimed to identify genetic variants known to be associated with muscle phenotypes relevant to sarcopenia. PubMed, Embase and Web of Science were systematically searched (from January 2004 to March 2019) using pre-defined search terms such as "aging", "sarcopenia", "skeletal muscle", "muscle strength" and "genetic association". Candidate gene association studies and genome wide association studies that examined the genetic association with muscle phenotypes in non-institutionalised adults aged ≥50 years were included. Fifty-four studies were included in the final analysis. Twenty-six genes and 88 DNA polymorphisms were analysed across the 54 studies. The ACTN3, ACE and VDR genes were the most frequently studied, although the IGF1/IGFBP3, TNFα, APOE, CNTF/R and UCP2/3 genes were also shown to be significantly associated with muscle phenotypes in two or more studies. Ten DNA polymorphisms (rs154410, rs2228570, rs1800169, rs3093059, rs1800629, rs1815739, rs1799752, rs7412, rs429358 and 192 bp allele) were significantly associated with muscle phenotypes in two or more studies. Through the identification of key gene variants, this review furthers the elucidation of genetic associations with muscle phenotypes associated with sarcopenia.
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Affiliation(s)
- Jedd Pratt
- Institute for Sport and Health, University College Dublin, Dublin, Ireland; (C.B.); (G.D.V.)
- Genomics Medicine Ireland, Dublin, Ireland; (S.E.); (A.W.R.)
| | - Colin Boreham
- Institute for Sport and Health, University College Dublin, Dublin, Ireland; (C.B.); (G.D.V.)
| | - Sean Ennis
- Genomics Medicine Ireland, Dublin, Ireland; (S.E.); (A.W.R.)
- UCD ACoRD, Academic Centre on Rare Diseases, University College Dublin, Dublin, Ireland
| | - Anthony W. Ryan
- Genomics Medicine Ireland, Dublin, Ireland; (S.E.); (A.W.R.)
| | - Giuseppe De Vito
- Institute for Sport and Health, University College Dublin, Dublin, Ireland; (C.B.); (G.D.V.)
- Department of Biomedical Sciences, University of Padova, Via F. Marzolo 3, 35131 Padova, Italy
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