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Li C, Wang Y, Sun X, Yang J, Ren Y, Jia J, Yang G, Liao M, Jin J, Shi X. Identification of different myofiber types in pigs muscles and construction of regulatory networks. BMC Genomics 2024; 25:400. [PMID: 38658807 PMCID: PMC11040794 DOI: 10.1186/s12864-024-10271-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/30/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Skeletal muscle is composed of muscle fibers with different physiological characteristics, which plays an important role in regulating skeletal muscle metabolism, movement and body homeostasis. The type of skeletal muscle fiber directly affects meat quality. However, the transcriptome and gene interactions between different types of muscle fibers are not well understood. RESULTS In this paper, we selected 180-days-old Large White pigs and found that longissimus dorsi (LD) muscle was dominated by fast-fermenting myofibrils and soleus (SOL) muscle was dominated by slow-oxidizing myofibrils by frozen sections and related mRNA and protein assays. Here, we selected LD muscle and SOL muscle for transcriptomic sequencing, and identified 312 differentially expressed mRNA (DEmRs), 30 differentially expressed miRNA (DEmiRs), 183 differentially expressed lncRNA (DElRs), and 3417 differentially expressed circRNA (DEcRs). The ceRNA network included ssc-miR-378, ssc-miR-378b-3p, ssc-miR-24-3p, XR_308817, XR_308823, SMIM8, MAVS and FOS as multiple core nodes that play important roles in muscle development. Moreover, we found that different members of the miR-10 family expressed differently in oxidized and glycolytic muscle fibers, among which miR-10a-5p was highly expressed in glycolytic muscle fibers (LD) and could target MYBPH gene mRNA. Therefore, we speculate that miR-10a-5p may be involved in the transformation of muscle fiber types by targeting the MYHBP gene. In addition, PPI analysis of differentially expressed mRNA genes showed that ACTC1, ACTG2 and ACTN2 gene had the highest node degree, suggesting that this gene may play a key role in the regulatory network of muscle fiber type determination. CONCLUSIONS We can conclude that these genes play a key role in regulating muscle fiber type transformation. Our study provides transcriptomic profiles and ceRNA interaction networks for different muscle fiber types in pigs, providing reference for the transformation of pig muscle fiber types and the improvement of meat quality.
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Affiliation(s)
- Chenchen Li
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yinuo Wang
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaohui Sun
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jinjin Yang
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yingchun Ren
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jinrui Jia
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Gongshe Yang
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mingzhi Liao
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Jianjun Jin
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Xin'e Shi
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Zhao Q, Du X, Liu F, Zhang Y, Qin W, Zhang Q. ECHDC3 Variant Regulates the Right Hippocampal Microstructural Integrity and Verbal Memory in Type 2 Diabetes Mellitus. Neuroscience 2024; 538:30-39. [PMID: 38070593 DOI: 10.1016/j.neuroscience.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/29/2023] [Accepted: 12/02/2023] [Indexed: 12/25/2023]
Abstract
ECHDC3 is a risk gene for white matter (WM) hyperintensity and is associated with insulin resistance. This study aimed to investigate whether ECHDC3 variants selectively regulate brain WM microstructures and episodic memory in patients with type 2 diabetes mellitus (T2DM). We enrolled 106 patients with T2DM and 111 healthy controls. A voxel-wise general linear model was employed to explore the interaction effect between ECHDC3 rs11257311 polymorphism and T2DM diagnosis on fractional anisotropy (FA). A linear modulated mediation analysis was conducted to examine the potential of FA value to mediate the influence of T2DM on episodic memory in an ECHDC3-dependent manner. We observed a noteworthy interaction between genotype and diagnosis on FA in the right inferior temporal WM, right anterior limb of the internal capsule, right frontal WM, and the right hippocampus. Modulated mediation analysis revealed a significant ECHDC3 modulation on the T2DM → right hippocampal FA → short-term memory pathway, with only rs11257311 G risk homozygote demonstrating significant mediation effect. Together, our findings provide evidence of ECHDC3 modulating the effect of T2DM on right hippocampal microstructural impairment and short-term memory decline, which might be a neuro-mechanism for T2DM related episodic memory impairment.
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Affiliation(s)
- Qiyu Zhao
- Department of Medical Imaging and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Xin Du
- Department of Medical Imaging and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Feng Liu
- Department of Medical Imaging and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yang Zhang
- Department of Medical Imaging and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Wen Qin
- Department of Medical Imaging and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China.
| | - Quan Zhang
- Department of Medical Imaging and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China.
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3
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Szabo E, Nagy B, Czajlik A, Komlodi T, Ozohanics O, Tretter L, Ambrus A. Mitochondrial Alpha-Keto Acid Dehydrogenase Complexes: Recent Developments on Structure and Function in Health and Disease. Subcell Biochem 2024; 104:295-381. [PMID: 38963492 DOI: 10.1007/978-3-031-58843-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The present work delves into the enigmatic world of mitochondrial alpha-keto acid dehydrogenase complexes discussing their metabolic significance, enzymatic operation, moonlighting activities, and pathological relevance with links to underlying structural features. This ubiquitous family of related but diverse multienzyme complexes is involved in carbohydrate metabolism (pyruvate dehydrogenase complex), the citric acid cycle (α-ketoglutarate dehydrogenase complex), and amino acid catabolism (branched-chain α-keto acid dehydrogenase complex, α-ketoadipate dehydrogenase complex); the complexes all function at strategic points and also participate in regulation in these metabolic pathways. These systems are among the largest multienzyme complexes with at times more than 100 protein chains and weights ranging up to ~10 million Daltons. Our chapter offers a wealth of up-to-date information on these multienzyme complexes for a comprehensive understanding of their significance in health and disease.
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Affiliation(s)
- Eszter Szabo
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Balint Nagy
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Andras Czajlik
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Timea Komlodi
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Oliver Ozohanics
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Laszlo Tretter
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Attila Ambrus
- Department of Biochemistry, Semmelweis University, Budapest, Hungary.
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Liu W, Chen S, Xie W, Wang Q, Luo Q, Huang M, Gu M, Lan P, Chen D. MCCC2 is a novel mediator between mitochondria and telomere and functions as an oncogene in colorectal cancer. Cell Mol Biol Lett 2023; 28:80. [PMID: 37828426 PMCID: PMC10571261 DOI: 10.1186/s11658-023-00487-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 09/04/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND The mitochondrial gene MCCC2, a subunit of the heterodimer of 3-methylcrotonyl-CoA carboxylase, plays a pivotal role in catabolism of leucine and isovaleric acid. The molecular mechanisms and prognostic value still need to be explored in the context of specific cancers, including colorectal cancer (CRC). METHODS In vitro and in vivo cell-based assays were performed to explore the role of MCCC2 in CRC cell proliferation, invasion, and migration. Mitochondrial morphology, membrane potential, intracellular reactive oxygen species (ROS), telomerase activity, and telomere length were examined and analyzed accordingly. Protein complex formation was detected by co-immunoprecipitation (CO-IP). Mitochondrial morphology was observed by transmission electron microscopy (TEM). The Cancer Genome Atlas (TCGA) CRC cohort analysis, qRT-PCR, and immunohistochemistry (IHC) were used to examine the MCCC2 expression level. The association between MCCC2 expression and various clinical characteristics was analyzed by chi-square tests. CRC patients' overall survival (OS) was analyzed by Kaplan-Meier analysis. RESULTS Ectopic overexpression of MCCC2 promoted cell proliferation, invasion, and migration, while MCCC2 knockdown (KD) or knockout (KO) inhibited cell proliferation, invasion, and migration. MCCC2 KD or KO resulted in reduced mitochondria numbers, but did not affect the gross ATP production in the cells. Mitochondrial fusion markers MFN1, MFN2, and OPA1 were all upregulated in MCCC2 KD or KO cells, which is in line with a phenomenon of more prominent mitochondrial fusion. Interestingly, telomere lengths of MCCC2 KD or KO cells were reduced more than control cells. Furthermore, we found that MCCC2 could specifically form a complex with telomere binding protein TRF2, and MCCC2 KD or KO did not affect the expression or activity of telomerase reverse transcriptase (TERT). Finally, MCCC2 expression was heightened in CRC, and patients with higher MCCC2 expression had favorable prognosis. CONCLUSIONS Together, we identified MCCC2 as a novel mediator between mitochondria and telomeres, and provided an additional biomarker for CRC stratification.
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Affiliation(s)
- Wanjun Liu
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, 26 Yuancun Er Heng Road, Guangzhou, 510655, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Si Chen
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, 26 Yuancun Er Heng Road, Guangzhou, 510655, Guangdong, China
| | - Wenqing Xie
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, 26 Yuancun Er Heng Road, Guangzhou, 510655, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qian Wang
- Department of Intensive Care Unit, The Sixth Affiliated Hospital, Sun Yat-sen University, 26 Yuancun Er Heng Road, Guangzhou, 510655, China
| | - Qianxin Luo
- Department of Intensive Care Unit, The Sixth Affiliated Hospital, Sun Yat-sen University, 26 Yuancun Er Heng Road, Guangzhou, 510655, China
| | - Minghan Huang
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, 26 Yuancun Er Heng Road, Guangzhou, 510655, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Minyi Gu
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Scientific Journal Center, The Sixth Affiliated Hospital, Sun Yat-sen University, 26 Yuancun Er Heng Road, Guangzhou, 510655, China
| | - Ping Lan
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, 26 Yuancun Er Heng Road, Guangzhou, 510655, Guangdong, China.
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, 26 Yuancun Er Heng Road, Guangzhou, 510655, China.
| | - Daici Chen
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, 26 Yuancun Er Heng Road, Guangzhou, 510655, Guangdong, China.
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
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5
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Whytock KL, Pino MF, Sun Y, Yu G, De Carvalho FG, Yeo RX, Vega RB, Parmar G, Divoux A, Kapoor N, Yi F, Cornnell H, Patten DA, Harper ME, Gardell SJ, Smith SR, Walsh MJ, Sparks LM. Comprehensive interrogation of human skeletal muscle reveals a dissociation between insulin resistance and mitochondrial capacity. Am J Physiol Endocrinol Metab 2023; 325:E291-E302. [PMID: 37584609 DOI: 10.1152/ajpendo.00143.2023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/10/2023] [Accepted: 08/10/2023] [Indexed: 08/17/2023]
Abstract
Insulin resistance and blunted mitochondrial capacity in skeletal muscle are often synonymous, however, this association remains controversial. The aim of this study was to perform an in-depth multifactorial comparison of skeletal muscle mitochondrial capacity between individuals who were lean and active (Active, n = 9), individuals with obesity (Obese, n = 9), and individuals with obesity, insulin resistance, and type 2 diabetes (T2D, n = 22). Mitochondrial capacity was assessed by ex vivo mitochondrial respiration with fatty-acid and glycolytic-supported protocols adjusted for mitochondrial content (mtDNA and citrate synthase activity). Supercomplex assembly was measured by Blue Native (BN)-PAGE and immunoblot. Tricarboxylic (TCA) cycle intermediates were assessed with targeted metabolomics. Exploratory transcriptomics and DNA methylation analyses were performed to uncover molecular differences affecting mitochondrial function among the three groups. We reveal no discernable differences in skeletal muscle mitochondrial content, mitochondrial capacity, supercomplex assembly, TCA cycle intermediates, and mitochondrial molecular profiles between obese individuals with and without T2D that had comparable levels of confounding factors (body mass index, age, and aerobic capacity). We highlight that lean, active individuals have greater mitochondrial content, mitochondrial capacity, supercomplex assembly, and TCA cycle intermediates. These phenotypical changes are reflected at the level of DNA methylation and gene transcription. The collective observation of comparable muscle mitochondrial capacity in individuals with obesity and T2D (vs. individuals without T2D) underscores a dissociation from skeletal muscle insulin resistance. Clinical trial number: NCT01911104.NEW & NOTEWORTHY Whether impaired mitochondrial capacity contributes to skeletal muscle insulin resistance is debated. Our multifactorial analysis shows no differences in skeletal muscle mitochondrial content, mitochondrial capacity, and mitochondrial molecular profiles between obese individuals with and without T2D that had comparable levels of confounding factors (BMI, age, aerobic capacity). We highlight that lean, active individuals have enhanced skeletal muscle mitochondrial capacity that is also reflected at the level of DNA methylation and gene transcription.
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Affiliation(s)
- Katie L Whytock
- Translational Research Institute, AdventHealth, Orlando, Florida, United States
| | - Maria F Pino
- Translational Research Institute, AdventHealth, Orlando, Florida, United States
| | - Yifei Sun
- Icahn School of Medicine at Mount Sinai, New York City, New York, United States
| | - GongXin Yu
- Translational Research Institute, AdventHealth, Orlando, Florida, United States
| | | | - Reichelle X Yeo
- Translational Research Institute, AdventHealth, Orlando, Florida, United States
| | - Rick B Vega
- Translational Research Institute, AdventHealth, Orlando, Florida, United States
| | - Gaganvir Parmar
- Department of Biochemistry Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Adeline Divoux
- Translational Research Institute, AdventHealth, Orlando, Florida, United States
| | - Nidhi Kapoor
- Translational Research Institute, AdventHealth, Orlando, Florida, United States
| | - Fancaho Yi
- Translational Research Institute, AdventHealth, Orlando, Florida, United States
| | - Heather Cornnell
- Translational Research Institute, AdventHealth, Orlando, Florida, United States
| | - David A Patten
- Department of Biochemistry Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Mary-Ellen Harper
- Department of Biochemistry Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Stephen J Gardell
- Translational Research Institute, AdventHealth, Orlando, Florida, United States
| | - Steven R Smith
- Translational Research Institute, AdventHealth, Orlando, Florida, United States
| | - Martin J Walsh
- Icahn School of Medicine at Mount Sinai, New York City, New York, United States
| | - Lauren M Sparks
- Translational Research Institute, AdventHealth, Orlando, Florida, United States
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6
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Makhnovskii PA, Lednev EM, Gavrilova AO, Kurochkina NS, Vepkhvadze TF, Shestakova MV, Popov DV. Dysregulation of early gene response to a mixed meal in skeletal muscle in obesity and type 2 diabetes. Physiol Genomics 2023; 55:468-477. [PMID: 37545425 DOI: 10.1152/physiolgenomics.00046.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/10/2023] [Accepted: 07/30/2023] [Indexed: 08/08/2023] Open
Abstract
Obesity- and type 2 diabetes mellitus-induced changes in the expression of protein-coding genes in human skeletal muscle were extensively examined at baseline (after an overnight fast). We aimed to compare the early transcriptomic response to a typical single meal in skeletal muscle of metabolically healthy subjects and obese individuals without and with type 2 diabetes. Transcriptomic response (RNA-seq) to a mixed meal (nutritional drink, ∼25 kJ/kg of body mass) was examined in the vastus lateralis muscle (1 h after a meal) in 7 healthy subjects and 14 obese individuals without or with type 2 diabetes. In all obese individuals, the transcriptome response to a meal was dysregulated (suppressed and altered) and associated with different biological processes compared with healthy control. To search for potential transcription factors regulating transcriptomic response to a meal, the enrichment of transcription factor-binding sites in individual promoters of the human skeletal muscle was examined. In obese individuals, the transcriptomic response is associated with a different set of transcription factors than that in healthy subjects. In conclusion, metabolic disorders are associated with a defect in the regulation of mixed meal/insulin-mediated gene expression-insulin resistance in terms of gene expression. Importantly, this dysregulation occurs in obese individuals without type 2 diabetes, i.e., at the first stage of the development of metabolic disorders.NEW & NOTEWORTHY In skeletal muscle of metabolically healthy subjects, a typical single meal normalized to body mass induces activation of various transcription factors, expression of numerous receptor tyrosine kinases associated with the insulin signaling cascade, and transcription regulators. In skeletal muscle of obese individuals without and with type 2 diabetes, this signaling network is poorly regulated at the transcriptional level, indicating dysregulation of the early gene response to a mixed meal.
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Affiliation(s)
- Pavel A Makhnovskii
- Institute of Biomedical Problems, Russian Academy of Sciences, Moscow, Russia
| | - Egor M Lednev
- Institute of Biomedical Problems, Russian Academy of Sciences, Moscow, Russia
- Diabetes Institute, National Medical Research Centre for Endocrinology, Moscow, Russia
| | - Alina O Gavrilova
- Diabetes Institute, National Medical Research Centre for Endocrinology, Moscow, Russia
| | - Nadia S Kurochkina
- Institute of Biomedical Problems, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana F Vepkhvadze
- Institute of Biomedical Problems, Russian Academy of Sciences, Moscow, Russia
- Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Marina V Shestakova
- Diabetes Institute, National Medical Research Centre for Endocrinology, Moscow, Russia
| | - Daniil V Popov
- Institute of Biomedical Problems, Russian Academy of Sciences, Moscow, Russia
- Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow, Russia
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Masson SWC, Madsen S, Cooke KC, Potter M, Vegas AD, Carroll L, Thillainadesan S, Cutler HB, Walder KR, Cooney GJ, Morahan G, Stöckli J, James DE. Leveraging genetic diversity to identify small molecules that reverse mouse skeletal muscle insulin resistance. eLife 2023; 12:RP86961. [PMID: 37494090 PMCID: PMC10371229 DOI: 10.7554/elife.86961] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023] Open
Abstract
Systems genetics has begun to tackle the complexity of insulin resistance by capitalising on computational advances to study high-diversity populations. 'Diversity Outbred in Australia (DOz)' is a population of genetically unique mice with profound metabolic heterogeneity. We leveraged this variance to explore skeletal muscle's contribution to whole-body insulin action through metabolic phenotyping and skeletal muscle proteomics of 215 DOz mice. Linear modelling identified 553 proteins that associated with whole-body insulin sensitivity (Matsuda Index) including regulators of endocytosis and muscle proteostasis. To enrich for causality, we refined this network by focusing on negatively associated, genetically regulated proteins, resulting in a 76-protein fingerprint of insulin resistance. We sought to perturb this network and restore insulin action with small molecules by integrating the Broad Institute Connectivity Map platform and in vitro assays of insulin action using the Prestwick chemical library. These complementary approaches identified the antibiotic thiostrepton as an insulin resistance reversal agent. Subsequent validation in ex vivo insulin-resistant mouse muscle and palmitate-induced insulin-resistant myotubes demonstrated potent insulin action restoration, potentially via upregulation of glycolysis. This work demonstrates the value of a drug-centric framework to validate systems-level analysis by identifying potential therapeutics for insulin resistance.
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Affiliation(s)
- Stewart W C Masson
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Søren Madsen
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Kristen C Cooke
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Meg Potter
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Alexis Diaz Vegas
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Luke Carroll
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, Australia
| | - Senthil Thillainadesan
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Harry B Cutler
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Ken R Walder
- School of Medicine, Deakin University, Geelong, Australia
| | - Gregory J Cooney
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, Murdoch, Australia
| | - Jacqueline Stöckli
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - David E James
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
- School of Medical Sciences University of Sydney, Sydney, Australia
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8
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Bunik V. The Therapeutic Potential of Vitamins B1, B3 and B6 in Charcot-Marie-Tooth Disease with the Compromised Status of Vitamin-Dependent Processes. BIOLOGY 2023; 12:897. [PMID: 37508330 PMCID: PMC10376249 DOI: 10.3390/biology12070897] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/11/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023]
Abstract
Understanding the molecular mechanisms of neurological disorders is necessary for the development of personalized medicine. When the diagnosis considers not only the disease symptoms, but also their molecular basis, treatments tailored to individual patients may be suggested. Vitamin-responsive neurological disorders are induced by deficiencies in vitamin-dependent processes. These deficiencies may occur due to genetic impairments of proteins whose functions are involved with the vitamins. This review considers the enzymes encoded by the DHTKD1, PDK3 and PDXK genes, whose mutations are observed in patients with Charcot-Marie-Tooth (CMT) disease. The enzymes bind or produce the coenzyme forms of vitamins B1 (thiamine diphosphate, ThDP) and B6 (pyridoxal-5'-phosphate, PLP). Alleviation of such disorders through administration of the lacking vitamin or its derivative calls for a better introduction of mechanistic knowledge to medical diagnostics and therapies. Recent data on lower levels of the vitamin B3 derivative, NAD+, in the blood of patients with CMT disease vs. control subjects are also considered in view of the NAD-dependent mechanisms of pathological axonal degeneration, suggesting the therapeutic potential of vitamin B3 in these patients. Thus, improved diagnostics of the underlying causes of CMT disease may allow patients with vitamin-responsive disease forms to benefit from the administration of the vitamins B1, B3, B6, their natural derivatives, or their pharmacological forms.
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Affiliation(s)
- Victoria Bunik
- Belozersky Institute of Physicochemical Biology, Department of Biokinetics, Lomonosov Moscow State University, 119234 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
- Department of Biochemistry, Sechenov University, 119048 Moscow, Russia
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9
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Stokes T, Cen HH, Kapranov P, Gallagher IJ, Pitsillides AA, Volmar C, Kraus WE, Johnson JD, Phillips SM, Wahlestedt C, Timmons JA. Transcriptomics for Clinical and Experimental Biology Research: Hang on a Seq. ADVANCED GENETICS (HOBOKEN, N.J.) 2023; 4:2200024. [PMID: 37288167 PMCID: PMC10242409 DOI: 10.1002/ggn2.202200024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Indexed: 06/09/2023]
Abstract
Sequencing the human genome empowers translational medicine, facilitating transcriptome-wide molecular diagnosis, pathway biology, and drug repositioning. Initially, microarrays are used to study the bulk transcriptome; but now short-read RNA sequencing (RNA-seq) predominates. Positioned as a superior technology, that makes the discovery of novel transcripts routine, most RNA-seq analyses are in fact modeled on the known transcriptome. Limitations of the RNA-seq methodology have emerged, while the design of, and the analysis strategies applied to, arrays have matured. An equitable comparison between these technologies is provided, highlighting advantages that modern arrays hold over RNA-seq. Array protocols more accurately quantify constitutively expressed protein coding genes across tissue replicates, and are more reliable for studying lower expressed genes. Arrays reveal long noncoding RNAs (lncRNA) are neither sparsely nor lower expressed than protein coding genes. Heterogeneous coverage of constitutively expressed genes observed with RNA-seq, undermines the validity and reproducibility of pathway analyses. The factors driving these observations, many of which are relevant to long-read or single-cell sequencing are discussed. As proposed herein, a reappreciation of bulk transcriptomic methods is required, including wider use of the modern high-density array data-to urgently revise existing anatomical RNA reference atlases and assist with more accurate study of lncRNAs.
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Affiliation(s)
- Tanner Stokes
- Faculty of ScienceMcMaster UniversityHamiltonL8S 4L8Canada
| | - Haoning Howard Cen
- Life Sciences InstituteUniversity of British ColumbiaVancouverV6T 1Z3Canada
| | | | - Iain J Gallagher
- School of Applied SciencesEdinburgh Napier UniversityEdinburghEH11 4BNUK
| | | | | | | | - James D. Johnson
- Life Sciences InstituteUniversity of British ColumbiaVancouverV6T 1Z3Canada
| | | | | | - James A. Timmons
- Miller School of MedicineUniversity of MiamiMiamiFL33136USA
- William Harvey Research InstituteQueen Mary University LondonLondonEC1M 6BQUK
- Augur Precision Medicine LTDStirlingFK9 5NFUK
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10
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Raina P, Guinea R, Chatsirisupachai K, Lopes I, Farooq Z, Guinea C, Solyom CA, de Magalhães JP. GeneFriends: gene co-expression databases and tools for humans and model organisms. Nucleic Acids Res 2022; 51:D145-D158. [PMID: 36454018 PMCID: PMC9825523 DOI: 10.1093/nar/gkac1031] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 12/05/2022] Open
Abstract
Gene co-expression analysis has emerged as a powerful method to provide insights into gene function and regulation. The rapid growth of publicly available RNA-sequencing (RNA-seq) data has created opportunities for researchers to employ this abundant data to help decipher the complexity and biology of genomes. Co-expression networks have proven effective for inferring the relationship between the genes, for gene prioritization and for assigning function to poorly annotated genes based on their co-expressed partners. To facilitate such analyses we created previously an online co-expression tool for humans and mice entitled GeneFriends. To continue providing a valuable tool to the scientific community, we have now updated the GeneFriends database and website. Here, we present the new version of GeneFriends, which includes gene and transcript co-expression networks based on RNA-seq data from 46 475 human and 34 322 mouse samples. The new database also encompasses tissue-specific gene co-expression networks for 20 human and 21 mouse tissues, dataset-specific gene co-expression maps based on TCGA and GTEx projects and gene co-expression networks for additional seven model organisms (fruit fly, zebrafish, worm, rat, yeast, cow and chicken). GeneFriends is freely available at http://www.genefriends.org/.
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Affiliation(s)
- Priyanka Raina
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Rodrigo Guinea
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Kasit Chatsirisupachai
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Inês Lopes
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Zoya Farooq
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Cristina Guinea
- UCAL - Universidad de Ciencias y Artes de América Latina, Faculty of Design, Lima 15026, Perú
| | - Csaba-Attila Solyom
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
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11
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Vorotnikov AV, Popov DV, Makhnovskii PA. Signaling and Gene Expression in Skeletal Muscles in Type 2 Diabetes: Current Results and OMICS Perspectives. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:1021-1034. [PMID: 36180992 DOI: 10.1134/s0006297922090139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 06/16/2023]
Abstract
Skeletal muscles mainly contribute to the emergence of insulin resistance, impaired glucose tolerance and the development of type 2 diabetes. Molecular mechanisms that regulate glucose uptake are diverse, including the insulin-dependent as most important, and others as also significant. They involve a wide range of proteins that control intracellular traffic and exposure of glucose transporters on the cell surface to create an extensive regulatory network. Here, we highlight advantages of the omics approaches to explore the insulin-regulated proteins and genes in human skeletal muscle with varying degrees of metabolic disorders. We discuss methodological aspects of the assessment of metabolic dysregulation and molecular responses of human skeletal muscle to insulin. The known molecular mechanisms of glucose uptake regulation and the first results of phosphoproteomic and transcriptomic studies are reviewed, which unveiled a large-scale array of insulin targets in muscle cells. They demonstrate that a clear depiction of changes that occur during metabolic dysfunction requires systemic and combined analysis at different levels of regulation, including signaling pathways, transcription factors, and gene expression. Such analysis seems promising to explore yet undescribed regulatory mechanisms of glucose uptake by skeletal muscle and identify the key regulators as potential therapeutic targets.
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Affiliation(s)
- Alexander V Vorotnikov
- Institute of Biomedical Problems, Russian Academy of Sciences, Moscow, 123007, Russia.
- National Medical Research Center of Cardiology, Ministry of Healthcare of the Russian Federation, Moscow, 121552, Russia
| | - Daniil V Popov
- Institute of Biomedical Problems, Russian Academy of Sciences, Moscow, 123007, Russia.
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Pavel A Makhnovskii
- Institute of Biomedical Problems, Russian Academy of Sciences, Moscow, 123007, Russia
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12
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Zhang R, Meng J, Yang S, Liu W, Shi L, Zeng J, Chang J, Liang B, Liu N, Xing D. Recent Advances on the Role of ATGL in Cancer. Front Oncol 2022; 12:944025. [PMID: 35912266 PMCID: PMC9326118 DOI: 10.3389/fonc.2022.944025] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 06/15/2022] [Indexed: 12/22/2022] Open
Abstract
The hypoxic state of the tumor microenvironment leads to reprogramming lipid metabolism in tumor cells. Adipose triglyceride lipase, also known as patatin-like phospholipase= domain-containing protein 2 and Adipose triglyceride lipase (ATGL), as an essential lipid metabolism-regulating enzyme in cells, is regulated accordingly under hypoxia induction. However, studies revealed that ATGL exhibits both tumor-promoting and tumor-suppressing effects, which depend on the cancer cell type and the site of tumorigenesis. For example, elevated ATGL expression in breast cancer is accompanied by enhanced fatty acid oxidation (FAO), enhancing cancer cells’ metastatic ability. In prostate cancer, on the other hand, tumor activity tends to be negatively correlated with ATGL expression. This review outlined the regulation of ATGL-mediated lipid metabolism pathways in tumor cells, emphasizing the Hypoxia-inducible factors 1 (HIF-1)/Hypoxia-inducible lipid droplet-associated (HIG-2)/ATGL axis, peroxisome proliferator-activated receptor (PPAR)/G0/G1 switch gene 2 (G0S2)/ATGL axis, and fat-specific protein 27 (FSP-27)/Early growth response protein 1 (EGR-1)/ATGL axis. In the light of recent research on different cancer types, the role of ATGL on tumorigenesis, tumor proliferation, and tumor metastasis was systemically reviewed.
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Affiliation(s)
- Renshuai Zhang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, China
- Qingdao Cancer Institute, Qingdao, China
| | - Jingsen Meng
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, China
- Qingdao Cancer Institute, Qingdao, China
| | - Shanbo Yang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, China
- Qingdao Cancer Institute, Qingdao, China
| | - Wenjing Liu
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, China
- Qingdao Cancer Institute, Qingdao, China
| | - Lingyu Shi
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, China
- Qingdao Cancer Institute, Qingdao, China
| | - Jun Zeng
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, China
- Qingdao Cancer Institute, Qingdao, China
| | - Jing Chang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, China
- Qingdao Cancer Institute, Qingdao, China
| | - Bing Liang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, China
- Qingdao Cancer Institute, Qingdao, China
| | - Ning Liu
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, China
- Qingdao Cancer Institute, Qingdao, China
- *Correspondence: Ning Liu, ; Dongming Xing,
| | - Dongming Xing
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, China
- Qingdao Cancer Institute, Qingdao, China
- School of Life Sciences, Tsinghua University, Beijing, China
- *Correspondence: Ning Liu, ; Dongming Xing,
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13
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Giannos P, Prokopidis K, Raleigh SM, Kelaiditi E, Hill M. Altered mitochondrial microenvironment at the spotlight of musculoskeletal aging and Alzheimer's disease. Sci Rep 2022; 12:11290. [PMID: 35788655 PMCID: PMC9253146 DOI: 10.1038/s41598-022-15578-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/27/2022] [Indexed: 11/23/2022] Open
Abstract
Emerging evidence has linked Alzheimer's disease (AD) onset with musculoskeletal aging via a muscle-brain crosstalk mediated by dysregulation of the mitochondrial microenvironment. This study investigated gene expression profiles from skeletal muscle tissues of older healthy adults to identify potential gene biomarkers whose dysregulated expression and protein interactome were involved in AD. Screening of the literature resulted in 12 relevant microarray datasets (GSE25941, GSE28392, GSE28422, GSE47881, GSE47969, GSE59880) in musculoskeletal aging and (GSE4757, GSE5281, GSE16759, GSE28146, GSE48350, GSE84422) in AD. Retrieved differentially expressed genes (DEGs) were used to construct two unique protein-protein interaction networks and clustering gene modules were identified. Overlapping module DEGs in the musculoskeletal aging and AD networks were ranked based on 11 topological algorithms and the five highest-ranked ones were considered as hub genes. The analysis revealed that the dysregulated expression of the mitochondrial microenvironment genes, NDUFAB1, UQCRC1, UQCRFS1, NDUFS3, and MRPL15, overlapped between both musculoskeletal aging and AD networks. Thus, these genes may have a potential role as markers of AD occurrence in musculoskeletal aging. Human studies are warranted to evaluate the functional role and prognostic value of these genes in aging populations with sarcopenia and AD.
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Affiliation(s)
- Panagiotis Giannos
- Society of Meta-research and Biomedical Innovation, London, UK. .,Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, South Kensington, London, SW7 2AZ, UK.
| | - Konstantinos Prokopidis
- Society of Meta-research and Biomedical Innovation, London, UK.,Department of Musculoskeletal Biology, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - Stuart M Raleigh
- Cardiovascular and Lifestyle Medicine Research Group, Centre for Sport, Exercise and Life Sciences, Coventry University, Coventry, UK
| | - Eirini Kelaiditi
- Faculty of Sport, Allied Health and Performance Science, St Mary's University Twickenham, Twickenham, UK
| | - Mathew Hill
- Centre for Sport, Exercise and Life Sciences, School of Life Sciences, Coventry University, Coventry, UK
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14
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Boyko AI, Karlina IS, Zavileyskiy LG, Aleshin VA, Artiukhov AV, Kaehne T, Ksenofontov AL, Ryabov SI, Graf AV, Tramonti A, Bunik VI. Delayed Impact of 2-Oxoadipate Dehydrogenase Inhibition on the Rat Brain Metabolism Is Linked to Protein Glutarylation. Front Med (Lausanne) 2022; 9:896263. [PMID: 35721081 PMCID: PMC9198357 DOI: 10.3389/fmed.2022.896263] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/28/2022] [Indexed: 12/19/2022] Open
Abstract
Background The DHTKD1-encoded 2-oxoadipate dehydrogenase (OADH) oxidizes 2-oxoadipate—a common intermediate of the lysine and tryptophan catabolism. The mostly low and cell-specific flux through these pathways, and similar activities of OADH and ubiquitously expressed 2-oxoglutarate dehydrogenase (OGDH), agree with often asymptomatic phenotypes of heterozygous mutations in the DHTKD1 gene. Nevertheless, OADH/DHTKD1 are linked to impaired insulin sensitivity, cardiovascular disease risks, and Charcot-Marie-Tooth neuropathy. We hypothesize that systemic significance of OADH relies on its generation of glutaryl residues for protein glutarylation. Using pharmacological inhibition of OADH and the animal model of spinal cord injury (SCI), we explore this hypothesis. Methods The weight-drop model of SCI, a single intranasal administration of an OADH-directed inhibitor trimethyl adipoyl phosphonate (TMAP), and quantification of the associated metabolic changes in the rat brain employ established methods. Results The TMAP-induced metabolic changes in the brain of the control, laminectomized (LE) and SCI rats are long-term and (patho)physiology-dependent. Increased glutarylation of the brain proteins, proportional to OADH expression in the control and LE rats, represents a long-term consequence of the OADH inhibition. The proportionality suggests autoglutarylation of OADH, supported by our mass-spectrometric identification of glutarylated K155 and K818 in recombinant human OADH. In SCI rats, TMAP increases glutarylation of the brain proteins more than OADH expression, inducing a strong perturbation in the brain glutathione metabolism. The redox metabolism is not perturbed by TMAP in LE animals, where the inhibition of OADH increases expression of deglutarylase sirtuin 5. The results reveal the glutarylation-imposed control of the brain glutathione metabolism. Glutarylation of the ODP2 subunit of pyruvate dehydrogenase complex at K451 is detected in the rat brain, linking the OADH function to the brain glucose oxidation essential for the redox state. Short-term inhibition of OADH by TMAP administration manifests in increased levels of tryptophan and decreased levels of sirtuins 5 and 3 in the brain. Conclusion Pharmacological inhibition of OADH affects acylation system of the brain, causing long-term, (patho)physiology-dependent changes in the expression of OADH and sirtuin 5, protein glutarylation and glutathione metabolism. The identified glutarylation of ODP2 subunit of pyruvate dehydrogenase complex provides a molecular mechanism of the OADH association with diabetes.
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Affiliation(s)
- Alexandra I Boyko
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Irina S Karlina
- N.V. Sklifosovsky Institute of Clinical Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Lev G Zavileyskiy
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Vasily A Aleshin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Department of Biological Chemistry, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Artem V Artiukhov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Department of Biological Chemistry, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Thilo Kaehne
- Institute of Experimental Internal Medicine, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Alexander L Ksenofontov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergey I Ryabov
- Russian Cardiology Research and Production Complex, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Anastasia V Graf
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Faculty of Nano-, Bio-, Informational, Cognitive and Socio-Humanistic Sciences and Technologies, Moscow Institute of Physics and Technology, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Angela Tramonti
- Institute of Molecular Biology and Pathology, Council of National Research, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University, Rome, Italy
| | - Victoria I Bunik
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Department of Biological Chemistry, Sechenov First Moscow State Medical University, Moscow, Russia
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15
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Bunik VI, Artiukhov AV, Kazantsev AV, Aleshin VA, Boyko AI, Ksenofontov AL, Lukashev NV, Graf AV. Administration of Phosphonate Inhibitors of Dehydrogenases of 2-Oxoglutarate and 2-Oxoadipate to Rats Elicits Target-Specific Metabolic and Physiological Responses. Front Chem 2022; 10:892284. [PMID: 35795216 PMCID: PMC9252169 DOI: 10.3389/fchem.2022.892284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/29/2022] [Indexed: 11/29/2022] Open
Abstract
In vitro and in cell cultures, succinyl phosphonate (SP) and adipoyl phosphonate (AP) selectively target dehydrogenases of 2-oxoglutarate (OGDH, encoded by OGDH/OGDHL) and 2-oxoadipate (OADH, encoded by DHTKD1), respectively. To assess the selectivity in animals, the effects of SP, AP, and their membrane-penetrating triethyl esters (TESP and TEAP) on the rat brain metabolism and animal physiology are compared. Opposite effects of the OGDH and OADH inhibitors on activities of OGDH, malate dehydrogenase, glutamine synthetase, and levels of glutamate, lysine, citrulline, and carnosine are shown to result in distinct physiological responses. ECG is changed by AP/TEAP, whereas anxiety is increased by SP/TESP. The potential role of the ester moiety in the uncharged precursors of the 2-oxo acid dehydrogenase inhibitors is estimated. TMAP is shown to be less efficient than TEAP, in agreement with lower lipophilicity of TMAP vs. TEAP. Non-monotonous metabolic and physiological impacts of increasing OADH inhibition are revealed. Compared to the non-treated animals, strong inhibition of OADH decreases levels of tryptophan and beta-aminoisobutyrate and activities of malate dehydrogenase and pyruvate dehydrogenase, increasing the R–R interval of ECG. Thus, both metabolic and physiological actions of the OADH-directed inhibitors AP/TEAP are different from those of the OGDH-directed inhibitors SP/TESP, with the ethyl ester being more efficient than methyl ester.
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Affiliation(s)
- Victoria I. Bunik
- Department of Biokinetics, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Department of Biochemistry, Sechenov University, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- *Correspondence: Victoria I. Bunik,
| | - Artem V. Artiukhov
- Department of Biokinetics, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Department of Biochemistry, Sechenov University, Moscow, Russia
| | - Alexey V. Kazantsev
- Department of Biokinetics, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Vasily A. Aleshin
- Department of Biokinetics, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Department of Biochemistry, Sechenov University, Moscow, Russia
| | - Alexandra I. Boyko
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander L. Ksenofontov
- Department of Biokinetics, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Anastasia V. Graf
- Department of Biokinetics, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
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16
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Timmons JA, Anighoro A, Brogan RJ, Stahl J, Wahlestedt C, Farquhar DG, Taylor-King J, Volmar CH, Kraus WE, Phillips SM. A human-based multi-gene signature enables quantitative drug repurposing for metabolic disease. eLife 2022; 11:68832. [PMID: 35037854 PMCID: PMC8763401 DOI: 10.7554/elife.68832] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 11/26/2021] [Indexed: 12/22/2022] Open
Abstract
Insulin resistance (IR) contributes to the pathophysiology of diabetes, dementia, viral infection, and cardiovascular disease. Drug repurposing (DR) may identify treatments for IR; however, barriers include uncertainty whether in vitro transcriptomic assays yield quantitative pharmacological data, or how to optimise assay design to best reflect in vivo human disease. We developed a clinical-based human tissue IR signature by combining lifestyle-mediated treatment responses (>500 human adipose and muscle biopsies) with biomarkers of disease status (fasting IR from >1200 biopsies). The assay identified a chemically diverse set of >130 positively acting compounds, highly enriched in true positives, that targeted 73 proteins regulating IR pathways. Our multi-gene RNA assay score reflected the quantitative pharmacological properties of a set of epidermal growth factor receptor-related tyrosine kinase inhibitors, providing insight into drug target specificity; an observation supported by deep learning-based genome-wide predicted pharmacology. Several drugs identified are suitable for evaluation in patients, particularly those with either acute or severe chronic IR.
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Affiliation(s)
- James A Timmons
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom.,Augur Precision Medicine LTD, Stirling, United Kingdom
| | | | | | - Jack Stahl
- Center for Therapeutic Innovation, Miller School of Medicine, University of Miami, Miami, United States
| | - Claes Wahlestedt
- Center for Therapeutic Innovation, Miller School of Medicine, University of Miami, Miami, United States
| | | | | | - Claude-Henry Volmar
- Center for Therapeutic Innovation, Miller School of Medicine, University of Miami, Miami, United States
| | | | - Stuart M Phillips
- Faculty of Science, Kinesiology, McMaster University, Hamilton, Canada
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17
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Prokopidis K, Giannos P, Witard OC, Peckham D, Ispoglou T. Aberrant mitochondrial homeostasis at the crossroad of musculoskeletal ageing and non-small cell lung cancer. PLoS One 2022; 17:e0273766. [PMID: 36067173 PMCID: PMC9447904 DOI: 10.1371/journal.pone.0273766] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/12/2022] [Indexed: 11/19/2022] Open
Abstract
Cancer cachexia is accompanied by muscle atrophy, sharing multiple common catabolic pathways with sarcopenia, including mitochondrial dysfunction. This study investigated gene expression from skeletal muscle tissues of older healthy adults, who are at risk of age-related sarcopenia, to identify potential gene biomarkers whose dysregulated expression and protein interference were involved in non-small cell lung cancer (NSCLC). Screening of the literature resulted in 14 microarray datasets (GSE25941, GSE28392, GSE28422, GSE47881, GSE47969, GSE59880 in musculoskeletal ageing; GSE118370, GSE33532, GSE19804, GSE18842, GSE27262, GSE19188, GSE31210, GSE40791 in NSCLC). Differentially expressed genes (DEGs) were used to construct protein-protein interaction networks and retrieve clustering gene modules. Overlapping module DEGs were ranked based on 11 topological algorithms and were correlated with prognosis, tissue expression, and tumour purity in NSCLC. The analysis revealed that the dysregulated expression of the mammalian mitochondrial ribosomal proteins, Mitochondrial Ribosomal Protein S26 (MRPS26), Mitochondrial Ribosomal Protein S17 (MRPS17), Mitochondrial Ribosomal Protein L18 (MRPL18) and Mitochondrial Ribosomal Protein L51 (MRPL51) were linked to reduced survival and tumour purity in NSCLC while tissue expression of the same genes followed an opposite direction in healthy older adults. These results support a potential link between the mitochondrial ribosomal microenvironment in ageing muscle and NSCLC. Further studies comparing changes in sarcopenia and NSCLC associated cachexia are warranted.
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Affiliation(s)
- Konstantinos Prokopidis
- Society of Meta-Research and Biomedical Innovation, London, United Kingdom
- Department of Musculoskeletal Biology, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Panagiotis Giannos
- Society of Meta-Research and Biomedical Innovation, London, United Kingdom
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
- * E-mail:
| | - Oliver C. Witard
- Faculty of Life Sciences and Medicine, Centre for Human and Applied Physiological Sciences, King’s College London, London, United Kingdom
| | - Daniel Peckham
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, United Kingdom
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18
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Cen HH, Hussein B, Botezelli JD, Wang S, Zhang JA, Noursadeghi N, Jessen N, Rodrigues B, Timmons JA, Johnson JD. Human and mouse muscle transcriptomic analyses identify insulin receptor mRNA downregulation in hyperinsulinemia-associated insulin resistance. FASEB J 2022; 36:e22088. [PMID: 34921686 PMCID: PMC9255858 DOI: 10.1096/fj.202100497rr] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 01/03/2023]
Abstract
Hyperinsulinemia is commonly viewed as a compensatory response to insulin resistance, yet studies have demonstrated that chronically elevated insulin may also drive insulin resistance. The molecular mechanisms underpinning this potentially cyclic process remain poorly defined, especially on a transcriptome-wide level. Transcriptomic meta-analysis in >450 human samples demonstrated that fasting insulin reliably and negatively correlated with INSR mRNA in skeletal muscle. To establish causality and study the direct effects of prolonged exposure to excess insulin in muscle cells, we incubated C2C12 myotubes with elevated insulin for 16 h, followed by 6 h of serum starvation, and established that acute AKT and ERK signaling were attenuated in this model of in vitro hyperinsulinemia. Global RNA-sequencing of cells both before and after nutrient withdrawal highlighted genes in the insulin receptor (INSR) signaling, FOXO signaling, and glucose metabolism pathways indicative of 'hyperinsulinemia' and 'starvation' programs. Consistently, we observed that hyperinsulinemia led to a substantial reduction in Insr gene expression, and subsequently a reduced surface INSR and total INSR protein, both in vitro and in vivo. Bioinformatic modeling combined with RNAi identified SIN3A as a negative regulator of Insr mRNA (and JUND, MAX, and MXI as positive regulators of Irs2 mRNA). Together, our analysis identifies mechanisms which may explain the cyclic processes underlying hyperinsulinemia-induced insulin resistance in muscle, a process directly relevant to the etiology and disease progression of type 2 diabetes.
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Affiliation(s)
- Haoning Howard Cen
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bahira Hussein
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - José Diego Botezelli
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Su Wang
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jiashuo Aaron Zhang
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nilou Noursadeghi
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Niels Jessen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Brian Rodrigues
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - James A Timmons
- Augur Precision Medicine LTD, Stirling University Innovation Park, Stirling, Scotland.,William Harvey Research Institute, Queen Mary University of London, London, UK
| | - James D Johnson
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
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19
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Piorońska W, Nwosu ZC, Han M, Büttner M, Ebert MP, Dooley S, Meyer C. Dysregulated paired related homeobox 1 impacts on hepatocellular carcinoma phenotypes. BMC Cancer 2021; 21:1006. [PMID: 34496784 PMCID: PMC8424914 DOI: 10.1186/s12885-021-08637-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 07/27/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a major cause of cancer-related death. Paired related homeobox 1 (PRRX1) is a transcription factor that regulates cell growth and differentiation, but its importance in HCC is unclear. METHODS We examined the expression pattern of PRRX1 in nine microarray datasets of human HCC tumour samples (n > 1100) and analyzed its function in HCC cell lines. In addition, we performed gene set enrichment, Kaplan-Meier overall survival analysis, metabolomics and functional assays. RESULTS PRRX1 is frequently upregulated in human HCC. Pathway enrichment analysis predicted a direct correlation between PRRX1 and focal adhesion and epithelial-mesenchymal transition. High expression of PRRX1 and low ZEB1 or high ZEB2 significantly predicted better overall survival in HCC patients. In contrast, metabolic processes correlated inversely and transcriptional analyses revealed that glycolysis, TCA cycle and amino acid metabolism were affected. These findings were confirmed by metabolomics analysis. At the phenotypic level, PRRX1 knockdown accelerated proliferation and clonogenicity in HCC cell lines. CONCLUSIONS Our results suggest that PRRX1 controls metabolism, has a tumour suppressive role, and may function in cooperation with ZEB1/2. These findings have functional relevance in HCC, including in understanding transcriptional control of distinct cancer hallmarks.
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Affiliation(s)
- Weronika Piorońska
- Department of Medicine II, Section Molecular Hepatology, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Zeribe Chike Nwosu
- Department of Medicine II, Section Molecular Hepatology, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany.,Current address: Department of Molecular and Integrative Physiology, Rogel Cancer Centre, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Mei Han
- Department of Medicine II, Section Molecular Hepatology, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany.,Current address: Department of Internal Medicine, the Second Hospital of Dalian Medical University, Shahekou District, Dalian City, Liaoning Province, China
| | - Michael Büttner
- The Metabolomics Core Technology Platform of the University of Heidelberg, Im Neuenheimer Feld 360, 69120, Heidelberg, Germany
| | - Matthias Philip Ebert
- Department of Medicine II, Section Molecular Hepatology, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Steven Dooley
- Department of Medicine II, Section Molecular Hepatology, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Christoph Meyer
- Department of Medicine II, Section Molecular Hepatology, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany.
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20
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McKendry J, Stokes T, Mcleod JC, Phillips SM. Resistance Exercise, Aging, Disuse, and Muscle Protein Metabolism. Compr Physiol 2021; 11:2249-2278. [PMID: 34190341 DOI: 10.1002/cphy.c200029] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Skeletal muscle is the organ of locomotion, its optimal function is critical for athletic performance, and is also important for health due to its contribution to resting metabolic rate and as a site for glucose uptake and storage. Numerous endogenous and exogenous factors influence muscle mass. Much of what is currently known regarding muscle protein turnover is owed to the development and use of stable isotope tracers. Skeletal muscle mass is determined by the meal- and contraction-induced alterations of muscle protein synthesis and muscle protein breakdown. Increased loading as resistance training is the most potent nonpharmacological strategy by which skeletal muscle mass can be increased. Conversely, aging (sarcopenia) and muscle disuse lead to the development of anabolic resistance and contribute to the loss of skeletal muscle mass. Nascent omics-based technologies have significantly improved our understanding surrounding the regulation of skeletal muscle mass at the gene, transcript, and protein levels. Despite significant advances surrounding the mechanistic intricacies that underpin changes in skeletal muscle mass, these processes are complex, and more work is certainly needed. In this article, we provide an overview of the importance of skeletal muscle, describe the influence that resistance training, aging, and disuse exert on muscle protein turnover and the molecular regulatory processes that contribute to changes in muscle protein abundance. © 2021 American Physiological Society. Compr Physiol 11:2249-2278, 2021.
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Affiliation(s)
- James McKendry
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
| | - Tanner Stokes
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
| | - Jonathan C Mcleod
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
| | - Stuart M Phillips
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
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21
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Lu X, Abdalla IM, Nazar M, Fan Y, Zhang Z, Wu X, Xu T, Yang Z. Genome-Wide Association Study on Reproduction-Related Body-Shape Traits of Chinese Holstein Cows. Animals (Basel) 2021; 11:1927. [PMID: 34203505 PMCID: PMC8300307 DOI: 10.3390/ani11071927] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/21/2021] [Accepted: 06/25/2021] [Indexed: 12/24/2022] Open
Abstract
Reproduction is an important production activity for dairy cows, and their reproductive performance can directly affect the level of farmers' income. To better understand the genomic regions and biological pathways of reproduction-related traits of dairy cows, in the present study, three body shape traits-Loin Strength (LS), Rump Angle (RA), and Pin Width (PW)-were selected as indicators of the reproductive ability of cows, and we conducted genome-wide association analyses on them. The heritability of these three traits was medium, ranging from 0.20 to 0.38. A total of 11 significant single-nucleotide polymorphisms (SNPs) were detected associated with these three traits. Bioinformatics analysis was performed on genes close to the significant SNPs (within 200 Kb) of LS, RA, and PW, and we found that these genes were totally enriched in 20 gene ontology terms and six KEGG signaling pathways. Finally, the five genes CDH12, TARP, PCDH9, DTHD1, and ARAP2 were selected as candidate genes that might affect LS. The six genes LOC781835, FSTL4, ATG4C, SH3BP4, DMP1, and DSPP were selected as candidate genes that might affect RA. The five genes USP6NL, CNTN3, LOC101907665, UPF2, and ECHDC3 were selected as candidate genes that might affect the PW of Chinese Holstein cows. Our results could provide useful biological information for the improvement of body shape traits and contribute to the genomic selection of Chinese Holstein cows.
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Affiliation(s)
- Xubin Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, China; (X.L.); (I.M.A.); (M.N.); (Y.F.); (Z.Z.); (X.W.)
| | - Ismail Mohamed Abdalla
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, China; (X.L.); (I.M.A.); (M.N.); (Y.F.); (Z.Z.); (X.W.)
| | - Mudasir Nazar
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, China; (X.L.); (I.M.A.); (M.N.); (Y.F.); (Z.Z.); (X.W.)
| | - Yongliang Fan
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, China; (X.L.); (I.M.A.); (M.N.); (Y.F.); (Z.Z.); (X.W.)
| | - Zhipeng Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, China; (X.L.); (I.M.A.); (M.N.); (Y.F.); (Z.Z.); (X.W.)
| | - Xinyue Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, China; (X.L.); (I.M.A.); (M.N.); (Y.F.); (Z.Z.); (X.W.)
| | - Tianle Xu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China;
| | - Zhangping Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, China; (X.L.); (I.M.A.); (M.N.); (Y.F.); (Z.Z.); (X.W.)
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22
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Molecular Transducers of Human Skeletal Muscle Remodeling under Different Loading States. Cell Rep 2021; 32:107980. [PMID: 32755574 PMCID: PMC7408494 DOI: 10.1016/j.celrep.2020.107980] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 02/27/2020] [Accepted: 07/09/2020] [Indexed: 12/11/2022] Open
Abstract
Loading of skeletal muscle changes the tissue phenotype reflecting altered metabolic and functional demands. In humans, heterogeneous adaptation to loading complicates the identification of the underpinning molecular regulators. A within-person differential loading and analysis strategy reduces heterogeneity for changes in muscle mass by ∼40% and uses a genome-wide transcriptome method that models each mRNA from coding exons and 3' and 5' untranslated regions (UTRs). Our strategy detects ∼3-4 times more regulated genes than similarly sized studies, including substantial UTR-selective regulation undetected by other methods. We discover a core of 141 genes correlated to muscle growth, which we validate from newly analyzed independent samples (n = 100). Further validating these identified genes via RNAi in primary muscle cells, we demonstrate that members of the core genes were regulators of protein synthesis. Using proteome-constrained networks and pathway analysis reveals notable relationships with the molecular characteristics of human muscle aging and insulin sensitivity, as well as potential drug therapies.
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23
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Antonaros F, Zenatelli R, Guerri G, Bertelli M, Locatelli C, Vione B, Catapano F, Gori A, Vitale L, Pelleri MC, Ramacieri G, Cocchi G, Strippoli P, Caracausi M, Piovesan A. The transcriptome profile of human trisomy 21 blood cells. Hum Genomics 2021; 15:25. [PMID: 33933170 PMCID: PMC8088681 DOI: 10.1186/s40246-021-00325-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/14/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Trisomy 21 (T21) is a genetic alteration characterised by the presence of an extra full or partial human chromosome 21 (Hsa21) leading to Down syndrome (DS), the most common form of intellectual disability (ID). It is broadly agreed that the presence of extra genetic material in T21 gives origin to an altered expression of genes located on Hsa21 leading to DS phenotype. The aim of this study was to analyse T21 and normal control blood cell gene expression profiles obtained by total RNA sequencing (RNA-Seq). RESULTS The results were elaborated by the TRAM (Transcriptome Mapper) software which generated a differential transcriptome map between human T21 and normal control blood cells providing the gene expression ratios for 17,867 loci. The obtained gene expression profiles were validated through real-time reverse transcription polymerase chain reaction (RT-PCR) assay and compared with previously published data. A post-analysis through transcriptome mapping allowed the identification of the segmental (regional) variation of the expression level across the whole genome (segment-based analysis of expression). Interestingly, the most over-expressed genes encode for interferon-induced proteins, two of them (MX1 and MX2 genes) mapping on Hsa21 (21q22.3). The altered expression of genes involved in mitochondrial translation and energy production also emerged, followed by the altered expression of genes encoding for the folate cycle enzyme, GART, and the folate transporter, SLC19A1. CONCLUSIONS The alteration of these pathways might be linked and involved in the manifestation of ID in DS.
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Affiliation(s)
- Francesca Antonaros
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Rossella Zenatelli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy.,Current Address: Department of Molecular and Translational Medicine (DMMT), University of Brescia, Viale Europa 11, 24123, Brescia, BS, Italy
| | - Giulia Guerri
- MAGI'S Lab, Via delle Maioliche 57/D, 38068, Rovereto, TN, Italy
| | - Matteo Bertelli
- MAGI'S Lab, Via delle Maioliche 57/D, 38068, Rovereto, TN, Italy
| | - Chiara Locatelli
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Via Massarenti 9, 40138, Bologna, BO, Italy
| | - Beatrice Vione
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Francesca Catapano
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy.,Current Address: Department of Medical Biotechnologies, University of Siena, Strada delle Scotte, 4, 53100, Siena, SI, Italy
| | - Alice Gori
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Lorenza Vitale
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Maria Chiara Pelleri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Giuseppe Ramacieri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Guido Cocchi
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138, Bologna, BO, Italy
| | - Pierluigi Strippoli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Maria Caracausi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy.
| | - Allison Piovesan
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
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24
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Bertozzi TM, Takahashi N, Hanin G, Kazachenka A, Ferguson-Smith AC. A spontaneous genetically induced epiallele at a retrotransposon shapes host genome function. eLife 2021; 10:e65233. [PMID: 33755012 PMCID: PMC8084528 DOI: 10.7554/elife.65233] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/22/2021] [Indexed: 12/14/2022] Open
Abstract
Intracisternal A-particles (IAPs) are endogenous retroviruses (ERVs) responsible for most insertional mutations in the mouse. Full-length IAPs harbour genes flanked by long terminal repeats (LTRs). Here, we identify a solo LTR IAP variant (Iap5-1solo) recently formed in the inbred C57BL/6J mouse strain. In contrast to the C57BL/6J full-length IAP at this locus (Iap5-1full), Iap5-1solo lacks DNA methylation and H3K9 trimethylation. The distinct DNA methylation levels between the two alleles are established during preimplantation development, likely due to loss of KRAB zinc finger protein binding at the Iap5-1solo variant. Iap5-1solo methylation increases and becomes more variable in a hybrid genetic background yet is unresponsive to maternal dietary methyl supplementation. Differential epigenetic modification of the two variants is associated with metabolic differences and tissue-specific changes in adjacent gene expression. Our characterisation of Iap5-1 as a genetically induced epiallele with functional consequences establishes a new model to study transposable element repression and host-element co-evolution.
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Affiliation(s)
- Tessa M Bertozzi
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Nozomi Takahashi
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Geula Hanin
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
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25
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Boyko AI, Artiukhov AV, Kaehne T, di Salvo ML, Bonaccorsi di Patti MC, Contestabile R, Tramonti A, Bunik VI. Isoforms of the DHTKD1-Encoded 2-Oxoadipate Dehydrogenase, Identified in Animal Tissues, Are not Observed upon the Human DHTKD1 Expression in Bacterial or Yeast Systems. BIOCHEMISTRY (MOSCOW) 2021; 85:920-929. [PMID: 33045952 DOI: 10.1134/s0006297920080076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Unlike the OGDH-encoded 2-oxoglutarate dehydrogenase (OGDH), which is an essential enzyme present in all animal tissues, expression of the DHTKD1-encoded isoenzyme, 2-oxoadipate dehydrogenase (OADH), depends on a number of factors, and mutant DHTKD1 phenotypes are rarely manifested. Physiological significance of OADH is also obscured by the fact that both isoenzymes transform 2-oxoglutarate and 2-oxoadipate. By analogy with other members of the 2-oxo acid dehydrogenases family, OADH is assumed to be a component of the multienzyme complex that catalyzes oxidative decarboxylation of 2-oxoadipate. This study aims at molecular characterization of OADH from animal tissues. Phylogenetic analysis of 2-oxo acid dehydrogenases reveals OADH only in animals and Dictyostelium discoideum slime mold, within a common branch with bacterial OGDH. Examination of partially purified animal OADH by immunoblotting and mass spectrometry identifies two OADH isoforms with molecular weights of about 130 and 70 kDa. These isoforms are not observed upon the expression of human DHTKD1 protein in either bacterial or yeast system, where the synthesized OADH is of expected molecular weight (about 100 kDa). Thus, the OADH isoforms present in animal tissues, may result from the animal-specific regulation of the DHTKD1 expression and/or posttranslational modifications of the encoded protein. Mapping of the peptides identified in the OADH preparations, onto the protein structure suggests that the 70-kDa isoform is truncated at the N-terminus, but retains the active site. Since the N-terminal domain of OGDH is required for the formation of the multienzyme complex, it is possible that the 70-kDa isoform catalyzes non-oxidative transformation of dicarboxylic 2-oxo acids that does not require the multienzyme structure. In this case, the ratio of the OADH isoforms in animal tissues may correspond to the ratio between the oxidative and non-oxidative decarboxylation of 2-oxoadipate.
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Affiliation(s)
- A I Boyko
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - A V Artiukhov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - T Kaehne
- Institute of Experimental Internal Medicine, Otto-von-Guericke University, Magdeburg, 39120, Germany
| | - M L di Salvo
- Department of Biological Sciences A. Rossi Fanelli, Sapienza University, Rome, 00185, Italy
| | | | - R Contestabile
- Department of Biological Sciences A. Rossi Fanelli, Sapienza University, Rome, 00185, Italy
| | - A Tramonti
- Department of Biological Sciences A. Rossi Fanelli, Sapienza University, Rome, 00185, Italy.,Institute of Molecular Biology and Pathology, Council of National Research, Rome, 00185, Italy
| | - V I Bunik
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.,Department of Biological Chemistry, Sechenov First Moscow State Medical University, Moscow, 119146, Russia
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26
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Artiukhov AV, Kazantsev AV, Lukashev NV, Bellinzoni M, Bunik VI. Selective Inhibition of 2-Oxoglutarate and 2-Oxoadipate Dehydrogenases by the Phosphonate Analogs of Their 2-Oxo Acid Substrates. Front Chem 2021; 8:596187. [PMID: 33511099 PMCID: PMC7835950 DOI: 10.3389/fchem.2020.596187] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/10/2020] [Indexed: 11/13/2022] Open
Abstract
Phosphonate analogs of pyruvate and 2-oxoglutarate are established specific inhibitors of cognate 2-oxo acid dehydrogenases. The present work develops application of this class of compounds to specific in vivo inhibition of 2-oxoglutarate dehydrogenase (OGDH) and its isoenzyme, 2-oxoadipate dehydrogenase (OADH). The isoenzymes-enriched preparations from the rat tissues with different expression of OADH and OGDH are used to characterize their interaction with 2-oxoglutarate (OG), 2-oxoadipate (OA) and the phosphonate analogs. Despite a 100-fold difference in the isoenzymes ratio in the heart and liver, similar Michaelis saturations by OG are inherent in the enzyme preparations from these tissues (KmOG = 0.45 ± 0.06 and 0.27 ± 0.026 mM, respectively), indicating no significant contribution of OADH to the OGDH reaction, or similar affinities of the isoenzymes to OG. However, the preparations differ in the catalysis of OADH reaction. The heart preparation, where OADH/OGDH ratio is ≈ 0.01, possesses low-affinity sites to OA (KmOA = 0.55 ± 0.07 mM). The liver preparation, where OADH/OGDH ratio is ≈ 1.6, demonstrates a biphasic saturation with OA: the low-affinity sites (Km,2OA = 0.45 ± 0.12 mM) are similar to those of the heart preparation; the high-affinity sites (Km,1OA = 0.008 ± 0.001 mM), revealed in the liver preparation only, are attributed to OADH. Phosphonate analogs of C5-C7 dicarboxylic 2-oxo acids inhibit OGDH and OADH competitively to 2-oxo substrates in all sites. The high-affinity sites for OA are affected the least by the C5 analog (succinyl phosphonate) and the most by the C7 one (adipoyl phosphonate). The opposite reactivity is inherent in both the low-affinity OA-binding sites and OG-binding sites. The C6 analog (glutaryl phosphonate) does not exhibit a significant preference to either OADH or OGDH. Structural analysis of the phosphonates binding to OADH and OGDH reveals the substitution of a tyrosine residue in OGDH for a serine residue in OADH among structural determinants of the preferential binding of the bulkier ligands to OADH. The consistent kinetic and structural results expose adipoyl phosphonate as a valuable pharmacological tool for specific in vivo inhibition of the DHTKD1-encoded OADH, a new member of mammalian family of 2-oxo acid dehydrogenases, up-regulated in some cancers and associated with diabetes and obesity.
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Affiliation(s)
- Artem V Artiukhov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Department of Biokinetics, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Marco Bellinzoni
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS, Université de Paris, Paris, France
| | - Victoria I Bunik
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Department of Biokinetics, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Department of Biochemistry, Sechenov University, Moscow, Russia
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27
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Baasch-Skytte T, Gunnarsson TP, Fiorenza M, Bangsbo J. Skeletal muscle proteins important for work capacity are altered with type 2 diabetes - Effect of 10-20-30 training. Physiol Rep 2021; 9:e14681. [PMID: 33426802 PMCID: PMC7797308 DOI: 10.14814/phy2.14681] [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: 10/28/2020] [Accepted: 11/01/2020] [Indexed: 11/24/2022] Open
Abstract
The study examined whether men with type 2 diabetes exhibit lower expression of muscle proteins important for exercise capacity, and whether exercise training promotes adaptations in these proteins. In a cross-sectional and longitudinal study, conducted at the University of Copenhagen. Twelve men with type 2 diabetes (T2D) were compared to eleven nondiabetes counterparts (ND) matched for age and body composition (body fat percentage). T2D underwent 10 weeks of high-intensity interval exercise training (10-20-30 training). T2D had lower expression of SOD1 (-62%; p < 0.001) and ETC complex V (-34%; p = 0.003), along with higher expression of ETC complex IV (+66%; p = 0.007), MFN2 (+62%; p = 0.001), and DRP1 (+30%; p = 0.028) compared to ND. T2D had higher (p < 0.001) expression of Na+ /K+ α1 (+98%), α2 (+114%), and NHE1 (+144%) than ND. In T2D, training increased exercise capacity (+9%; p < 0.001) as well as expression of SOD2 (+44%; p = 0.029), ETC complex II (+25%; p = 0.035), III (+52%; p = 0.041), IV (+23%; p = 0.005), and V (+21%; p = 0.035), CS activity (+32%; p = 0.006) as well as Na+ /K+ α1 (+24%; p = 0.034), Kir6.2 (+36%; p = 0.029), and MCT1 (+20%; p = 0.007). Men with type 2 diabetes exhibited altered expression of a multitude of skeletal muscle proteins important for exercise capacity. Ten weeks of 10-20-30 training upregulated expression of muscle proteins regulating antioxidant defense, mitochondrial function, and ion handling while enhancing exercise capacity in men with type 2 diabetes.
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Affiliation(s)
- Thomas Baasch-Skytte
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Thomas P Gunnarsson
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Matteo Fiorenza
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Jens Bangsbo
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
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28
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Nikpay M, Lau P, Soubeyrand S, Whytock KL, Beehler K, Pileggi C, Ghosh S, Harper ME, Dent R, McPherson R. SGCG rs679482 Associates With Weight Loss Success in Response to an Intensively Supervised Outpatient Program. Diabetes 2020; 69:2017-2026. [PMID: 32527767 DOI: 10.2337/db20-0219] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/07/2020] [Indexed: 02/07/2023]
Abstract
Weight loss in response to energy restriction is highly variable, and identification of genetic contributors can provide insights into underlying biology. Leveraging 1000 Genomes imputed genotypes, we carried out genome-wide association study (GWAS) analysis in 551 unrelated obese subjects of European ancestry who participated in an intensively supervised weight loss program with replication of promising signals in an independent sample of 1,331 obese subjects who completed the program at a later date. By single nucleotide polymorphism-based and sib-pair analysis, we show that that weight loss is a heritable trait, with estimated heritability (h 2 = 0.49) within the range reported for obesity. We find rs679482, intronic to SGCG (sarcoglycan γ), highly expressed in skeletal muscle, to concordantly associate with weight loss in discovery and replication samples reaching GWAS significance in the combined meta-analysis (β = -0.35, P = 1.7 × 10-12). Located in a region of open chromatin, rs679482 is predicted to bind DMRT2, and allele-specific transcription factor binding analysis indicates preferential binding of DMRT2 to rs679482-A. Concordantly, rs679482-A impairs native repressor activity and increases basal and DMRT2-mediated enhancer activity. These findings confirm that weight loss is a heritable trait and provide evidence by which a novel variant in SGCG, rs679482, leads to impaired diet response.
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Affiliation(s)
- Majid Nikpay
- Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, Canada
| | - Paulina Lau
- Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, Canada
| | | | - Katey L Whytock
- Translational Research Institute for Metabolism and Diabetes, AdventHealth, Orlando, FL
| | - Kaitlyn Beehler
- Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, Canada
| | - Chantal Pileggi
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Sujoy Ghosh
- Duke-NUS Medical School, Singapore, Singapore
| | - Mary-Ellen Harper
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Robert Dent
- Weight Management Clinic, The Ottawa Hospital, Ottawa, Canada
| | - Ruth McPherson
- Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, Canada
- Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, Canada
- Division of Cardiology, University of Ottawa Heart Institute, Ottawa, Canada
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29
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Abstract
ADP-ribosylation is an intricate and versatile posttranslational modification involved in the regulation of a vast variety of cellular processes in all kingdoms of life. Its complexity derives from the varied range of different chemical linkages, including to several amino acid side chains as well as nucleic acids termini and bases, it can adopt. In this review, we provide an overview of the different families of (ADP-ribosyl)hydrolases. We discuss their molecular functions, physiological roles, and influence on human health and disease. Together, the accumulated data support the increasingly compelling view that (ADP-ribosyl)hydrolases are a vital element within ADP-ribosyl signaling pathways and they hold the potential for novel therapeutic approaches as well as a deeper understanding of ADP-ribosylation as a whole.
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Affiliation(s)
| | - Luca Palazzo
- Institute for the Experimental Endocrinology and Oncology, National Research Council of Italy, 80145 Naples, Italy
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
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30
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Gray ID, Kross AR, Renfrew ME, Wood P. Precision Medicine in Lifestyle Medicine: The Way of the Future? Am J Lifestyle Med 2020; 14:169-186. [PMID: 32231483 PMCID: PMC7092395 DOI: 10.1177/1559827619834527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/21/2018] [Accepted: 02/08/2019] [Indexed: 02/06/2023] Open
Abstract
Precision medicine has captured the imagination of the medical community with visions of therapies precisely targeted to the specific individual's genetic, biological, social, and environmental profile. However, in practice it has become synonymous with genomic medicine. As such its successes have been limited, with poor predictive or clinical value for the majority of people. It adds little to lifestyle medicine, other than in establishing why a healthy lifestyle is effective in combatting chronic disease. The challenge of lifestyle medicine remains getting people to actually adopt, sustain, and naturalize a healthy lifestyle, and this will require an approach that treats the patient as a person with individual needs and providing them with suitable types of support. The future of lifestyle medicine is holistic and person-centered rather than technological.
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Affiliation(s)
- Ian D. Gray
- Avondale College of Higher Education, Cooranbong,
New South Wales, Australia
| | - Andrea R. Kross
- Avondale College of Higher Education, Cooranbong,
New South Wales, Australia
| | - Melanie E. Renfrew
- Avondale College of Higher Education, Cooranbong,
New South Wales, Australia
| | - Paul Wood
- Avondale College of Higher Education, Cooranbong,
New South Wales, Australia
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31
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Joanisse S, Lim C, McKendry J, Mcleod JC, Stokes T, Phillips SM. Recent advances in understanding resistance exercise training-induced skeletal muscle hypertrophy in humans. F1000Res 2020; 9. [PMID: 32148775 PMCID: PMC7043134 DOI: 10.12688/f1000research.21588.1] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/18/2020] [Indexed: 12/22/2022] Open
Abstract
Skeletal muscle plays a pivotal role in the maintenance of physical and metabolic health and, critically, mobility. Accordingly, strategies focused on increasing the quality and quantity of skeletal muscle are relevant, and resistance exercise is foundational to the process of functional hypertrophy. Much of our current understanding of skeletal muscle hypertrophy can be attributed to the development and utilization of stable isotopically labeled tracers. We know that resistance exercise and sufficient protein intake act synergistically and provide the most effective stimuli to enhance skeletal muscle mass; however, the molecular intricacies that underpin the tremendous response variability to resistance exercise-induced hypertrophy are complex. The purpose of this review is to discuss recent studies with the aim of shedding light on key regulatory mechanisms that dictate hypertrophic gains in skeletal muscle mass. We also aim to provide a brief up-to-date summary of the recent advances in our understanding of skeletal muscle hypertrophy in response to resistance training in humans.
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Affiliation(s)
- Sophie Joanisse
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, ON, Canada
| | - Changhyun Lim
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, ON, Canada
| | - James McKendry
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, ON, Canada
| | - Jonathan C Mcleod
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, ON, Canada
| | - Tanner Stokes
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, ON, Canada
| | - Stuart M Phillips
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, ON, Canada
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32
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Artiukhov AV, Grabarska A, Gumbarewicz E, Aleshin VA, Kähne T, Obata T, Kazantsev AV, Lukashev NV, Stepulak A, Fernie AR, Bunik VI. Synthetic analogues of 2-oxo acids discriminate metabolic contribution of the 2-oxoglutarate and 2-oxoadipate dehydrogenases in mammalian cells and tissues. Sci Rep 2020; 10:1886. [PMID: 32024885 PMCID: PMC7002488 DOI: 10.1038/s41598-020-58701-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/03/2020] [Indexed: 02/06/2023] Open
Abstract
The biological significance of the DHTKD1-encoded 2-oxoadipate dehydrogenase (OADH) remains obscure due to its catalytic redundancy with the ubiquitous OGDH-encoded 2-oxoglutarate dehydrogenase (OGDH). In this work, metabolic contributions of OADH and OGDH are discriminated by exposure of cells/tissues with different DHTKD1 expression to the synthesized phosphonate analogues of homologous 2-oxodicarboxylates. The saccharopine pathway intermediates and phosphorylated sugars are abundant when cellular expressions of DHTKD1 and OGDH are comparable, while nicotinate and non-phosphorylated sugars are when DHTKD1 expression is order(s) of magnitude lower than that of OGDH. Using succinyl, glutaryl and adipoyl phosphonates on the enzyme preparations from tissues with varied DHTKD1 expression reveals the contributions of OADH and OGDH to oxidation of 2-oxoadipate and 2-oxoglutarate in vitro. In the phosphonates-treated cells with the high and low DHTKD1 expression, adipate or glutarate, correspondingly, are the most affected metabolites. The marker of fatty acid β-oxidation, adipate, is mostly decreased by the shorter, OGDH-preferring, phosphonate, in agreement with the known OGDH dependence of β-oxidation. The longest, OADH-preferring, phosphonate mostly affects the glutarate level. Coupled decreases in sugars and nicotinate upon the OADH inhibition link the perturbation in glucose homeostasis, known in OADH mutants, to the nicotinate-dependent NAD metabolism.
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Affiliation(s)
- Artem V Artiukhov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Aneta Grabarska
- Department of Biochemistry and Molecular Biology of Medical University of Lublin, Lublin, Poland
| | - Ewelina Gumbarewicz
- Department of Biochemistry and Molecular Biology of Medical University of Lublin, Lublin, Poland
| | - Vasily A Aleshin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Thilo Kähne
- Institute of Experimental Internal Medicine, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Toshihiro Obata
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Department of Biochemistry, George W. Beadle Center, University of Nebraska-Lincoln, Lincoln, NE, 68588-0664, USA
| | | | | | - Andrzej Stepulak
- Department of Biochemistry and Molecular Biology of Medical University of Lublin, Lublin, Poland
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Victoria I Bunik
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
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33
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Jansen HT, Trojahn S, Saxton MW, Quackenbush CR, Evans Hutzenbiler BD, Nelson OL, Cornejo OE, Robbins CT, Kelley JL. Hibernation induces widespread transcriptional remodeling in metabolic tissues of the grizzly bear. Commun Biol 2019; 2:336. [PMID: 31531397 PMCID: PMC6744400 DOI: 10.1038/s42003-019-0574-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/12/2019] [Indexed: 12/20/2022] Open
Abstract
Revealing the mechanisms underlying the reversible physiology of hibernation could have applications to both human and animal health as hibernation is often associated with disease-like states. The present study uses RNA-sequencing to reveal the tissue and seasonal transcriptional changes occurring in grizzly bears (Ursus arctos horribilis). Comparing hibernation to other seasons, bear adipose has a greater number of differentially expressed genes than liver and skeletal muscle. During hyperphagia, adipose has more than 900 differentially expressed genes compared to active season. Hibernation is characterized by reduced expression of genes associated with insulin signaling, muscle protein degradation, and urea production, and increased expression within muscle protein anabolic pathways. Across all three tissues we find a subset of shared differentially expressed genes, some of which are uncharacterized, that together may reflect a common regulatory mechanism. The identified gene families could be useful for developing novel therapeutics to treat human and animal diseases.
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Affiliation(s)
- Heiko T. Jansen
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA 99164 USA
| | - Shawn Trojahn
- School of Biological Sciences, Washington State University, Pullman, WA 99164 USA
| | - Michael W. Saxton
- School of Biological Sciences, Washington State University, Pullman, WA 99164 USA
| | - Corey R. Quackenbush
- School of Biological Sciences, Washington State University, Pullman, WA 99164 USA
| | - Brandon D. Evans Hutzenbiler
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA 99164 USA
- School of the Environment, Washington State University, Pullman, WA 99164 USA
| | - O. Lynne Nelson
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164 USA
| | - Omar E. Cornejo
- School of Biological Sciences, Washington State University, Pullman, WA 99164 USA
| | - Charles T. Robbins
- School of Biological Sciences, Washington State University, Pullman, WA 99164 USA
- School of the Environment, Washington State University, Pullman, WA 99164 USA
| | - Joanna L. Kelley
- School of Biological Sciences, Washington State University, Pullman, WA 99164 USA
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34
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Timmons JA, Volmar C, Crossland H, Phillips BE, Sood S, Janczura KJ, Törmäkangas T, Kujala UM, Kraus WE, Atherton PJ, Wahlestedt C. Longevity-related molecular pathways are subject to midlife "switch" in humans. Aging Cell 2019; 18:e12970. [PMID: 31168962 PMCID: PMC6612641 DOI: 10.1111/acel.12970] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 04/30/2019] [Accepted: 05/03/2019] [Indexed: 12/12/2022] Open
Abstract
Emerging evidence indicates that molecular aging may follow nonlinear or discontinuous trajectories. Whether this occurs in human neuromuscular tissue, particularly for the noncoding transcriptome, and independent of metabolic and aerobic capacities, is unknown. Applying our novel RNA method to quantify tissue coding and long noncoding RNA (lncRNA), we identified ~800 transcripts tracking with age up to ~60 years in human muscle and brain. In silico analysis demonstrated that this temporary linear "signature" was regulated by drugs, which reduce mortality or extend life span in model organisms, including 24 inhibitors of the IGF-1/PI3K/mTOR pathway that mimicked, and 5 activators that opposed, the signature. We profiled Rapamycin in nondividing primary human myotubes (n = 32 HTA 2.0 arrays) and determined the transcript signature for reactive oxygen species in neurons, confirming that our age signature was largely regulated in the "pro-longevity" direction. Quantitative network modeling demonstrated that age-regulated ncRNA equaled the contribution of protein-coding RNA within structures, but tended to have a lower heritability, implying lncRNA may better reflect environmental influences. Genes ECSIT, UNC13, and SKAP2 contributed to a network that did not respond to Rapamycin, and was associated with "neuron apoptotic processes" in protein-protein interaction analysis (FDR = 2.4%). ECSIT links inflammation with the continued age-related downwards trajectory of mitochondrial complex I gene expression (FDR < 0.01%), implying that sustained inhibition of ECSIT may be maladaptive. The present observations link, for the first time, model organism longevity programs with the endogenous but temporary genome-wide responses to aging in humans, revealing a pattern that may ultimately underpin personalized rates of health span.
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Affiliation(s)
- James A. Timmons
- Division of Genetics and Molecular MedicineKing's College LondonLondonUK
- Scion HouseStirling University Innovation ParkStirlingUK
| | - Claude‐Henry Volmar
- Department of Psychiatry and Behavioral Sciences, Center for Therapeutic InnovationUniversity of Miami Miller School of MedicineMiamiFlorida
| | - Hannah Crossland
- Division of Genetics and Molecular MedicineKing's College LondonLondonUK
- School of Medicine, Royal Derby HospitalUniversity of NottinghamDerbyUK
| | | | - Sanjana Sood
- Division of Genetics and Molecular MedicineKing's College LondonLondonUK
| | - Karolina J. Janczura
- Department of Psychiatry and Behavioral Sciences, Center for Therapeutic InnovationUniversity of Miami Miller School of MedicineMiamiFlorida
| | - Timo Törmäkangas
- Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
| | - Urho M. Kujala
- Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
| | | | | | - Claes Wahlestedt
- Department of Psychiatry and Behavioral Sciences, Center for Therapeutic InnovationUniversity of Miami Miller School of MedicineMiamiFlorida
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35
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Reference quantitative transcriptome dataset for adult Caenorhabditis elegans. Data Brief 2019; 25:104152. [PMID: 31440537 PMCID: PMC6700341 DOI: 10.1016/j.dib.2019.104152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 02/06/2023] Open
Abstract
Caenorhabditis elegans is a nematode widely used in biology and genomics as a model organism. We provide an integrated, quantitative reference map for the transcriptome of whole, wild type Bristol N2 strain C. elegans worms. The map has been obtained by meta-analysis of 110 gene expression profiles available in Gene Expression Omnibus (GEO) repository and integrated using the computational biology tool Transcriptome Mapper (TRAM). Following probe assignment to the relative locus and intra- and inter-sample normalization (in particular using the scaled quantile method), a mean, consensus reference value is provided for 45,932 transcripts, along with standard deviation. Expression values are all mapped in the context of genomic coordinates. The map provides easy access to relationships among expression values of different genes in this standard condition, highlights genomic segments with relatively high over-/under-expression and may serve as a reference to test for gene expression variation for both individual genes and the whole transcriptome in specific biological conditions (e.g. mutated strains or differently grown worms).
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