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Liu Y, Ma Y, Yang W, Lin Q, Xing Y, Shao H, Li P, He Y, Duan W, Wei X. Integrated proteomics and metabolomics analysis of sclerosis-related proteins and femoral head necrosis following internal fixation of femoral neck fractures. Sci Rep 2024; 14:13207. [PMID: 38851808 PMCID: PMC11162501 DOI: 10.1038/s41598-024-63837-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 06/03/2024] [Indexed: 06/10/2024] Open
Abstract
Femoral head necrosis (FHN) is a serious complication after femoral neck fractures (FNF), often linked to sclerosis around screw paths. Our study aimed to uncover the proteomic and metabolomic underpinnings of FHN and sclerosis using integrated proteomics and metabolomics analyses. We identified differentially expressed proteins (DEPs) and metabolites (DEMs) among three groups: patients with FNF (Group A), sclerosis (Group B), and FHN (Group C). Using the Kyoto Encyclopedia of Genes and Genomes and Gene Ontology enrichment analyses, we examined the roles of these proteins and metabolites. Our findings highlight the significant differences across the groups, with 218 DEPs and 44 DEMs identified between the sclerosis and FNF groups, 247 DEPs and 31 DEMs between the FHN and sclerosis groups, and a stark 682 DEPs and 94 DEMs between the FHN and FNF groups. Activities related to carbonate dehydratase and hydrolase were similar in the FHN and sclerosis groups, whereas extracellular region and lysosome were prevalent in the FHN and FNF groups. Our study also emphasized the involvement of the PI3K-Akt pathway in sclerosis and FHN. Moreover, the key metabolic pathways were implicated in glycerophospholipid metabolism and retrograde endocannabinoid signaling. Using western blotting, we confirmed the pivotal role of specific genes/proteins such as ITGB5, TNXB, CA II, and CA III in sclerosis and acid phosphatase 5 and cathepsin K in FHN. This comprehensive analyses elucidates the molecular mechanisms behind sclerosis and FHN and suggests potential biomarkers and therapeutic targets, paving the way for improved treatment strategies. Further validation of the findings is necessary to strengthen the robustness and reliability of the results.
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Affiliation(s)
- Yang Liu
- Department of Orthopaedics, Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, No. 382, Wuyi Road, Taiyuan, 030001, Shanxi, China
| | - Yongsheng Ma
- Department of Orthopaedics, Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, No. 382, Wuyi Road, Taiyuan, 030001, Shanxi, China
| | - Wenming Yang
- Department of Orthopaedics, Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, No. 382, Wuyi Road, Taiyuan, 030001, Shanxi, China
| | - Qitai Lin
- Department of Orthopaedics, Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, No. 382, Wuyi Road, Taiyuan, 030001, Shanxi, China
| | - Yugang Xing
- Department of Orthopaedics, Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, No. 382, Wuyi Road, Taiyuan, 030001, Shanxi, China
| | - Huifeng Shao
- School of Mechanical Engineering, Hangzhou Dianzi University, Hangzhou, 310018, China
- Key Laboratory of 3D Printing Process and Equipment of Zhejiang Province, School of Mechanical Engineering, Zhejiang University, No. 866, Yuhang Tang Road, Hangzhou, 310027, Zhejiang, China
| | - Pengcui Li
- Department of Orthopaedics, Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, No. 382, Wuyi Road, Taiyuan, 030001, Shanxi, China
| | - Yong He
- Key Laboratory of 3D Printing Process and Equipment of Zhejiang Province, School of Mechanical Engineering, Zhejiang University, No. 866, Yuhang Tang Road, Hangzhou, 310027, Zhejiang, China.
| | - Wangping Duan
- Department of Orthopaedics, Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, No. 382, Wuyi Road, Taiyuan, 030001, Shanxi, China.
| | - Xiaochun Wei
- Department of Orthopaedics, Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, No. 382, Wuyi Road, Taiyuan, 030001, Shanxi, China
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Peña-Martín J, Belén García-Ortega M, Palacios-Ferrer JL, Díaz C, Ángel García M, Boulaiz H, Valdivia J, Jurado JM, Almazan-Fernandez FM, Arias Santiago S, Vicente F, Del Val C, Pérez Del Palacio J, Marchal JA. Identification of novel biomarkers in the early diagnosis of malignant melanoma by untargeted liquid chromatography coupled to high-resolution mass spectrometry-based metabolomics: a pilot study. Br J Dermatol 2024; 190:740-750. [PMID: 38214572 DOI: 10.1093/bjd/ljae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
BACKGROUND Malignant melanoma (MM) is a highly aggressive form of skin cancer whose incidence continues to rise worldwide. If diagnosed at an early stage, it has an excellent prognosis, but mortality increases significantly at advanced stages after distant spread. Unfortunately, early detection of aggressive melanoma remains a challenge. OBJECTIVES To identify novel blood-circulating biomarkers that may be useful in the diagnosis of MM to guide patient counselling and appropriate disease management. METHODS In this study, 105 serum samples from 26 healthy patients and 79 with MM were analysed using an untargeted approach by liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS) to compare the metabolomic profiles of both conditions. Resulting data were subjected to both univariate and multivariate statistical analysis to select robust biomarkers. The classification model obtained from this analysis was further validated with an independent cohort of 12 patients with stage I MM. RESULTS We successfully identified several lipidic metabolites differentially expressed in patients with stage I MM vs. healthy controls. Three of these metabolites were used to develop a classification model, which exhibited exceptional precision (0.92) and accuracy (0.94) when validated on an independent sample. CONCLUSIONS These results demonstrate that metabolomics using LC-HRMS is a powerful tool to identify and quantify metabolites in bodily fluids that could serve as potential early diagnostic markers for MM.
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Affiliation(s)
- Jesús Peña-Martín
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM)
- Department of Human Anatomy and Embryology, Faculty of Medicine
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Excellence Research Unit "Modeling Nature" (MNat)
| | - María Belén García-Ortega
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Excellence Research Unit "Modeling Nature" (MNat)
| | - José Luis Palacios-Ferrer
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM)
- Department of Human Anatomy and Embryology, Faculty of Medicine
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Excellence Research Unit "Modeling Nature" (MNat)
| | - Caridad Díaz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía. Parque Tecnológico Ciencias de la Salud, Granada, Spain
| | - María Ángel García
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM)
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Excellence Research Unit "Modeling Nature" (MNat)
- Department of Biochemistry 3 and Immunology, Faculty of Medicine
| | - Houria Boulaiz
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM)
- Department of Human Anatomy and Embryology, Faculty of Medicine
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Excellence Research Unit "Modeling Nature" (MNat)
| | - Javier Valdivia
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Department of Oncology
| | - José Miguel Jurado
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Department of Oncology
| | - Francisco M Almazan-Fernandez
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Department of Dermatology, San Cecilio University Hospital, Granada, Spain
| | - Salvador Arias Santiago
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Department of Dermatology, Virgen de las Nieves University Hospital, Granada, Spain
| | - Francisca Vicente
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía. Parque Tecnológico Ciencias de la Salud, Granada, Spain
| | - Coral Del Val
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Department of Computer Science and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI), University of Granada, Granada, Spain
| | - José Pérez Del Palacio
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía. Parque Tecnológico Ciencias de la Salud, Granada, Spain
| | - Juan Antonio Marchal
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM)
- Department of Human Anatomy and Embryology, Faculty of Medicine
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Excellence Research Unit "Modeling Nature" (MNat)
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Schiaffino S, Hughes SM, Murgia M, Reggiani C. MYH13, a superfast myosin expressed in extraocular, laryngeal and syringeal muscles. J Physiol 2024; 602:427-443. [PMID: 38160435 DOI: 10.1113/jp285714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
MYH13 is a unique type of sarcomeric myosin heavy chain (MYH) first detected in mammalian extraocular (EO) muscles and later also in vocal muscles, including laryngeal muscles of some mammals and syringeal muscles of songbirds. All these muscles are specialized in generating very fast contractions while producing relatively low force, a design appropriate for muscles acting against a much lower load than most skeletal muscles inserting into the skeleton. The definition of the physiological properties of muscle fibres containing MYH13 has been complicated by the mixed fibre type composition of EO muscles and the coexistence of different MYH types within the same fibre. A major advance in this area came from studies on isolated recombinant myosin motors and the demonstration that the affinity of actin-bound human MYH13 for ADP is much weaker than those of fast-type MYH1 (type 2X) and MYH2 (type 2A). This property is consistent with a very fast detachment of myosin from actin, a major determinant of shortening velocity. The MYH13 gene arose early during vertebrate evolution but was characterized only in mammals and birds and appears to have been lost in some teleost fish. The MYH13 gene is located at the 3' end of the mammalian fast/developmental gene cluster and in a similar position to the orthologous cluster in syntenic regions of the songbird genome. MYH13 gene regulation is controlled by a super-enhancer in the mammalian locus and deletion of the neighbouring fast MYH1 and MYH4 genes leads to abnormal MYH13 expression in mouse leg muscles.
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Affiliation(s)
| | - Simon M Hughes
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College, London, UK
| | - Marta Murgia
- Department of Biomedical Sciences, University of Padova, Padua, Italy
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Carlo Reggiani
- Department of Biomedical Sciences, University of Padova, Padua, Italy
- Science and Research Center Koper, Institute for Kinesiology Research, Koper, Slovenia
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4
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Reggiani C, Murgia M. Comment on "Fiber-type traps: revisiting common misconceptions about skeletal muscle fiber types with application to motor control, biomechanics, physiology, and biology". J Appl Physiol (1985) 2024; 136:437-438. [PMID: 38353629 DOI: 10.1152/japplphysiol.00008.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 02/16/2024] Open
Affiliation(s)
- Carlo Reggiani
- Department of Biomedical Sciences, University of Padova, Padua, Italy
- Science and Research Center Koper, Institute for Kinesiology Research, Koper, Slovenia
| | - Marta Murgia
- Department of Biomedical Sciences, University of Padova, Padua, Italy
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
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Nakamura S, Miyachi Y, Shinjo A, Yokomizo H, Takahashi M, Nakatani K, Izumi Y, Otsuka H, Sato N, Sakamoto R, Miyazawa T, Bamba T, Ogawa Y. Improved endurance capacity of diabetic mice during SGLT2 inhibition: Role of AICARP, an AMPK activator in the soleus. J Cachexia Sarcopenia Muscle 2023; 14:2866-2881. [PMID: 37941098 PMCID: PMC10751436 DOI: 10.1002/jcsm.13350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 08/02/2023] [Accepted: 09/11/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Diabetes is associated with an increased risk of deleterious changes in muscle mass and function or sarcopenia, leading to physical inactivity and worsening glycaemic control. Given the negative energy balance during sodium-glucose cotransporter-2 (SGLT2) inhibition, whether SGLT2 inhibitors affect skeletal muscle mass and function is a matter of concern. However, how SGLT2 inhibition affects the skeletal muscle function in patients with diabetes remains insufficiently explored. We aimed to explore the effects of canagliflozin (CANA), an SGLT2 inhibitor, on skeletal muscles in genetically diabetic db/db mice focusing on the differential responses of oxidative and glycolytic muscles. METHODS Db/db mice were treated with CANA for 4 weeks. We measured running distance and handgrip strength to assess skeletal muscle function during CANA treatment. At the end of the experiment, we performed a targeted metabolome analysis of the skeletal muscles. RESULTS CANA treatment improved the reduced endurance capacity, as revealed by running distance in db/db mice (414.9 ± 52.8 vs. 88.7 ± 22.7 m, P < 0.05). Targeted metabolome analysis revealed that 5-aminoimidazole-4-carboxamide-1-β-D-ribofuranosyl 5'-monophosphate (AICARP), a naturally occurring AMP-activated protein kinase (AMPK) activator, increased in the oxidative soleus muscle (P < 0.05), but not in the glycolytic extensor digitorum longus muscle (P = 0.4376), with increased levels of AMPK phosphorylation (P < 0.01). CONCLUSIONS This study highlights the potential role of the AICARP/AMPK pathway in oxidative rather than glycolytic skeletal muscles during SGLT2 inhibition, providing novel insights into the mechanism by which SGLT2 inhibitors improve endurance capacity in patients with type 2 diabetes.
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Affiliation(s)
- Shintaro Nakamura
- Department of Medicine and Bioregulatory Science, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Yasutaka Miyachi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Akihito Shinjo
- Department of Medicine and Bioregulatory Science, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Hisashi Yokomizo
- Department of Medicine and Bioregulatory Science, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Masatomo Takahashi
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Kohta Nakatani
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Yoshihiro Izumi
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Hiroko Otsuka
- Department of Medicine and Bioregulatory Science, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Naoichi Sato
- Department of Medicine and Bioregulatory Science, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Ryuichi Sakamoto
- Department of Medicine and Bioregulatory Science, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Takashi Miyazawa
- Department of Medicine and Bioregulatory Science, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Takeshi Bamba
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Yoshihiro Ogawa
- Department of Medicine and Bioregulatory Science, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
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6
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Du Q, Wang X, Chen J, Wang Y, Liu W, Wang L, Liu H, Jiang L, Nie Z. Machine learning encodes urine and serum metabolic patterns for autoimmune disease discrimination, classification and metabolic dysregulation analysis. Analyst 2023; 148:4318-4330. [PMID: 37547947 DOI: 10.1039/d3an01051a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
There is a wide variety of autoimmune diseases (ADs) with complex pathogenesis and their accurate diagnosis is difficult to achieve because of their vague symptoms. Metabolomics has been proven to be an efficient tool in the analysis of metabolic disorders to provide clues about the mechanism and diagnosis of diseases. Previous studies of the metabolomics analysis of ADs were not competent in their discrimination. Herein, a liquid chromatography tandem mass spectrometry (LC-MS) strategy combined with machine learning is proposed for the discrimination and classification of ADs. Urine and serum samples were collected from 267 subjects consisting of 127 healthy controls (HC) and 140 AD patients, including those with rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), sicca syndrome (SS), ankylosing spondylitis (AS), systemic scleroderma (SSc) and connective tissue disease (CTD). Machine learning algorithms were encoded for the discrimination and classification of ADs with metabolomic patterns obtained by LC-MS, and satisfactory results were achieved. Notably, urine samples exhibited higher accuracy for disease differentiation and triage than serum samples. Apart from that, differential metabolites were selected and metabolite panels were evaluated to demonstrate their representativeness. Metabolic dysregulations were also investigated to gain more knowledge about the pathogenesis of ADs. This research provides a promising method for the application of metabolomics combined with machine learning in precision medicine.
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Affiliation(s)
- Qiuyao Du
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junyu Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiran Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenlan Liu
- Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Liping Wang
- Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Huihui Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lixia Jiang
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province 341000, China.
| | - Zongxiu Nie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
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Smith JAB, Murach KA, Dyar KA, Zierath JR. Exercise metabolism and adaptation in skeletal muscle. Nat Rev Mol Cell Biol 2023; 24:607-632. [PMID: 37225892 PMCID: PMC10527431 DOI: 10.1038/s41580-023-00606-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 05/26/2023]
Abstract
Viewing metabolism through the lens of exercise biology has proven an accessible and practical strategy to gain new insights into local and systemic metabolic regulation. Recent methodological developments have advanced understanding of the central role of skeletal muscle in many exercise-associated health benefits and have uncovered the molecular underpinnings driving adaptive responses to training regimens. In this Review, we provide a contemporary view of the metabolic flexibility and functional plasticity of skeletal muscle in response to exercise. First, we provide background on the macrostructure and ultrastructure of skeletal muscle fibres, highlighting the current understanding of sarcomeric networks and mitochondrial subpopulations. Next, we discuss acute exercise skeletal muscle metabolism and the signalling, transcriptional and epigenetic regulation of adaptations to exercise training. We address knowledge gaps throughout and propose future directions for the field. This Review contextualizes recent research of skeletal muscle exercise metabolism, framing further advances and translation into practice.
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Affiliation(s)
- Jonathon A B Smith
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Kevin A Murach
- Molecular Mass Regulation Laboratory, Exercise Science Research Center, Department of Health, Human Performance and Recreation, University of Arkansas, Fayetteville, AR, USA
| | - Kenneth A Dyar
- Metabolic Physiology, Institute for Diabetes and Cancer, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Juleen R Zierath
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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8
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Van der Stede T, Spaas J, de Jager S, De Brandt J, Hansen C, Stautemas J, Vercammen B, De Baere S, Croubels S, Van Assche CH, Pastor BC, Vandenbosch M, Van Thienen R, Verboven K, Hansen D, Bové T, Lapauw B, Van Praet C, Decaestecker K, Vanaudenaerde B, Eijnde BO, Gliemann L, Hellsten Y, Derave W. Extensive profiling of histidine-containing dipeptides reveals species- and tissue-specific distribution and metabolism in mice, rats, and humans. Acta Physiol (Oxf) 2023; 239:e14020. [PMID: 37485756 DOI: 10.1111/apha.14020] [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: 03/31/2023] [Revised: 06/26/2023] [Accepted: 07/13/2023] [Indexed: 07/25/2023]
Abstract
AIM Histidine-containing dipeptides (HCDs) are pleiotropic homeostatic molecules with potent antioxidative and carbonyl quenching properties linked to various inflammatory, metabolic, and neurological diseases, as well as exercise performance. However, the distribution and metabolism of HCDs across tissues and species are still unclear. METHODS Using a sensitive UHPLC-MS/MS approach and an optimized quantification method, we performed a systematic and extensive profiling of HCDs in the mouse, rat, and human body (in n = 26, n = 25, and n = 19 tissues, respectively). RESULTS Our data show that tissue HCD levels are uniquely produced by carnosine synthase (CARNS1), an enzyme that was preferentially expressed by fast-twitch skeletal muscle fibres and brain oligodendrocytes. Cardiac HCD levels are remarkably low compared to other excitable tissues. Carnosine is unstable in human plasma, but is preferentially transported within red blood cells in humans but not rodents. The low abundant carnosine analogue N-acetylcarnosine is the most stable plasma HCD, and is enriched in human skeletal muscles. Here, N-acetylcarnosine is continuously secreted into the circulation, which is further induced by acute exercise in a myokine-like fashion. CONCLUSION Collectively, we provide a novel basis to unravel tissue-specific, paracrine, and endocrine roles of HCDs in human health and disease.
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Affiliation(s)
- Thibaux Van der Stede
- Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
- Department of Nutrition, Exercise and Sports, Copenhagen University, Copenhagen, Denmark
| | - Jan Spaas
- Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
- University MS Center (UMSC) Hasselt, Pelt, Belgium
- BIOMED Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Sarah de Jager
- Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
| | - Jana De Brandt
- BIOMED Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
- REVAL Rehabilitation Research Center, Hasselt University, Hasselt, Belgium
| | - Camilla Hansen
- Department of Nutrition, Exercise and Sports, Copenhagen University, Copenhagen, Denmark
| | - Jan Stautemas
- Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
| | - Bjarne Vercammen
- Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
| | - Siegrid De Baere
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, Ghent, Belgium
| | - Siska Croubels
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, Ghent, Belgium
| | - Charles-Henri Van Assche
- The Maastricht MultiModal Molecular Imaging (M4I) institute, Maastricht University, Maastricht, The Netherlands
| | - Berta Cillero Pastor
- The Maastricht MultiModal Molecular Imaging (M4I) institute, Maastricht University, Maastricht, The Netherlands
| | - Michiel Vandenbosch
- The Maastricht MultiModal Molecular Imaging (M4I) institute, Maastricht University, Maastricht, The Netherlands
| | - Ruud Van Thienen
- Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
| | - Kenneth Verboven
- BIOMED Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
- REVAL Rehabilitation Research Center, Hasselt University, Hasselt, Belgium
| | - Dominique Hansen
- BIOMED Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
- REVAL Rehabilitation Research Center, Hasselt University, Hasselt, Belgium
- Heart Center Hasselt, Jessa Hospital Hasselt, Hasselt, Belgium
| | - Thierry Bové
- Department of Cardiac Surgery, Ghent University Hospital, Ghent, Belgium
| | - Bruno Lapauw
- Department of Endocrinology, Ghent University Hospital, Ghent, Belgium
| | - Charles Van Praet
- Department of Urology, Ghent University Hospital, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Karel Decaestecker
- Department of Urology, Ghent University Hospital, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Bart Vanaudenaerde
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Bert O Eijnde
- University MS Center (UMSC) Hasselt, Pelt, Belgium
- SMRC Sports Medical Research Center, BIOMED Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
- Division of Sport Science, Stellenbosch University, Stellenbosch, South Africa
| | - Lasse Gliemann
- Department of Nutrition, Exercise and Sports, Copenhagen University, Copenhagen, Denmark
| | - Ylva Hellsten
- Department of Nutrition, Exercise and Sports, Copenhagen University, Copenhagen, Denmark
| | - Wim Derave
- Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
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Luo L, Chua YJB, Liu T, Liang K, Chua MWJ, Ma W, Goh JW, Wang Y, Su J, Ho YS, Li CW, Liu KH, Teh BT, Yu K, Shyh-Chang N. Muscle Injuries Induce a Prostacyclin-PPARγ/PGC1a-FAO Spike That Boosts Regeneration. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023:e2301519. [PMID: 37140179 PMCID: PMC10375192 DOI: 10.1002/advs.202301519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/14/2023] [Indexed: 05/05/2023]
Abstract
It is well-known that muscle regeneration declines with aging, and aged muscles undergo degenerative atrophy or sarcopenia. While exercise and acute injury are both known to induce muscle regeneration, the molecular signals that help trigger muscle regeneration have remained unclear. Here, mass spectrometry imaging (MSI) is used to show that injured muscles induce a specific subset of prostanoids during regeneration, including PGG1, PGD2, and the prostacyclin PGI2. The spike in prostacyclin promotes skeletal muscle regeneration via myoblasts, and declines with aging. Mechanistically, the prostacyclin spike promotes a spike in PPARγ/PGC1a signaling, which induces a spike in fatty acid oxidation (FAO) to control myogenesis. LC-MS/MS and MSI further confirm that an early FAO spike is associated with normal regeneration, but muscle FAO became dysregulated during aging. Functional experiments demonstrate that the prostacyclin-PPARγ/PGC1a-FAO spike is necessary and sufficient to promote both young and aged muscle regeneration, and that prostacyclin can synergize with PPARγ/PGC1a-FAO signaling to restore aged muscles' regeneration and physical function. Given that the post-injury prostacyclin-PPARγ-FAO spike can be modulated pharmacologically and via post-exercise nutrition, this work has implications for how prostacyclin-PPARγ-FAO might be fine-tuned to promote regeneration and treat muscle diseases of aging.
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Affiliation(s)
- Lanfang Luo
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
- Beijing Institute for Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yan-Jiang Benjamin Chua
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore City, 119077, Singapore
- Genome Institute of Singapore, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore City, 138672, Singapore
| | - Taoyan Liu
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
- Beijing Institute for Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, P. R. China
| | - Kun Liang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
- Beijing Institute for Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Min-Wen Jason Chua
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore City, 119077, Singapore
- Genome Institute of Singapore, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore City, 138672, Singapore
| | - Wenwu Ma
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
- Beijing Institute for Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Jun-Wei Goh
- Genome Institute of Singapore, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore City, 138672, Singapore
| | - Yuefan Wang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
- Beijing Institute for Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Jiali Su
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
- Beijing Institute for Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Ying Swan Ho
- Bioprocessing Technology Institute, Agency for Science Technology and Research, Singapore City, 138668, Singapore
| | - Chun-Wei Li
- Department of Clinical Nutrition, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, P. R. China
| | - Ke Hui Liu
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
- Beijing Institute for Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, P. R. China
| | - Bin Tean Teh
- Laboratory of Cancer Therapeutics, Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore City, 169857, Singapore
- Division of Medical Science, Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore City, 119074, Singapore
| | - Kang Yu
- Department of Clinical Nutrition, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, P. R. China
| | - Ng Shyh-Chang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
- Beijing Institute for Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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Ma W, Luo L, Liang K, Liu T, Su J, Wang Y, Li J, Zhou SK, Shyh-Chang N. XAI-enabled neural network analysis of metabolite spatial distributions. Anal Bioanal Chem 2023; 415:2819-2830. [PMID: 37083759 DOI: 10.1007/s00216-023-04694-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 04/22/2023]
Abstract
We used deep neural networks to process the mass spectrometry imaging (MSI) data of mouse muscle (young vs aged) and human cancer (tumor vs normal adjacent) tissues, with the aim of using explainable artificial intelligence (XAI) methods to rapidly identify biomarkers that can distinguish different classes of tissues, from several thousands of metabolite features. We also modified classic neural network architectures to construct a deep convolutional neural network that is more suitable for processing high-dimensional MSI data directly, instead of using dimension reduction techniques, and compared it to seven other machine learning analysis methods' performance in classification accuracy. After ascertaining the superiority of Channel-ResNet10, we used a novel channel selection-based XAI method to identify the key metabolite features that were responsible for its learning accuracy. These key metabolite biomarkers were then processed using MetaboAnalyst for pathway enrichment mapping. We found that Channel-ResNet10 was superior to seven other machine learning methods for MSI analysis, reaching > 98% accuracy in muscle aging and colorectal cancer datasets. We also used a novel channel selection-based XAI method to find that in young and aged muscle tissues, the differentially distributed metabolite biomarkers were especially enriched in the propanoate metabolism pathway, suggesting it as a novel target pathway for anti-aging therapy.
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Affiliation(s)
- Wenwu Ma
- Department of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Lanfang Luo
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Kun Liang
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Taoyan Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Jiali Su
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Yuefan Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Jun Li
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
- Center for Medical Imaging Robotics, Analytic Computing & Learning (MIRACLE), School of Biomedical Engineering &, Suzhou Institute for Advance Research, University of Science and Technology of China, Suzhou, China
| | - S Kevin Zhou
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
- Center for Medical Imaging Robotics, Analytic Computing & Learning (MIRACLE), School of Biomedical Engineering &, Suzhou Institute for Advance Research, University of Science and Technology of China, Suzhou, China
| | - Ng Shyh-Chang
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
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11
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Yang Q, Cai Y, Guo S, Wang Z, Qiu S, Zhang A. Localization analysis of metabolites from complex biological samples-recent analytical technique of mass spectrometry imaging. Front Mol Biosci 2023; 10:1169449. [PMID: 37152901 PMCID: PMC10160367 DOI: 10.3389/fmolb.2023.1169449] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 04/13/2023] [Indexed: 05/09/2023] Open
Affiliation(s)
- Qiang Yang
- GAP Center and Graduate School, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Ying Cai
- GAP Center and Graduate School, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Sifan Guo
- GAP Center and Graduate School, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Zhibo Wang
- GAP Center and Graduate School, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan Medical University, Haikou, China
- *Correspondence: Shi Qiu, ; Aihua Zhang,
| | - Aihua Zhang
- GAP Center and Graduate School, Heilongjiang University of Chinese Medicine, Harbin, China
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan Medical University, Haikou, China
- *Correspondence: Shi Qiu, ; Aihua Zhang,
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