1
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Chen HC, Liu YW, Chang KC, Wu YW, Chen YM, Chao YK, You MY, Lundy DJ, Lin CJ, Hsieh ML, Cheng YC, Prajnamitra RP, Lin PJ, Ruan SC, Chen DHK, Shih ESC, Chen KW, Chang SS, Chang CMC, Puntney R, Moy AW, Cheng YY, Chien HY, Lee JJ, Wu DC, Hwang MJ, Coonen J, Hacker TA, Yen CLE, Rey FE, Kamp TJ, Hsieh PCH. Gut butyrate-producers confer post-infarction cardiac protection. Nat Commun 2023; 14:7249. [PMID: 37945565 PMCID: PMC10636175 DOI: 10.1038/s41467-023-43167-5] [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: 07/30/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
The gut microbiome and its metabolites are increasingly implicated in several cardiovascular diseases, but their role in human myocardial infarction (MI) injury responses have yet to be established. To address this, we examined stool samples from 77 ST-elevation MI (STEMI) patients using 16 S V3-V4 next-generation sequencing, metagenomics and machine learning. Our analysis identified an enriched population of butyrate-producing bacteria. These findings were then validated using a controlled ischemia/reperfusion model using eight nonhuman primates. To elucidate mechanisms, we inoculated gnotobiotic mice with these bacteria and found that they can produce beta-hydroxybutyrate, supporting cardiac function post-MI. This was further confirmed using HMGCS2-deficient mice which lack endogenous ketogenesis and have poor outcomes after MI. Inoculation increased plasma ketone levels and provided significant improvements in cardiac function post-MI. Together, this demonstrates a previously unknown role of gut butyrate-producers in the post-MI response.
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Affiliation(s)
- Hung-Chih Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Yen-Wen Liu
- Division of Cardiology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan
| | - Kuan-Cheng Chang
- Division of Cardiovascular Medicine, China Medical University Hospital, Taichung, 40447, Taiwan
- School of Medicine, China Medical University, Taichung, 40402, Taiwan
| | - Yen-Wen Wu
- Cardiovascular Medical Center, Far Eastern Memorial Hospital, New Taipei City, 220, Taiwan
| | - Yi-Ming Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Yu-Kai Chao
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Min-Yi You
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - David J Lundy
- Graduate Institute of Biomedical Materials and Tissue Engineering, Taipei Medical University, Taipei, 110, Taiwan
| | - Chen-Ju Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Marvin L Hsieh
- Model Organisms Research Core, Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Yu-Che Cheng
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Ray P Prajnamitra
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Po-Ju Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Shu-Chian Ruan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | | | - Edward S C Shih
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Ke-Wei Chen
- Division of Cardiovascular Medicine, China Medical University Hospital, Taichung, 40447, Taiwan
| | - Shih-Sheng Chang
- Division of Cardiovascular Medicine, China Medical University Hospital, Taichung, 40447, Taiwan
- School of Medicine, China Medical University, Taichung, 40402, Taiwan
| | - Cindy M C Chang
- Model Organisms Research Core, Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Riley Puntney
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Amy Wu Moy
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Yuan-Yuan Cheng
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Hsin-Yuan Chien
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Jia-Jung Lee
- Division of Nephrology, Department of Medicine, Kaohsiung Medical University & Hospital, Kaohsiung, 807, Taiwan
| | - Deng-Chyang Wu
- Division of Gastroenterology, Department of Medicine, Kaohsiung Medical University & Hospital, Kaohsiung, 807, Taiwan
| | - Ming-Jing Hwang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Jennifer Coonen
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Timothy A Hacker
- Model Organisms Research Core, Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - C-L Eric Yen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Federico E Rey
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Timothy J Kamp
- Department of Medicine and Stem Cell and Regenerative Medicine Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Patrick C H Hsieh
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan.
- Department of Medicine and Stem Cell and Regenerative Medicine Center, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Institute of Medical Genomics and Proteomics and Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, 100, Taiwan.
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2
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Ortega M, Molina-García T, Gavara J, de Dios E, Pérez-Solé N, Marcos-Garcés V, Chorro FJ, Rios-Navarro C, Ruiz-Sauri A, Bodi V. Novel Targets Regulating the Role of Endothelial Cells and Angiogenesis after Infarction: A RNA Sequencing Analysis. Int J Mol Sci 2023; 24:15698. [PMID: 37958681 PMCID: PMC10649670 DOI: 10.3390/ijms242115698] [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: 10/05/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Endothelial cells (ECs) are a key target for cardioprotection due to their role in preserving cardiac microvasculature and homeostasis after myocardial infarction (MI). Our goal is to identify the genes involved in post-MI EC proliferation, EC apoptosis, and angiogenesis regulation via RNA-sequencing transcriptomic datasets. Using eight studies from the Gene Expression Omnibus, RNA-sequencing data from 92 mice submitted to different times of coronary ischemia or sham were chosen. Functional enrichment analysis was performed based on gene ontology biological processes (BPs). Apoptosis-related BPs are activated up to day 3 after ischemia onset, whereas endothelial proliferation occurs from day 3 onwards, including an overrepresentation of up to 37 genes. Endothelial apoptosis post-MI is triggered via both the extrinsic and intrinsic signaling pathways, as reflected by the overrepresentation of 13 and 2 specific genes, respectively. BPs implicated in new vessel formation are upregulated soon after ischemia onset, whilst the mechanisms aiming at angiogenesis repression can be detected at day 3. Overall, 51 pro-angiogenic and 29 anti-angiogenic factors displayed altered transcriptomic expression post-MI. This is the first study using RNA sequencing datasets to evaluate the genes participating in post-MI endothelium physiology and angiogenesis regulation. These novel data could lay the groundwork to advance understanding of the implication of ECs after MI.
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Affiliation(s)
- María Ortega
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (M.O.); (T.M.-G.); (N.P.-S.); (V.M.-G.); (F.J.C.); (V.B.)
| | - Tamara Molina-García
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (M.O.); (T.M.-G.); (N.P.-S.); (V.M.-G.); (F.J.C.); (V.B.)
| | - Jose Gavara
- Centro de Biomateriales e Ingeniería Tisular, Universidad Politécnica de Valencia, 46010 Valencia, Spain;
| | - Elena de Dios
- Centro de Investigación Biomédica en Red (CIBER)-CV, 28029 Madrid, Spain;
| | - Nerea Pérez-Solé
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (M.O.); (T.M.-G.); (N.P.-S.); (V.M.-G.); (F.J.C.); (V.B.)
| | - Victor Marcos-Garcés
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (M.O.); (T.M.-G.); (N.P.-S.); (V.M.-G.); (F.J.C.); (V.B.)
- Cardiology Department, Hospital Clínico Universitario, 46010 Valencia, Spain
| | - Francisco J. Chorro
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (M.O.); (T.M.-G.); (N.P.-S.); (V.M.-G.); (F.J.C.); (V.B.)
- Centro de Investigación Biomédica en Red (CIBER)-CV, 28029 Madrid, Spain;
- Cardiology Department, Hospital Clínico Universitario, 46010 Valencia, Spain
- Department of Medicine, University of Valencia, 46010 Valencia, Spain
| | - Cesar Rios-Navarro
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (M.O.); (T.M.-G.); (N.P.-S.); (V.M.-G.); (F.J.C.); (V.B.)
- Department of Pathology, University of Valencia, 46010 Valencia, Spain
| | - Amparo Ruiz-Sauri
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (M.O.); (T.M.-G.); (N.P.-S.); (V.M.-G.); (F.J.C.); (V.B.)
- Department of Pathology, University of Valencia, 46010 Valencia, Spain
| | - Vicente Bodi
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (M.O.); (T.M.-G.); (N.P.-S.); (V.M.-G.); (F.J.C.); (V.B.)
- Centro de Investigación Biomédica en Red (CIBER)-CV, 28029 Madrid, Spain;
- Cardiology Department, Hospital Clínico Universitario, 46010 Valencia, Spain
- Department of Medicine, University of Valencia, 46010 Valencia, Spain
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3
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Arif M, Matyas C, Mukhopadhyay P, Yokus B, Trojnar E, Paloczi J, Paes-Leme B, Zhao S, Lohoff FW, Haskó G, Pacher P. Data-driven transcriptomics analysis identifies PCSK9 as a novel key regulator in liver aging. GeroScience 2023; 45:3059-3077. [PMID: 37726433 PMCID: PMC10643490 DOI: 10.1007/s11357-023-00928-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023] Open
Abstract
The liver, as a crucial metabolic organ, undergoes significant pathological changes during the aging process, which can have a profound impact on overall health. To gain a comprehensive understanding of these alterations, we employed data-driven approaches, along with biochemical methods, histology, and immunohistochemistry techniques, to systematically investigate the effects of aging on the liver. Our study utilized a well-established rat aging model provided by the National Institute of Aging. Systems biology approaches were used to analyze genome-wide transcriptomics data from liver samples obtained from young (4-5 months old) and aging (20-21 months old) Fischer 344 rats. Our findings revealed pathological changes occurring in various essential biological processes in aging livers. These included mitochondrial dysfunction, increased oxidative/nitrative stress, decreased NAD + content, impaired amino acid and protein synthesis, heightened inflammation, disrupted lipid metabolism, enhanced apoptosis, senescence, and fibrosis. These results were validated using independent datasets from both human and rat aging studies. Furthermore, by employing co-expression network analysis, we identified novel driver genes responsible for liver aging, confirmed our findings in human aging subjects, and pointed out the cellular localization of the driver genes using single-cell RNA-sequencing human data. Our study led to the discovery and validation of a liver-specific gene, proprotein convertase subtilisin/kexin type 9 (PCSK9), as a potential therapeutic target for mitigating the pathological processes associated with aging in the liver. This finding envisions new possibilities for developing interventions aimed to improve liver health during the aging process.
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Affiliation(s)
- Muhammad Arif
- Laboratory of Cardiovascular Physiology and Tissue Injury, National Institute On Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
- Section On Fibrotic Disorders, National Institute On Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Csaba Matyas
- Laboratory of Cardiovascular Physiology and Tissue Injury, National Institute On Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Partha Mukhopadhyay
- Laboratory of Cardiovascular Physiology and Tissue Injury, National Institute On Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Burhan Yokus
- Laboratory of Cardiovascular Physiology and Tissue Injury, National Institute On Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Eszter Trojnar
- Laboratory of Cardiovascular Physiology and Tissue Injury, National Institute On Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Janos Paloczi
- Laboratory of Cardiovascular Physiology and Tissue Injury, National Institute On Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Bruno Paes-Leme
- Laboratory of Cardiovascular Physiology and Tissue Injury, National Institute On Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Suxian Zhao
- Laboratory of Cardiovascular Physiology and Tissue Injury, National Institute On Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Falk W Lohoff
- Section On Clinical Genomics and Experimental Therapeutics, National Institute On Alcohol Abuse and Alcoholism National Institutes of Health, Bethesda, MD, USA
| | - György Haskó
- Department of Anesthesiology, Columbia University, New York, NY, USA
| | - Pal Pacher
- Laboratory of Cardiovascular Physiology and Tissue Injury, National Institute On Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA.
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4
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Li S, Zhai J, Chu W, Geng X, Wang D, Jiao L, Lu G, Chan WY, Sun K, Sun Y, Chen ZJ, Du Y. Alleviation of Limosilactobacillus reuteri in polycystic ovary syndrome protects against circadian dysrhythmia-induced dyslipidemia via capric acid and GALR1 signaling. NPJ Biofilms Microbiomes 2023; 9:47. [PMID: 37422471 DOI: 10.1038/s41522-023-00415-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 06/22/2023] [Indexed: 07/10/2023] Open
Abstract
Knowledge gaps that limit the development of therapies for polycystic ovary syndrome (PCOS) concern various environmental factors that impact clinical characteristics. Circadian dysrhythmia contributes to glycometabolic and reproductive hallmarks of PCOS. Here, we illustrated the amelioration of Limosilactobacillus reuteri (L. reuteri) on biorhythm disorder-ignited dyslipidemia of PCOS via a microbiota-metabolite-liver axis. A rat model of long-term (8 weeks) darkness treatment was used to mimic circadian dysrhythmia-induced PCOS. Hepatic transcriptomics certified by in vitro experiments demonstrated that increased hepatic galanin receptor 1 (GALR1) due to darkness exposure functioned as a critical upstream factor in the phosphoinositide 3-kinase (PI3K)/protein kinase B pathway to suppress nuclear receptors subfamily 1, group D, member 1 (NR1D1) and promoted sterol regulatory element binding protein 1 (SREBP1), inducing lipid accumulation in the liver. Further investigations figured out a restructured microbiome-metabolome network following L. reuteri administration to protect darkness rats against dyslipidemia. Notably, L. reuteri intervention resulted in the decrease of Clostridium sensu stricto 1 and Ruminococcaceae UCG-010 as well as gut microbiota-derived metabolite capric acid, which could further inhibit GALR1-NR1D1-SREBP1 pathway in the liver. In addition, GALR antagonist M40 reproduced similar ameliorative effects as L. reuteri to protect against dyslipidemia. While exogenous treatment of capric acid restrained the protective effects of L. reuteri in circadian disruption-induced PCOS through inhibiting GALR1-dependent hepatic lipid metabolism. These findings purport that L. reuteri could serve for circadian disruption-associated dyslipidemia. Manipulation of L. reuteri-capric acid-GALR1 axis paves way for clinical therapeutic strategies to prevent biorhythm disorder-ignited dyslipidemia in PCOS women.
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Affiliation(s)
- Shang Li
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, 200135, China
| | - Junyu Zhai
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, 200135, China
| | - Weiwei Chu
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, 200135, China
| | - Xueying Geng
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, 200135, China
| | - Dongshuang Wang
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, 200135, China
| | - Luwei Jiao
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, 200135, China
| | - Gang Lu
- The Chinese University of Hong Kong-Shandong University Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wai-Yee Chan
- The Chinese University of Hong Kong-Shandong University Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kang Sun
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, 200135, China
| | - Yun Sun
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, 200135, China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200135, China.
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, 200135, China.
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong Provincial Key Laboratory of Reproductive Medicine, Jinan, Shandong, 250012, China.
- NMU-SD Suzhou Collaborative Innovation Center for Reproductive Medicine, Suzhou, Jiangsu, China.
| | - Yanzhi Du
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200135, China.
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, 200135, China.
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5
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Wang RS, Maron BA, Loscalzo J. Multiomics Network Medicine Approaches to Precision Medicine and Therapeutics in Cardiovascular Diseases. Arterioscler Thromb Vasc Biol 2023; 43:493-503. [PMID: 36794589 PMCID: PMC10038904 DOI: 10.1161/atvbaha.122.318731] [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: 11/07/2022] [Accepted: 01/30/2023] [Indexed: 02/17/2023]
Abstract
Cardiovascular diseases (CVD) are the leading cause of death worldwide and display complex phenotypic heterogeneity caused by many convergent processes, including interactions between genetic variation and environmental factors. Despite the identification of a large number of associated genes and genetic loci, the precise mechanisms by which these genes systematically influence the phenotypic heterogeneity of CVD are not well understood. In addition to DNA sequence, understanding the molecular mechanisms of CVD requires data from other omics levels, including the epigenome, the transcriptome, the proteome, as well as the metabolome. Recent advances in multiomics technologies have opened new precision medicine opportunities beyond genomics that can guide precise diagnosis and personalized treatment. At the same time, network medicine has emerged as an interdisciplinary field that integrates systems biology and network science to focus on the interactions among biological components in health and disease, providing an unbiased framework through which to integrate systematically these multiomics data. In this review, we briefly present such multiomics technologies, including bulk omics and single-cell omics technologies, and discuss how they can contribute to precision medicine. We then highlight network medicine-based integration of multiomics data for precision medicine and therapeutics in CVD. We also include a discussion of current challenges, potential limitations, and future directions in the study of CVD using multiomics network medicine approaches.
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Affiliation(s)
- Rui-Sheng Wang
- Division of Cardiovascular Medicine
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Joseph Loscalzo
- Division of Cardiovascular Medicine
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
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6
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Cinato M, Mardani I, Miljanovic A, Drevinge C, Laudette M, Bollano E, Henricsson M, Tolö J, Bauza Thorbrügge M, Levin M, Lindbom M, Arif M, Pacher P, Andersson L, Olofsson CS, Borén J, Levin MC. Cardiac Plin5 interacts with SERCA2 and promotes calcium handling and cardiomyocyte contractility. Life Sci Alliance 2023; 6:e202201690. [PMID: 36717246 PMCID: PMC9887753 DOI: 10.26508/lsa.202201690] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/17/2023] [Accepted: 01/17/2023] [Indexed: 01/31/2023] Open
Abstract
The adult heart develops hypertrophy to reduce ventricular wall stress and maintain cardiac function in response to an increased workload. Although pathological hypertrophy generally progresses to heart failure, physiological hypertrophy may be cardioprotective. Cardiac-specific overexpression of the lipid-droplet protein perilipin 5 (Plin5) promotes cardiac hypertrophy, but it is unclear whether this response is beneficial. We analyzed RNA-sequencing data from human left ventricle and showed that cardiac PLIN5 expression correlates with up-regulation of cardiac contraction-related processes. To investigate how elevated cardiac Plin5 levels affect cardiac contractility, we generated mice with cardiac-specific overexpression of Plin5 (MHC-Plin5 mice). These mice displayed increased left ventricular mass and cardiomyocyte size but preserved heart function. Quantitative proteomics identified sarcoplasmic/endoplasmic reticulum Ca2+ ATPase 2 (SERCA2) as a Plin5-interacting protein. In situ proximity ligation assay further confirmed the Plin5/SERCA2 interaction. Live imaging showed increases in intracellular Ca2+ release during contraction, Ca2+ removal during relaxation, and SERCA2 function in MHC-Plin5 versus WT cardiomyocytes. These results identify a role of Plin5 in improving cardiac contractility through enhanced Ca2+ signaling.
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Affiliation(s)
- Mathieu Cinato
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, Sahlgrenska Academy at University of Gothenburgand Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Ismena Mardani
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, Sahlgrenska Academy at University of Gothenburgand Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Azra Miljanovic
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, Sahlgrenska Academy at University of Gothenburgand Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Christina Drevinge
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, Sahlgrenska Academy at University of Gothenburgand Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Marion Laudette
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, Sahlgrenska Academy at University of Gothenburgand Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Entela Bollano
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, Sahlgrenska Academy at University of Gothenburgand Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Marcus Henricsson
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, Sahlgrenska Academy at University of Gothenburgand Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Johan Tolö
- Department of Physiology/Metabolic Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Marcos Bauza Thorbrügge
- Department of Physiology/Metabolic Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Max Levin
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, Sahlgrenska Academy at University of Gothenburgand Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Malin Lindbom
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, Sahlgrenska Academy at University of Gothenburgand Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Muhammad Arif
- Laboratory of Cardiovascular Physiology and Tissue Injury, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Pal Pacher
- Laboratory of Cardiovascular Physiology and Tissue Injury, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Linda Andersson
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, Sahlgrenska Academy at University of Gothenburgand Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Charlotta S Olofsson
- Department of Physiology/Metabolic Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Jan Borén
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, Sahlgrenska Academy at University of Gothenburgand Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Malin C Levin
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, Sahlgrenska Academy at University of Gothenburgand Sahlgrenska University Hospital, Gothenburg, Sweden
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7
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Clasen F, Nunes PM, Bidkhori G, Bah N, Boeing S, Shoaie S, Anastasiou D. Systematic diet composition swap in a mouse genome-scale metabolic model reveals determinants of obesogenic diet metabolism in liver cancer. iScience 2023; 26:106040. [PMID: 36844450 PMCID: PMC9947310 DOI: 10.1016/j.isci.2023.106040] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/08/2022] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
Dietary nutrient availability and gene expression, together, influence tissue metabolic activity. Here, we explore whether altering dietary nutrient composition in the context of mouse liver cancer suffices to overcome chronic gene expression changes that arise from tumorigenesis and western-style diet (WD). We construct a mouse genome-scale metabolic model and estimate metabolic fluxes in liver tumors and non-tumoral tissue after computationally varying the composition of input diet. This approach, called Systematic Diet Composition Swap (SyDiCoS), revealed that, compared to a control diet, WD increases production of glycerol and succinate irrespective of specific tissue gene expression patterns. Conversely, differences in fatty acid utilization pathways between tumor and non-tumor liver are amplified with WD by both dietary carbohydrates and lipids together. Our data suggest that combined dietary component modifications may be required to normalize the distinctive metabolic patterns that underlie selective targeting of tumor metabolism.
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Affiliation(s)
- Frederick Clasen
- Cancer Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London SE1 9RT, UK
| | - Patrícia M. Nunes
- Cancer Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Gholamreza Bidkhori
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London SE1 9RT, UK
| | - Nourdine Bah
- Bioinformatics and Biostatistics Science Technology Platform, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stefan Boeing
- Bioinformatics and Biostatistics Science Technology Platform, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London SE1 9RT, UK
- Science for Life Laboratory (SciLifeLab), KTH - Royal Institute of Technology, Tomtebodavägen 23, 171 65 Solna, Stockholm, Sweden
| | - Dimitrios Anastasiou
- Cancer Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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8
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Interaction between Acute Hepatic Injury and Early Coagulation Dysfunction on Mortality in Patients with Acute Myocardial Infarction. J Clin Med 2023; 12:jcm12041534. [PMID: 36836066 PMCID: PMC9966038 DOI: 10.3390/jcm12041534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/04/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND In acute myocardial infarction (AMI), acute hepatic injury is an independent risk factor for prognosis and is associated with complex coagulation dynamics. This study aims to determine the interaction between acute hepatic injury and coagulation dysfunction on outcomes in AMI patients. METHODS The Medical Information Mart for Intensive Care (MIMIC-III) database was used to identify AMI patients who underwent liver function testing within 24 h of admission. After ruling out previous hepatic injury, patients were divided into the hepatic injury group and the nonhepatic injury group based on whether the alanine transaminase (ALT) level at admission was >3 times the upper limit of normal (ULN). The primary outcome was intensive care unit (ICU) mortality. RESULTS Among 703 AMI patients (67.994% male, median age 65.139 years (55.757-76.859)), acute hepatic injury occurred in 15.220% (n = 107). Compared with the nonhepatic injury group, patients with hepatic injury had a higher Elixhauser comorbidity index (ECI) score (12 (6-18) vs. 7 (1-12), p < 0.001) and more severe coagulation dysfunction (85.047% vs. 68.960%, p < 0.001). In addition, acute hepatic injury was associated with increased in-hospital mortality (odds ratio (OR) = 3.906; 95% CI: 2.053-7.433; p < 0.001), ICU mortality (OR = 4.866; 95% CI: 2.489-9.514; p < 0.001), 28-day mortality (OR = 4.129; 95% CI: 2.215-7.695; p < 0.001) and 90-day mortality (OR = 3.407; 95% CI: 1.883-6.165; p < 0.001) only in patients with coagulation disorder but not with normal coagulation. Unlike patients with coagulation disorder and normal liver, patients with both coagulation disorder and acute hepatic injury had greater odds of ICU mortality (OR = 8.565; 95% CI: 3.467-21.160; p < 0.001) than those with normal coagulation. CONCLUSIONS The effects of acute hepatic injury on prognosis are likely to be modulated by early coagulation disorder in AMI patients.
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9
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Ahmed A, Syed JN, Chi L, Wang Y, Perez-Romero C, Lee D, Kocaqi E, Caballero A, Yang J, Escalante-Covarrubias Q, Ishimura A, Suzuki T, Aguilar-Arnal L, Gonzales GB, Kim KH, Delgado-Olguín P. KDM8 epigenetically controls cardiac metabolism to prevent initiation of dilated cardiomyopathy. NATURE CARDIOVASCULAR RESEARCH 2023; 2:174-191. [PMID: 38665902 PMCID: PMC11041705 DOI: 10.1038/s44161-023-00214-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/05/2023] [Indexed: 04/28/2024]
Abstract
Cardiac metabolism is deranged in heart failure, but underlying mechanisms remain unclear. Here, we show that lysine demethylase 8 (Kdm8) maintains an active mitochondrial gene network by repressing Tbx15, thus preventing dilated cardiomyopathy leading to lethal heart failure. Deletion of Kdm8 in mouse cardiomyocytes increased H3K36me2 with activation of Tbx15 and repression of target genes in the NAD+ pathway before dilated cardiomyopathy initiated. NAD+ supplementation prevented dilated cardiomyopathy in Kdm8 mutant mice, and TBX15 overexpression blunted NAD+-activated cardiomyocyte respiration. Furthermore, KDM8 was downregulated in human hearts affected by dilated cardiomyopathy, and higher TBX15 expression defines a subgroup of affected hearts with the strongest downregulation of genes encoding mitochondrial proteins. Thus, KDM8 represses TBX15 to maintain cardiac metabolism. Our results suggest that epigenetic dysregulation of metabolic gene networks initiates myocardium deterioration toward heart failure and could underlie heterogeneity of dilated cardiomyopathy.
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Affiliation(s)
- Abdalla Ahmed
- Department of Translational Medicine, The Hospital for Sick Children, Toronto, Ontario Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario Canada
| | - Jibran Nehal Syed
- Department of Translational Medicine, The Hospital for Sick Children, Toronto, Ontario Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario Canada
| | - Lijun Chi
- Department of Translational Medicine, The Hospital for Sick Children, Toronto, Ontario Canada
| | - Yaxu Wang
- Department of Translational Medicine, The Hospital for Sick Children, Toronto, Ontario Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario Canada
| | - Carmina Perez-Romero
- Department of Translational Medicine, The Hospital for Sick Children, Toronto, Ontario Canada
| | - Dorothy Lee
- Department of Translational Medicine, The Hospital for Sick Children, Toronto, Ontario Canada
- Department of Physiology, University of Toronto, Toronto, Ontario Canada
| | - Etri Kocaqi
- Department of Translational Medicine, The Hospital for Sick Children, Toronto, Ontario Canada
| | - Amalia Caballero
- Department of Translational Medicine, The Hospital for Sick Children, Toronto, Ontario Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario Canada
| | - Jielin Yang
- Department of Translational Medicine, The Hospital for Sick Children, Toronto, Ontario Canada
| | - Quetzalcoatl Escalante-Covarrubias
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México
| | - Akihiko Ishimura
- Division of Functional Genomics, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| | - Takeshi Suzuki
- Division of Functional Genomics, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| | - Lorena Aguilar-Arnal
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México
| | - Gerard Bryan Gonzales
- Division of Human Nutrition and Health, Wageningen University, Wageningen, Netherlands
| | - Kyoung-Han Kim
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa and University of Ottawa Heart Institute, Ottawa, Ontario Canada
| | - Paul Delgado-Olguín
- Department of Translational Medicine, The Hospital for Sick Children, Toronto, Ontario Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario Canada
- Heart & Stroke Richard Lewar Centre of Excellence, Toronto, Ontario Canada
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10
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Filosa A, Sawamiphak S. Heart development and regeneration-a multi-organ effort. FEBS J 2023; 290:913-930. [PMID: 34894086 DOI: 10.1111/febs.16319] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 10/22/2021] [Accepted: 12/10/2021] [Indexed: 12/15/2022]
Abstract
Development of the heart, from early morphogenesis to functional maturation, as well as maintenance of its homeostasis are tasks requiring collaborative efforts of cardiac tissue and different extra-cardiac organ systems. The brain, lymphoid organs, and gut are among the interaction partners that can communicate with the heart through a wide array of paracrine signals acting at local or systemic level. Disturbance of cardiac homeostasis following ischemic injury also needs immediate response from these distant organs. Our hearts replace dead muscles with non-contractile fibrotic scars. We have learned from animal models capable of scarless repair that regenerative capability of the heart does not depend only on competency of the myocardium and cardiac-intrinsic factors but also on long-range molecular signals originating in other parts of the body. Here, we provide an overview of inter-organ signals that take part in development and regeneration of the heart. We highlight recent findings and remaining questions. Finally, we discuss the potential of inter-organ modulatory approaches for possible therapeutic use.
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Affiliation(s)
- Alessandro Filosa
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Suphansa Sawamiphak
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.,DZHK (German Center for Cardiovascular Research), Partner Site Berlin, Germany
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11
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Ortega M, Ríos-Navarro C, Gavara J, de Dios E, Perez-Solé N, Marcos-Garcés V, Ferrández-Izquierdo A, Bodí V, Ruiz-Saurí A. Meta-Analysis of Extracellular Matrix Dynamics after Myocardial Infarction Using RNA-Sequencing Transcriptomic Database. Int J Mol Sci 2022; 23:ijms232415615. [PMID: 36555255 PMCID: PMC9779146 DOI: 10.3390/ijms232415615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
Extracellular matrix (ECM) changes after myocardial infarction (MI) need precise regulation, and next-generation sequencing technologies provide omics data that can be used in this context. We performed a meta-analysis using RNA-sequencing transcriptomic datasets to identify genes involved in post-MI ECM turnover. Eight studies available in Gene Expression Omnibus were selected following the inclusion criteria. We compare RNA-sequencing data from 92 mice submitted to permanent coronary ligation or sham, identifying differentially expressed genes (p-value < 0.05 and Log2FoldChange ≥ 2). Functional enrichment analysis was performed based on Gene Ontology biological processes (BPs). BPs implicated in response to extracellular stimulus, regulation of ECM organization, and ECM disassembly were detected soon after ischemia onset. ECM disassembly occurred between days one to seven post-MI, compared with ECM assembly from day seven onwards. We identified altered mRNA expression of 19 matrix metalloproteinases and four tissue inhibitors of metalloproteinases at post-infarcted ECM remodeling and altered transcriptomic expression of 42 genes encoding 26 collagen subunits at the fibrotic stage. To our knowledge, this is the first meta-analysis using RNA-sequencing datasets to evaluate post-infarcted cardiac interstitium healing, revealing previously unknown mechanisms and molecules actively implicated in ECM remodeling post-MI, which warrant further validation.
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Affiliation(s)
- María Ortega
- INCLIVA health Research Institute, 46010 Valencia, Spain
| | | | - Jose Gavara
- Centro de Biomateriales e Ingeniería Tisular, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Elena de Dios
- Department of Medicine, University of Valencia,46010 Valencia, Spain
- Centro de Investigación Biomédica en Red (CIBER)-CV, 28029 Madrid, Spain
| | | | - Victor Marcos-Garcés
- INCLIVA health Research Institute, 46010 Valencia, Spain
- Cardiology Department, Hospital Clínico Universitario, 46010 Valencia, Spain
| | - Antonio Ferrández-Izquierdo
- INCLIVA health Research Institute, 46010 Valencia, Spain
- Department of Pathology, University of Valencia, 46010 Valencia, Spain
- Pathology Department, Hospital Clínico Universitario, 46010 Valencia, Spain
| | - Vicente Bodí
- INCLIVA health Research Institute, 46010 Valencia, Spain
- Department of Medicine, University of Valencia,46010 Valencia, Spain
- Centro de Investigación Biomédica en Red (CIBER)-CV, 28029 Madrid, Spain
- Cardiology Department, Hospital Clínico Universitario, 46010 Valencia, Spain
- Correspondence: ; Tel.: +34-96-3862658
| | - Amparo Ruiz-Saurí
- INCLIVA health Research Institute, 46010 Valencia, Spain
- Department of Pathology, University of Valencia, 46010 Valencia, Spain
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12
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Aminian-Dehkordi J, Valiei A, Mofrad MRK. Emerging computational paradigms to address the complex role of gut microbial metabolism in cardiovascular diseases. Front Cardiovasc Med 2022; 9:987104. [PMID: 36299869 PMCID: PMC9589059 DOI: 10.3389/fcvm.2022.987104] [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: 07/05/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
The human gut microbiota and its associated perturbations are implicated in a variety of cardiovascular diseases (CVDs). There is evidence that the structure and metabolic composition of the gut microbiome and some of its metabolites have mechanistic associations with several CVDs. Nevertheless, there is a need to unravel metabolic behavior and underlying mechanisms of microbiome-host interactions. This need is even more highlighted when considering that microbiome-secreted metabolites contributing to CVDs are the subject of intensive research to develop new prevention and therapeutic techniques. In addition to the application of high-throughput data used in microbiome-related studies, advanced computational tools enable us to integrate omics into different mathematical models, including constraint-based models, dynamic models, agent-based models, and machine learning tools, to build a holistic picture of metabolic pathological mechanisms. In this article, we aim to review and introduce state-of-the-art mathematical models and computational approaches addressing the link between the microbiome and CVDs.
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Affiliation(s)
| | | | - Mohammad R. K. Mofrad
- Department of Bioengineering and Mechanical Engineering, University of California, Berkeley, Berkeley, CA, United States
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13
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Proteomics Reveals Long-Term Alterations in Signaling and Metabolic Pathways Following Both Myocardial Infarction and Chemically Induced Denervation. Neurochem Res 2022; 47:2416-2430. [PMID: 35716295 DOI: 10.1007/s11064-022-03636-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 10/18/2022]
Abstract
Myocardial infraction (MI) is the principal risk factor for the onset of heart failure (HF). Investigations regarding the physiopathology of MI progression to HF have revealed the concerted engagement of other tissues, such as the autonomic nervous system and the medulla oblongata (MO), giving rise to systemic effects, important in the regulation of heart function. Cardiac sympathetic afferent denervation following application of resiniferatoxin (RTX) attenuates cardiac remodelling and restores cardiac function following MI. While the physiological responses are well documented in numerous species, the underlying molecular responses during the initiation and progression from MI to HF remains unclear. We obtained multi-tissue time course proteomics with a murine model of HF induced by MI in conjunction with RTX application. We isolated tissue sections from the left ventricle (LV), MO, cervical spinal cord and cervical vagal nerves at four time points over a 12-week study. Bioinformatic analyses consistently revealed a high statistical enrichment for metabolic pathways in all tissues and treatments, implicating a central role of mitochondria in the tissue-cellular response to both MI and RTX. In fact, the additional functional pathways found to be enriched in these tissues, involving the cytoskeleton, vesicles and signal transduction, could be downstream of responses initiated by mitochondria due to changes in neuronal pulse frequency after a shock such as MI or the modification of such frequency communication from the heart to the brain after RTX application. Development of future experiments, based on our proteomic results, should enable the dissection of more precise mechanisms whereby metabolic changes in neuronal and cardiac tissues can effectively ameliorate the negative physiological effects of MI via RTX application.
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14
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Sun F, Ou J, Shoffner AR, Luan Y, Yang H, Song L, Safi A, Cao J, Yue F, Crawford GE, Poss KD. Enhancer selection dictates gene expression responses in remote organs during tissue regeneration. Nat Cell Biol 2022; 24:685-696. [PMID: 35513710 DOI: 10.1038/s41556-022-00906-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 03/23/2022] [Indexed: 12/14/2022]
Abstract
Acute trauma stimulates local repair mechanisms but can also impact structures distant from the injury, for example through the activity of circulating factors. To study the responses of remote tissues during tissue regeneration, we profiled transcriptomes of zebrafish brains after experimental cardiac damage. We found that the transcription factor gene cebpd was upregulated remotely in brain ependymal cells as well as kidney tubular cells, in addition to its local induction in epicardial cells. cebpd mutations altered both local and distant cardiac injury responses, altering the cycling of epicardial cells as well as exchange between distant fluid compartments. Genome-wide profiling and transgenesis identified a hormone-responsive enhancer near cebpd that exists in a permissive state, enabling rapid gene expression in heart, brain and kidney after cardiac injury. Deletion of this sequence selectively abolished cebpd induction in remote tissues and disrupted fluid regulation after injury, without affecting its local cardiac expression response. Our findings suggest a model to broaden gene function during regeneration in which enhancer regulatory elements define short- and long-range expression responses to injury.
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Affiliation(s)
- Fei Sun
- Duke Regeneration Center, Duke University, Durham, NC, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Jianhong Ou
- Duke Regeneration Center, Duke University, Durham, NC, USA
| | - Adam R Shoffner
- Duke Regeneration Center, Duke University, Durham, NC, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Yu Luan
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Hongbo Yang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Lingyun Song
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.,Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC, USA
| | - Alexias Safi
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.,Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC, USA
| | - Jingli Cao
- Cardiovascular Research Institute, Weill Cornell Medical College, New York, NY, USA.,Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.,Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC, USA
| | - Kenneth D Poss
- Duke Regeneration Center, Duke University, Durham, NC, USA. .,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA.
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15
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He J, Liu Q, Wang J, Xu F, Fan Y, He R, Yan R, Zhu L. Identification of the metabolic remodeling profile in the early-stage of myocardial ischemia and the contributory role of mitochondrion. Bioengineered 2022; 13:11106-11121. [PMID: 35470774 PMCID: PMC9161979 DOI: 10.1080/21655979.2022.2068882] [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] [Indexed: 11/29/2022] Open
Abstract
Cardiac remodeling is the primary pathological feature of chronic heart failure. Prompt inhibition of remodeling in acute coronary syndrome has been a standard procedure, but the morbidity and mortality are still high. Exploring the characteristics of ischemia in much earlier stages and identifying its biomarkers are essential for introducing novel mechanisms and therapeutic strategies. Metabolic and structural remodeling of mitochondrion is identified to play key roles in ischemic heart disease. The mitochondrial metabolic features in early ischemia have not previously been described. In the present study, we established a mouse heart in early ischemia and explored the mitochondrial metabolic profile using metabolomics analysis. We also discussed the role of mitochondrion in the global cardiac metabolism. Transmission electron microscopy revealed that mitochondrial structural injury was invoked at 8 minutes post-coronary occlusion. In total, 75 metabolites in myocardium and 26 in mitochondria were screened out. About 23% of the differentiated metabolites in mitochondria overlapped with the differentiated metabolites in myocardium; Total 81% of the perturbed metabolic pathway in mitochondria overlapped with the perturbed pathway in myocardium, and these pathways accounted for 50% of the perturbed pathway in myocardium. Purine metabolism was striking and mechanically important. In conclusion, in the early ischemia, myocardium exacerbated metabolic remodeling. Mitochondrion was a contributor to the myocardial metabolic disorder. Purine metabolism may be a potential biomarker for early ischemia diagnosis. Our study introduced a perspective for prompt identification of ischemia.
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Affiliation(s)
- Jun He
- Department of Cardiovascular Internal Medicine, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China
| | - Qian Liu
- School of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China
| | - Jie Wang
- School of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China
| | - Fangjing Xu
- School of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China
| | - Yucheng Fan
- School of Basic Medicine, Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China
| | - Ruhua He
- Department of Cardiovascular Internal Medicine, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China
| | - Ru Yan
- Department of Cardiovascular Internal Medicine, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China
| | - Li Zhu
- Department of Radiology, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China
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16
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Neogi U, Elaldi N, Appelberg S, Ambikan A, Kennedy E, Dowall S, Bagci BK, Gupta S, Rodriguez JE, Svensson-Akusjärvi S, Monteil V, Vegvari A, Benfeitas R, Banerjea A, Weber F, Hewson R, Mirazimi A. Multi-omics insights into host-viral response and pathogenesis in Crimean-Congo hemorrhagic fever viruses for novel therapeutic target. eLife 2022; 11:76071. [PMID: 35437144 PMCID: PMC9018070 DOI: 10.7554/elife.76071] [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: 12/03/2021] [Accepted: 03/15/2022] [Indexed: 12/25/2022] Open
Abstract
The pathogenesis and host-viral interactions of the Crimean–Congo hemorrhagic fever orthonairovirus (CCHFV) are convoluted and not well evaluated. Application of the multi-omics system biology approaches, including biological network analysis in elucidating the complex host-viral response, interrogates the viral pathogenesis. The present study aimed to fingerprint the system-level alterations during acute CCHFV-infection and the cellular immune responses during productive CCHFV-replication in vitro. We used system-wide network-based system biology analysis of peripheral blood mononuclear cells (PBMCs) from a longitudinal cohort of CCHF patients during the acute phase of infection and after one year of recovery (convalescent phase) followed by untargeted quantitative proteomics analysis of the most permissive CCHFV-infected Huh7 and SW13 cells. In the RNAseq analysis of the PBMCs, comparing the acute and convalescent-phase, we observed system-level host’s metabolic reprogramming towards central carbon and energy metabolism (CCEM) with distinct upregulation of oxidative phosphorylation (OXPHOS) during CCHFV-infection. Upon application of network-based system biology methods, negative coordination of the biological signaling systems like FOXO/Notch axis and Akt/mTOR/HIF-1 signaling with metabolic pathways during CCHFV-infection were observed. The temporal quantitative proteomics in Huh7 showed a dynamic change in the CCEM over time and concordant with the cross-sectional proteomics in SW13 cells. By blocking the two key CCEM pathways, glycolysis and glutaminolysis, viral replication was inhibited in vitro. Activation of key interferon stimulating genes during infection suggested the role of type I and II interferon-mediated antiviral mechanisms both at the system level and during progressive replication. Crimean-Congo hemorrhagic fever (CCHF) is an emerging disease that is increasingly spreading to new populations. The condition is now endemic in almost 30 countries in sub-Saharan Africa, South-Eastern Europe, the Middle East and Central Asia. CCHF is caused by a tick-borne virus and can cause uncontrolled bleeding. It has a mortality rate of up to 40%, and there are currently no vaccines or effective treatments available. All viruses depend entirely on their hosts for reproduction, and they achieve this through hijacking the molecular machinery of the cells they infect. However, little is known about how the CCHF virus does this and how the cells respond. To understand more about the relationship between the cell’s metabolism and viral replication, Neogi, Elaldi et al. studied immune cells taken from patients during an infection and one year later. The gene activity of the cells showed that the virus prefers to hijack processes known as central carbon and energy metabolism. These are the main regulator of the cellular energy supply and the production of essential chemicals. By using cancer drugs to block these key pathways, Neogi, Elaldi et al. could reduce the viral reproduction in laboratory cells. These findings provide a clearer understanding of how the CCHF virus replicates inside human cells. By interfering with these processes, researchers could develop new antiviral strategies to treat the disease. One of the cancer drugs tested in cells, 2-DG, has been approved for emergency use against COVID-19 in some countries. Neogi, Elaldi et al. are now studying this further in animals with the hope of reaching clinical trials in the future.
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Affiliation(s)
- Ujjwal Neogi
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm, Sweden.,Manipal Institute of Virology (MIV), Manipal Academy of Higher Education, Manipal, India
| | - Nazif Elaldi
- Department of Infectious Diseases and Clinical Microbiology, Medical Faculty, Cumhuriyet University, Sivas, Turkey
| | | | - Anoop Ambikan
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Emma Kennedy
- Public Health England, Porton Down, Salisbury, United Kingdom.,Oxford Brookes University, Oxford, United Kingdom
| | - Stuart Dowall
- Public Health England, Porton Down, Salisbury, United Kingdom
| | - Binnur K Bagci
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Sivas Cumhuriyet University, Sivas, Turkey
| | - Soham Gupta
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Jimmy E Rodriguez
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Sara Svensson-Akusjärvi
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Vanessa Monteil
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Akos Vegvari
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rui Benfeitas
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Akhil Banerjea
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Friedemann Weber
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Giessen, Germany
| | - Roger Hewson
- Public Health England, Porton Down, Salisbury, United Kingdom.,Oxford Brookes University, Oxford, United Kingdom.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ali Mirazimi
- Public Health Agency of Sweden, Solna, Sweden.,Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm, Sweden.,National Veterinary Institute, Uppsala, Sweden
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17
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Arif M, Zhang C, Li X, Güngör C, Çakmak B, Arslantürk M, Tebani A, Özcan B, Subaş O, Zhou W, Piening B, Turkez H, Fagerberg L, Price N, Hood L, Snyder M, Nielsen J, Uhlen M, Mardinoglu A. iNetModels 2.0: an interactive visualization and database of multi-omics data. Nucleic Acids Res 2021; 49:W271-W276. [PMID: 33849075 DOI: 10.1101/2021.11.10.468051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/10/2021] [Accepted: 03/29/2021] [Indexed: 05/20/2023] Open
Abstract
It is essential to reveal the associations between various omics data for a comprehensive understanding of the altered biological process in human wellness and disease. To date, very few studies have focused on collecting and exhibiting multi-omics associations in a single database. Here, we present iNetModels, an interactive database and visualization platform of Multi-Omics Biological Networks (MOBNs). This platform describes the associations between the clinical chemistry, anthropometric parameters, plasma proteomics, plasma metabolomics, as well as metagenomics for oral and gut microbiome obtained from the same individuals. Moreover, iNetModels includes tissue- and cancer-specific Gene Co-expression Networks (GCNs) for exploring the connections between the specific genes. This platform allows the user to interactively explore a single feature's association with other omics data and customize its particular context (e.g. male/female specific). The users can also register their data for sharing and visualization of the MOBNs and GCNs. Moreover, iNetModels allows users who do not have a bioinformatics background to facilitate human wellness and disease research. iNetModels can be accessed freely at https://inetmodels.com without any limitation.
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Affiliation(s)
- Muhammad Arif
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm SE-171 21, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm SE-171 21, Sweden
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan Province, PR 450001, China
| | - Xiangyu Li
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm SE-171 21, Sweden
| | - Cem Güngör
- Bash Biotech Inc, 600 West Broadway, Suite 700, San Diego, CA, USA
| | - Buğra Çakmak
- Bash Biotech Inc, 600 West Broadway, Suite 700, San Diego, CA, USA
| | - Metin Arslantürk
- Bash Biotech Inc, 600 West Broadway, Suite 700, San Diego, CA, USA
| | - Abdellah Tebani
- Department of Metabolic Biochemistry, Rouen University Hospital, 76000 Rouen, France
- Normandie Univ, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France
| | - Berkay Özcan
- Bash Biotech Inc, 600 West Broadway, Suite 700, San Diego, CA, USA
| | - Oğuzhan Subaş
- Bash Biotech Inc, 600 West Broadway, Suite 700, San Diego, CA, USA
| | - Wenyu Zhou
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Brian Piening
- Providence Cancer Center, Oregon Area, Portland, OR, USA
| | - Hasan Turkez
- Department of Medical Biology, Faculty of Medicine, Atatürk University, Erzurum, Turkey
| | - Linn Fagerberg
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm SE-171 21, Sweden
| | | | - Leroy Hood
- Institute of Systems Biology, Seattle, USA
| | - Michael Snyder
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm SE-171 21, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm SE-171 21, Sweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London SE1 9RT, UK
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18
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Odongo R, Çakır T. Working together. eLife 2021; 10:69863. [PMID: 34100721 PMCID: PMC8186899 DOI: 10.7554/elife.69863] [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: 06/03/2021] [Accepted: 06/03/2021] [Indexed: 11/29/2022] Open
Abstract
Heart attacks have a ripple effect on how other organs exchange biomolecules that help the heart respond to injury.
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Affiliation(s)
- Regan Odongo
- Gebze Technical University, Gebze, Kocaeli, Turkey
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19
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Arif M, Klevstig M, Benfeitas R, Doran S, Turkez H, Uhlén M, Clausen M, Wikström J, Etal D, Zhang C, Levin M, Mardinoglu A, Boren J. Integrative transcriptomic analysis of tissue-specific metabolic crosstalk after myocardial infarction. eLife 2021; 10:66921. [PMID: 33972017 PMCID: PMC8186902 DOI: 10.7554/elife.66921] [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: 01/26/2021] [Accepted: 04/25/2021] [Indexed: 12/14/2022] Open
Abstract
Myocardial infarction (MI) promotes a range of systemic effects, many of which are unknown. Here, we investigated the alterations associated with MI progression in heart and other metabolically active tissues (liver, skeletal muscle, and adipose) in a mouse model of MI (induced by ligating the left ascending coronary artery) and sham-operated mice. We performed a genome-wide transcriptomic analysis on tissue samples obtained 6- and 24 hr post MI or sham operation. By generating tissue-specific biological networks, we observed: (1) dysregulation in multiple biological processes (including immune system, mitochondrial dysfunction, fatty-acid beta-oxidation, and RNA and protein processing) across multiple tissues post MI and (2) tissue-specific dysregulation in biological processes in liver and heart post MI. Finally, we validated our findings in two independent MI cohorts. Overall, our integrative analysis highlighted both common and specific biological responses to MI across a range of metabolically active tissues. The human body is like a state-of-the-art car, where each part must work together with all the others. When a car breaks down, most of the time the problem is not isolated to only one part, as it is an interconnected system. Diseases in the human body can also have systemic effects, so it is important to study their implications throughout the body. Most studies of heart attacks focus on the direct impact on the heart and the cardiovascular system. Learning more about how heart attacks affect rest of the body may help scientists identify heart attacks early or create improved treatments. Arif and Klevstig et al. show that heart attacks affect the metabolism throughout the body. In the experiments, mice underwent a procedure that mimics either a heart attack or a fake procedure. Then, Arif and Klevstig et al. compared the activity of genes in the heart, muscle, liver and fat tissue of the two groups of mice 6- and 24-hours after the operations. This revealed disruptions in the immune system, metabolism and the production of proteins. The experiments also showed that changes in the activity of four important genes are key to these changes. This suggests that this pattern of changes could be used as a way to identify heart attacks. The experiments show that heart attacks have important effects throughout the body, especially on metabolism. These discoveries may help scientists learn more about the underlying biological processes and develop new treatments that prevent the harmful systemic effects of heart attacks and boost recovery.
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Affiliation(s)
- Muhammad Arif
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Martina Klevstig
- Department of Molecular and Clinical Medicine, University of Gothenburg, The Wallenberg Laboratory, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Rui Benfeitas
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Stephen Doran
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, United Kingdom
| | - Hasan Turkez
- Department of Medical Biology, Faculty of Medicine, Atatürk University, Erzurum, Turkey
| | - Mathias Uhlén
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Maryam Clausen
- Translational Genomics, BioPharmaceuticals R&D, Discovery Sciences, AstraZeneca, Gothenburg, Sweden
| | - Johannes Wikström
- Bioscience Cardiovascular, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Damla Etal
- Translational Genomics, BioPharmaceuticals R&D, Discovery Sciences, AstraZeneca, Gothenburg, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Malin Levin
- Department of Molecular and Clinical Medicine, University of Gothenburg, The Wallenberg Laboratory, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.,Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, United Kingdom
| | - Jan Boren
- Department of Molecular and Clinical Medicine, University of Gothenburg, The Wallenberg Laboratory, Sahlgrenska University Hospital, Gothenburg, Sweden
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