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Perry AS, Amancherla K, Huang X, Lance ML, Farber-Eger E, Gajjar P, Amrute J, Stolze L, Zhao S, Sheng Q, Joynes CM, Peng Z, Tanaka T, Drakos SG, Lavine KJ, Selzman C, Visker JR, Shankar TS, Ferrucci L, Das S, Wilcox J, Patel RB, Kalhan R, Shah SJ, Walker KA, Wells Q, Tucker N, Nayor M, Shah RV, Khan SS. Clinical-transcriptional prioritization of the circulating proteome in human heart failure. Cell Rep Med 2024; 5:101704. [PMID: 39226894 DOI: 10.1016/j.xcrm.2024.101704] [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: 12/15/2023] [Revised: 06/15/2024] [Accepted: 08/07/2024] [Indexed: 09/05/2024]
Abstract
Given expanding studies in epidemiology and disease-oriented human studies offering hundreds of associations between the human "ome" and disease, prioritizing molecules relevant to disease mechanisms among this growing breadth is important. Here, we link the circulating proteome to human heart failure (HF) propensity (via echocardiographic phenotyping and clinical outcomes) across the lifespan, demonstrating key pathways of fibrosis, inflammation, metabolism, and hypertrophy. We observe a broad array of genes encoding proteins linked to HF phenotypes and outcomes in clinical populations dynamically expressed at a transcriptional level in human myocardium during HF and cardiac recovery (several in a cell-specific fashion). Many identified targets do not have wide precedent in large-scale genomic discovery or human studies, highlighting the complementary roles for proteomic and tissue transcriptomic discovery to focus epidemiological targets to those relevant in human myocardium for further interrogation.
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Affiliation(s)
- Andrew S Perry
- Vanderbilt Translational and Clinical Cardiovascular Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kaushik Amancherla
- Vanderbilt Translational and Clinical Cardiovascular Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Xiaoning Huang
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Eric Farber-Eger
- Vanderbilt Translational and Clinical Cardiovascular Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Priya Gajjar
- Sections of Cardiovascular Medicine and Preventive Medicine and Epidemiology, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Junedh Amrute
- Cardiology Division, Washington University School of Medicine, St. Louis, MO, USA
| | - Lindsey Stolze
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shilin Zhao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Quanhu Sheng
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cassandra M Joynes
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Zhongsheng Peng
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Stavros G Drakos
- Division of Cardiovascular Medicine, University of Utah and Nora Eccles Harrison Cardiovascular Research and Training Institute (CVRTI), Salt Lake City, UT, USA
| | - Kory J Lavine
- Cardiology Division, Washington University School of Medicine, St. Louis, MO, USA
| | - Craig Selzman
- Department of Cardiac Surgery, University of Utah School of Medicine, Division of Cardiothoracic Surgery, University of Utah and Nora Eccles Harrison Cardiovascular Research and Training Institute (CVRTI), Salt Lake City, UT, USA
| | - Joseph R Visker
- Division of Cardiovascular Medicine, University of Utah and Nora Eccles Harrison Cardiovascular Research and Training Institute (CVRTI), Salt Lake City, UT, USA
| | - Thirupura S Shankar
- Division of Cardiovascular Medicine, University of Utah and Nora Eccles Harrison Cardiovascular Research and Training Institute (CVRTI), Salt Lake City, UT, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Saumya Das
- Cardiovascular Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jane Wilcox
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ravi B Patel
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ravi Kalhan
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Sanjiv J Shah
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Keenan A Walker
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Quinn Wells
- Vanderbilt Translational and Clinical Cardiovascular Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Matthew Nayor
- Sections of Cardiovascular Medicine and Preventive Medicine and Epidemiology, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Ravi V Shah
- Vanderbilt Translational and Clinical Cardiovascular Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Sadiya S Khan
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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McLouth CJ, Maglinger B, Frank JA, Hazelwood HS, Harp JP, Cranford W, Pahwa S, Sheikhi L, Dornbos D, Trout AL, Stowe AM, Fraser JF, Pennypacker KR. The differential proteomic response to ischemic stroke in appalachian subjects treated with mechanical thrombectomy. J Neuroinflammation 2024; 21:205. [PMID: 39154085 PMCID: PMC11330053 DOI: 10.1186/s12974-024-03201-9] [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: 05/30/2024] [Accepted: 08/09/2024] [Indexed: 08/19/2024] Open
Abstract
INTRODUCTION The Appalachia region of North America is known to have significant health disparities, specifically, worse risk factors and outcomes for stroke. Appalachians are more likely to have comorbidities related to stroke, such as diabetes, obesity, and tobacco use, and are often less likely to have stroke interventions, such as mechanical thrombectomy (MT), for emergent large vessel occlusion (ELVO). As our Comprehensive Stroke Center directly serves stroke subjects from both Appalachian and non-Appalachian areas, inflammatory proteomic biomarkers were identified associated with stroke outcomes specific to subjects residing in Appalachia. METHODS There were 81 subjects that met inclusion criteria for this study. These subjects underwent MT for ELVO, and carotid arterial blood samples acquired at time of intervention were sent for proteomic analysis. Samples were processed in accordance with the Blood And Clot Thrombectomy Registry And Collaboration (BACTRAC; clinicaltrials.gov; NCT03153683). Statistical analyses were utilized to examine whether relationships between protein expression and outcomes differed by Appalachian status for functional (NIH Stroke Scale; NIHSS and Modified Rankin Score; mRS), and cognitive outcomes (Montreal Cognitive Assessment; MoCA). RESULTS No significant differences were found in demographic data or co-morbidities when comparing Appalachian to non-Appalachian subjects. However, time from stroke onset to treatment (last known normal) was significantly longer and edema volume significantly higher in patients from Appalachia. Further, when comparing Appalachian to non-Appalachian subjects, there were significant unadjusted differences in the NIHSS functional outcome. A comprehensive analysis of 184 proteins from Olink proteomic (92 Cardiometabolic and 92 Inflammation panels) showed that the association between protein expression outcomes significantly differed by Appalachian status for seven proteins for the NIHSS, two proteins for the MoCA, and three for the mRS. CONCLUSION Our study utilizes an ELVO tissue bank and registry to investigate the intracranial/intravascular proteomic environment occurring at the time of thrombectomy. We found that patients presenting from Appalachian areas have different levels of proteomic expression at the time of MT when compared to patients presenting from non-Appalachian areas. These proteins differentially relate to stroke outcome and could be used as prognostic biomarkers, or as targets for novel therapies. The identification of a disparate proteomic response in Appalachian patients provides initial insight to the biological basis for health disparity. Nevertheless, further investigations through community-based studies are imperative to elucidate the underlying causes of this differential response.
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Affiliation(s)
- Christopher J McLouth
- Department of Biostatistics, University of Kentucky, Lexington, KY, USA
- Department of Neurology, University of Kentucky, Lexington, KY, USA
| | - Benton Maglinger
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jacqueline A Frank
- Department of Neurosurgery, University of Kentucky, Lexington, KY, USA
- Center for Advanced Translational Stroke Science, Department of Neurology and Neuroscience Building BBSRB Office B463, University of Kentucky, Lexington, KY, 40536, USA
| | | | - Jordan P Harp
- Department of Neurology, University of Kentucky, Lexington, KY, USA
- Center for Advanced Translational Stroke Science, Department of Neurology and Neuroscience Building BBSRB Office B463, University of Kentucky, Lexington, KY, 40536, USA
| | - Will Cranford
- Department of Biostatistics, University of Kentucky, Lexington, KY, USA
| | - Shivani Pahwa
- Department of Neurosurgery, University of Kentucky, Lexington, KY, USA
- Department of Radiology, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, University of Kentucky, Lexington, KY, USA
| | - Lila Sheikhi
- Department of Neurology, University of Kentucky, Lexington, KY, USA
- Department of Neurosurgery, University of Kentucky, Lexington, KY, USA
- Department of Radiology, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, University of Kentucky, Lexington, KY, USA
| | - David Dornbos
- Department of Neurosurgery, University of Kentucky, Lexington, KY, USA
- Department of Radiology, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, University of Kentucky, Lexington, KY, USA
| | - Amanda L Trout
- Department of Neurosurgery, University of Kentucky, Lexington, KY, USA
- Center for Advanced Translational Stroke Science, Department of Neurology and Neuroscience Building BBSRB Office B463, University of Kentucky, Lexington, KY, 40536, USA
| | - Ann M Stowe
- Department of Neurology, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, University of Kentucky, Lexington, KY, USA
- Center for Advanced Translational Stroke Science, Department of Neurology and Neuroscience Building BBSRB Office B463, University of Kentucky, Lexington, KY, 40536, USA
| | - Justin F Fraser
- Department of Neurology, University of Kentucky, Lexington, KY, USA
- Department of Neurosurgery, University of Kentucky, Lexington, KY, USA
- Department of Radiology, University of Kentucky, Lexington, KY, USA
- Center for Advanced Translational Stroke Science, Department of Neurology and Neuroscience Building BBSRB Office B463, University of Kentucky, Lexington, KY, 40536, USA
| | - Keith R Pennypacker
- Department of Neurology, University of Kentucky, Lexington, KY, USA.
- Department of Neuroscience, University of Kentucky, Lexington, KY, USA.
- Center for Advanced Translational Stroke Science, Department of Neurology and Neuroscience Building BBSRB Office B463, University of Kentucky, Lexington, KY, 40536, USA.
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Zeng H, Lan B, Li B, Xie H, Zhao E, Liu X, Xue X, Sun J, Su L, Zhang Y. The role and mechanism of thrombospondin-4 in pulmonary arterial hypertension associated with congenital heart disease. Respir Res 2024; 25:313. [PMID: 39154161 PMCID: PMC11330619 DOI: 10.1186/s12931-024-02932-w] [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: 04/14/2024] [Accepted: 07/31/2024] [Indexed: 08/19/2024] Open
Abstract
BACKGROUND Due to a special hemodynamic feature, pulmonary vascular disease in pulmonary arterial hypertension associated with congenital heart disease (PAH-CHD) has two stages: reversible and irreversible. So far, the mechanism involved in the transition from reversible to irreversible stage is elusive. Moreover, no recognized and reliable assessments to distinguish these two stages are available. Furthermore, we found that compared with control and reversible PAH, thrombospondin-4 (THBS4) was significantly upregulated in irreversible group by bioinformatic analysis. Hence, we further verify and investigate the expression and role of THBS4 in PAH-CHD. METHODS We established the monocrotaline plus aorto-cava shunt-induced (MCT-AV) rat model. We measured the expression of THBS4 in lung tissues from MCT-AV rats. Double immunofluorescence staining of lung tissue for THBS4 and α-SMA (biomarker of smooth muscle cells) or vWF (biomarker of endothelial cells) to identify the location of THBS4 in the pulmonary artery. Primary pulmonary artery smooth muscle cells (PASMCs) were cultivated, identified, and used in this study. THBS4 was inhibited and overexpressed by siRNA and plasmid, respectively, to explore the effect of THBS4 on phenotype transformation, proliferation, apoptosis, and migration of PASMCs. The effect of THBS4 on pulmonary vascular remodeling was evaluated in vivo by adeno-associated virus which suppressed THBS4 expression. Circulating level of THBS4 in patients with PAH-CHD was measured by ELISA. RESULTS THBS4 was upregulated in the lung tissues of MCT-AV rats, and was further upregulated in severe pulmonary vascular lesions. And THBS4 was expressed mainly in PASMCs. When THBS4 was inhibited, contractile markers α-SMA and MYH11 were upregulated, while the proliferative marker PCNA was decreased, the endothelial-mensenchymal transition marker N-cad was downregulated, proapototic marker BAX was increased. Additionally, proliferation and migration of PASMCs was inhibited and apoptosis was increased. Conversely, THBS4 overexpression resulted in opposite effects. And the impact of THBS4 on PASMCs was probably achieved through the regulation of the PI3K/AKT pathway. THBS4 suppression attenuated pulmonary vascular remodeling. Furthermore, compared with patients with simple congenital heart disease and mild PAH-CHD, the circulating level of THBS4 was higher in patients with severe PAH-CHD. CONCLUSIONS THBS4 is a promising biomarker to distinguish reversible from irreversible PAH-CHD before repairing the shunt. THBS4 is a potential treatment target in PAH-CHD, especially in irreversible stage.
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Affiliation(s)
- Haowei Zeng
- Department of Cardiovascular Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Beidi Lan
- Department of Cardiovascular Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Bingyi Li
- Department of Cardiovascular Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Hang Xie
- Department of Cardiovascular Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Enfa Zhao
- Department of Ultrasound, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, China
| | - Xiaoqin Liu
- Department of Cardiovascular Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaoyi Xue
- Department of Cardiovascular Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jingyan Sun
- Department of Cardiovascular Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Linjie Su
- Department of Cardiovascular Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yushun Zhang
- Department of Cardiovascular Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
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Sun HJ, Lu QB, Zhu XX, Ni ZR, Su JB, Fu X, Chen G, Zheng GL, Nie XW, Bian JS. Pharmacology of Hydrogen Sulfide and Its Donors in Cardiometabolic Diseases. Pharmacol Rev 2024; 76:846-895. [PMID: 38866561 DOI: 10.1124/pharmrev.123.000928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/13/2024] [Accepted: 06/10/2024] [Indexed: 06/14/2024] Open
Abstract
Cardiometabolic diseases (CMDs) are major contributors to global mortality, emphasizing the critical need for novel therapeutic interventions. Hydrogen sulfide (H2S) has garnered enormous attention as a significant gasotransmitter with various physiological, pathophysiological, and pharmacological impacts within mammalian cardiometabolic systems. In addition to its roles in attenuating oxidative stress and inflammatory response, burgeoning research emphasizes the significance of H2S in regulating proteins via persulfidation, a well known modification intricately associated with the pathogenesis of CMDs. This review seeks to investigate recent updates on the physiological actions of endogenous H2S and the pharmacological roles of various H2S donors in addressing diverse aspects of CMDs across cellular, animal, and clinical studies. Of note, advanced methodologies, including multiomics, intestinal microflora analysis, organoid, and single-cell sequencing techniques, are gaining traction due to their ability to offer comprehensive insights into biomedical research. These emerging approaches hold promise in characterizing the pharmacological roles of H2S in health and diseases. We will critically assess the current literature to clarify the roles of H2S in diseases while also delineating the opportunities and challenges they present in H2S-based pharmacotherapy for CMDs. SIGNIFICANCE STATEMENT: This comprehensive review covers recent developments in H2S biology and pharmacology in cardiometabolic diseases CMDs. Endogenous H2S and its donors show great promise for the management of CMDs by regulating numerous proteins and signaling pathways. The emergence of new technologies will considerably advance the pharmacological research and clinical translation of H2S.
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Affiliation(s)
- Hai-Jian Sun
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China (H.-J.S., X.-X.Z., Z.-R.N., J.-B.S., X.F., G.C., G.-L.Z.); Department of Endocrinology, Affiliated Hospital of Jiangnan University, Jiangnan University, Wuxi, Jiangsu, China (Q.-B.L.); Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital, Shenzhen, Guangdong, China (X.-W.N.); and Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China (J.-S.B.)
| | - Qing-Bo Lu
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China (H.-J.S., X.-X.Z., Z.-R.N., J.-B.S., X.F., G.C., G.-L.Z.); Department of Endocrinology, Affiliated Hospital of Jiangnan University, Jiangnan University, Wuxi, Jiangsu, China (Q.-B.L.); Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital, Shenzhen, Guangdong, China (X.-W.N.); and Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China (J.-S.B.)
| | - Xue-Xue Zhu
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China (H.-J.S., X.-X.Z., Z.-R.N., J.-B.S., X.F., G.C., G.-L.Z.); Department of Endocrinology, Affiliated Hospital of Jiangnan University, Jiangnan University, Wuxi, Jiangsu, China (Q.-B.L.); Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital, Shenzhen, Guangdong, China (X.-W.N.); and Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China (J.-S.B.)
| | - Zhang-Rong Ni
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China (H.-J.S., X.-X.Z., Z.-R.N., J.-B.S., X.F., G.C., G.-L.Z.); Department of Endocrinology, Affiliated Hospital of Jiangnan University, Jiangnan University, Wuxi, Jiangsu, China (Q.-B.L.); Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital, Shenzhen, Guangdong, China (X.-W.N.); and Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China (J.-S.B.)
| | - Jia-Bao Su
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China (H.-J.S., X.-X.Z., Z.-R.N., J.-B.S., X.F., G.C., G.-L.Z.); Department of Endocrinology, Affiliated Hospital of Jiangnan University, Jiangnan University, Wuxi, Jiangsu, China (Q.-B.L.); Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital, Shenzhen, Guangdong, China (X.-W.N.); and Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China (J.-S.B.)
| | - Xiao Fu
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China (H.-J.S., X.-X.Z., Z.-R.N., J.-B.S., X.F., G.C., G.-L.Z.); Department of Endocrinology, Affiliated Hospital of Jiangnan University, Jiangnan University, Wuxi, Jiangsu, China (Q.-B.L.); Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital, Shenzhen, Guangdong, China (X.-W.N.); and Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China (J.-S.B.)
| | - Guo Chen
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China (H.-J.S., X.-X.Z., Z.-R.N., J.-B.S., X.F., G.C., G.-L.Z.); Department of Endocrinology, Affiliated Hospital of Jiangnan University, Jiangnan University, Wuxi, Jiangsu, China (Q.-B.L.); Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital, Shenzhen, Guangdong, China (X.-W.N.); and Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China (J.-S.B.)
| | - Guan-Li Zheng
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China (H.-J.S., X.-X.Z., Z.-R.N., J.-B.S., X.F., G.C., G.-L.Z.); Department of Endocrinology, Affiliated Hospital of Jiangnan University, Jiangnan University, Wuxi, Jiangsu, China (Q.-B.L.); Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital, Shenzhen, Guangdong, China (X.-W.N.); and Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China (J.-S.B.)
| | - Xiao-Wei Nie
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China (H.-J.S., X.-X.Z., Z.-R.N., J.-B.S., X.F., G.C., G.-L.Z.); Department of Endocrinology, Affiliated Hospital of Jiangnan University, Jiangnan University, Wuxi, Jiangsu, China (Q.-B.L.); Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital, Shenzhen, Guangdong, China (X.-W.N.); and Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China (J.-S.B.)
| | - Jin-Song Bian
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China (H.-J.S., X.-X.Z., Z.-R.N., J.-B.S., X.F., G.C., G.-L.Z.); Department of Endocrinology, Affiliated Hospital of Jiangnan University, Jiangnan University, Wuxi, Jiangsu, China (Q.-B.L.); Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital, Shenzhen, Guangdong, China (X.-W.N.); and Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China (J.-S.B.)
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Helal SA, El-Sherbeni AA, El-Kadi AOS. 11-Hydroxyeicosatetraenoics induces cellular hypertrophy in an enantioselective manner. Front Pharmacol 2024; 15:1438567. [PMID: 39188949 PMCID: PMC11345585 DOI: 10.3389/fphar.2024.1438567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Accepted: 07/08/2024] [Indexed: 08/28/2024] Open
Abstract
Background R/S enantiomers of 11-hydroxyeicosatertraenoic acid (11-HETE) are formed from arachidonic acid by enzymatic and non-enzymatic pathways. 11-HETE is predominately formed by the cytochrome P450 1B1 (CYP1B1). The role of CYP1B1 in the development of cardiovascular diseases is well established. Objectives This study aimed to assess the cellular hypertrophic effect of 11-HETE enantiomers in human RL-14 cardiomyocyte cell line and to examine their association with CYP1B1 levels. Methods Human fetal ventricular cardiomyocyte, RL-14 cells, were treated with 20 µM (R) or (S) 11-HETE for 24 h. Thereafter, cellular hypertrophic markers and cell size were then determined using real-time polymerase chain reaction (RT-PCR) and phase-contrast imaging, respectively. The mRNA and protein levels of selected CYPs were determined using RT-PCR and Western blot, respectively. In addition, we examined the effect of (R) and (S) 11-HETE on CYP1B1 catalytic activity using human recombinant CYP1B1 and human liver microsomes. Results Both (R) and (S) 11-HETE induced cellular hypertrophic markers and cell surface area in RL-14 cells. Both enantiomers significantly upregulated CYP1B1, CYP1A1, CYP4F2, and CYP4A11 at the mRNA and protein levels, however, the effect of the S-enantiomer was more pronounced. Furthermore, 11(S)-HETE increased the mRNA and protein levels of CYP2J and CYP4F2, whereas 11(R)-HETE increased only CYP4F2. Only 11(S)-HETE significantly increased the catalytic activity of CYP1B1 in recombinant human CYP1B1, suggesting allosteric activation in an enantioselective manner. Conclusion Our study provides the first evidence that 11-HETE can induce cellular hypertrophy in RL-14 cells via the increase in CYP1B1 mRNA, protein, and activity levels.
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Affiliation(s)
- Sara A. Helal
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
- Department of Biochemistry, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Ahmed A. El-Sherbeni
- Department of Clinical Pharmacy, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Ayman O. S. El-Kadi
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
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Park S, Laskow TC, Chen J, Guha P, Dawn B, Kim D. Microphysiological systems for human aging research. Aging Cell 2024; 23:e14070. [PMID: 38180277 PMCID: PMC10928588 DOI: 10.1111/acel.14070] [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: 06/30/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Recent advances in microphysiological systems (MPS), also known as organs-on-a-chip (OoC), enable the recapitulation of more complex organ and tissue functions on a smaller scale in vitro. MPS therefore provide the potential to better understand human diseases and physiology. To date, numerous MPS platforms have been developed for various tissues and organs, including the heart, liver, kidney, blood vessels, muscle, and adipose tissue. However, only a few studies have explored using MPS platforms to unravel the effects of aging on human physiology and the pathogenesis of age-related diseases. Age is one of the risk factors for many diseases, and enormous interest has been devoted to aging research. As such, a human MPS aging model could provide a more predictive tool to understand the molecular and cellular mechanisms underlying human aging and age-related diseases. These models can also be used to evaluate preclinical drugs for age-related diseases and translate them into clinical settings. Here, we provide a review on the application of MPS in aging research. First, we offer an overview of the molecular, cellular, and physiological changes with age in several tissues or organs. Next, we discuss previous aging models and the current state of MPS for studying human aging and age-related conditions. Lastly, we address the limitations of current MPS and present future directions on the potential of MPS platforms for human aging research.
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Affiliation(s)
- Seungman Park
- Department of Mechanical EngineeringUniversity of Nevada, Las VegasLas VegasNevadaUSA
| | - Thomas C. Laskow
- Department of MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Jingchun Chen
- Nevada Institute of Personalized MedicineUniversity of Nevada, Las VegasLas VegasNevadaUSA
| | - Prasun Guha
- Nevada Institute of Personalized MedicineUniversity of Nevada, Las VegasLas VegasNevadaUSA
- School of Life SciencesUniversity of Nevada, Las VegasLas VegasNevadaUSA
| | - Buddhadeb Dawn
- Department of Internal Medicine, Kirk Kerkorian School of MedicineUniversity of Nevada, Las VegasLas VegasNevadaUSA
| | - Deok‐Ho Kim
- Department of MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of Biomedical EngineeringJohns Hopkins UniversityBaltimoreMarylandUSA
- Center for Microphysiological SystemsJohns Hopkins UniversityBaltimoreMarylandUSA
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Genaro K, Luo ZD. Pathophysiological roles of thrombospondin-4 in disease development. Semin Cell Dev Biol 2024; 155:66-73. [PMID: 37391348 PMCID: PMC10753034 DOI: 10.1016/j.semcdb.2023.06.007] [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: 06/11/2023] [Accepted: 06/21/2023] [Indexed: 07/02/2023]
Abstract
Thrombospondin-4 (TSP-4) belongs to the extracellular matrix glycoprotein family of thrombospondins (TSPs). The multidomain, pentameric structure of TSP-4 allows its interactions with numerous extracellular matrix components, proteins and signaling molecules that enable its modulation to various physiological and pathological processes. Characterization of TSP-4 expression under development and pathogenesis of disorders has yielded important insights into mechanisms underlying the unique role of TSP-4 in mediating various processes including cell-cell, cell-extracellular matrix interactions, cell migration, proliferation, tissue remodeling, angiogenesis, and synaptogenesis. Maladaptation of these processes in response to pathological insults and stress can accelerate the development of disorders including skeletal dysplasia, osteoporosis, degenerative joint disease, cardiovascular diseases, tumor progression/metastasis and neurological disorders. Overall, the diverse functions of TSP-4 suggest that it may be a potential marker or therapeutic target for prognosis, diagnosis, and treatment of various pathological conditions upon further investigations. This review article highlights recent findings on the role of TSP-4 in both physiological and pathological conditions with a focus on what sets it apart from other TSPs.
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Affiliation(s)
- Karina Genaro
- Department of Anesthesiology & Perioperative Care, School of Medicine, University of California Irvine, Irvine, CA 92697, USA
| | - Z David Luo
- Department of Anesthesiology & Perioperative Care, School of Medicine, University of California Irvine, Irvine, CA 92697, USA.
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8
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Reitz CJ, Kuzmanov U, Gramolini AO. Multi-omic analyses and network biology in cardiovascular disease. Proteomics 2023; 23:e2200289. [PMID: 37691071 DOI: 10.1002/pmic.202200289] [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: 03/17/2023] [Revised: 08/11/2023] [Accepted: 08/22/2023] [Indexed: 09/12/2023]
Abstract
Heart disease remains a leading cause of death in North America and worldwide. Despite advances in therapies, the chronic nature of cardiovascular diseases ultimately results in frequent hospitalizations and steady rates of mortality. Systems biology approaches have provided a new frontier toward unraveling the underlying mechanisms of cell, tissue, and organ dysfunction in disease. Mapping the complex networks of molecular functions across the genome, transcriptome, proteome, and metabolome has enormous potential to advance our understanding of cardiovascular disease, discover new disease biomarkers, and develop novel therapies. Computational workflows to interpret these data-intensive analyses as well as integration between different levels of interrogation remain important challenges in the advancement and application of systems biology-based analyses in cardiovascular research. This review will focus on summarizing the recent developments in network biology-level profiling in the heart, with particular emphasis on modeling of human heart failure. We will provide new perspectives on integration between different levels of large "omics" datasets, including integration of gene regulatory networks, protein-protein interactions, signaling networks, and metabolic networks in the heart.
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Affiliation(s)
- Cristine J Reitz
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, Ontario, Canada
| | - Uros Kuzmanov
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, Ontario, Canada
| | - Anthony O Gramolini
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, Ontario, Canada
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Allam S, Levenson-Palmer R, Chia Chang Z, Kaur S, Cernuda B, Raman A, Booth A, Dobbins S, Suppa G, Yang J, Buraei Z. Inactivation influences the extent of inhibition of voltage-gated Ca +2 channels by Gem-implications for channelopathies. Front Physiol 2023; 14:1155976. [PMID: 37654674 PMCID: PMC10466392 DOI: 10.3389/fphys.2023.1155976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 07/21/2023] [Indexed: 09/02/2023] Open
Abstract
Voltage-gated Ca2+ channels (VGCC) directly control muscle contraction and neurotransmitter release, and slower processes such as cell differentiation, migration, and death. They are potently inhibited by RGK GTP-ases (Rem, Rem2, Rad, and Gem/Kir), which decrease Ca2+ channel membrane expression, as well as directly inhibit membrane-resident channels. The mechanisms of membrane-resident channel inhibition are difficult to study because RGK-overexpression causes complete or near complete channel inhibition. Using titrated levels of Gem expression in Xenopus oocytes to inhibit WT P/Q-type calcium channels by ∼50%, we show that inhibition is dependent on channel inactivation. Interestingly, fast-inactivating channels, including Familial Hemiplegic Migraine mutants, are more potently inhibited than WT channels, while slow-inactivating channels, such as those expressed with the Cavβ2a auxiliary subunit, are spared. We found similar results in L-type channels, and, remarkably, Timothy Syndrome mutant channels were insensitive to Gem inhibition. Further results suggest that RGKs slow channel recovery from inactivation and further implicate RGKs as likely modulating factors in channelopathies.
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Affiliation(s)
- Salma Allam
- Department of Biology, Pace University, New York, NY, United States
| | - Rose Levenson-Palmer
- Department of Biological Sciences, Columbia University, New York, NY, United States
| | | | - Sukhjinder Kaur
- Department of Biology, Pace University, New York, NY, United States
| | - Bryan Cernuda
- Department of Biology, Pace University, New York, NY, United States
| | - Ananya Raman
- Department of Biology, Pace University, New York, NY, United States
| | - Audrey Booth
- Department of Biology, Pace University, New York, NY, United States
| | - Scott Dobbins
- Department of Biological Sciences, Columbia University, New York, NY, United States
| | - Gabrielle Suppa
- Department of Biology, Pace University, New York, NY, United States
| | - Jian Yang
- Department of Biological Sciences, Columbia University, New York, NY, United States
| | - Zafir Buraei
- Department of Biology, Pace University, New York, NY, United States
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10
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Padula G, Garces GR, Fernández ME, Vercellini R, Arias DO, García PP, Giovambattista G. Preliminary transcriptomic analysis of peripheral blood from German Shepherd dogs with degenerative joint disease for the identification of diagnostic biomarkers. Gene 2023; 872:147455. [PMID: 37254296 DOI: 10.1016/j.gene.2023.147455] [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: 10/15/2022] [Revised: 04/08/2023] [Accepted: 04/25/2023] [Indexed: 06/01/2023]
Abstract
OBJECTIVE Degenerative joint disease (DJD) includes a group of disorders characterised by the deterioration of the articular cartilage. In this study, we investigated the transcriptomic profile of peripheral blood in German Shepherd dogs with DJD to identify putative diagnostic biomarkers. METHODS Differential gene expression (DGE) and gene ontology (GO) analyses of the bulk RNA-seq experiment were performed in a cohort of 12 adult dogs (five cases and seven controls, classified by clinical and radiographic analyses). RESULTS Radiographs of cases revealed severe signs of progressive DJD. Two up-regulated (LOC106559672 and THBS4) and one down-regulated (LOC106559235) differentially expressed genes (adjusted p value < 0.05) were identified. The DGE with log2 fold change < -1.5 and > 1.5 and non-adjusted p < 0.01 were selected for GO analysis. No significant enrichment terms were observed in the selected threshold. CONCLUSION The gene-encoding protein THBS4 is correlated with DJD severity and long noncoding RNA LOC106559235 is probably involved in the DJD process. The THBS4 gene should be considered a good biomarker for DJD in dogs. Future studies using independent cohorts will be necessary to validate the present results.
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Affiliation(s)
- Gisel Padula
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, 60 y 118 S/N, 1900 La Plata, Argentina; Facultad de Ciencias Naturales y Museo UNLP, 60 y 122, 1900 La Plata, Argentina
| | - Gabriela Rudd Garces
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, 60 y 118 S/N, 1900 La Plata, Argentina
| | - María Elena Fernández
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, 60 y 118 S/N, 1900 La Plata, Argentina
| | - Rosario Vercellini
- Servicio de Radiología, Facultad de Ciencias Veterinarias UNLP, 60 y 118 S/N, 1900 La Plata, Argentina
| | - Daniel Osvaldo Arias
- Servicio de Radiología, Facultad de Ciencias Veterinarias UNLP, 60 y 118 S/N, 1900 La Plata, Argentina
| | - Pilar Peral García
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, 60 y 118 S/N, 1900 La Plata, Argentina
| | - Guillermo Giovambattista
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, 60 y 118 S/N, 1900 La Plata, Argentina.
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11
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Xu X, Elkenani M, Tan X, Hain JK, Cui B, Schnelle M, Hasenfuss G, Toischer K, Mohamed BA. DNA Methylation Analysis Identifies Novel Epigenetic Loci in Dilated Murine Heart upon Exposure to Volume Overload. Int J Mol Sci 2023; 24:ijms24065885. [PMID: 36982963 PMCID: PMC10059258 DOI: 10.3390/ijms24065885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Left ventricular (LV) dilatation, a prominent risk factor for heart failure (HF), precedes functional deterioration and is used to stratify patients at risk for arrhythmias and cardiac mortality. Aberrant DNA methylation contributes to maladaptive cardiac remodeling and HF progression following pressure overload and ischemic cardiac insults. However, no study has examined cardiac DNA methylation upon exposure to volume overload (VO) despite being relatively common among HF patients. We carried out global methylome analysis of LV harvested at a decompensated HF stage following exposure to VO induced by aortocaval shunt. VO resulted in pathological cardiac remodeling, characterized by massive LV dilatation and contractile dysfunction at 16 weeks after shunt. Although methylated DNA was not markedly altered globally, 25 differentially methylated promoter regions (DMRs) were identified in shunt vs. sham hearts (20 hypermethylated and 5 hypomethylated regions). The validated hypermethylated loci in Junctophilin-2 (Jph2), Signal peptidase complex subunit 3 (Spcs3), Vesicle-associated membrane protein-associated protein B (Vapb), and Inositol polyphosphate multikinase (Ipmk) were associated with the respective downregulated expression and were consistently observed in dilated LV early after shunt at 1 week after shunt, before functional deterioration starts to manifest. These hypermethylated loci were also detected peripherally in the blood of the shunt mice. Altogether, we have identified conserved DMRs that could be novel epigenetic biomarkers in dilated LV upon VO exposure.
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Affiliation(s)
- Xingbo Xu
- Department of Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), 37075 Göttingen, Germany
| | - Manar Elkenani
- Department of Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), 37075 Göttingen, Germany
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Xiaoying Tan
- DZHK (German Centre for Cardiovascular Research), 37075 Göttingen, Germany
- Department of Nephrology and Rheumatology, University Medical Center of Göttingen, 37075 Göttingen, Germany
| | - Jara Katharina Hain
- Department of Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Baolong Cui
- Department of Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), 37075 Göttingen, Germany
| | - Moritz Schnelle
- DZHK (German Centre for Cardiovascular Research), 37075 Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Gerd Hasenfuss
- Department of Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), 37075 Göttingen, Germany
| | - Karl Toischer
- Department of Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), 37075 Göttingen, Germany
| | - Belal A Mohamed
- Department of Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), 37075 Göttingen, Germany
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12
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Bian R, Xu X, Li W. Uncovering the molecular mechanisms between heart failure and end-stage renal disease via a bioinformatics study. Front Genet 2023; 13:1037520. [PMID: 36704339 PMCID: PMC9871391 DOI: 10.3389/fgene.2022.1037520] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 12/20/2022] [Indexed: 01/12/2023] Open
Abstract
Background: Heart failure (HF) is not only a common complication in patients with end-stage renal disease (ESRD) but also a major cause of death. Although clinical studies have shown that there is a close relationship between them, the mechanism of its occurrence is unclear. The aim of this study is to explore the molecular mechanisms between HF and ESRD through comprehensive bioinformatics analysis, providing a new perspective on the crosstalk between these two diseases. Methods: The HF and ESRD datasets were downloaded from the Gene Expression Omnibus (GEO) database; we identified and analyzed common differentially expressed genes (DEGs). First, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set variation analyses (GSVA) were applied to explore the potential biological functions and construct protein-protein interaction (PPI) networks. Also, four algorithms, namely, random forest (RF), Boruta algorithm, logical regression of the selection operator (LASSO), and support vector machine-recursive feature elimination (SVM-RFE), were used to identify the candidate genes. Subsequently, the diagnostic efficacy of hub genes for HF and ESRD was evaluated using eXtreme Gradient Boosting (XGBoost) algorithm. CIBERSORT was used to analyze the infiltration of immune cells. Thereafter, we predicted target microRNAs (miRNAs) using databases (miRTarBase, TarBase, and ENOCRI), and transcription factors (TFs) were identified using the ChEA3 database. Cytoscape software was applied to construct mRNA-miRNA-TF regulatory networks. Finally, the Drug Signatures Database (DSigDB) was used to identify potential drug candidates. Results: A total of 68 common DEGs were identified. The enrichment analysis results suggest that immune response and inflammatory factors may be common features of the pathophysiology of HF and ESRD. A total of four hub genes (BCL6, CCL5, CNN1, and PCNT) were validated using RF, LASSO, Boruta, and SVM-RFE algorithms. Their AUC values were all greater than 0.8. Immune infiltration analysis showed that immune cells such as macrophages, neutrophils, and NK cells were altered in HF myocardial tissue, while neutrophils were significantly correlated with all four hub genes. Finally, 11 target miRNAs and 10 TFs were obtained, and miRNA-mRNA-TF regulatory network construction was performed. In addition, 10 gene-targeted drugs were discovered. Conclusion: Our study revealed important crosstalk between HF and ESRD. These common pathways and pivotal genes may provide new ideas for further clinical treatment and experimental studies.
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Joshua J, Caswell J, O’Sullivan ML, Wood G, Fonfara S. Feline myocardial transcriptome in health and in hypertrophic cardiomyopathy-A translational animal model for human disease. PLoS One 2023; 18:e0283244. [PMID: 36928240 PMCID: PMC10019628 DOI: 10.1371/journal.pone.0283244] [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: 12/05/2022] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is the most common heart disease in cats, characterized by primary left ventricular hypertrophy. Feline HCM closely resembles human HCM and is suggested as translational animal model for the human disease. A genetic cause is established in humans and suspected for cats, but little is known about the gene expression and pathways involved in the pathogenesis of HCM. To investigate the myocardial transcriptome changes in HCM, RNA sequencing was conducted on left ventricle (LV) and left atrium (LA) samples of healthy cats and cats with HCM (each n = 5; 20 samples). Ingenuity Pathway Analysis was used to determine functional pathways, regulators, and networks. Distinct gene expression profiles were identified in the LV and LA of the feline healthy and HCM myocardium. Analysis of differentially expressed mRNAs (>2 fold; FDR < 0.01) found chamber-specific (LV vs. LA) expression in both healthy and HCM groups, with higher transcriptional activity in the LA. Genes that contribute to the distinct structure and function of each chamber in health and HCM were identified in the regional comparison. The gene expression profiles of HCM compared to healthy hearts revealed disease related genes, including THBS4 and KLHL33 (LV), FAM177B and THRSP (LA), the latter 3 have not been reported for the myocardium so far, as the top differently expressed genes in the HCM heart. Differently expressed genes and functional pathways found in the HCM heart are associated with cardiac remodeling and fibrosis, inflammation, microvascular changes, calcium signaling and cardiac metabolism, with some regional differences. RhoGDI-RhoGTPase signaling, integrin and ILK signaling pathways, the LXR/RXR pathway in the LA, and the PPARα/RXRα, HIF1α and CXCR4 pathways in the LV might be of particular importance in the HCM disease process. This study identified region-specific myocardial gene transcription patterns as well as novel genes and pathways associated with HCM.
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Affiliation(s)
- Jessica Joshua
- University of Guelph, Ontario Veterinary College, Department of Pathobiology, Guelph, Ontario, Canada
- University of Guelph, Ontario Veterinary College, Department of Clinical Studies, Guelph, Ontario, Canada
| | - Jeff Caswell
- University of Guelph, Ontario Veterinary College, Department of Pathobiology, Guelph, Ontario, Canada
| | - M. Lynne O’Sullivan
- University of Prince Edward Island, Department of Companion Animals, Charlottetown, Prince Edward Island, Canada
| | - Geoffrey Wood
- University of Guelph, Ontario Veterinary College, Department of Pathobiology, Guelph, Ontario, Canada
| | - Sonja Fonfara
- University of Guelph, Ontario Veterinary College, Department of Clinical Studies, Guelph, Ontario, Canada
- * E-mail:
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14
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Boyang C, Yuexing L, Yiping Y, Haiyang Y, Xufei Z, Liancheng G, Yunzhi C. Construction and analysis of heart failure diagnosis model based on random forest and artificial neural network. Medicine (Baltimore) 2022; 101:e31097. [PMID: 36254001 PMCID: PMC9575800 DOI: 10.1097/md.0000000000031097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Heart failure is a global health problem and the number of sufferers is increasing as the population grows and ages. Existing diagnostic techniques for heart failure have various limitations in the clinical setting and there is a need to develop a new diagnostic model to complement the existing diagnostic methods. In recent years, with the development and improvement of gene sequencing technology, more genes associated with heart failure have been identified. We screened for differentially expressed genes in heart failure using available gene expression data from the Gene Expression Omnibus database and identified 6 important genes by a random forest classifier (ASPN, MXRA5, LUM, GLUL, CNN1, and SERPINA3). And we have successfully constructed a new heart failure diagnostic model using an artificial neural network and validated its diagnostic efficacy in a public dataset. We calculated heart failure-related differentially expressed genes and obtained 24 candidate genes by random forest classification, and selected the top 6 genes as important genes for subsequent analysis. The prediction weights of the genes of interest were determined by the neural network model and the model scores were evaluated in 2 independent sample datasets (GSE16499 and GSE57338 datasets). Since the weights of RNA-seq predictions for constructing neural network models were theoretically more suitable for disease classification of RNA-seq data, the GSE57338 dataset had the best performance in the validation results. The diagnostic model derived from our study can be of clinical value in determining the likelihood of HF occurring through cardiac biopsy. In the meantime, we need to further investigate the accuracy of the diagnostic model based on the results of our study.
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Affiliation(s)
- Chen Boyang
- School of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Li Yuexing
- School of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Yan Yiping
- School of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Yu Haiyang
- School of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Zhang Xufei
- School of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Guan Liancheng
- Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Chen Yunzhi
- School of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
- * Correspondence: Chen Yunzhi, School of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China (e-mail: )
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15
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Song Y, Jiang Y, Shi L, He C, Zhang W, Xu Z, Yang M, Xu Y. Comprehensive analysis of key m5C modification-related genes in type 2 diabetes. Front Genet 2022; 13:1015879. [PMID: 36276976 PMCID: PMC9582283 DOI: 10.3389/fgene.2022.1015879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Background: 5-methylcytosine (m5C) RNA methylation plays a significant role in several human diseases. However, the functional role of m5C in type 2 diabetes (T2D) remains unclear.Methods: The merged gene expression profiles from two Gene Expression Omnibus (GEO) datasets were used to identify m5C-related genes and T2D-related differentially expressed genes (DEGs). Least-absolute shrinkage and selection operator (LASSO) regression analysis was performed to identify optimal predictors of T2D. After LASSO regression, we constructed a diagnostic model and validated its accuracy. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted to confirm the biological functions of DEGs. Gene Set Enrichment Analysis (GSEA) was used to determine the functional enrichment of molecular subtypes. Weighted gene co-expression network analysis (WGCNA) was used to select the module that correlated with the most pyroptosis-related genes. Protein-protein interaction (PPI) network was established using the STRING database, and hub genes were identified using Cytoscape software. The competitive endogenous RNA (ceRNA) interaction network of the hub genes was obtained. The CIBERSORT algorithm was applied to analyze the interactions between hub gene expression and immune infiltration.Results: m5C-related genes were significantly differentially expressed in T2D and correlated with most T2D-related DEGs. LASSO regression showed that ZBTB4 could be a predictive gene for T2D. GO, KEGG, and GSEA indicated that the enriched modules and pathways were closely related to metabolism-related biological processes and cell death. The top five genes were identified as hub genes in the PPI network. In addition, a ceRNA interaction network of hub genes was obtained. Moreover, the expression levels of the hub genes were significantly correlated with the abundance of various immune cells.Conclusion: Our findings may provide insights into the molecular mechanisms underlying T2D based on its pathophysiology and suggest potential biomarkers and therapeutic targets for T2D.
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Affiliation(s)
- Yaxian Song
- Department of Endocrinology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yan Jiang
- Department of Endocrinology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Li Shi
- Department of Endocrinology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chen He
- Department of Geriatric Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Wenhua Zhang
- Department of Endocrinology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Zhao Xu
- Department of Endocrinology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Mengshi Yang
- Department of Endocrinology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yushan Xu
- Department of Endocrinology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
- *Correspondence: Yushan Xu,
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16
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Spurrell CH, Barozzi I, Kosicki M, Mannion BJ, Blow MJ, Fukuda-Yuzawa Y, Slaven N, Afzal SY, Akiyama JA, Afzal V, Tran S, Plajzer-Frick I, Novak CS, Kato M, Lee EA, Garvin TH, Pham QT, Kronshage AN, Lisgo S, Bristow J, Cappola TP, Morley MP, Margulies KB, Pennacchio LA, Dickel DE, Visel A. Genome-wide fetalization of enhancer architecture in heart disease. Cell Rep 2022; 40:111400. [PMID: 36130500 PMCID: PMC9534044 DOI: 10.1016/j.celrep.2022.111400] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/10/2022] [Accepted: 09/01/2022] [Indexed: 11/22/2022] Open
Abstract
Heart disease is associated with re-expression of key transcription factors normally active only during prenatal development of the heart. However, the impact of this reactivation on the regulatory landscape in heart disease is unclear. Here, we use RNA-seq and ChIP-seq targeting a histone modification associated with active transcriptional enhancers to generate genome-wide enhancer maps from left ventricle tissue from up to 26 healthy controls, 18 individuals with idiopathic dilated cardiomyopathy (DCM), and five fetal hearts. Healthy individuals have a highly reproducible epigenomic landscape, consisting of more than 33,000 predicted heart enhancers. In contrast, we observe reproducible disease-associated changes in activity at 6,850 predicted heart enhancers. Combined analysis of adult and fetal samples reveals that the heart disease epigenome and transcriptome both acquire fetal-like characteristics, with 3,400 individual enhancers sharing fetal regulatory properties. We also provide a comprehensive data resource (http://heart.lbl.gov) for the mechanistic exploration of DCM etiology.
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Affiliation(s)
- Cailyn H Spurrell
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Iros Barozzi
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michael Kosicki
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Brandon J Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Matthew J Blow
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Yoko Fukuda-Yuzawa
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Neil Slaven
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sarah Y Afzal
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jennifer A Akiyama
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Veena Afzal
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stella Tran
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Catherine S Novak
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Momoe Kato
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Elizabeth A Lee
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tyler H Garvin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Quan T Pham
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anne N Kronshage
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Steven Lisgo
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - James Bristow
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Thomas P Cappola
- Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Michael P Morley
- Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Kenneth B Margulies
- Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; Comparative Biochemistry Program, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, Merced, CA 95343, USA.
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17
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Abraham S, Lindo C, Peoples J, Cox A, Lytle E, Nguyen V, Mehta M, Alvarez JD, Yooseph S, Pacher P, Ebert SN. Maternal binge alcohol consumption leads to distinctive acute perturbations in embryonic cardiac gene expression profiles. Alcohol Clin Exp Res 2022; 46:1433-1448. [PMID: 35692084 DOI: 10.1111/acer.14880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 05/09/2022] [Accepted: 06/01/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND Excessive alcohol consumption during pregnancy is associated with high risk of congenital heart defects, but it is unclear how alcohol specifically affects heart development during the acute aftermath of a maternal binge drinking episode. We hypothesize that administration of a single maternal binge dose of alcohol to pregnant mice at embryonic day 9.5 (E9.5) causes perturbations in the expression patterns of specific genes in the developing heart in the acute period (1-3 days) following the binge episode. To test this hypothesis and identify strong candidate ethanol-sensitive target genes of interest, we adapted a mouse binge alcohol model that is associated with a high incidence of congenital heart defects as described below. METHODS/RESULTS Pregnant mice were administered a single dose of alcohol (2.5 g/kg in saline) or control (saline alone) via oral gavage. To evaluate the impact of maternal binge alcohol on cardiac gene expression profiles, we isolated embryonic hearts from both groups (n = 5/group) at 24, 48, and 72 h post-gavage for transcriptomic analyses. RNA was extracted and evaluated using quantitative RNA-sequencing (RNA-Seq) methods. To identify a cohort of binge-altered cardiac genes, we set the threshold for change at >2.0-fold difference with adjusted p < 0.05 versus control. RNA-Seq analysis of cardiac gene expression revealed that of the 17 genes that were altered within the first 48 h post-binge, with the largest category consisting of transcription factors (Alx1, Alx4, HoxB7, HoxD8, and Runx2), followed by signaling molecules (Adamts18, Dkk2, Rtl1, and Wnt7a). Furthermore, multiple comparative and pathway analyses suggested that several of the candidate genes identified through differential RNA-Seq analysis may interact through certain common pathways. To investigate this further, we performed gene-specific qPCR analyses for three representative candidate targets: Runx2, Wnt7a, and Mlxipl. Notably, only Wnt7a showed significantly (p < 0.05) decreased expression in response to maternal binge alcohol in the qPCR assays. CONCLUSIONS These findings identify Wnt7a and a short list of potential other candidate genes and pathways for further study, which could provide mechanistic insights into how maternal binge alcohol consumption produces congenital cardiac malformations.
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Affiliation(s)
- Shani Abraham
- Division of Metabolic and Cardiovascular Science, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Chad Lindo
- Division of Metabolic and Cardiovascular Science, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Jessica Peoples
- Division of Metabolic and Cardiovascular Science, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Amanda Cox
- Division of Metabolic and Cardiovascular Science, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Erika Lytle
- Division of Metabolic and Cardiovascular Science, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Vu Nguyen
- Division of Metabolic and Cardiovascular Science, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Meeti Mehta
- Division of Metabolic and Cardiovascular Science, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Jose D Alvarez
- Division of Metabolic and Cardiovascular Science, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Shibu Yooseph
- Department of Computer Science, Genomics and Bioinformatics Cluster, College of Engineering and Computer Science, University of Central Florida, Orlando, Florida, USA
| | - Pal Pacher
- Laboratory of Cardiovascular Physiology and Tissue Injury, National Institute of Alcohol and Alcohol Abuse (NIAAA), The National Institutes of Health (NIH), Rockville, Maryland, USA
| | - Steven N Ebert
- Division of Metabolic and Cardiovascular Science, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
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18
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Froese N, Cordero J, Abouissa A, Trogisch FA, Grein S, Szaroszyk M, Wang Y, Gigina A, Korf-Klingebiel M, Bosnjak B, Davenport CF, Wiehlmann L, Geffers R, Riechert E, Jürgensen L, Boileau E, Lin Y, Dieterich C, Förster R, Bauersachs J, Ola R, Dobreva G, Völkers M, Heineke J. Analysis of myocardial cellular gene expression during pressure overload reveals matrix based functional intercellular communication. iScience 2022; 25:103965. [PMID: 35281736 PMCID: PMC8908217 DOI: 10.1016/j.isci.2022.103965] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/22/2021] [Accepted: 02/18/2022] [Indexed: 11/16/2022] Open
Abstract
To identify cellular mechanisms responsible for pressure overload triggered heart failure, we isolated cardiomyocytes, endothelial cells, and fibroblasts as most abundant cell types from mouse hearts in the subacute and chronic stages after transverse aortic constriction (TAC) and performed RNA-sequencing. We detected highly cell-type specific transcriptional responses with characteristic time courses and active intercellular communication. Cardiomyocytes after TAC exerted an early and sustained upregulation of inflammatory and matrix genes and a concomitant suppression of metabolic and ion channel genes. Fibroblasts, in contrast, showed transient early upregulation of inflammatory and matrix genes and downregulation of angiogenesis genes, but sustained induction of cell cycle and ion channel genes during TAC. Endothelial cells transiently induced cell cycle and extracellular matrix genes early after TAC, but exerted a long-lasting upregulation of inflammatory genes. As we found that matrix production by multiple cell types triggers pathological cellular responses, it might serve as a future therapeutic target. TAC induces matrix and growth, but reduces contraction genes in cardiomyocytes TAC induces genes related to matrix, inflammation, and cell cycle in endothelial cells TAC induces matrix and inflammation, but reduces angiogenesis genes in fibroblasts Matrix proteins trigger growth, proliferation, and migration in cardiac cells
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Affiliation(s)
- Natali Froese
- Department of Cardiology and Angiology, Hannover Medical School, 30625 Hannover, Germany
| | - Julio Cordero
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, 68167 Mannheim, Germany
| | - Aya Abouissa
- Department of Cardiovascular Physiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Ludolf-Krehl-Str. 7-11, 68167 Mannheim, Germany
| | - Felix A Trogisch
- Department of Cardiovascular Physiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Ludolf-Krehl-Str. 7-11, 68167 Mannheim, Germany
| | - Steve Grein
- Department of Cardiovascular Physiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Ludolf-Krehl-Str. 7-11, 68167 Mannheim, Germany
| | - Malgorzata Szaroszyk
- Department of Cardiology and Angiology, Hannover Medical School, 30625 Hannover, Germany
| | - Yong Wang
- Department of Cardiology and Angiology, Hannover Medical School, 30625 Hannover, Germany
| | - Anna Gigina
- Department of Cardiology and Angiology, Hannover Medical School, 30625 Hannover, Germany
| | | | | | - Colin F Davenport
- Research Core Unit Genomics, Hannover Medical School, 30625 Hannover, Germany
| | - Lutz Wiehlmann
- Research Core Unit Genomics, Hannover Medical School, 30625 Hannover, Germany
| | - Robert Geffers
- Genome Analytics, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
| | - Eva Riechert
- Department of Internal Medicine III, Medical Faculty of Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany
| | - Lonny Jürgensen
- Department of Internal Medicine III, Medical Faculty of Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany
| | - Etienne Boileau
- Department of Internal Medicine III, Medical Faculty of Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany.,Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, 69120 Heidelberg, Germany
| | - Yanzhu Lin
- Department of Experimental Pharmacology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, 68167 Mannheim, Germany
| | - Christoph Dieterich
- Department of Internal Medicine III, Medical Faculty of Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany.,Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, 69120 Heidelberg, Germany
| | | | - Johann Bauersachs
- Department of Cardiology and Angiology, Hannover Medical School, 30625 Hannover, Germany
| | - Roxana Ola
- Department of Experimental Pharmacology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, 68167 Mannheim, Germany
| | - Gergana Dobreva
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, 68167 Mannheim, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Mirko Völkers
- Department of Internal Medicine III, Medical Faculty of Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Joerg Heineke
- Department of Cardiovascular Physiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Ludolf-Krehl-Str. 7-11, 68167 Mannheim, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
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19
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Chen J, Liu HF, Qiao LB, Wang FB, Wang L, Lin Y, Liu J. Global RNA editing identification and characterization during human pluripotent-to-cardiomyocyte differentiation. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 26:879-891. [PMID: 34760335 PMCID: PMC8551472 DOI: 10.1016/j.omtn.2021.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/05/2021] [Accepted: 10/01/2021] [Indexed: 01/19/2023]
Abstract
RNA editing is widely involved in stem cell differentiation and development; however, RNA editing events during human cardiomyocyte differentiation have not yet been characterized and elucidated. Here, we identified genome-wide RNA editing sites and systemically characterized their genomic distribution during four stages of human cardiomyocyte differentiation. It was found that the expression level of ADAR1 affected the global number of adenosine to inosine (A-to-I) editing sites but not the editing degree. Next, we identified 43, 163, 544, and 141 RNA editing sites that contribute to changes in amino acid sequences, variation in alternative splicing, alterations in miRNA-target binding, and changes in gene expression, respectively. Generally, RNA editing showed a stage-specific pattern with 211 stage-shared editing sites. Interestingly, cardiac muscle contraction and heart-disease-related pathways were enriched by cardio-specific editing genes, emphasizing the connection between cardiomyocyte differentiation and heart diseases from the perspective of RNA editing. Finally, it was found that these RNA editing sites are also related to several congenital and noncongenital heart diseases. Together, our study provides a new perspective on cardiomyocyte differentiation and offers more opportunities to understand the mechanisms underlying cell fate determination, which can promote the development of cardiac regenerative medicine and therapies for human heart diseases.
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Affiliation(s)
- Juan Chen
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Hui-Fang Liu
- Department of Endocrinology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430014, China
| | - Li-Bo Qiao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Fang-Bin Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Lu Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Yan Lin
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Jian Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China.,Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, Anhui 230009, China
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20
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Chunhacha P, Pinkaew D, Sinthujaroen P, Bowles DE, Fujise K. Fortilin inhibits p53, halts cardiomyocyte apoptosis, and protects the heart against heart failure. Cell Death Discov 2021; 7:310. [PMID: 34689154 PMCID: PMC8542040 DOI: 10.1038/s41420-021-00692-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 01/01/2023] Open
Abstract
Heart failure (HF) has reached epidemic proportions in developed countries, affecting over 20 million people worldwide. Despite modern medical and device therapies, 60–70% of HF patients still die within 5 years of diagnosis as it relentlessly progresses through pervasive apoptotic loss of cardiomyocytes. Although fortilin, a 172-amino-acid anti-p53 molecule, is one of the most expressed proteins in the heart, its precise role there has remained unknown. Also unclear is how cardiomyocytes are protected against apoptosis. Here, we report that failing human hearts express less fortilin than do non-failing hearts. We also found that mice lacking fortilin in the heart (fortilinKO-heart) die by 9 weeks of age due to extensive cardiomyocyte apoptosis and severe HF, which suggests that fortilin sustains cardiomyocyte viability. The lack of fortilin is also associated with drastic upregulation of p53 target genes in the hearts. The heart-specific deletion of p53 in fortilinKO-heart mice extends their life spans from 9 to 18 weeks by mitigating cardiomyocyte apoptosis. Our data suggest that fortilin is a novel cardiac p53 inhibitor and that its inadequate expression in failing hearts and subsequent overactivation of the p53 apoptosis pathway in cardiomyocytes exacerbates HF.
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Affiliation(s)
- Preedakorn Chunhacha
- Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA, 98109, USA.,Department of Biochemistry and Microbiology, and Cell-based Drug and Health Product Development Research Unit (CDD), Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Decha Pinkaew
- Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Patuma Sinthujaroen
- Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA, 98109, USA.,Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, 90110, Thailand
| | - Dawn E Bowles
- Division of Surgical Sciences, Department of Surgery, Duke University, Durham, NC, 27710, USA
| | - Ken Fujise
- Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA, 98109, USA.
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21
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Klaas M, Mäemets-Allas K, Heinmäe E, Lagus H, Cárdenas-León CG, Arak T, Eller M, Kingo K, Kankuri E, Jaks V. Thrombospondin-4 Is a Soluble Dermal Inflammatory Signal That Selectively Promotes Fibroblast Migration and Keratinocyte Proliferation for Skin Regeneration and Wound Healing. Front Cell Dev Biol 2021; 9:745637. [PMID: 34631719 PMCID: PMC8495264 DOI: 10.3389/fcell.2021.745637] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/06/2021] [Indexed: 01/05/2023] Open
Abstract
Thrombospondin-4 (THBS4) is a non-structural extracellular matrix molecule associated with tissue regeneration and a variety of pathological processes characterized by increased cell proliferation and migration. However, the mechanisms of how THBS4 regulates cell behavior as well as the pathways contributing to its effects have remained largely unexplored. In the present study we investigated the role of THBS4 in skin regeneration both in vitro and in vivo. We found that THBS4 expression was upregulated in the dermal compartment of healing skin wounds in humans as well as in mice. Application of recombinant THBS4 protein promoted cutaneous wound healing in mice and selectively stimulated migration of primary fibroblasts as well as proliferation of keratinocytes in vitro. By using a combined proteotranscriptomic pathway analysis approach we discovered that β-catenin acted as a hub for THBS4-dependent cell signaling and likely plays a key role in promoting its downstream effects. Our results suggest that THBS4 is an important contributor to wound healing and its incorporation into novel wound healing therapies may be a promising strategy for treatment of cutaneous wounds.
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Affiliation(s)
- Mariliis Klaas
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | | | - Elizabeth Heinmäe
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Heli Lagus
- Department of Plastic Surgery and Wound Healing Centre, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | | | - Terje Arak
- Surgery Clinic, Tartu University Hospital, Tartu, Estonia
| | - Mart Eller
- Surgery Clinic, Tartu University Hospital, Tartu, Estonia
| | - Külli Kingo
- Dermatology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Esko Kankuri
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Viljar Jaks
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.,Dermatology Clinic, Tartu University Hospital, Tartu, Estonia
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22
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Zhao K, Yang CX, Li P, Sun W, Kong XQ. Epigenetic role of N6-methyladenosine (m6A) RNA methylation in the cardiovascular system. J Zhejiang Univ Sci B 2021; 21:509-523. [PMID: 32633106 DOI: 10.1631/jzus.b1900680] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
As the most prevalent and abundant transcriptional modification in the eukaryotic genome, the continuous and dynamic regulation of N6-methyladenosine (m6A) has been shown to play a vital role in physiological and pathological processes of cardiovascular diseases (CVDs), such as ischemic heart failure (HF), myocardial hypertrophy, myocardial infarction (MI), and cardiomyogenesis. Regulation is achieved by modulating the expression of m6A enzymes and their downstream cardiac genes. In addition, this process has a major impact on different aspects of internal biological metabolism and several other external environmental effects associated with the development of CVDs. However, the exact molecular mechanism of m6A epigenetic regulation has not been fully elucidated. In this review, we outline recent advances and discuss potential therapeutic strategies for managing m6A in relation to several common CVD-related metabolic disorders and external environmental factors. Note that an appropriate understanding of the biological function of m6A in the cardiovascular system will pave the way towards exploring the mechanisms responsible for the development of other CVDs and their associated symptoms. Finally, it can provide new insights for the development of novel therapeutic agents for use in clinical practice.
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Affiliation(s)
- Kun Zhao
- Department of Cardiology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Chuan-Xi Yang
- Department of Cardiology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Peng Li
- Department of Cardiology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Wei Sun
- Department of Cardiology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Xiang-Qing Kong
- Department of Cardiology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
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23
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Luo X, Yin J, Dwyer D, Yamawaki T, Zhou H, Ge H, Han CY, Shkumatov A, Snyder K, Ason B, Li CM, Homann O, Stolina M. Chamber-enriched gene expression profiles in failing human hearts with reduced ejection fraction. Sci Rep 2021; 11:11839. [PMID: 34088950 PMCID: PMC8178406 DOI: 10.1038/s41598-021-91214-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 05/17/2021] [Indexed: 02/07/2023] Open
Abstract
Heart failure with reduced ejection fraction (HFrEF) constitutes 50% of HF hospitalizations and is characterized by high rates of mortality. To explore the underlying mechanisms of HFrEF etiology and progression, we studied the molecular and cellular differences in four chambers of non-failing (NF, n = 10) and HFrEF (n = 12) human hearts. We identified 333 genes enriched within NF heart subregions and often associated with cardiovascular disease GWAS variants. Expression analysis of HFrEF tissues revealed extensive disease-associated transcriptional and signaling alterations in left atrium (LA) and left ventricle (LV). Common left heart HFrEF pathologies included mitochondrial dysfunction, cardiac hypertrophy and fibrosis. Oxidative stress and cardiac necrosis pathways were prominent within LV, whereas TGF-beta signaling was evident within LA. Cell type composition was estimated by deconvolution and revealed that HFrEF samples had smaller percentage of cardiomyocytes within the left heart, higher representation of fibroblasts within LA and perivascular cells within the left heart relative to NF samples. We identified essential modules associated with HFrEF pathology and linked transcriptome discoveries with human genetics findings. This study contributes to a growing body of knowledge describing chamber-specific transcriptomics and revealed genes and pathways that are associated with heart failure pathophysiology, which may aid in therapeutic target discovery.
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Affiliation(s)
- Xin Luo
- Genome Analysis Unit, Amgen Research, 1120 Veterans BLVD, South San Francisco, CA, 94010, USA
| | - Jun Yin
- Genome Analysis Unit, Amgen Research, 1120 Veterans BLVD, South San Francisco, CA, 94010, USA
| | - Denise Dwyer
- Department of Cardiometabolic Disorders, Amgen Research, One Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - Tracy Yamawaki
- Genome Analysis Unit, Amgen Research, 1120 Veterans BLVD, South San Francisco, CA, 94010, USA
| | - Hong Zhou
- Genome Analysis Unit, Amgen Research, 1120 Veterans BLVD, South San Francisco, CA, 94010, USA
| | - Hongfei Ge
- Department of Cardiometabolic Disorders, Amgen Research, 1120 Veterans BLVD, South San Francisco, CA, 94010, USA
| | - Chun-Ya Han
- Department of Cardiometabolic Disorders, Amgen Research, One Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - Artem Shkumatov
- TS&BA Pathology, Amgen Research, 1120 Veterans BLVD, South San Francisco, CA, 94010, USA
| | - Karen Snyder
- Clinical Biomarkers, Amgen Research, 1120 Veterans BLVD, South San Francisco, CA, 94010, USA
| | - Brandon Ason
- Department of Cardiometabolic Disorders, Amgen Research, 1120 Veterans BLVD, South San Francisco, CA, 94010, USA
| | - Chi-Ming Li
- Genome Analysis Unit, Amgen Research, 1120 Veterans BLVD, South San Francisco, CA, 94010, USA
| | - Oliver Homann
- Genome Analysis Unit, Amgen Research, 1120 Veterans BLVD, South San Francisco, CA, 94010, USA
| | - Marina Stolina
- Department of Cardiometabolic Disorders, Amgen Research, One Amgen Center Drive, Thousand Oaks, CA, 91320, USA.
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24
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Martens MD, Fernando AS, Gordon JW. A new trick for an old dog? Myocardial-specific roles for prostaglandins as mediators of ischemic injury and repair. Am J Physiol Heart Circ Physiol 2021; 320:H2169-H2184. [PMID: 33861147 DOI: 10.1152/ajpheart.00872.2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The small lipid-derived paracrine signaling molecules known as prostaglandins have been recognized for their ability to modulate many facets of cardiovascular physiology since their initial discovery more than 85 years ago. Although the role of prostaglandins in the vasculature has gained significant attention across time, a handful of historical studies have also directly implicated the cardiomyocyte in both prostaglandin synthesis and release. Recently, our understanding of how prostaglandin receptor modulation impacts and contributes to myocardial structure and function has gained attention while leaving most other components of myocardial prostaglandin metabolism and signaling unexplored. This mini-review highlights both the key historical studies that underpin modern prostaglandin research in the heart, while concurrently presenting the latest findings related to how prostaglandin metabolism and signaling impact myocardial injury and repair.
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Affiliation(s)
- Matthew D Martens
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Science, University of Manitoba, Winnipeg, Manitoba, Canada.,The Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Amy S Fernando
- The Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Joseph W Gordon
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Science, University of Manitoba, Winnipeg, Manitoba, Canada.,College of Nursing, Rady Faculty of Health Science, University of Manitoba, Winnipeg, Manitoba, Canada.,The Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
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25
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Okabe M, Yamamoto K, Miyazaki Y, Motojima M, Ohtsuka M, Pastan I, Yokoo T, Matsusaka T. Indirect podocyte injury manifested in a partial podocytectomy mouse model. Am J Physiol Renal Physiol 2021; 320:F922-F933. [PMID: 33719575 DOI: 10.1152/ajprenal.00602.2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In progressive glomerular diseases, segmental podocyte injury often expands, leading to global glomerulosclerosis by unclear mechanisms. To study the expansion of podocyte injury, we established a new mosaic mouse model in which a fraction of podocytes express human (h)CD25 and can be injured by the immunotoxin LMB2. hCD25+ and hCD25- podocytes were designed to express tdTomato and enhanced green fluorescent protein (EGFP), respectively, which enabled cell sorting analysis of podocytes. After the injection of LMB2, mosaic mice developed proteinuria and glomerulosclerosis. Not only tdTomato+ podocytes but also EGFP+ podocytes were decreased in number and showed damage, as evidenced by a decrease in nephrin and an increase in desmin at both protein and RNA levels. Transcriptomics analysis found a decrease in the glucocorticoid-induced transcript 1 gene and an increase in the thrombospondin 4, heparin-binding EGF-like growth factor, and transforming growth factor-β genes in EGFP+ podocytes; these genes may be candidate mediators of secondary podocyte damage. Pathway analysis suggested that focal adhesion, integrin-mediated cell adhesion, and focal adhesion-phosphatidylinositol 3-kinase-Akt-mammalian target of rapamycin signaling are involved in secondary podocyte injury. Finally, treatment of mosaic mice with angiotensin II receptor blocker markedly ameliorated secondary podocyte injury. This mosaic podocyte injury model has distinctly demonstrated that damaged podocytes cause secondary podocyte damage, which may be a promising therapeutic target in progressive kidney diseases.NEW & NOTEWORTHY This novel mosaic model has demonstrated that when a fraction of podocytes is injured, other podocytes are subjected to secondary injury. This spreading of injury may occur ubiquitously irrespective of the primary cause of podocyte injury, leading to end-stage renal failure. Understanding the molecular mechanism of secondary podocyte injury and its prevention is important for the treatment of progressive kidney diseases. This model will be a powerful tool for studying the indirect podocyte injury.
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Affiliation(s)
- Masahiro Okabe
- Division of Nephrology and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan.,Department of Basic Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Kazuyoshi Yamamoto
- Division of Nephrology and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan.,Department of Basic Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Yoichi Miyazaki
- Division of Nephrology and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan
| | - Masaru Motojima
- Department of Clinical Pharmacology, Tokai University School of Medicine, Isehara, Japan
| | - Masato Ohtsuka
- Department of Basic Medicine, Tokai University School of Medicine, Isehara, Japan.,Institute of Medical Science, Tokai University School of Medicine, Isehara, Japan
| | - Ira Pastan
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Takashi Yokoo
- Division of Nephrology and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan
| | - Taiji Matsusaka
- Department of Basic Medicine, Tokai University School of Medicine, Isehara, Japan.,Institute of Medical Science, Tokai University School of Medicine, Isehara, Japan
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Ma Q, Ma H, Xu F, Wang X, Sun W. Microfluidics in cardiovascular disease research: state of the art and future outlook. MICROSYSTEMS & NANOENGINEERING 2021; 7:19. [PMID: 34567733 PMCID: PMC8433381 DOI: 10.1038/s41378-021-00245-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/08/2021] [Accepted: 01/16/2021] [Indexed: 05/21/2023]
Abstract
Due to extremely severe morbidity and mortality worldwide, it is worth achieving a more in-depth and comprehensive understanding of cardiovascular diseases. Tremendous effort has been made to replicate the cardiovascular system and investigate the pathogenesis, diagnosis and treatment of cardiovascular diseases. Microfluidics can be used as a versatile primary strategy to achieve a holistic picture of cardiovascular disease. Here, a brief review of the application of microfluidics in comprehensive cardiovascular disease research is presented, with specific discussions of the characteristics of microfluidics for investigating cardiovascular diseases integrally, including the study of pathogenetic mechanisms, the development of accurate diagnostic methods and the establishment of therapeutic treatments. Investigations of critical pathogenetic mechanisms for typical cardiovascular diseases by microfluidic-based organ-on-a-chip are categorized and reviewed, followed by a detailed summary of microfluidic-based accurate diagnostic methods. Microfluidic-assisted cardiovascular drug evaluation and screening as well as the fabrication of novel delivery vehicles are also reviewed. Finally, the challenges with and outlook on further advancing the use of microfluidics technology in cardiovascular disease research are highlighted and discussed.
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Affiliation(s)
- Qingming Ma
- School of Pharmacy, Qingdao University, Qingdao, 266071 China
| | - Haixia Ma
- Center for Prenatal Diagnosis, Zibo Maternal and Child Health Care Hospital, Zibo, 255000 China
| | - Fenglan Xu
- Department of Clinical Pharmacy, The Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, 212001 China
| | - Xinyu Wang
- Institute of Thermal Science and Technology, Shandong University, Jinan, 250061 China
| | - Wentao Sun
- Center for Basic Medical Research, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences & School of Medicine, Nankai University, Tianjin, 300457 China
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Li D, Lin H, Li L. Multiple Feature Selection Strategies Identified Novel Cardiac Gene Expression Signature for Heart Failure. Front Physiol 2020; 11:604241. [PMID: 33304275 PMCID: PMC7693561 DOI: 10.3389/fphys.2020.604241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/15/2020] [Indexed: 02/02/2023] Open
Abstract
Heart failure (HF) is a serious condition in which the support of blood pumped by the heart is insufficient to meet the demands of body at a normal cardiac filling pressure. Approximately 26 million patients worldwide are suffering from heart failure and about 17–45% of patients with heart failure die within 1-year, and the majority die within 5-years admitted to a hospital. The molecular mechanisms underlying the progression of heart failure have been poorly studied. We compared the gene expression profiles between patients with heart failure (n = 177) and without heart failure (n = 136) using multiple feature selection strategies and identified 38 HF signature genes. The support vector machine (SVM) classifier based on these 38 genes evaluated with leave-one-out cross validation (LOOCV) achieved great performance with sensitivity of 0.983 and specificity of 0.963. The network analysis suggested that the hub gene SMOC2 may play important roles in HF. Other genes, such as FCN3, HMGN2, and SERPINA3, also showed great promises. Our results can facilitate the early detection of heart failure and can reveal its molecular mechanisms.
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Affiliation(s)
- Dan Li
- Department of Cardiovascular Medicine, First Hospital Affiliated to Harbin Medical University, Harbin, China
| | - Hong Lin
- Internal Medicine-Cardiovascular Department, Harbin Chest Hospital, Harbin, China
| | - Luyifei Li
- Department of Cardiovascular Medicine, First Hospital Affiliated to Harbin Medical University, Harbin, China
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Russell-Hallinan A, Neary R, Watson CJ, Baugh JA. Repurposing From Oncology to Cardiology: Low-Dose 5-Azacytidine Attenuates Pathological Cardiac Remodeling in Response to Pressure Overload Injury. J Cardiovasc Pharmacol Ther 2020; 26:375-385. [PMID: 33264040 DOI: 10.1177/1074248420979235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Recent evidence suggests that transcriptional reprogramming is involved in the pathogenesis of cardiac remodeling (cardiomyocyte hypertrophy and fibrosis) and the development of heart failure. 5-Azacytidine (5aza), an inhibitor of DNA methylation approved for hematological malignancies, has previously demonstrated beneficial effects on cardiac remodeling in hypertension. The aim of our work was to investigate whether pressure overload is associated with alterations in DNA methylation and if intervention with low-dose 5aza can attenuate the associated pathological changes. METHODS AND RESULTS C57Bl6/J mice underwent surgical constriction of the aortic arch for 8 weeks. Mice began treatment 4 weeks post-surgery with either vehicle or 5aza (5 mg/kg). Cardiac structure and function was examined in vivo using echocardiography followed by post mortem histological assessment of hypertrophy and fibrosis. Global DNA methylation was examined by immunostaining for 5-methylcytosine (5MeC) and assessment of DNA methyltransferase expression. The results highlighted that pressure overload-induced pathological cardiac remodeling is associated with increased DNA methylation (elevated cardiac 5MeC positivity and Dnmt1 expression). Administration of 5aza attenuated pathological remodeling and diastolic dysfunction. These beneficial changes were mirrored by a treatment-related reduction in global 5MeC levels and expression of Dnmt1 and Dnmt3B in the heart. CONCLUSION DNA methylation plays an important role in the pathogenesis of pressure overload-induced cardiac remodeling. Therapeutic intervention with 5aza, at a dose 5 times lower than clinically given for oncology treatment, attenuated myocardial hypertrophy and fibrosis. Our work supports the rationale for its potential use in cardiac pathologies associated with aberrant cardiac wound healing.
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Affiliation(s)
- Adam Russell-Hallinan
- Wellcome-Wolfson Institute for Experimental Medicine, 1596Queen's University Belfast, Northern Ireland, United Kingdom.,UCD School of Medicine, Conway Institute, 231327University College Dublin, Belfield, Dublin, Ireland
| | - Roisin Neary
- UCD School of Medicine, Conway Institute, 231327University College Dublin, Belfield, Dublin, Ireland
| | - Chris J Watson
- Wellcome-Wolfson Institute for Experimental Medicine, 1596Queen's University Belfast, Northern Ireland, United Kingdom
| | - John A Baugh
- UCD School of Medicine, Conway Institute, 231327University College Dublin, Belfield, Dublin, Ireland
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Peng Z, Sun H, Bunpetch V, Koh Y, Wen Y, Wu D, Ouyang H. The regulation of cartilage extracellular matrix homeostasis in joint cartilage degeneration and regeneration. Biomaterials 2020; 268:120555. [PMID: 33285440 DOI: 10.1016/j.biomaterials.2020.120555] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 11/05/2020] [Accepted: 11/18/2020] [Indexed: 12/31/2022]
Abstract
Osteoarthritis (OA) is a major cause of disability and socioeconomic loss worldwide. However, the current pharmacological approaches used to treat OA are largely palliative. Being the hallmark of OA, the cartilage extracellular matrix (ECM) destruction and abnormal homeostasis is gaining more attention as a therapeutic target in cartilage regeneration. Moreover, during the progression of OA, the cartilage ECM shows significant pathological alternations, which can be promising biomarkers in identifying the pathological stages of OA. In this review, we summarize the role of abnormal ECM homeostasis in the joint cartilage during OA. Furthermore, we provide an update on the cartilage ECM derived biomarkers and regenerative medicine therapies targeting cartilage ECM which includes preclinical animal models study and clinical trials.
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Affiliation(s)
- Zhi Peng
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, And Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, And Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Heng Sun
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, And Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, And Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Varitsara Bunpetch
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, And Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, And Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Yiwen Koh
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, And Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Ya Wen
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, And Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, And Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Dongmei Wu
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, And Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, And Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Hongwei Ouyang
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, And Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, And Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China; Department of Sports Medicine, Zhejiang University School of Medicine, Hangzhou, China; China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, China.
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Schmidt M, Hopp L, Arakelyan A, Kirsten H, Engel C, Wirkner K, Krohn K, Burkhardt R, Thiery J, Loeffler M, Loeffler-Wirth H, Binder H. The Human Blood Transcriptome in a Large Population Cohort and Its Relation to Aging and Health. Front Big Data 2020; 3:548873. [PMID: 33693414 PMCID: PMC7931910 DOI: 10.3389/fdata.2020.548873] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023] Open
Abstract
Background: The blood transcriptome is expected to provide a detailed picture of an organism's physiological state with potential outcomes for applications in medical diagnostics and molecular and epidemiological research. We here present the analysis of blood specimens of 3,388 adult individuals, together with phenotype characteristics such as disease history, medication status, lifestyle factors, and body mass index (BMI). The size and heterogeneity of this data challenges analytics in terms of dimension reduction, knowledge mining, feature extraction, and data integration. Methods: Self-organizing maps (SOM)-machine learning was applied to study transcriptional states on a population-wide scale. This method permits a detailed description and visualization of the molecular heterogeneity of transcriptomes and of their association with different phenotypic features. Results: The diversity of transcriptomes is described by personalized SOM-portraits, which specify the samples in terms of modules of co-expressed genes of different functional context. We identified two major blood transcriptome types where type 1 was found more in men, the elderly, and overweight people and it upregulated genes associated with inflammation and increased heme metabolism, while type 2 was predominantly found in women, younger, and normal weight participants and it was associated with activated immune responses, transcriptional, ribosomal, mitochondrial, and telomere-maintenance cell-functions. We find a striking overlap of signatures shared by multiple diseases, aging, and obesity driven by an underlying common pattern, which was associated with the immune response and the increase of inflammatory processes. Conclusions: Machine learning applications for large and heterogeneous omics data provide a holistic view on the diversity of the human blood transcriptome. It provides a tool for comparative analyses of transcriptional signatures and of associated phenotypes in population studies and medical applications.
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Affiliation(s)
- Maria Schmidt
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Leipzig, Germany
| | - Lydia Hopp
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Leipzig, Germany
| | - Arsen Arakelyan
- BIG, Group of Bioinformatics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | - Holger Kirsten
- IMISE, Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.,Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Christoph Engel
- IMISE, Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.,Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Kerstin Wirkner
- IMISE, Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.,Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Knut Krohn
- Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany.,Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University of Leipzig, Leipzig, Germany
| | - Ralph Burkhardt
- Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany.,Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University of Leipzig, Leipzig, Germany
| | - Joachim Thiery
- Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany.,Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University of Leipzig, Leipzig, Germany
| | - Markus Loeffler
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Leipzig, Germany.,IMISE, Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.,Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Henry Loeffler-Wirth
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Leipzig, Germany
| | - Hans Binder
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Leipzig, Germany.,Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
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Mollanoori H, Rahmati Y, Hassani B, Esmaeili S, Amini K, Teimourian S. Screening the underlying molecular mechanisms involved in the development of heart failure. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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McLellan MA, Skelly DA, Dona MSI, Squiers GT, Farrugia GE, Gaynor TL, Cohen CD, Pandey R, Diep H, Vinh A, Rosenthal NA, Pinto AR. High-Resolution Transcriptomic Profiling of the Heart During Chronic Stress Reveals Cellular Drivers of Cardiac Fibrosis and Hypertrophy. Circulation 2020; 142:1448-1463. [PMID: 32795101 PMCID: PMC7547893 DOI: 10.1161/circulationaha.119.045115] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Supplemental Digital Content is available in the text. Background: Cardiac fibrosis is a key antecedent to many types of cardiac dysfunction including heart failure. Physiological factors leading to cardiac fibrosis have been recognized for decades. However, the specific cellular and molecular mediators that drive cardiac fibrosis, and the relative effect of disparate cell populations on cardiac fibrosis, remain unclear. Methods: We developed a novel cardiac single-cell transcriptomic strategy to characterize the cardiac cellulome, the network of cells that forms the heart. This method was used to profile the cardiac cellular ecosystem in response to 2 weeks of continuous administration of angiotensin II, a profibrotic stimulus that drives pathological cardiac remodeling. Results: Our analysis provides a comprehensive map of the cardiac cellular landscape uncovering multiple cell populations that contribute to pathological remodeling of the extracellular matrix of the heart. Two phenotypically distinct fibroblast populations, Fibroblast-Cilp and Fibroblast-Thbs4, emerged after induction of tissue stress to promote fibrosis in the absence of smooth muscle actin–expressing myofibroblasts, a key profibrotic cell population. After angiotensin II treatment, Fibroblast-Cilp develops as the most abundant fibroblast subpopulation and the predominant fibrogenic cell type. Mapping intercellular communication networks within the heart, we identified key intercellular trophic relationships and shifts in cellular communication after angiotensin II treatment that promote the development of a profibrotic cellular microenvironment. Furthermore, the cellular responses to angiotensin II and the relative abundance of fibrogenic cells were sexually dimorphic. Conclusions: These results offer a valuable resource for exploring the cardiac cellular landscape in health and after chronic cardiovascular stress. These data provide insights into the cellular and molecular mechanisms that promote pathological remodeling of the mammalian heart, highlighting early transcriptional changes that precede chronic cardiac fibrosis.
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Affiliation(s)
- Micheal A McLellan
- The Jackson Laboratory, Bar Harbor, ME (M.A.M., D.A.S., G.T.S., R.P., N.A.R.).,Graduate School of Biomedical Sciences, Tufts University, Boston, MA (M.A.M.)
| | - Daniel A Skelly
- The Jackson Laboratory, Bar Harbor, ME (M.A.M., D.A.S., G.T.S., R.P., N.A.R.)
| | - Malathi S I Dona
- Baker Heart and Diabetes Research Institute, Melbourne, Victoria, Australia (M.S.I.D., G.E.F., T.L.G., C.D.C., A.R.P.)
| | - Galen T Squiers
- The Jackson Laboratory, Bar Harbor, ME (M.A.M., D.A.S., G.T.S., R.P., N.A.R.)
| | - Gabriella E Farrugia
- Baker Heart and Diabetes Research Institute, Melbourne, Victoria, Australia (M.S.I.D., G.E.F., T.L.G., C.D.C., A.R.P.)
| | - Taylah L Gaynor
- Baker Heart and Diabetes Research Institute, Melbourne, Victoria, Australia (M.S.I.D., G.E.F., T.L.G., C.D.C., A.R.P.)
| | - Charles D Cohen
- Baker Heart and Diabetes Research Institute, Melbourne, Victoria, Australia (M.S.I.D., G.E.F., T.L.G., C.D.C., A.R.P.)
| | - Raghav Pandey
- The Jackson Laboratory, Bar Harbor, ME (M.A.M., D.A.S., G.T.S., R.P., N.A.R.)
| | - Henry Diep
- Centre for Cardiovascular Biology and Disease Research, La Trobe University, Melbourne, Victoria, Australia (T.L.G, C.D.C., H.D., A.V., A.R.P.)
| | - Antony Vinh
- Centre for Cardiovascular Biology and Disease Research, La Trobe University, Melbourne, Victoria, Australia (T.L.G, C.D.C., H.D., A.V., A.R.P.)
| | - Nadia A Rosenthal
- The Jackson Laboratory, Bar Harbor, ME (M.A.M., D.A.S., G.T.S., R.P., N.A.R.)
| | - Alexander R Pinto
- Baker Heart and Diabetes Research Institute, Melbourne, Victoria, Australia (M.S.I.D., G.E.F., T.L.G., C.D.C., A.R.P.).,Centre for Cardiovascular Biology and Disease Research, La Trobe University, Melbourne, Victoria, Australia (T.L.G, C.D.C., H.D., A.V., A.R.P.)
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Muppala S, Rahman MT, Krukovets I, Verbovetskiy D, Pluskota E, Fleischman A, Vince DG, Plow EF, Stenina-Adognravi O. The P387 thrombospondin-4 variant promotes accumulation of macrophages in atherosclerotic lesions. FASEB J 2020; 34:11529-11545. [PMID: 32686880 DOI: 10.1096/fj.201901434rrrr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 05/12/2020] [Accepted: 05/29/2020] [Indexed: 11/11/2022]
Abstract
Thrombospondin-4 (TSP4) is a pro-angiogenic protein that has been implicated in tissue remodeling and local vascular inflammation. TSP4 and, in particular, its SNP variant, P387 TSP4, have been associated with cardiovascular disease. Macrophages are central to initiation and resolution of inflammation and development of atherosclerotic lesions, but the effects of the P387 TSP4 on macrophages remain essentially unknown. We examined the effects of the P387 TSP4 variant on macrophages in cell culture and in vivo in a murine model of atherosclerosis. Furthermore, the levels and distributions of the two TSP4 variants were assessed in human atherosclerotic arteries. In ApoE- /- /P387-TSP4 knock-in mice, lesions size measured by Oil Red O did not change, but the lesions accumulated more macrophages than lesions bearing A387 TSP4. The levels of inflammatory markers were increased in lesions of ApoE- / - /P387-TSP4 knock-in mice compared to ApoE- / - mice. Lesions in human arteries from individuals carrying the P387 variant had higher levels of TSP4 and higher macrophage accumulation. P387 TSP4 was more active in supporting adhesion of cultured human and mouse macrophages in experiments using recombinant TSP4 variants and in cells derived from P387-TSP4 knock-in mice. TSP4 supports the adhesion of macrophages and their accumulation in atherosclerotic lesions without changing the size of lesions. P387 TSP4 is more active in supporting these pro-inflammatory events in the vascular wall, which may contribute to the increased association of P387 TSP4 with cardiovascular disease.
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Affiliation(s)
- Santoshi Muppala
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, USA
| | | | - Irene Krukovets
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Dmitriy Verbovetskiy
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Elzbieta Pluskota
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Aaron Fleischman
- Department of Biomedical Engineering, Cleveland Clinic, Cleveland, OH, USA
| | - D Geoffrey Vince
- Department of Biomedical Engineering, Cleveland Clinic, Cleveland, OH, USA
| | - Edward F Plow
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Olga Stenina-Adognravi
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, USA
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Fajarda O, Duarte-Pereira S, Silva RM, Oliveira JL. Merging microarray studies to identify a common gene expression signature to several structural heart diseases. BioData Min 2020; 13:8. [PMID: 32670412 PMCID: PMC7346458 DOI: 10.1186/s13040-020-00217-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/05/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Heart disease is the leading cause of death worldwide. Knowing a gene expression signature in heart disease can lead to the development of more efficient diagnosis and treatments that may prevent premature deaths. A large amount of microarray data is available in public repositories and can be used to identify differentially expressed genes. However, most of the microarray datasets are composed of a reduced number of samples and to obtain more reliable results, several datasets have to be merged, which is a challenging task. The identification of differentially expressed genes is commonly done using statistical methods. Nonetheless, these methods are based on the definition of an arbitrary threshold to select the differentially expressed genes and there is no consensus on the values that should be used. RESULTS Nine publicly available microarray datasets from studies of different heart diseases were merged to form a dataset composed of 689 samples and 8354 features. Subsequently, the adjusted p-value and fold change were determined and by combining a set of adjusted p-values cutoffs with a list of different fold change thresholds, 12 sets of differentially expressed genes were obtained. To select the set of differentially expressed genes that has the best accuracy in classifying samples from patients with heart diseases and samples from patients with no heart condition, the random forest algorithm was used. A set of 62 differentially expressed genes having a classification accuracy of approximately 95% was identified. CONCLUSIONS We identified a gene expression signature common to different cardiac diseases and supported our findings by showing their involvement in the pathophysiology of the heart. The approach used in this study is suitable for the identification of gene expression signatures, and can be extended to different diseases.
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Affiliation(s)
- Olga Fajarda
- IEETA/DETI, University of Aveiro, Aveiro, 3810-193 Portugal
| | - Sara Duarte-Pereira
- IEETA/DETI, University of Aveiro, Aveiro, 3810-193 Portugal
- Department of Medical Sciences and iBiMED-Institute of Biomedicine, University of Aveiro, Aveiro, 3810-193 Portugal
| | - Raquel M. Silva
- IEETA/DETI, University of Aveiro, Aveiro, 3810-193 Portugal
- Department of Medical Sciences and iBiMED-Institute of Biomedicine, University of Aveiro, Aveiro, 3810-193 Portugal
- Current Address: Universidade Católica Portuguesa, Faculdade de Medicina Dentária, CIIS-Centro de Investigação Interdisciplinar em Saúde, Campus de Viseu, Viseu, 3504-505 Portugal
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Reese-Petersen AL, Olesen MS, Karsdal MA, Svendsen JH, Genovese F. Atrial fibrillation and cardiac fibrosis: A review on the potential of extracellular matrix proteins as biomarkers. Matrix Biol 2020; 91-92:188-203. [PMID: 32205152 DOI: 10.1016/j.matbio.2020.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 03/04/2020] [Accepted: 03/04/2020] [Indexed: 01/06/2023]
Abstract
The involvement of fibrosis as an underlying pathology in heart diseases is becoming increasingly clear. In recent years, fibrosis has been granted a causative role in heart diseases and is now emerging as a major contributor to Atrial Fibrillation (AF) pathogenesis. AF is the most common arrhythmia encountered in the clinic, but the substrate for AF is still being debated. Consensus in the field is a combination of cardiac tissue remodeling, inflammation and genetic predisposition. The extracellular matrix (ECM) is subject of growing investigation, since measuring circulatory biomarkers of ECM formation and degradation provides both diagnostic and prognostic information. However, fibrosis is not just fibrosis. Each specific collagen biomarker holds information on regulatory mechanisms, as well as information about which section of the ECM is being remodeled, providing a detailed description of cardiac tissue homeostasis. This review entails an overview of the implication of fibrosis in AF, the different collagens and their significance, and the potential of using biomarkers of ECM remodeling as tools for understanding AF pathogenesis and identifying patients at risk for further disease progression.
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Affiliation(s)
| | - Morten S Olesen
- Labratory of Molecular Cardiology, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | | | - Jesper H Svendsen
- Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
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Effects of thrombospondin-4 on pro-inflammatory phenotype differentiation and apoptosis in macrophages. Cell Death Dis 2020; 11:53. [PMID: 31974349 PMCID: PMC6978349 DOI: 10.1038/s41419-020-2237-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/25/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023]
Abstract
Thrombospondin-4 (TSP-4) attracted renewed attention recently as a result of assignment of new functions to this matricellular protein in cardiovascular, muscular, and nervous systems. We have previously reported that TSP-4 promotes local vascular inflammation in a mouse atherosclerosis model. A common variant of TSP-4, P387-TSP-4, was associated with increased cardiovascular disease risk in human population studies. In a mouse atherosclerosis model, TSP-4 had profound effect on accumulation of macrophages in lesions, which prompted us to examine its effects on macrophages in more detail. We examined the effects of A387-TSP-4 and P387-TSP-4 on mouse macrophages in cell culture and in vivo in the model of LPS-induced peritonitis. In tissues and in cell culture, TSP-4 expression was associated with inflammation: TSP-4 expression was upregulated in peritoneal tissues in LPS-induced peritonitis, and pro-inflammatory signals, INFγ, GM-CSF, and LPS, induced TSP-4 expression in macrophages in vivo and in cell culture. Deficiency in TSP-4 in macrophages from Thbs4−/− mice reduced the expression of pro-inflammatory macrophage markers, suggesting that TSP-4 facilitates macrophage differentiation into a pro-inflammatory phenotype. Expression of TSP-4, especially more active P387-TSP-4, was associated with higher cellular apoptosis. Cultured macrophages displayed increased adhesion to TSP-4 and reduced migration in presence of TSP-4, and these responses were further increased with P387 variant. We concluded that TSP-4 expression in macrophages increases their accumulation in tissues during the acute inflammatory process and supports macrophage differentiation into a pro-inflammatory phenotype. In a model of acute inflammation, TSP-4 supports pro-inflammatory macrophage apoptosis, a response that is closely related to their pro-inflammatory activity and release of pro-inflammatory signals. P387-TSP-4 was found to be the more active form of TSP-4 in all examined functions.
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Hua X, Wang YY, Jia P, Xiong Q, Hu Y, Chang Y, Lai S, Xu Y, Zhao Z, Song J. Multi-level transcriptome sequencing identifies COL1A1 as a candidate marker in human heart failure progression. BMC Med 2020; 18:2. [PMID: 31902369 PMCID: PMC6943904 DOI: 10.1186/s12916-019-1469-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 11/19/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Heart failure (HF) has been recognized as a global pandemic with a high rate of hospitalization, morbidity, and mortality. Although numerous advances have been made, its representative molecular signatures remain largely unknown, especially the role of genes in HF progression. The aim of the present prospective follow-up study was to reveal potential biomarkers associated with the progression of heart failure. METHODS We generated multi-level transcriptomic data from a cohort of left ventricular heart tissue collected from 21 HF patients and 9 healthy donors. By using Masson staining to calculate the fibrosis percentage for each sample, we applied lasso regression model to identify the genes associated with fibrosis as well as progression. The genes were further validated by immunohistochemistry (IHC) staining in the same cohort and qRT-PCR using another independent cohort (20 HF and 9 healthy donors). Enzyme-linked immunosorbent assay (ELISA) was used to measure the plasma level in a validation cohort (139 HF patients) for predicting HF progression. RESULTS Based on the multi-level transcriptomic data, we examined differentially expressed genes [mRNAs, microRNAs, and long non-coding RNAs (lncRNAs)] in the study cohort. The follow-up functional annotation and regulatory network analyses revealed their potential roles in regulating extracellular matrix. We further identified several genes that were associated with fibrosis. By using the survival time before transplantation, COL1A1 was identified as a potential biomarker for HF progression and its upregulation was confirmed by both IHC and qRT-PCR. Furthermore, COL1A1 content ≥ 256.5 ng/ml in plasma was found to be associated with poor survival within 1 year of heart transplantation from heart failure [hazard ratio (HR) 7.4, 95% confidence interval (CI) 3.5 to 15.8, Log-rank p value < 1.0 × 10- 4]. CONCLUSIONS Our results suggested that COL1A1 might be a plasma biomarker of HF and associated with HF progression, especially to predict the 1-year survival from HF onset to transplantation.
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Affiliation(s)
- Xiumeng Hua
- Department of Cardiac Surgery, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167A Beilishi Road, Xi Cheng District, Beijing, 10037, China
| | - Yin-Ying Wang
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St, Houston, TX, 77030, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St, Houston, TX, 77030, USA
| | - Qing Xiong
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St, Houston, TX, 77030, USA
| | - Yiqing Hu
- Department of Cardiac Surgery, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167A Beilishi Road, Xi Cheng District, Beijing, 10037, China
| | - Yuan Chang
- Department of Cardiac Surgery, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167A Beilishi Road, Xi Cheng District, Beijing, 10037, China
| | - Songqing Lai
- Department of Cardiac Surgery, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167A Beilishi Road, Xi Cheng District, Beijing, 10037, China
| | - Yong Xu
- Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St, Houston, TX, 77030, USA. .,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, 1200 Pressler St, Houston, TX, 77030, USA. .,Department of Biomedical Informatics, Vanderbilt University Medical Center, 2525 West End Avenue, Nashville, TN, 37203, USA.
| | - Jiangping Song
- Department of Cardiac Surgery, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167A Beilishi Road, Xi Cheng District, Beijing, 10037, China.
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Defining decreased protein succinylation of failing human cardiac myofibrils in ischemic cardiomyopathy. J Mol Cell Cardiol 2019; 138:304-317. [PMID: 31836543 DOI: 10.1016/j.yjmcc.2019.11.159] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/23/2019] [Accepted: 11/27/2019] [Indexed: 12/20/2022]
Abstract
Succinylation is a post-translational modification of protein lysine residues with succinyl groups derived from succinyl CoA. Succinylation is considered a significant post-translational modification with the potential to impact protein function which is highly conserved across numerous species. The role of succinylation in the heart, especially in heart failure and myofibril mechanics, remains largely unexplored. Mechanical parameters were measured in myofibrils isolated from failing hearts of ischemic cardiomyopathy patients and non-failing donor controls. We employed mass spectrometry to quantify differential protein expression in myofibrils from failing ischemic cardiomyopathy hearts compared to non-failing hearts. In addition, we combined peptide enrichment by immunoprecipitation with liquid chromatography tandem mass spectrometry to quantitatively analyze succinylated lysine residues in these myofibrils. Several key parameters of sarcomeric mechanical interactions were altered in myofibrils isolated from failing ischemic cardiomyopathy hearts, including lower resting tension and a faster rate of activation. Of the 100 differentially expressed proteins, 46 showed increased expression in ischemic heart failure, while 54 demonstrated decreased expression in ischemic heart failure. Our quantitative succinylome analysis identified a total of 572 unique succinylated lysine sites located on 181 proteins, with 307 significantly changed succinylation events. We found that 297 succinyl-Lys demonstrated decreased succinylation on 104 proteins, while 10 residues demonstrated increased succinylation on 4 proteins. Investigating succinyl CoA generation, enzyme activity assays demonstrated that α-ketoglutarate dehydrogenase and succinate dehydrogenase activities were significantly decreased in ischemic heart failure. An activity assay for succinyl CoA synthetase demonstrated a significant increase in ischemic heart failure. Taken together, our findings support the hypothesis that succinyl CoA production is decreased and succinyl CoA turnover is increased in ischemic heart failure, potentially resulting in an overall decrease in the mitochondrial succinyl CoA pool, which may contribute to decreased myofibril protein succinylation in heart failure.
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Ni L, Scott L, Campbell HM, Pan X, Alsina KM, Reynolds J, Philippen LE, Hulsurkar M, Lagor WR, Li N, Wehrens XHT. Atrial-Specific Gene Delivery Using an Adeno-Associated Viral Vector. Circ Res 2019; 124:256-262. [PMID: 30582449 DOI: 10.1161/circresaha.118.313811] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
RATIONALE Somatic overexpression in mice using an adeno-associated virus (AAV) as gene transfer vectors has become a valuable tool to analyze the roles of specific genes in cardiac diseases. The lack of atrial-specific AAV vector has been a major obstacle for studies into the pathogenesis of atrial diseases. Moreover, gene therapy studies for atrial fibrillation would benefit from atrial-specific vectors. Atrial natriuretic factor (ANF) promoter drives gene expression specifically in atrial cardiomyocytes. OBJECTIVE To establish the platform of atrial specific in vivo gene delivery by AAV-ANF. METHODS AND RESULTS We constructed AAV vectors based on serotype 9 (AAV9) that are driven by the atrial-specific ANF promoter. Hearts from mice injected with AAV9-ANF-GFP (green fluorescent protein) exhibited strong and atrial-specific GFP expression without notable GFP in ventricular tissue. In contrast, similar vectors containing a cardiac troponin T promoter (AAV9-TNT4-GFP) showed GFP expression in all 4 chambers of the heart, while AAV9 with an enhanced chicken β-actin promoter (AAV-enCB-GFP) caused ubiquitous GFP expression. Next, we used Rosa26mT/mG (membrane-targeted tandem dimer Tomato/membrane-targeted GFP), a double-fluorescent Cre reporter mouse that expresses membrane-targeted tandem dimer Tomato before Cre-mediated excision, and membrane-targeted GFP after excision. AAV9-ANF-Cre led to highly efficient LoxP recombination in membrane-targeted tandem dimer Tomato/membrane-targeted green fluorescent protein mice with high specificity for the atria. We measured the frequency of transduced cardiomyocytes in atria by detecting Cre-dependent GFP expression from the Rosa26mT/mG allele. AAV9 dose was positively correlated with the number of GFP-positive atrial cardiomyocytes. Finally, we assessed whether the AAV9-ANF-Cre vector could be used to induce atrial-specific gene knockdown in proof-of-principle experiments using conditional JPH2 (junctophilin-2) knockdown mice. Four weeks after AAV9-ANF-Cre injection, a strong reduction in atrial expression of JPH2 protein was observed. Furthermore, there was evidence for abnormal Ca2+ handling in atrial myocytes isolated from mice with atrial-restricted JPH2 deficiency. CONCLUSIONS AAV9-ANF vectors produce efficient, dose-dependent, and atrial-specific gene expression following a single-dose systemic delivery in mice. This vector is a novel reagent for both mechanistic and gene therapy studies on atrial diseases.
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Affiliation(s)
- Li Ni
- From the Cardiovascular Research Institute (L.N., L.S., H.M.C., X.P., K.M.A., J.R., L.E.P., M.H., W.R.L., N.L., X.H.T.W.), Baylor College of Medicine, Houston, TX
- Department of Molecular Physiology and Biophysics (L.N., L.S., H.M.C., X.P., K.M.A., J.R., L.E.P., M.H., W.R.L., N.L., X.H.T.W.), Baylor College of Medicine, Houston, TX
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (L.N.)
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (L.N.)
| | - Larry Scott
- From the Cardiovascular Research Institute (L.N., L.S., H.M.C., X.P., K.M.A., J.R., L.E.P., M.H., W.R.L., N.L., X.H.T.W.), Baylor College of Medicine, Houston, TX
- Department of Molecular Physiology and Biophysics (L.N., L.S., H.M.C., X.P., K.M.A., J.R., L.E.P., M.H., W.R.L., N.L., X.H.T.W.), Baylor College of Medicine, Houston, TX
| | - Hannah M Campbell
- From the Cardiovascular Research Institute (L.N., L.S., H.M.C., X.P., K.M.A., J.R., L.E.P., M.H., W.R.L., N.L., X.H.T.W.), Baylor College of Medicine, Houston, TX
- Department of Molecular Physiology and Biophysics (L.N., L.S., H.M.C., X.P., K.M.A., J.R., L.E.P., M.H., W.R.L., N.L., X.H.T.W.), Baylor College of Medicine, Houston, TX
| | - Xiaolu Pan
- From the Cardiovascular Research Institute (L.N., L.S., H.M.C., X.P., K.M.A., J.R., L.E.P., M.H., W.R.L., N.L., X.H.T.W.), Baylor College of Medicine, Houston, TX
- Department of Molecular Physiology and Biophysics (L.N., L.S., H.M.C., X.P., K.M.A., J.R., L.E.P., M.H., W.R.L., N.L., X.H.T.W.), Baylor College of Medicine, Houston, TX
| | - Katherina M Alsina
- From the Cardiovascular Research Institute (L.N., L.S., H.M.C., X.P., K.M.A., J.R., L.E.P., M.H., W.R.L., N.L., X.H.T.W.), Baylor College of Medicine, Houston, TX
- Department of Molecular Physiology and Biophysics (L.N., L.S., H.M.C., X.P., K.M.A., J.R., L.E.P., M.H., W.R.L., N.L., X.H.T.W.), Baylor College of Medicine, Houston, TX
| | - Julia Reynolds
- From the Cardiovascular Research Institute (L.N., L.S., H.M.C., X.P., K.M.A., J.R., L.E.P., M.H., W.R.L., N.L., X.H.T.W.), Baylor College of Medicine, Houston, TX
- Department of Molecular Physiology and Biophysics (L.N., L.S., H.M.C., X.P., K.M.A., J.R., L.E.P., M.H., W.R.L., N.L., X.H.T.W.), Baylor College of Medicine, Houston, TX
| | - Leonne E Philippen
- From the Cardiovascular Research Institute (L.N., L.S., H.M.C., X.P., K.M.A., J.R., L.E.P., M.H., W.R.L., N.L., X.H.T.W.), Baylor College of Medicine, Houston, TX
- Department of Molecular Physiology and Biophysics (L.N., L.S., H.M.C., X.P., K.M.A., J.R., L.E.P., M.H., W.R.L., N.L., X.H.T.W.), Baylor College of Medicine, Houston, TX
| | - Mohit Hulsurkar
- From the Cardiovascular Research Institute (L.N., L.S., H.M.C., X.P., K.M.A., J.R., L.E.P., M.H., W.R.L., N.L., X.H.T.W.), Baylor College of Medicine, Houston, TX
- Department of Molecular Physiology and Biophysics (L.N., L.S., H.M.C., X.P., K.M.A., J.R., L.E.P., M.H., W.R.L., N.L., X.H.T.W.), Baylor College of Medicine, Houston, TX
| | - William R Lagor
- From the Cardiovascular Research Institute (L.N., L.S., H.M.C., X.P., K.M.A., J.R., L.E.P., M.H., W.R.L., N.L., X.H.T.W.), Baylor College of Medicine, Houston, TX
- Department of Molecular Physiology and Biophysics (L.N., L.S., H.M.C., X.P., K.M.A., J.R., L.E.P., M.H., W.R.L., N.L., X.H.T.W.), Baylor College of Medicine, Houston, TX
| | - Na Li
- From the Cardiovascular Research Institute (L.N., L.S., H.M.C., X.P., K.M.A., J.R., L.E.P., M.H., W.R.L., N.L., X.H.T.W.), Baylor College of Medicine, Houston, TX
- Department of Molecular Physiology and Biophysics (L.N., L.S., H.M.C., X.P., K.M.A., J.R., L.E.P., M.H., W.R.L., N.L., X.H.T.W.), Baylor College of Medicine, Houston, TX
- Department of Medicine (Section of Cardiovascular Research) (N.L.), Baylor College of Medicine, Houston, TX
| | - Xander H T Wehrens
- From the Cardiovascular Research Institute (L.N., L.S., H.M.C., X.P., K.M.A., J.R., L.E.P., M.H., W.R.L., N.L., X.H.T.W.), Baylor College of Medicine, Houston, TX
- Department of Molecular Physiology and Biophysics (L.N., L.S., H.M.C., X.P., K.M.A., J.R., L.E.P., M.H., W.R.L., N.L., X.H.T.W.), Baylor College of Medicine, Houston, TX
- Department of Medicine (Cardiology) (X.H.T.W.), Baylor College of Medicine, Houston, TX
- Department of Pediatrics (X.H.T.W.), Baylor College of Medicine, Houston, TX
- Department of Neuroscience (X.H.T.W.), Baylor College of Medicine, Houston, TX
- Center for Space Medicine (X.H.T.W.), Baylor College of Medicine, Houston, TX
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Luzum JA, Ting C, Peterson EL, Gui H, Shugg T, Williams LK, Li L, Sadee W, Wang D, Lanfear DE. Association of Regulatory Genetic Variants for Protein Kinase Cα with Mortality and Drug Efficacy in Patients with Heart Failure. Cardiovasc Drugs Ther 2019; 33:693-700. [PMID: 31728800 DOI: 10.1007/s10557-019-06909-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
PURPOSE Protein kinase C alpha (gene: PRKCA) is a key regulator of cardiac contractility. Two genetic variants have recently been discovered to regulate PRKCA expression in failing human heart tissue (rs9909004 [T → C] and rs9303504 [C → G]). The association of those variants with clinical outcomes in patients with heart failure (HF), and their interaction with HF drug efficacy, is unknown. METHODS Patients with HF in a prospective registry starting in 2007 were genotyped by whole genome array (n = 951). The primary outcome was all-cause mortality. Cox proportional hazards models adjusted for established clinical risk factors and genomic ancestry tested the independent association of rs9909004 or rs9303504 and the variant interactions with cornerstone HF pharmacotherapies (beta-blockers or angiotensin-converting enzyme inhibitors/angiotensin receptor blockers) in additive genetic models. RESULTS The minor allele of rs9909004, but not of rs9303504, was independently associated with a decreased risk for all-cause mortality: adjusted HR = 0.81 (95% CI = 0.67-0.98), p = 0.032. The variants did not significantly interact with mortality benefit associated with cornerstone HF pharmacotherapies (p > 0.1 for all). CONCLUSIONS A recently discovered cardiac-specific regulatory variant for PRKCA (rs9909004) was independently associated with a decreased risk for all-cause mortality in patients with HF. The variant did not interact with mortality benefit associated with cornerstone HF pharmacotherapies.
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Affiliation(s)
- Jasmine A Luzum
- Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA. .,Center for Individualized and Genomic Medicine Research (CIGMA), Henry Ford Health System, Detroit, MI, USA.
| | - Christopher Ting
- Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Edward L Peterson
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
| | - Hongsheng Gui
- Center for Individualized and Genomic Medicine Research (CIGMA), Henry Ford Health System, Detroit, MI, USA
| | - Tyler Shugg
- Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - L Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Henry Ford Health System, Detroit, MI, USA
| | - Liang Li
- Department of Medical Genetics, Southern Medical University, Guangzhou, China
| | - Wolfgang Sadee
- Center for Pharmacogenomics and Department of Cancer Biology and Genetics, College of Medicine, Ohio State University, Columbus, OH, USA
| | - Danxin Wang
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - David E Lanfear
- Center for Individualized and Genomic Medicine Research (CIGMA), Henry Ford Health System, Detroit, MI, USA.,Heart and Vascular Institute, Henry Ford Health System, Detroit, MI, USA
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Li Y, Meng Q, Yang M, Liu D, Hou X, Tang L, Wang X, Lyu Y, Chen X, Liu K, Yu AM, Zuo Z, Bi H. Current trends in drug metabolism and pharmacokinetics. Acta Pharm Sin B 2019; 9:1113-1144. [PMID: 31867160 PMCID: PMC6900561 DOI: 10.1016/j.apsb.2019.10.001] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 08/23/2019] [Accepted: 09/09/2019] [Indexed: 12/15/2022] Open
Abstract
Pharmacokinetics (PK) is the study of the absorption, distribution, metabolism, and excretion (ADME) processes of a drug. Understanding PK properties is essential for drug development and precision medication. In this review we provided an overview of recent research on PK with focus on the following aspects: (1) an update on drug-metabolizing enzymes and transporters in the determination of PK, as well as advances in xenobiotic receptors and noncoding RNAs (ncRNAs) in the modulation of PK, providing new understanding of the transcriptional and posttranscriptional regulatory mechanisms that result in inter-individual variations in pharmacotherapy; (2) current status and trends in assessing drug-drug interactions, especially interactions between drugs and herbs, between drugs and therapeutic biologics, and microbiota-mediated interactions; (3) advances in understanding the effects of diseases on PK, particularly changes in metabolizing enzymes and transporters with disease progression; (4) trends in mathematical modeling including physiologically-based PK modeling and novel animal models such as CRISPR/Cas9-based animal models for DMPK studies; (5) emerging non-classical xenobiotic metabolic pathways and the involvement of novel metabolic enzymes, especially non-P450s. Existing challenges and perspectives on future directions are discussed, and may stimulate the development of new research models, technologies, and strategies towards the development of better drugs and improved clinical practice.
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Affiliation(s)
- Yuhua Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510275, China
- The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Qiang Meng
- College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Mengbi Yang
- School of Pharmacy, the Chinese University of Hong Kong, Hong Kong, China
| | - Dongyang Liu
- Drug Clinical Trial Center, Peking University Third Hospital, Beijing 100191, China
| | - Xiangyu Hou
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lan Tang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xin Wang
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yuanfeng Lyu
- School of Pharmacy, the Chinese University of Hong Kong, Hong Kong, China
| | - Xiaoyan Chen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Kexin Liu
- College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Ai-Ming Yu
- UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Zhong Zuo
- School of Pharmacy, the Chinese University of Hong Kong, Hong Kong, China
| | - Huichang Bi
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510275, China
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Pepin ME, Drakos S, Ha CM, Tristani-Firouzi M, Selzman CH, Fang JC, Wende AR, Wever-Pinzon O. DNA methylation reprograms cardiac metabolic gene expression in end-stage human heart failure. Am J Physiol Heart Circ Physiol 2019; 317:H674-H684. [PMID: 31298559 PMCID: PMC6843013 DOI: 10.1152/ajpheart.00016.2019] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 05/15/2019] [Accepted: 06/13/2019] [Indexed: 12/24/2022]
Abstract
Heart failure (HF) is a leading cause of morbidity and mortality in the United States and worldwide. As a multifactorial syndrome with unpredictable clinical outcomes, identifying the common molecular underpinnings that drive HF pathogenesis remains a major focus of investigation. Disruption of cardiac gene expression has been shown to mediate a common final cascade of pathological hallmarks wherein the heart reactivates numerous developmental pathways. Although the central regulatory mechanisms that drive this cardiac transcriptional reprogramming remain unknown, epigenetic contributions are likely. In the current study, we examined whether the epigenome, specifically DNA methylation, is reprogrammed in HF to potentiate a pathological shift in cardiac gene expression. To accomplish this, we used paired-end whole genome bisulfite sequencing and next-generation RNA sequencing of left ventricle tissue obtained from seven patients with end-stage HF and three nonfailing donor hearts. We found that differential methylation was localized to promoter-associated cytosine-phosphate-guanine islands, which are established regulatory regions of downstream genes. Hypermethylated promoters were associated with genes involved in oxidative metabolism, whereas promoter hypomethylation enriched glycolytic pathways. Overexpression of plasmid-derived DNA methyltransferase 3A in vitro was sufficient to lower the expression of numerous oxidative metabolic genes in H9c2 rat cardiomyoblasts, further supporting the importance of epigenetic factors in the regulation of cardiac metabolism. Last, we identified binding-site competition via hypermethylation of the nuclear respiratory factor 1 (NRF1) motif, an established upstream regulator of mitochondrial biogenesis. These preliminary observations are the first to uncover an etiology-independent shift in cardiac DNA methylation that corresponds with altered metabolic gene expression in HF.NEW & NOTEWORTHY The failing heart undergoes profound metabolic changes because of alterations in cardiac gene expression, reactivating glycolytic genes and suppressing oxidative metabolic genes. In the current study, we discover that alterations to cardiac DNA methylation encode this fetal-like metabolic gene reprogramming. We also identify novel epigenetic interference of nuclear respiratory factor 1 via hypermethylation of its downstream promoter targets, further supporting a novel contribution of DNA methylation in the metabolic remodeling of heart failure.
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Affiliation(s)
- Mark E Pepin
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, Alabama
| | - Stavros Drakos
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - Chae-Myeong Ha
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Martin Tristani-Firouzi
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah
| | - Craig H Selzman
- Division of Cardiothoracic Surgery, Department of Surgery, University of Utah, Salt Lake City, Utah
| | - James C Fang
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - Adam R Wende
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, Alabama
| | - Omar Wever-Pinzon
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah, Salt Lake City, Utah
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43
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Curran J, Burkhoff D, Kloner RA. Beyond Reperfusion: Acute Ventricular Unloading and Cardioprotection During Myocardial Infarction. J Cardiovasc Transl Res 2019; 12:95-106. [PMID: 30671717 PMCID: PMC6497619 DOI: 10.1007/s12265-019-9863-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 01/02/2019] [Indexed: 12/21/2022]
Abstract
Heart failure is a major cause of morbidity and mortality around the world, and myocardial infarction is its leading cause. Myocardial infarction destroys viable myocardium, and this dead tissue is replaced by a non-contractile scar that results in impaired cardiac function and a significantly increased likelihood of the patient developing heart failure. Limiting infarct scar size has been the target of pre-clinical and clinical investigations for decades. However, beyond reperfusion, few therapies have translated into the clinic that limit its formation. New approaches are needed. This review will focus on new clinical and pre-clinical data demonstrating that acute ventricular unloading prior to reperfusion by means of percutaneous left ventricular support devices reduces ischemia-reperfusion injury and limits infarct scar size. Emphasis will be given to summarizing our current mechanistic understanding of this new therapeutic approach to treating myocardial infarction.
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Affiliation(s)
| | | | - Robert A Kloner
- Huntington Medical Research Institutes, Pasadena, CA, USA
- University of Southern California, Los Angeles, CA, USA
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44
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Kmietczyk V, Riechert E, Kalinski L, Boileau E, Malovrh E, Malone B, Gorska A, Hofmann C, Varma E, Jürgensen L, Kamuf-Schenk V, Altmüller J, Tappu R, Busch M, Most P, Katus HA, Dieterich C, Völkers M. m 6A-mRNA methylation regulates cardiac gene expression and cellular growth. Life Sci Alliance 2019; 2:e201800233. [PMID: 30967445 PMCID: PMC6458851 DOI: 10.26508/lsa.201800233] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 03/22/2019] [Accepted: 03/22/2019] [Indexed: 01/25/2023] Open
Abstract
Conceptually similar to modifications of DNA, mRNAs undergo chemical modifications, which can affect their activity, localization, and stability. The most prevalent internal modification in mRNA is the methylation of adenosine at the N6-position (m6A). This returns mRNA to a role as a central hub of information within the cell, serving as an information carrier, modifier, and attenuator for many biological processes. Still, the precise role of internal mRNA modifications such as m6A in human and murine-dilated cardiac tissue remains unknown. Transcriptome-wide mapping of m6A in mRNA allowed us to catalog m6A targets in human and murine hearts. Increased m6A methylation was found in human cardiomyopathy. Knockdown and overexpression of the m6A writer enzyme Mettl3 affected cell size and cellular remodeling both in vitro and in vivo. Our data suggest that mRNA methylation is highly dynamic in cardiomyocytes undergoing stress and that changes in the mRNA methylome regulate translational efficiency by affecting transcript stability. Once elucidated, manipulations of methylation of specific m6A sites could be a powerful approach to prevent worsening of cardiac function.
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Affiliation(s)
- Vivien Kmietczyk
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Eva Riechert
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Laura Kalinski
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Etienne Boileau
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
- Section of Bioinformatics and Systems Cardiology, Department of Cardiology, Angiology, and Pneumology and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Ellen Malovrh
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Brandon Malone
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
- Section of Bioinformatics and Systems Cardiology, Department of Cardiology, Angiology, and Pneumology and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Agnieszka Gorska
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Christoph Hofmann
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Eshita Varma
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Lonny Jürgensen
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Verena Kamuf-Schenk
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Rewati Tappu
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Martin Busch
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Patrick Most
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Hugo A Katus
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Christoph Dieterich
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
- Section of Bioinformatics and Systems Cardiology, Department of Cardiology, Angiology, and Pneumology and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Mirko Völkers
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
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45
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Maly K, Schaible I, Riegger J, Brenner RE, Meurer A, Zaucke F. The Expression of Thrombospondin-4 Correlates with Disease Severity in Osteoarthritic Knee Cartilage. Int J Mol Sci 2019; 20:ijms20020447. [PMID: 30669608 PMCID: PMC6359043 DOI: 10.3390/ijms20020447] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 01/11/2019] [Accepted: 01/17/2019] [Indexed: 12/13/2022] Open
Abstract
Osteoarthritis (OA) is a progressive joint disease characterized by a continuous degradation of the cartilage extracellular matrix (ECM). The expression of the extracellular glycoprotein thrombospondin-4 (TSP-4) is known to be increased in injured tissues and involved in matrix remodeling, but its role in articular cartilage and, in particular, in OA remains elusive. In the present study, we analyzed the expression and localization of TSP-4 in healthy and OA knee cartilage by reverse transcription polymerase chain reaction (RT-PCR), immunohistochemistry, and immunoblot. We found that TSP-4 protein expression is increased in OA and that expression levels correlate with OA severity. TSP-4 was not regulated at the transcriptional level but we detected changes in the anchorage of TSP-4 in the altered ECM using sequential protein extraction. We were also able to detect pentameric and fragmented TSP-4 in the serum of both healthy controls and OA patients. Here, the total protein amount was not significantly different but we identified specific degradation products that were more abundant in sera of OA patients. Future studies will reveal if these fragments have the potential to serve as OA-specific biomarkers.
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Affiliation(s)
- Kathrin Maly
- Dr. Rolf M. Schwiete Research Unit for Osteoarthritis, Orthopaedic University Hospital Friedrichsheim gGmbH, Marienburgstraße 2, 60528 Frankfurt/Main, Germany.
| | - Inna Schaible
- Dr. Rolf M. Schwiete Research Unit for Osteoarthritis, Orthopaedic University Hospital Friedrichsheim gGmbH, Marienburgstraße 2, 60528 Frankfurt/Main, Germany.
| | - Jana Riegger
- Division for Biochemistry of Joint and Connective Tissue Diseases, Department of Orthopaedics, University of Ulm, Oberer Eselsberg 45, 89081 Ulm, Germany.
| | - Rolf E Brenner
- Division for Biochemistry of Joint and Connective Tissue Diseases, Department of Orthopaedics, University of Ulm, Oberer Eselsberg 45, 89081 Ulm, Germany.
| | - Andrea Meurer
- Dr. Rolf M. Schwiete Research Unit for Osteoarthritis, Orthopaedic University Hospital Friedrichsheim gGmbH, Marienburgstraße 2, 60528 Frankfurt/Main, Germany.
| | - Frank Zaucke
- Dr. Rolf M. Schwiete Research Unit for Osteoarthritis, Orthopaedic University Hospital Friedrichsheim gGmbH, Marienburgstraße 2, 60528 Frankfurt/Main, Germany.
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46
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Sweet ME, Cocciolo A, Slavov D, Jones KL, Sweet JR, Graw SL, Reece TB, Ambardekar AV, Bristow MR, Mestroni L, Taylor MRG. Transcriptome analysis of human heart failure reveals dysregulated cell adhesion in dilated cardiomyopathy and activated immune pathways in ischemic heart failure. BMC Genomics 2018; 19:812. [PMID: 30419824 PMCID: PMC6233272 DOI: 10.1186/s12864-018-5213-9] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 10/31/2018] [Indexed: 01/17/2023] Open
Abstract
Background Current heart failure (HF) treatment is based on targeting symptoms and left ventricle dysfunction severity, relying on a common HF pathway paradigm to justify common treatments for HF patients. This common strategy may belie an incomplete understanding of heterogeneous underlying mechanisms and could be a barrier to more precise treatments. We hypothesized we could use RNA-sequencing (RNA-seq) in human heart tissue to delineate HF etiology-specific gene expression signatures. Results RNA-seq from 64 human left ventricular samples: 37 dilated (DCM), 13 ischemic (ICM), and 14 non-failing (NF). Using a multi-analytic approach including covariate adjustment for age and sex, differentially expressed genes (DEGs) were identified characterizing HF and disease-specific expression. Pathway analysis investigated enrichment for biologically relevant pathways and functions. DCM vs NF and ICM vs NF had shared HF-DEGs that were enriched for the fetal gene program and mitochondrial dysfunction. DCM-specific DEGs were enriched for cell-cell and cell-matrix adhesion pathways. ICM-specific DEGs were enriched for cytoskeletal and immune pathway activation. Using the ICM and DCM DEG signatures from our data we were able to correctly classify the phenotypes of 24/31 ICM and 32/36 DCM samples from publicly available replication datasets. Conclusions Our results demonstrate the commonality of mitochondrial dysfunction in end-stage HF but more importantly reveal key etiology-specific signatures. Dysfunctional cell-cell and cell-matrix adhesion signatures typified DCM whereas signals related to immune and fibrotic responses were seen in ICM. These findings suggest that transcriptome signatures may distinguish end-stage heart failure, shedding light on underlying biological differences between ICM and DCM. Electronic supplementary material The online version of this article (10.1186/s12864-018-5213-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mary E Sweet
- Human Medical Genetics and Genomics, University of Colorado, Aurora, CO, USA
| | - Andrea Cocciolo
- Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado, Aurora, CO, USA
| | - Dobromir Slavov
- Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado, Aurora, CO, USA
| | - Kenneth L Jones
- Department of Pediatrics, Section of Hematology, Oncology, and Bone Marrow Transplant, University of Colorado, Aurora, CO, USA
| | - Joseph R Sweet
- Department of Statistics, E. & J. Gallo, Modesto, CA, USA
| | - Sharon L Graw
- Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado, Aurora, CO, USA
| | - T Brett Reece
- Department of Cardiothoracic Surgery, University of Colorado Hospital, Aurora, CO, USA
| | - Amrut V Ambardekar
- Division of Cardiology, Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Michael R Bristow
- Division of Cardiology, Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Luisa Mestroni
- Human Medical Genetics and Genomics, University of Colorado, Aurora, CO, USA.,Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado, Aurora, CO, USA
| | - Matthew R G Taylor
- Human Medical Genetics and Genomics, University of Colorado, Aurora, CO, USA. .,Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado, Aurora, CO, USA.
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47
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Wang C, Yang H, Gao C. Potential biomarkers for heart failure. J Cell Physiol 2018; 234:9467-9474. [PMID: 30370655 DOI: 10.1002/jcp.27632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 09/27/2018] [Indexed: 12/13/2022]
Abstract
In this study, we identified candidate biomarkers for heart failure (HF). The gene expression profile GSE57338, containing 117 ischemic cardiomyopathic HF and 136 control samples, was downloaded and analyzed using various bioinformatics approaches. In total, 376 differentially expressed genes (DEGs) were identified, and four modules were explored in protein-protein interaction networks. DEGs (including ankyrin repeat and SOCS box-containing 14 [ASB14]) in the modules were mainly categorized by the function. Several relationships including interferon regulatory factor 1 (IRF1)-C-C motif chemokine ligand 5 (CCL5) were revealed in the transcription factor microRNA target gene regulatory network. Gene-drug analysis revealed 11 DEGs (such as the cluster of differentiation 163 [CD163]) for the target drugs. Data verification analysis identified 118 overlapping DEGs including ASB14, CD163, and CCL5. ASB14 may be involved in HF progression via protein ubiquitination and CCL5 may be involved in HF via the IRF1-CCL5 interaction. Genes including CD163 are potential biomarkers for HF.
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Affiliation(s)
- Che Wang
- Department of Cardiology, Henan Provincial People's Hospital, Fuwai Central China Cardiovascular Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Honghui Yang
- Department of Cardiology, Henan Provincial People's Hospital, Fuwai Central China Cardiovascular Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Chuanyu Gao
- Department of Cardiology, Henan Provincial People's Hospital, Fuwai Central China Cardiovascular Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
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48
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Andenæs K, Lunde IG, Mohammadzadeh N, Dahl CP, Aronsen JM, Strand ME, Palmero S, Sjaastad I, Christensen G, Engebretsen KVT, Tønnessen T. The extracellular matrix proteoglycan fibromodulin is upregulated in clinical and experimental heart failure and affects cardiac remodeling. PLoS One 2018; 13:e0201422. [PMID: 30052659 PMCID: PMC6063439 DOI: 10.1371/journal.pone.0201422] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/13/2018] [Indexed: 01/01/2023] Open
Abstract
Pressure overload of the heart leads to cardiac remodeling that may progress into heart failure, a common, morbid and mortal condition. Increased mechanistic insight into remodeling is instrumental for development of novel heart failure treatment. Cardiac remodeling comprises cardiomyocyte hypertrophic growth, extracellular matrix alterations including fibrosis, and inflammation. Fibromodulin is a small leucine-rich proteoglycan that regulates collagen fibrillogenesis. Fibromodulin is expressed in the cardiac extracellular matrix, however its role in the heart remains largely unknown. We investigated fibromodulin levels in myocardial biopsies from heart failure patients and mice, subjected fibromodulin knock-out (FMOD-KO) mice to pressure overload by aortic banding, and overexpressed fibromodulin in cultured cardiomyocytes and cardiac fibroblasts using adenovirus. Fibromodulin was 3-10-fold upregulated in hearts of heart failure patients and mice. Both cardiomyocytes and cardiac fibroblasts expressed fibromodulin, and its expression was increased by pro-inflammatory stimuli. Without stress, FMOD-KO mice showed no cardiac phenotype. Upon aortic banding, left ventricles of FMOD-KO mice developed mildly exacerbated hypertrophic remodeling compared to wild-type mice, with increased cardiomyocyte size and altered infiltration of leukocytes. There were no differences in mortality, left ventricle dilatation, dysfunction or expression of heart failure markers. Although collagen amount and cross-linking were comparable in FMOD-KO and wild-type, overexpression of fibromodulin in cardiac fibroblasts in vitro decreased their migratory capacity and expression of fibrosis-associated molecules, i.e. the collagen-cross linking enzyme lysyl oxidase, transglutaminase 2 and periostin. In conclusion, despite a robust fibromodulin upregulation in clinical and experimental heart failure, FMOD-KO mice showed a relatively mild hypertrophic phenotype. In cultured cardiac fibroblasts, fibromodulin has anti-fibrotic effects.
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Affiliation(s)
- Kine Andenæs
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway
- KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, Oslo, Norway
| | - Ida G. Lunde
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway
- KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, Oslo, Norway
- Centre for Molecular Medicine Norway, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Naiyereh Mohammadzadeh
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway
- KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, Oslo, Norway
| | - Christen P. Dahl
- KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, Oslo, Norway
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
- Department of Cardiology, Oslo University Hospital, Oslo, Norway
| | - Jan Magnus Aronsen
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway
- Bjørknes College, Oslo, Norway
| | - Mari E. Strand
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway
- KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, Oslo, Norway
| | - Sheryl Palmero
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway
- KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, Oslo, Norway
| | - Ivar Sjaastad
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway
- KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, Oslo, Norway
| | - Geir Christensen
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway
- KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, Oslo, Norway
| | - Kristin V. T. Engebretsen
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway
- KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, Oslo, Norway
- Department of Surgery, Vestre Viken Hospital, Drammen, Norway
| | - Theis Tønnessen
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway
- KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, Oslo, Norway
- Department of Cardiothoracic Surgery, Oslo University Hospital, Oslo, Norway
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49
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Nair NU, Das A, Amit U, Robinson W, Park SG, Basu M, Lugo A, Leor J, Ruppin E, Hannenhalli S. Putative functional genes in idiopathic dilated cardiomyopathy. Sci Rep 2018; 8:66. [PMID: 29311597 PMCID: PMC5758757 DOI: 10.1038/s41598-017-18524-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 12/12/2017] [Indexed: 12/16/2022] Open
Abstract
Idiopathic dilated cardiomyopathy (DCM) is a complex disorder with a genetic and an environmental component involving multiple genes, many of which are yet to be discovered. We integrate genetic, epigenetic, transcriptomic, phenotypic, and evolutionary features into a method - Hridaya, to infer putative functional genes underlying DCM in a genome-wide fashion, using 213 human heart genomes and transcriptomes. Many genes identified by Hridaya are experimentally shown to cause cardiac complications. We validate the top predicted genes, via five different genome-wide analyses: First, the predicted genes are associated with cardiovascular functions. Second, their knockdowns in mice induce cardiac abnormalities. Third, their inhibition by drugs cause cardiac side effects in human. Fourth, they tend to have differential exon usage between DCM and normal samples. Fifth, analyzing 213 individual genotypes, we show that regulatory polymorphisms of the predicted genes are associated with elevated risk of cardiomyopathy. The stratification of DCM patients based on cardiac expression of the functional genes reveals two subgroups differing in key cardiac phenotypes. Integrating predicted functional genes with cardiomyocyte drug treatment experiments reveals novel potential drug targets. We provide a list of investigational drugs that target the newly identified functional genes that may lead to cardiac side effects.
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Affiliation(s)
- Nishanth Ulhas Nair
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, 20742, USA.
| | - Avinash Das
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, 20742, USA
| | - Uri Amit
- The Neufeld Cardiac Research Institute, Tel Aviv University, Tel Aviv-Yafo, Israel
- Tamman Cardiovascular Research Institute, Sheba Medical Center, Ramat Gan, Israel
- The Dr. Pinchas Borenstein Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel
- Department of Radiation Oncology, Sheba Medical Center, Tel-Hashomer, Israel
| | - Welles Robinson
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, 20742, USA
| | - Seung Gu Park
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, 20742, USA
| | - Mahashweta Basu
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, 20742, USA
| | - Alex Lugo
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, 20742, USA
| | - Jonathan Leor
- The Neufeld Cardiac Research Institute, Tel Aviv University, Tel Aviv-Yafo, Israel
- Tamman Cardiovascular Research Institute, Sheba Medical Center, Ramat Gan, Israel
| | - Eytan Ruppin
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, 20742, USA
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Sridhar Hannenhalli
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, 20742, USA.
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50
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Kumari N, Gaur H, Bhargava A. Cardiac voltage gated calcium channels and their regulation by β-adrenergic signaling. Life Sci 2017; 194:139-149. [PMID: 29288765 DOI: 10.1016/j.lfs.2017.12.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/17/2017] [Accepted: 12/24/2017] [Indexed: 01/08/2023]
Abstract
Voltage-gated calcium channels (VGCCs) are the predominant source of calcium influx in the heart leading to calcium-induced calcium release and ultimately excitation-contraction coupling. In the heart, VGCCs are modulated by the β-adrenergic signaling. Signaling through β-adrenergic receptors (βARs) and modulation of VGCCs by β-adrenergic signaling in the heart are critical signaling and changes to these have been significantly implicated in heart failure. However, data related to calcium channel dysfunction in heart failure is divergent and contradictory ranging from reduced function to no change in the calcium current. Many recent studies have highlighted the importance of functional and spatial microdomains in the heart and that may be the key to answer several puzzling questions. In this review, we have briefly discussed the types of VGCCs found in heart tissues, their structure, and significance in the normal and pathological condition of the heart. More importantly, we have reviewed the modulation of VGCCs by βARs in normal and pathological conditions incorporating functional and structural aspects. There are different types of βARs, each having their own significance in the functioning of the heart. Finally, we emphasize the importance of location of proteins as it relates to their function and modulation by co-signaling molecules. Its implication on the studies of heart failure is speculated.
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Affiliation(s)
- Neema Kumari
- Ion Channel Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana 502285, India
| | - Himanshu Gaur
- Ion Channel Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana 502285, India
| | - Anamika Bhargava
- Ion Channel Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana 502285, India.
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