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Qiu Z, Cui J, Huang Q, Qi B, Xia Z. Roles of O-GlcNAcylation in Mitochondrial Homeostasis and Cardiovascular Diseases. Antioxidants (Basel) 2024; 13:571. [PMID: 38790676 PMCID: PMC11117601 DOI: 10.3390/antiox13050571] [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: 03/25/2024] [Revised: 04/28/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
Protein posttranslational modifications are important factors that mediate the fine regulation of signaling molecules. O-linked β-N-acetylglucosamine-modification (O-GlcNAcylation) is a monosaccharide modification on N-acetylglucosamine linked to the hydroxyl terminus of serine and threonine of proteins. O-GlcNAcylation is responsive to cellular stress as a reversible and posttranslational modification of nuclear, mitochondrial and cytoplasmic proteins. Mitochondrial proteins are the main targets of O-GlcNAcylation and O-GlcNAcylation is a key regulator of mitochondrial homeostasis by directly regulating the mitochondrial proteome or protein activity and function. Disruption of O-GlcNAcylation is closely related to mitochondrial dysfunction. More importantly, the O-GlcNAcylation of cardiac proteins has been proven to be protective or harmful to cardiac function. Mitochondrial homeostasis is crucial for cardiac contractile function and myocardial cell metabolism, and the imbalance of mitochondrial homeostasis plays a crucial role in the pathogenesis of cardiovascular diseases (CVDs). In this review, we will focus on the interactions between protein O-GlcNAcylation and mitochondrial homeostasis and provide insights on the role of mitochondrial protein O-GlcNAcylation in CVDs.
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Affiliation(s)
- Zhen Qiu
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan 430060, China; (Z.Q.); (J.C.); (Q.H.)
| | - Jiahui Cui
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan 430060, China; (Z.Q.); (J.C.); (Q.H.)
| | - Qin Huang
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan 430060, China; (Z.Q.); (J.C.); (Q.H.)
| | - Biao Qi
- Department of Anesthesiology, Hubei 672 Orthopaedics Hospital of Integrated Chinese and Western Medicine, Wuhan Orthopaedics Hospital of Intergrated Traditional Medicine Chinese and Western Medicine, The Affiliated Hospital of Wuhan Sports University, Wuhan 430070, China
| | - Zhongyuan Xia
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan 430060, China; (Z.Q.); (J.C.); (Q.H.)
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Pandey R, Roberts ML, Wang J, Pereckas M, Jensen D, Greene AS, Widlansky ME, Liang M. Proteomic Profiles of Human Arterioles Isolated From Fresh Adipose Tissue or Following Overnight Storage. J Transl Med 2024; 104:102036. [PMID: 38408704 PMCID: PMC11098693 DOI: 10.1016/j.labinv.2024.102036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 01/20/2024] [Accepted: 02/20/2024] [Indexed: 02/28/2024] Open
Abstract
Arterioles are key determinants of the total peripheral vascular resistance, which, in turn, is a key determinant of arterial blood pressure. However, the amount of protein available from one isolated human arteriole may be less than 5 μg, making proteomic analysis challenging. In addition, obtaining human arterioles requires manual dissection of unfrozen clinical specimens. This limits its feasibility, especially for powerful multicenter clinical studies in which clinical specimens need to be shipped overnight to a research laboratory for arteriole isolation. We performed a study to address low-input, test overnight tissue storage and develop a reference human arteriolar proteomic profile. In tandem mass tag proteomics, use of a booster channel consisting of human induced pluripotent stem cell-derived endothelial and vascular smooth muscle cells (1:5 ratio) increased the number of proteins detected in a human arteriole segment with a false discovery rate of <0.01 from 1051 to more than 3000. The correlation coefficient of proteomic profile was similar between replicate arterioles isolated freshly, following cold storage, or before and after the cold storage (1-way analysis of variance; P = .60). We built a human arteriolar proteomic profile consisting of 3832 proteins based on the analysis of 12 arteriole samples from 3 subjects. Of 1945 blood pressure-relevant proteins that we curated, 476 (12.5%) were detected in the arteriolar proteome, which was a significant overrepresentation (χ2 test; P < .05). These findings demonstrate that proteomic analysis is feasible with arterioles isolated from human adipose tissue following cold overnight storage and provide a reference human arteriolar proteome profile highly valuable for studies of arteriole-related traits.
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Affiliation(s)
- Rajan Pandey
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin; Department of Physiology, University of Arizona College of Medicine-Tucson, Tucson, Arizona
| | - Michelle L Roberts
- Division of Cardiovascular Medicine, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Jingli Wang
- Division of Cardiovascular Medicine, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Michaela Pereckas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - David Jensen
- Division of Cardiovascular Medicine, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
| | | | - Michael E Widlansky
- Division of Cardiovascular Medicine, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin.
| | - Mingyu Liang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin; Department of Physiology, University of Arizona College of Medicine-Tucson, Tucson, Arizona.
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Wu X, Zhang H. Omics Approaches Unveiling the Biology of Human Atherosclerotic Plaques. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:482-498. [PMID: 38280419 PMCID: PMC10988765 DOI: 10.1016/j.ajpath.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 12/16/2023] [Accepted: 12/20/2023] [Indexed: 01/29/2024]
Abstract
Atherosclerosis is a chronic inflammatory disease of the arterial wall, characterized by the buildup of plaques with the accumulation and transformation of lipids, immune cells, vascular smooth muscle cells, and necrotic cell debris. Plaques with collagen-poor thin fibrous caps infiltrated by macrophages and lymphocytes are considered unstable because they are at the greatest risk of rupture and clinical events. However, the current histologic definition of plaque types may not fully capture the complex molecular nature of atherosclerotic plaque biology and the underlying mechanisms contributing to plaque progression, rupture, and erosion. The advances in omics technologies have changed the understanding of atherosclerosis plaque biology, offering new possibilities to improve risk prediction and discover novel therapeutic targets. Genomic studies have shed light on the genetic predisposition to atherosclerosis, and integrative genomic analyses expedite the translation of genomic discoveries. Transcriptomic, proteomic, metabolomic, and lipidomic studies have refined the understanding of the molecular signature of atherosclerotic plaques, aiding in data-driven hypothesis generation for mechanistic studies and offering new prospects for biomarker discovery. Furthermore, advancements in single-cell technologies and emerging spatial analysis techniques have unveiled the heterogeneity and plasticity of plaque cells. This review discusses key omics-based discoveries that have advanced the understanding of human atherosclerotic plaque biology, focusing on insights derived from omics profiling of human atherosclerotic vascular specimens.
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Affiliation(s)
- Xun Wu
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Hanrui Zhang
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, New York.
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4
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Chen H, Zhao M, Li Y, Wang Q, Xing Y, Bian C, Li J. A study on the ultimate mechanical properties of middle-aged and elderly human aorta based on uniaxial tensile test. Front Bioeng Biotechnol 2024; 12:1357056. [PMID: 38576445 PMCID: PMC10991712 DOI: 10.3389/fbioe.2024.1357056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 03/07/2024] [Indexed: 04/06/2024] Open
Abstract
Background The mechanical properties of the aorta are particularly important in clinical medicine and forensic science, serving as basic data for further exploration of aortic disease or injury mechanisms. Objective To study the influence of various factors (age, gender, test direction, anatomical location, and pathological characteristics) on the mechanical properties and thickness of the aorta. Methods In this study, a total of 24 aortas (age range: 54-88 years old) were collected, one hundred and seventy-four dog-bone-shaped samples were made, and then the uniaxial tensile test was run, finally, pathological grouping was performed through histological staining. Results Atherosclerotic plaques were mainly distributed near the openings of blood vessel branches. The distribution was most severe in the abdominal aorta, followed by the aortic arch. Aortic atherosclerosis was a more severe trend in the male group. In the comparison of thickness, there were no significant differences in age (over 50 years) and test direction, the average thickness of the aorta was greater in the male group than the female group and decreased progressively from the ascending aorta to the abdominal aorta. Comparing the mechanical parameters, various parameters are mainly negatively correlated with age, especially in the circumferential ascending aorta (εp "Y = -0.01402*X + 1.762, R2 = 0.6882", εt "Y = -0.01062*X + 1.250, R2 = 0.6772"); the parameters of males in the healthy group were larger, while the parameters of females were larger in atherosclerosis group; the aorta has anisotropy, the parameters in the circumferential direction were greater than those in the axial direction; the parameters of the ascending aorta were the largest in the circumferential direction, the ultimate stress [σp "1.69 (1.08,2.32)"] and ultimate elastic modulus [E2"8.28 (6.67,10.25)"] of the abdominal aorta were significantly larger in the axial direction; In the circumferential direction, the stress [σp "2.2 (1.31,3.98)", σt "0.13 (0.09,0.31)"] and ultimate elastic modulus (E2 "14.10 ± 7.21") of adaptive intimal thickening were greater than those of other groups, the strain (εp "0.82 ± 0.17", εt "0.53 ± 0.14") of pathological intimal thickening was the largest in the pathological group. Conclusion The present study systematically analyzed the influence of age, sex, test direction, anatomical site, and pathological characteristics on the biomechanical properties of the aorta, described the distribution of aortic atherosclerosis, and illustrated the characteristics of aortic thickness changes. At the same time, new insights into the grouping of pathological features were presented.
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Affiliation(s)
- Hongbing Chen
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Engineering Research Center for Criminal Investigation Technology, Chongqing, China
- Chongqing Key Laboratory of Forensic Medicine, Chongqing, China
| | - Minzhu Zhao
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Engineering Research Center for Criminal Investigation Technology, Chongqing, China
- Chongqing Key Laboratory of Forensic Medicine, Chongqing, China
| | - Yongguo Li
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Engineering Research Center for Criminal Investigation Technology, Chongqing, China
- Chongqing Key Laboratory of Forensic Medicine, Chongqing, China
| | - Qi Wang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Engineering Research Center for Criminal Investigation Technology, Chongqing, China
- Chongqing Key Laboratory of Forensic Medicine, Chongqing, China
| | - Yu Xing
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Engineering Research Center for Criminal Investigation Technology, Chongqing, China
- Chongqing Key Laboratory of Forensic Medicine, Chongqing, China
| | - Cunhao Bian
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Engineering Research Center for Criminal Investigation Technology, Chongqing, China
- Chongqing Key Laboratory of Forensic Medicine, Chongqing, China
| | - Jianbo Li
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Chongqing Engineering Research Center for Criminal Investigation Technology, Chongqing, China
- Chongqing Key Laboratory of Forensic Medicine, Chongqing, China
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Wu CT, Du D, Chen L, Dai R, Liu C, Yu G, Bhardwaj S, Parker SJ, Zhang Z, Clarke R, Herrington DM, Wang Y. CAM3.0: determining cell type composition and expression from bulk tissues with fully unsupervised deconvolution. Bioinformatics 2024; 40:btae107. [PMID: 38407991 PMCID: PMC10924278 DOI: 10.1093/bioinformatics/btae107] [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: 04/03/2023] [Revised: 01/13/2024] [Accepted: 02/25/2024] [Indexed: 02/28/2024] Open
Abstract
MOTIVATION Complex tissues are dynamic ecosystems consisting of molecularly distinct yet interacting cell types. Computational deconvolution aims to dissect bulk tissue data into cell type compositions and cell-specific expressions. With few exceptions, most existing deconvolution tools exploit supervised approaches requiring various types of references that may be unreliable or even unavailable for specific tissue microenvironments. RESULTS We previously developed a fully unsupervised deconvolution method-Convex Analysis of Mixtures (CAM), that enables estimation of cell type composition and expression from bulk tissues. We now introduce CAM3.0 tool that improves this framework with three new and highly efficient algorithms, namely, radius-fixed clustering to identify reliable markers, linear programming to detect an initial scatter simplex, and a smart floating search for the optimum latent variable model. The comparative experimental results obtained from both realistic simulations and case studies show that the CAM3.0 tool can help biologists more accurately identify known or novel cell markers, determine cell proportions, and estimate cell-specific expressions, complementing the existing tools particularly when study- or datatype-specific references are unreliable or unavailable. AVAILABILITY AND IMPLEMENTATION The open-source R Scripts of CAM3.0 is freely available at https://github.com/ChiungTingWu/CAM3/(https://github.com/Bioconductor/Contributions/issues/3205). A user's guide and a vignette are provided.
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Affiliation(s)
- Chiung-Ting Wu
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, United States
| | - Dongping Du
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, United States
| | - Lulu Chen
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, United States
| | - Rujia Dai
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, United States
| | - Chunyu Liu
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, United States
| | - Guoqiang Yu
- Department of Automation, Tsinghua University, Beijing 100084, P. R. China
| | - Saurabh Bhardwaj
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, United States
- Department of Electrical and Instrumentation Engineering, Thapar Institute of Engineering & Technology, Punjab 147004, India
| | - Sarah J Parker
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Zhen Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, United States
| | - Robert Clarke
- The Hormel Institute, University of Minnesota, Austin, MN 55912, United States
| | - David M Herrington
- Department of Internal Medicine, Wake Forest University, Winston-Salem, NC 27157, United States
| | - Yue Wang
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, United States
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Lin HF, Wu MN, Chen CY, Lim K, Juo SHH, Chen CS. Thrombospondin-1 associated with carotid intima-media thickness among individuals with hypertension. J Investig Med 2024; 72:279-286. [PMID: 38217383 DOI: 10.1177/10815589241228589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
In vivo and in vitro studies have demonstrated that thrombospondin-1 (TSP-1) is involved in atherosclerotic pathogenesis. However, the role of TSP-1 in clinical atherosclerosis remains unknown. This cross-sectional study investigated the relationship between TSP-1 and carotid intima-media thickness (IMT) and examined whether it interacts with conventional cardiovascular risk factors. A total of 587 participants were enrolled from February 2018 to December 2021. TSP-1 was dichotomized based on median value. Carotid IMT was measured bilaterally in each segment, and the average value was taken as the overall IMT variable. Analysis of covariance models were used to ascertain the main and interaction effects of cardiovascular risk factors and circulating TSP-1 levels on carotid IMT. Those with high TSP-1 (n = 294) had significantly higher carotid IMT than did those with low TSP-1 (n = 293; 0.74 ± 0.12 vs 0.72 ± 0.11 mm; p = 0.011). After the combined effects of TSP-1 and vascular risk factors on carotid IMT were evaluated, an interaction effect on IMT was observed between TSP-1 and hypertension (adjusted F = 8.760; p = 0.003). Stratification analysis revealed that individuals with hypertension and high TSP-1 had significantly higher IMT than did those with low TSP-1 (adjusted p = 0.007). However, this difference was not observed in normotensive individuals (adjusted p = 0.636). In conclusion, this is the first study to provide clinical data supporting the correlation between TSP-1 and atherosclerosis. TSP-1 may be a crucial marker of increased susceptibility to atherosclerosis in individuals with hypertension.
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Affiliation(s)
- Hsiu-Fen Lin
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Neurology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Meng-Ni Wu
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Neurology, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chien-Yuan Chen
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Kelly Lim
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Suh-Hang Hank Juo
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
- Institute of Translational Medicine and New Drug Development, China Medical University, Taichung, Taiwan
- Drug Development Center, China Medical University, Taichung, Taiwan
| | - Cheng-Sheng Chen
- Department of Psychiatry, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Psychiatry, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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Yang F, Xu F, Zhang H, Gill D, Larsson SC, Li X, Cui H, Yuan S. Proteomic insights into the associations between obesity, lifestyle factors, and coronary artery disease. BMC Med 2023; 21:485. [PMID: 38049831 PMCID: PMC10696760 DOI: 10.1186/s12916-023-03197-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/27/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND We aimed to investigate the protein pathways linking obesity and lifestyle factors to coronary artery disease (CAD). METHODS Summary-level genome-wide association statistics of CAD were obtained from the CARDIoGRAMplusC4D consortium (60,801 cases and 123,504 controls) and the FinnGen study (R8, 39,036 cases and 303,463 controls). Proteome-wide Mendelian randomization (MR) analysis was conducted to identify CAD-associated blood proteins, supplemented by colocalization analysis to minimize potential bias caused by linkage disequilibrium. Two-sample MR analyses were performed to assess the associations of genetically predicted four obesity measures and 13 lifestyle factors with CAD risk and CAD-associated proteins' levels. A two-step network MR analysis was conducted to explore the mediating effects of proteins in the associations between these modifiable factors and CAD. RESULTS Genetically predicted levels of 41 circulating proteins were associated with CAD, and 17 of them were supported by medium to high colocalization evidence. PTK7 (protein tyrosine kinase-7), RGMB (repulsive guidance molecule BMP co-receptor B), TAGLN2 (transgelin-2), TIMP3 (tissue inhibitor of metalloproteinases 3), and VIM (vimentin) were identified as promising therapeutic targets. Several proteins were found to mediate the associations between some modifiable factors and CAD, with PCSK9, C1S, AGER (advanced glycosylation end product-specific receptor), and MST1 (mammalian Ste20-like kinase 1) exhibiting highest frequency among the mediating networks. CONCLUSIONS This study suggests pathways explaining the associations of obesity and lifestyle factors with CAD from alterations in blood protein levels. These insights may be used to prioritize therapeutic intervention for further study.
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Affiliation(s)
- Fangkun Yang
- Department of Cardiology, First Affiliated Hospital of Ningbo University (Ningbo First Hospital), School of Medicine, Ningbo University, 59 Liuting Road, Ningbo, 315010, China
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Ningbo, China
- Cardiovascular Disease Clinical Medical Research Center of Ningbo, Ningbo, Zhejiang, China
| | - Fengzhe Xu
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Han Zhang
- Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dipender Gill
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Susanna C Larsson
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Unit of Medical Epidemiology, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Xue Li
- Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Hanbin Cui
- Department of Cardiology, First Affiliated Hospital of Ningbo University (Ningbo First Hospital), School of Medicine, Ningbo University, 59 Liuting Road, Ningbo, 315010, China.
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Ningbo, China.
- Cardiovascular Disease Clinical Medical Research Center of Ningbo, Ningbo, Zhejiang, China.
| | - Shuai Yuan
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
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Mahoney SA, Dey AK, Basisty N, Herman AB. Identification and functional analysis of senescent cells in the cardiovascular system using omics approaches. Am J Physiol Heart Circ Physiol 2023; 325:H1039-H1058. [PMID: 37656130 PMCID: PMC10908411 DOI: 10.1152/ajpheart.00352.2023] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023]
Abstract
Cardiovascular disease (CVD) is a leading cause of morbidity and mortality worldwide, and senescent cells have emerged as key contributors to its pathogenesis. Senescent cells exhibit cell cycle arrest and secrete a range of proinflammatory factors, termed the senescence-associated secretory phenotype (SASP), which promotes tissue dysfunction and exacerbates CVD progression. Omics technologies, specifically transcriptomics and proteomics, offer powerful tools to uncover and define the molecular signatures of senescent cells in cardiovascular tissue. By analyzing the comprehensive molecular profiles of senescent cells, omics approaches can identify specific genetic alterations, gene expression patterns, protein abundances, and metabolite levels associated with senescence in CVD. These omics-based discoveries provide insights into the mechanisms underlying senescence-induced cardiovascular damage, facilitating the development of novel diagnostic biomarkers and therapeutic targets. Furthermore, integration of multiple omics data sets enables a systems-level understanding of senescence in CVD, paving the way for precision medicine approaches to prevent or treat cardiovascular aging and its associated complications.
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Affiliation(s)
- Sophia A Mahoney
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, Colorado, United States
| | - Amit K Dey
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States
| | - Nathan Basisty
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States
| | - Allison B Herman
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States
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Momenzadeh A, Kreimer S, Guo D, Ayres M, Berman D, Chyu KY, Shah PK, Milewicz D, Azizzadeh A, Meyer JG, Parker S. Differentiation between Descending Thoracic Aortic Diseases using Machine Learning and Plasma Proteomic Signatures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538468. [PMID: 37162892 PMCID: PMC10168345 DOI: 10.1101/2023.04.26.538468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Background Descending thoracic aortic aneurysms and dissections can go undetected until severe and catastrophic, and few clinical indices exist to screen for aneurysms or predict risk of dissection. Methods This study generated a plasma proteomic dataset from 75 patients with descending type B dissection (Type B) and 62 patients with descending thoracic aortic aneurysm (DTAA). Standard statistical approaches were compared to supervised machine learning (ML) algorithms to distinguish Type B from DTAA cases. Quantitatively similar proteins were clustered based on linkage distance from hierarchical clustering and ML models were trained with uncorrelated protein lists across various linkage distances with hyperparameter optimization using 5-fold cross validation. Permutation importance (PI) was used for ranking the most important predictor proteins of ML classification between disease states and the proteins among the top 10 PI protein groups were submitted for pathway analysis. Results Of the 1,549 peptides and 198 proteins used in this study, no peptides and only one protein, hemopexin (HPX), were significantly different at an adjusted p-value <0.01 between Type B and DTAA cases. The highest performing model on the training set (Support Vector Classifier) and its corresponding linkage distance (0.5) were used for evaluation of the test set, yielding a precision-recall area under the curve of 0.7 to classify between Type B from DTAA cases. The five proteins with the highest PI scores were immunoglobulin heavy variable 6-1 (IGHV6-1), lecithin-cholesterol acyltransferase (LCAT), coagulation factor 12 (F12), HPX, and immunoglobulin heavy variable 4-4 (IGHV4-4). All proteins from the top 10 most important correlated groups generated the following significantly enriched pathways in the plasma of Type B versus DTAA patients: complement activation, humoral immune response, and blood coagulation. Conclusions We conclude that ML may be useful in differentiating the plasma proteome of highly similar disease states that would otherwise not be distinguishable using statistics, and, in such cases, ML may enable prioritizing important proteins for model prediction.
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Affiliation(s)
- Amanda Momenzadeh
- Department of Computational Biomedicine, Cedars Sinai Medical Center, Los Angeles, California, USA
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Simion Kreimer
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Dongchuan Guo
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas
| | - Matthew Ayres
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Daniel Berman
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
- Cedars-Sinai Imaging Department, Cedars Sinai Medical Center, Lost Angeles, California, USA
| | - Kuang-Yuh Chyu
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Prediman K Shah
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Dianna Milewicz
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas
| | - Ali Azizzadeh
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Jesse G. Meyer
- Department of Computational Biomedicine, Cedars Sinai Medical Center, Los Angeles, California, USA
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Sarah Parker
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles California, USA
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Nieddu G, Formato M, Lepedda AJ. Searching for Atherosclerosis Biomarkers by Proteomics: A Focus on Lesion Pathogenesis and Vulnerability. Int J Mol Sci 2023; 24:15175. [PMID: 37894856 PMCID: PMC10607641 DOI: 10.3390/ijms242015175] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Plaque rupture and thrombosis are the most important clinical complications in the pathogenesis of stroke, coronary arteries, and peripheral vascular diseases. The identification of early biomarkers of plaque presence and susceptibility to ulceration could be of primary importance in preventing such life-threatening events. With the improvement of proteomic tools, large-scale technologies have been proven valuable in attempting to unravel pathways of atherosclerotic degeneration and identifying new circulating markers to be utilized either as early diagnostic traits or as targets for new drug therapies. To address these issues, different matrices of human origin, such as vascular cells, arterial tissues, plasma, and urine, have been investigated. Besides, proteomics was also applied to experimental atherosclerosis in order to unveil significant insights into the mechanisms influencing atherogenesis. This narrative review provides an overview of the last twenty years of omics applications to the study of atherogenesis and lesion vulnerability, with particular emphasis on lipoproteomics and vascular tissue proteomics. Major issues of tissue analyses, such as plaque complexity, sampling, availability, choice of proper controls, and lipoproteins purification, will be raised, and future directions will be addressed.
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Affiliation(s)
| | | | - Antonio Junior Lepedda
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (G.N.); (M.F.); Antonio Junior Lepedda (A.J.L.)
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11
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Theofilatos K, Stojkovic S, Hasman M, van der Laan SW, Baig F, Barallobre-Barreiro J, Schmidt LE, Yin S, Yin X, Burnap S, Singh B, Popham J, Harkot O, Kampf S, Nackenhorst MC, Strassl A, Loewe C, Demyanets S, Neumayer C, Bilban M, Hengstenberg C, Huber K, Pasterkamp G, Wojta J, Mayr M. Proteomic Atlas of Atherosclerosis: The Contribution of Proteoglycans to Sex Differences, Plaque Phenotypes, and Outcomes. Circ Res 2023; 133:542-558. [PMID: 37646165 PMCID: PMC10498884 DOI: 10.1161/circresaha.123.322590] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 08/09/2023] [Accepted: 08/13/2023] [Indexed: 09/01/2023]
Abstract
BACKGROUND Using proteomics, we aimed to reveal molecular types of human atherosclerotic lesions and study their associations with histology, imaging, and cardiovascular outcomes. METHODS Two hundred nineteen carotid endarterectomy samples were procured from 120 patients. A sequential protein extraction protocol was employed in conjunction with multiplexed, discovery proteomics. To focus on extracellular proteins, parallel reaction monitoring was employed for targeted proteomics. Proteomic signatures were integrated with bulk, single-cell, and spatial RNA-sequencing data, and validated in 200 patients from the Athero-Express Biobank study. RESULTS This extensive proteomics analysis identified plaque inflammation and calcification signatures, which were inversely correlated and validated using targeted proteomics. The inflammation signature was characterized by the presence of neutrophil-derived proteins, such as S100A8/9 (calprotectin) and myeloperoxidase, whereas the calcification signature included fetuin-A, osteopontin, and gamma-carboxylated proteins. The proteomics data also revealed sex differences in atherosclerosis, with large-aggregating proteoglycans versican and aggrecan being more abundant in females and exhibiting an inverse correlation with estradiol levels. The integration of RNA-sequencing data attributed the inflammation signature predominantly to neutrophils and macrophages, and the calcification and sex signatures to smooth muscle cells, except for certain plasma proteins that were not expressed but retained in plaques, such as fetuin-A. Dimensionality reduction and machine learning techniques were applied to identify 4 distinct plaque phenotypes based on proteomics data. A protein signature of 4 key proteins (calponin, protein C, serpin H1, and versican) predicted future cardiovascular mortality with an area under the curve of 75% and 67.5% in the discovery and validation cohort, respectively, surpassing the prognostic performance of imaging and histology. CONCLUSIONS Plaque proteomics redefined clinically relevant patient groups with distinct outcomes, identifying subgroups of male and female patients with elevated risk of future cardiovascular events.
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Affiliation(s)
- Konstantinos Theofilatos
- King’s British Heart Foundation Centre, Kings College London, United Kingdom (K.T., M.H., F.B., J.B.B., L.E.S., S.Y., X.Y., S.B., B.S., J.P., M.M.)
| | - Stefan Stojkovic
- Division of Cardiology, Department of Internal Medicine II (S.S., O.H., C.H., J.W., M.M.), Medical University of Vienna, Austria
| | - Maria Hasman
- King’s British Heart Foundation Centre, Kings College London, United Kingdom (K.T., M.H., F.B., J.B.B., L.E.S., S.Y., X.Y., S.B., B.S., J.P., M.M.)
| | - Sander W. van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, the Netherlands (S.W.v.d.L., G.P.)
| | - Ferheen Baig
- King’s British Heart Foundation Centre, Kings College London, United Kingdom (K.T., M.H., F.B., J.B.B., L.E.S., S.Y., X.Y., S.B., B.S., J.P., M.M.)
| | - Javier Barallobre-Barreiro
- King’s British Heart Foundation Centre, Kings College London, United Kingdom (K.T., M.H., F.B., J.B.B., L.E.S., S.Y., X.Y., S.B., B.S., J.P., M.M.)
| | - Lukas Emanuel Schmidt
- King’s British Heart Foundation Centre, Kings College London, United Kingdom (K.T., M.H., F.B., J.B.B., L.E.S., S.Y., X.Y., S.B., B.S., J.P., M.M.)
| | - Siqi Yin
- King’s British Heart Foundation Centre, Kings College London, United Kingdom (K.T., M.H., F.B., J.B.B., L.E.S., S.Y., X.Y., S.B., B.S., J.P., M.M.)
| | - Xiaoke Yin
- King’s British Heart Foundation Centre, Kings College London, United Kingdom (K.T., M.H., F.B., J.B.B., L.E.S., S.Y., X.Y., S.B., B.S., J.P., M.M.)
| | - Sean Burnap
- King’s British Heart Foundation Centre, Kings College London, United Kingdom (K.T., M.H., F.B., J.B.B., L.E.S., S.Y., X.Y., S.B., B.S., J.P., M.M.)
| | - Bhawana Singh
- King’s British Heart Foundation Centre, Kings College London, United Kingdom (K.T., M.H., F.B., J.B.B., L.E.S., S.Y., X.Y., S.B., B.S., J.P., M.M.)
| | - Jude Popham
- King’s British Heart Foundation Centre, Kings College London, United Kingdom (K.T., M.H., F.B., J.B.B., L.E.S., S.Y., X.Y., S.B., B.S., J.P., M.M.)
| | - Olesya Harkot
- Division of Cardiology, Department of Internal Medicine II (S.S., O.H., C.H., J.W., M.M.), Medical University of Vienna, Austria
| | - Stephanie Kampf
- Division of Vascular Surgery, Department of Surgery (S.K., C.N.), Medical University of Vienna, Austria
| | | | - Andreas Strassl
- Division of Cardiovascular and Interventional Radiology, Department of Biomedical Imaging and Image-Guided Therapy (A.S., C.L.), Medical University of Vienna, Austria
| | - Christian Loewe
- Division of Cardiovascular and Interventional Radiology, Department of Biomedical Imaging and Image-Guided Therapy (A.S., C.L.), Medical University of Vienna, Austria
| | - Svitlana Demyanets
- Department of Laboratory Medicine (S.D.), Medical University of Vienna, Austria
| | - Christoph Neumayer
- Division of Vascular Surgery, Department of Surgery (S.K., C.N.), Medical University of Vienna, Austria
| | - Martin Bilban
- Core Facilities (M.B.), Medical University of Vienna, Austria
| | - Christian Hengstenberg
- Division of Cardiology, Department of Internal Medicine II (S.S., O.H., C.H., J.W., M.M.), Medical University of Vienna, Austria
| | - Kurt Huber
- Third Medical Department, Wilhelminenspital, and Sigmund Freud University, Medical Faculty, Vienna, Austria (K.H.)
| | - Gerard Pasterkamp
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, the Netherlands (S.W.v.d.L., G.P.)
| | - Johann Wojta
- Division of Cardiology, Department of Internal Medicine II (S.S., O.H., C.H., J.W., M.M.), Medical University of Vienna, Austria
- Ludwig Boltzmann Institute for Cardiovascular Research, Vienna, Austria (J.W.)
| | - Manuel Mayr
- King’s British Heart Foundation Centre, Kings College London, United Kingdom (K.T., M.H., F.B., J.B.B., L.E.S., S.Y., X.Y., S.B., B.S., J.P., M.M.)
- Division of Cardiology, Department of Internal Medicine II (S.S., O.H., C.H., J.W., M.M.), Medical University of Vienna, Austria
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12
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Blaser MC, Buffolo F, Halu A, Turner ME, Schlotter F, Higashi H, Pantano L, Clift CL, Saddic LA, Atkins SK, Rogers MA, Pham T, Vromman A, Shvartz E, Sukhova GK, Monticone S, Camussi G, Robson SC, Body SC, Muehlschlegel JD, Singh SA, Aikawa M, Aikawa E. Multiomics of Tissue Extracellular Vesicles Identifies Unique Modulators of Atherosclerosis and Calcific Aortic Valve Stenosis. Circulation 2023; 148:661-678. [PMID: 37427430 PMCID: PMC10527599 DOI: 10.1161/circulationaha.122.063402] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 06/02/2023] [Indexed: 07/11/2023]
Abstract
BACKGROUND Fewer than 50% of patients who develop aortic valve calcification have concomitant atherosclerosis, implying differential pathogenesis. Although circulating extracellular vesicles (EVs) act as biomarkers of cardiovascular diseases, tissue-entrapped EVs are associated with early mineralization, but their cargoes, functions, and contributions to disease remain unknown. METHODS Disease stage-specific proteomics was performed on human carotid endarterectomy specimens (n=16) and stenotic aortic valves (n=18). Tissue EVs were isolated from human carotid arteries (normal, n=6; diseased, n=4) and aortic valves (normal, n=6; diseased, n=4) by enzymatic digestion, (ultra)centrifugation, and a 15-fraction density gradient validated by proteomics, CD63-immunogold electron microscopy, and nanoparticle tracking analysis. Vesiculomics, comprising vesicular proteomics and small RNA-sequencing, was conducted on tissue EVs. TargetScan identified microRNA targets. Pathway network analyses prioritized genes for validation in primary human carotid artery smooth muscle cells and aortic valvular interstitial cells. RESULTS Disease progression drove significant convergence (P<0.0001) of carotid artery plaque and calcified aortic valve proteomes (2318 proteins). Each tissue also retained a unique subset of differentially enriched proteins (381 in plaques; 226 in valves; q<0.05). Vesicular gene ontology terms increased 2.9-fold (P<0.0001) among proteins modulated by disease in both tissues. Proteomics identified 22 EV markers in tissue digest fractions. Networks of proteins and microRNA targets changed by disease progression in both artery and valve EVs revealed shared involvement in intracellular signaling and cell cycle regulation. Vesiculomics identified 773 proteins and 80 microRNAs differentially enriched by disease exclusively in artery or valve EVs (q<0.05); multiomics integration found tissue-specific EV cargoes associated with procalcific Notch and Wnt signaling in carotid arteries and aortic valves, respectively. Knockdown of tissue-specific EV-derived molecules FGFR2, PPP2CA, and ADAM17 in human carotid artery smooth muscle cells and WNT5A, APP, and APC in human aortic valvular interstitial cells significantly modulated calcification. CONCLUSIONS The first comparative proteomics study of human carotid artery plaques and calcified aortic valves identifies unique drivers of atherosclerosis versus aortic valve stenosis and implicates EVs in advanced cardiovascular calcification. We delineate a vesiculomics strategy to isolate, purify, and study protein and RNA cargoes from EVs entrapped in fibrocalcific tissues. Integration of vesicular proteomics and transcriptomics by network approaches revealed novel roles for tissue EVs in modulating cardiovascular disease.
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Affiliation(s)
- Mark C. Blaser
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Fabrizio Buffolo
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Arda Halu
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Mandy E. Turner
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Florian Schlotter
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Hideyuki Higashi
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Lorena Pantano
- T H Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Cassandra L. Clift
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Louis A. Saddic
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Boston University School of Medicine, Boston, MA, USA
| | - Samantha K. Atkins
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Maximillian A. Rogers
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Tan Pham
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Amélie Vromman
- Center for Excellence in Vascular Biology, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Eugenia Shvartz
- Center for Excellence in Vascular Biology, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Galina K Sukhova
- Center for Excellence in Vascular Biology, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Silvia Monticone
- Division of Internal Medicine and Hypertension, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Giovanni Camussi
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Simon C. Robson
- Center for Inflammation Research, Department of Anesthesia, Critical Care and Pain Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School
| | - Simon C. Body
- Boston University School of Medicine, Boston, MA, USA
| | - Jochen D. Muehlschlegel
- Center for Perioperative Genomics, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sasha A. Singh
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Center for Excellence in Vascular Biology, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Elena Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Center for Excellence in Vascular Biology, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
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13
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Gao J, Hou T. Cardiovascular disease treatment using traditional Chinese medicine:Mitochondria as the Achilles' heel. Biomed Pharmacother 2023; 164:114999. [PMID: 37311280 DOI: 10.1016/j.biopha.2023.114999] [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: 04/08/2023] [Revised: 05/30/2023] [Accepted: 06/07/2023] [Indexed: 06/15/2023] Open
Abstract
Cardiovascular disease (CVD), involving the pathological alteration of the heart or blood vessels, is one of the main causes of disability and death worldwide, with an estimated 18.6 million deaths per year. CVDs are caused by a variety of risk factors, including inflammation, hyperglycemia, hyperlipidemia, and increased oxidative stress. Mitochondria, the hub of ATP production and the main generator of reactive oxygen species (ROS), are linked to multiple cellular signaling pathways that regulate the progression of CVD and therefore are recognized as an essential target for CVD management. Initial treatment of CVD generally focuses on diet and lifestyle interventions; proper drugs or surgery can prolong or save the patient's life. Traditional Chinese medicine (TCM), a holistic medical care system with an over 2500-year history, has been proven to be efficient in curing CVD and other illnesses, with a strengthening effect on the body. However, the mechanisms underlying TCM alleviation of CVD remain elusive. Recent studies have recognized that TCM can alleviate cardiovascular disease by manipulating the quality and function of mitochondria. This review systematically summarizes the association of mitochondria with cardiovascular risk factors, and the relationships between mitochondrial dysfunction and CVD progression. We will investigate the research progress of managing cardiovascular disease by TCM and cover widely used TCMs that target mitochondria for the treatment of cardiovascular disease.
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Affiliation(s)
- Jie Gao
- Chengdu Integrated TCM and Western Medicine Hospital and Chengdu University of Traditional Chinese Medicine, Chengdu 610041 China
| | - Tianshu Hou
- Chengdu Integrated TCM and Western Medicine Hospital and Chengdu University of Traditional Chinese Medicine, Chengdu 610041 China.
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14
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Rao L, Peng B, Li T. Nonnegative matrix factorization analysis and multiple machine learning methods identified IL17C and ACOXL as novel diagnostic biomarkers for atherosclerosis. BMC Bioinformatics 2023; 24:196. [PMID: 37173646 PMCID: PMC10176911 DOI: 10.1186/s12859-023-05244-w] [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: 01/04/2023] [Accepted: 03/21/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Atherosclerosis is the common pathological basis for many cardiovascular and cerebrovascular diseases. The purpose of this study is to identify the diagnostic biomarkers related to atherosclerosis through machine learning algorithm. METHODS Clinicopathological parameters and transcriptomics data were obtained from 4 datasets (GSE21545, GSE20129, GSE43292, GSE100927). A nonnegative matrix factorization algorithm was used to classify arteriosclerosis patients in GSE21545 dataset. Then, we identified prognosis-related differentially expressed genes (DEGs) between the subtypes. Multiple machine learning methods to detect pivotal markers. Discrimination, calibration and clinical usefulness of the predicting model were assessed using area under curve, calibration plot and decision curve analysis respectively. The expression level of the feature genes was validated in GSE20129, GSE43292, GSE100927. RESULTS 2 molecular subtypes of atherosclerosis was identified, and 223 prognosis-related DEGs between the 2 subtypes were identified. These genes are not only related to epithelial cell proliferation, mitochondrial dysfunction, but also to immune related pathways. Least absolute shrinkage and selection operator, random forest, support vector machine- recursive feature elimination show that IL17C and ACOXL were identified as diagnostic markers of atherosclerosis. The prediction model displayed good discrimination and good calibration. Decision curve analysis showed that this model was clinically useful. Moreover, IL17C and ACOXL were verified in other 3 GEO datasets, and also have good predictive performance. CONCLUSION IL17C and ACOXL were diagnostic genes of atherosclerosis and associated with higher incidence of ischemic events.
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Affiliation(s)
- Li Rao
- Department of Geriatrics, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
| | - Bo Peng
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
- Cardiovascular Research Institute of Wuhan University, Wuhan, 430060, Hubei, China
- Hubei Key Laboratory of Cardiology, Wuhan, 430060, Hubei, China
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
| | - Tao Li
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China.
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15
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Raos D, Prkačin I, Delalić Đ, Bulum T, Lovrić Benčić M, Jug J. Postoperative Hyperuricemia-A Risk Factor in Elective Cardiosurgical Patients. Metabolites 2023; 13:metabo13050590. [PMID: 37233631 DOI: 10.3390/metabo13050590] [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: 03/13/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Hyperuricemia is a well-known cardiovascular risk factor. The aim of our study was to investigate the connection between postoperative hyperuricemia and poor outcomes after elective cardiac surgery compared to patients without postoperative hyperuricemia. In this retrospective study, a total of 227 patients after elective cardiac surgery were divided into two groups: 42 patients with postoperative hyperuricemia (mean age 65.14 ± 8.9 years) and a second group of 185 patients without it (mean age 62.67 ± 7.45 years). The time spent on mechanical ventilation (hours) and in the intensive care unit (days) were taken as the primary outcome measures while the secondary measure comprised postoperative complications. The preoperative patient characteristics were similar. Most of the patients were men. The EuroSCORE value of assessing the risk was not different between the groups nor the comorbidities. Among the most common comorbidities was hypertension, seen in 66% of all patients (69% in patients with postoperative hyperuricemia and 63.7% in those without it). A group of patients with postoperative hyperuricemia had a prolonged time of treatment in the intensive care unit (p = 0.03), as well as a prolonged duration of mechanical ventilation (p < 0.01) and a significantly higher incidence of the following postoperative complications: circulatory instability and/or low cardiac output syndrome (LCOS) (χ2 = 4486, p < 0.01), renal failure and/or continuous venovenous hemodiafiltration (CVVHDF's) (χ2 = 10,241, p < 0.001), and mortality (χ2 = 5.22, p < 0.01). Compared to patients without postoperative hyperuricemia, elective cardiac patients with postoperative hyperuricemia have prolonged postoperative treatment in intensive care units, extended durations of mechanically assisted ventilation, and a higher incidence of postoperative circulatory instability, renal failure, and death.
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Affiliation(s)
- Dominik Raos
- Institute of Emergency Medicine of Zagreb County, 10000 Zagreb, Croatia
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Ingrid Prkačin
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
- Department of Internal Medicine, Merkur University Hospital, 10000 Zagreb, Croatia
| | - Điđi Delalić
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Tomislav Bulum
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
- Department of Diabetes, Vuk Vrhovac University Clinic for Diabetes, Endocrinology, and Metabolic Diseases, Merkur University Hospital, 10000 Zagreb, Croatia
| | - Martina Lovrić Benčić
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
- Department for Ischemic Heart Disease, University Clinic of Cardiovascular Diseases, Clinical Hospital Center Zagreb, 10000 Zagreb, Croatia
| | - Juraj Jug
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
- Health Center Zagreb-West, 10000 Zagreb, Croatia
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16
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Kocsmár É, Schmid M, Cosenza-Contreras M, Kocsmár I, Föll M, Krey L, Barta BA, Rácz G, Kiss A, Werner M, Schilling O, Lotz G, Bronsert P. Proteome alterations in human autopsy tissues in relation to time after death. Cell Mol Life Sci 2023; 80:117. [PMID: 37020120 PMCID: PMC10075177 DOI: 10.1007/s00018-023-04754-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 02/17/2023] [Accepted: 03/07/2023] [Indexed: 04/07/2023]
Abstract
Protein expression is a primary area of interest for routine histological diagnostics and tissue-based research projects, but the limitations of its post-mortem applicability remain largely unclear. On the other hand, tissue specimens obtained during autopsies can provide unique insight into advanced disease states, especially in cancer research. Therefore, we aimed to identify the maximum post-mortem interval (PMI) which is still suitable for characterizing protein expression patterns, to explore organ-specific differences in protein degradation, and to investigate whether certain proteins follow specific degradation kinetics. Therefore, the proteome of human tissue samples obtained during routine autopsies of deceased patients with accurate PMI (6, 12, 18, 24, 48, 72, 96 h) and without specific diseases that significantly affect tissue preservation, from lungs, kidneys and livers, was analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). For the kidney and liver, significant protein degradation became apparent at 48 h. For the lung, the proteome composition was rather static for up to 48 h and substantial protein degradation was detected only at 72 h suggesting that degradation kinetics appear to be organ specific. More detailed analyses suggested that proteins with similar post-mortem kinetics are not primarily shared in their biological functions. The overrepresentation of protein families with analogous structural motifs in the kidney indicates that structural features may be a common factor in determining similar postmortem stability. Our study demonstrates that a longer post-mortem period may have a significant impact on proteome composition, but sampling within 24 h may be appropriate, as degradation is within acceptable limits even in organs with faster autolysis.
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Affiliation(s)
- Éva Kocsmár
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - Marlene Schmid
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Miguel Cosenza-Contreras
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ildikó Kocsmár
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
- Department of Urology, Semmelweis University, Budapest, Hungary
| | - Melanie Föll
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Khoury College of Computer Sciences, Northeastern University, Boston, USA
| | - Leah Krey
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bálint András Barta
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Gergely Rácz
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - András Kiss
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - Martin Werner
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Schilling
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany.
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Gábor Lotz
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - Peter Bronsert
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany.
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- Biobank Comprehensive Cancer Center Freiburg, University Medical Center, Freiburg, Germany.
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17
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Karere GM, Glenn JP, Li G, Konar A, VandeBerg JL, Cox LA. Potential miRNA biomarkers and therapeutic targets for early atherosclerotic lesions. Sci Rep 2023; 13:3467. [PMID: 36859458 PMCID: PMC9977938 DOI: 10.1038/s41598-023-29074-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/30/2023] [Indexed: 03/03/2023] Open
Abstract
Identification of potential therapeutic targets and biomarkers indicative of burden of early atherosclerosis that occur prior to advancement to life-threatening unstable plaques is the key to eradication of CAD prevalence and incidences. We challenged 16 baboons with a high cholesterol, high fat diet for 2 years and evaluated early-stage atherosclerotic lesions (fatty streaks, FS, and fibrous plaques, FP) in formalin-fixed common iliac arteries (CIA). We used small RNA sequencing to identify expressed miRNAs in CIA and in baseline blood samples of the same animals. We found 412 expressed miRNAs in CIA and 356 in blood samples. Eight miRNAs (miR-7975, -486-5p, -451a, -191-5p, -148a-3p, -17-5p, -378c, and -144-3p) were differentially expressed between paired fatty streak lesion and no-lesion sites of the tissue, and 27 miRNAs (e.g., miR-92a-3p, -5001, -342-3p, miR-28-3p, -21-5p, -221-3p, 146a-5p, and -16-5p) in fibrous plaques. The expression of 14 blood miRNAs significantly correlated with extent of lesions and the number of plaques. We identified coordinately regulated miRNA-gene networks in which miR-17-5p and miR-146a-5p are central hubs and miR-5001 and miR-7975 are potentially novel miRNAs associated with early atherosclerosis. In summary, we have identified miRNAs expressed in lesions and in blood that correlate with lesion burden and are potential therapeutic targets and biomarkers. These findings are a first step in elucidating miRNA regulated molecular mechanisms that underlie early atherosclerosis in a baboon model, enabling translation of our findings to humans.
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Affiliation(s)
- Genesio M Karere
- Department of Internal Medicine, Section on Molecular Medicine, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.
| | - Jeremy P Glenn
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Ge Li
- Department of Internal Medicine, Section on Molecular Medicine, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Ayati Konar
- Department of Internal Medicine, Section on Molecular Medicine, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - John L VandeBerg
- Department of Human Genetics, South Texas Diabetes and Obesity Institute, The University of Texas Rio Grande Valley, Brownville, Harlingen, Edinburg, TX, 78520, USA
| | - Laura A Cox
- Department of Internal Medicine, Section on Molecular Medicine, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
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18
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Matuck B, Ferraz da Silva LF, Warner BM, Byrd KM. The need for integrated research autopsies in the era of precision oral medicine. J Am Dent Assoc 2023; 154:194-205. [PMID: 36710158 PMCID: PMC9974796 DOI: 10.1016/j.adaj.2022.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/18/2022] [Accepted: 11/20/2022] [Indexed: 01/29/2023]
Abstract
BACKGROUND Autopsy has benefited the practice of medicine for centuries; however, its use to advance the practice of oral health care is relatively limited. In the era of precision oral medicine, the research autopsy is poised to play an important role in understanding oral-systemic health, including infectious disease, autoimmunity, craniofacial genetics, and cancer. TYPES OF STUDIES REVIEWED The authors reviewed relevant articles that used medical and dental research autopsies to summarize the advantages of minimally invasive autopsies of dental, oral, and craniofacial tissues and to outline practices for supporting research autopsies of the oral and craniofacial complex. RESULTS The authors provide a historical summary of research autopsy in dentistry and provide a perspective on the value of autopsies for high-resolution multiomic studies to benefit precision oral medicine. As the promise of high-resolution multiomics is being realized, there is a need to integrate the oral and craniofacial complex into the practice of autopsy in medicine. Furthermore, the collaboration of autopsy centers with researchers will accelerate the understanding of dental, oral, and craniofacial tissues as part of the whole body. CONCLUSIONS Autopsies must integrate oral and craniofacial tissues as part of biobanking procedures. As new technologies allow for high-resolution, multimodal phenotyping of human samples, using optimized sampling procedures will allow for unprecedented understanding of common and rare dental, oral, and craniofacial diseases in the future. PRACTICAL IMPLICATIONS The COVID-19 pandemic highlighted the oral cavity as a site for viral infection and transmission potential; this was only discovered via clinical autopsies. The realization of the integrated autopsy's value in full body health initiatives will benefit patients across the globe.
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Affiliation(s)
- Bruno Matuck
- Department of Pathology, School of Medicine University of São Paulo, São Paulo, Brazil
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Blake M. Warner
- Salivary Disorders Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Kevin Matthew Byrd
- Salivary Disorders Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lab of Oral & Craniofacial Innovation (LOCI), Department of Innovation and Technology Research, ADA Science & Research Institute, Gaithersburg, MD, USA
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19
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Hu A, Zhang J, Shen H. Progress in Targeted Mass Spectrometry (Parallel Accumulation-Serial Fragmentation) and Its Application in Plasma/Serum Proteomics. Methods Mol Biol 2023; 2628:339-352. [PMID: 36781796 DOI: 10.1007/978-1-0716-2978-9_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Targeted mass spectrometry using multiple reaction monitoring (MRM) or parallel reaction monitoring (PRM) has been commonly used for protein biomarker validation in plasma, serum, or other clinically relevant specimens due to its high specificity, selectivity, and multiplexing capability compared with immunoassays. As the emerging mode termed parallel accumulation-serial fragmentation (prmPASEF) significantly improved analyte throughput (100-1000), sensitivity (attomole level), and acquisition speed, it promises to broaden the application of targeted mass spectrometry to simultaneous biomarker discovery and validation with high accuracy. Here, we summarize the general approach of the MRM and PRM techniques used for serum/plasma proteomics and describe a detailed step-by-step procedure for the development of MRM/PRM assays for secreted proteins.
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Affiliation(s)
- Anqi Hu
- Institutes of Biomedical Sciences and Minhang Hospital, Fudan University, Shanghai, China
| | - Jiayi Zhang
- Institutes of Biomedical Sciences and Minhang Hospital, Fudan University, Shanghai, China
| | - Huali Shen
- Institutes of Biomedical Sciences and Minhang Hospital, Fudan University, Shanghai, China.
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20
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Zhang J, Hu A, Chen X, Shen F, Zhang L, Lin Y, Shen H. Pan‐targeted quantification of deep and comprehensive cancer serum proteome improves cancer detection. VIEW 2023. [DOI: 10.1002/viw.20220039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Jiayi Zhang
- Minhang Hospital and Institutes of Biomedical Sciences Fudan University Shanghai China
| | - Anqi Hu
- Minhang Hospital and Institutes of Biomedical Sciences Fudan University Shanghai China
| | - Xuguang Chen
- Informatization Office Fudan University Shanghai China
| | - Fenglin Shen
- Minhang Hospital and Institutes of Biomedical Sciences Fudan University Shanghai China
| | - Lei Zhang
- Minhang Hospital and Institutes of Biomedical Sciences Fudan University Shanghai China
| | - Yuxiang Lin
- Department of Breast Surgery Fujian Medical University Union Hospital Fuzhou China
- Department of General Surgery Fujian Medical University Union Hospital Fuzhou China
- Breast Cancer Institute Fujian Medical University Fuzhou China
| | - Huali Shen
- Minhang Hospital and Institutes of Biomedical Sciences Fudan University Shanghai China
- NHC Key Laboratory of Glycoconjugates Research Fudan University Shanghai China
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21
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Chandran M, S S, Abhirami, Chandran A, Jaleel A, Plakkal Ayyappan J. Defining atherosclerotic plaque biology by mass spectrometry-based omics approaches. Mol Omics 2023; 19:6-26. [PMID: 36426765 DOI: 10.1039/d2mo00260d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Atherosclerosis is the principal cause of vascular diseases and one of the leading causes of worldwide death. Even though several insights into its natural course, risk factors and interventions have been identified, it is still an ongoing global pandemic. Since the structure and biochemical composition of the plaques show high heterogeneity, a comprehensive understanding of the intraplaque composition, its microenvironment, and the mechanisms of the progression and instability across different vascular beds at their progression stages is crucial for better risk stratification and treatment modalities. Even though several cell-based studies, animal studies, and extensive multicentric population studies have been conducted concerning cardiovascular diseases for assessing the risk factors and plaque biology, the studies on human clinical samples are very limited. New novel approaches utilize samples from percutaneous coronary interventions, which could possibly gain more access to clinical samples at different stages of the diseases without complex invasive resections. As an emerging technological platform in disease discovery research, mass spectrometry-based omics technologies offer capabilities for a comprehensive understanding of the mechanisms linked to several vascular diseases. Here, we discuss the cellular and molecular processes of atherosclerosis, different mass spectrometry-based omics approaches, and the studies mostly done on clinical samples of atheroma plaque using mass spectrometry-based proteomics, metabolomics and lipidomics approaches.
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Affiliation(s)
- Mahesh Chandran
- Translational Nanomedicine and Lifestyle Disease Research Laboratory, Department of Biochemistry, University of Kerala, Thiruvananthapuram 695034, Kerala, India. .,Department of Biotechnology, University of Kerala, Thiruvananthapuram 695034, Kerala, India.,Mass Spectrometry and Proteomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695012, India
| | - Sudhina S
- Translational Nanomedicine and Lifestyle Disease Research Laboratory, Department of Biochemistry, University of Kerala, Thiruvananthapuram 695034, Kerala, India.
| | - Abhirami
- Translational Nanomedicine and Lifestyle Disease Research Laboratory, Department of Biochemistry, University of Kerala, Thiruvananthapuram 695034, Kerala, India.
| | - Akash Chandran
- Department of Nanoscience and Nanotechnology, University of Kerala, Kariavattom, Thiruvananthapuram-695581, Kerala, India
| | - Abdul Jaleel
- Mass Spectrometry and Proteomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695012, India
| | - Janeesh Plakkal Ayyappan
- Translational Nanomedicine and Lifestyle Disease Research Laboratory, Department of Biochemistry, University of Kerala, Thiruvananthapuram 695034, Kerala, India. .,Department of Biotechnology, University of Kerala, Thiruvananthapuram 695034, Kerala, India.,Department of Nanoscience and Nanotechnology, University of Kerala, Kariavattom, Thiruvananthapuram-695581, Kerala, India.,Centre for Advanced Cancer Research, Department of Biochemistry, University of Kerala, Thiruvananthapuram 695034, Kerala, India
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22
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Lin L, Liu S, Chen Z, Xia Y, Xie J, Fu M, Lu D, Wu Y, Shen H, Yang P, Qian J. Anatomically resolved transcriptome and proteome landscapes reveal disease‐relevant molecular signatures and systematic changes in heart function of end‐stage dilated cardiomyopathy. VIEW 2022. [DOI: 10.1002/viw.20220040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Ling Lin
- Institutes of Biomedical Sciences of Shanghai Medical School & Minhang Hospital Fudan University Shanghai China
- Department of Cardiology Shanghai Institute of Cardiovascular Diseases Zhongshan Hospital Fudan University Shanghai China
| | - Shanshan Liu
- Institutes of Biomedical Sciences of Shanghai Medical School & Minhang Hospital Fudan University Shanghai China
| | - Zhangwei Chen
- Department of Cardiology Shanghai Institute of Cardiovascular Diseases Zhongshan Hospital Fudan University Shanghai China
| | - Yan Xia
- Department of Cardiology Shanghai Institute of Cardiovascular Diseases Zhongshan Hospital Fudan University Shanghai China
| | - Juanjuan Xie
- Institutes of Biomedical Sciences of Shanghai Medical School & Minhang Hospital Fudan University Shanghai China
| | - Mingqiang Fu
- Department of Cardiology Shanghai Institute of Cardiovascular Diseases Zhongshan Hospital Fudan University Shanghai China
| | - Danbo Lu
- Department of Cardiology Shanghai Institute of Cardiovascular Diseases Zhongshan Hospital Fudan University Shanghai China
| | - Yuan Wu
- Department of Cardiology Shanghai Institute of Cardiovascular Diseases Zhongshan Hospital Fudan University Shanghai China
| | - Huali Shen
- Institutes of Biomedical Sciences of Shanghai Medical School & Minhang Hospital Fudan University Shanghai China
| | - Pengyuan Yang
- Institutes of Biomedical Sciences of Shanghai Medical School & Minhang Hospital Fudan University Shanghai China
- Department of chemistry Fudan University Shanghai China
| | - Juying Qian
- Department of Cardiology Shanghai Institute of Cardiovascular Diseases Zhongshan Hospital Fudan University Shanghai China
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23
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Wang A, Li Y, Wang Z, Xin G, You Y, Sun M, Miao L, Li L, Pan Y, Liu J. Proteomic analysis revealed the pharmacological mechanism of Xueshuantong injection in preventing early acute myocardial infarction injury. Front Pharmacol 2022; 13:1010079. [PMID: 36618918 PMCID: PMC9811672 DOI: 10.3389/fphar.2022.1010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Acute myocardial infarction (AMI) is a common and life-threatening cardiovascular disease. However, there is a lack of pathology and drug studies on AMI within 20 min. Xueshuantong injection (XST) is mainly composed of Panax notoginseng saponins, which can dilate blood vessels and improve blood circulation, and is clinically used in the treatment of cardiovascular and cerebrovascular diseases. Purpose: The study aimed to investigate the protective mechanism of Xueshuantong injection against acute myocardial infarction within 20 min in rats by proteomic methods and molecular docking. Method: The male Sprague-Dawley rat acute myocardial infarction model was established by LAD ligation, and Xueshuantong injection (38 mg/kg) was injected into the caudal vein 15 min before surgery. Cardiac function evaluation, morphological observation, label-free quantitative proteomics, Western blotting analysis, molecular docking, and affinity measurement were applied in this study. Results: In a span of 20 min after acute myocardial infarction, the model group showed significant cardiac function impairment. Xueshuantong injection can significantly improve cardiac function and prevent pathological injury of myocardial tissue. A total of 117 vital differentially expressed proteins were identified by proteomic analysis, including 80 differentially expressed proteins (DEPs) in the sham group compared with model rats (Sham: model) and 43 DEPs in model rats compared with the Xueshuantong injection group (Model: XST). The treatment of Xueshuantong injection mainly involves "poly(A) RNA binding" and "cadherin binding involved in cell-cell adhesion." The differentially expressed levels of the pathways related to proteins Echdc2, Gcdh, Dlst, and Nampt, as well as 14-3-3 family proteins Ywhaz and Ywhab, could be quantitatively confirmed by WB. Molecular docking analysis and SPR analysis revealed that Ywhaz has a generally stable binding with five Xueshuantong injection components. Conclusion: Xueshuantong injection (XST) could protect rat myocardial function injury against AMI in 20 min. Echdc2, Ywhaz, Gcdh, Ywhab, Nampt, and Dlst play an essential role in this protective effect. In particular, Ywhaz might be the core target of Xueshuantong injection when treating acute myocardial infarction in the early stage. This study promoted the understanding of the protective mechanism of Xueshuantong injection in 20 min injury of acute myocardial infarction and contributed to the identification of possible targets of Xueshuantong injection.
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Affiliation(s)
- Aoao Wang
- National Clinical Research Center for Cardiovascular Diseases of Traditional Chinese Medicine, Institute of Basic Medical Sciences of Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ying Li
- National Clinical Research Center for Cardiovascular Diseases of Traditional Chinese Medicine, Institute of Basic Medical Sciences of Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ziyan Wang
- National Clinical Research Center for Cardiovascular Diseases of Traditional Chinese Medicine, Institute of Basic Medical Sciences of Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Gaojie Xin
- National Clinical Research Center for Cardiovascular Diseases of Traditional Chinese Medicine, Institute of Basic Medical Sciences of Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yue You
- National Clinical Research Center for Cardiovascular Diseases of Traditional Chinese Medicine, Institute of Basic Medical Sciences of Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Mingqian Sun
- National Clinical Research Center for Cardiovascular Diseases of Traditional Chinese Medicine, Institute of Basic Medical Sciences of Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lan Miao
- National Clinical Research Center for Cardiovascular Diseases of Traditional Chinese Medicine, Institute of Basic Medical Sciences of Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lei Li
- National Clinical Research Center for Cardiovascular Diseases of Traditional Chinese Medicine, Institute of Basic Medical Sciences of Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China,*Correspondence: Lei Li, ; Yinghong Pan, ; Jianxun Liu,
| | - Yinghong Pan
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China,*Correspondence: Lei Li, ; Yinghong Pan, ; Jianxun Liu,
| | - Jianxun Liu
- National Clinical Research Center for Cardiovascular Diseases of Traditional Chinese Medicine, Institute of Basic Medical Sciences of Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China,*Correspondence: Lei Li, ; Yinghong Pan, ; Jianxun Liu,
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24
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Proteomic Insights into Cardiac Fibrosis: From Pathophysiological Mechanisms to Therapeutic Opportunities. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248784. [PMID: 36557919 PMCID: PMC9781843 DOI: 10.3390/molecules27248784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
Cardiac fibrosis is a common pathophysiologic process in nearly all forms of heart disease which refers to excessive deposition of extracellular matrix proteins by cardiac fibroblasts. Activated fibroblasts are the central cellular effectors in cardiac fibrosis, and fibrotic remodelling can cause several cardiac dysfunctions either by reducing the ejection fraction due to a stiffened myocardial matrix, or by impairing electric conductance. Recently, there is a rising focus on the proteomic studies of cardiac fibrosis for pathogenesis elucidation and potential biomarker mining. This paper summarizes the current knowledge of molecular mechanisms underlying cardiac fibrosis, discusses the potential of imaging and circulating biomarkers available to recognize different phenotypes of this lesion, reviews the currently available and potential future therapies that allow individualized management in reversing progressive fibrosis, as well as the recent progress on proteomic studies of cardiac fibrosis. Proteomic approaches using clinical specimens and animal models can provide the ability to track pathological changes and new insights into the mechanisms underlining cardiac fibrosis. Furthermore, spatial and cell-type resolved quantitative proteomic analysis may also serve as a minimally invasive method for diagnosing cardiac fibrosis and allowing for the initiation of prophylactic treatment.
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25
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Dos Santos Liberato SF, da Cruz Vegian MR, Abu Hasna A, de Alvarenga JA, Dos Santos JG, Tini ÍRP, Amêndola I, Junqueira JC, de Oliveira LD. Antibiofilm action of Persea americana glycolic extract over Acinetobacter baumannii and absence of toxicity in Galleria mellonella. JOURNAL OF COMPLEMENTARY & INTEGRATIVE MEDICINE 2022; 19:905-911. [PMID: 34265885 DOI: 10.1515/jcim-2021-0051] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
OBJECTIVES This study aimed to evaluate the antibiofilm activity and toxicity of the glycolic extract of Persea americana "P. americana" over multidrug-resistant strains of Acinetobacter baumannii "A. baumannii" as alternative therapy to be investigated. METHODS A bacterial inoculum of each bacterial strain (4a, 5a, 9a, 12a, ATCC 19606) of A. baumannii was prepared and adjusted by the spectrophotometer. The microdilution broth method was performed to determine the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). P. americana glycolic extracts were obtained of the tree stalk and leaves. The biofilm viability was tested by MTT assay after 5 min exposure. The toxicity of the extracts was tested by invertebrate model Galleria mellonella. The data were analyzed by ANOVA, Tukey test and log-rank method (α=0.05). RESULTS The extract showed an inhibitory and bactericidal action over all the tested strains with the lowest MIC value observed for the reference strain (3.12 mg/mL). The extract did not demonstrate toxicity in any of the tested concentrations (12.5, 25 and 50 mg/mL) in Galleria mellonella larvae, with a survival percentage above 80% after 168 h. CONCLUSIONS The glycolic extract of P. americana has microbicidal and antibiofilm activity on multidrug-resistant clinical strains of A. baumannii and showed low toxicity for the invertebrate model G. mellonella.
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Affiliation(s)
| | - Mariana Raquel da Cruz Vegian
- Department of Bioscience and Oral Diagnosis, Institute of Science and Technology, São Paulo State University - UNESP, São Paulo, Brazil
| | - Amjad Abu Hasna
- Department of Restorative Dentistry, Endodontics division, Institute of Science and Technology, São Paulo State University - UNESP, São Paulo, Brazil
| | - Janaína Araújo de Alvarenga
- Department of Bioscience and Oral Diagnosis, Institute of Science and Technology, São Paulo State University - UNESP, São Paulo, Brazil
| | - Juliana Guimarães Dos Santos
- Department of Bioscience and Oral Diagnosis, Institute of Science and Technology, São Paulo State University - UNESP, São Paulo, Brazil
| | - Ítalo Rigotti Pereira Tini
- Department of Bioscience and Oral Diagnosis, Institute of Science and Technology, São Paulo State University - UNESP, São Paulo, Brazil
| | - Isabela Amêndola
- Department of Bioscience and Oral Diagnosis, Institute of Science and Technology, São Paulo State University - UNESP, São Paulo, Brazil
| | - Juliana Campos Junqueira
- Department of Bioscience and Oral Diagnosis, Institute of Science and Technology, São Paulo State University - UNESP, São Paulo, Brazil
| | - Luciane Dias de Oliveira
- Department of Bioscience and Oral Diagnosis, Institute of Science and Technology, São Paulo State University - UNESP, São Paulo, Brazil
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26
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Wu CT, Shen M, Du D, Cheng Z, Parker SJ, Lu Y, Van Eyk JE, Yu G, Clarke R, Herrington DM, Wang Y. Cosbin: cosine score-based iterative normalization of biologically diverse samples. BIOINFORMATICS ADVANCES 2022; 2:vbac076. [PMID: 36330358 PMCID: PMC9614059 DOI: 10.1093/bioadv/vbac076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 10/02/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022]
Abstract
Motivation Data normalization is essential to ensure accurate inference and comparability of gene expression measures across samples or conditions. Ideally, gene expression data should be rescaled based on consistently expressed reference genes. However, to normalize biologically diverse samples, the most commonly used reference genes exhibit striking expression variability and size-factor or distribution-based normalization methods can be problematic when the amount of asymmetry in differential expression is significant. Results We report an efficient and accurate data-driven method—Cosine score-based iterative normalization (Cosbin)—to normalize biologically diverse samples. Based on the Cosine scores of cross-condition expression patterns, the Cosbin pipeline iteratively eliminates asymmetric differentially expressed genes, identifies consistently expressed genes, and calculates sample-wise normalization factors. We demonstrate the superior performance and enhanced utility of Cosbin compared with six representative peer methods using both simulation and real multi-omics expression datasets. Implemented in open-source R scripts and specifically designed to address normalization bias due to significant asymmetry in differential expression across multiple conditions, the Cosbin tool complements rather than replaces the existing methods and will allow biologists to more accurately detect true molecular signals among diverse phenotypic groups. Availability and implementation The R scripts of Cosbin pipeline are freely available at https://github.com/MinjieSh/Cosbin. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
| | | | - Dongping Du
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Zuolin Cheng
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Sarah J Parker
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yingzhou Lu
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Guoqiang Yu
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Robert Clarke
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - David M Herrington
- Department of Internal Medicine, Wake Forest University, Winston-Salem, NC 27157, USA
| | - Yue Wang
- To whom correspondence should be addressed.
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27
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Decano JL, Aikawa M, Singh SA. Promise of a Novel Bedside-to-Bench Paradigm: Can Percutaneous Coronary Intervention Proteomics Balloon Into Clinical Practice? Arterioscler Thromb Vasc Biol 2022; 42:865-867. [PMID: 35616034 DOI: 10.1161/atvbaha.122.317802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Julius L Decano
- From the Center for Interdisciplinary Cardiovascular Sciences (J.L.D., M.A., S.A.S.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Masanori Aikawa
- From the Center for Interdisciplinary Cardiovascular Sciences (J.L.D., M.A., S.A.S.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Center for Excellence in Vascular Biology (M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Channing Division of Network Medicine (M.A.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Sasha A Singh
- From the Center for Interdisciplinary Cardiovascular Sciences (J.L.D., M.A., S.A.S.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
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28
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Dawkins JF, Ehdaie A, Rogers R, Soetkamp D, Valle J, Holm K, Sanchez L, Tremmel I, Nawaz A, Shehata M, Wang X, Prakosa A, Yu J, Van Eyk JE, Trayanova N, Marbán E, Cingolani E. Biological substrate modification suppresses ventricular arrhythmias in a porcine model of chronic ischaemic cardiomyopathy. Eur Heart J 2022; 43:2139-2156. [PMID: 35262692 PMCID: PMC9649918 DOI: 10.1093/eurheartj/ehac042] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 08/15/2023] Open
Abstract
AIMS Cardiomyopathy patients are prone to ventricular arrhythmias (VA) and sudden cardiac death. Current therapies to prevent VA include radiofrequency ablation to destroy slowly conducting pathways of viable myocardium which support re-entry. Here, we tested the reverse concept, namely that boosting local tissue viability in zones of slow conduction might eliminate slow conduction and suppress VA in ischaemic cardiomyopathy. METHODS AND RESULTS Exosomes are extracellular vesicles laden with bioactive cargo. Exosomes secreted by cardiosphere-derived cells (CDCEXO) reduce scar and improve heart function after intramyocardial delivery. In a VA-prone porcine model of ischaemic cardiomyopathy, we injected CDCEXO or vehicle into zones of delayed conduction defined by electroanatomic mapping. Up to 1-month post-injection, CDCEXO, but not the vehicle, decreased myocardial scar, suppressed slowly conducting electrical pathways, and inhibited VA induction by programmed electrical stimulation. In silico reconstruction of electrical activity based on magnetic resonance images accurately reproduced the suppression of VA inducibility by CDCEXO. Strong anti-fibrotic effects of CDCEXO, evident histologically and by proteomic analysis from pig hearts, were confirmed in a co-culture assay of cardiomyocytes and fibroblasts. CONCLUSION Biological substrate modification by exosome injection may be worth developing as a non-destructive alternative to conventional ablation for the prevention of recurrent ventricular tachyarrhythmias.
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Affiliation(s)
- James F. Dawkins
- Smidt Heart Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA
| | - Ashkan Ehdaie
- Smidt Heart Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA
| | - Russell Rogers
- Smidt Heart Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA
| | - Daniel Soetkamp
- Smidt Heart Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA
| | - Jackelyn Valle
- Smidt Heart Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA
| | - Kevin Holm
- Smidt Heart Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA
| | - Lizbeth Sanchez
- Smidt Heart Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA
| | - Ileana Tremmel
- Smidt Heart Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA
| | - Asma Nawaz
- Smidt Heart Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA
| | - Michael Shehata
- Smidt Heart Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA
| | - Xunzhang Wang
- Smidt Heart Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA
| | - Adityo Prakosa
- Alliance for Cardiovascular Diagnostic and Treatment Innovation, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Joseph Yu
- Alliance for Cardiovascular Diagnostic and Treatment Innovation, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jennifer E Van Eyk
- Smidt Heart Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA
| | - Natalia Trayanova
- Alliance for Cardiovascular Diagnostic and Treatment Innovation, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Eduardo Marbán
- Smidt Heart Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA
| | - Eugenio Cingolani
- Smidt Heart Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA
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Lu Y, Wu CT, Parker SJ, Cheng Z, Saylor G, Van Eyk JE, Yu G, Clarke R, Herrington DM, Wang Y. COT: an efficient and accurate method for detecting marker genes among many subtypes. BIOINFORMATICS ADVANCES 2022; 2:vbac037. [PMID: 35673616 PMCID: PMC9163574 DOI: 10.1093/bioadv/vbac037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/10/2022] [Accepted: 05/16/2022] [Indexed: 01/27/2023]
Abstract
Motivation Ideally, a molecularly distinct subtype would be composed of molecular features that are expressed uniquely in the subtype of interest but in no others-so-called marker genes (MGs). MG plays a critical role in the characterization, classification or deconvolution of tissue or cell subtypes. We and others have recognized that the test statistics used by most methods do not exactly satisfy the MG definition and often identify inaccurate MG. Results We report an efficient and accurate data-driven method, formulated as a Cosine-based One-sample Test (COT) in scatter space, to detect MG among many subtypes using subtype expression profiles. Fundamentally different from existing approaches, the test statistic in COT precisely matches the mathematical definition of an ideal MG. We demonstrate the performance and utility of COT on both simulated and real gene expression and proteomics data. The open source Python/R tool will allow biologists to efficiently detect MG and perform a more comprehensive and unbiased molecular characterization of tissue or cell subtypes in many biomedical contexts. Nevertheless, COT complements not replaces existing methods. Availability and implementation The Python COT software with a detailed user's manual and a vignette are freely available at https://github.com/MintaYLu/COT. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Yingzhou Lu
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Chiung-Ting Wu
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Sarah J Parker
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Zuolin Cheng
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Georgia Saylor
- Department of Internal Medicine, Wake Forest University, Winston-Salem, NC 27157, USA
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Guoqiang Yu
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Robert Clarke
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - David M Herrington
- Department of Internal Medicine, Wake Forest University, Winston-Salem, NC 27157, USA
| | - Yue Wang
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA,To whom correspondence should be addressed.
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Kayashima Y, Clanton CA, Lewis AM, Sun X, Hiller S, Huynh P, Wilder J, Hagaman J, Li F, Maeda-Smithies N, Harris EN. Reduction of Stabilin-2 Contributes to a Protection Against Atherosclerosis. Front Cardiovasc Med 2022; 9:818662. [PMID: 35360009 PMCID: PMC8963368 DOI: 10.3389/fcvm.2022.818662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/16/2022] [Indexed: 01/05/2023] Open
Abstract
We have previously identified a novel atherosclerosis quantitative trait locus (QTL), Arch atherosclerosis 5 (Aath5), on mouse chromosome 10 by three-way QTL analyses between Apoe−/− mice on a DBA/2J, 129S6 and C57BL/6J background. The DBA/2J haplotype at the Aath5 locus was associated with smaller plaque size. One of the candidate genes underlying Aath5 was Stabilin-2 (Stab2), which encodes a clearance receptor for hyaluronan (HA) predominantly expressed in liver sinusoidal endothelial cells (LSECs). However, the role of Stab2 in atherosclerosis is unknown. A congenic line of Apoe−/− mice carrying Aath5 covering the Stab2DBA allele on a background of 129S6 confirmed the small reductions of atherosclerotic plaque development. To further determine whether Stab2 is an underlying gene for Aath5, we generated Stab2−/−Apoe−/− mice on a C57BL/6J background. When fed with a Western diet for 8 weeks, Stab2−/−Apoe−/− males developed approximately 30% smaller plaques than Stab2+/+Apoe−/− mice. HA was accumulated in circulation but not in major organs in the Stab2 deficient mice. STAB2-binding molecules that are involved in atherosclerosis, including acLDL, apoptotic cells, heparin and vWF were not likely the direct cause of the protection in the Stab2−/−Apoe−/− males. These data indicate that reduction of Stab2 is protective against atherosclerotic plaque development, and that Stab2 is a contributing gene underlying Aath5, although its effect is small. To test whether non-synonymous amino acid changes unique to DBA/2J affect the function of STAB2 protein, we made HEK293 cell lines expressing STAB2129 or STAB2DBA proteins, as well as STAB2129 proteins carrying each of five DBA-unique replacements that have been predicted to be deleterious. These mutant cells were capable of internalizing 125I -HA and DiI-acLDL similarly to the control cells. These results indicate that the amino acid changes unique to DBA/2J are not affecting the function of STAB2 protein, and support our previous observation that the reduced transcription of Stab2 in the liver sinusoid as a consequence of the insertion of a viral-derived sequence, intracisternal A particle, is the primary contributor to the athero-protection conferred by the DBA/2J allele.
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Affiliation(s)
- Yukako Kayashima
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- *Correspondence: Yukako Kayashima
| | - Connor A. Clanton
- Department of Biochemistry, University of Nebraska, Lincoln, NE, United States
| | - Amanda M. Lewis
- Department of Biochemistry, University of Nebraska, Lincoln, NE, United States
| | - Xinghui Sun
- Department of Biochemistry, University of Nebraska, Lincoln, NE, United States
| | - Sylvia Hiller
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Phillip Huynh
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jennifer Wilder
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - John Hagaman
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Feng Li
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Nobuyo Maeda-Smithies
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Edward N. Harris
- Department of Biochemistry, University of Nebraska, Lincoln, NE, United States
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The Application of Autopsy and Explanted Heart Samples in Scientific Research. Cardiovasc Pathol 2022; 59:107424. [DOI: 10.1016/j.carpath.2022.107424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/09/2022] [Accepted: 03/09/2022] [Indexed: 12/28/2022] Open
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Saril A, Kocaturk M, Shimada K, Uemura A, Akgün E, Levent P, Baykal AT, Prieto AM, Agudelo CF, Tanaka R, Ceron JJ, Koch J, Yilmaz Z. Serum Proteomic Changes in Dogs with Different Stages of Chronic Heart Failure. Animals (Basel) 2022; 12:ani12040490. [PMID: 35203200 PMCID: PMC8868296 DOI: 10.3390/ani12040490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/04/2022] [Accepted: 02/14/2022] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Canine MMVD is a progressive chronic disease with variable clinical signs, with some patients remaining completely asymptomatic while others develop CHF. Here, the aims of the pilot study were to evaluate serum proteins by proteomic analysis in dogs at different stages of chronic heart failure (CHF) due to degenerative mitral valve disease (MMVD), and how these proteins can change after a conventional treatment. Study revealed 157 different proteins; 11 were up- and 21 down-regulated at a statistically significant level in dogs with CHF compared to controls. Based on the bioinformatic analysis, protein–protein interactions between complement proteins, fibrinogen subtypes and others (albumin precursor, serpins, inter-alpha-trypsin inhibitor heavy chain, fetuin, clusterin, apolipoproteins, and alpha-glycoproteins) showed that pathophysiology of CHF seems to be more sophisticated than we had thought. These proteins are associated with several cellular, biologic, and metabolic processes such as immune-inflammatory responses, hemostasis, oxidative stress, and energy metabolism, which might be detrimental in the progression of canine CHF. Their molecular and biological functions as well as roles in the signaling pathways, such as inflammation, cadherin signaling, nicotinic acetylcholine receptor signaling and Wnt signaling make them possible biomarkers and therapeutic targets for the diagnosis and treatments in dogs with different stages of CHF. Abstract MMVD, the most common cause of CHF in dogs, is a chronic disease with variable clinical signs, with some patients remaining asymptomatic while others develop CHF. Here, we aimed to evaluate serum proteins by proteomic analysis in dogs at different stages of CHF due to MMVD, and proteome behaviors after conventional treatment. A total of 32 dogs were divided equally into four groups—stage A (healthy/controls), stage B2 (asymptomatic), stage C and stage D (symptomatic)—according to the ACVIM consensus. Serum proteomes were evaluated using LC/MS-based label-free differential proteome analysis. The study revealed 157 different proteins; 11 were up- and 21 down-regulated in dogs with CHF compared to controls. In stage B2 dogs, angiotensinogen (AGT) was up-regulated, but immunoglobulin iota chain-like, lipopolysaccharide-binding protein, and carboxypeptidase (CPN) were down-regulated. In stage C dogs, complement C3 (C3) and inter-alpha-trypsin inhibitor heavy chain were up-regulated, but hemopexin, and actin-cytoplasmic-1 (ACT-1) were down-regulated. In stage D dogs, AGT was up-regulated, whereas tetranectin, paraoxonase-1, adiponectin and ACT-1 were down-regulated. A decrease in CPN, C3 and AGT and an increase in ACT-1 were observed after treatment of dogs in stage C. This pilot study identified that dogs at different stages of CHF show different serum protein composition which has potential to be biomarker for diagnose and treatment monitorization.
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Affiliation(s)
- Ahmet Saril
- Department of Internal Medicine, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey; (A.S.); (M.K.); (P.L.); (Z.Y.)
| | - Meric Kocaturk
- Department of Internal Medicine, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey; (A.S.); (M.K.); (P.L.); (Z.Y.)
| | - Kazumi Shimada
- Department of Veterinary Surgery, Faculty of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan;
- Correspondence:
| | - Akiko Uemura
- Laboratory of Veterinary Surgery, Department of Clinical Veterinary Medicine, Division of Veterinary Research, Obihiro University of Agriculture and Veterinary Medicine, Sapporo 080-8555, Japan;
| | - Emel Akgün
- Department of Medical Biochemistry, Acibadem University School of Medicine, Istanbul 34750, Turkey; (E.A.); (A.T.B.)
| | - Pinar Levent
- Department of Internal Medicine, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey; (A.S.); (M.K.); (P.L.); (Z.Y.)
| | - Ahmet Tarik Baykal
- Department of Medical Biochemistry, Acibadem University School of Medicine, Istanbul 34750, Turkey; (E.A.); (A.T.B.)
| | - Alberto Muñoz Prieto
- Clinic for Internal Diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000 Zagreb, Croatia;
| | - Carlos Fernando Agudelo
- Small Animal Clinic, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Palackého Tř. 1946/1, 612 42 Brno, Czech Republic;
| | - Ryou Tanaka
- Department of Veterinary Surgery, Faculty of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan;
| | - Jose Joaquin Ceron
- Interdisciplinary Laboratory of Clinical Analysis, Interlab-UMU, Regional Campus of International Excellence, University of Murcia, Espinardo, 30100 Murcia, Spain;
| | - Jorgen Koch
- Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg, Denmark;
| | - Zeki Yilmaz
- Department of Internal Medicine, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey; (A.S.); (M.K.); (P.L.); (Z.Y.)
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Chen L, Wu CT, Lin CH, Dai R, Liu C, Clarke R, Yu G, Van Eyk JE, Herrington DM, Wang Y. swCAM: estimation of subtype-specific expressions in individual samples with unsupervised sample-wise deconvolution. Bioinformatics 2022; 38:1403-1410. [PMID: 34904628 PMCID: PMC8826012 DOI: 10.1093/bioinformatics/btab839] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 10/30/2021] [Accepted: 12/10/2021] [Indexed: 02/04/2023] Open
Abstract
MOTIVATION Complex biological tissues are often a heterogeneous mixture of several molecularly distinct cell subtypes. Both subtype compositions and subtype-specific (STS) expressions can vary across biological conditions. Computational deconvolution aims to dissect patterns of bulk tissue data into subtype compositions and STS expressions. Existing deconvolution methods can only estimate averaged STS expressions in a population, while many downstream analyses such as inferring co-expression networks in particular subtypes require subtype expression estimates in individual samples. However, individual-level deconvolution is a mathematically underdetermined problem because there are more variables than observations. RESULTS We report a sample-wise Convex Analysis of Mixtures (swCAM) method that can estimate subtype proportions and STS expressions in individual samples from bulk tissue transcriptomes. We extend our previous CAM framework to include a new term accounting for between-sample variations and formulate swCAM as a nuclear-norm and ℓ2,1-norm regularized matrix factorization problem. We determine hyperparameter values using cross-validation with random entry exclusion and obtain a swCAM solution using an efficient alternating direction method of multipliers. Experimental results on realistic simulation data show that swCAM can accurately estimate STS expressions in individual samples and successfully extract co-expression networks in particular subtypes that are otherwise unobtainable using bulk data. In two real-world applications, swCAM analysis of bulk RNASeq data from brain tissue of cases and controls with bipolar disorder or Alzheimer's disease identified significant changes in cell proportion, expression pattern and co-expression module in patient neurons. Comparative evaluation of swCAM versus peer methods is also provided. AVAILABILITY AND IMPLEMENTATION The R Scripts of swCAM are freely available at https://github.com/Lululuella/swCAM. A user's guide and a vignette are provided. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Lulu Chen
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Chiung-Ting Wu
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Chia-Hsiang Lin
- Department of Electrical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Rujia Dai
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Chunyu Liu
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Robert Clarke
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Guoqiang Yu
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - David M Herrington
- Department of Internal Medicine, Wake Forest University, Winston-Salem, NC 27157, USA
| | - Yue Wang
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
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Xing C, Jiang Z, Wang Y. Downregulation of NAGLU in VEC Increases Abnormal Accumulation of Lysosomes and Represents a Predictive Biomarker in Early Atherosclerosis. Front Cell Dev Biol 2022; 9:797047. [PMID: 35155448 PMCID: PMC8826576 DOI: 10.3389/fcell.2021.797047] [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: 10/18/2021] [Accepted: 12/27/2021] [Indexed: 12/23/2022] Open
Abstract
Cardiovascular diseases (CVDs), predominantly caused by atherosclerosis (AS), are the leading cause of mortality worldwide. Although a great number of previous studies have attempted to reveal the molecular mechanism of AS, the underlying mechanism has not been fully elucidated. The aberrant expression profiling of vascular endothelial cells (VECs) gene in early atherosclerosis (EAS) was analyzed according to the dataset (GSE132651) downloaded from the Gene Expression Omnibus (GEO) database. We primarily performed functional annotation analysis on the downregulated genes (DRGs). We further identified that α-N-acetylglucosaminidase (NAGLU), one of the DRGs, played a critical role in the progression of EAS. NAGLU is a key enzyme for the degradation of heparan sulfate (HS), and its deficiency could cause lysosomal accumulation and lead to dysfunctions of VECs. We found that siRNA knockdown of NAGLU in human umbilical vein endothelial cell (HUVEC) aggravated the abnormal accumulation of lysosomes and HS. In addition, the expression of NAGLU was reduced in the EAS model constructed by ApoE−/- mice. Furthermore, we also showed that heparin-binding EGF-like growth factor (HB-EGF) protein was upregulated while NAGLU knockdown in HUVEC could specifically bind to vascular endothelial growth factor receptor 2 (VEGFR2) and promote its phosphorylation, ultimately activating the phosphorylation levels of extracellular signal-regulated kinases (ERKs). However, the application of selective VEGFR2 and ERKs inhibitors, SU5614 and PD98059, respectively, could reverse the abnormal lysosomal storage caused by NAGLU knockdown. These results indicated that downregulation of NAGLU in HUVEC increases the abnormal accumulation of lysosomes and may be a potential biomarker for the diagnosis of EAS.
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Affiliation(s)
- Changchang Xing
- Department of Cardiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhongyi Jiang
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Wang
- Department of Cardiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Yi Wang,
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Comparative assessment and novel strategy on methods for imputing proteomics data. Sci Rep 2022; 12:1067. [PMID: 35058491 PMCID: PMC8776850 DOI: 10.1038/s41598-022-04938-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 01/04/2022] [Indexed: 11/09/2022] Open
Abstract
Missing values are a major issue in quantitative proteomics analysis. While many methods have been developed for imputing missing values in high-throughput proteomics data, a comparative assessment of imputation accuracy remains inconclusive, mainly because mechanisms contributing to true missing values are complex and existing evaluation methodologies are imperfect. Moreover, few studies have provided an outlook of future methodological development. We first re-evaluate the performance of eight representative methods targeting three typical missing mechanisms. These methods are compared on both simulated and masked missing values embedded within real proteomics datasets, and performance is evaluated using three quantitative measures. We then introduce fused regularization matrix factorization, a low-rank global matrix factorization framework, capable of integrating local similarity derived from additional data types. We also explore a biologically-inspired latent variable modeling strategy—convex analysis of mixtures—for missing value imputation and present preliminary experimental results. While some winners emerged from our comparative assessment, the evaluation is intrinsically imperfect because performance is evaluated indirectly on artificial missing or masked values not authentic missing values. Nevertheless, we show that our fused regularization matrix factorization provides a novel incorporation of external and local information, and the exploratory implementation of convex analysis of mixtures presents a biologically plausible new approach.
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Buja LM, Zhao B, Segura A, Lelenwa L, McDonald M, Michaud K. Cardiovascular pathology: guide to practice and training. Cardiovasc Pathol 2022. [DOI: 10.1016/b978-0-12-822224-9.00001-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Saddic L, Orosco A, Guo D, Milewicz DM, Troxlair D, Heide RV, Herrington D, Wang Y, Azizzadeh A, Parker SJ. Proteomic analysis of descending thoracic aorta identifies unique and universal signatures of aneurysm and dissection. JVS Vasc Sci 2022; 3:85-181. [PMID: 35280433 PMCID: PMC8914561 DOI: 10.1016/j.jvssci.2022.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/05/2022] [Indexed: 01/05/2023] Open
Abstract
Objective Methods Results Conclusions Diseases of the descending thoracic aorta such as aneurysms and dissections carry a high degree of morbidity and mortality. At present, a complete understanding is still lacking of the genetics that drive these diseases and why some aortic segments dissect in the presence or absence of an aneurysm. We compared and contrasted the whole proteome expression of descending aortas from patients with normal, dissected, aneurysmal, and aneurysmal with dissected pathology aortic tissue. We uncovered potential tissue markers that might serve as future targets for therapy or predictors of disease progression.
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Affiliation(s)
- Louis Saddic
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, Calif
| | - Amanda Orosco
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, Calif
| | - Dongchuan Guo
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Tex
| | - Dianna M. Milewicz
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Tex
| | - Dana Troxlair
- Department of Pathology, Louisiana State University, New Orleans, La
| | | | - David Herrington
- Department of Cardiovascular Medicine, Wake Forest University, Winston-Salem, NC
| | - Yue Wang
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, Va
| | - Ali Azizzadeh
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, Calif
| | - Sarah J. Parker
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, Calif
- Correspondence: Sarah J. Parker, PhD, Department of Cardiology, Smidt Heart Institute, Cedars Sinai Medical Center, AHSP A9228, 8700 Beverly Blvd, Los Angeles, CA 90048
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Leopold JA. Personalizing treatments for patients based on cardiovascular phenotyping. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2022; 7:4-16. [PMID: 36778892 PMCID: PMC9913616 DOI: 10.1080/23808993.2022.2028548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Introduction Cardiovascular disease persists as the leading cause of death worldwide despite continued advances in diagnostics and therapeutics. Our current approach to patients with cardiovascular disease is rooted in reductionism, which presupposes that all patients share a similar phenotype and will respond the same to therapy; however, this is unlikely as cardiovascular diseases exhibit complex heterogeneous phenotypes. Areas covered With the advent of high-throughput platforms for omics testing, phenotyping cardiovascular diseases has advanced to incorporate large-scale molecular data with classical history, physical examination, and laboratory results. Findings from genomics, proteomics, and metabolomics profiling have been used to define more precise cardiovascular phenotypes and predict adverse outcomes in population-based and disease-specific patient cohorts. These molecular data have also been utilized to inform drug efficacy based on a patient's unique phenotype. Expert opinion Multiscale phenotyping of cardiovascular disease has revealed diversity among patients that can be used to personalize pharmacotherapies and predict outcomes. Nonetheless, precision phenotyping for cardiovascular disease remains a nascent field that has not yet translated into widespread clinical practice despite its many potential advantages for patient care. Future endeavors that demonstrate improved pharmacotherapeutic responses and associated reduction in adverse events will facilitate mainstream adoption of precision cardiovascular phenotyping.
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Affiliation(s)
- Jane A. Leopold
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, 77 Ave Louis Pasteur, NRB0630K, Boston, Massachusetts, USA
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González-Arostegui LG, Rubio CP, Cerón JJ, Tvarijonaviciute A, Muñoz-Prieto A. Proteomics in dogs: a systematic review. Res Vet Sci 2021; 143:107-114. [PMID: 35007798 DOI: 10.1016/j.rvsc.2021.12.026] [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: 10/11/2021] [Revised: 12/17/2021] [Accepted: 12/29/2021] [Indexed: 10/19/2022]
Abstract
Proteomic analysis is having a rapid development as a method for the detection of biomarkers of diseases in dogs. Dogs in addition to their importance as companion animals, serve as important animal models for research. This study aims to systematically review evidence regarding the studies performed in proteomics in dogs, and specifically those made in serum, saliva, urine and/or plasma. Information searched in October 2020, January 2021 and August 2021, for English language publications of the last decade (2010-2020) were obtained from electronic databases. Screening, data extraction and risk of bias assessment were undertaken by two investigators. The risk of bias was evaluated using the Review Manager (RevMan 5) tool. Meta-analysis and case report studies were not included in this review. Through the screening process a total of 557 publications were identified after the removal of duplicates. Out of these, 65 were fully evaluated and 44 of these were included in the review. Most studies evaluated the proteome of disease and compared it with a healthy population, and most of the articles included were made on serum, followed by saliva. The overall risk of bias for all studies was high, due to an absence in the generation of random sequence. Overall proteomic analysis has allowed the discovery of new physiopathological pathways of diseases and potential biomarkers in the dog, which are addressed in this review.
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Affiliation(s)
- Luis Guillermo González-Arostegui
- Interdisciplinary Laboratory of Clinical Analysis (Interlab-UMU), Veterinary School, Campus of Excellence Mare Nostrum, University of Murcia, Campus Espinardo, 30100 Murcia, Spain
| | - Camila Peres Rubio
- Interdisciplinary Laboratory of Clinical Analysis (Interlab-UMU), Veterinary School, Campus of Excellence Mare Nostrum, University of Murcia, Campus Espinardo, 30100 Murcia, Spain; Department of Animal and Food Science, School of Veterinary Science, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - José Joaquín Cerón
- Interdisciplinary Laboratory of Clinical Analysis (Interlab-UMU), Veterinary School, Campus of Excellence Mare Nostrum, University of Murcia, Campus Espinardo, 30100 Murcia, Spain
| | - Asta Tvarijonaviciute
- Interdisciplinary Laboratory of Clinical Analysis (Interlab-UMU), Veterinary School, Campus of Excellence Mare Nostrum, University of Murcia, Campus Espinardo, 30100 Murcia, Spain.
| | - Alberto Muñoz-Prieto
- Clinic for Internal Diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000 Zagreb, Croatia
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Proteomic Studies of Blood and Vascular Wall in Atherosclerosis. Int J Mol Sci 2021; 22:ijms222413267. [PMID: 34948066 PMCID: PMC8707794 DOI: 10.3390/ijms222413267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/02/2021] [Accepted: 12/07/2021] [Indexed: 12/12/2022] Open
Abstract
The review is devoted to the analysis of literature data related to the role of proteomic studies in the study of atherosclerotic cardiovascular diseases. Diagnosis of patients with atherosclerotic plaques before clinical manifestations is an arduous task. The review presents the results of research on the new proteomic potential biomarkers of coronary heart disease, coronary atherosclerosis, acute coronary syndrome, myocardial infarction, carotid artery atherosclerosis. Also, the analysis of literature data on proteomic studies of the vascular wall was carried out. To assess the involvement of proteins in the pathological process of atherosclerosis, it is important to investigate the specific relationships between proteins in the arteries, expression and concentration of proteins. The development of proteomic technologies has made it possible to analyse the number of proteins associated with the development of the disease. Analysis of the proteomic profile of the vascular wall in atherosclerosis can help to detect possible diagnostically significant protein structures or potential biomarkers of the disease and develop novel approaches to the diagnosis of atherosclerosis and its complications.
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Cathepsin C Is Involved in Macrophage M1 Polarization via p38/MAPK Pathway in Sudden Cardiac Death. Cardiovasc Ther 2021; 2021:6139732. [PMID: 34737793 PMCID: PMC8536465 DOI: 10.1155/2021/6139732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/27/2021] [Indexed: 12/28/2022] Open
Abstract
This study was aimed at identifying molecular markers associated with the pathogenesis of sudden cardiac death (SCD). It provides a proteomic analysis of human left anterior descending coronary artery from subjects diagnosed with SCD through histological examination and cases of nondisease accidental deaths through autopsy. A total of 2784 proteins were obtained from label-free quantitative proteomic analysis. This included a total of 265 differential proteins which were involved in SCD-related processes, such as inflammation, muscle system process regulation, metal ion transport, and lysosomal pathway. Western blotting was carried out to measure the expressions of cathepsin C (CTSC), focal adhesion kinase (FAK), p-FAK, and proteins related to the p38/MAPK signaling pathway, whereas immunohistochemistry was performed to determine the localization and expression of CTSC, TNF-α, and CD206 in arterial tissues. It was found that CTSC were the most expressed proteins with a significant upward trend in SCD cases. Besides, CTSC regulated macrophage polarization to M1 through the FAK-induced p38/MAPK signaling pathway. This promoted the release of inflammatory factors and eventually increased the inflammatory response. In conclusion, this study implies that CTSC may be one of the key molecular targets for promoting macrophage M1 polarization in SCD, which may provide new therapeutic insights into the treatment of inflammatory diseases.
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Forbes T, Pauza AG, Adams JC. In the balance: how do thrombospondins contribute to the cellular pathophysiology of cardiovascular disease? Am J Physiol Cell Physiol 2021; 321:C826-C845. [PMID: 34495764 DOI: 10.1152/ajpcell.00251.2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Thrombospondins (TSPs) are multidomain, secreted proteins that associate with cell surfaces and extracellular matrix. In mammals, there is a large body of data on functional roles of various TSP family members in cardiovascular disease (CVD), including stroke, cardiac remodeling and fibrosis, atherosclerosis, and aortic aneurysms. Coding single nucleotide polymorphisms (SNPs) of TSP1 or TSP4 are also associated with increased risk of several forms of CVD. Whereas interactions and functional effects of TSPs on a variety of cell types have been studied extensively, the molecular and cellular basis for the differential effects of the SNPs remains under investigation. Here, we provide an integrative review on TSPs, their roles in CVD and cardiovascular cell physiology, and known properties and mechanisms of TSP SNPs relevant to CVD. In considering recent expansions to knowledge of the fundamental cellular roles and mechanisms of TSPs, as well as the effects of wild-type and variant TSPs on cells of the cardiovascular system, we aim to highlight knowledge gaps and areas for future research or of translational potential.
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Affiliation(s)
- Tessa Forbes
- Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Audrys G Pauza
- Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Josephine C Adams
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
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Ahmed M, Lai TH, Kim DR. A Small Fraction of Progenitors Differentiate Into Mature Adipocytes by Escaping the Constraints on the Cell Structure. Front Cell Dev Biol 2021; 9:753042. [PMID: 34708046 PMCID: PMC8542793 DOI: 10.3389/fcell.2021.753042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/10/2021] [Indexed: 11/13/2022] Open
Abstract
Differentiating 3T3-L1 pre-adipocytes are a mixture of non-identical culture cells. It is vital to identify the cell types that respond to the induction stimulus to understand the pre-adipocyte potential and the mature adipocyte behavior. To test this hypothesis, we deconvoluted the gene expression profiles of the cell culture of MDI-induced 3T3-L1 cells. Then we estimated the fractions of the sub-populations and their changes in time. We characterized the sub-populations based on their specific expression profiles. Initial cell cultures comprised three distinct phenotypes. A small fraction of the starting cells responded to the induction and developed into mature adipocytes. Unresponsive cells were probably under structural constraints or were committed to differentiating into alternative phenotypes. Using the same population gene markers, similar proportions were found in induced human primary adipocyte cell cultures. The three sub-populations had diverse responses to treatment with various drugs and compounds. Only the response of the maturating sub-population resembled that estimated from the profiles of the mixture. We then showed that even at a low division rate, a small fraction of cells could increase its share in a dynamic two-populations model. Finally, we used a cell cycle expression index to validate that model. To sum, pre-adipocytes are a mixture of different cells of which a limited fraction become mature adipocytes.
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Affiliation(s)
- Mahmoud Ahmed
- Department of Biochemistry and Convergence Medical Sciences, Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, South Korea
| | - Trang Huyen Lai
- Department of Biochemistry and Convergence Medical Sciences, Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, South Korea
| | - Deok Ryong Kim
- Department of Biochemistry and Convergence Medical Sciences, Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, South Korea
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44
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Grootaert MOJ, Bennett MR. Vascular smooth muscle cells in atherosclerosis: time for a re-assessment. Cardiovasc Res 2021; 117:2326-2339. [PMID: 33576407 PMCID: PMC8479803 DOI: 10.1093/cvr/cvab046] [Citation(s) in RCA: 151] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 02/04/2021] [Indexed: 12/12/2022] Open
Abstract
Vascular smooth muscle cells (VSMCs) are key participants in both early and late-stage atherosclerosis. VSMCs invade the early atherosclerotic lesion from the media, expanding lesions, but also forming a protective fibrous cap rich in extracellular matrix to cover the 'necrotic' core. Hence, VSMCs have been viewed as plaque-stabilizing, and decreased VSMC plaque content-often measured by expression of contractile markers-associated with increased plaque vulnerability. However, the emergence of lineage-tracing and transcriptomic studies has demonstrated that VSMCs comprise a much larger proportion of atherosclerotic plaques than originally thought, demonstrate multiple different phenotypes in vivo, and have roles that might be detrimental. VSMCs down-regulate contractile markers during atherosclerosis whilst adopting alternative phenotypes, including macrophage-like, foam cell-like, osteochondrogenic-like, myofibroblast-like, and mesenchymal stem cell-like. VSMC phenotypic switching can be studied in tissue culture, but also now in the media, fibrous cap and deep-core region, and markedly affects plaque formation and markers of stability. In this review, we describe the different VSMC plaque phenotypes and their presumed cellular and paracrine functions, the regulatory mechanisms that control VSMC plasticity, and their impact on atherogenesis and plaque stability.
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Affiliation(s)
- Mandy O J Grootaert
- Division of Cardiovascular Medicine, University of Cambridge, Box 110, ACCI, Addenbrookes Hospital, CB2 0QQ Cambridge, UK
| | - Martin R Bennett
- Division of Cardiovascular Medicine, University of Cambridge, Box 110, ACCI, Addenbrookes Hospital, CB2 0QQ Cambridge, UK
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Lanzer P, Hannan FM, Lanzer JD, Janzen J, Raggi P, Furniss D, Schuchardt M, Thakker R, Fok PW, Saez-Rodriguez J, Millan A, Sato Y, Ferraresi R, Virmani R, St Hilaire C. Medial Arterial Calcification: JACC State-of-the-Art Review. J Am Coll Cardiol 2021; 78:1145-1165. [PMID: 34503684 PMCID: PMC8439554 DOI: 10.1016/j.jacc.2021.06.049] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 01/07/2023]
Abstract
Medial arterial calcification (MAC) is a chronic systemic vascular disorder distinct from atherosclerosis that is frequently but not always associated with diabetes mellitus, chronic kidney disease, and aging. MAC is also a part of more complex phenotypes in numerous less common diseases. The hallmarks of MAC include disseminated and progressive precipitation of calcium phosphate within the medial layer, a prolonged and clinically silent course, and compromise of hemodynamics associated with chronic limb-threatening ischemia. MAC increases the risk of complications during vascular interventions and mitigates their outcomes. With the exception of rare monogenetic defects affecting adenosine triphosphate metabolism, MAC pathogenesis remains unknown, and causal therapy is not available. Implementation of genetics and omics-based approaches in research recognizing the critical importance of calcium phosphate thermodynamics holds promise to unravel MAC molecular pathogenesis and to provide guidance for therapy. The current state of knowledge concerning MAC is reviewed, and future perspectives are outlined.
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Affiliation(s)
- Peter Lanzer
- Middle German Heart Center-Bitterfeld, Bitterfeld-Wolfen Health Care Center, Bitterfeld, Germany.
| | - Fadil M Hannan
- Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Jan D Lanzer
- Institute for Computational Biomedicine, Bioquant, Faculty of Medicine, Heidelberg University, Heidelberg, Germany; Department of Internal Medicine II, Heidelberg University Hospital, Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Heidelberg, Germany
| | | | - Paolo Raggi
- Division of Cardiology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Dominic Furniss
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Mirjam Schuchardt
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität and Humboldt Universität Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - Rajesh Thakker
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Pak-Wing Fok
- Department of Mathematical Sciences, University of Delaware, Newark, Delaware, USA
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Bioquant, Faculty of Medicine, Heidelberg University, Heidelberg, Germany
| | - Angel Millan
- Institute of Materials Science, University of Zaragoza, Zaragoza, Spain
| | - Yu Sato
- CVPath Institute, Gaithersburg, Maryland, USA
| | | | | | - Cynthia St Hilaire
- Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Abudupataer M, Zhu S, Yan S, Xu K, Zhang J, Luo S, Ma W, Alam MF, Tang Y, Huang H, Chen N, Wang L, Yan G, Li J, Lai H, Wang C, Zhu K, Zhang W. Aorta smooth muscle-on-a-chip reveals impaired mitochondrial dynamics as a therapeutic target for aortic aneurysm in bicuspid aortic valve disease. eLife 2021; 10:69310. [PMID: 34486519 PMCID: PMC8451027 DOI: 10.7554/elife.69310] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 08/18/2021] [Indexed: 12/11/2022] Open
Abstract
Background: Bicuspid aortic valve (BAV) is the most common congenital cardiovascular disease in general population and is frequently associated with the development of thoracic aortic aneurysm (TAA). There is no effective strategy to intervene with TAA progression due to an incomplete understanding of the pathogenesis. Insufficiency of NOTCH1 expression is highly related to BAV-TAA, but the underlying mechanism remains to be clarified. Methods: A comparative proteomics analysis was used to explore the biological differences between non-diseased and BAV-TAA aortic tissues. A microfluidics-based aorta smooth muscle-on-a-chip model was constructed to evaluate the effect of NOTCH1 deficiency on contractile phenotype and mitochondrial dynamics of human aortic smooth muscle cells (HAoSMCs). Results: Protein analyses of human aortic tissues showed the insufficient expression of NOTCH1 and impaired mitochondrial dynamics in BAV-TAA. HAoSMCs with NOTCH1-knockdown exhibited reduced contractile phenotype and were accompanied by attenuated mitochondrial fusion. Furthermore, we identified that mitochondrial fusion activators (leflunomide and teriflunomide) or mitochondrial fission inhibitor (Mdivi-1) partially rescued the disorders of mitochondrial dynamics in HAoSMCs derived from BAV-TAA patients. Conclusions: The aorta smooth muscle-on-a-chip model simulates the human pathophysiological parameters of aorta biomechanics and provides a platform for molecular mechanism studies of aortic disease and related drug screening. This aorta smooth muscle-on-a-chip model and human tissue proteomic analysis revealed that impaired mitochondrial dynamics could be a potential therapeutic target for BAV-TAA. Funding: National Key R and D Program of China, National Natural Science Foundation of China, Shanghai Municipal Science and Technology Major Project, Shanghai Science and Technology Commission, and Shanghai Municipal Education Commission. To function properly, the heart must remain a one-way system, pumping out oxygenated blood into the aorta – the largest artery in the body – so it can be distributed across the organism. The aortic valve, which sits at the entrance of the aorta, is a key component of this system. Its three flaps (or ‘cusps’) are pushed open when the blood exits the heart, and they shut tightly so it does not flow back in the incorrect direction. Nearly 1.4% of people around the world are born with ‘bicuspid’ aortic valves that only have two flaps. These valves may harden or become leaky, forcing the heart to work harder. This defect is also associated with bulges on the aorta which progressively weaken the artery, sometimes causing it to rupture. Open-heart surgery is currently the only way to treat these bulges (or ‘aneurysms’), as no drug exists that could slow down disease progression. This is partly because the biological processes involved in the aneurysms worsening and bursting open is unclear. Recent studies have highlighted that many individuals with bicuspid aortic valves also have lower levels of a protein known as NOTCH1, which plays a key signalling role for cells. Problems in the mitochondria – the structures that power up a cell – are also observed. However, it is not known how these findings are connected or linked with the aneurysms developing. To answer this question, Abudupataer et al. analyzed the proteins present in diseased and healthy aortic muscle cells, confirming a lower production of NOTCH1 and impaired mitochondria in diseased tissues. They also created an ‘aorta-on-a-chip’ model where aortic muscle cells were grown in the laboratory under conditions resembling those found in the body – including the rhythmic strain that the aorta is under because of the heart beating. Abudupataer et al. then reduced NOTCH1 levels in healthy samples, which made the muscle tissue less able to contract and reduced the activity of the mitochondria. Applying drugs that tweak mitochondrial activity helped tissues from patients with bicuspid aortic valves to work better. These compounds could potentially benefit individuals with deficient aortic valves, but experiments in animals and clinical trials would be needed first to confirm the results and assess safety. The aorta-on-a-chip model developed by Abudupataer et al. also provides a platform to screen for drugs and examine the molecular mechanisms at play in aortic diseases.
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Affiliation(s)
- Mieradilijiang Abudupataer
- Department of Cardiac Surgery and Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shichao Zhu
- Department of Cardiac Surgery and Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shiqiang Yan
- Institutes of Biomedical Sciences and the Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai, China
| | - Kehua Xu
- Institutes of Biomedical Sciences and the Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jingjing Zhang
- Institutes of Biomedical Sciences and the Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shaman Luo
- Institutes of Biomedical Sciences and the Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai, China.,The State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China
| | - Wenrui Ma
- Department of Cardiac Surgery and Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Md Fazle Alam
- Institutes of Biomedical Sciences and the Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai, China.,The State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China
| | - Yuyi Tang
- Institutes of Biomedical Sciences and the Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hui Huang
- Institutes of Biomedical Sciences and the Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai, China
| | - Nan Chen
- Department of Cardiac Surgery and Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Li Wang
- Institutes of Biomedical Sciences and the Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai, China
| | - Guoquan Yan
- Institutes of Biomedical Sciences and the Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jun Li
- Department of Cardiac Surgery and Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China.,Institutes of Biomedical Sciences and the Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hao Lai
- Department of Cardiac Surgery and Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chunsheng Wang
- Department of Cardiac Surgery and Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Kai Zhu
- Department of Cardiac Surgery and Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Weijia Zhang
- Department of Cardiac Surgery and Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China.,Institutes of Biomedical Sciences and the Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai, China.,The State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China
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Doran S, Arif M, Lam S, Bayraktar A, Turkez H, Uhlen M, Boren J, Mardinoglu A. Multi-omics approaches for revealing the complexity of cardiovascular disease. Brief Bioinform 2021; 22:bbab061. [PMID: 33725119 PMCID: PMC8425417 DOI: 10.1093/bib/bbab061] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/20/2021] [Accepted: 02/05/2021] [Indexed: 02/06/2023] Open
Abstract
The development and progression of cardiovascular disease (CVD) can mainly be attributed to the narrowing of blood vessels caused by atherosclerosis and thrombosis, which induces organ damage that will result in end-organ dysfunction characterized by events such as myocardial infarction or stroke. It is also essential to consider other contributory factors to CVD, including cardiac remodelling caused by cardiomyopathies and co-morbidities with other diseases such as chronic kidney disease. Besides, there is a growing amount of evidence linking the gut microbiota to CVD through several metabolic pathways. Hence, it is of utmost importance to decipher the underlying molecular mechanisms associated with these disease states to elucidate the development and progression of CVD. A wide array of systems biology approaches incorporating multi-omics data have emerged as an invaluable tool in establishing alterations in specific cell types and identifying modifications in signalling events that promote disease development. Here, we review recent studies that apply multi-omics approaches to further understand the underlying causes of CVD and provide possible treatment strategies by identifying novel drug targets and biomarkers. We also discuss very recent advances in gut microbiota research with an emphasis on how diet and microbial composition can impact the development of CVD. Finally, we present various biological network analyses and other independent studies that have been employed for providing mechanistic explanation and developing treatment strategies for end-stage CVD, namely myocardial infarction and stroke.
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Affiliation(s)
- Stephen Doran
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, SE1 9RT, United Kingdom
| | - Muhammad Arif
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Simon Lam
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, SE1 9RT, United Kingdom
| | - Abdulahad Bayraktar
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, SE1 9RT, United Kingdom
| | - Hasan Turkez
- Department of Medical Biology, Faculty of Medicine, Atatürk University, Erzurum, Turkey
| | - Mathias Uhlen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jan Boren
- Institute of Medicine, Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital Gothenburg, Sweden
| | - Adil Mardinoglu
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, SE1 9RT, United Kingdom
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
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Molecular Dysfunctions of Mitochondria-Associated Endoplasmic Reticulum Contacts in Atherosclerosis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:2424509. [PMID: 34336087 PMCID: PMC8321742 DOI: 10.1155/2021/2424509] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 07/11/2021] [Indexed: 02/05/2023]
Abstract
Atherosclerosis is a chronic lipid-driven inflammatory disease that results in the formation of lipid-rich and immune cell-rich plaques in the arterial wall, which has high morbidity and mortality in the world. The mechanism of atherosclerosis is still unclear now. Potential hypotheses involved in atherosclerosis are chronic inflammation theory, lipid percolation theory, mononuclear-macrophage theory, endothelial cell (EC) injury theory, and smooth muscle cell (SMC) mutation theory. Changes of phospholipids, glucose, critical proteins, etc. on mitochondria-associated endoplasmic reticulum membrane (MAM) can cause the progress of atherosclerosis. This review describes the structural and functional interaction between mitochondria and endoplasmic reticulum (ER) and explains the role of critical molecules in the structure of MAM during atherosclerosis.
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Applying Proteomics and Integrative "Omics" Strategies to Decipher the Chronic Kidney Disease-Related Atherosclerosis. Int J Mol Sci 2021; 22:ijms22147492. [PMID: 34299112 PMCID: PMC8305100 DOI: 10.3390/ijms22147492] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 02/07/2023] Open
Abstract
Patients with chronic kidney disease (CKD) are at increased risk of atherosclerosis and premature mortality, mainly due to cardiovascular events. However, well-known risk factors, which promote “classical” atherosclerosis are alone insufficient to explain the high prevalence of atherosclerosis-related to CKD (CKD-A). The complexity of the molecular mechanisms underlying the acceleration of CKD-A is still to be defied. To obtain a holistic picture of these changes, comprehensive proteomic approaches have been developed including global protein profiling followed by functional bioinformatics analyses of dysregulated pathways. Furthermore, proteomics surveys in combination with other “omics” techniques, i.e., transcriptomics and metabolomics as well as physiological assays provide a solid ground for interpretation of observed phenomena in the context of disease pathology. This review discusses the comprehensive application of various “omics” approaches, with emphasis on proteomics, to tackle the molecular mechanisms underlying CKD-A progression. We summarize here the recent findings derived from global proteomic approaches and underline the potential of utilizing integrative systems biology, to gain a deeper insight into the pathogenesis of CKD-A and other disorders.
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