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author:("Ma, longgang")
1.  Using systems biology approaches to understand cardiac inflammation and extracellular matrix remodeling in the setting of myocardial infarction 
Inflammation and extracellular matrix (ECM) remodeling are important components regulating the response of the left ventricle (LV) to myocardial infarction (MI). Significant cellular and molecular level contributors can be identified by analyzing data acquired through high-throughput genomic and proteomic technologies that provide expression levels for thousands of genes and proteins. Large scale data provide both temporal and spatial information that need to be analyzed and interpreted using systems biology approaches in order to integrate this information into dynamic models that predict and explain mechanisms of cardiac healing post-MI. In this review, we summarize the systems biology approaches needed to computationally simulate post-MI remodeling, including data acquisition, data analysis for biomarker classification and identification, data integration to build dynamic models, and data interpretation for biological functions. An example for applying a systems biology approach to ECM remodeling is presented as a reference illustration.
PMCID: PMC3990867  PMID: 24741709
mathematical modeling; differential equations; biclustering; myocardial infarction; matrix metalloproteinase; LV remodeling; review
2.  Negative Elongation Factor Controls Energy Homeostasis in Cardiomyocytes 
Cell reports  2014;7(1):79-85.
SUMMARY
Negative elongation factor (NELF) is known to enforce promoter-proximal pausing of RNA polymerase II (Pol II), a pervasive phenomenon observed across multicellular genomes. However, the physiological impact of NELF on tissue homeostasis remains unclear. Here, we show that whole-body conditional deletion of the B subunit of NELF (NELF-B) in adult mice results in cardiomyopathy and impaired response to cardiac stress. Tissue-specific knockout of NELF-B confirms its cell-autonomous function in cardiomyocytes. NELF directly supports transcription of those genes encoding rate-limiting enzymes in fatty acid oxidation (FAO) and the tricarboxylic acid (TCA) cycle. NELF also shares extensively transcriptional target genes with peroxisome proliferator-activated receptor α (PPARα), a master regulator of energy metabolism in the myocardium. Mechanistically, NELF helps stabilize the transcription initiation complex at the metabolism-related genes. Our findings strongly indicate that NELF is part of the PPARα-mediated transcription regulatory network that maintains metabolic homeostasis in cardiomyocytes.
doi:10.1016/j.celrep.2014.02.028
PMCID: PMC4277258  PMID: 24656816
3.  Obese and diabetic KKAy mice show increased mortality but improved cardiac function following myocardial infarction 
Background
Introduction of the yellow obese gene (Ay) into mice (KKAy) results in obesity and diabetes by 5 weeks of age.
Methods
Using this model of type 2 diabetes, we evaluated male and female 6–8 month old wild type (WT, n=10) and KKAy (n=22) mice subjected to myocardial infraction (MI) and sacrificed at day (d) 7.
Results
Despite similar infarct sizes (50±4% for WT and 49±2% for KKAy, p=N.S.), the 7 d post-MI survival was 70% (n=7/10) in WT mice and 45% (n=10/22) in KKAy mice (p<0.05). Plasma glucose levels were 1.4 fold increased in KKAy mice at baseline, compared to WT (p<0.05). Glucose levels did not change in WT mice but decreased 38% in KKAy post-MI (p<0.05). End-diastolic and end-systolic dimensions post-MI were smaller and fractional shortening improved in the KKAy (5±1% in WT and 10±2% in KKAy, p<0.05 for all). The improved cardiac function in KKAy was accompanied by reduced macrophage numbers and collagen I and III levels (both p<0.05). Griffonia (Bandeiraea) simplicifolia lectin-I staining for vessel density demonstrated fewer vessels in KKAy infarcts (5.9±0.5%) compared to WT infarcts (7.3±0.1%, p<0.05).
Conclusion
In conclusion, our study in KKAy mice revealed a paradoxical reduced post-MI survival but improved cardiac function through reduced inflammation, extracellular matrix accumulation, and neovascularization in the infarct region. These results indicate a dual role effect of obesity in the post-MI response.
doi:10.1016/j.carpath.2013.06.002
PMCID: PMC3965668  PMID: 23896047
obesity; diabetes; extracellular matrix; heart failure; inflammation; myocardial infarction
4.  Texas 3-Step decellularization protocol: Looking at the cardiac extracellular matrix 
Journal of proteomics  2013;86:10.1016/j.jprot.2013.05.004.
The extracellular matrix (ECM) is a critical tissue component, providing structural support as well as important regulatory signaling cues to govern cellular growth, metabolism, and differentiation. The study of ECM proteins, however, is hampered by the low solubility of ECM components in common solubilizing reagents. ECM proteins are often not detected during proteomics analyses using unbiased approaches due to solubility issues and relatively low abundance compared to highly abundant cytoplasmic and mitochondrial proteins. Decellularization has become a common technique for ECM protein-enrichment and is frequently used in engineering studies. Solubilizing the ECM after decellularization for further proteomic examination has not been previously explored in depth. In this study, we describe testing of a series of protocols that enabled us to develop a novel optimized strategy for the enrichment and solubilization of ECM components. Following tissue decellularization, we use acid extraction and enzymatic deglycosylation to facilitate resolubilization. The end result is the generation of three fractions for each sample: soluble components, cellular components, and an insoluble ECM fraction. These fractions, developed in mass spectrometry-compatible buffers, are amenable to proteomics analysis. The developed protocol allows identification (by mass spectrometry) and quantification (by mass spectrometry or immunoblotting) of ECM components in tissue samples.
Biological significance
The study of extracellular matrix (ECM) proteins in pathological and non-pathological conditions is often hampered by the low solubility of ECM components in common solubilizing reagents. Additionally, ECM proteins are often not detected during global proteomic analyses due to their relatively low abundance compared to highly abundant cytoplasmic and mitochondrial proteins. In this manuscript we describe testing of a series of protocols that enabled us to develop a final novel optimized strategy for the enrichment and solubilization of ECM components. The end result is the generation of three fractions for each sample: soluble components, cellular components, and an insoluble ECM fraction. By analysis of each independent fraction, differences in protein levels can be detected that in normal conditions would be masked. These fractions are amenable to mass spectrometry analysis to identify and quantify ECM components in tissue samples. The manuscript places a strong emphasis on the immediate practical relevance of the method, particularly when using mass spectrometry approaches; additionally, the optimized method was validated and compared to other methodologies described in the literature.
doi:10.1016/j.jprot.2013.05.004
PMCID: PMC3879953  PMID: 23681174
Extracellular matrix; Enrichment; Decellularization; Heart; Solubility; Matrix metalloproteinases
5.  Is Isolated Systolic Hypertension Worse than Combined Systolic/Diastolic Hypertension? 
doi:10.1111/jch.12011
PMCID: PMC4032063  PMID: 23126357
editorial; isolated systolic hypertension; combined systolic/diastolic hypertension; endothelial dysfunction; MMP; vascular calcification
6.  Heart Rate Reduction 
Hypertension  2012;59(5):908-910.
doi:10.1161/HYPERTENSIONAHA.111.186494
PMCID: PMC3996900  PMID: 22493078
7.  Matrix Metalloproteinase-28 Deletion Amplifies Inflammatory and Extracellular Matrix Responses to Cardiac Aging 
To determine if matrix metalloproteinase (MMP)-28 mediates cardiac aging, wild-type (WT) and MMP-28−/− young (7 ± 1 months, n = 9 each) and old (20 ± 2 months, n = 7 each) female mice were evaluated. MMP-28 expression in the left ventricle (LV) increased 42% in old WT mice compared to young controls (p < 0.05). By Doppler echocardiography, LV function declined at 20 ± 2 months of age for both groups. However, dobutamine stress responses were similar, indicating that cardiac reserve was maintained. Plasma proteomic profiling revealed that macrophage inflammatory protein (MIP)-1 α, MIP-1β and MMP-9 plasma levels did not change in WT old mice but were significantly elevated in MMP-28−/− old mice (all p < 0.05), suggestive of a higher inflammatory status when MMP-28 is deleted. RT2-PCR gene array and immunoblotting analyses demonstrated that MIP-1α and MMP-9 gene and protein levels in the LV were also higher in MMP-28−/− old mice (all p < 0.05). Macrophage numbers in the LV increased similarly in WT and MMP-28−/− old mice, compared to respective young controls (both p < 0.05). Collagen content was not different among the WT and MMP-28−/− young and old mice. In conclusion, LV inflammation increases with age, and MMP-28 deletion further elevates inflammation and extracellular matrix responses, without altering macrophage numbers or collagen content.
doi:10.1017/S1431927611012220
PMCID: PMC3972008  PMID: 22153350
MMP-28; cardiac aging; extracellular matrix; inflammation; macrophage; collagen; left ventricle; mice
8.  Cardiac Wound Healing Post-myocardial Infarction: A Novel Method to Target Extracellular Matrix Remodeling in the Left Ventricle 
Myocardial infarction (MI) is a leading cause of death worldwide. Permanent ligation of the left anterior descending coronary artery (LAD) is a commonly used surgical model to study post-MI effects in mice. LAD occlusion induces a robust wound healing response that includes extracellular matrix (ECM) remodeling. This chapter provides a detailed guide on the surgical procedure to permanently ligate the LAD. Additionally, we describe a prototype method to enrich cardiac tissue for ECM, which allows one to focus on ECM remodeling in the left ventricle following surgically induced MI in mice.
doi:10.1007/978-1-62703-505-7_18
PMCID: PMC3970183  PMID: 24029944
Myocardial infarction; Cardiac wound healing; Mice; Extracellular matrix; Matrix metalloproteinases; Inflammation; Decellularization
9.  DHA derivatives of fish oil as dietary supplements: a nutrition-based drug discovery approach for therapies to prevent metabolic cardiotoxicity 
Expert opinion on drug discovery  2012;7(8):711-721.
Introduction
During the early 1970s, Danish physicians Jorn Dyerberg and colleagues observed that Greenland Eskimos consuming fatty fishes exhibited low incidences of heart disease. Fish oil is now one of the most commonly consumed dietary supplements. In 2004, concentrated fish oil was approved as a drug by the FDA for the treatment of hyperlipidemia. Fish oil contains two major omega-3 fatty acids: eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). With advancements in lipid concentration and purification techniques, EPA- or DHA-enriched products are now commercially available, and the availability of these components in isolation allows their individual effects to be examined. Newly synthesized derivatives and endogenously discovered metabolites of DHA exhibit therapeutic utility for obesity, metabolic syndrome and cardiovascular disease.
Areas covered
This review summarizes our current knowledge on the distinct effects of EPA and DHA to prevent metabolic syndrome and reduce cardiotoxicity risk. Since EPA is an integral component of fish oil, we will briefly review EPA effects, but our main theme will be to summarize effects of the DHA derivatives that are available today. We focus on using nutrition-based drug discovery to explore the potential of DHA derivatives for the treatment of obesity, metabolic syndrome and cardiovascular diseases.
Expert opinion
The safety and efficacy evaluation of DHA derivatives will provide novel biomolecules for the drug discovery arsenal. Novel nutritional-based drug discoveries of DHA derivatives or metabolites may provide realistic and alternative strategies for the treatment of metabolic and cardiovascular disease.
doi:10.1517/17460441.2012.694862
PMCID: PMC3969443  PMID: 22724444
cardiovascular disease; dietary supplement; docosahexaenoic acid; eicosapentaenoic acid; fish oil; metabolic syndrome; obesity
10.  Matrix Metalloproteinase-28 Deletion Exacerbates Cardiac Dysfunction and Rupture Following Myocardial Infarction in Mice by Inhibiting M2 Macrophage Activation 
Circulation research  2012;112(4):675-688.
Rationale
Matrix metalloproteinase (MMP)-28 regulates the inflammatory and extracellular matrix (ECM) responses in cardiac aging, but the roles of MMP-28 after myocardial infarction (MI) have not been explored.
Objective
To determine the impact of MMP-28 deletion on post-MI remodeling of the left ventricle (LV)
Methods and Results
Adult C57BL/6J wild type (WT, n=76) and MMP null (MMP-28−/−, n=86) mice of both sexes were subjected to permanent coronary artery ligation to create MI. MMP-28 expression decreased post-MI, and its cell source shifted from myocytes to macrophages. MMP-28 deletion increased day 7 mortality as a result of increased cardiac rupture post-MI. MMP-28−/− mice exhibited larger LV volumes, worse LV dysfunction, a worse LV remodeling index, and increased lung edema. Plasma MMP-9 levels were unchanged in the MMP-28−/− mice but increased in WT mice at day 7 post-MI. The mRNA levels of inflammatory and ECM proteins were attenuated in the infarct regions of MMP-28−/− mice, indicating reduced inflammatory and ECM responses. M2 macrophage activation was impaired when MMP-28 was absent. MMP-28 deletion also led to decreased collagen deposition and fewer myofibroblasts. Collagen cross-linking was impaired, due to decreased expression and activation of lysyl oxidase in the infarcts of MMP-28−/− mice. The LV tensile strength at day 3 post-MI, however, was similar between the two genotypes
Conclusions
MMP-28 deletion aggravated MI induced LV dysfunction and rupture, due to defective inflammatory response and scar formation by suppressing M2 macrophage activation.
doi:10.1161/CIRCRESAHA.111.300502
PMCID: PMC3597388  PMID: 23261783
Myocardial infarction; MMP-28; fibroblast; macrophage phenotype; inflammation
11.  Myofibroblasts and the extracellular matrix network in post-myocardial infarction cardiac remodeling 
Pflugers Archiv  2014;466(6):1113-1127.
The cardiac extracellular matrix (ECM) fills the space between cells, supports tissue organization, and transduces mechanical, chemical, and biological signals to regulate homeostasis of the left ventricle (LV). Following myocardial infarction (MI), a multitude of ECM proteins are synthesized to replace myocyte loss and form a reparative scar. Activated fibroblasts (myofibroblasts) are the primary source of ECM proteins, thus playing a key role in cardiac repair. A balanced turnover of ECM through regulation of synthesis by myofibroblasts and degradation by matrix metalloproteinases (MMPs) is critical for proper scar formation. In this review, we summarize the current literature on the roles of myofibroblasts, MMPs, and ECM proteins in MI-induced LV remodeling. In addition, we discuss future research directions that are needed to further elucidate the molecular mechanisms of ECM actions to optimize cardiac repair.
doi:10.1007/s00424-014-1463-9
PMCID: PMC4033805  PMID: 24519465
Extracellular matrix; MMP-9; Myocardial infarction; Myofibroblast; Proteomics; Review
12.  Extracellular Matrix and Fibroblast Communication Following Myocardial Infarction 
The extracellular matrix (ECM) provides structural support by serving as a scaffold for cells, and as such the ECM maintains normal tissue homeostasis and mediates the repair response following injury. In response to myocardial infarction (MI), ECM expression is generally upregulated in the left ventricle (LV), which regulates LV remodeling by modulating scar formation. The ECM directly affects scar formation by regulating growth factor release and cell adhesion, and indirectly affects scar formation by regulating the inflammatory, angiogenic, and fibroblast responses. This review summarizes the current literature on ECM expression patterns and fibroblast mechanisms in the myocardium, focusing on the ECM response to MI. In addition, we discuss future research areas that are needed to better understand the molecular mechanisms of ECM action, both in general and as a means to optimize infarct healing.
doi:10.1007/s12265-012-9398-z
PMCID: PMC3518752  PMID: 22926488
extracellular matrix; myocardial infarction; fibroblasts; cardiac myocytes; cell-ECM communication; proteomics
13.  Neutrophil roles in left ventricular remodeling following myocardial infarction 
Polymorphonuclear granulocytes (PMNs; neutrophils) serve as key effector cells in the innate immune system and provide the first line of defense against invading microorganisms. In addition to producing inflammatory cytokines and chemokines and undergoing a respiratory burst that stimulates the release of reactive oxygen species, PMNs also degranulate to release components that kill pathogens. Recently, neutrophil extracellular traps have been shown to be an alternative way to trap microorganisms and contain infection. PMN-derived granule components are also involved in multiple non-infectious inflammatory processes, including the response to myocardial infarction (MI). In this review, we will discuss the biological characteristics, recruitment, activation, and removal of PMNs, as well as the roles of PMN-derived granule proteins in inflammation and innate immunity, focusing on the MI setting when applicable. We also discuss future perspectives that will direct research in PMN biology.
doi:10.1186/1755-1536-6-11
PMCID: PMC3681584  PMID: 23731794
PMNs; Myocardial infarction; Inflammation; Innate immunity; Degranulation; Matrix metalloproteinases
14.  Mathematical modeling and stability analysis of macrophage activation in left ventricular remodeling post-myocardial infarction 
BMC Genomics  2012;13(Suppl 6):S21.
Background
About 6 million Americans suffer from heart failure and 70% of heart failure cases are caused by myocardial infarction (MI). Following myocardial infarction, increased cytokines induce two major types of macrophages: classically activated macrophages which contribute to extracellular matrix destruction and alternatively activated macrophages which contribute to extracellular matrix construction. Though experimental results have shown the transitions between these two types of macrophages, little is known about the dynamic progression of macrophages activation. Therefore, the objective of this study is to analyze macrophage activation patterns post-MI.
Results
We have collected experimental data from adult C57 mice and built a framework to represent the regulatory relationships among cytokines and macrophages. A set of differential equations were established to characterize the regulatory relationships for macrophage activation in the left ventricle post-MI based on the physical chemistry laws. We further validated the mathematical model by comparing our computational results with experimental results reported in the literature. By applying Lyaponuv stability analysis, the established mathematical model demonstrated global stability in homeostasis situation and bounded response to myocardial infarction.
Conclusions
We have established and validated a mathematical model for macrophage activation post-MI. The stability analysis provided a possible strategy to intervene the balance of classically and alternatively activated macrophages in this study. The results will lay a strong foundation to understand the mechanisms of left ventricular remodelling post-MI.
doi:10.1186/1471-2164-13-S6-S21
PMCID: PMC3481436  PMID: 23134700
15.  Correction: Toll-Like Receptor (TLR) 2 and TLR4 Differentially Regulate Doxorubicin Induced Cardiomyopathy in Mice 
PLoS ONE  2012;7(10):10.1371/annotation/e82f77a8-3d29-44be-a9ef-7abc6c7e584a.
doi:10.1371/annotation/e82f77a8-3d29-44be-a9ef-7abc6c7e584a
PMCID: PMC3491864
16.  Toll-Like Receptor (TLR) 2 and TLR4 Differentially Regulate Doxorubicin Induced Cardiomyopathy in Mice 
PLoS ONE  2012;7(7):e40763.
Recent evidence indicates that toll-like receptor (TLR) 2 and 4 are involved in the pathogenesis of dilated cardiomyopathy (DCM), but the exact mechanisms of their actions have not been elucidated. We explored the therapeutic potential of blocking TLRs in mice with established cardiomyopathy. Cardiomyopathy was generated by a single intraperitoneal injection of doxorubicin (10 mg/kg). Two weeks later, the mice were treated with TLR2 or TLR4 neutralizing antibody. Blocking TLR2, but not TLR4, activity not only reduced mortality, but also attenuated doxorubicin-induced cardiac dysfunction by 20% and inhibited myocardial fibrosis. To determine the differential effects of blocking TLR2 and TLR4 in chronic cardiomyopathy, mice were injected with doxorubicin (3.5 mg/kg) once a week for 8 weeks, followed by treatment with TLR2 or TLR4 neutralizing antibody for 40 days. Blocking TLR2 activity blunted cardiac dysfunction by 13% and inhibited cardiac fibrosis, which was associated with a significant suppression of myocardial inflammation. The underlying mechanism involved interrupting the interaction of TLR2 with its endogenous ligands, resulting in attenuation of inflammation and fibrosis. In contrast, blocking TLR4 exacerbated cardiac dysfunction and fibrosis by amplifying inflammation and suppressing autophagy. Our studies demonstrate that TLR2 and TLR4 play distinct roles in the progression of doxorubicin-induced DCM. TLR4 activity is crucial for the resolution of inflammation and cardiac fibrosis, while blocking TLR2 activity has therapeutic potential for the treatment of DCM.
doi:10.1371/journal.pone.0040763
PMCID: PMC3396603  PMID: 22808256
17.  Plasma Fractionation Enriches Post-Myocardial Infarction Samples Prior to Proteomics Analysis 
Following myocardial infarction (MI), matrix metalloproteinase-9 (MMP-9) levels increase, and MMP-9 deletion improves post-MI remodeling of the left ventricle (LV). We provide here a technical report on plasma-analysis from wild type (WT) and MMP-9 null mice using fractionation and mass-spectrometry-based proteomics. MI was induced by coronary artery ligation in male WT and MMP-9 null mice (4–8 months old; n = 3/genotype). Plasma was collected on days 0 (pre-) and 1 post-MI. Plasma proteins were fractionated and proteins in the lowest (fraction 1) and highest (fraction 12) molecular weight fractions were separated by 1-D SDS-PAGE, digested in-gel with trypsin and analyzed by HPLC-ESI-MS/MS on an Orbitrap Velos. We tried five different fractionation protocols, before reaching an optimized protocol that allowed us to identify over 100 proteins. Serum amyloid A substantially increased post-MI in both genotypes, while alpha-2 macroglobulin increased only in the null samples. In fraction 12, extracellular matrix proteins were observed only post-MI. Interestingly, fibronectin-1, a substrate of MMP-9, was identified at both day 0 and day 1 post-MI in the MMP-9 null mice but was only identified post-MI in the WT mice. In conclusion, plasma fractionation offers an improved depletion-free method to evaluate plasma changes following MI.
doi:10.1155/2012/397103
PMCID: PMC3385641  PMID: 22778955

Results 1-17 (17)