Divide and conquer: the application of organelle proteomics to heart failure.

Chronic heart failure is a worldwide cause of mortality and morbidity and is the final outcome of a number of different etiologies. This reflects both the complexity of the disease and our incomplete understanding of its underlying molecular mechanisms. One experimental approach to address this is to study subcellular organelles and how their functions are activated and synchronized under physiological and pathological conditions.

Overview: the maturing of proteomics in cardiovascular research.

Proteomic technologies are used to study the complexity of proteins, their roles, and biological functions. It is based on the premise that the diversity of proteins, comprising their isoforms, and posttranslational modifications (PTMs) underlies biology. Based on an annotated human cardiac protein database, 62% have at least one PTM (phosphorylation currently dominating), whereas ≈25% have more than one type of modification.

Analysis of protein composition of rabbit aqueous humor following two different cataract surgery incision procedures using 2-DE and LC-MS/MS.

Background: The aqueous humor (AH), a liquid of the anterior and posterior chamber of the eye, comprises many proteins with various roles and important biological functions. Many of these proteins have not been identified yet and their functions in AH are still unknown. Recently, our laboratory published the protein database of AH obtained from healthy rabbits which expanded known protein identifications by 65%.

Hemoglobin depletion from plasma: considerations for proteomic discovery in sickle cell disease and other hemolytic processes.

Purpose: Hemoglobin (Hb) depletion with nickel affinity chromatography has been shown to increase the number of proteins identified in proteomic studies of erythrocytes, but limited data exist on the application of this technique in depletion of Hb from plasma or serum required for clinical biomarker studies. The aim of this study was to explore the potential of using nickel-beads for Hb depletion of plasma.

Experimental Design: Nickel–nitrilotriacetic acid (Ni–NTA) affinity chromatography was used to deplete Hb from hemolyzed plasma samples obtained from children with sickle cell disease (SCD, n=7) and normal human plasma (n=4).

Report from the Wellcome Trust/EBA “Perspectives in Clinical Proteomics” retreat--a strategy to implement next-generation proteomic analyses to the clinic for patient benefit: pathway to translation.

Proteomics has long been thought to hold the promise of producing results of clinical utility which will influence patient treatment and outcomes. A recent Wellcome Trust/EBI meeting and retreat--“Perspectives in Clinical Proteomics”--brought together experts from a broad range of stakeholder groups with an interest in ensuring proteomics achieves this aim. This viewpoint presents views derived from these forums, proposing a pathway for the development of next-generation proteomic analyses in the clinical setting from selection of candidates through to their validation and ultimate demonstration of utility through health technology assessments.

Multiplex assays for biomarker research and clinical application: translational science coming of age.

Over the last decade, translational science has come into the focus of academic medicine, and significant intellectual and financial efforts have been made to initiate a multitude of bench-to-bedside projects. The quest for suitable biomarkers that will significantly change clinical practice has become one of the biggest challenges in translational medicine. Quantitative measurement of proteins is a critical step in biomarker discovery.

Primary results from the SmartDelay determined AV optimization: a comparison to other AV delay methods used in cardiac resynchronization therapy (SMART-AV) trial: a randomized trial comparing empirical, echocardiography-guided, and algorithmic atrioventricular delay programming in cardiac resynchronization therapy.

Background: one variable that may influence cardiac resynchronization therapy response is the programmed atrioventricular (AV) delay. The SmartDelay determined av optimization: a comparison to other AV delay methods used in cardiac resynchronization therapy (SMART-AV) trial prospectively randomized patients to a fixed empirical AV delay (120 milliseconds), echocardiographically optimized AV delay, or AV delay optimized with SmartDelay, an electrogram-based algorithm.

Methods And Results: a total of 1014 patients (68% men; mean age, 66 ± 11 years; mean left ventricular ejection fraction, 25 ± 7%) who met enrollment criteria received a cardiac resynchronization therapy defibrillator, and 980 patients were randomized in a 1:1:1 ratio.

Site-mapping of in vitro S-nitrosation in cardiac mitochondria: implications for cardioprotection.

S-nitrosation (SNO) of mitochondrial protein cysteines can be cardioprotective. Several targets have been implicated, yet the scope and identification of specific residues has not been fully assessed. To address this, a comprehensive assessment of mitochondrial SNO-modifiable cysteines was performed to determine nitric oxide (NO) susceptible pathways and identify novel mechanisms of oxidative cardioprotection.

Parallel proteomics to improve coverage and confidence in the partially annotated Oryctolagus cuniculus mitochondrial proteome.

The ability to decipher the dynamic protein component of any system is determined by the inherent limitations of the technologies used, the complexity of the sample, and the existence of an annotated genome. In the absence of an annotated genome, large-scale proteomic investigations can be technically difficult. Yet the functional and biological species differences across animal models can lead to selection of partially or nonannotated organisms over those with an annotated genome.

Abl tyrosine kinase phosphorylates nonmuscle Myosin light chain kinase to regulate endothelial barrier function.

Nonmuscle myosin light chain kinase (nmMLCK), a multi-functional cytoskeletal protein critical to vascular homeostasis, is highly regulated by tyrosine phosphorylation. We identified multiple novel c-Abl-mediated nmMLCK phosphorylation sites by mass spectroscopy analysis (including Y231, Y464, Y556, Y846) and examined their influence on nmMLCK function and human lung endothelial cell (EC) barrier regulation. Tyrosine phosphorylation of nmMLCK increased kinase activity, reversed nmMLCK-mediated inhibition of Arp2/3-mediated actin polymerization, and enhanced binding to the critical actin-binding phosphotyrosine protein, cortactin.

Highly divergent mitochondrial ATP synthase complexes in Tetrahymena thermophila.

The F-type ATP synthase complex is a rotary nano-motor driven by proton motive force to synthesize ATP. Its F(1) sector catalyzes ATP synthesis, whereas the F(o) sector conducts the protons and provides a stator for the rotary action of the complex. Components of both F(1) and F(o) sectors are highly conserved across prokaryotes and eukaryotes.

Development of a qualitative sequential immunoassay for characterizing the intrinsic properties of circulating cardiac troponin I.

Background: With myocardial infarction (MI), cardiac troponin is released from the heart into circulation, where it can be detected with immunoassays independently quantifying cardiac troponin I (cTnI) or cTnT. There is, however, no single immunoassay that sequentially probes the posttranslational modification status of cTnI or directly characterizes whether circulating cTnI is bound to cTnC and/or cTnT. Here we describe the development of a qualitative immunoassay to directly probe the primary and ternary structure of circulating cTnI through diffractive optics technology (dotLab System, Axela).

Expanding the mouse embryonic stem cell proteome: combining three proteomic approaches.

The current study used three different proteomic strategies, which differed by their extent of intact protein separation, to examine the proteome of a pluripotent mouse embryonic stem cell line, R1. Proteins from whole-cell lysates were subjected either to 2-D-LC, or 1-DE, or were unfractionated prior to enzymatic digestion and subsequent analysis by MS. The results yielded 1895 identified non-redundant proteins and, for 128 of these, the specific isoform could be determined based on detection of an isoform-specific peptide.

Identifying patients at high risk of a cardiovascular event in the near future: current status and future directions: report of a national heart, lung, and blood institute working group.

The National Heart, Lung, and Blood Institute convened working group to provide basic and clinical research recommendations to the National Heart, Lung, and Blood Institute on the development of an integrated approach for identifying those individuals who are at high risk for cardiovascular event such as acute coronary syndromes (ACS) or sudden cardiac death in the “near term.” The working group members defined near-term as occurring within 1 year of the time of assessment. The participants reviewed current clinical cardiology practices for risk assessment and state-of-the-science techniques in several areas, including biomarkers, proteomics, genetics, psychosocial factors, imaging, coagulation, and vascular and myocardial susceptibility.

Ultrastructure and regulation of lateralized connexin43 in the failing heart.

Rationale: Gap junctions mediate cell-to-cell electric coupling of cardiomyocytes. The primary gap junction protein in the working myocardium, connexin43 (Cx43), exhibits increased localization at the lateral membranes of cardiomyocytes in a variety of heart diseases, although the precise location and function of this population is unknown.

Objective: To define the subcellular location of lateralized gap junctions at the light and electron microscopic level, and further characterize the biochemical regulation of gap junction turnover.

Modulation of mitochondrial proteome and improved mitochondrial function by biventricular pacing of dyssynchronous failing hearts.

Background: Cardiac resynchronization therapy (CRT) improves chamber mechanoenergetics and morbidity and mortality of patients manifesting heart failure with ventricular dyssynchrony; however, little is known about the molecular changes underlying CRT benefits. We hypothesized that mitochondria may play an important role because of their involvement in energy production.

Methods And Results: Mitochondria isolated from the left ventricle in a canine model of dyssynchronous or resynchronized (CRT) heart failure were analyzed by a classical, gel-based, proteomic approach.

The C terminus of cardiac troponin I stabilizes the Ca2+-activated state of tropomyosin on actin filaments.

Rationale: Ca(2+) control of troponin-tropomyosin position on actin regulates cardiac muscle contraction. The inhibitory subunit of troponin, cardiac troponin (cTn)I is primarily responsible for maintaining a tropomyosin conformation that prevents crossbridge cycling. Despite extensive characterization of cTnI, the precise role of its C-terminal domain (residues 193 to 210) is unclear.

Phosphorylation of the F(1)F(o) ATP synthase beta subunit: functional and structural consequences assessed in a model system.

Rationale: We previously discovered several phosphorylations to the beta subunit of the mitochondrial F(1)F(o) ATP synthase complex in isolated rabbit myocytes on adenosine treatment, an agent that induces cardioprotection. The role of these phosphorylations is unknown.

Objective: The present study focuses on the functional consequences of phosphorylation of the ATP synthase complex beta subunit by generating nonphosphorylatable and phosphomimetic analogs in a model system, Saccharomyces cerevisiae.

Comparison of multiplex immunoassay platforms.

Background: Candidate biomarkers discovered with high-throughput proteomic techniques (along with many biomarkers reported in the literature) must be rigorously validated. The simultaneous quantitative assessment of multiple potential biomarkers across large cohorts presents a major challenge to the field. Multiplex immunoassays represent a promising solution, with the potential to provide quantitative data via parallel analyses.

Identification and functionality of proteomes secreted by rat cardiac stem cells and neonatal cardiomyocytes.

In the heart, the proteomes secreted by both cardiac stem cells (CSCs) and cardiac myocytes could act synergistically, but the identification and functionality of the proteins comprising the individual secretomes have not yet been described. In this study, we have identified proteins present in the media obtained from cultured rat CSCs and from cultured neonatal rat ventricular myocytes (NRVMs) and compared them with proteins identified in the media alone. Briefly, 83 unique proteins were identified after analysis by RPLC and MS.

Uromodulin levels associate with a common UMOD variant and risk for incident CKD.

Common variants in the region of the UMOD gene, which encodes uromodulin (Tamm-Horsfall protein), associate with chronic kidney disease (CKD) and estimated GFR (eGFR). Whether uromodulin levels associate with UMOD variants or with the risk for developing CKD is unknown. We conducted an age- and gender-matched case-control study (n = 200) of incident CKD (eGFR <60 ml/min per 1.

Murine model of surgically induced acute aortic dissection type A.

Objectives: This study aimed at developing a murine model of surgically induced acute aortic dissection type A for investigation of the formation and progression of acute aortic dissection and to test whether this system could be used for biomarker discovery.

Methods: Adult fibrillin-1 deficient, Fbn1(C1039G/+) mice and wild-type mice were anesthetized, ventilated, and the ascending aorta exposed via hemisternotomy. We hypothesized that acute aortic dissection could be induced either by injecting autologous blood into the aortic wall or by injury to the wall with aortic clamping.

SmartDelay determined AV optimization: a comparison of AV delay methods used in cardiac resynchronization therapy (SMART-AV): rationale and design.

Background: The clinical benefit of cardiac resynchronization therapy (CRT) for patients with moderate-to-severely symptomatic heart failure, left ventricular systolic dysfunction, and ventricular conduction delay is established. However, some patients do not demonstrate clinical improvement following CRT. It is unclear whether systematic optimization of the programmed atrioventricular (AV) delay improves the rate of clinical response.

Preparation of proteins and peptides for mass spectrometry analysis in a bottom-up proteomics workflow.

This unit outlines the steps required to prepare a sample for MS analysis following protein separation or enrichment by gel electrophoresis, liquid chromatography, and affinity capture within the context of a bottom-up proteomics workflow in which the protein is first broken up into peptides, either by chemical or enzymatic digestion, prior to MS analysis. Also included are protocols for enrichment at the peptide level, including phosphopeptide enrichment and reversed-phase chromatography for sample purification immediately prior to MS analysis. Finally, there is a discussion regarding the types of MS technologies commonly used to analyze proteomics samples, as well as important parameters that should be considered when analyzing the MS data to ensure stringent and robust protein identifications and characterization.