Improving Veteran Engagement with Virtual Care Technologies: a Veterans Health Administration State of the Art Conference Research Agenda.

Although the availability of virtual care technologies in the Veterans Health Administration (VHA) continues to expand, ensuring engagement with these technologies among Veterans remains a challenge. VHA Health Services Research & Development convened a Virtual Care State of The Art (SOTA) conference in May 2022 to create a research agenda for improving virtual care access, engagement, and outcomes. This article reports findings from the Virtual Care SOTA engagement workgroup, which comprised fourteen VHA subject matter experts representing VHA clinical care, research, administration, and operations. Workgroup members reviewed current evidence on factors and strategies that may affect Veteran engagement with virtual care technologies and generated key questions to address evidence gaps. The workgroup agreed that although extensive literature exists on factors that affect Veteran engagement, more work is needed to identify effective strategies to increase and sustain engagement. Workgroup members identified key priorities for research on Veteran engagement with virtual care technologies through a series of breakout discussion groups and ranking exercises. The top three priorities were to (1) understand the Veteran journey from active service to VHA enrollment and beyond, and when and how virtual care technologies can best be introduced along that journey to maximize engagement and promote seamless care; (2) utilize the meaningful relationships in a Veteran's life, including family, friends, peers, and other informal or formal caregivers, to support Veteran adoption and sustained use of virtual care technologies; and (3) test promising strategies in meaningful combinations to promote Veteran adoption and/or sustained use of virtual care technologies. Research in these priority areas has the potential to help VHA refine strategies to improve virtual care user engagement, and by extension, outcomes.

Determinants and outcome correlates of engagement with a mobile mental health intervention for depression and anxiety in middle-aged and older adults.

OBJECTIVES: To examine baseline factors (i.e., age, gender, mobile device proficiency, sensory impairment) associated with app engagement in a 12-week mental health app intervention and to explore whether app engagement predicts changes in depression and anxiety symptoms among middle-aged and older adults. METHOD: Mobile device proficiency, sensory impairment, depression, and anxiety symptoms were measured using questionnaires. App engagement was defined by metrics characterizing the core intervention features (i.e., messages sent to therapist, mindfulness meditation minutes, action tasks completed). Multiple regressions and multilevel models were conducted. RESULTS: Forty-nine participants (M age = 57.40, SD = 11.09 years) enrolled. Women (ß = .35, p < .05) and participants with less sensory impairment completed more action tasks (ß = -.40, p < .05). Depressive and anxiety symptoms measured within the app declined significantly across treatment. Clinical significant improvements were observed for depression in 48.9% and for anxiety in 40% of participants. App engagement metrics were not predictive of depression or anxiety symptoms, either incrementally in time-lagged models or cumulatively in hierarchical linear regression analyses. CONCLUSION: App engagement is multifaceted; participants engaged differently by gender and ability. Participation in this digital mental health intervention reduced depression and anxiety symptoms, but these findings should be interpreted with caution as the study did not include a control condition. Our findings underscore the importance of considering individual factors that may influence use of a digital mental health intervention.

A Randomized Clinical Trial of Clinician-Supported PTSD Coach in VA Primary Care Patients.

BACKGROUND: Posttraumatic stress disorder (PTSD) is common in primary care patients; however, evidence-based treatments are typically only available in specialty mental healthcare settings and often not accessed. OBJECTIVE: To test the effectiveness of a brief primary care-based treatment, Clinician-Supported PTSD Coach (CS PTSD Coach) was compared with Primary Care Mental Health Integration-Treatment as Usual (PCMHI-TAU) in (1) reducing PTSD severity, (2) engaging veterans in specialty mental health care, and (3) patient satisfaction with care. DESIGN: Multi-site randomized pragmatic clinical trial. PARTICIPANTS: A total of 234 veterans with PTSD symptoms who were not currently accessing PTSD treatment. INTERVENTION: CS PTSD Coach was designed to be implemented in Veterans Affairs PCMHI and combines mental health clinician support with the "PTSD Coach" mobile app. Four 30-min sessions encourage daily use of symptom management strategies. MAIN MEASURES: PTSD severity was measured by clinician-rated interviews pre- and post-treatment (8 weeks). Self-report measures assessed PTSD, depression, and quality of life at pretreatment, posttreatment, and 16- and 24-week follow-ups, and patient satisfaction at post-treatment. Mental healthcare utilization was extracted from medical records. KEY RESULTS: Clinician-rated PTSD severity did not differ by condition at post-treatment. CS PTSD Coach participants improved more on patient-reported PTSD severity at post-treatment than TAU participants (D = .28, p = .021). Coach participants who continued to have problematic PTSD symptoms at post-treatment were not more likely to engage in 2 sessions of specialty mental health treatment than TAU participants. Coach participants engaged in 74% more sessions in the intervention and reported higher treatment satisfaction than TAU participants (p < .001). CONCLUSIONS: A structured 4-session intervention designed to align with patient preferences for care resulted in more patient-reported PTSD symptom relief, greater utilization of mental health treatment, and overall treatment satisfaction than TAU, but not more clinician-rated PTSD symptom relief or engagement in specialty mental health.

Internet-based family training with telephone coaching to promote mental health treatment initiation among veterans with posttraumatic stress disorder: A pilot study.

Posttraumatic stress disorder (PTSD) is common among military veterans, yet many affected veterans do not seek treatment. Family members of these veterans often experience compromised well-being and a desire for the veteran to receive mental health care. The Veterans Affairs (VA)-Community Reinforcement and Family Training (VA-CRAFT) for PTSD is an internet-based intervention intended to teach veterans' family members skills to encourage veterans to initiate mental health care. This study assessed the feasibility, acceptability, and potential efficacy of VA-CRAFT with telephone coaching in a sample of 12 spouses and intimate partners of veterans with PTSD. Participants completed the intervention over 12 weeks and were assessed pre- and posttreatment. For feasibility, 75.0% (n = 9) of participants completed the intervention and reported few difficulties and ease of use. Supporting acceptability, all nine completers had mostly favorable impressions of the intervention and perceived it as helpful. Finally, six (50.0%) participants got the PTSD-affected veteran to engage in mental health care; however, aside from potentially increasing treatment talk frequency, outcome expectancy, and self-efficacy, ds = 0.60-1.08, no apparent improvements were observed for any well-being outcomes, ds = 0.01-0.40. Although the findings are promising, given the study limitations, future research is required to evaluate this approach in a full-scale randomized controlled trial.

A highly multiplexed quantitative phosphosite assay for biology and preclinical studies.

Reliable methods to quantify dynamic signaling changes across diverse pathways are needed to better understand the effects of disease and drug treatment in cells and tissues but are presently lacking. Here, we present SigPath, a targeted mass spectrometry (MS) assay that measures 284 phosphosites in 200 phosphoproteins of biological interest. SigPath probes a broad swath of signaling biology with high throughput and quantitative precision. We applied the assay to investigate changes in phospho-signaling in drug-treated cancer cell lines, breast cancer preclinical models, and human medulloblastoma tumors. In addition to validating previous findings, SigPath detected and quantified a large number of differentially regulated phosphosites newly associated with disease models and human tumors at baseline or with drug perturbation. Our results highlight the potential of SigPath to monitor phosphoproteomic signaling events and to nominate mechanistic hypotheses regarding oncogenesis, response, and resistance to therapy.

Prion protein quantification in human cerebrospinal fluid as a tool for prion disease drug development.

Reduction of native prion protein (PrP) levels in the brain is an attractive strategy for the treatment or prevention of human prion disease. Clinical development of any PrP-reducing therapeutic will require an appropriate pharmacodynamic biomarker: a practical and robust method for quantifying PrP, and reliably demonstrating its reduction in the central nervous system (CNS) of a living patient. Here we evaluate the potential of ELISA-based quantification of human PrP in human cerebrospinal fluid (CSF) to serve as a biomarker for PrP-reducing therapeutics. We show that CSF PrP is highly sensitive to plastic adsorption during handling and storage, but its loss can be minimized by the addition of detergent. We find that blood contamination does not affect CSF PrP levels, and that CSF PrP and hemoglobin are uncorrelated, together suggesting that CSF PrP is CNS derived, supporting its relevance for monitoring the tissue of interest and in keeping with high PrP abundance in brain relative to blood. In a cohort with controlled sample handling, CSF PrP exhibits good within-subject test-retest reliability (mean coefficient of variation, 13% in samples collected 8-11 wk apart), a sufficiently stable baseline to allow therapeutically meaningful reductions in brain PrP to be readily detected in CSF. Together, these findings supply a method for monitoring the effect of a PrP-reducing drug in the CNS, and will facilitate development of prion disease therapeutics with this mechanism of action.

Patterns of substrate affinity, competition, and degradation kinetics underlie biological activity of thalidomide analogs.

Pharmacologic agents that modulate ubiquitin ligase activity to induce protein degradation are a major new class of therapeutic agents, active in a number of hematologic malignancies. However, we currently have a limited understanding of the determinants of activity of these agents and how resistance develops. We developed and used a novel quantitative, targeted mass spectrometry (MS) assay to determine the relative activities, kinetics, and cell-type specificity of thalidomide and 4 analogs, all but 1 of which are in clinical use or clinical trials for hematologic malignancies. Thalidomide analogs bind the CRL4CRBN ubiquitin ligase and induce degradation of particular proteins, but each of the molecules studied has distinct patterns of substrate specificity that likely underlie the clinical activity and toxicities of each drug. Our results demonstrate that the activity of molecules that induce protein degradation depends on the strength of ligase-substrate interaction in the presence of drug, the levels of the ubiquitin ligase, and the expression level of competing substrates. These findings highlight a novel mechanism of resistance to this class of drugs mediated by competition between substrates for access to a limiting pool of the ubiquitin ligase. We demonstrate that increased expression of a nonessential substrate can lead to decreased degradation of other substrates that are critical for antineoplastic activity of the drug, resulting in drug resistance. These studies provide general rules that govern drug-dependent substrate degradation and key differences between thalidomide analog activity in vitro and in vivo.

Digital Clinics and Mobile Technology Implementation for Mental Health Care.

PURPOSE OF REVIEW: Interest in digital mental health, especially smartphone apps, has expanded in light of limited access to mental health services and the need for remote care during COVID-19. Digital clinics, in which apps are blended into routine care, offer a potential solution to common implementation challenges including low user engagement and lack of clinical integration of apps. RECENT FINDINGS: While the number of mental health apps available in commercial marketplaces continues to rise, there are few examples of successful implementation of these apps into care settings. We review one example of a digital clinic created within an academic medical center and another within the Department of Veterans Affairs. We then discuss how implementation science can inform new efforts to effectively integrate mental health technologies across diverse use cases. Integrating mental health apps into care settings is feasible but requires careful attention to multiple domains that will influence implementation success, including characteristics of the innovation (e.g., utility and complexity of the app), the recipients of the technology (e.g., patients and clinicians), and context (e.g., healthcare system buy-in, reimbursement, and regulatory policies). Examples of effective facilitation strategies that can be utilized to improve implementation efforts include co-production of technology involving all end users, specialized trainings for staff and patients, creation of new team members to aid in app usage (e.g., digital navigators), and re-design of clinical workflows.

Domain-specific Quantification of Prion Protein in Cerebrospinal Fluid by Targeted Mass Spectrometry.

Therapies currently in preclinical development for prion disease seek to lower prion protein (PrP) expression in the brain. Trials of such therapies are likely to rely on quantification of PrP in cerebrospinal fluid (CSF) as a pharmacodynamic biomarker and possibly as a trial endpoint. Studies using PrP ELISA kits have shown that CSF PrP is lowered in the symptomatic phase of disease, a potential confounder for reading out the effect of PrP-lowering drugs in symptomatic patients. Because misfolding or proteolytic cleavage could potentially render PrP invisible to ELISA even if its concentration were constant or increasing in disease, we sought to establish an orthogonal method for CSF PrP quantification. We developed a multi-species targeted mass spectrometry method based on multiple reaction monitoring (MRM) of nine PrP tryptic peptides quantified relative to an isotopically labeled recombinant protein standard for human samples, or isotopically labeled synthetic peptides for nonhuman species. Analytical validation experiments showed process replicate coefficients of variation below 15%, good dilution linearity and recovery, and suitable performance for both CSF and brain homogenate and across humans as well as preclinical species of interest. In n = 55 CSF samples from individuals referred to prion surveillance centers with rapidly progressive dementia, all six human PrP peptides, spanning the N- and C-terminal domains of PrP, were uniformly reduced in prion disease cases compared with individuals with nonprion diagnoses. Thus, lowered CSF PrP concentration in prion disease is a genuine result of the disease process and not an artifact of ELISA-based measurement. As a result, dose-finding studies for PrP lowering drugs may need to be conducted in presymptomatic at-risk individuals rather than in symptomatic patients. We provide a targeted mass spectrometry-based method suitable for preclinical quantification of CSF PrP as a tool for drug development.

Secretion induces cell pH dynamics impacting assembly-disassembly of the fusion protein complex: A combined fluorescence and atomic force microscopy study.

A wide range of cellular activities including protein folding and cell secretion, such as neurotransmission or insulin release, are all governed by intracellular pH homeostasis, underscoring the importance of pH on critical life processes. Nano- scale pH measurements of cells and biomolecules therefore hold great promise in understanding a plethora of cellular functions, in addition to disease detection and therapy. In the current study, a novel approach using cadmium telluride quantum dots (CdTeQDs) as pH sensors, combined with fluorescent imaging, spectrofluorimetry, atomic force microscopy (AFM), and Western blot analysis, enabled the study of intracellular pH dynamics at 1 milli-pH sensitivity and 80nm pixel resolution, during insulin secretion. Additionally, the pH-dependent interaction between membrane fusion proteins, also called the soluble N-ethylmaleimide-sensitive factor activating protein receptor (SNARE), was determined. Glucose stimulation of CdTeQD-loaded insulin secreting Min-6 mouse insulinoma cell line demonstrated the initial (5-6min) intracellular acidification reflected as a loss in QD fluorescence, followed by alkalization and a return to resting pH in 10min. Analysis of the SNARE complex in insulin secreting Min-6 cells demonstrated an initial gain followed by loss of complexed SNAREs in 10min. Stabilization of the SNARE complex at low intracellular pH is further supported by results from studies utilizing both native and AFM measurements of liposome-reconstituted recombinant neuronal SNAREs, providing a molecular understanding of the role of pH during cell secretion.

Spontaneous Glycan Reattachment Following N-Glycanase Treatment of Influenza and HIV Vaccine Antigens.

In cells, asparagine/N-linked glycans are added to glycoproteins cotranslationally, in an attachment process that supports proper folding of the nascent polypeptide. We found that following pruning of N-glycan by the amidase PNGase F, the principal influenza vaccine antigen and major viral spike protein hemagglutinin (HA) spontaneously reattached N-glycan to its de-N-glycosylated positions when the amidase was removed from solution. This reaction, which we term N-glycanation, was confirmed by site-specific analysis of HA glycoforms by mass spectrometry prior to PNGase F exposure, during exposure to PNGase F, and after amidase removal. Iterative rounds of de-N-glycosylation followed by N-glycanation could be repeated at least three times and were observed for other viral glycoproteins/vaccine antigens, including the envelope glycoprotein (Env) from HIV. Covalent N-glycan reattachment was nonenzymatic as it occurred in the presence of metal ions that inhibit PNGase F activity. Rather, N-glycanation relied on a noncovalent assembly between protein and glycan, formed in the presence of the amidase, where linearization of the glycoprotein prevented this retention and subsequent N-glycanation. This reaction suggests that under certain experimental conditions, some glycoproteins can organize self-glycan addition, highlighting a remarkable self-assembly principle that may prove useful for re-engineering therapeutic glycoproteins such as influenza HA or HIV Env, where glycan sequence and structure can markedly affect bioactivity and vaccine efficacy.

Nanoscale imaging using differential expansion microscopy.

Expensive and time-consuming approaches of immunoelectron microscopy of biopsy tissues continues to serve as the gold-standard for diagnostic pathology. The recent development of the new approach of expansion microscopy (ExM) capable of fourfold lateral expansion of biological specimens for their morphological examination at approximately 70 nm lateral resolution using ordinary diffraction limited optical microscopy, is a major advancement in cellular imaging. Here we report (1) an optimized fixation protocol for retention of cellular morphology while obtaining optimal expansion, (2) an ExM procedure for up to eightfold lateral and over 500-fold volumetric expansion, (3) demonstrate that ExM is anisotropic or differential between tissues, cellular organelles and domains within organelles themselves, and (4) apply image analysis and machine learning (ML) approaches to precisely assess differentially expanded cellular structures. We refer to this enhanced ExM approach combined with ML as differential expansion microscopy (DiExM), applicable to profiling biological specimens at the nanometer scale. DiExM holds great promise for the precise, rapid and inexpensive diagnosis of disease from pathological specimen slides.

A Qualitative Examination of Stay Quit Coach, A Mobile Application for Veteran Smokers With Posttraumatic Stress Disorder.

INTRODUCTION: Smoking is a lethal public health problem that is common in US military veterans, particularly those with posttraumatic stress disorder (PTSD). Mobile applications (apps) to promote smoking cessation are a scalable and low-cost approach that may facilitate treatment engagement. METHODS: This qualitative study examined the acceptability, user experience, and perceptions of a smoking cessation app, Stay Quit Coach (SQC), when incorporated into evidence-based smoking cessation treatment. US military veterans with PTSD who smoked at least five cigarettes per day for 15 of the past 30 days and stated an interested in cessation were eligible to participate. Participants' baseline comfort levels with mobile technology was measured using the Perceptions of Mobile Phone Interventions Questionnaire-Patient version (PMPIQ-P). At treatment end, semi-structured qualitative interviews were conducted. RESULTS: Twenty participants were enrolled and 17 (85.0%) participated in the qualitative interview at treatment end. PMPIQ-P scores at baseline ranged from 4.97 to 5.25 (SDs = 0.73-1.04), reflecting moderately high comfort with mobile technology among participants. Qualitative analyses indicated that most participants: (1) endorsed mobile technology as an appealing format for smoking cessation treatment, due to convenience and instantaneous access; and (2) expressed highest perceived helpfulness for interactive app features. Recommendations to improve SQC clustered into four thematic areas: (1) increasing personalization, (2) including more self-tracking features, (3) increasing visual cues, and (4) sharing progress with peers. CONCLUSIONS: SQC was perceived as an acceptable and useful tool to support smoking cessation in a sample of veteran smokers with PTSD. Qualitative data provided valuable insights that can inform the continued development of SQC and other apps for smoking cessation. IMPLICATIONS: Given the high lethality associated with cigarette smoking, it is crucial to identify scalable, low-risk strategies to promote smoking cessation, particularly in high-risk populations. Mobile technology is a promising approach that can be used to augment evidence-based smoking cessation treatment. Results of this qualitative study support the use of the SQC mobile app when incorporated into evidence-based smoking cessation treatment for veterans with PTSD and provide future directions for refinement of the SQC app. These findings also highlight the importance of using a patient-centered approach in designing apps intended for a clinical population.

Technology use and preferences for mental health self-management interventions among older veterans.

OBJECTIVES: The United States Department of Veterans Affairs offers numerous technology-delivered interventions to self-manage mental health problems. It is unknown, however, what barriers older military veterans face to using these technologies and how willing they would be to use technologies for mental health concerns. METHODS: Seventy-seven veterans (Mage = 69.16 years; SD = 7.10) completed interviews in a concurrent mixed methods study. Interviewers asked about technology ownership and described four modalities of delivering self-management interventions: printed materials, DVDs, Internet, and mobile apps. Interviewers obtained feedback about each modality's benefits, barriers, and facilitators. Participants ranked their self-management modalities preferences alone and compared with counseling. Multivariable adjusted logistic regression and qualitative analyses were conducted to investigate the reasons contributing to preferences. RESULTS: Most reported owning a computer (84.4%), having home Internet (80.5%), and a smartphone (70.1%). Participants preferred printed materials (35.1%) over mobile apps (28.6%), Internet (24.7%), and DVDs (13.0%). Lower computer proficiency was associated with preferring DVDs; higher proficiency was associated with Internet and mobile interventions. Residing in an urban area was associated with mobile apps. When counseling was an option, 66% identified this as their first preference. Qualitative findings showed veterans' desire for information, training, and provider support with technology. CONCLUSIONS: Older veterans reported high technology ownership rates but varied preferences for self-management interventions. Notably, two-thirds preferred some form of technology, which points to the importance of ensuring that providers offer existing technology-delivered interventions to older veterans. Veterans' strong preference for counseling emphasizes the need for human support alongside self-management.

Clinician Perceptions Related to the Use of the CBT-I Coach Mobile App.

Objective: Clinicians' perceptions of CBT-I Coach, a patient-facing mobile app for cognitive-behavioral therapy for insomnia (CBT-I), are critical to its adoption and integration into practice. Diffusion of innovations theory emphasizes the influence of perceptions, including the relative advantage to current practice, the compatibility to clinicians' needs, the complexity, the innovation's trialability, and observability. This study intended to evaluate the use and perceptions of CBT-I Coach among Veterans Affairs (VA)-trained CBT-I clinicians. Participants and Methods: Clinicians (N = 108) were surveyed about their use, feedback, and perceptions of CBT-I Coach a year after the app became available. Results: Overall perceptions of CBT-I Coach were favorable. Fifty percent of clinicians reported using CBT-I Coach, with 98% intending to continue use. The app was perceived to increase sleep diary completion and homework compliance. Clinicians viewed the app as providing accessibility to helpful tools and improving patient engagement. Of those not using the app, 83% endorsed intention to use it. Reasons for nonuse were lack of patient access to smart phones, not being aware of the app, not having time to learn it, and inability to directly access app data. Those who reported using CBT-I Coach had more favorable perceptions across all constructs (p < .01 - p < .001), except relative advantage, compared to nonusers. Users perceived it as less complex and more compatible with their practice than nonusers. Conclusions: Continued efforts are needed to increase adoption and enhance use of CBT-I Coach, as well as study if reported benefits can be evidenced more directly.

Nanothermometry Reveals Calcium-Induced Remodeling of Myosin.

Ions greatly influence protein structure-function and are critical to health and disease. A 10, 000-fold higher calcium in the sarcoplasmic reticulum (SR) of muscle suggests elevated calcium levels near active calcium channels at the SR membrane and the impact of localized high calcium on the structure-function of the motor protein myosin. In the current study, combined quantum dot (QD)-based nanothermometry and circular dichroism (CD) spectroscopy enabled detection of previously unknown enthalpy changes and associated structural remodeling of myosin, impacting its function following exposure to elevated calcium. Cadmium telluride QDs adhere to myosin, function as thermal sensors, and reveal that exposure of myosin to calcium is exothermic, resulting in lowering of enthalpy, a decrease in alpha helical content measured using CD spectroscopy, and the consequent increase in motor efficiency. Isolated muscle fibers subjected to elevated levels of calcium further demonstrate fiber lengthening and decreased motility of actin filaments on myosin-functionalized substrates. Our results, in addition to providing new insights into our understanding of muscle structure-function, establish a novel approach to understand the enthalpy of protein-ion interactions and the accompanying structural changes that may occur within the protein molecule.

Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes.

Profiling post-translational modifications represents an alternative dimension to gene expression data in characterizing cellular processes. Many cellular responses to drugs are mediated by changes in cellular phosphosignaling. We sought to develop a common platform on which phosphosignaling responses could be profiled across thousands of samples, and created a targeted MS assay that profiles a reduced-representation set of phosphopeptides that we show to be strong indicators of responses to chemical perturbagens.To develop the assay, we investigated the coordinate regulation of phosphosites in samples derived from three cell lines treated with 26 different bioactive small molecules. Phosphopeptide analytes were selected from these discovery studies by clustering and picking 1 to 2 proxy members from each cluster. A quantitative, targeted parallel reaction monitoring assay was developed to directly measure 96 reduced-representation probes. Sample processing for proteolytic digestion, protein quantification, peptide desalting, and phosphopeptide enrichment have been fully automated, making possible the simultaneous processing of 96 samples in only 3 days, with a plate phosphopeptide enrichment variance of 12%. This highly reproducible process allowed ∼95% of the reduced-representation phosphopeptide probes to be detected in ∼200 samples.The performance of the assay was evaluated by measuring the probes in new samples generated under treatment conditions from discovery experiments, recapitulating the observations of deeper experiments using a fraction of the analytical effort. We measured these probes in new experiments varying the treatments, cell types, and timepoints to demonstrate generalizability. We demonstrated that the assay is sensitive to disruptions in common signaling pathways (e.g. MAPK, PI3K/mTOR, and CDK). The high-throughput, reduced-representation phosphoproteomics assay provides a platform for the comparison of perturbations across a range of biological conditions, suitable for profiling thousands of samples. We believe the assay will prove highly useful for classification of known and novel drug and genetic mechanisms through comparison of phosphoproteomic signatures.

Nanothermometry Measure of Muscle Efficiency.

Despite recent advances in thermometry, determination of temperature at the nanometer scale in single molecules to live cells remains a challenge that holds great promise in disease detection among others. In the present study, we use a new approach to nanometer scale thermometry with a spatial and thermal resolution of 80 nm and 1 mK respectively, by directly associating 2 nm cadmium telluride quantum dots (CdTe QDs) to the subject under study. The 2 nm CdTe QDs physically adhered to bovine cardiac and rabbit skeletal muscle myosin, enabling the determination of heat released when ATP is hydrolyzed by both myosin motors. Greater heat loss reflects less work performed by the motor, hence decreased efficiency. Surprisingly, we found rabbit skeletal myosin to be more efficient than bovine cardiac. We have further extended this approach to demonstrate the gain in efficiency of Drosophila melanogaster skeletal muscle overexpressing the PGC-1α homologue spargel, a known mediator of improved exercise performance in humans. Our results establish a novel approach to determine muscle efficiency with promise for early diagnosis and treatment of various metabolic disorders including cancer.

Aptamer-Based Proteomic Profiling Reveals Novel Candidate Biomarkers and Pathways in Cardiovascular Disease.

BACKGROUND: Single-stranded DNA aptamers are oligonucleotides of ≈50 base pairs in length selected for their ability to bind proteins with high specificity and affinity. Emerging DNA aptamer-based technologies may address limitations of existing proteomic techniques, including low sample throughput, which have hindered proteomic analyses of large cohorts. METHODS: To identify early biomarkers of myocardial injury, we applied an aptamer-based proteomic platform that measures 1129 proteins to a clinically relevant perturbational model of planned myocardial infarction (PMI), patients undergoing septal ablation for hypertrophic cardiomyopathy. Blood samples were obtained before and at 10 and 60 minutes after PMI, and protein changes were assessed by repeated-measures analysis of variance. The generalizability of our PMI findings was evaluated in a spontaneous myocardial infarction cohort (Wilcoxon rank-sum). We then tested the platform's ability to detect associations between proteins and Framingham Risk Score components in the Framingham Heart Study, performing regression analyses for each protein versus each clinical trait. RESULTS: We found 217 proteins that significantly changed in the peripheral vein blood after PMI in a derivation cohort (n=15; P<5.70E-5). Seventy-nine of these proteins were validated in an independent PMI cohort (n=15; P<2.30E-4); >85% were directionally consistent and reached nominal significance. We detected many protein changes that are novel in the context of myocardial injury, including Dickkopf-related protein 4, a WNT pathway inhibitor (peak increase 124%, P=1.29E-15) and cripto, a growth factor important in cardiac development (peak increase 64%, P=1.74E-4). Among the 40 validated proteins that increased within 1 hour after PMI, 23 were also elevated in patients with spontaneous myocardial infarction (n=46; P<0.05). Framingham Heart Study analyses revealed 156 significant protein associations with the Framingham Risk Score (n=899), including aminoacylase 1 (ß=0.3386, P=2.54E-22) and trigger factor 2 (ß=0.2846, P=5.71E-17). Furthermore, we developed a novel workflow integrating DNA-based immunoaffinity with mass spectrometry to analytically validate aptamer specificity. CONCLUSIONS: Our results highlight an emerging proteomics tool capable of profiling >1000 low-abundance analytes with high sensitivity and high precision, applicable both to well-phenotyped perturbational studies and large human cohorts, as well.

Deep, Quantitative Coverage of the Lysine Acetylome Using Novel Anti-acetyl-lysine Antibodies and an Optimized Proteomic Workflow.

Introduction of antibodies specific for acetylated lysine has significantly improved the detection of endogenous acetylation sites by mass spectrometry. Here, we describe a new, commercially available mixture of anti-lysine acetylation (Kac) antibodies and show its utility for in-depth profiling of the acetylome. Specifically, seven complementary monoclones with high specificity for Kac were combined into a final anti-Kac reagent which results in at least a twofold increase in identification of Kac peptides over a commonly used Kac antibody. We outline optimal antibody usage conditions, effective offline basic reversed phase separation, and use of state-of-the-art LC-MS technology for achieving unprecedented coverage of the acetylome. The methods were applied to quantify acetylation sites in suberoylanilide hydroxamic acid-treated Jurkat cells. Over 10,000 Kac peptides from over 3000 Kac proteins were quantified from a single stable isotope labeling by amino acids in cell culture labeled sample using 7.5 mg of peptide input per state. This constitutes the deepest coverage of acetylation sites in quantitative experiments obtained to-date. The approach was also applied to breast tumor xenograft samples using isobaric mass tag labeling of peptides (iTRAQ4, TMT6 and TMT10-plex reagents) for quantification. Greater than 6700 Kac peptides from over 2300 Kac proteins were quantified using 1 mg of tumor protein per iTRAQ 4-plex channel. The novel reagents and methods we describe here enable quantitative, global acetylome analyses with depth and sensitivity approaching that obtained for other well-studied post-translational modifications such as phosphorylation and ubiquitylation, and should have widespread application in biological and clinical studies employing mass spectrometry-based proteomics.