Publications by authors named "David J Clark"

285 Publications

Proteogenomic characterization of pancreatic ductal adenocarcinoma.

Cell 2021 Sep;184(19):5031-5052.e26

Department of Oncology, Johns Hopkins University, Baltimore, MD 21205, USA.

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient survival. Toward understanding the underlying molecular alterations that drive PDAC oncogenesis, we conducted comprehensive proteogenomic analysis of 140 pancreatic cancers, 67 normal adjacent tissues, and 9 normal pancreatic ductal tissues. Proteomic, phosphoproteomic, and glycoproteomic analyses were used to characterize proteins and their modifications. In addition, whole-genome sequencing, whole-exome sequencing, methylation, RNA sequencing (RNA-seq), and microRNA sequencing (miRNA-seq) were performed on the same tissues to facilitate an integrated proteogenomic analysis and determine the impact of genomic alterations on protein expression, signaling pathways, and post-translational modifications. To ensure robust downstream analyses, tumor neoplastic cellularity was assessed via multiple orthogonal strategies using molecular features and verified via pathological estimation of tumor cellularity based on histological review. This integrated proteogenomic characterization of PDAC will serve as a valuable resource for the community, paving the way for early detection and identification of novel therapeutic targets.
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http://dx.doi.org/10.1016/j.cell.2021.08.023DOI Listing
September 2021

Defining candidate mRNA and protein EV biomarkers to discriminate ccRCC and pRCC from non-malignant renal cells in vitro.

Med Oncol 2021 Jul 31;38(9):105. Epub 2021 Jul 31.

The Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.

Renal cell carcinoma (RCC) accounts for over 400,000 new cases and 175,000 deaths annually. Diagnostic RCC biomarkers may prevent overtreatment in patients with early disease. Extracellular vesicles (EVs) are a promising source of RCC biomarkers because EVs carry proteins and messenger RNA (mRNA) among other biomolecules. We aimed to identify biomarkers and assess biological functions of EV cargo from clear cell RCC (ccRCC), papillary RCC (pRCC), and benign kidney cell lines. EVs were enriched from conditioned cell media by size exclusion chromatography. The EV proteome was assessed using Tandem Mass Tag mass spectrometry (TMT-MS) and NanoString nCounter technology was used to profile 770 cancer-related mRNA present in EVs. The heterogeneity of protein and mRNA abundance and identification highlighted the heterogeneity of EV cargo, even between cell lines of a similar pathological group (e.g., ccRCC or pRCC). Overall, 1726 proteins were quantified across all EV samples, including 181 proteins that were detected in all samples. In the targeted profiling of mRNA by NanoString, 461 mRNAs were detected in EVs from at least one cell line, including 159 that were present in EVs from all cell lines. In addition to a shared EV cargo signature, pRCC, ccRCC, and/or benign renal cell lines also showed unique signatures. Using this multi-omics approach, we identified 34 protein candidate pRCC EV biomarkers and 20 protein and 8 mRNA candidate ccRCC EV biomarkers for clinical validation.
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http://dx.doi.org/10.1007/s12032-021-01554-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8325656PMC
July 2021

Unbiased Proteomic and Phosphoproteomic Analysis Identifies Response Signatures and Novel Susceptibilities After Combined MEK and mTOR Inhibition in BRAF Mutant Glioma.

Mol Cell Proteomics 2021 Jul 21;20:100123. Epub 2021 Jul 21.

Division of Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Division of Neuropathology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. Electronic address:

The mitogen-activated protein kinase pathway is one of the most frequently altered pathways in cancer. It is involved in the control of cell proliferation, invasion, and metabolism, and can cause resistance to therapy. A number of aggressive malignancies, including melanoma, colon cancer, and glioma, are driven by a constitutively activating missense mutation (V600E) in the v-Raf murine sarcoma viral oncogene homolog B (BRAF) component of the pathway. Mitogen-activated protein kinase kinase (MEK) inhibition is initially effective in targeting these cancers, but reflexive activation of mammalian target of rapamycin (mTOR) signaling contributes to frequent therapy resistance. We have previously demonstrated that combination treatment with the MEK inhibitor trametinib and the dual mammalian target of rapamycin complex 1/2 inhibitor TAK228 improves survival and decreases vascularization in a BRAF mutant glioma model. To elucidate the mechanism of action of this combination therapy and understand the ensuing tumor response, we performed comprehensive unbiased proteomic and phosphoproteomic characterization of BRAF mutant glioma xenografts after short-course treatment with trametinib and TAK228. We identified 13,313 proteins and 30,928 localized phosphosites, of which 12,526 proteins and 17,444 phosphosites were quantified across all samples (data available via ProteomeXchange; identifier PXD022329). We identified distinct response signatures for each monotherapy and combination therapy and validated that combination treatment inhibited activation of the mitogen-activated protein kinase and mTOR pathways. Combination therapy also increased apoptotic signaling, suppressed angiogenesis signaling, and broadly suppressed the activity of the cyclin-dependent kinases. In response to combination therapy, both epidermal growth factor receptor and class 1 histone deacetylase proteins were activated. This study reports a detailed (phospho)proteomic analysis of the response of BRAF mutant glioma to combined MEK and mTOR pathway inhibition and identifies new targets for the development of rational combination therapies for BRAF-driven tumors.
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http://dx.doi.org/10.1016/j.mcpro.2021.100123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8363840PMC
July 2021

Chronic Pain is Associated With Reduced Sympathetic Nervous System Reactivity During Simple and Complex Walking Tasks: Potential Cerebral Mechanisms.

Chronic Stress (Thousand Oaks) 2021 Jan-Dec;5:24705470211030273. Epub 2021 Jul 7.

Pain Research & Intervention Center of Excellence, University of Florida, University of Florida, Gainesville, FL, USA.

Background: Autonomic dysregulation may lead to blunted sympathetic reactivity in chronic pain states. Autonomic responses are controlled by the central autonomic network (CAN). Little research has examined sympathetic reactivity and associations with brain CAN structures in the presence of chronic pain; thus, the present study aims to investigate how chronic pain influences sympathetic reactivity and associations with CAN brain region volumes.

Methods: Sympathetic reactivity was measured as change in skin conductance level (ΔSCL) between a resting reference period and walking periods for typical and complex walking tasks (obstacle and dual-task). Participants included 31 people with (n = 19) and without (n = 12) chronic musculoskeletal pain. Structural 3 T MRI was used to determine gray matter volume associations with ΔSCL in regions of the CAN (i.e., brainstem, amygdala, insula, and anterior cingulate cortex).

Results: ΔSCL varied across walking tasks (main effect p = 0.036), with lower ΔSCL in chronic pain participants compared to controls across trials 2 and 3 under the obstacle walking condition. ΔSCL during typical walking was associated with multiple CAN gray matter volumes, including brainstem, bilateral insula, amygdala, and right caudal anterior cingulate cortex (p's < 0.05). The difference in ΔSCL from typical-to-obstacle walking were associated with volumes of the midbrain segment of the brainstem and anterior segment of the circular sulcus of the insula (p's < 0.05), with no other significant associations. The difference in ΔSCL from typical-to-dual task walking was associated with the bilateral caudal anterior cingulate cortex, and left rostral cingulate cortex (p's < 0.05).

Conclusions: Sympathetic reactivity is blunted during typical and complex walking tasks in persons with chronic pain. Additionally, blunted sympathetic reactivity is associated with CAN brain structure, with direction of association dependent on brain region. These results support the idea that chronic pain may negatively impact typical autonomic responses needed for walking performance via its potential impact on the brain.
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http://dx.doi.org/10.1177/24705470211030273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8267022PMC
July 2021

Comparison of Long-Term Outcomes in Men versus Women Undergoing Percutaneous Coronary Intervention.

Am J Cardiol 2021 08 6;153:1-8. Epub 2021 Jul 6.

Department of Cardiology, Austin Health, Melbourne, Australia; University of Melbourne, Melbourne, Australia. Electronic address:

There has been a significant decrease in mortality associated with coronary artery disease (CAD) in recent decades, although at discordant rates between men and women. Using a well-established multicenter registry, we sought to examine the impact of gender on long-term mortality stratified by indication for percutaneous coronary intervention (PCI). Data from 54,440 consecutive patients (12,805, 23.5% women) undergoing PCI from the Victorian Cardiac Outcomes Registry (2013 to 2018) were analyzed. We aimed to compare gender-related differences of patients undergoing PCI for stable angina pectoris (SAP), non-ST-elevation acute coronary syndrome (NSTEACS) and ST-elevation myocardial infarction (STEMI). The primary outcome was long-term all-cause mortality. Female patients were older across all indications (SAP: 67 vs 71 years, NSTEACS: 64 vs 69 years, STEMI 61 vs 67 years; p value for all <0.001), with age-adjusted higher rates of diabetes mellitus (p value for all <0.02) and renal impairment (p value for all <0.001), and were more likely to have femoral artery access for intervention (p value for all <0.001). Unadjusted in-hospital and 30-day mortality rates were comparable between men and women across all indications. Compared to men, women had a higher rate of unadjusted long-term mortality (9.0% vs 7.37%; p <0.001). However, after adjusting for variables significant on univariate analysis, female gender was independently associated with improved long-term survival (HR 0.76, 95% CI 0.66 to 0.87; p <0.001). In conclusion, contrary to previous studies, despite being older with a differing clinical profile and interventional approach, women undergoing PCI have a long-term survival advantage.
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http://dx.doi.org/10.1016/j.amjcard.2021.05.013DOI Listing
August 2021

Prevalence of neutralising antibodies against SARS-CoV-2 in acute infection and convalescence: A systematic review and meta-analysis.

PLoS Negl Trop Dis 2021 07 8;15(7):e0009551. Epub 2021 Jul 8.

Departments of Clinical Sciences and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.

Background: Individuals infected with SARS-CoV-2 develop neutralising antibodies. We investigated the proportion of individuals with SARS-CoV-2 neutralising antibodies after infection and how this proportion varies with selected covariates.

Methodology/principal Findings: This systematic review and meta-analysis examined the proportion of individuals with SARS-CoV-2 neutralising antibodies after infection and how these proportions vary with selected covariates. Three models using the maximum likelihood method assessed these proportions by study group, covariates and individually extracted data (protocol CRD42020208913). A total of 983 reports were identified and 27 were included. The pooled (95%CI) proportion of individuals with neutralising antibodies was 85.3% (83.5-86.9) using the titre cut off >1:20 and 83.9% (82.2-85.6), 70.2% (68.1-72.5) and 54.2% (52.0-56.5) with titres >1:40, >1:80 and >1:160, respectively. These proportions were higher among patients with severe COVID-19 (e.g., titres >1:80, 84.8% [80.0-89.2], >1:160, 74.4% [67.5-79.7]) than those with mild presentation (56.7% [49.9-62.9] and 44.1% [37.3-50.6], respectively) and lowest among asymptomatic infections (28.6% [17.9-39.2] and 10.0% [3.7-20.1], respectively). IgG and neutralising antibody levels correlated poorly.

Conclusions/significance: 85% of individuals with proven SARS-CoV-2 infection had detectable neutralising antibodies. This proportion varied with disease severity, study setting, time since infection and the method used to measure antibodies.
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http://dx.doi.org/10.1371/journal.pntd.0009551DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8291969PMC
July 2021

High-Throughput Analyses of Glycans, Glycosites, and Intact Glycopeptides Using C4-and C18/MAX-Tips and Liquid Handling System.

Curr Protoc 2021 Jul;1(7):e186

Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, Maryland.

Protein glycosylation is one of the most common and diverse modifications. Aberrant protein glycosylation has been reported to associate with various diseases. High-throughput and comprehensive characterization of glycoproteins is crucial for structural and functional studies of altered glycosylation in biological, physiological, and pathological processes. In this protocol, we detail a workflow for comprehensive analyses of intact glycopeptides (IGPs), glycosylation sites, and glycans from N-linked glycoproteins. By utilizing liquid handling systems, our workflow could enrich IGPs in a high-throughput manner while reducing sample processing time and human error involved in traditional proteomics sample processing techniques. Together, our workflow enables a high-throughput enrichment of glycans, glycosites, and intact glycopeptides from complex biological or clinical samples. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Enzymatic digestion of glycoproteins using C4-tips Basic Protocol 2: Intact glycopeptide analysis using C18/MAX-tips Basic Protocol 3: Glycan and glycosite analysis.
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http://dx.doi.org/10.1002/cpz1.186DOI Listing
July 2021

Brain activity during walking in older adults: Implications for compensatory versus dysfunctional accounts.

Neurobiol Aging 2021 09 31;105:349-364. Epub 2021 May 31.

Department of Applied Physiology and Kinesiology, University of Florida, Gainesville, FL, USA; Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL, USA.

A prominent trend in the functional brain imaging literature is that older adults exhibit increased brain activity compared to young adults to perform a given task. This phenomenon has been extensively studied for cognitive tasks, with the field converging on interpretations described in two alternative accounts. One account interprets over-activation in older adults as reflecting neural dysfunction (increased brain activity - indicates poorer performance), whereas another interprets it as neural compensation (increased brain activity - supports better performance). Here we review studies that have recorded brain activity and walking measurements in older adults, and we categorize their findings as reflecting either neural dysfunction or neural compensation. Based on this synthesis, we recommend including multiple task difficulty levels in future work to help differentiate if and when compensation fails as the locomotion task becomes more difficult. Using multiple task difficulty levels with neuroimaging will lead to a more advanced understanding of how age-related changes in locomotor brain activity fit with existing accounts of brain aging and support the development of targeted neural rehabilitation techniques.
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http://dx.doi.org/10.1016/j.neurobiolaging.2021.05.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8338893PMC
September 2021

Safety and Long-Term Clinical Outcomes of Fractional Flow Reserve Guided Coronary Revascularisation.

Heart Lung Circ 2021 Sep 26;30(9):1343-1347. Epub 2021 Mar 26.

Department of Cardiology, Austin Health, Melbourne, Vic, Australia; University of Melbourne, Melbourne, Vic, Australia. Electronic address:

Background: Increasingly, fractional flow reserve (FFR) is employed to assess coronary artery stenoses although there is limited real world long-term outcome data with a recent report questioning its safety. This study aimed to assess the in-hospital complications and clinical outcomes up to 10 years after FFR-guided revascularisation at a tertiary Australian hospital.

Methods: The cohort comprised 274 consecutive patients undergoing FFR from 2010 to 2015 with follow-up to 2020. In-hospital complications and long-term outcomes were compared between patients with FFR≤0.80 and FFR>0.80. Major adverse cardiac events (MACE) comprised cardiac death, myocardial infarction (MI) and target vessel revascularisation (TVR).

Results: The FFR was ≤0.80 in 166 and >0.80 in 108 patients. Stable coronary disease was present in 95%. Revascularisation was undertaken in 86.7% of the FFR≤0.80 group and in 2.8% of the group with an FFR>0.80. In-hospital adverse events were 3.3% with no pressure wire-related coronary dissection, stroke or death. At median follow-up of 5 years, patients with FFR≤0.80 and FFR>0.80 had a similar rate of cardiac death (2.6% versus 5.0%, p=0.335) and MI (2.6% versus 6.9%, p=0.154). In the FFR>0.80 group, MACE (17.8% v 7.9%; p=0.018) and TVR (12.9% v 5.3%; p=0.033) were significantly higher.

Conclusion: This observational study highlights the safety and long-term effectiveness of FFR-guided coronary revascularisation in patients with predominantly stable disease.
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http://dx.doi.org/10.1016/j.hlc.2021.02.009DOI Listing
September 2021

Rehabilitation with accurate adaptability walking tasks or steady state walking: A randomized clinical trial in adults post-stroke.

Clin Rehabil 2021 Aug 16;35(8):1196-1206. Epub 2021 Mar 16.

Department of Physical Therapy, University of Florida, Gainesville, FL, USA.

Objective: To assess changes in walking function and walking-related prefrontal cortical activity following two post-stroke rehabilitation interventions: an accurate adaptability (ACC) walking intervention and a steady state (SS) walking intervention.

Design: Randomized, single blind, parallel group clinical trial.

Setting: Hospital research setting.

Subjects: Adults with chronic post-stroke hemiparesis and walking deficits.

Interventions: ACC emphasized stepping accuracy and walking adaptability, while SS emphasized steady state, symmetrical stepping. Both included 36 sessions led by a licensed physical therapist. ACC walking tasks recruit cortical regions that increase corticospinal tract activation, while SS walking activates the corticospinal tract less intensely.

Main Measures: The primary functional outcome measure was preferred steady state walking speed. Prefrontal brain activity during walking was measured with functional near infrared spectroscopy to assess executive control demands. Assessments were conducted at baseline, post-intervention (three months), and follow-up (six months).

Results: Thirty-eight participants were randomized to the study interventions (mean age 59.6 ± 9.1 years; mean months post-stroke 18.0 ± 10.5). Preferred walking speed increased from baseline to post-intervention by 0.13 ± 0.11 m/s in the ACC group and by 0.14 ± 0.13 m/s in the SS group. The Time × Group interaction was not statistically significant ( = 0.86). Prefrontal fNIRS during walking decreased from baseline to post-intervention, with a marginally larger effect in the ACC group ( = 0.05).

Conclusions: The ACC and SS interventions produced similar changes in walking function. fNIRS suggested a potential benefit of ACC training for reducing demand on prefrontal (executive) resources during walking.
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http://dx.doi.org/10.1177/02692155211001682DOI Listing
August 2021

Comparison of Long-Term Outcomes After Percutaneous Coronary Intervention in Patients With Insulin-Treated Versus Non-Insulin Treated Diabetes Mellitus.

Am J Cardiol 2021 06 3;148:36-43. Epub 2021 Mar 3.

School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia; Department of Cardiology, Royal Melbourne Hospital, Melbourne, Australia; Department of Medicine, University of Melbourne, Melbourne, Australia. Electronic address:

There are conflicting data on whether patients with insulin-treated diabetes mellitus (ITDM) have poorer outcomes compared with non-insulin treated diabetic (non-ITDM) patients following percutaneous coronary intervention (PCI). We therefore compared clinical outcomes following PCI in ITDM versus non-ITDM patients. We prospectively collected data on 4,579 patients with diabetes underwent PCI between 2005 and 2014 in a large multicenter registry and dichotomized them as having ITDM (n = 1,111) or non-ITDM (n = 3,468). The non-ITDM group was further divided into diet control only (diet-DM; n = 786) and those taking oral hypoglycemic agents (OHG-DM; n = 2,639), and clinical outcomes were compared with ITDM patients. Median follow-up for long-term mortality was 4.2 years (IQR 2.0 to 6.6 years). ITDM patients were more likely to be female, obese, and have severe renal impairment (all p <0.001). Procedural characteristics were similar other than a greater use of drug-eluting stents in ITDM patients. On multivariable analysis, ITDM was an independent predictor of 12-month major adverse cardiovascular and cerebrovascular events (MACCE; OR 1.26, 95% CI 1.02 to1.55, p = 0.03). Dividing the non-ITDM group further by treatment, a progressively higher rate of 12-month MACCE across the 3 groups was observed (13.5% vs 17.9% vs 21.8%; p <0.001). Long-term mortality was similar in the diet-DM and OHG-DM groups, but significantly higher in the ITDM group on Kaplan-Meier analysis (log-rank p <0.001). In conclusion, there is a clear gradient of adverse outcomes with escalation of therapy from diet control to OHGs to insulin.
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http://dx.doi.org/10.1016/j.amjcard.2021.02.025DOI Listing
June 2021

Invasive versus Conservative Management in Patients ≥85 years presenting with Non-ST Elevation Myocardial Infarction.

Intern Med J 2021 Mar 1. Epub 2021 Mar 1.

Department of Cardiology, Austin Health, Melbourne, Victoria, Australia.

Background: Guidelines recommend early coronary angiography (CA) in patients with non-ST-elevation myocardial infarction (NSTEMI), irrespective of age. However, elderly patients are less likely to be treated according to these guidelines due to their perceived high risk and medical comorbidities. Whether an invasive strategy is associated with improved survival in patients aged ≥85 years remains uncertain due to their exclusion from randomised trials.

Methods: Consecutive patients aged ≥85 years presenting to a tertiary centre with NSTEMI between 2008-18 were included in this retrospective cohort study. Patients were stratified based on whether they underwent invasive management with CA with a view to revascularisation versus conservative management. The primary outcome was long-term mortality.

Results: Of 7,591 patients with NSTEMI, 1052 patients ≥85years were included. 99(9.4%) patients underwent CA. Those undergoing CA were more likely to be younger, male, live independently, without mobility or cognitive issues (all p<0.01). Overall, 495(47%) patients died during a mean follow-up of 1.3±1 year. On Cox regression, after adjusting for age, pre-morbid functional status, cognition and cardiovascular risk factors, invasive management was the strongest predictor for survival (HR 0.47; 95%CI 0.26-0.85; p=0.01). Invasive management was associated with a trend to increased risk of in-hospital bleeding (6.1% vs 2.6%, p=0.054) with no significant difference in stroke (2.0% vs 3.8%, p=0.37).

Conclusion: In patients aged ≥85 years who presented with NSTEMI, invasive management was associated with improved survival without significant differences in bleeding or stroke. A randomised controlled study assessing the efficacy and safety of invasive management in very elderly patients with NSTEMI is warranted. This article is protected by copyright. All rights reserved.
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http://dx.doi.org/10.1111/imj.15258DOI Listing
March 2021

The yeast ISW1b ATP-dependent chromatin remodeler is critical for nucleosome spacing and dinucleosome resolution.

Sci Rep 2021 Feb 18;11(1):4195. Epub 2021 Feb 18.

Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Building 6A Room 2A02, 6 Center Drive, Bethesda, MD, 20892, USA.

Isw1 and Chd1 are ATP-dependent nucleosome-spacing enzymes required to establish regular arrays of phased nucleosomes near transcription start sites of yeast genes. Cells lacking both Isw1 and Chd1 have extremely disrupted chromatin, with weak phasing, irregular spacing and a propensity to form close-packed dinucleosomes. The Isw1 ATPase subunit occurs in two different remodeling complexes: ISW1a (composed of Isw1 and Ioc3) and ISW1b (composed of Isw1, Ioc2 and Ioc4). The Ioc4 subunit of ISW1b binds preferentially to the H3-K36me3 mark. Here we show that ISW1b is primarily responsible for setting nucleosome spacing and resolving close-packed dinucleosomes, whereas ISW1a plays only a minor role. ISW1b and Chd1 make additive contributions to dinucleosome resolution, such that neither enzyme is capable of resolving all dinucleosomes on its own. Loss of the Set2 H3-K36 methyltransferase partly phenocopies loss of Ioc4, resulting in increased dinucleosome levels with only a weak effect on nucleosome spacing, suggesting that Set2-mediated H3-K36 trimethylation contributes to ISW1b-mediated dinucleosome separation. The H4 tail domain is required for normal nucleosome spacing but not for dinucleosome resolution. We conclude that the nucleosome spacing and dinucleosome resolving activities of ISW1b and Chd1 are critical for normal global chromatin organisation.
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http://dx.doi.org/10.1038/s41598-021-82842-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7892562PMC
February 2021

Does Falls Efficacy Influence the Relationship Between Forward and Backward Walking Speed After Stroke?

Phys Ther 2021 05;101(5)

University of Florida, Gainesville, Florida, USA.

Objective: Forward walking speed (FWS) is known to be an important predictor of mobility, falls, and falls-related efficacy poststroke. However, backward walking speed (BWS) is emerging as an assessment tool to reveal mobility deficits in people poststroke that may not be apparent with FWS alone. Since backward walking is more challenging than forward walking, falls efficacy may play a role in the relationship between one's preferred FWS and BWS. We tested the hypothesis that people with lower falls efficacy would have a stronger positive relationship between FWS and BWS than those with higher falls efficacy.

Methods: Forty-five individuals (12.9 ± 5.6 months poststroke) participated in this observational study. We assessed FWS with the 10-meter walk test and BWS with the 3-meter backward walk test. The modified Falls-Efficacy Scale (mFES) quantified falls efficacy. A moderated regression analysis examined the hypothesis.

Results: FWS was positively associated with BWS (R2 = 0.26). The addition of the interaction term FWS × mFES explained 7.6% additional variance in BWS. As hypothesized, analysis of the interaction revealed that people with lower falls efficacy (mFES ≤ 6.6) had a significantly positive relationship between their preferred FWS and BWS, whereas people with higher falls efficacy (mFES > 6.6) had no relationship between their walking speed in the 2 directions.

Conclusions: FWS is positively related to BWS poststroke, but this relationship is influenced by one's perceived falls efficacy. Our results suggest that BWS can be predicted from FWS in people with lower falls efficacy, but as falls efficacy increases, BWS becomes a separate and unassociated construct from FWS.

Impact: This study provides unique evidence that the degree of falls efficacy significantly influences the relationship between FWS and BWS poststroke. Physical therapists should examine both FWS and BWS in people with higher falls efficacy, but further investigation is warranted for those with lower falls efficacy.
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http://dx.doi.org/10.1093/ptj/pzab050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8152901PMC
May 2021

Global histone protein surface accessibility in yeast indicates a uniformly loosely packed genome with canonical nucleosomes.

Epigenetics Chromatin 2021 Jan 11;14(1). Epub 2021 Jan 11.

Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA.

Background: The vast majority of methods available to characterize genome-wide chromatin structure exploit differences in DNA accessibility to nucleases or chemical crosslinking. We developed a novel method to gauge genome-wide accessibility of histone protein surfaces within nucleosomes by assessing reactivity of engineered cysteine residues with a thiol-specific reagent, biotin-maleimide (BM).

Results: Yeast nuclei were obtained from cells expressing the histone mutant H2B S116C, in which a cysteine resides near the center of the external flat protein surface of the nucleosome. BM modification revealed that nucleosomes are generally equivalently accessible throughout the S. cerevisiae genome, including heterochromatic regions, suggesting limited, higher-order chromatin structures in which this surface is obstructed by tight nucleosome packing. However, we find that nucleosomes within 500 bp of transcription start sites exhibit the greatest range of accessibility, which correlates with the density of chromatin remodelers. Interestingly, accessibility is not well correlated with RNA polymerase density and thus the level of gene expression. We also investigated the accessibility of cysteine mutations designed to detect exposure of histone surfaces internal to the nucleosome thought to be accessible in actively transcribed genes: H3 102, is at the H2A-H2B dimer/H3-H4 tetramer interface, and H3 A110C, resides at the H3-H3 interface. However, in contrast to the external surface site, we find that neither of these internal sites were found to be appreciably exposed.

Conclusions: Overall, our finding that nucleosomes surfaces within S. cerevisiae chromatin are equivalently accessible genome-wide is consistent with a globally uncompacted chromatin structure lacking substantial higher-order organization. However, we find modest differences in accessibility that correlate with chromatin remodelers but not transcription, suggesting chromatin poised for transcription is more accessible than actively transcribed or intergenic regions. In contrast, we find that two internal sites remain inaccessible, suggesting that such non-canonical nucleosome species generated during transcription are rapidly and efficiently converted to canonical nucleosome structure and thus not widely present in native chromatin.
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http://dx.doi.org/10.1186/s13072-020-00381-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7802155PMC
January 2021

Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma.

Cancer Cell 2021 03 7;39(3):361-379.e16. Epub 2021 Jan 7.

Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.

We present a proteogenomic study of 108 human papilloma virus (HPV)-negative head and neck squamous cell carcinomas (HNSCCs). Proteomic analysis systematically catalogs HNSCC-associated proteins and phosphosites, prioritizes copy number drivers, and highlights an oncogenic role for RNA processing genes. Proteomic investigation of mutual exclusivity between FAT1 truncating mutations and 11q13.3 amplifications reveals dysregulated actin dynamics as a common functional consequence. Phosphoproteomics characterizes two modes of EGFR activation, suggesting a new strategy to stratify HNSCCs based on EGFR ligand abundance for effective treatment with inhibitory EGFR monoclonal antibodies. Widespread deletion of immune modulatory genes accounts for low immune infiltration in immune-cold tumors, whereas concordant upregulation of multiple immune checkpoint proteins may underlie resistance to anti-programmed cell death protein 1 monotherapy in immune-hot tumors. Multi-omic analysis identifies three molecular subtypes with high potential for treatment with CDK inhibitors, anti-EGFR antibody therapy, and immunotherapy, respectively. Altogether, proteogenomics provides a systematic framework to inform HNSCC biology and treatment.
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http://dx.doi.org/10.1016/j.ccell.2020.12.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7946781PMC
March 2021

Correction: Chromatin remodeler Ino80C acts independently of H2A.Z to evict promoter nucleosomes and stimulate transcription of highly expressed genes in yeast.

Nucleic Acids Res 2021 01;49(1):599

Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1093/nar/gkaa1212DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7797040PMC
January 2021

Comparison of Long-Term Mortality in Patients With Single Coronary Narrowing and Diabetes Mellitus to That of Patients With Multivessel Coronary Narrowing Without Diabetes Mellitus.

Am J Cardiol 2021 03 5;142:1-4. Epub 2020 Dec 5.

Department of Cardiology, Austin Health, Melbourne, Australia; The University of Melbourne, Parkville, Victoria, Australia. Electronic address:

It is well recognized that patients with diabetes mellitus (DM) and multivessel coronary artery disease (MVD) undergoing percutaneous coronary intervention (PCI) have poorer long-term outcomes compared with those undergoing coronary artery bypass grafting. However, the relative impact of DM status and extent of coronary artery disease on long term mortality in patients undergoing PCI is unknown. We sought to compare patients with DM undergoing PCI for single and multivessel disease to their non-DM counterparts. Overall, 34,690 consecutive patients undergoing PCI from the Melbourne Interventional Group registry (2005 to 2017) were included (mean age 64.5 ± 12 years, 76.6% male). Our cohort was stratified by the presence of DM and extent of CAD (DM-SVD [single-vessel disease] [n = 2,669], DM-MVD [n = 6,118], no-DM-SVD [n = 10,993], no-DM-MVD [n = 14,910]). DM-SVD and no-DM-MVD cohorts demonstrated comparable baseline cardiovascular risk profiles, although the no-DM-MVD cohort had higher rates of prior myocardial infarction, while the DM-SVD cohort had a higher proportion of patients with renal impairment. Over a median follow-up of 4.8 (IQR 2.0 to 8.2) years, 6,031 (17.5%) patients died. Using the no-DM-SVD group as the reference category, adjusted risk of mortality was highest in the MVD-DM cohort (HR 1.90; 95% CI 1.71 to 2.09). Similar adjusted risk of long-term mortality was observed in the DM-SVD (HR 1.32, 95%CI 1.15 to 1.51) and no-DM-MVD (HR 1.30, 95%CI 1.20 to 1.40) groups. In conclusion, we found that the long-term mortality of patients with DM and SVD undergoing PCI was the risk equivalent of non-DM patients with MVD.
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http://dx.doi.org/10.1016/j.amjcard.2020.11.036DOI Listing
March 2021

IgG Seroconversion and Pathophysiology in Severe Acute Respiratory Syndrome Coronavirus 2 Infection.

Emerg Infect Dis 2021 01 30;27(1). Epub 2020 Nov 30.

We investigated the dynamics of seroconversion in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. During March 29-May 22, 2020, we collected serum samples and associated clinical data from 177 persons in London, UK, who had SARS-CoV-2 infection. We measured IgG against SARS-CoV-2 and compared antibody levels with patient outcomes, demographic information, and laboratory characteristics. We found that 2.0%-8.5% of persons did not seroconvert 3-6 weeks after infection. Persons who seroconverted were older, were more likely to have concurrent conditions, and had higher levels of inflammatory markers. Non-White persons had higher antibody concentrations than those who identified as White; these concentrations did not decline during follow-up. Serologic assay results correlated with disease outcome, race, and other risk factors for severe SARS-CoV-2 infection. Serologic assays can be used in surveillance to clarify the duration and protective nature of humoral responses to SARS-CoV-2 infection.
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http://dx.doi.org/10.3201/eid2701.203074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7774532PMC
January 2021

Innovations in Geroscience to enhance mobility in older adults.

Exp Gerontol 2020 12 22;142:111123. Epub 2020 Oct 22.

University of Florida, Department of Psychology, 945 Center Drive, Gainesville, FL 32611, United States. Electronic address:

Aging is the primary risk factor for functional decline; thus, understanding and preventing disability among older adults has emerged as an important public health challenge of the 21st century. The science of gerontology - or geroscience - has the practical purpose of "adding life to the years." The overall goal of geroscience is to increase healthspan, which refers to extending the portion of the lifespan in which the individual experiences enjoyment, satisfaction, and wellness. An important facet of this goal is preserving mobility, defined as the ability to move independently. Despite this clear purpose, this has proven to be a challenging endeavor as mobility and function in later life are influenced by a complex interaction of factors across multiple domains. Moreover, findings over the past decade have highlighted the complexity of walking and how targeting multiple systems, including the brain and sensory organs, as well as the environment in which a person lives, can have a dramatic effect on an older person's mobility and function. For these reasons, behavioral interventions that incorporate complex walking tasks and other activities of daily living appear to be especially helpful for improving mobility function. Other pharmaceutical interventions, such as oxytocin, and complementary and alternative interventions, such as massage therapy, may enhance physical function both through direct effects on biological mechanisms related to mobility, as well as indirectly through modulation of cognitive and socioemotional processes. Thus, the purpose of the present review is to describe evolving interventional approaches to enhance mobility and maintain healthspan in the growing population of older adults in the United States and countries throughout the world. Such interventions are likely to be greatly assisted by technological advances and the widespread adoption of virtual communications during and after the COVID-19 era.
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http://dx.doi.org/10.1016/j.exger.2020.111123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7581361PMC
December 2020

Integrated Proteomic and Glycoproteomic Characterization of Human High-Grade Serous Ovarian Carcinoma.

Cell Rep 2020 10;33(3):108276

Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA. Electronic address:

Many gene products exhibit great structural heterogeneity because of an array of modifications. These modifications are not directly encoded in the genomic template but often affect the functionality of proteins. Protein glycosylation plays a vital role in proper protein functions. However, the analysis of glycoproteins has been challenging compared with other protein modifications, such as phosphorylation. Here, we perform an integrated proteomic and glycoproteomic analysis of 83 prospectively collected high-grade serous ovarian carcinoma (HGSC) and 23 non-tumor tissues. Integration of the expression data from global proteomics and glycoproteomics reveals tumor-specific glycosylation, uncovers different glycosylation associated with three tumor clusters, and identifies glycosylation enzymes that were correlated with the altered glycosylation. In addition to providing a valuable resource, these results provide insights into the potential roles of glycosylation in the pathogenesis of HGSC, with the possibility of distinguishing pathological outcomes of ovarian tumors from non-tumors, as well as classifying tumor clusters.
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http://dx.doi.org/10.1016/j.celrep.2020.108276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7970828PMC
October 2020

Obstacle Negotiation in Older Adults: Prefrontal Activation Interpreted Through Conceptual Models of Brain Aging.

Innov Aging 2020 10;4(4):igaa034. Epub 2020 Aug 10.

Brain Rehabilitation Research Center, Malcom Randall VA Medical Center, Gainesville, Florida.

Background And Objectives: The influence of interindividual differences on brain activation during obstacle negotiation and the implications for walking performance are poorly understood in older adults. This study investigated the extent to which prefrontal recruitment during obstacle negotiation is explained by differences in age, executive function, and sex. These data were interpreted according to the Compensation-Related Utilization of Neural Circuits Hypothesis (CRUNCH) framework of brain aging. We also tested the association between prefrontal recruitment and walking performance.

Research Design And Methods: Prefrontal oxygenated hemoglobin concentration (OHb) was measured during typical walking () and obstacle negotiation () tasks in 50 adults aged 65 years and older using functional near-infrared spectroscopy. The primary outcome was the change in prefrontal recruitment (∆PFR), measured as ∆OHb minus ∆OHb. Multiple regression was used to test the relationship between ∆PFR and age, executive function measured by the Trail Making Test, and sex. Pearson's correlation coefficient was used to investigate the association between ∆PFR and the cost of walking speed relative to walking.

Results: Age, executive function, and their interaction significantly predicted greater ∆PFR ( = 0.34, = .01). Participants were subgrouped according to age and executive function to examine the interaction effects. Adults of lower age and with lower executive function exhibited greater ∆PFR during compared to their peers with higher executive function ( = .03). Adults of advanced age exhibited a ceiling of prefrontal recruitment during obstacle negotiation, regardless of executive function level ( = .87). Greater ∆PFR was significantly associated with a smaller cost of ( = 0.3, = .03).

Discussion And Implications: These findings are consistent with the CRUNCH framework: neural inefficiency where a greater amount of brain activation is needed for task performance at a similar level, compensatory overactivation to prevent a steeper decline in task performance, and capacity limitation with a recruitment ceiling effect.
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http://dx.doi.org/10.1093/geroni/igaa034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7508296PMC
August 2020

A consensus guide to using functional near-infrared spectroscopy in posture and gait research.

Gait Posture 2020 10 18;82:254-265. Epub 2020 Sep 18.

Laboratory for Early Markers of Neurodegeneration (LEMON), Center for the Study of Movement, Cognition, and Mobility (CMCM), Neurological Institute, Tel Aviv Sourasky Medical Center, Israel; Department of Neurology, Sackler School of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.

Background: Functional near-infrared spectroscopy (fNIRS) is increasingly used in the field of posture and gait to investigate patterns of cortical brain activation while people move freely. fNIRS methods, analysis and reporting of data vary greatly across studies which in turn can limit the replication of research, interpretation of findings and comparison across works.

Research Question And Methods: Considering these issues, we propose a set of practical recommendations for the conduct and reporting of fNIRS studies in posture and gait, acknowledging specific challenges related to clinical groups with posture and gait disorders.

Results: Our paper is organized around three main sections: 1) hardware set up and study protocols, 2) artefact removal and data processing and, 3) outcome measures, validity and reliability; it is supplemented with a detailed checklist.

Significance: This paper was written by a core group of members of the International Society for Posture and Gait Research and posture and gait researchers, all experienced in fNIRS research, with the intent of assisting the research community to lead innovative and impactful fNIRS studies in the field of posture and gait, whilst ensuring standardization of research.
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http://dx.doi.org/10.1016/j.gaitpost.2020.09.012DOI Listing
October 2020

A Cross-species Model of Dual-Task Walking in Young and Older Humans and Rats.

Front Aging Neurosci 2020 2;12:276. Epub 2020 Sep 2.

Department of Aging and Geriatric Research, College of Medicine, University of Florida, Gainesville, FL, United States.

: Dual-task walking is common in daily life but becomes more difficult with aging. Little is known about the neurobiological mechanisms affecting competing cognitive demands. Translational studies with human and animal models are needed to address this gap. This pilot study investigated the feasibility of implementing a novel cross-species dual-task model in humans and rats and aimed to establish preliminary evidence that the model induces a dual-task cost. : Young and older humans and rats performed an object discrimination task (OD), a baseline task of typical walking (baseline), an alternation turning task on a Figure 8 walking course (Alt), and a dual-task combining object discrimination with the alternation task (AltOD). Primary behavioral assessments including walking speed and correct selections for object discrimination and turning direction. In humans, left prefrontal cortex activity was measured with functional near-infrared spectroscopy (fNIRS). : Human subjects generally performed well on all tasks, but the older adults exhibited a trend for a slowing of walking speed immediately before the turning decision for Alt and AltOD compared to baseline. Older adults also had heightened prefrontal activity relative to young adults for the Alt and AltOD tasks. Older rodents required more training than young rodents to learn the alternation task. When tested on AltOD with and without a 15-s delay between trials, older rodents exhibited a substantial performance deficit for the delayed version on the initial day of testing. Old rats, however, did not show a significant slowing in walking speed with increasing task demand, as was evident in the young rats. : This study demonstrates the feasibility and challenges associated with implementing a cross-species dual-task model. While there was preliminary evidence of dual-task cost in both humans and rats, the magnitude of effects was small and not consistent across species. This is likely due to the relative ease of each task in humans and the walking component in rats not being sufficiently challenging. Future versions of this test should make the cognitive tasks more challenging and the motor task in rats more complex.
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http://dx.doi.org/10.3389/fnagi.2020.00276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7492995PMC
September 2020

SMARTphone-based, early cardiac REHABilitation in patients with acute coronary syndromes: a randomized controlled trial.

Coron Artery Dis 2021 Aug;32(5):432-440

Department of Cardiology, Austin Health.

Background: There are well-documented treatment gaps in secondary prevention of coronary heart disease with a lack of clearly defined strategies to assist early physical activity after acute coronary syndromes (ACS). Smartphone technology may provide an innovative platform to close these gaps.

Objectives: The primary goal of this study was to assess whether a smartphone-based, early cardiac rehabilitation program improved exercise capacity in patients with ACS.

Methods: A total of 206 patients with ACS across six tertiary Australian hospitals were included in this randomized controlled trial. Participants were randomized to usual care (UC; including referral to traditional cardiac rehabilitation), with or without an adjunctive smartphone-based cardiac rehabilitation program (S-CRP) upon hospital discharge. The primary endpoint was change in exercise capacity, measured by the change in 6-minute walk test distance at 8 weeks when compared to baseline, between groups. Secondary endpoints included uptake and adherence to cardiac rehabilitation, changes in cardiac risk factors, psychological well-being and quality of life status.

Results: Of the 168 patients with complete follow-up (age 56 ± 10 years; 16% females), 83 were in the S-CRP. At 8-week follow-up, the S-CRP group had a clinically significant improvement in 6-minute walk test distance (Δ117 ± 76 vs. Δ91 ± 110 m; P = 0.02). Patients in the S-CRP were more likely to participate (87% vs. 51%, P < 0.001) and adhere (72% vs. 22%, P < 0.001) to a cardiac rehabilitation program. Compared to UC, patients receiving S-CRP had similar smoking cessation rates, LDL-cholesterol levels, blood pressure reduction, depression, anxiety and quality of life measures (all P = NS).

Conclusion: In patients with ACS, a S-CRP, as an adjunct to UC improved exercise capacity at 8 weeks in addition to participation and adherence to cardiac rehabilitation (Australian New Zealand Clinical Trials Registry; ACTRN12616000426482).
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http://dx.doi.org/10.1097/MCA.0000000000000938DOI Listing
August 2021

Combining Frontal Transcranial Direct Current Stimulation With Walking Rehabilitation to Enhance Mobility and Executive Function: A Pilot Clinical Trial.

Neuromodulation 2021 Jul 18;24(5):950-959. Epub 2020 Aug 18.

Department of Clinical and Health Psychology, Center for Cognitive Aging and Memory, McKnight Brain Institute, University of Florida, Gainesville, FL, USA.

Objectives: This pilot study assessed whether frontal lobe transcranial direct current stimulation (tDCS) combined with complex walking rehabilitation is feasible, safe, and shows preliminary efficacy for improving walking and executive function.

Materials And Methods: Participants were randomized to one of the following 18-session interventions: active tDCS and rehabilitation with complex walking tasks (Active/Complex); sham tDCS and rehabilitation with complex walking tasks (Sham/Complex); or sham tDCS and rehabilitation with typical walking (Sham/Typical). Active tDCS was delivered over F3 (cathode) and F4 (anode) scalp locations for 20 min at 2 mA intensity. Outcome measures included tests of walking function, executive function, and prefrontal activity measured by functional near infrared spectroscopy.

Results: Ninety percent of participants completed the intervention protocol successfully. tDCS side effects of tingling or burning sensations were low (average rating less than two out of 10). All groups demonstrated gains in walking performance based on within-group effect sizes (d ≥ 0.50) for one or more assessments. The Sham/Typical group showed the greatest gains for walking based on between-group effect sizes. For executive function, the Active/Complex group showed the greatest gains based on moderate to large between-group effect sizes (d = 0.52-1.11). Functional near-infrared spectroscopy (fNIRS) findings suggest improved prefrontal cortical activity during walking.

Conclusions: Eighteen sessions of walking rehabilitation combined with tDCS is a feasible and safe intervention for older adults. Preliminary effects size data indicate a potential improvement in executive function by adding frontal tDCS to walking rehabilitation. This study justifies future larger clinical trials to better understand the benefits of combining tDCS with walking rehabilitation.
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http://dx.doi.org/10.1111/ner.13250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7889743PMC
July 2021

Proteomic approaches for characterizing renal cell carcinoma.

Clin Proteomics 2020 29;17:28. Epub 2020 Jul 29.

Department of Pathology, The Johns Hopkins University, Baltimore, MD 21231 USA.

Renal cell carcinoma is among the top 15 most commonly diagnosed cancers worldwide, comprising multiple sub-histologies with distinct genomic, proteomic, and clinicopathological features. Proteomic methodologies enable the detection and quantitation of protein profiles associated with the disease state and have been explored to delineate the dysregulated cellular processes associated with renal cell carcinoma. In this review we highlight the reports that employed proteomic technologies to characterize tissue, blood, and urine samples obtained from renal cell carcinoma patients. We describe the proteomic approaches utilized and relate the results of studies in the larger context of renal cell carcinoma biology. Moreover, we discuss some unmet clinical needs and how emerging proteomic approaches can seek to address them. There has been significant progress to characterize the molecular features of renal cell carcinoma; however, despite the large-scale studies that have characterized the genomic and transcriptomic profiles, curative treatments are still elusive. Proteomics facilitates a direct evaluation of the functional modules that drive pathobiology, and the resulting protein profiles would have applications in diagnostics, patient stratification, and identification of novel therapeutic interventions.
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http://dx.doi.org/10.1186/s12014-020-09291-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7391522PMC
July 2020

High-dimensional Cytometry (ExCYT) and Mass Spectrometry of Myeloid Infiltrate in Clinically Localized Clear Cell Renal Cell Carcinoma Identifies Novel Potential Myeloid Targets for Immunotherapy.

Mol Cell Proteomics 2020 11 31;19(11):1850-1859. Epub 2020 Jul 31.

Bloomberg-Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Department of Oncology, Johns Hopkins School of Medicine and The Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA. Electronic address:

Renal Cell Carcinoma (RCC) is one of the most commonly diagnosed cancers worldwide with research efforts dramatically improving understanding of the biology of the disease. To investigate the role of the immune system in treatment-naïve clear cell Renal Cell Carcinoma (ccRCC), we interrogated the immune infiltrate in patient-matched ccRCC tumor samples, benign normal adjacent tissue (NAT) and peripheral blood mononuclear cells (PBMCs isolated from whole blood, focusing our attention on the myeloid cell infiltrate. Using flow cytometric, MS, and ExCYT analysis, we discovered unique myeloid populations in PBMCs across patient samples. Furthermore, normal adjacent tissues and ccRCC tissues contained numerous myeloid populations with a unique signature for both tissues. Enrichment of the immune cell (CD45) fraction and subsequent gene expression analysis revealed a number of myeloid-related genes that were differentially expressed. These data provide evidence, for the first time, of an immunosuppressive and pro-tumorigenic role of myeloid cells in early, clinically localized ccRCC. The identification of a number of immune proteins for therapeutic targeting provides a rationale for investigation into the potential efficacy of earlier intervention with single-agent or combination immunotherapy for ccRCC.
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http://dx.doi.org/10.1074/mcp.RA120.002049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7664124PMC
November 2020

Interplay among ATP-Dependent Chromatin Remodelers Determines Chromatin Organisation in Yeast.

Biology (Basel) 2020 Jul 25;9(8). Epub 2020 Jul 25.

Division of Developmental Biology, NICHD, National Institutes of Health, Bethesda, MD 20892, USA.

Cellular DNA is packaged into chromatin, which is composed of regularly-spaced nucleosomes with occasional gaps corresponding to active regulatory elements, such as promoters and enhancers, called nucleosome-depleted regions (NDRs). This chromatin organisation is primarily determined by the activities of a set of ATP-dependent remodeling enzymes that are capable of moving nucleosomes along DNA, or of evicting nucleosomes altogether. In yeast, the nucleosome-spacing enzymes are ISW1 (Imitation SWitch protein 1), Chromodomain-Helicase-DNA-binding (CHD)1, ISW2 (Imitation SWitch protein 2) and INOsitol-requiring 80 (INO80); the nucleosome eviction enzymes are the SWItching/Sucrose Non-Fermenting (SWI/SNF) family, the Remodeling the Structure of Chromatin (RSC) complexes and INO80. We discuss the contributions of each set of enzymes to chromatin organisation. ISW1 and CHD1 are the major spacing enzymes; loss of both enzymes results in major chromatin disruption, partly due to the appearance of close-packed di-nucleosomes. ISW1 and CHD1 compete to set nucleosome spacing on most genes. ISW1 is dominant, setting wild type spacing, whereas CHD1 sets short spacing and may dominate on highly-transcribed genes. We propose that the competing remodelers regulate spacing, which in turn controls the binding of linker histone (H1) and therefore the degree of chromatin folding. Thus, genes with long spacing bind more H1, resulting in increased chromatin compaction. RSC, SWI/SNF and INO80 are involved in NDR formation, either directly by nucleosome eviction or repositioning, or indirectly by affecting the size of the complex that resides in the NDR. The nature of this complex is controversial: some suggest that it is a RSC-bound "fragile nucleosome", whereas we propose that it is a non-histone transcription complex. In either case, this complex appears to serve as a barrier to nucleosome formation, resulting in the formation of phased nucleosomal arrays on both sides.
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http://dx.doi.org/10.3390/biology9080190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7466152PMC
July 2020
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