29 results on '"Douglas J. Chapski"'
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2. Unwind to the beat: chromatin and cardiac conduction
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Douglas J. Chapski and Thomas M. Vondriska
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Medicine - Abstract
How chromatin accessibility and structure endow highly specialized cells with their unique phenotypes is an area of intense investigation. In the mammalian heart, an exclusive subset of cardiac cells comprise the conduction system. Many molecular components of this system are well studied and genetic variation in some of the components induces abnormal cardiac conduction. However, genetic risk for cardiac arrhythmias in human populations also occurs in noncoding regions. A study by Bhattacharyya, Kollipara, et al. in this issue of the JCI examines how chromatin accessibility and structure may explain the mechanisms by which noncoding variants increase susceptibility to cardiac arrhythmias. We discuss the implications of these findings for cell type–specific gene regulation and highlight potential therapeutic strategies to engineer locus-specific epigenomic remodeling in vivo.
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- 2023
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3. Rtf1 Transcriptionally Regulates Neonatal and Adult Cardiomyocyte Biology
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Adam D. Langenbacher, Fei Lu, Lauren Crisman, Zi Yi Stephanie Huang, Douglas J. Chapski, Thomas M. Vondriska, Yibin Wang, Chen Gao, and Jau-Nian Chen
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cardiomyocyte ,heart ,Rtf1 ,PAF1 complex ,transcription regulation ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
The PAF1 complex component Rtf1 is an RNA Polymerase II-interacting transcription regulatory protein that promotes transcription elongation and the co-transcriptional monoubiquitination of histone 2B. Rtf1 plays an essential role in the specification of cardiac progenitors from the lateral plate mesoderm during early embryogenesis, but its requirement in mature cardiac cells is unknown. Here, we investigate the importance of Rtf1 in neonatal and adult cardiomyocytes using knockdown and knockout approaches. We demonstrate that loss of Rtf1 activity in neonatal cardiomyocytes disrupts cell morphology and results in a breakdown of sarcomeres. Similarly, Rtf1 ablation in mature cardiomyocytes of the adult mouse heart leads to myofibril disorganization, disrupted cell–cell junctions, fibrosis, and systolic dysfunction. Rtf1 knockout hearts eventually fail and exhibit structural and gene expression defects resembling dilated cardiomyopathy. Intriguingly, we observed that loss of Rtf1 activity causes a rapid change in the expression of key cardiac structural and functional genes in both neonatal and adult cardiomyocytes, suggesting that Rtf1 is continuously required to support expression of the cardiac gene program.
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- 2023
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4. genomeSidekick: A user-friendly epigenomics data analysis tool
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Junjie Chen, Ashley J. Zhu, René R. S. Packard, Thomas M. Vondriska, and Douglas J. Chapski
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epigenomics ,chromatin ,data visualization ,Shiny app ,bioinformatics ,Computer applications to medicine. Medical informatics ,R858-859.7 - Abstract
Recent advances in epigenomics measurements have resulted in a preponderance of genomic sequencing datasets that require focused analyses to discover mechanisms governing biological processes. In addition, multiple epigenomics experiments are typically performed within the same study, thereby increasing the complexity and difficulty of making meaningful inferences from large datasets. One gap in the sequencing data analysis pipeline is the availability of tools to efficiently browse genomic data for scientists that do not have bioinformatics training. To bridge this gap, we developed genomeSidekick, a graphical user interface written in R that allows researchers to perform bespoke analyses on their transcriptomic and chromatin accessibility or chromatin immunoprecipitation data without the need for command line tools. Importantly, genomeSidekick outputs lists of up- and downregulated genes or chromatin features with differential accessibility or occupancy; visualizes omics data using interactive volcano plots; performs Gene Ontology analyses locally; and queries PubMed for selected gene candidates for further evaluation. Outputs can be saved using the user interface and the code underlying genomeSidekick can be edited for custom analyses. In summary, genomeSidekick brings wet lab scientists and bioinformaticians into a shared fluency with the end goal of driving mechanistic discovery.
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- 2022
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5. DNA Methylation-Based Prediction of Post-operative Atrial Fibrillation
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Matthew A. Fischer, Aman Mahajan, Maximilian Cabaj, Todd H. Kimball, Marco Morselli, Elizabeth Soehalim, Douglas J. Chapski, Dennis Montoya, Colin P. Farrell, Jennifer Scovotti, Claudia T. Bueno, Naomi A. Mimila, Richard J. Shemin, David Elashoff, Matteo Pellegrini, Emma Monte, and Thomas M. Vondriska
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post-operative atrial fibrillation (POAF) ,epigenomics ,DNA methylation ,cardiac surgery ,precision medicine ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
BackgroundAtrial fibrillation (AF) is the most common sustained cardiac arrhythmia and post-operative atrial fibrillation (POAF) is a major healthcare burden, contributing to an increased risk of stroke, kidney failure, heart attack and death. Genetic studies have identified associations with AF, but no molecular diagnostic exists to predict POAF based on pre-operative measurements. Such a tool would be of great value for perioperative planning to improve patient care and reduce healthcare costs. In this pilot study of epigenetic precision medicine in the perioperative period, we carried out bisulfite sequencing to measure DNA methylation status in blood collected from patients prior to cardiac surgery to identify biosignatures of POAF.MethodsWe enrolled 221 patients undergoing cardiac surgery in this prospective observational study. DNA methylation measurements were obtained from blood samples drawn from awake patients prior to surgery. After controlling for clinical and methylation covariates, we analyzed DNA methylation loci in the discovery cohort of 110 patients for association with POAF. We also constructed predictive models for POAF using clinical and DNA methylation data. We subsequently performed targeted analyses of a separate cohort of 101 cardiac surgical patients to measure the methylation status solely of significant methylation loci in the discovery cohort.ResultsA total of 47 patients in the discovery cohort (42.7%) and 43 patients in the validation cohort (42.6%) developed POAF. We identified 12 CpGs that were statistically significant in the discovery cohort after correcting for multiple hypothesis testing. Of these sites, 6 were amenable to targeted bisulfite sequencing and chr16:24640902 was statistically significant in the validation cohort. In addition, the methylation POAF prediction model had an AUC of 0.79 in the validation cohort.ConclusionsWe have identified DNA methylation biomarkers that can predict future occurrence of POAF associated with cardiac surgery. This research demonstrates the use of precision medicine to develop models combining epigenomic and clinical data to predict disease.
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- 2022
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6. Transcriptional, Electrophysiological, and Metabolic Characterizations of hESC-Derived First and Second Heart Fields Demonstrate a Potential Role of TBX5 in Cardiomyocyte Maturation
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Arash Pezhouman, Ngoc B. Nguyen, Alexander J. Sercel, Thang L. Nguyen, Ali Daraei, Shan Sabri, Douglas J. Chapski, Melton Zheng, Alexander N. Patananan, Jason Ernst, Kathrin Plath, Thomas M. Vondriska, Michael A. Teitell, and Reza Ardehali
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first and second heart fields ,single cell RNA seq ,action potential ,hESC-derived cardiomyocyte ,maturity ,regenerative medicine ,Biology (General) ,QH301-705.5 - Abstract
Background: Human embryonic stem cell-derived cardiomyocytes (hESC-CMs) can be used as a source for cell delivery to remuscularize the heart after myocardial infarction. Despite their therapeutic potential, the emergence of ventricular arrhythmias has limited their application. We previously developed a double reporter hESC line to isolate first heart field (FHF: TBX5+NKX2-5+) and second heart field (SHF: TBX5-NKX2-5+) CMs. Herein, we explore the role of TBX5 and its effects on underlying gene regulatory networks driving phenotypical and functional differences between these two populations.Methods: We used a combination of tools and techniques for rapid and unsupervised profiling of FHF and SHF populations at the transcriptional, translational, and functional level including single cell RNA (scRNA) and bulk RNA sequencing, atomic force and quantitative phase microscopy, respirometry, and electrophysiology.Results: Gene ontology analysis revealed three biological processes attributed to TBX5 expression: sarcomeric structure, oxidative phosphorylation, and calcium ion handling. Interestingly, migratory pathways were enriched in SHF population. SHF-like CMs display less sarcomeric organization compared to FHF-like CMs, despite prolonged in vitro culture. Atomic force and quantitative phase microscopy showed increased cellular stiffness and decreased mass distribution over time in FHF compared to SHF populations, respectively. Electrophysiological studies showed longer plateau in action potentials recorded from FHF-like CMs, consistent with their increased expression of calcium handling genes. Interestingly, both populations showed nearly identical respiratory profiles with the only significant functional difference being higher ATP generation-linked oxygen consumption rate in FHF-like CMs. Our findings suggest that FHF-like CMs display more mature features given their enhanced sarcomeric alignment, calcium handling, and decreased migratory characteristics. Finally, pseudotime analyses revealed a closer association of the FHF population to human fetal CMs along the developmental trajectory.Conclusion: Our studies reveal that distinguishing FHF and SHF populations based on TBX5 expression leads to a significant impact on their downstream functional properties. FHF CMs display more mature characteristics such as enhanced sarcomeric organization and improved calcium handling, with closer positioning along the differentiation trajectory to human fetal hearts. These data suggest that the FHF CMs may be a more suitable candidate for cardiac regeneration.
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- 2021
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7. Laparoscopic Sleeve Gastrectomy in Patients with Severe Obesity Restores Adaptive Responses Leading to Nonalcoholic Steatohepatitis
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Noemí Cabré, Fedra Luciano-Mateo, Douglas J. Chapski, Gerard Baiges-Gaya, Salvador Fernández-Arroyo, Anna Hernández-Aguilera, Helena Castañé, Elisabet Rodríguez-Tomàs, Marta París, Fàtima Sabench, Daniel Del Castillo, Josep M. del Bas, Mercedes Tomé, Clément Bodineau, Alejandro Sola-García, José López-Miranda, Alejandro Martín-Montalvo, Raúl V. Durán, Thomas M. Vondriska, Manuel Rosa-Garrido, Jordi Camps, Javier A. Menéndez, and Jorge Joven
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bariatric surgery ,DNA methylation ,energy metabolism ,epigenetics ,functional studies ,glutaminolysis ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
The surgically induced remission of liver disease represents a model to investigate the signalling processes that trigger the development of nonalcoholic steatohepatitis with the aim of identifying novel therapeutic targets. We recruited patients with severe obesity with or without nonalcoholic steatohepatitis and obtained liver and plasma samples before and after laparoscopic sleeve gastrectomy for immunoblotting, immunocytochemical, metabolomic, transcriptomic and epigenetic analyses. Functional studies were performed in HepG2 cells and primary hepatocytes. Surgery was associated with a decrease in the inflammatory response and revealed the role of mitogen-activated protein kinases. Nonalcoholic steatohepatitis was associated with an increased glutaminolysis-induced production of α-ketoglutarate and the hyperactivation of mammalian target of rapamycin complex 1. These changes were crucial for adenosine monophosphate-activated protein kinase/mammalian target of rapamycin-driven pathways that modulated hepatocyte survival by coordinating apoptosis and autophagy and affected methylation-related epigenomic remodelling enzymes. Hepatic transcriptome signatures and differentially methylated genomic regions distinguished patients with and without steatohepatitis. Our results suggest that the increased glutaminolysis-induced α-ketoglutarate production and the mammalian target of rapamycin complex 1 dysregulation play a crucial role in the inefficient adaptive responses leading to steatohepatitis in obesity.
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- 2022
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8. Spatial Principles of Chromatin Architecture Associated With Organ-Specific Gene Regulation
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Douglas J. Chapski, Manuel Rosa-Garrido, Nan Hua, Frank Alber, and Thomas M. Vondriska
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transcription ,chromatin conformation capture ,genomics ,chromatin structure ,epigenetics ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Packaging of the genome in the nucleus is a non-random process that is thought to directly contribute to cell type-specific transcriptomes, although this hypothesis remains untested. Epigenome architecture, as assayed by chromatin conformation capture techniques, such as Hi-C, has recently been described in the mammalian cardiac myocyte and found to be remodeled in the setting of heart failure. In the present study, we sought to determine whether the structural features of the epigenome are conserved between different cell types by investigating Hi-C and RNA-seq data from heart and liver. Investigation of genes with enriched expression in heart or liver revealed nuanced interaction paradigms between organs: first, the log2 ratios of heart:liver (or liver:heart) intrachromosomal interactions are higher in organ-specific gene sets (p = 0.009), suggesting that organ-specific genes have specialized chromatin structural features. Despite similar number of total interactions between cell types, intrachromosomal interaction profiles in heart but not liver demonstrate that genes forming promoter-to-transcription-end-site loops in the cardiac nucleus tend to be involved in cardiac-related pathways. The same analysis revealed an analogous organ-specific interaction profile for liver-specific loop genes. Investigation of A/B compartmentalization (marker of chromatin accessibility) revealed that in the heart, 66.7% of cardiac-specific genes are in compartment A, while 66.1% of liver-specific genes are found in compartment B, suggesting that there exists a cardiac chromatin topology that allows for expression of cardiac genes. Analyses of interchromosomal interactions revealed a relationship between interchromosomal interaction count and organ-specific gene localization (p = 2.2 × 10−16) and that, for both organs, regions of active or inactive chromatin tend to segregate in 3D space (i.e., active with active, inactive with inactive). 3D models of topologically associating domains (TADs) suggest that TADs tend to interact with regions of similar compartmentalization across chromosomes, revealing trans structural interactions contributing to genomic compartmentalization at distinct structural scales. These models reveal discordant nuclear compaction strategies, with heart packaging compartment A genes preferentially toward the center of the nucleus and liver exhibiting preferential arrangement toward the periphery. Taken together, our data suggest that intra- and interchromosomal chromatin architecture plays a role in orchestrating tissue-specific gene expression.
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- 2019
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9. Integrative transcriptomics and cell systems analyses reveal protective pathways controlled by Igfbp‐3 in anthracycline‐induced cardiotoxicity
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Junjie Chen, Douglas J. Chapski, Jeremy Jong, Jerome Awada, Yijie Wang, Dennis J. Slamon, Thomas M. Vondriska, and René R. Sevag Packard
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Genetics ,Molecular Biology ,Biochemistry ,Biotechnology - Published
- 2023
10. Telescope: an interactive tool for managing large scale analysis from mobile devices.
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Jaqueline J. Brito, Thiago Mosqueiro, Douglas J. Chapski, Juan De la Hoz, Paulo Matias, Lana S. Martin, Matteo Pellegrinni, and Serghei Mangul
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- 2019
11. Histone H1.0 Couples Cellular Mechanical Behaviors to Chromatin Structure
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Shuaishuai Hu, Douglas J. Chapski, Natalie Gehred, Todd H. Kimball, Tatiana Gromova, Angelina Flores, Amy C. Rowat, Junjie Chen, René R. Sevag Packard, Emily Olszewski, Jennifer Davis, Christoph D. Rau, Timothy A. McKinsey, Manuel Rosa Garrido, and Thomas M. Vondriska
- Abstract
SummaryTuning of genome structure and function is accomplished by chromatin binding proteins, which determine the transcriptome and phenotype of the cell. We sought to investigate how communication between extracellular stress and chromatin structure may regulate cellular mechanical behaviors. We demonstrate that the linker histone H1.0, which compacts nucleosomes into higher order chromatin fibers, controls genome organization and cellular stress response. Histone H1.0 has privileged expression in fibroblasts across tissue types in mice and humans, and modulation of its expression is necessary and sufficient to mount a myofibroblast phenotype in these cells. Depletion of histone H1.0 prevents transforming growth factor beta (TGF-β)-induced fibroblast contraction, proliferation and migration in a histone H1 isoform-specific manner via inhibition of a transcriptome comprised of extracellular matrix, cytoskeletal and contractile genes. Histone H1.0 is associated with local regulation of gene expression via mechanisms involving chromatin fiber compaction and reprogramming of histone acetylation, rendering the cell stiffer in response to cytokine stimulation. Knockdown of histone H1.0 prevented locus-specific histone H3 lysine 27 acetylation by TGF-βand decreased levels of both HDAC1 and the chromatin reader BRD4, thereby preventing transcription of a fibrotic gene program. Transient depletion of histone H1.0in vivodecompacts chromatin and prevents fibrosis in cardiac muscle, thereby linking chromatin structure with fibroblast phenotype in response to extracellular stress. Our work identifies an unexpected role of linker histones to orchestrate cellular mechanical behaviors, directly coupling cellular force generation, nuclear organization and gene transcription.Graphical Abstract
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- 2022
12. Abstract P2007: Bmal1 Drives Postnatal Cardiac Hypertrophy Via Circadian Chromatin Remodeling Of The Pro-hypertrophic Gene Sik1
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Adrian Arrieta, Anna Reese, David Wong, Douglas J Chapski, Manuel Rosa-Garrido, Ashley Zhu, and Thomas M Vondriska
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Physiology ,Cardiology and Cardiovascular Medicine - Abstract
Background: During neonatal cardiac development, myocytes integrate cues such as changes in blood pressure and circulating hormones to execute a temporal genetic response that drives physiological cardiac hypertrophy. Chromatin remodeling precedes the adult heart’s response to growth stimuli, yet the temporal nature of neonatal chromatin remodeling is unclear. In other tissues, genes regulated by the master circadian rhythm factor BMAL1 display circadian oscillations in histone acetylation and nucleosome and RNAP II occupancy. We hypothesized that BMAL1 regulates temporal chromatin remodeling and expression of genes critical for neonatal cardiac hypertrophy. Methods: BMAL1 chromatin immunoprecipitation sequencing (ChIP-Seq) and assay for transposase-accessible chromatin and sequencing (ATAC-Seq) data from murine hearts were analyzed to identify genes at which BMAL1 may drive chromatin remodeling. To interrogate myocyte time-of-day dependent response to growth stimuli, neonatal rat ventricular myocytes (NRVM) were subjected to serum shock synchronization to drive oscillatory BMAL1 expression, followed by treatment with the growth stimulus phenylephrine (PE) at the peak and trough of BMAL1 expression. BMAL1 was knocked down via siRNA and hypertrophy was assessed by measurement of cell size and of RT-PCR of fetal genes (Nppa and Nppb). Results: BMAL1 ChIP-Seq data revealed myocyte-specific BMAL1 localization to regions exhibiting an open chromatin signature based on ATAC-seq, including the pro-hypertrophic gene salt-inducible kinase 1 ( Sik1 ). Serum shock induced oscillations of BMAL1 and histone H3.3: administration of PE at the peak of BMAL1 expression induced a 30% increase in cell size and 2-fold increase in fetal gene expression. PE given at the trough of BMAL1 expression affected neither cell size nor fetal genes, demonstrating a critical role for the circadian clock in myocyte growth. BMAL1 knockdown: decreased expression of its known target and partner clock gene, Per2 , as well as expression of Sik1, Nppa , and Nppb ; decreased myocyte size by 30%; and increased expression of histone H3.3. Conclusions: These data indicate that BMAL1 temporally regulates myocyte growth by modulating histone stoichiometry and expression of Sik1 .
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- 2022
13. DNA Methylation-Based Prediction of Post-operative Atrial Fibrillation
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Matthew A. Fischer, Aman Mahajan, Maximilian Cabaj, Todd H. Kimball, Marco Morselli, Elizabeth Soehalim, Douglas J. Chapski, Dennis Montoya, Colin P. Farrell, Jennifer Scovotti, Claudia T. Bueno, Naomi A. Mimila, Richard J. Shemin, David Elashoff, Matteo Pellegrini, Emma Monte, and Thomas M. Vondriska
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screening and diagnosis ,DNA methylation ,precision medicine ,Prevention ,Human Genome ,Cardiovascular ,4.1 Discovery and preclinical testing of markers and technologies ,Detection ,Heart Disease ,Good Health and Well Being ,Clinical Research ,epigenomics ,post-operative atrial fibrillation ,Genetics ,Cardiology and Cardiovascular Medicine ,cardiac surgery ,4.2 Evaluation of markers and technologies - Abstract
BackgroundAtrial fibrillation (AF) is the most common sustained cardiac arrhythmia and post-operative atrial fibrillation (POAF) is a major healthcare burden, contributing to an increased risk of stroke, kidney failure, heart attack and death. Genetic studies have identified associations with AF, but no molecular diagnostic exists to predict POAF based on pre-operative measurements. Such a tool would be of great value for perioperative planning to improve patient care and reduce healthcare costs. In this pilot study of epigenetic precision medicine in the perioperative period, we carried out bisulfite sequencing to measure DNA methylation status in blood collected from patients prior to cardiac surgery to identify biosignatures of POAF.MethodsWe enrolled 221 patients undergoing cardiac surgery in this prospective observational study. DNA methylation measurements were obtained from blood samples drawn from awake patients prior to surgery. After controlling for clinical and methylation covariates, we analyzed DNA methylation loci in the discovery cohort of 110 patients for association with POAF. We also constructed predictive models for POAF using clinical and DNA methylation data. We subsequently performed targeted analyses of a separate cohort of 101 cardiac surgical patients to measure the methylation status solely of significant methylation loci in the discovery cohort.ResultsA total of 47 patients in the discovery cohort (42.7%) and 43 patients in the validation cohort (42.6%) developed POAF. We identified 12 CpGs that were statistically significant in the discovery cohort after correcting for multiple hypothesis testing. Of these sites, 6 were amenable to targeted bisulfite sequencing and chr16:24640902 was statistically significant in the validation cohort. In addition, the methylation POAF prediction model had an AUC of 0.79 in the validation cohort.ConclusionsWe have identified DNA methylation biomarkers that can predict future occurrence of POAF associated with cardiac surgery. This research demonstrates the use of precision medicine to develop models combining epigenomic and clinical data to predict disease.
- Published
- 2021
14. The anti-aging protein Klotho affects early postnatal myogenesis by downregulating Jmjd3 and the canonical Wnt pathway
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Cynthia M. McKee, Douglas J. Chapski, Michelle Wehling‐Henricks, Manuel Rosa‐Garrido, Makoto Kuro‐o, Thomas M. Vondriska, and James G. Tidball
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Jumonji Domain-Containing Histone Demethylases ,Down-Regulation ,Gene Expression Regulation, Developmental ,Muscle Development ,Biochemistry ,Cell Line ,Mice, Inbred C57BL ,Myoblasts ,Mice ,Genetics ,Animals ,Molecular Biology ,Klotho Proteins ,Wnt Signaling Pathway ,Biotechnology - Abstract
Modulating the number of muscle stems cells, called satellite cells, during early postnatal development produces long-term effects on muscle growth. We tested the hypothesis that high expression levels of the anti-aging protein Klotho in early postnatal myogenesis increase satellite cell numbers by influencing the epigenetic regulation of genes that regulate myogenesis. Our findings show that elevated klotho expression caused a transient increase in satellite cell numbers and slowed muscle fiber growth, followed by a period of accelerated muscle growth that leads to larger fibers. Klotho also transcriptionally downregulated the H3K27 demethylase Jmjd3, leading to increased H3K27 methylation and decreased expression of genes in the canonical Wnt pathway, which was associated with a delay in muscle differentiation. In addition, Klotho stimulation and Jmjd3 downregulation produced similar but not additive reductions in the expression of Wnt4, Wnt9a, and Wnt10a in myogenic cells, indicating that inhibition occurred through a common pathway. Together, our results identify a novel pathway through which Klotho influences myogenesis by reducing the expression of Jmjd3, leading to reductions in the expression of Wnt genes and inhibition of canonical Wnt signaling.
- Published
- 2021
15. Abstract 115: Cell-type-specific Gene Expression And Transcriptional Networks Reveal Adamts2 As A Powerful Regulator Of Cardiac Homeostasis During Heart Failure
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Caitlin Lahue, Christoph Rau, Manuel Rosa Garrido, Douglas J. Chapski, Shuxun Ren, Thomas M. Vondriska, and Yibin Wang
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ADAMTS2 ,Physiology ,Heart failure ,Transcriptional Networks ,Gene expression ,Cell type specific ,medicine ,Regulator ,Biology ,Cardiology and Cardiovascular Medicine ,medicine.disease ,Homeostasis ,Cell biology - Abstract
Background: Heart failure (HF) is a highly heterogeneous disorder characterized by the interactions of multiple genetic and environmental factors as well as the interaction of different cell types in the heart. Although reductionistic approaches have successfully identified many genes involved in HF, heritability studies suggest that many genes have resisted discovery through these approaches. By utilizing cell-type-specific gene expression paired with transcriptomic data from a large cohort of mice, we sought to identify important drivers of HF using a systems genetics approach. Methods and Results: Mice from 93 unique inbred lines of the Hybrid Mouse Diversity Panel were given 30 ug/g/day of isoproterenol for three weeks via osmotic minipump to induce heart failure. Transcriptomes were generated from these mice and the weighted Maximal Information Component Analysis (wMICA) algorithm was applied to generate transcriptomic gene networks. Cardiomyocytes and Fibroblasts were isolated from both control and isoproterenol-treated adult C57BL/6J hearts using a Langendorff apparatus (n=3 per sex/treatment) and transcriptomes were generated. Significantly differentially expressed genes were identified using DESEQ2 and used to query the wMICA-derived network, identifying the gene Adamts2 as a potential regulator of cardiac hypertrophy. Follow-up in vitro and in vivo work has demonstrated that Adamts2 knockdown significantly blunts the hypertrophic effect of isoproterenol on cardiomyocytes while simultaneously reducing fibroblast proliferation and increasing apoptosis as measured by TUNEL staining. Careful examination of the gene network reveals evidence of paracrine signaling between cardiomyocytes and fibroblasts and suggests a key trans-cell-type role of Adamts2 in the regulation of HF after catecholamine stimulation. Conclusion: Co-expression network algorithms combined with cell-type-specific transcriptomics identified Adamts2 as a driver of HF. Adamts2 plays an important role via paracrine signaling in the proliferative response of fibroblasts and the hypertrophic response of cardiomyocytes to catecholamines. Further mechanistic analysis of Adamts2 will further reveal its role in the progression of heart failure.
- Published
- 2021
16. Early adaptive chromatin remodeling events precede pathologic phenotypes and are reinforced in the failing heart
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Thomas M. Vondriska, Matteo Pellegrini, Shuxun Ren, Rosibel J. Mason, Yibin Wang, Manuel Rosa-Garrido, Douglas J. Chapski, Marco Morselli, Maximilian Cabaj, and Elizabeth Soehalim
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Medical Physiology ,Gene Expression ,Cardiorespiratory Medicine and Haematology ,Inbred C57BL ,Cardiovascular ,Epigenesis, Genetic ,Chromosome conformation capture ,Histones ,Mice ,2.1 Biological and endogenous factors ,Myocytes, Cardiac ,Aetiology ,Promoter Regions, Genetic ,Mice, Knockout ,Chromatin accessibility ,DNA methylation ,biology ,Chromatin ,Cell biology ,Heart Disease ,Histone ,Enhancer Elements, Genetic ,Phenotype ,Cardiology and Cardiovascular Medicine ,Cardiac ,Enhancer Elements ,Knockout ,Heart failure ,Cardiomegaly ,Chromatin remodeling ,Promoter Regions ,Genetic ,Enhancers ,Genetics ,Animals ,Epigenetics ,Enhancer ,Molecular Biology ,Heart Failure ,Myocytes ,Animal ,Human Genome ,DNA Methylation ,CTCF ,Chromatin Assembly and Disassembly ,Rats ,Mice, Inbred C57BL ,Disease Models, Animal ,Cardiovascular System & Hematology ,Disease Models ,biology.protein ,Epigenesis ,Transcription Factors - Abstract
The temporal nature of chromatin structural changes underpinning pathologic transcription are poorly understood. We measured chromatin accessibility and DNA methylation to study the contribution of chromatin remodeling at different stages of cardiac hypertrophy and failure. ATAC-seq and reduced representation bisulfite sequencing were performed in cardiac myocytes after transverse aortic constriction (TAC) or depletion of the chromatin structural protein CTCF. Early compensation to pressure overload showed changes in chromatin accessibility and DNA methylation preferentially localized to intergenic and intronic regions. Most methylation and accessibility changes observed in enhancers and promoters at the late phase (3 weeks after TAC) were established at an earlier time point (3 days after TAC), before heart failure manifests. Enhancers were paired with genes based on chromatin conformation capture data: while enhancer accessibility generally correlated with changes in gene expression, this feature, nor DNA methylation, was alone sufficient to predict transcription of all enhancer interacting genes. Enrichment of transcription factors and active histone marks at these regions suggests that enhancer activity coordinates with other epigenetic factors to determine gene transcription. In support of this hypothesis, ChIP-qPCR demonstrated increased enhancer and promoter occupancy of GATA4 and NKX2.5 at Itga9 and Nppa, respectively, concomitant with increased transcription of these genes in the diseased heart. Lastly, we demonstrate that accessibility and DNA methylation are imperfect predictors of chromatin structure at the scale of A/B compartmentalization—rather, accessibility, DNA methylation, transcription factors and other histone marks work within these domains to determine gene expression. These studies establish that chromatin reorganization during early compensation after pathologic stimuli is maintained into the later decompensatory phases of heart failure. The findings reveal the rules for how local chromatin features govern gene expression in the context of global genomic structure and identify chromatin remodeling events for therapeutic targeting in disease.
- Published
- 2021
17. Taking Data Science to Heart: Next Scale of Gene Regulation
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Douglas J. Chapski and Thomas M. Vondriska
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Big Data ,Process (engineering) ,Bioinformatics ,Big data ,Context (language use) ,Genomics ,030204 cardiovascular system & hematology ,Biology ,Cardiorespiratory Medicine and Haematology ,Cardiovascular ,Article ,Machine Learning ,03 medical and health sciences ,0302 clinical medicine ,Genetics ,Humans ,030212 general & internal medicine ,Transcriptomics ,Epigenomics ,Regulation of gene expression ,business.industry ,Scale (chemistry) ,Data Science ,Human Genome ,Cardiovascular disease ,Data science ,Chromatin ,Heart Disease ,Gene Expression Regulation ,Networking and Information Technology R&D (NITRD) ,Cardiovascular System & Hematology ,Generic health relevance ,Cardiology and Cardiovascular Medicine ,business ,Biotechnology - Abstract
PURPOSE OF REVIEW: Technical advances have facilitated high-throughput measurements of the genome in the context of cardiovascular biology. These techniques bring a deluge of gargantuan datasets, which in turn present two fundamentally new opportunities for innovation—data processing and knowledge integration—toward the goal of meaningful basic and translational discoveries. RECENT FINDINGS: Big data, integrative analyses, and machine learning have brought cardiac investigations to the cutting edge of chromatin biology, not only to reveal basic principles of gene regulation in the heart, but also to aid in the design of targeted epigenetic therapies. SUMMARY: Cardiac studies using big data are only beginning to integrate the millions of recorded data points and the tools of machine learning are aiding this process. Future experimental design should take into consideration insights from existing genomic datasets, thereby focusing on heretofore unexplored epigenomic contributions to disease pathology.
- Published
- 2021
18. Abstract 15945: Temporal Analyses of Chromatin Accessibility, Dna Methylation and Epigenomic Structure Identify Mechanisms of Locus-specific Regulation in the Heart
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Shuxun Ren, Manuel Rosa-Garrido, Rosibel J. Mason, Douglas J. Chapski, Marco Morselli, Maximilian Cabaj, Yibin Wang, Thomas M. Vondriska, and Matteo Pellegrini
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chemistry.chemical_classification ,business.industry ,Locus (genetics) ,Chromatin ,Cell biology ,Pathogenesis ,Enzyme ,chemistry ,Physiology (medical) ,Chromatin modifying enzymes ,DNA methylation ,Medicine ,Epigenetics ,Cardiology and Cardiovascular Medicine ,business ,Epigenomics - Abstract
Heart failure can be induced or ameliorated in animal models by regulation of chromatin modifying enzymes, yet the chromatin level actions of these enzymes during pathogenesis is unknown. Because many histone modifiers and transcription factors regulate gene expression, we sought to directly measure chromatin accessibility through an unbiased method (ATAC-seq) that reports the status of a given locus at any time—the sum total of all epigenetic modifiers—in a mouse model of pressure overload hypertrophy. Early compensation of pressure overload at 3 days was associated with widespread changes in chromatin accessibility and DNA methylation, primarily in noncoding regions. The majority of changes that persisted to the decompensated phase (3weeks) were already established at the earlier time point, revealing a temporal nature of epigenomic compensation to pathologic stimuli. A cardiac-specific CTCF depletion model was used to examine basal cardiac chromatin function and revealed that disruption of this structure by loss of CTCF causes widespread changes in accessibility and methylation distinct from those in pressure overload. Less than half of the gene expression changes occurring at either time point after pressure overload were explained by DNA methylation alone and accessibility was likewise an imperfect predictor of transcription. Distal enhancers were paired with genes based on chromatin structural data and the regulatory actions of these elements examined in the context of DNA methylation and accessibility: enhancer actions require specific combinations of transcription factors and histone modifications at different stages of disease and to execute aspecific transcriptional event (methylation or accessibility alone was insufficient to predict the behavior). For example, the subset of differentially accessible enhancers in both 3 weeks TACand CTCF depletion significantly overlaps with cardiac transcription factors Gata4 (p=4.13x10 -6 ),Nkx2-5 (p=2.49x10 -5 ) and P300 (p=8.38x10 -7 ). In summary, these studies characterize the logic employed at coding, regulatory, and noncoding regions to regulate chromatin accessibility and transcription, providing a resource of epigenomic data at distinct temporal stages of heart failure.
- Published
- 2020
19. Glutaminolysis-induced mTORC1 activation drives non-alcoholic steatohepatitis progression
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Douglas J. Chapski, Alejandro Sola-García, Jordi Camps, Elisabet Rodríguez-Tomàs, Javier A. Menendez, Noemí Cabré, Alejandro Martin-Montalvo, Mercedes Tomé, Thomas M. Vondriska, Salvador Fernández-Arroyo, Helena Castañé, Daniel Del Castillo, Raúl V. Durán, Gerard Baiges-Gaya, Jose Lopez-Miranda, Manuel Rosa-Garrido, Clément Bodineau, Josep M. del Bas, Fàtima Sabench, Fedra Luciano-Mateo, Marta París, Anna Hernández-Aguilera, and Jorge Joven
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0301 basic medicine ,Glutaminolysis ,Hepatology ,business.industry ,Autophagy ,Fatty liver ,mTORC1 ,medicine.disease ,Transcriptome ,03 medical and health sciences ,Liver disease ,030104 developmental biology ,0302 clinical medicine ,Cancer research ,Medicine ,030211 gastroenterology & hepatology ,Steatohepatitis ,business ,Epigenomics - Abstract
Background & Aims A holistic insight on the relationship between obesity and metabolic dysfunction-associated fatty liver disease is an unmet clinical need. Omics investigations can be used to investigate the multifaceted role of altered mitochondrial pathways to promote nonalcoholic steatohepatitis, a major risk factor for liver disease-associated death. There are no specific treatments but remission via surgery might offer an opportunity to examine the signaling processes that govern the complex spectrum of chronic liver diseases observed in extreme obesity. We aim to assess the emerging relationship between metabolism, methylation and liver disease. Methods We tailed the flow of information, before and after steatohepatitis remission, from biochemical, histological, and multi-omics analyses in liver biopsies from patients with extreme obesity and successful bariatric surgery. Functional studies were performed in HepG2 cells and primary hepatocytes. Results The reversal of hepatic mitochondrial dysfunction and the control of oxidative stress and inflammatory responses revealed the regulatory role of mitogen-activated protein kinases. The reversible metabolic rearrangements leading to steatohepatitis increased the glutaminolysis-induced production of α-ketoglutarate and the hyperactivation of mammalian target of rapamycin complex 1. These changes were crucial for the adenosine monophosphate-activated protein kinase/mammalian target of rapamycin-driven pathways that modulated hepatocyte survival by coordinating apoptosis and autophagy. The signaling activity of α-ketoglutarate and the associated metabolites also affected methylation-related epigenomic remodeling enzymes. Integrative analysis of hepatic transcriptome signatures and differentially methylated genomic regions distinguished patients with and without steatohepatitis. Conclusion We provide evidence supporting the multifaceted potential of the increased glutaminolysis-induced α-ketoglutarate production and the mammalian target of rapamycin complex 1 dysregulation as a conceivable source of the inefficient adaptive responses leading to steatohepatitis. Lay summary Steatohepatitis is a frequent and threatening complication of extreme obesity without specific treatment. Omics technologies can be used to identify therapeutic targets. We highlight increased glutaminolysis-induced α-ketoglutarate production as a potential source of signals promoting and exacerbating steatohepatitis.
- Published
- 2020
20. High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure
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Niels Galjart, Todd Kimball, Emma Monte, Shuxun Ren, Anthony D. Schmitt, Enrique Balderas, Elaheh Karbassi, Douglas J. Chapski, Thomas M. Vondriska, Peipei Ping, Bing Ren, David A. Liem, Matteo Pellegrini, Manuel Rosa-Garrido, Elizabeth Soehalim, Yibin Wang, Tsai-Ting Shih, and Cell biology
- Subjects
0301 basic medicine ,heart failure ,Cardiorespiratory Medicine and Haematology ,Bioinformatics ,Cardiovascular ,Chromosome conformation capture ,Mice ,Original Research Articles ,2.1 Biological and endogenous factors ,Myocytes, Cardiac ,Aetiology ,Epigenomics ,Cardiac myocyte ,Chromatin ,3. Good health ,Cell biology ,Heart Disease ,Public Health and Health Services ,ComputingMethodologies_DOCUMENTANDTEXTPROCESSING ,Cardiology and Cardiovascular Medicine ,hypertrophy ,Cardiac ,Knockout ,Clinical Sciences ,Bioengineering ,Cardiomegaly ,Biology ,Chromatin remodeling ,03 medical and health sciences ,Genetic ,Physiology (medical) ,Genetics ,genomics ,Animals ,Humans ,Pressure overload ,Heart Failure ,Myocytes ,Human Genome ,Epigenome ,Chromatin Assembly and Disassembly ,030104 developmental biology ,Cardiovascular System & Hematology ,CTCF ,epigenomics ,Epigenesis ,Genome-Wide Association Study - Abstract
Supplemental Digital Content is available in the text., Background: Cardiovascular disease is associated with epigenomic changes in the heart; however, the endogenous structure of cardiac myocyte chromatin has never been determined. Methods: To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin conformation capture (Hi-C) and DNA sequencing were performed in adult cardiac myocytes following development of pressure overload–induced hypertrophy. Mice with cardiac-specific deletion of CTCF (a ubiquitous chromatin structural protein) were generated to explore the role of this protein in chromatin structure and cardiac phenotype. Transcriptome analyses by RNA-seq were conducted as a functional readout of the epigenomic structural changes. Results: Depletion of CTCF was sufficient to induce heart failure in mice, and human patients with heart failure receiving mechanical unloading via left ventricular assist devices show increased CTCF abundance. Chromatin structural analyses revealed interactions within the cardiac myocyte genome at 5-kb resolution, enabling examination of intra- and interchromosomal events, and providing a resource for future cardiac epigenomic investigations. Pressure overload or CTCF depletion selectively altered boundary strength between topologically associating domains and A/B compartmentalization, measurements of genome accessibility. Heart failure involved decreased stability of chromatin interactions around disease-causing genes. In addition, pressure overload or CTCF depletion remodeled long-range interactions of cardiac enhancers, resulting in a significant decrease in local chromatin interactions around these functional elements. Conclusions: These findings provide a high-resolution chromatin architecture resource for cardiac epigenomic investigations and demonstrate that global structural remodeling of chromatin underpins heart failure. The newly identified principles of endogenous chromatin structure have key implications for epigenetic therapy.
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- 2017
21. Telescope: an interactive tool for managing large-scale analysis from mobile devices
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Thiago Mosqueiro, Jaqueline J. Brito, Alexander Zelikovsky, Juan Fernando de la Hoz, Paulo Matias, Jeremy Rotman, Matteo Pellegrini, Lana S. Martin, Douglas J. Chapski, Serghei Mangul, and Victor Xue
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Big Data ,high-throughput computing ,bioinformatics analysis ,job scheduler ,Computer science ,Interface (computing) ,Big data ,Health Informatics ,Encryption ,law.invention ,Telescope ,03 medical and health sciences ,User-Computer Interface ,0302 clinical medicine ,User experience design ,Human–computer interaction ,law ,Technical Note ,Data Mining ,030304 developmental biology ,0303 health sciences ,business.industry ,Computational Biology ,Usability ,bioinformatics ,Computer Science Applications ,User interface ,business ,Mobile device ,030217 neurology & neurosurgery ,Software - Abstract
Background In today's world of big data, computational analysis has become a key driver of biomedical research. High-performance computational facilities are capable of processing considerable volumes of data, yet often lack an easy-to-use interface to guide the user in supervising and adjusting bioinformatics analysis via a tablet or smartphone. Results To address this gap we proposed Telescope, a novel tool that interfaces with high-performance computational clusters to deliver an intuitive user interface for controlling and monitoring bioinformatics analyses in real-time. By leveraging last generation technology now ubiquitous to most researchers (such as smartphones), Telescope delivers a friendly user experience and manages conectivity and encryption under the hood. Conclusions Telescope helps to mitigate the digital divide between wet and computational laboratories in contemporary biology. By delivering convenience and ease of use through a user experience not relying on expertise with computational clusters, Telescope can help researchers close the feedback loop between bioinformatics and experimental work with minimal impact on the performance of computational tools. Telescope is freely available at https://github.com/Mangul-Lab-USC/telescope.
- Published
- 2019
22. Direct visualization of cardiac transcription factories reveals regulatory principles of nuclear architecture during pathological remodeling
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Yong Wu, Elaheh Karbassi, Shuxun Ren, Thomas M. Vondriska, Yibin Wang, Douglas J. Chapski, Enrico Stefani, and Manuel Rosa-Garrido
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0301 basic medicine ,Transcription factories ,Epigenomics ,Transcription, Genetic ,Medical Physiology ,RNA polymerase II ,030204 cardiovascular system & hematology ,Cardiorespiratory Medicine and Haematology ,Cardiovascular ,Mice ,0302 clinical medicine ,Transcription (biology) ,Gene expression ,Transcriptional regulation ,2.1 Biological and endogenous factors ,Myocytes, Cardiac ,Aetiology ,In Situ Hybridization ,In Situ Hybridization, Fluorescence ,Regulation of gene expression ,Heart ,Chromatin ,Cell biology ,Molecular Imaging ,RNA Polymerase II ,Cardiology and Cardiovascular Medicine ,Cardiac ,Transcription ,Biotechnology ,Transcriptional Activation ,1.1 Normal biological development and functioning ,Bioengineering ,Biology ,Heart disease ,Chromatin structure ,Fluorescence ,Article ,03 medical and health sciences ,Genetic ,Underpinning research ,Genetics ,Animals ,Humans ,Molecular Biology ,Heart Failure ,Myocytes ,Human Genome ,Newborn ,030104 developmental biology ,Cardiovascular System & Hematology ,Animals, Newborn ,Gene Expression Regulation ,biology.protein ,Digestive Diseases - Abstract
Heart failure is associated with hypertrophying of cardiomyocytes and changes in transcriptional activity. Studies from rapidly dividing cells in culture have suggested that transcription may be compartmentalized into factories within the nucleus, but this phenomenon has not been tested in vivo and the role of nuclear architecture in cardiac gene regulation is unknown. While alterations to transcription have been linked to disease, little is known about the regulation of the spatial organization of transcription and its properties in the pathological setting. In the present study, we investigate the structural features of endogenous transcription factories in the heart and determine the principles connecting chromatin structure to transcriptional regulation in vivo. Super-resolution imaging of endogenous RNA polymerase II clusters in neonatal and adult cardiomyocytes revealed distinct properties of transcription factories in response to pathological stress: neonatal nuclei demonstrated changes in number of clusters, with parallel increases in nuclear area, while the adult nuclei underwent changes in size and intensity of RNA polymerase II foci. Fluorescence in situ hybridization-based labeling of genes revealed locus-specific relationships between expression change and anatomical localization-with respect to nuclear periphery and heterochromatin regions, both sites associated with gene silencing-in the nuclei of cardiomyocytes in hearts (but not liver hepatocytes) of mice subjected to pathologic stimuli that induce heart failure. These findings demonstrate a role for chromatin organization and rearrangement of nuclear architecture for cell type-specific transcription in vivo during disease. RNA polymerase II ChIP and chromatin conformation capture studies in the same model system demonstrate formation and reorganization of distinct nuclear compartments regulating gene expression. These findings reveal locus-specific compartmentalization of stress-activated, housekeeping and silenced genes in the anatomical context of the endogenous nucleus, revealing basic principles of global chromatin structure and nuclear architecture in the regulation of gene expression in healthy and diseased conditions.
- Published
- 2019
23. Epigenomes in Cardiovascular Disease
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Manuel Rosa-Garrido, Thomas M. Vondriska, and Douglas J. Chapski
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0301 basic medicine ,Epigenomics ,RNA, Untranslated ,Physiology ,Cell Survival ,Clinical Sciences ,Reviews ,Disease ,Computational biology ,Biology ,Cardiorespiratory Medicine and Haematology ,Genome ,Histone Deacetylases ,Epigenesis, Genetic ,Transcriptome ,Histones ,Cardiovascular Physiological Phenomena ,03 medical and health sciences ,Genetic ,Humans ,Genetic Predisposition to Disease ,genetics ,Grand Challenges ,Translational medicine ,Untranslated ,DNA Methylation ,Chromatin Assembly and Disassembly ,Chromatin ,Nucleosomes ,cardiovascular diseases ,030104 developmental biology ,Cardiovascular System & Hematology ,DNA methylation ,ComputingMethodologies_DOCUMENTANDTEXTPROCESSING ,RNA ,Gene-Environment Interaction ,Cardiology and Cardiovascular Medicine ,Epigenesis - Abstract
Supplemental Digital Content is available in the text., If unifying principles could be revealed for how the same genome encodes different eukaryotic cells and for how genetic variability and environmental input are integrated to impact cardiovascular health, grand challenges in basic cell biology and translational medicine may succumb to experimental dissection. A rich body of work in model systems has implicated chromatin-modifying enzymes, DNA methylation, noncoding RNAs, and other transcriptome-shaping factors in adult health and in the development, progression, and mitigation of cardiovascular disease. Meanwhile, deployment of epigenomic tools, powered by next-generation sequencing technologies in cardiovascular models and human populations, has enabled description of epigenomic landscapes underpinning cellular function in the cardiovascular system. This essay aims to unpack the conceptual framework in which epigenomes are studied and to stimulate discussion on how principles of chromatin function may inform investigations of cardiovascular disease and the development of new therapies.
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- 2018
24. P1594Role of CTCF in maintenance of global chromatin architecture in the heart
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T. Kimball, I. Shih, Thomas M. Vondriska, M. Rosa Garrido, B. Ren, E. Soehalim, E. Balderas, Yibin Wang, A. Schmitt, Douglas J. Chapski, and N.J. Galjart
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0301 basic medicine ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,CTCF ,business.industry ,Medicine ,Architecture ,Cardiology and Cardiovascular Medicine ,business ,030226 pharmacology & pharmacy ,Chromatin ,Cell biology - Published
- 2017
25. SAT-278-Integrated analysis of dna methylation and mRNA expression to identify mechanisms of non-alcoholic steatohepatitis
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Salvador Fernández-Arroyo, Douglas J. Chapski, F. Luciano, Noemí Cabré, Thomas M. Vondriska, Anna Hernández-Aguilera, Jordi Camps, Manuel Rosa-Garrido, Jorge Joven, Gerard Baiges, and Elisabet Rodríguez
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Hepatology ,Mrna expression ,DNA methylation ,medicine ,Non alcoholic ,Biology ,Steatohepatitis ,medicine.disease ,Molecular biology - Published
- 2019
26. Abstract 319: Structural Reorganization of Cardiac Transcription Factories Mediates Transcriptional Changes in Response to Stress
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Elaheh Karbassi, Douglas J. Chapski, Manuel Rosa Garrido, Yong Wu, Thomas M. Vondriska, and Emma Monte
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Transcription factories ,Stress (mechanics) ,Physiology ,Biology ,Cardiology and Cardiovascular Medicine ,Cell biology - Abstract
The heart’s response to stress entails precise gene expression changes to affect the metabolic and structural features of the cardiomyocyte. The changes in gene expression are mediated by structural alterations in the packaging of the genome. However, the manner in which the three-dimensional architecture of the genome is established is unknown. In non-cardiac cells, genes that are actively transcribed are thought to reside in transcriptionally permissive compartments called transcription factories. The structural principles for achieving cardiac-specific transcription are not understood. We sought to understand the functional nature of cardiac transcription factories: whether they are stable structures (to which genes move in and out of) or are transiently formed around genes in response to cardiac stimuli. Using 5-fluorouridine incorporation into nascent RNA, we quantified changes in RNA polymerase II-mediated transcription in cardiomyocytes upon hypertrophic stress. Furthermore, we characterized the spatial distribution of transcription factories, marked by RNA polymerase II, from adult mice subjected to pressure overload. Using super-resolution microscopy, our analyses revealed reorganization of RNA polymerase II, evidenced by a significant increase in the distance between clusters (130nm in sham to 132.5nm in failing hearts, p=0.02) and a 38% increase in cluster intensity in failing hearts. To understand regulation of cardiac gene expression, we used DNA fluorescence in situ hybridization to map the nuclear position of the gene for SERCA2a (atp2a2), which is down regulated in disease. In failing hearts, we measured increased association of atp2a2 with the nuclear envelope (0/159 loci in sham to 11/278 loci in failure) and increased colocalization with heterochromatin (53/160 loci in sham versus 139/290 loci in failure), providing a structural mechanism for the decrease in SERCA2a expression. In contrast, atp2a2 positioning in the liver remained unaffected, with the majority of loci colocalizing with heterochromatin. These findings show that RNA polymerase II is redistributed to affect transcriptional programming and characterize for the first time the structural rearrangements in chromatin that underpin cardiac pathology.
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- 2016
27. Relationship of disease-associated gene expression to cardiac phenotype is buffered by genetic diversity and chromatin regulation
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Douglas J. Chapski, James N. Weiss, Rachel Lopez, Jessica Wang, Aldons J. Lusis, Joseph M Kim, Manuel Rosa Garrido, Elaheh Karbassi, Thomas M. Vondriska, Yibin Wang, N. Wisniewski, Emma Monte, and Christoph C Rau
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0301 basic medicine ,Genomic and “Polyomic” Studies of Cardiovascular and Inflammatory Diseases ,Physiology ,Gene Expression ,Cardiomegaly ,Biology ,Transcriptome ,03 medical and health sciences ,Mice ,Gene expression ,Genetic variation ,Genetics ,Animals ,Myocytes, Cardiac ,Gene ,Transcription factor ,Regulation of gene expression ,Myocardium ,Genetic Variation ,Heart ,Phenotype ,Chromatin ,030104 developmental biology ,Gene Expression Regulation ,Female ,Signal Transduction ,Transcription Factors - Abstract
Expression of a cohort of disease-associated genes, some of which are active in fetal myocardium, is considered a hallmark of transcriptional change in cardiac hypertrophy models. How this transcriptome remodeling is affected by the common genetic variation present in populations is unknown. We examined the role of genetics, as well as contributions of chromatin proteins, to regulate cardiac gene expression and heart failure susceptibility. We examined gene expression in 84 genetically distinct inbred strains of control and isoproterenol-treated mice, which exhibited varying degrees of disease. Unexpectedly, fetal gene expression was not correlated with hypertrophic phenotypes. Unbiased modeling identified 74 predictors of heart mass after isoproterenol-induced stress, but these predictors did not enrich for any cardiac pathways. However, expanded analysis of fetal genes and chromatin remodelers as groups correlated significantly with individual systemic phenotypes. Yet, cardiac transcription factors and genes shown by gain-/loss-of-function studies to contribute to hypertrophic signaling did not correlate with cardiac mass or function in disease. Because the relationship between gene expression and phenotype was strain specific, we examined genetic contribution to expression. Strikingly, strains with similar transcriptomes in the basal heart did not cluster together in the isoproterenol state, providing comprehensive evidence that there are different genetic contributors to physiological and pathological gene expression. Furthermore, the divergence in transcriptome similarity versus genetic similarity between strains is organ specific and genome-wide, suggesting chromatin is a critical buffer between genetics and gene expression.
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- 2016
28. Positive Feedback in Cardioprotection
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Douglas J. Chapski, Emma Monte, and Thomas M. Vondriska
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Cardioprotection ,medicine.medical_specialty ,education.field_of_study ,Physiology ,business.industry ,Population ,Ischemia ,medicine.disease ,Surgery ,Coronary artery disease ,Internal medicine ,Heart failure ,medicine ,Cardiology ,Ischemic preconditioning ,Myocardial infarction ,Cardiology and Cardiovascular Medicine ,education ,business ,Reperfusion injury - Abstract
Coronary artery disease is becoming an increasingly common cause of heart failure, with ≈65% of heart failure patients in the United States having ischemic heart disease.1 Each year, 635 000 people in the United States experience their first myocardial infarction (MI), with another 280 000 having a recurrent MI.2 This results in 125 664 deaths, with 15% of MI patients dying in the first year.2 Although mortality rates for MI are declining, survivors have an increased risk of death from 1.5% to 15% over the general population due in large part to an estimated 24% of MI patients ultimately developing heart failure.2,3 Thus, there is a clear clinical need to prevent myocardial cell death to reduce mortality due to acute MI, but also to improve long-term outcomes by minimizing subsequent development of heart failure. Coronary heart disease as a whole costs the United States $195.2 billion a year, with the cost expected to double by 2030,2 underscoring the need for the discovery of translatable approaches to prevent ischemic cell death. Article, see p 1268 Ischemia/reperfusion injury causes cell death because of a well-described, albeit very complex, process involving lack of oxygen, calcium overload, disruption of the sarcolemma, ATP depletion, and reactive oxygen species generation.4,5 Almost 3 decades ago, Murry et al6 described the cardioprotective effect of ischemic preconditioning, wherein short bouts of ischemia/reperfusion before a prolonged ischemic episode were shown to reduce subsequent infarct size. This observation has since been confirmed in hundreds of laboratories and extended to multiple mammalian species and other organ systems, demonstrating that the innate protective mechanisms activated by brief ischemia/reperfusion are conserved. Moreover, subsequent investigations have shown that pharmacological agents can induce selective arms of the complex physiological response to brief ischemia/reperfusion, reaping some …
- Published
- 2014
29. The mTORC1 pathway stimulates glutamine metabolism and cell proliferation by repressing SIRT4
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John Blenis, Chenggang Li, Douglas J. Chapski, Lewis C. Cantley, Sarah-Maria Fendt, Andrew Y. Choo, Gregory Stephanopoulos, Tasha Morrison, Andrey A. Parkhitko, Jane J. Yu, Alfred Csibi, Marcia C. Haigis, Elizabeth P. Henske, George Poulogiannis, Jamie M. Dempsey, and Seung Min Jeong
- Subjects
Male ,Transcription, Genetic ,Glutamine ,Transplantation, Heterologous ,mTORC1 ,Mechanistic Target of Rapamycin Complex 1 ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Article ,Mitochondrial Proteins ,chemistry.chemical_compound ,Mice ,Biosynthesis ,Glutamate Dehydrogenase ,Neoplasms ,Tuberous Sclerosis Complex 2 Protein ,Animals ,Humans ,Sirtuins ,Cell Proliferation ,Glutaminolysis ,Cell growth ,Biochemistry, Genetics and Molecular Biology(all) ,Glutamate dehydrogenase ,TOR Serine-Threonine Kinases ,Tumor Suppressor Proteins ,Ubiquitination ,Neoplasms, Experimental ,Embryo, Mammalian ,Activating Transcription Factors ,Cell biology ,Mitochondria ,Citric acid cycle ,Biochemistry ,chemistry ,Multiprotein Complexes ,Sirtuin ,biology.protein ,Female ,biological phenomena, cell phenomena, and immunity ,Energy Metabolism ,Neoplasm Transplantation ,DNA Damage - Abstract
Proliferating mammalian cells use glutamine as a source of nitrogen and as a key anaplerotic source to provide metabolites to the tricarboxylic acid cycle (TCA) for biosynthesis. Recently, mammalian target of rapamycin complex 1 (mTORC1) activation has been correlated with increased nutrient uptake and metabolism, but no molecular connection to glutaminolysis has been reported. Here, we show that mTORC1 promotes glutamine anaplerosis by activating glutamate dehydrogenase (GDH). This regulation requires transcriptional repression of SIRT4, the mitochondrial-localized sirtuin that inhibits GDH. Mechanistically, mTORC1 represses SIRT4 by promoting the proteasome-mediated destabilization of cAMP-responsive element binding 2 (CREB2). Thus, a relationship between mTORC1, SIRT4, and cancer is suggested by our findings. Indeed, SIRT4 expression is reduced in human cancer, and its overexpression reduces cell proliferation, transformation, and tumor development. Finally, our data indicate that targeting nutrient metabolism in energy-addicted cancers with high mTORC1 signaling may be an effective therapeutic approach. ispartof: Cell vol:153 issue:4 pages:840-54 ispartof: location:United States status: published
- Published
- 2013
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