Review
Cardiac & Cardiovascular Systems
Tatiana Gromova, Natalie D. Gehred, Thomas M. Vondriska
Summary: This review explores the biological significance of cellular heterogeneity in the heart through an analysis of single-cell transcriptomics. It evaluates new models for cardiac function and discusses the role of cell-to-cell variability in development and disease. Additionally, emerging epigenomic approaches combined with single-cell RNA-sequencing are presented as tools to understand gene regulation and cell phenotype variability.
CARDIOVASCULAR RESEARCH
(2023)
Review
Cell Biology
Jasvinder Singh Bhatti, Naina Khullar, Rajesh Vijayvergiya, Umashanker Navik, Gurjit Kaur Bhatti, P. Hemachandra Reddy
Summary: Heart disorders are a major issue in aging, with mitochondria playing a critical role in their development. Both environmental and genetic factors are important in controlling mitochondrial functions. Aging hearts are more prone to heart-related complications compared to younger hearts. While advanced technologies and procedures are used for prevention and treatment, there is still a need for a novel and effective strategy for timely diagnosis and treatment.
AGEING RESEARCH REVIEWS
(2023)
Review
Biochemical Research Methods
Elias Orouji, Ayush T. Raman
Summary: The human genome is shaped by a variety of histone modifications, which play a crucial role in determining chromatin states and organization. Using statistical models and computational tools, noncoding regions of DNA can be annotated and combinatorial histone marks inferred. These marks enable the discovery of genomic function and activity, and their patterns change in different cell conditions.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Cardiac & Cardiovascular Systems
Yuliang Feng, Liuyang Cai, Wanzi Hong, Chunxiang Zhang, Ning Tan, Mingyang Wang, Cheng Wang, Feng Liu, Xiaohong Wang, Jianyong Ma, Chen Gao, Mohit Kumar, Yuanxi Mo, Qingshan Geng, Changjun Luo, Yan Lin, Haiyang Chen, Shuang-Yin Wang, Michael J. Watson, Anil G. Jegga, Roger A. Pedersen, Ji-Dong Fu, Zhao Wang, Guo-Chang Fan, Sakthivel Sadayappan, Yigang Wang, Siim Pauklin, Feng Huang, Wei Huang, Lei Jiang
Summary: This study investigates the role of 3-dimensional chromatin topology in dilated cardiomyopathy (DCM) by analyzing the epigenome and transcriptome maps of DCM and nonfailing heart tissues. The research reveals that the reprogramming of chromatin topology is associated with transcriptional dysregulation in DCM, with the key transcription factor HAND1 implicated in the process. The findings provide insights into the pathogenesis of DCM and highlight the importance of chromatin organization in heart failure.
Article
Oncology
Dieter Weichenhan, Daniel B. Lipka, Pavlo Lutsik, Ashish Goyal, Christoph Plass
Summary: Epigenetic patterns in cells control gene expression and determine cell phenotype. Altered epigenomes in cancer cells can be used as biomarkers for cancer detection and classification. Furthermore, the cancer epigenome can predict response to different therapeutic approaches.
SEMINARS IN CANCER BIOLOGY
(2022)
Review
Genetics & Heredity
Laura Mateu-Arrom, Lluis Puig
Summary: Psoriasis is a complex disease influenced by both genetic and environmental factors. Advances in genomic and epigenomic studies have provided insight into the underlying mechanisms of psoriasis, leading to the development of new drugs. This review aims to summarize the current evidence on the genetic and epigenetic mechanisms of psoriasis.
Article
Cardiac & Cardiovascular Systems
Jason D. Roberts, Eric Vittinghoff, Ake T. Lu, Alvaro Alonso, Biqi Wang, Colleen M. Sitlani, Pedrum Mohammadi-Shemirani, Myriam Fornage, Jelena Kornej, Jennifer A. Brody, Dan E. Arking, Honghuang Lin, Susan R. Heckbert, Ivana Prokic, Mohsen Ghanbari, Allan C. Skanes, Traci M. Bartz, Marco Perez, Kent D. Taylor, Steven A. Lubitz, Patrick T. Ellinor, Kathryn L. Lunetta, James S. Pankow, Guillaume Pare, Nona Sotoodehnia, Emelia J. Benjamin, Steve Horvath, Gregory M. Marcus
Summary: The study identified associations between epigenetic age acceleration measures and incident atrial fibrillation, indicating the importance of biological aging independent of chronological age. However, the potential underlying causal relationship remains unclear. These aging processes may be modifiable and not constrained by the immutable factor of time.
Article
Genetics & Heredity
Kaori Hara-Isono, Kazuki Yamazawa, Satsuki Tanaka, Eriko Nishi, Maki Fukami, Masayo Kagami
Summary: The paternal deletions involving KCNQ1OT1:TSS-DMR in the two patients resulted in increased CDKN1C expression and severe growth failure.
JOURNAL OF MEDICAL GENETICS
(2022)
Article
Cardiac & Cardiovascular Systems
A. Dushani C. U. Ranasinghe, Maggie Holohan, Kalyn M. Borger, Deborah L. Donahue, Rafael D. Kuc, Martin Gerig, Andrew Kim, Victoria A. Ploplis, Francis J. Castellino, Margaret A. Schwarz
Summary: The expression and activation of SPHK2 can affect the acetylation of pulmonary artery smooth muscle cells, which may serve as a new therapeutic target for reducing vascular remodeling in pulmonary hypertension.
CIRCULATION RESEARCH
(2023)
Article
Ophthalmology
Michaella Hulley, Thandiswa Ngcungcu, Michele Ramsay, Susan Williams
Summary: The feasibility of using a non-invasive technique, the EYEPRIMTM conjunctival cell impression device, to harvest sufficient RNA from conjunctival cells for whole-transcriptome sequencing was investigated. Conjunctival cells were collected from 40 participants using the EYEPRIMTM conjunctival cell impression device. RNA extraction, library construction, and transcriptome sequencing were successfully performed, with sufficient yield and quality of RNA obtained. This technique provides a convenient alternative to studying eye diseases using post-mortem tissues or surgical excisions.
EXPERIMENTAL EYE RESEARCH
(2023)
Article
Public, Environmental & Occupational Health
Karri Silventoinen, Hannu Lahtinen, George Davey Smith, Tim T. Morris, Pekka Martikainen
Summary: This study used a polygenic score for height to reveal the associations between height, socioeconomic position, and coronary heart disease incidence. The results showed clear gradients for residual height in relation to education, social class, and income, with a stronger association for residual height. These findings support the role of material and social living conditions in childhood as contributing factors to the association of height with both socioeconomic position and CHD risk.
JOURNAL OF EPIDEMIOLOGY AND COMMUNITY HEALTH
(2023)
Article
Peripheral Vascular Disease
Fumihiko Takeuchi, Yi-Qiang Liang, Masato Isono, Mia Yang Ang, Kotaro Mori, Norihiro Kato
Summary: This study evaluated the effects of antihypertensive drugs on the heart and kidney through in vivo phenotypic evaluation and transcriptomic analysis. The results showed that certain drugs had protective effects on end-organ damages independent of blood pressure lowering. The study also found significant differences in gene expression changes between different organs.
Review
Peripheral Vascular Disease
Emma F. Magavern, Helen R. Warren, Fu L. Ng, Claudia P. Cabrera, Patricia B. Munroe, Mark J. Caulfield
Summary: At the dawn of the new decade, a wealth of knowledge about polygenic risk for essential hypertension has been supplied by genome-wide association studies. Future innovations may translate this knowledge into clinical benefits, offering opportunities for understanding and treating polygenic hypertension using big data.
Article
Neurosciences
Chun Su, Mariana Argenziano, Sumei Lu, James A. Pippin, Matthew C. Pahl, Michelle E. Leonard, Diana L. Cousminer, Matthew E. Johnson, Chiara Lasconi, Andrew D. Wells, Alessandra Chesi, Struan F. A. Grant
Summary: This study integrated transcriptomics, epigenomics, and chromatin conformation changes to identify potential causal genes associated with neurodevelopmental disorders. The findings suggest that regulatory mechanisms during neuronal differentiation involve long-range interactions between cis-regulatory elements and developmental-stage-specific genes. The identified effector genes were enriched in pathways related to neuronal development and chromatin organization, providing valuable insights into the genetic and developmental basis of neurodevelopmental disorders.
PROGRESS IN NEUROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Di Zhang, Yanxiang Deng, Petra Kukanja, Eneritz Agirre, Marek Bartosovic, Mingze Dong, Cong Ma, Sai Ma, Graham Su, Shuozhen Bao, Yang Liu, Yang Xiao, Gorazd B. Rosoklija, Andrew J. Dwork, J. John Mann, Kam W. Leong, Maura Boldrini, Liya Wang, Maximilian Haeussler, Benjamin J. Raphael, Yuval Kluger, Goncalo Castelo-Branco, Rong Fan
Summary: Emerging spatial technologies such as spatial transcriptomics and spatial epigenomics have become powerful tools in profiling cellular states in tissue contexts. However, current methods only capture one layer of omics information at a time, limiting the examination of mechanistic relationships in molecular biology. In this study, two technologies are presented for joint profiling of the epigenome and transcriptome at a genome-wide, spatially resolved, and near-single-cell resolution. These technologies provide new insights into spatial epigenetic priming, differentiation, and gene regulation within tissue architecture.
Article
Cardiac & Cardiovascular Systems
Elaheh Karbassi, Manuel Rosa-Garrido, Douglas J. Chapski, Yong Wu, Shuxun Ren, Yibin Wang, Enrico Stefani, Thomas M. Vondriska
JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY
(2019)
Article
Neurosciences
Enrique Balderas, Natalia S. Torres, Manuel Rosa-Garrido, Dipayan Chaudhuri, Ligia Toro, Enrico Stefani, Riccardo Olcese
JOURNAL OF PHYSIOLOGY-LONDON
(2019)
Article
Biology
Jaqueline J. Brito, Thiago Mosqueiro, Jeremy Rotman, Victor Xue, Douglas J. Chapski, Juan De la Hoz, Paulo Matias, Lana S. Martin, Alex Zelikovsky, Matteo Pellegrini, Serghei Mangul
Article
Cardiac & Cardiovascular Systems
Alessandro Bertero, Manuel Rosa-Garrido
Summary: Recent technological advancements in chromatin biology have revealed that chromatin folding in 3D space is non-random, hierarchical, and complex. While 3D chromatin structure is partially encoded in the primary sequence, a substantial portion of the genome appears to be dynamic. Additionally, evidence suggests that some 3D chromatin structure is functionally linked to gene regulation, influenced by various nuclear processes. This has led to investigations on the role of 3D chromatin topology dynamics in heart development and disease.
JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY
(2021)
Editorial Material
Cardiac & Cardiovascular Systems
Emma Louise Robinson, Chukwuemeka George Anene-Nzelu, Manuel Rosa-Garrido, Roger S. Y. Foo
Summary: Epigenetic regulation is crucial for the homeostasis of every tissue and organ, especially in the cardiovascular system. Understanding the signaling from the cardiac epigenome is essential for unraveling the molecular underpinnings of cardiovascular disease and development.
JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY
(2021)
Review
Cardiac & Cardiovascular Systems
Douglas J. Chapski, Thomas M. Vondriska
Summary: The advancements in technology have enabled high-throughput measurements of the genome in cardiovascular biology, leading to a flood of immense datasets that offer new opportunities for data processing and knowledge integration for meaningful discoveries. Big data, integrative analyses, and machine learning have brought cardiac investigations to the forefront of chromatin biology, with potential implications for targeted epigenetic therapies. Future research should consider insights from existing genomic datasets to explore uncharted epigenomic contributions to disease pathology.
CURRENT CARDIOLOGY REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Cynthia M. McKee, Douglas J. Chapski, Michelle Wehling-Henricks, Manuel Rosa-Garrido, Makoto Kuro-O, Thomas M. Vondriska, James G. Tidball
Summary: This study reveals that modulation of muscle stem cell numbers during early postnatal development has long-term effects on muscle growth. The anti-aging protein Klotho influences myogenesis by increasing satellite cell numbers and influencing the epigenetic regulation of genes involved in myogenesis. Klotho reduces the expression of Jmjd3, leading to decreased expression of Wnt genes and inhibition of canonical Wnt signaling, which delays muscle differentiation.
Article
Cardiac & Cardiovascular Systems
Douglas J. Chapski, Maximilian Cabaj, Marco Morselli, Rosibel J. Mason, Elizabeth Soehalim, Shuxun Ren, Matteo Pellegrini, Yibin Wang, Thomas M. Vondriska, Manuel Rosa-Garrido
Summary: The study revealed that chromatin remodeling during early compensation after pathologic stimuli persists into the later decompensatory phases of heart failure. The findings provide insights into how local chromatin features govern gene expression within the context of global genomic structure and highlight chromatin remodeling events that could be targeted for therapeutic interventions in disease.
JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Noemi Cabre, Fedra Luciano-Mateo, Douglas J. Chapski, Gerard Baiges-Gaya, Salvador Fernandez-Arroyo, Anna Hernandez-Aguilera, Helena Castane, Elisabet Rodriguez-Tomas, Marta Paris, Fatima Sabench, Daniel Del Castillo, Josep M. del Bas, Mercedes Tome, Clement Bodineau, Alejandro Sola-Garcia, Jose Lopez-Miranda, Alejandro Martin-Montalvo, Raul Duran, Thomas M. Vondriska, Manuel Rosa-Garrido, Jordi Camps, Javier A. Menendez, Jorge Joven
Summary: The study investigates the signaling processes involved in the development of nonalcoholic steatohepatitis using a surgically induced remission model of liver disease. The results suggest that surgery can decrease the inflammatory response and reveal the role of mitogen-activated protein kinases. Furthermore, increased glutaminolysis-induced production of alpha-ketoglutarate and dysregulation of mammalian target of rapamycin complex 1 play a crucial role in the inefficient adaptive responses leading to steatohepatitis in obesity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Yang Cao, Laurent Vergnes, Yu-Chen Wang, Calvin Pan, Karthickeyan Chella Krishnan, Timothy M. Moore, Manuel Rosa-Garrido, Todd H. Kimball, Zhiqiang Zhou, Sarada Charugundla, Christoph D. Rau, Marcus M. Seldin, Jessica Wang, Yibin Wang, Thomas M. Vondriska, Karen Reue, Aldons J. Lusis
Summary: This study reveals that sex differences in mitochondrial DNA levels and function in the heart contribute to sex biases in functions relevant to heart failure, and identifies Acsl6 as a mitochondrial sex-biased regulator of diastolic function. By conducting genetic studies in mice and analyzing human cohorts, the authors find that heart mitochondrial DNA levels and function are reduced in females compared to males, and the expression of genes encoding mitochondrial proteins is higher in males. The study also shows that mitochondrial gene expression is highly correlated with diastolic function, an important trait in HFpEF.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Lu Wang, Thanh Nguyen, Manuel Rosa-Garrido, Yang Zhou, David C. Cleveland, Jianyi Zhang
Summary: The study investigates the relationship between somatic-cell lineage and hiPSC-CM production by comparing the yield and functional properties of CMs differentiated from iPSCs reprogrammed from human atrial or ventricular cardiac fibroblasts. The study demonstrates that the tissue of origin and sublocation within the cardiac tissue have marginal effects on the differentiation process, but differences in electrophysiological properties and transcription profiles between cardiac and non-cardiac derived cardiomyocytes exist.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Cardiac & Cardiovascular Systems
Douglas J. Chapski, Manuel Rosa-Garrido, Nan Hua, Frank Ajber, Thomas M. Vondriska
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2019)
