Review
Oncology
Richard Sean Lee, Kirti Sad, Dorelle V. Fawwal, Jennifer Marie Spangle
Summary: Breast cancer is a frequent and deadly disease in women, with histone-modifying enzymes playing a role in treatment response and patient outcomes. Epigenetic changes to chromatin affect the tumor environment and can be targeted for breast cancer treatment. Understanding these mechanisms may improve therapeutic interventions and patient outcomes.
Article
Multidisciplinary Sciences
Quan Wu, Yuichi Shichino, Takaya Abe, Taeko Suetsugu, Ayaka Omori, Hiroshi Kiyonari, Shintaro Iwasaki, Fumio Matsuzaki
Summary: This study reveals that Fbl, a ribosomal RNA methyltransferase, controls translational efficiencies of epigenetic modifiers during neural stem cell (NSC) development, thereby playing a potential role as a clock in the development of the cerebral cortex.
NATURE COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
Eduardo Izquierdo-Torres, Andres Hernandez-Oliveras, Dalia Lozano-Arriaga, Angel Zarain-Herzberg
Summary: Obesity and cancer are complex medical conditions that are closely related. Understanding the mechanism of obesity and cancer development is crucial for public health. This review article explores the impact of lifestyle on obesity and cancer at the cellular and molecular level, as well as the regulation of gene expression by metabolic products.
JOURNAL OF NUTRITIONAL BIOCHEMISTRY
(2022)
Article
Genetics & Heredity
Stefan Butz, Nina Schmolka, Ino D. Karemaker, Rodrigo Villasenor, Isabel Schwarz, Silvia Domcke, Esther C. H. Uijttewaal, Julian Jude, Florian Lienert, Arnaud R. Krebs, Nathalie P. de Wagenaar, Xue Bao, Johannes Zuber, Ulrich Elling, Dirk Schuebeler, Tuncay Baubec
Summary: Genomic imprinting is regulated by DNA methylation of imprinting control regions (ICRs) with parental-specificity. The epigenetic states of ICRs, despite having an identical DNA sequence, are determined by genetic and epigenetic factors. Through iterative integration of ICRs and DNA sequences, this study identified the DNA sequence features required for maintaining the epigenetic states in embryonic stem cells. Additionally, ATF7IP and ZMYM2 were found to be important for the stability of DNA and H3K9 methylation at ICRs in embryonic stem cells.
Article
Medicine, Research & Experimental
Samadrita Bhattacharyya, Rahul K. Kollipara, Gabriela Orquera-Tornakian, Sean Goetsch, Minzhe Zhang, Cameron Perry, Boxun Li, John M. Shelton, Minoti Bhakta, Jialei Duan, Yang Xie, Guanghua Xiao, Bret M. Evers, Gary C. Hon, Ralf Kittler, Nikhil V. Munshi
Summary: A comprehensive CCS-enriched CRE database named CCS-ATAC was established for studying CCS-wide and component-specific regulatory functions. CCS component-specific gene regulatory networks (GRNs) were constructed using transcription factor (TF) motifs, and specific TF sub-networks were identified and confirmed. CCS-ATAC was leveraged to improve annotation of existing human variants related to cardiac rhythm, and a potential dysregulated enhancer-target pair by a specific SNP was nominated.
JOURNAL OF CLINICAL INVESTIGATION
(2023)
Review
Endocrinology & Metabolism
Annalisa Roberti, Agustin F. Fernandez, Mario F. Fraga
Summary: NNMT acts as a key link between cellular metabolism and epigenetic gene regulation, playing a central role in various pathologies. Targeting NNMT pathways represents a current pharmaceutical challenge for treating a range of metabolic-related diseases and cancers.
MOLECULAR METABOLISM
(2021)
Review
Genetics & Heredity
Benjamin Carter, Keji Zhao
Summary: Single-cell sequencing methods have shown heterogeneity in gene expression levels among morphologically similar cells, with epigenomic information contributing to the regulation of gene expression.Recent studies suggest that variations in chromatin organization collectively define gene expression heterogeneity among otherwise similar cells.
NATURE REVIEWS GENETICS
(2021)
Review
Cardiac & Cardiovascular Systems
Krishnega Murugasamy, Aastha Munjal, Nagalingam Ravi Sundaresan
Summary: The heart, as a highly metabolically active organ, primarily uses fatty acids as an energy source. SIRT3, a deacetylase, plays a crucial role in regulating cardiac metabolism. Increasing SIRT3 levels or activity can alleviate cardiac pathologies, as SIRT3 targets mitochondrial proteins involved in energy metabolism. This review emphasizes the importance of SIRT3 as a master regulator of cardiac metabolism and discusses potential therapeutic strategies for improving cardiac health.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2022)
Article
Biochemical Research Methods
Dongbo Lu, Caroline A. Foley, Shama Birla, Austin J. Hepperla, Jeremy M. Simon, Lindsey James, Nathaniel A. Hathaway
Summary: CRISPR-Cas9 systems have been developed for gene expression regulation through fusions with epigenetic regulators or chemical-mediated strategies. This chemical approach utilizes a new chemical epigenetic modifier (CEM) to optimize gene targeting by linking it to catalytically inactive Cas9 (dCas9) and FKBP.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Oncology
Cheemala Ashok, Neha Ahuja, Subhashis Natua, Jharna Mishra, Atul Samaiya, Sanjeev Shukla
Summary: ESRP1 plays a significant role in cancer progression, with elevated expression in carcinoma in situ and reduced expression in hypoxic cancer cells. The transcription factor E2F1 and CpG hydroxymethylation are key factors in upregulating ESRP1 expression, while hypoxia-induced TET3 downregulation leads to E2F1 repression, contributing to diminished ESRP1 expression in hypoxic conditions.
Review
Physiology
Magda Correia, Bruno Bernardes de Jesus, Sandrina Nobrega-Pereira
Summary: Heart disease is the leading cause of mortality in developed countries, characterized by loss of cardiomyocytes leading to heart failure. While adult mammalian hearts have limited regenerative capacity, neonatal hearts have stronger regenerative potential. The role of metabolic pathways and lncRNAs in cardiac regeneration requires further research.
FRONTIERS IN PHYSIOLOGY
(2021)
Review
Microbiology
Lynise C. Pillay, Lucpah Nekati, Phuti J. Makhwitine, Sizwe I. Ndlovu
Summary: The discovery of silent biosynthetic gene clusters in fungi provides vast opportunities for utilizing their encoded secondary metabolites, including for pharmaceutical applications. Fungi in endosymbiosis relationship with plants have been recognized as potential future sources for clinically relevant agents. The regulatory mechanisms governing the expression of silent biosynthetic gene clusters in fungi remain unknown, limiting their exploitation in the laboratory. Epigenetic modification using small molecular compounds has shown promising results in activating the expression of silent biosynthetic gene clusters. This review comprehensively analyzes the secondary metabolite profiles expressed after treatment with various epigenetic modifiers.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Immunology
Carmen A. Buttler, Edward B. Chuong
Summary: Recent advances in regulatory genomic technologies have led to significant progress in understanding the transcriptional networks underlying mammalian immune responses. Epigenomic studies profiling immune cells have revealed detailed genome-wide maps of regulatory elements, with endogenous retroviruses unexpectedly emerging as allies in regulating human immune systems.
IMMUNOLOGICAL REVIEWS
(2022)
Review
Hematology
Andrew B. Das, Carlos C. Smith-Diaz, Margreet C. M. Vissers
Summary: The development of epigenetic therapies has shown promise in diseases like acute myeloid leukemia, but issues such as patient response heterogeneity and resistance may be partly attributed to epigenetic heterogeneity. Combination therapy targeting both driver mutations and epigenetic plasticity could be a key strategy in addressing these challenges.
Article
Clinical Neurology
Yannick Braun, Katharina Filipski, Simon Bernatz, Peter Baumgarten, Bastian Roller, Jenny Zinke, Pia S. Zeiner, Elena Ilina, Christian Senft, Michael W. Ronellenfitsch, Karl H. Plate, Oliver Baehr, Elke Hattingen, Joachim P. Steinbach, Michel Mittelbronn, Patrick N. Harter
Summary: This study aims to characterize metabolic features in different molecular subgroups of gliomas, focusing on the impact of metabolic alterations on patient outcomes. Results showed that DNA methylation patterns of metabolic genes can distinguish between IDHmut and IDHwt gliomas, and mitochondrial DNA copy number and immune cell content analysis can predict patient survival under anti-angiogenic therapy. Genomic signatures related to metabolism could indicate specific tumor subgroups with metabolic vulnerabilities.
NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Natascha Sommers, Nasim Alebrahimdehkordi, Oleg Pak, Fenja Knoepp, Ievgen Strielkov, Susan Scheibe, Eric Dufour, Ana Andjelkovic, Akylbek Sydykov, Alireza Saraji, Aleksandar Petrovic, Karin Quanz, Matthias Heckert, Manish Kumar, Joel Wahl, Simone Kraut, Werner Seeger, Ralph T. Schermuly, Hossein A. Ghofrani, Kerstin Ramser, Thomas Braun, Howard T. Jacobs, Norbert Weissmann, Marten Szibor
Review
Cardiac & Cardiovascular Systems
Giovanni Maroli, Thomas Braun
Summary: Knowledge on regulating CM proliferation and differentiation has grown rapidly, but poor regenerative potential of the postnatal heart and incomplete maturation of iPSC-derived CMs are significant challenges for future therapies.
CARDIOVASCULAR RESEARCH
(2021)
Article
Cell Biology
Isabelle Salwig, Birgit Spitznagel, Marion Wiesnet, Thomas Braun
Summary: Optical clearing combined with deep imaging allows for organ-wide visualization of cell dynamics in three dimensions for exploring the regenerative processes in spatial context, showing the stages of bronchiolar epithelial renewal following injury and the regenerative capacity of respiratory epithelium.
HISTOCHEMISTRY AND CELL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Kee-Pyo Kim, Jinmi Choi, Juyong Yoon, Jan M. Bruder, Borami Shin, Jonghun Kim, Marcos J. Arauzo-Bravo, Dong Han, Guangming Wu, Dong Wook Han, Johnny Kim, Patrick Cramer, Hans R. Schoeler
Summary: A chemical screen targeting major epigenetic pathways can identify permissive epigenetic states that enhance reprogramming competence of transcription factors. In this study, inhibiting specific epigenetic roadblocks simultaneously was found to dramatically improve the reprogramming ability of most OCT factors and enable dismantling species-dependent reprogramming competence of certain transcription factors such as OCT6.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Cardiac & Cardiovascular Systems
Lei Wang, Megan Rice, Sandra Swist, Thomas Kubin, Fan Wu, Shengpeng Wang, Simone Kraut, Norbert Weissmann, Thomas Boettger, Matthew Wheeler, Andre Schneider, Thomas Braun
Summary: The study revealed that BMP9 and BMP10 act directly on VSMCs for induction and maintenance of their contractile state. The effects of BMP9/10 in VSMCs are mediated by different combinations of BMP type 1 receptors in a vessel bed-specific manner, offering new opportunities to manipulate blood pressure in the pulmonary circulation.
Article
Biochemistry & Molecular Biology
Jacqueline Heger, Christine Hirschhaeuser, Julia Bornbaum, Akylbek Sydykov, Astrid Dempfle, Andre Schneider, Thomas Braun, Klaus-Dieter Schlueter, Rainer Schulz
Summary: The creation of MAO-B knockout mice demonstrates that the lack of cardiomyocyte MAO-B can protect the heart from I/R injury and reduce infarct size.
FREE RADICAL BIOLOGY AND MEDICINE
(2021)
Article
Biochemical Research Methods
Clemens Neufert, Christina Heichler, Thomas Brabletz, Kristina Scheibe, Verawan Boonsanay, Florian R. Greten, Markus F. Neurath
Summary: This protocol introduces a method utilizing mouse models to study colorectal cancer, including induction of tumor growth using azoxymethane and dextran sodium sulfate. Through analysis of tumor growth and metastasis, researchers can gain insights into mechanisms of tumor development, suitable for early assessment of novel drugs and clinical treatment strategies.
Article
Multidisciplinary Sciences
Alessandro Ianni, Poonam Kumari, Shahriar Tarighi, Nicolas G. Simonet, Daniela Popescu, Stefan Guenther, Soraya Holper, Andreas Schmidt, Christian Smolka, Shijing Yue, Marcus Kruger, Claudia Fiorillo, Alejandro Vaquero, Eva Bober, Thomas Braun
Summary: Adaptation to different forms of environmental stress is crucial for maintaining cellular functions and survival, with nucleolus playing a decisive role as a signaling hub; SIRT7 is an essential component for regulating p53 stability during stress responses induced by UV irradiation; Through ATR-mediated phosphorylation, SIRT7 promotes deacetylation of NPM, affecting ubiquitination and stabilization of p53 in response to genotoxic stress.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Cell & Tissue Engineering
Azimeh Akhlaghpour, Adeleh Taei, Seyyed Abolghasem Ghadami, Zahra Bahadori, Saeed Yakhkeshi, Sepideh Molamohammadi, Tahereh Kiani, Azam Samadian, Zahra Ghezelayagh, Newsha Haghparast, Keynoosh Khalooghi, Thomas Braun, Hossein Baharvand, Seyedeh-Nafiseh Hassani
Summary: The developing chicken embryo is found to be a permissive host for analyzing the pluripotency potential of hPSCs. Both naive-like and primed hPSCs can form robust chimerism when transplanted at matched developmental stages, but only naive-like hPSCs show reduced ability to form chimera when injected at non-matched developmental stages. Conclusively, contribution to chick embryogenesis serves as an informative and versatile test to identify different pluripotent states of hPSCs.
Article
Cell & Tissue Engineering
Kee-Pyo Kim, Cui Li, Daria Bunina, Hyun-Woo Jeong, Julia Ghelman, Juyong Yoon, Borami Shin, Hongryeol Park, Dong Wook Han, Judith B. Zaugg, Johnny Kim, Tanja Kuhlmann, Ralf H. Adams, Kyung-Min Noh, Steven A. Goldman, Hans R. Schoeler
Summary: By transducing an optimized transcription factor combination into a permissive donor phenotype, pericyte-derived iOPCs (PC-iOPCs) can overcome the limitations of inefficient generation and limited expansion and differentiation competence. PC-iOPCs are stably expandable and functionally myelinogenic with high differentiation competence.
Review
Biochemistry & Molecular Biology
Kee-Pyo Kim, Dong Wook Han, Johnny Kim, Hans R. Schoeler
Summary: The ectopic expression of Oct4, Sox2, Klf4 and c-Myc can reprogram somatic cells into induced pluripotent stem cells (iPSCs), with Oct4 not always being necessary for reprogramming. Different Oct family members and species display varying reprogramming capacities, indicating a complex mechanism for reprogramming. Epigenomes of donor cells can affect the reprogramming competence of Oct proteins.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2021)
Article
Multidisciplinary Sciences
Yanpu Chen, Felipe F. Luttmann, Eric Schoger, Hans R. Schoeler, Laura C. Zelarayan, Kee-Pyo Kim, Jody J. Haigh, Johnny Kim, Thomas Braun
Summary: Research shows that expression of OSKM genes in adult cardiomyocytes can induce these cells to dedifferentiate, conferring regenerative capacity to the heart. This short-term dedifferentiation and reprogramming can ameliorate myocardial damage and facilitate heart regeneration.
Article
Biochemistry & Molecular Biology
Alessandro Ianni, Poonam Kumari, Shahriar Tarighi, Flavia Rita Argento, Eleonora Fini, Giacomo Emmi, Alessandra Bettiol, Thomas Braun, Domenico Prisco, Claudia Fiorillo, Matteo Becatti
Summary: GCA patients exhibit systemic oxidative stress, with a reduced expression of nuclear sirtuins, suggesting a potential involvement in GCA pathogenesis. Further studies are required to explore the impact of these alterations.
Article
Biochemistry & Molecular Biology
Holger Loerchner, Juan M. Adrian-Segarra, Christian Waechter, Roxanne Wagner, Maria Elisa Goes, Nathalie Brachmann, Krishnamoorthy Sreenivasan, Astrid Wietelmann, Stefan Guenther, Nicolas Doll, Thomas Braun, Jochen Poeling
Summary: This study discovered that simultaneous and rapid activation of OSMR and LIFR after myocardial infarction (MI) can protect the functional and structural integrity of the infarcted heart, and this can be achieved by using engineered human-like OSM.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Respiratory System
Stanislav Keranov, Oliver Doerr, Leili Jafari, Christian Troidl, Christoph Liebetrau, Steffen Kriechbaum, Till Keller, Sandra Voss, Timm Bauer, Jakob Lorenz, Manuel J. Richter, Khodr Tello, Henning Gall, Hossein A. Ghofrani, Eckhard Mayer, Christoph B. Wiedenroth, Stefan Guth, Holger Loerchner, Jochen Poeling, Prakash Chelladurai, Soni Savai Pullamsetti, Thomas Braun, Werner Seeger, Christian W. Hamm, Holger Nef
Summary: The study revealed that CILP1 is a novel biomarker associated with maladaptive RV function and PH, with significant differences in its concentrations among different cardiac pathology groups, showing potential in predicting maladaptive RV function.
EUROPEAN RESPIRATORY JOURNAL
(2021)
