Article
Biochemistry & Molecular Biology
Hosub Shin, Woo Lee Choi, Joo Young Lim, Jin Hoe Huh
Summary: Epigenetic modifications play important roles in cellular processes and have potential applications in plant breeding. Understanding epimutations in crops is crucial for developing useful traits. Plant breeding through epigenome editing can expand the use of genetic resources and alleviate concerns about genetically modified crops.
Article
Endocrinology & Metabolism
Amanda L. Morin, Phyo W. Win, Angela Z. Lin, Christina A. Castellani
Summary: Bidirectional crosstalk between the nuclear and mitochondrial genomes is crucial for cell functioning. Mitochondrial DNA copy number and heteroplasmy can influence mitochondrial function, nuclear genome, and contribute to overall health and disease. Mitochondria act as environmental biosensors, conveying essential information about cell state to the nuclear genome. Cellular communication between mitochondrial variation and nuclear epigenome can occur through modifications of metabolites and intermediates, affecting epigenetic modifications.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Plant Sciences
Fangming Zhu, Mingyan Li, Manwen Yan, Fei Qiao, Xuefei Jiang
Summary: DNA methylation plays a crucial role in plants' response to osmotic stress, with genes related to plant hormone synthesis, signal transduction, osmoregulatory substance, and antioxidant enzymes rapidly responding. Additionally, demethylation of key enzyme genes can alleviate the inhibition of cell growth caused by osmotic stress.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Biochemistry & Molecular Biology
Qiong Wu, Anders E. Berglund, Arnold B. Etame
Summary: Glioblastoma is highly resistant to standard therapies and the durability of response to the best chemotherapy agent, Temozolomide, is often short-lived due to tumor resistance. The need for therapies that can provide synergy to chemoradiation is urgent, as adaptive resistance evolution in GBM is facilitated through treatment-induced epigenetic modifications. Understanding and targeting these epigenetic modifications associated with GBM resistance is a top priority.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Oncology
Irfete S. Fetahu, Sabine Taschner-Mandl
Summary: Neuroblastoma is a common solid tumor in infants, with genetic and epigenetic alterations playing a key role in its pathogenesis. Aberrant DNA methylation, disrupted histone modification patterns, and abnormal expression of non-coding RNAs are major epigenetic changes associated with NB.
CANCER AND METASTASIS REVIEWS
(2021)
Review
Nutrition & Dietetics
Paola Ungaro, Immacolata Cristina Nettore, Fabiana Franchini, Giuseppe Palatucci, Giovanna Muscogiuri, Annamaria Colao, Paolo Emidio Macchia
Summary: Ketogenic diets are effective in the treatment of obesity, metabolic diseases, and other conditions. However, limited data is available on the epigenetic changes associated with these diets.
Review
Plant Sciences
Jun-Li Wang, Dong-Wei Di, Pan Luo, Li Zhang, Xiao-Feng Li, Guang-Qin Guo, Lei Wu
Summary: This review focuses on the molecular mechanisms through which epigenetic modifications regulate auxin biosynthesis, demonstrating that complex signaling pathways affect gene expression and subsequently protein production.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Oncology
Francisco Gimeno-Valiente, Gerardo Lopez-Rodas, Josefa Castillo, Luis Franco
Summary: This review focuses on the interconnections between epigenetics and alternative splicing in the development of cancer. It discusses the mechanisms involved in these interconnections and the potential diagnostic and therapeutic tools that can be derived from them. The reversible nature of epigenetic alterations and the possibility of correcting aberrant alternative splicing offer promising therapeutic possibilities for cancer treatment.
Review
Environmental Sciences
Arijit Chakraborty, Soma Ghosh, Bratisha Biswas, Sreemanta Pramanik, Jerome Nriagu, Subhamoy Bhowmick
Summary: Arsenic exposure can cause harmful epigenetic alterations, leading to various health complications. This review summarizes the mechanisms underlying arsenic-induced epigenetic changes and proposes therapeutic strategies to alleviate the global burden of arsenic poisoning.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Review
Biotechnology & Applied Microbiology
Nicolas Marx, Peter Eisenhut, Marcus Weinguny, Gerald Klanert, Nicole Borth
Summary: Recent advances have greatly improved our understanding of Chinese hamster ovary (CHO) cells as hosts for producing biopharmaceuticals. Despite progress in characterizing CHO cells on different omics levels, our understanding of its epigenetic regulation is still incomplete. This review provides an overview of epigenetic regulation in CHO cells and discusses its significance in shaping cell phenotype. The review also presents current state-of-the-art technologies for manipulating epigenetic networks and controlling gene expression.
BIOTECHNOLOGY ADVANCES
(2022)
Review
Plant Sciences
Kajal Samantara, Aalok Shiv, Lorenna Lopes de Sousa, Karansher Singh Sandhu, Parichita Priyadarshini, Sourav Ranjan Mohapatra
Summary: Epigenetics is an important mechanism that can help plants cope with various stressors by altering gene expression without involving changes in DNA sequences. It provides diversity to aid plants in responding to the impacts of climate change.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2021)
Article
Reproductive Biology
Jingjing Qian, Fan Guo
Summary: Both human and mouse oocytes have unique epigenomic landscapes. New measurement technologies allow us to study genome regulation at different levels, including DNA methylation, transcription, and chromatin accessibility. Recent studies have also explored the relationship between different histone modifications and DNA methylation, revealing the mechanisms behind oocyte DNA methylome formation.
BIOLOGY OF REPRODUCTION
(2022)
Review
Neurosciences
Julia Reichard, Geraldine Zimmer-Bensch
Summary: Neurodevelopmental diseases are characterized by diverse neurological and psychiatric symptoms, with disrupted brain development leading to functional deficits. Genetic and environmental factors during corticogenesis can contribute to deficits in neuronal identity, proportion or function, implicating the cerebral cortex in various disorders. Epigenetic mechanisms, including DNA methylation, histone modifications, chromatin remodeling, and non-coding RNAs, play a role in regulating neuronal development and have been associated with NDDs of varying phenotypes.
FRONTIERS IN NEUROSCIENCE
(2021)
Review
Oncology
Junyuan Xie, Li Gan, Bingjian Xue, Xinxing Wang, Xinhong Pei
Summary: Breast cancer remains the leading cause of cancer-related death in women worldwide. Non-coding RNAs, especially lncRNAs, have been found to play important roles in breast cancer. The study of epigenetic modifications has also contributed to the understanding of the role of ncRNAs in breast cancer.
FRONTIERS IN ONCOLOGY
(2023)
Review
Pharmacology & Pharmacy
Miklos Toth
Summary: This review explores how drugs of different classes, including those with therapeutic and abuse potential, can alter brain functions and behaviors through the epigenome. The epigenome, established during development, can be modified throughout life by various drugs with clinical utility and abuse potential. Epigenetic effects may play a central role in a drug's therapeutic or abuse potential, or may produce beneficial or adverse side effects independently from the main effect.
ANNUAL REVIEW OF PHARMACOLOGY AND TOXICOLOGY, VOL 61, 2021
(2021)
Article
Cardiac & Cardiovascular Systems
Naveed Akbar, Adam T. Braithwaite, Emma M. Corr, Graeme J. Koelwyn, Coen van Solingen, Clement Cochain, Antoine-Emmanuel Saliba, Alastair Corbin, Daniela Pezzolla, Malene Moller Jorgensen, Rikke Baek, Laurienne Edgar, Carla De Villiers, Mala Gunadasa-Rohling, Abhirup Banerjee, Daan Paget, Charlotte Lee, Eleanor Hogg, Adam Costin, Raman Dhaliwal, Errin Johnson, Thomas Krausgruber, Joey Riepsaame, Genevieve E. Melling, Mayooran Shanmuganathan, Christoph Bock, David R. F. Carter, Keith M. Channon, Paul R. Riley, Irina A. Udalova, Kathryn J. Moore, Daniel Anthony, Robin P. Choudhury
Summary: Acute myocardial infarction leads to a rapid increase in blood neutrophils. While chemokine elevation has been considered their source, this study shows that endothelial cell activation can release extracellular vesicles (EVs) that promote mobilization of neutrophils from the spleen to peripheral blood. These EVs carry VCAM-1 and miRNA-126, and their accumulation in the spleen induces inflammatory gene expression and mobilizes splenic neutrophils.
CARDIOVASCULAR RESEARCH
(2023)
Article
Pathology
Laura Sabater, Jean B. Gossart, Inmaculada Hernandez, Daniel Rico, Andy Blanchard, Lee A. Borthwick, Andrew J. Fisher, Joaquim Majo, Kasim Jiwa, Amy Collins, Giuseppe Abbate, Fiona Oakley, Derek A. Mann, Jelena Mann
Summary: miRNAs play a crucial role in regulating gene expression in idiopathic pulmonary fibrosis (IPF). This study compared the expression levels of miRNAs in fibroblastic foci (FF), whole IPF lung tissue, and cultured IPF fibroblasts, and found that FF had a unique and distinct miRNA composition. The differences in miRNA composition between FF and cultured IPF fibroblasts affected multiple signaling pathways, highlighting the importance of characterizing FF biology as a functionally discrete tissue microenvironment.
AMERICAN JOURNAL OF PATHOLOGY
(2023)
Article
Immunology
Ram Vinay Pandey, Johanna Strobl, Anna Redl, Luisa Unterluggauer, Laura Gail, Lisa Kleissl, Sophie Mueller, Denise Atzmueller, Victoria Fife-Gernedl, Thomas Krausgruber, Hanna Knaus, Margit Mitterbauer, Philipp Wohlfarth, Werner Rabitsch, Christoph Bock, Georg Stary
Summary: Allogeneic hematopoietic stem-cell transplantation (HSCT) aims to rebuild the host's immune system using donor stem cells. However, there are complications that can affect the success of HSCT, such as leukemia relapse or graft-versus-host-disease (GvHD). This study investigated the regulatory processes involved in T cell recovery after HSCT, using multi-omics analysis of T cells from the skin and blood. The findings revealed the importance of epigenetic regulation and identified specific epigenetic regulators in restoring T cell homeostasis after transplantation.
CLINICAL IMMUNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Giulia Borsi, Krishna Motheramgari, Heena Dhiman, Martina Baumann, Elly Sinkala, Max Sauerland, Julian Riba, Nicole Borth
Summary: This study investigated the variability and diversity of individual cell transcriptomes in CHO and HEK293 cells under different culture conditions using full-length coverage single-cell RNA sequencing. The results showed a batch effect in CHO cells and highlighted the impact of the cell cycle on transcriptome variation.
JOURNAL OF BIOTECHNOLOGY
(2023)
Article
Endocrinology & Metabolism
Zora Messner, David Carro-Vazquez, Judith Haschka, Johannes Grillari, Heinrich Resch, Christian Muschitz, Peter Pietschmann, Jochen Zwerina, Matthias Hackl, Roland Kocijan
Summary: This study investigated circulating miRNAs as potential biomarkers for monitoring treatment response in women with postmenopausal osteoporosis on denosumab therapy. The results showed significant changes in expression of seven miRNAs after two years of treatment, which correlated with changes in bone mineral density and bone turnover markers.
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2023)
Article
Multidisciplinary Sciences
Johanna Klughammer, Daria Romanovskaia, Amelie Nemc, Annika Posautz, Charlotte A. Seid, Linda C. Schuster, Melissa C. Keinath, Juan Sebastian Lugo Ramos, Lindsay Kosack, Ann Evankow, Dieter Printz, Stefanie Kirchberger, Bekir Erguener, Paul Datlinger, Nikolaus Fortelny, Christian Schmidl, Matthias Farlik, Kaja Skjaerven, Andreas Bergthaler, Miriam Liedvogel, Denise Thaller, Pamela A. Burger, Marcela Hermann, Martin Distel, Daniel L. Distel, Anna Kuebber-Heiss, Christoph Bock
Summary: This study maps DNA methylation in 535 vertebrates and 45 invertebrates and establishes a reference dataset for cross-species analysis. It quantifies the association between DNA methylation and genomic DNA sequence throughout vertebrate evolution and reveals a deeply conserved association of DNA methylation with tissue type. The study also identifies evolutionary changes in DNA methylation at gene promoters for orthologous genes.
NATURE COMMUNICATIONS
(2023)
Article
Geriatrics & Gerontology
Isabella Pototschnig, Ursula Feiler, Clemens Diwoky, Paul W. Vesely, Thomas Rauchenwald, Margret Paar, Latifa Bakiri, Laura Pajed, Peter Hofer, Karl Kashofer, Nyamdelger Sukhbaatar, Gabriele Schoiswohl, Thomas Weichhart, Gerald Hoefler, Christoph Bock, Martin Pichler, Erwin F. Wagner, Rudolf Zechner, Martina Schweiger
Summary: In this study, CHX207 fibrosarcoma cells were used as a novel tool to study the mediators and metabolic consequences of CAC in C57BL/6 mice compared to non-cachectic MCA207-tumour-bearing mice. The results showed that IL-6 plays a crucial role in the development of CAC caused by CHX207 tumors.
JOURNAL OF CACHEXIA SARCOPENIA AND MUSCLE
(2023)
Review
Biochemistry & Molecular Biology
Daniel Kent, Letizia Marchetti, Aneta Mikulasova, Lisa J. J. Russell, Daniel Rico
Summary: The human and mouse genomes are complex due to regulatory elements in the non-coding genome, resulting in various cell types. Recent advances in epigenomic profiling have identified non-coding gene promoters and enhancers. Broad H3K4me3 domains (H3K4me3-BDs) are associated with constitutive gene expression and tumour suppressor genes. Dysregulated gene expression and tumourigenesis in cancer are associated with H3K4me3-BDs over oncogenes. The interaction between H3K4me3-BDs and super-enhancers (SE) is an important mechanism to identify treatments for SE driven cancers.
Article
Immunology
Thomas Krausgruber, Anna Redl, Daniele Barreca, Konstantin Doberer, Daria Romanovskaia, Lina Dobnikar, Maria Guarini, Luisa Unterluggauer, Lisa Kleissl, Denise Atzmuller, Carolina Mayerhofer, Aglaja Kopf, Simona Saluzzo, Clarice X. Lim, Praveen Rexie, Thomas Weichhart, Christoph Bock, George Stary
Summary: By analyzing granulomas from sarcoidosis patients, researchers reconstructed the gene regulatory networks involved in granuloma formation. They found that granulomas adopt aspects of lymphoid organ development and involve processes related to immunometabolism, cytokine and chemokine signaling, and extracellular matrix remodeling. Three cell types, including metabolically reprogrammed macrophages, cytokine-producing Th17.1 cells, and fibroblasts with inflammatory and tissue-remodeling phenotypes, were identified as key players in granuloma formation. Inhibiting one of the identified processes attenuated granuloma formation in a mouse model of sarcoidosis.
Article
Biochemistry & Molecular Biology
Maninder Heer, Luca Giudice, Claudia Mengoni, Rosalba Giugno, Daniel Rico
Summary: Researchers have developed a new method called Esearch3D to identify active enhancers using network theory approaches. This method calculates the likelihood of enhancer activity in intergenic regions by analyzing the folding of chromatin in the three-dimensional nuclear space, and regions predicted to have high enhancer activity are shown to be enriched in annotations indicative of enhancer activity.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Gastroenterology & Hepatology
Patrick Starlinger, Laura Brunnthaler, Chantal McCabe, David Pereyra, Jonas Santol, Jessica Steadman, Matthias Hackl, Susanna Skalicky, Hubert Hackl, Raphael Gronauer, Daniel O'Brien, Renate Kain, Petra Hirsova, Gregory J. Gores, Chen Wang, Thomas Gruenberger, Rory L. Smoot, Alice Assinger
Summary: Through the analysis of blood and tissue samples from patients, this study explores the early transcriptional changes during liver regeneration and their differences in individuals with dysfunctional liver regeneration.
Article
Biotechnology & Applied Microbiology
Neza Novak, Martina Baumann, Amy Friss, Victor Cairns, Christine DeMaria, Nicole Borth
Summary: Long non-coding RNAs (lncRNAs) were found to be correlated with productivity in mAb producer CHO clones. Overexpression or deletion of candidate lncRNAs showed that their expression levels were closely related to productivity. Deletion of one lncRNA region affected cell growth and productivity. These findings demonstrate the feasibility and usefulness of engineering lncRNA expression in production cell lines.
METABOLIC ENGINEERING
(2023)
Article
Multidisciplinary Sciences
Diana Swolin-Eide, Gun Forsander, Auste Pundziute Lycka, Daniel Novak, Johannes Grillari, Andreas B. Diendorfer, Matthias Hackl, Per Magnusson
Summary: This case-control study aimed to investigate potential differences in circulating miRNAs between young individuals with long-duration type 1 diabetes (T1D) and healthy controls, as well as the expression of these identified miRNAs across different tissues. The results showed that 27 miRNAs were upregulated and one was downregulated in T1D. Six of these miRNAs were tissue-enriched. These findings have important implications for studying biomarkers for diabetes-related complications.
SCIENTIFIC REPORTS
(2023)
Article
Physiology
Matthijs Luxen, Peter J. Zwiers, Femke Meester, Rianne M. Jongman, Timara Kuiper, Jill Moser, Marianne Pultar, Susanna Skalicky, Andreas B. Diendorfer, Matthias Hackl, Matijs van Meurs, Grietje Molema
Summary: This study investigated the microRNA and mRNA transcription patterns in different microvascular compartments of the mouse kidney cortex. Unique microRNA and mRNA profiles were identified, providing important molecular information for studying microvascular heterogeneity in the kidney in health and disease.
AMERICAN JOURNAL OF PHYSIOLOGY-RENAL PHYSIOLOGY
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
Aneta Mikulasova, Dan Kent, Marco Trevisan-Herraz, Nefeli Karataraki, Kent F. M. Fung, Cody Ashby, Agata Cieslak, Shmuel Yaccoby, Frits van Rhee, Maurizio Zangari, Sharmilan Thanendrarajan, Carolina Schinke, Gareth J. Morgan, Vahid Asnafi, Salvatore Spicuglia, Chris A. Brackley, Anne E. Corcoran, Sophie Hambleton, Brian A. Walker, Daniel Rico, Lisa J. Russell
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)