Review
Cell Biology
Dipanwita Das, Nandini Karthik, Reshma Taneja
Summary: Inflammation is a crucial immune response against infection and tissue damage, but chronic inflammation is linked to cancer development. Immune cells produce inflammatory mediators to facilitate tumor growth, while aberrant expression of inflammatory factors by tumor cells recruits immune cells for mutual crosstalk, creating a conducive environment for tumor growth.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Chemistry, Physical
Giovanni Scala, Mathilde N. Delaval, Sourav P. Mukherjee, Antonio Federico, Timur O. Khaliullin, Naveena Yanamala, Liliya M. Fatkhutdinova, Elena R. Kisin, Dario Greco, Bengt Fadeel, Anna A. Shvedova
Summary: The study revealed that MWCNTs exert epigenetic effects in the lungs, potentially driving subsequent gene expression changes. Muscle contraction, immune system/inflammation, and extracellular matrix pathways were the most affected pathways.
Article
Immunology
Stephanie Shiau, Stephen M. Arpadi, Yanhan Shen, Anyelina Cantos, Christian Vivar Ramon, Jayesh Shah, Grace Jang, Jennifer J. Manly, Adam M. Brickman, Andrea A. Baccarelli, Michael T. Yin
Summary: The study observed accelerated aging using DNA methylation biomarkers in African American older individuals with HIV, revealing significant differences in biomarker measurements compared to the control group and associations between aging biomarkers and cognitive function.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Biochemical Research Methods
Wubin Ding, Diljeet Kaur, Steve Horvath, Wanding Zhou
Summary: Researchers have developed informatics infrastructure and methods for DNA methylation analysis in multiple species, including domesticated animals and laboratory mice. They have created a data-driven analysis pipeline for species inference, genome-specific data preprocessing, and regression modeling. Comparative analysis has revealed the dynamics of epigenome evolution in different genomic territories and tissue types, and specific methylation differences related to mouse strain phenotypes have been identified. These methods expand epigenome research to a wide range of species by streamlining DNA methylation array analysis for undesigned genomes.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Geriatrics & Gerontology
Raul Fernandez Perez, Juan Jose Alba-Linares, Juan Ramon Tejedor, Agustin Fernandez Fernandez, Miguel Calero, Aurora Roman-Dominguez, Consuelo Borras, Jose Vina, Jesus Avila, Miguel Medina, Mario Fernandez Fraga
Summary: The study reveals the presence of dementia-associated epigenetic patterns before diagnosis, highlighting the potential importance of these epigenetic alterations in the development of dementia. The findings suggest that epigenetic biomarkers based on peripheral tissues may be useful for disease detection.
JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES
(2022)
Review
Immunology
Anthony M. Joudi, Carla P. Reyes Flores, Benjamin D. Singer
Summary: FoxP3(+) regulatory T cells play a crucial role in maintaining immune homeostasis, self-tolerance, and resolving inflammation and tissue damage. However, their plasticity in inflammatory microenvironments could lead to loss of function and contribute to inflammatory pathology, presenting a barrier to Treg cell immunotherapy. Understanding the determinants of Treg cell stability and utilizing epigenetic mechanisms could enhance the efficacy and minimize toxicity of Treg cell-based therapeutics.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Psychiatry
Weijing Wang, Weilong Li, Wenjie Jiang, Haijun Lin, Yili Wu, Yanhua Wen, Chunsheng Xu, Xiaocao Tian, Shuxia Li, Qihua Tan, Dongfeng Zhang
Summary: Cognitive ability plays a crucial role in the well-being of aging populations. Through an epigenome-wide association study on monozygotic twins, specific epigenetic variations significantly involved in functional genes and pathways related to cognitive function were identified. This research may offer insights for new diagnostic biomarkers and therapeutic targets for cognitive dysfunction.
JOURNAL OF PSYCHIATRIC RESEARCH
(2021)
Article
Cell Biology
Jayakanthan Kabeerdoss, Debashish Danda, Ruchika Goel, Hindhumathi Mohan, Sumita Danda, R. Hal Scofield
Summary: CD8 T cells may play a major role in the immunopathogenesis of inflammation in TA, while gamma delta T cells may have a regulatory role.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Immunology
Christian Gerecke, Caue Egea Rodrigues, Thomas Homann, Burkhard Kleuser
Summary: This study reviews the mechanisms by which TET proteins regulate immune cell maturation and function, as well as the complex interplay between TET expression and activity in inflammatory processes. The findings suggest that modulating TET enzymes could be a novel approach for treating inflammation-related diseases.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Eshaan Patnaik, Chikezie Madu, Yi Lu
Summary: Epigenetics plays a crucial role in gene regulation and tumor development. DNA methylation inhibitors and histone deacetylase inhibitors can restore normal gene expression and be effective against cancer. Understanding epigenetic modifications and utilizing inhibitors offer new possibilities for cancer research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Simeon Santourlidis, Wolfgang A. Schulz, Marcos J. Arauzo-Bravo, Daniela Gerovska, Pauline Ott, Marcelo L. Bendhack, Mohamed Hassan, Lars Erichsen
Summary: Epigenetic mechanisms play a fundamental role in the initiation and development of melanoma, but research in this area is relatively limited compared to other cancers. This review provides a brief summary of the epigenetic aspects relevant to melanoma pathogenesis and introduces new perspectives from epigenetic research in other cancers that may have potential for melanoma diagnosis and therapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cardiac & Cardiovascular Systems
Daniel A. Bizjak, Ole Ammerpohl, Sebastian Vw Schulz, Janine Wendt, Juergen M. Steinacker, Marion Flechtner-Mors
Summary: This study investigated pro-inflammatory markers and epigenetic risk factors in the saliva of obese children. The findings suggest that CRP concentrations and methylation status in saliva can be used as non-invasive methods for early detection of non-communicable diseases in children and adolescents.
NUTRITION METABOLISM AND CARDIOVASCULAR DISEASES
(2022)
Review
Environmental Sciences
Maja Srut
Summary: The effect of environmental pollutants on epigenetic changes, including DNA methylation, histone modifications, and non-coding RNAs, is a major concern in ecotoxicology. Earthworms have been widely used as models to study the impact of environmental stress on epigenetic mechanisms and to explore the possibility of epigenetic inheritance. However, there are still many knowledge gaps that need to be filled in.
Article
Environmental Sciences
Arce Domingo-Relloso, Anne Bozack, Samara Kiihl, Zulema Rodriguez-Hernandez, Pilar Rentero-Garrido, J. Antonio Casasnovas, Montserrat Leon-Latre, Tamara Garcia-Barrera, J. Luis Gomez-Ariza, Belen Moreno, Ana Cenarro, Griselda de Marco, Faruque Parvez, Abu B. Siddique, Hasan Shahriar, Mohammad N. Uddin, Tariqul Islam, Ana Navas-Acien, Mary Gamble, Maria Tellez-Plaza
Summary: The study identified common 5-hmC and 5-mC signatures in two populations exposed to varying levels of inorganic As, but differences in As-related epigenetic sites across the study populations may also reflect low and high As-specific associations. This work contributes to a deeper understanding of potential epigenetic dysregulations of As, with further research needed to confirm biological consequences associated with DIP2C epigenetic regulation and investigate the role of 5-hmC and 5-mC separately in As-induced health disorders at different exposure levels.
ENVIRONMENTAL RESEARCH
(2022)
Article
Multidisciplinary Sciences
Zhenhui Zhong, Suhua Feng, Sascha H. Duttke, Magdalena E. Potok, Yiwei Zhang, Javier Gallego-Bartolom, Wanlu Liu, Steven E. Jacobsen
Summary: DNA methylation influences chromatin accessibility, particularly in heterochromatin, in plants. Different sequence contexts of DNA methylation interact with each other, and methylation can impact chromatin structure through mechanisms other than transcription. Increased chromatin accessibility is associated with enhanced long-range chromatin interactions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Cell Biology
Katerina O. Gospodinova, Ditte Olsen, Mathias Kaas, Susan M. Anderson, Jonathan Phillips, Rosie M. Walker, Mairead L. Bermingham, Abigail L. Payne, Panagiotis Giannopoulos, Divya Pandya, Tara L. Spires-Jones, Catherine M. Abbott, David J. Porteous, Simon Glerup, Kathryn L. Evans
Summary: This study reveals a novel role for SORCS2 in DNA double-strand break formation, showing that loss of SORCS2 leads to increased DSB levels and reduced neuronal viability. These findings contribute to our understanding of the pathogenesis of neurodegenerative disorders.
CELLULAR AND MOLECULAR NEUROBIOLOGY
(2023)
Article
Neurosciences
Marissa C. Vacher, Claire S. Durrant, Jamie Rose, Ailsa J. Hall, Tara L. Spires-Jones, Frank Gunn-Moore, Mark P. Dagleish
Summary: Toothed whales, such as odontocetes, develop neuropathology similar to Alzheimer's disease, including amyloid plaques and hyperphosphorylated tau accumulation, suggesting that they may be affected by AD-like neurodegeneration.
EUROPEAN JOURNAL OF NEUROSCIENCE
(2023)
Article
Multidisciplinary Sciences
Niamh B. B. McNamara, David A. D. Munro, Nadine Bestard-Cuche, Akiko Uyeda, Jeroen F. J. Bogie, Alana Hoffmann, Rebecca K. K. Holloway, Irene Molina-Gonzalez, Katharine E. E. Askew, Stephen Mitchell, William Mungall, Michael Dodds, Carsten Dittmayer, Jonathan Moss, Jamie Rose, Stefan Szymkowiak, Lukas Amann, Barry W. W. McColl, Marco Prinz, Tara L. L. Spires-Jones, Werner Stenzel, Karen Horsburgh, Jerome J. A. Hendriks, Clare Pridans, Rieko Muramatsu, Anna Williams, Josef Priller, Veronique E. E. Miron
Summary: This study reveals the crucial role of resident microglia in maintaining myelin health in the central nervous system. Microglia are involved in regulating myelin growth, preserving myelin integrity, and influencing cognitive function. Disruption of the TGF beta 1-TGF beta R1 axis is implicated in the mechanism underlying the loss of myelin health. The findings suggest that targeting microglia could be a potential therapeutic approach for conditions with dysregulated myelin growth and integrity.
Review
Clinical Neurology
Makis Tzioras, Robert I. McGeachan, Claire S. Durrant, Tara L. Spires-Jones
Summary: Alzheimer's disease is a neurodegenerative disorder characterized by cognitive decline and the presence of amyloid-beta and tau protein aggregates in the brain. Synaptic loss plays a crucial role in cognitive decline, and the spread of pathology is mediated by soluble forms of amyloid-beta and tau. Understanding the mechanisms of synaptic degeneration is essential for developing new therapeutic approaches for Alzheimer's disease.
NATURE REVIEWS NEUROLOGY
(2023)
Article
Neurosciences
Anna E. Furtjes, Ryan Arathimos, Jonathan R. I. Coleman, James H. Cole, Simon R. Cox, Ian J. Deary, Javier de la Fuente, James W. Madole, Elliot M. Tucker-Drob, Stuart J. Ritchie
Summary: Understanding the neurodegenerative mechanisms of cognitive decline can help detect health issues in late life. This study explores the genetic links between brain morphometry, aging, and cognitive ability using Genomic Principal Components Analysis. The analysis reveals moderate shared genetic etiology between brain-wide morphometry and cognitive aging, suggesting a potential genetic basis for age-related cognitive decline.
HUMAN BRAIN MAPPING
(2023)
Article
Biochemistry & Molecular Biology
V. Kartik Chundru, Riccardo E. Marioni, James G. D. Prendergast, Tian Lin, Allan J. Beveridge, Nicholas G. Martin, Grant W. Montgomery, David A. Hume, Ian J. Deary, Peter M. Visscher, Naomi R. Wray, Allan F. McRae
Summary: Testing the effect of rare variants on phenotypic variation is challenging due to the need for large cohorts. This study investigates the effect of rare genetic variants on DNA methylation (DNAm) and demonstrates their role in phenotypic variation. The study also shows that extreme levels of DNAm have functional consequences on gene expression.
HUMAN MOLECULAR GENETICS
(2023)
Article
Geriatrics & Gerontology
Ashleigh C. Duthie, Jean Hannah, G. David Batty, Ian J. Deary, John M. Starr, Daniel J. Smith, Tom C. Russ
Summary: This study investigated the association between lithium levels in drinking water and the rate of dementia using data from the Scottish Mental Survey 1932. The results showed that lithium levels in drinking water are very low in Scotland, and extremely low levels of lithium are not associated with an increased risk of dementia. However, there was a slight trend towards increased risk in females at lithium levels below 2.1 mu g/L.
INTERNATIONAL JOURNAL OF GERIATRIC PSYCHIATRY
(2023)
Correction
Genetics & Heredity
Ceres Fernandez-Rozadilla, Maria Timofeeva, Zhishan Chen, Philip Law, Minta Thomas, Stephanie Schmit, Virginia Diez-Obrero, Li Hsu, Juan Fernandez-Tajes, Claire Palles, Kitty Sherwood, Sarah Briggs, Victoria Svinti, Kevin Donnelly, Susan Farrington, James Blackmur, Peter Vaughan-Shaw, Xiao-ou Shu, Jirong Long, Qiuyin Cai, Xingyi Guo, Yingchang Lu, Peter Broderick, James Studd, Jeroen Huyghe, Tabitha Harrison, David Conti, Christopher Dampier, Mathew Devall, Fredrick Schumacher, Marilena Melas, Gad Rennert, Mireia Obon-Santacana, Vicente Martin-Sanchez, Ferran Moratalla-Navarro, Jae Hwan Oh, Jeongseon Kim, Sun Ha Jee, Keum Ji Jung, Sun-Seog Kweon, Min-Ho Shin, Aesun Shin, Yoon-Ok Ahn, Dong-Hyun Kim, Isao Oze, Wanqing Wen, Keitaro Matsuo, Koichi Matsuda, Chizu Tanikawa, Zefang Ren, Yu-Tang Gao, Wei-Hua Jia, John Hopper, Mark Jenkins, Aung Ko Win, Rish Pai, Jane Figueiredo, Robert Haile, Steven Gallinger, Michael Woods, Polly Newcomb, David Duggan, Jeremy Cheadle, Richard Kaplan, Timothy Maughan, Rachel Kerr, David Kerr, Iva Kirac, Jan Bohm, Lukka-Pekka Mecklin, Pekka Jousilahti, Paul Knekt, Lauri Aaltonen, Harri Rissanen, Eero Pukkala, Johan Eriksson, Tatiana Cajuso, Ulrika Hanninen, Johanna Kondelin, Kimmo Palin, Tomas Tanskanen, Laura Renkonen-Sinisalo, Brent Zanke, Satu Mannisto, Demetrius Albanes, Stephanie Weinstein, Edward Ruiz-Narvaez, Julie Palmer, Daniel Buchanan, Elizabeth Platz, Kala Visvanathan, Cornelia Ulrich, Erin Siegel, Stefanie Brezina, Andrea Gsur, Peter Campbell, Jenny Chang-Claude, Michael Hoffmeister, Hermann Brenner, Martha Slattery, John Potter, Konstantinos Tsilidis, Matthias Schulze, Marc Gunter, Neil Murphy, Antoni Castells, Sergi Castellvi-Bel, Leticia Moreira, Volker Arndt, Anna Shcherbina, Mariana Stern, Bens Pardamean, Timothy Bishop, Graham Giles, Melissa Southey, Gregory Idos, Kevin McDonnell, Zomoroda Abu-Ful, Joel Greenson, Katerina Shulman, Flavio Lejbkowicz, Kenneth Offit, Yu-Ru Su, Robert Steinfelder, Temitope Keku, Bethany van Guelpen, Thomas Hudson, Heather Hampel, Rachel Pearlman, Sonja Berndt, Richard Hayes, Marie Elena Martinez, Sushma Thomas, Douglas Corley, Paul Pharoah, Susanna Larsson, Yun Yen, Heinz-Josef Lenz, Emily White, Li Li, Kimberly Doheny, Elizabeth Pugh, Tameka Shelford, Andrew Chan, Marcia Cruz-Correa, Annika Lindblom, David Hunter, Amit Joshi, Clemens Schafmayer, Peter Scacheri, Anshul Kundaje, Deborah Nickerson, Robert Schoen, Jochen Hampe, Zsofia Stadler, Pavel Vodicka, Ludmila Vodickova, Veronika Vymetalkova, Nickolas Papadopoulos, Chistopher Edlund, William Gauderman, Duncan Thomas, David Shibata, Amanda Toland, Sanford Markowitz, Andre Kim, Stephen Chanock, Franzel van Duijnhoven, Edith Feskens, Lori Sakoda, Manuela Gago-Dominguez, Alicja Wolk, Alessio Naccarati, Barbara Pardini, Liesel FitzGerald, Soo Chin Lee, Shuji Ogino, Stephanie Bien, Charles Kooperberg, Christopher Li, Yi Lin, Ross Prentice, Conghui Qu, Stephane Bezieau, Catherine Tangen, Elaine Mardis, Taiki Yamaji, Norie Sawada, Motoki Iwasaki, Christopher Haiman, Loic Le Marchand, Anna Wu, Chenxu Qu, Caroline McNeil, Gerhard Coetzee, Caroline Hayward, Ian Deary, Sarah Harris, Evropi Theodoratou, Stuart Reid, Marion Walker, Li Yin Ooi, Victor Moreno, Graham Casey, Stephen Gruber, Ian Tomlinson, Wei Zheng, Malcolm Dunlop, Richard Houlston, Ulrike Peters
Article
Genetics & Heredity
Xiaotong Wang, Alicia Walker, Joana A. Revez, Guiyan Ni, Mark J. Adams, Andrew M. McIntosh, Peter M. Psychiatric Genomics Consortium, Peter M. Visscher, Naomi R. Wray
Summary: In polygenic score (PGS) analysis, the coefficient of determination (R-2) is used to evaluate efficacy. However, in real data analyses, R-2 has been found to exceed the theoretical upper limit of the out-of-sample prediction calculated by SNP-based heritability (h(SNP)(2)). This is likely due to heterogeneities in cohort-specific h(SNP)(2) and genetic correlations between cohorts. We provide simulated and real data evidence to support these observations and emphasize the need for a better approach to address between-cohort heterogeneity.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Medicine, General & Internal
Robert A. Hillary, Daniel D. McCartney, Hannah Smith, Elena Bernabeu, Danni Gadd, Aleksandra Chybowska, Yipeng M. Cheng, Lee Murphy, Nicola L. Wrobel, Archie M. Campbell, Rosie E. Walker, Caroline Hayward, Kathryn Evans, Andrew McIntosh, Riccardo Marioni
Summary: This study investigated the association between blood DNA methylation and the prevalence of 14 disease states and the incidence of 19 disease states in a population of over 18,000 Scottish individuals. The findings identified over 100 associations between blood methylation sites and common disease states, suggesting that blood DNA methylation could serve as a potential marker for various common diseases.
Article
Cell Biology
Yipeng Cheng, Danni A. Gadd, Christian Gieger, Karla Monterrubio-Gomez, Yufei Zhang, Imrich Berta, Michael J. Stam, Natalia Szlachetka, Evgenii Lobzaev, Nicola Wrobel, Lee Murphy, Archie Campbell, Cliff Nangle, Rosie M. Walker, Chloe Fawns-Ritchie, Annette Peters, Wolfgang Rathmann, David J. Porteous, Kathryn L. Evans, Andrew M. McIntosh, Timothy I. Cannings, Melanie Waldenberger, Andrea Ganna, Daniel L. McCartney, Catalina A. Vallejos, Riccardo E. Marioni
Summary: This study developed 10-year risk prediction models for incident type 2 diabetes (T2D) using blood-based DNA methylation data, showing improved performance beyond standard risk factors typically used for T2D prediction.
Correction
Biology
Danni A. Gadd, Robert F. Hillary, Daniel L. McCartney, Shaza B. Zaghlool, Anna J. Stevenson, Yipeng Cheng, Chloe Fawns-Ritchie, Cliff Nangle, Archie Campbell, Robin Flaig, Sarah E. Harris, Rosie M. Walker, Liu Shi, Elliot M. Tucker-Drob, Christian Gieger, Annette Peters, Melanie Waldenberger, Johannes Graumann, Allan F. McRae, Ian J. Deary, David J. Porteous, Caroline Hayward, Peter M. Visscher, Simon R. Cox, Kathryn L. Evans, Andrew M. McIntosh, Karsten Suhre, Riccardo E. Marioni
Article
Cell Biology
Yeda Wu, Slavina B. Goleva, Lindsay B. Breidenbach, Minsoo Kim, Stuart Macgregor, Michael J. Gandal, Lea K. Davis, Naomi R. Wray
Summary: The study conducted a genome-wide association analysis to explore the genetic factors related to diverticular disease (DivD) of the intestine. The results indicated significant associations between DivD development and specific cell types and genes. The study also proposed a polygenic score that can effectively predict the risk of DivD and identified potential mechanisms involved in DivD development through statistical and bioinformatic analyses.
Article
Cell Biology
Eduardo A. Maury, Maxwell A. Sherman, Giulio Genovese, Thomas G. Gilgenast, Tushar Kamath, S. J. Burris, Prashanth Rajarajan, Erin Flaherty, Schahram Akbarian, Andrew Chess, Steven A. McCarroll, Po-Ru Loh, Jennifer E. Phillips-Cremins, Kristen J. Brennand, Evan Z. Macosko, James T. R. Walters, Michael O'Donovan, Patrick Sullivan, Jonathan Sebat, Eunjung A. Lee, Christopher A. Walsh
Summary: This study suggests that somatic copy-number variants (sCNVs) may play a potential role in the risk of schizophrenia (SCZ). Early-developmental sCNVs were more common in SCZ cases, including recurrent somatic deletions in the NRXN1 gene. Additionally, recurrent intragenic deletions of the ABCB11 gene were observed in treatment-resistant SCZ cases.