Article
Oncology
Xiaoli Luo, Yi Hu, Junwei Shen, Xinwen Liu, Tao Wang, Li Li, Jue Li
Summary: This study used RNA-seq and MeDIP-seq technologies to observe gene expression and DNA methylation changes in an AMI mouse model. We found a large number of differential methylation positions and differentially expressed genes at different stages of AMI. Especially, the 6-hour stage of AMI showed significant changes in DEGs and enriched functional pathways in KEGG, suggesting it may be the most critical stage of AMI. We also identified genes that showed a negative correlation between mRNA expression and DNA methylation, and confirmed their function through experimental validation.
CLINICAL EPIGENETICS
(2022)
Article
Cardiac & Cardiovascular Systems
Yuru Han, Baoyu Duan, Jing Wu, Yanjun Zheng, Yinchen Gu, Xiaomeng Cai, Changlian Lu, Xubo Wu, Yanfei Li, Xuefeng Gu
Summary: This study utilized RNA-seq and MeDIP-seq to analyze the genetic and epigenetic features of myocardial infarction (MI) at the early stages, revealing changes in gene expression and methylation regions associated with immune response, apoptosis, and energy metabolism. The study identified potential drug targets in genes related to apoptosis and inflammation, as well as highlighted the importance of methylation changes in genes affecting processes such as cardiac muscle contraction and angiogenesis during MI progression.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2022)
Article
Genetics & Heredity
Yuezhen Tian, Xuemei Yang, Jianwen Du, Weidan Zeng, Weiwei Wu, Jiang Di, Xixia Huang, Kechuan Tian
Summary: The study utilized MeDIP-seq to obtain a genome-wide methylation map of hair follicle development in Super Merino sheep, identifying 65 genes with both differential methylation and expression. Differential methylation genes were found enriched in signaling pathways related to hair follicle development, and further exploration of WNT2 gene function revealed its promotion of skin and hair follicle growth and development. The results provide a theoretical basis for further research on sheep hair follicle development and gene regulation mechanisms.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Nhan Nguyen, Matthias Lienhard, Ralf Herwig, Jos Kleinjans, Danyel Jennen
Summary: In this study, the DNA methylation profile and gene expression changes in response to Epirubicin treatment were analyzed in human cardiac microtissues. The results revealed multiple differentially methylated genes that may be involved in cardiac dysfunction mechanisms. These findings provide valuable insights into the toxic effects of Epirubicin on the heart.
FRONTIERS IN BIOSCIENCE-LANDMARK
(2022)
Article
Cell Biology
Kamalnath S. Rajagopalan, Sara Kazeminia, Logan M. Glasstetter, Rahele A. Farahani, Xiang-Yang Zhu, Hui Tang, Kyra L. Jordan, Alejandro R. Chade, Amir Lerman, Lilach O. Lerman, Alfonso Eirin
Summary: Autologous mesenchymal stem/stromal cells (MSCs) have therapeutic effects in various diseases. Metabolic syndrome (MetS) can induce epigenetic alterations in mitochondria-related genes in porcine MSCs, but this can be modulated by vitamin C. These findings contribute to the development of strategies to mitigate the detrimental effects of MetS on MSCs.
Article
Environmental Sciences
Yujian Sang, Jianhui Liu, Xiangyang Li, Guiqing Zhou, Yue Zhang, Leqiang Gao, Yanzhi Zhao, Xianqing Zhou
Summary: This study revealed that SiNPs caused extensive methylation changes in the genome of GC-2 cells, identifying 428 hyper-methylated genes and 398 hypo-methylated genes. Gene Ontology and pathway analysis showed that differential DNA methylation induced by SiNPs was probably involved with abnormal transcription and translation, mitochondrial damage, and cell apoptosis.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2021)
Review
Medicine, General & Internal
Akanksha Sood, Gadha Mohiyiddeen, Gaity Ahmad, Cheryl Fitzgerald, Andrew Watson, Lamiya Mohiyiddeen
Summary: The use of growth hormone (GH) as an adjuvant treatment in IVF has uncertain effects on live birth rates and number of oocytes retrieved in normal responders. However, it may slightly increase the number of oocytes retrieved and pregnancy rates in poor responders. The results need to be interpreted cautiously due to small sample sizes, bias, and variability in GH doses and regimens used in the trials. Additional research is needed to further define the role of GH in IVF as adjuvant therapy.
COCHRANE DATABASE OF SYSTEMATIC REVIEWS
(2021)
Article
Genetics & Heredity
Joan Sabria-Back, Ana Monteagudo-Sanchez, Marta Sanchez-Delgado, Anne C. Ferguson-Smith, Olga Gomez, Africa Pertierra Cartada, Jair Tenorio, Julian Nevado, Pablo Lapunzina, Arrate Pereda Aguirre, Carles Gimenez Sevilla, Estefania Toro Toro, Guiomar Perez de Nanclares, David Monk
Summary: Kagami-Ogata syndrome (KOS14) and Temple syndrome (TS14) are associated with reciprocal alterations within the chr14q32 imprinted domain. A work-up strategy for preimplantation genetic testing (PGT) was presented to avoid the transmission of a causative micro-deletion. PGT was successfully offered to identify an unaffected embryo and transfer it, resulting in the birth of a healthy baby.
JOURNAL OF MEDICAL GENETICS
(2022)
Article
Multidisciplinary Sciences
Purva Singh, Samantha G. Lessard, Piali Mukherjee, Brennan Rourke, Miguel Otero
Summary: The phenotypic changes in articular chondrocytes during osteoarthritis are associated with alterations in DNA methylation patterns, which may contribute to cartilage destruction. By combining in vitro culture systems with RNA sequencing and enhanced bisulfite sequencing, researchers identified transcriptomic and epigenomic changes in hypertrophic differentiation of chondrocytes. The integrative analyses revealed associations between methylation changes and gene expression during hypertrophic differentiation, suggesting new therapeutic targets may be uncovered.
ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Ping Zhang, Yongke Lu, Yanli Li, Kesheng Wang, Huimei An, Yunlong Tan
Summary: This study identified a number of methylated genes and pathways associated with tardive dyskinesia (TD) in schizophrenia patients. These findings may provide potential biomarkers for TD and serve as a resource for replication in other populations.
Article
Andrology
Simona Ioana Enoiu, Marie Berg Nygaard, Mona Bungum, Soren Ziebe, Morten Ronn Petersen, Kristian Almstrup
Summary: This study investigated the membrane integrity and fusion proteins in spermatozoa from men in couples experiencing total fertilisation failure (TFF) during in vitro fertilisation (IVF). The results indicate that the expression of fusion proteins and the integrity of spermatozoa play a crucial role in achieving fertilisation during IVF.
Article
Genetics & Heredity
Mathias Schwartz, Sabrina Ibadioune, Albain Chansavang, Sophie Vacher, Sandrine M. Caputo, Helene Delhomelle, Jennifer Wong, Khadija Abidallah, Virginie Moncoutier, Veronique Becette, Tatiana Popova, Voreak Suybeng, Antoine De Pauw, Marc-Henri Stern, Chrystelle Colas, Emmanuelle Mouret-Fourme, Dominique Stoppa-Lyonnet, Lisa Golmard, Ivan Bieche, Julien Masliah-Planchon
Summary: Mosaic BRCA1 promoter methylation is associated with an increased risk of early-onset breast cancer, triple-negative breast cancer, and ovarian cancer. This de novo event could contribute to hereditary breast/ovarian cancer pedigrees, especially in families with affected relatives showing high prevalence of BRCA1meth. Detection of BRCA1meth may indicate involvement of BRCA1 in tumorigenesis in affected probands.
JOURNAL OF MEDICAL GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Christopher Riccardi, Iacopo Passeri, Lisa Cangioli, Camilla Fagorzi, Marco Fondi, Alessio Mengoni
Summary: DNA methylation is a commonly observed epigenetic modification found in both eukaryotes and prokaryotes, and it is implicated in various biological phenomena such as gene regulation and adaptation to the environment. Advances in third-generation sequencing technologies have enabled the direct detection of genome-wide methylation profiles, providing opportunities to understand and utilize the epigenomic landscape at the individual and population levels. Here, we introduce a pipeline called MeStudio, which analyzes and combines genome-wide methylation profiles with genomic features, allowing for the identification of DNA methylation in coding and noncoding sequences. We demonstrate the utility and performance of MeStudio using single-molecule real-time sequencing outputs from Sinorhizobium meliloti strains.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Hernan Guillermo Hernandez, Gloria Cristina Aranzazu-Moya, Efrain Hernando Pinzon-Reyes
Summary: The objective of this study was to identify DNA methylation patterns of heavy smokers in oral rinse samples. Genome-wide DNA methylation data from Gene Expression Omnibus GSE70977 was analyzed, including 71 epigenomes of cancer-free subjects and 139 oral-cancer patients' epigenomes. Differential DNA methylation was determined using bioinformatics packages, and candidate biomarker genes were identified. The results suggest that AHRR, ADAMTS2, and FAM184B genes may serve as biomarkers in oral rinse samples of heavy smokers.
Article
Genetics & Heredity
Jing Fu, Ju Zhang, Li Yang, Nan Ding, Liya Yue, Xiangli Zhang, Dandan Lu, Xinmiao Jia, Cuidan Li, Chongye Guo, Zhe Yin, Xiaoyuan Jiang, Yongliang Zhao, Fei Chen, Dongsheng Zhou
Summary: The study systematically investigated the methylation features of Klebsiella pneumoniae and identified 15 methylation motifs. The distribution patterns of these motifs in the genome were analyzed and the methylation dynamics were characterized at single-base resolution. The findings provide useful insights into the epigenetic regulation of K. pneumoniae and other bacterial species.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Public, Environmental & Occupational Health
Meredith O'Connor, Margarita Moreno-Betancur, Sharon Goldfeld, Melissa Wake, George Patton, Terence Dwyer, Mimi L. K. Tang, Richard Saffery, Jeffrey M. Craig, Jane Loke, David Burgner, Craig A. Olsson, LifeCourse Cohort Investigators
INTERNATIONAL JOURNAL OF EPIDEMIOLOGY
(2022)
Article
Immunology
Cindy Pham, Siroon Bekkering, Martin O'Hely, David Burgner, Sarah Thomson, Peter Vuillermin, Fiona Collier, Wolfgang Marx, Toby Mansell, Christos Symeonides, Peter D. Sly, Mimi L. K. Tang, Richard Saffery, Anne-Louise Ponsonby, B. I. S. Investigator Group BIS Invest Grp
Summary: This study found a link between inflammation at birth and emotional and behavioral problems in children at the age of two, and showed that the inflammation partially mediated the association between socioeconomic disadvantage and these problems.
BRAIN BEHAVIOR AND IMMUNITY
(2022)
Article
Clinical Neurology
Michaela-Kristina Keck, Martin Sill, Andrea Wittmann, Piyush Joshi, Damian Stichel, Pengbo Beck, Konstantin Okonechnikow, Philipp Sievers, Annika K. Wefers, Federico Roncaroli, Shivaram Avula, Martin G. McCabe, James T. Hayden, Pieter Wesseling, Ingrid Ora, Monica Nister, Mariette E. G. Kranendonk, Bastiaan B. J. Tops, Michal Zapotocky, Josef Zamecnik, Alexandre Vasiljevic, Tanguy Fenouil, David Meyronet, Katja von Hoff, Ulrich Schuller, Hugues Loiseau, Dominique Figarella-Branger, Christof M. Kramm, Dominik Sturm, David Scheie, Tuomas Rauramaa, Jouni Pesola, Johannes Gojo, Christine Haberler, Sebastian Brandner, Tom Jacques, Alexandra Sexton Oates, Richard Saffery, Ewa Koscielniak, Suzanne J. Baker, Stephen Yip, Matija Snuderl, Nasir Ud Din, David Samuel, Kathrin Schramm, Mirjam Blattner-Johnson, Florian Selt, Jonas Ecker, Till Milde, Andreas von Deimling, Andrey Korshunov, Arie Perry, Stefan M. Pfister, Felix Sahm, David A. Solomon, David T. W. Jones
Summary: Pediatric central nervous system (CNS) tumors are the leading cause of cancer-related death in children aged 0-14 years. A newly identified CNS tumor type characterized by PLAGL1/2 amplification and a lack of recurrent genetic alterations has been described. These tumors are composed of primitive embryonal-like cells and are associated with intermediate survival, but the cell of origin and optimal treatment strategies are yet to be determined.
ACTA NEUROPATHOLOGICA
(2023)
Article
Medicine, General & Internal
Ahmed Elhakeem, Justiina Ronkainen, Toby Mansell, Katherine Lange, Tuija M. M. Mikkola, Binisha H. H. Mishra, Rama J. J. Wahab, Tim Cadman, Tiffany Yang, David Burgner, Johan G. G. Eriksson, Marjo-Riitta Jaervelin, Romy Gaillard, Vincent W. V. Jaddoe, Terho Lehtimaeki, Olli T. T. Raitakari, Richard Saffery, Melissa Wake, John Wright, Sylvain Sebert, Deborah A. A. Lawlor
Summary: This study examined the associations between common pregnancy and perinatal complications and offspring metabolic traits using data from eight population-based cohort studies. The findings indicate that these complications are mainly associated with metabolic traits in newborns, with little evidence of long-term impact on older offspring.
Article
Environmental Sciences
Sarah Thomson, Katherine Drummond, Martin O'Hely, Christos Symeonides, Chitra Chandran, Toby Mansell, Richard Saffery, Peter Sly, Jochen Mueller, Peter Vuillermin, Anne-Louise Ponsonby
Summary: This study investigated whether maternal and child central carbon metabolism is involved in the development of autism spectrum disorder (ASD). They found that higher prenatal levels of di-(2-ethylhexyl) phthalate (DEHP) were associated with upregulation of maternal non-oxidative energy metabolism pathways and increased ASD symptoms in children at 2 and 4 years of age.
ENVIRONMENT INTERNATIONAL
(2023)
Article
Cardiac & Cardiovascular Systems
Ahmed Elhakeem, Amy E. Taylor, Hazel M. Inskip, Jonathan Y. Huang, Toby Mansell, Carina Rodrigues, Federica Asta, Sophia M. Blaauwendraad, Siri E. Haberg, Jane Halliday, Margreet W. Harskamp-van Ginkel, Jian-Rong He, Vincent W. V. Jaddoe, Sharon Lewis, Gillian M. Maher, Yannis Manios, Fergus P. McCarthy, Irwin K. M. Reiss, Franca Rusconi, Theodosia Salika, Muriel Tafflet, Xiu Qiu, Bjorn O. Asvold, David Burgner, Jerry K. Y. Chan, Luigi Gagliardi, Romy Gaillard, Barbara Heude, Maria C. Magnus, George Moschonis, Deirdre Murray, Scott M. Nelson, Daniela Porta, Richard Saffery, Henrique Barros, Johan G. Eriksson, Tanja G. M. Vrijkotte, Deborah A. Lawlor
Summary: This study aimed to examine the associations of assisted reproductive technology (ART) conception with offspring cardiometabolic health outcomes and whether these associations differ with age. The researchers found small and statistically non-significant differences in offspring cardiometabolic outcomes between ART-conceived and naturally conceived offspring. The study concluded that these findings should reassure individuals receiving ART, but longer-term follow-up is needed to investigate changes in the risks of hypertension, dyslipidaemia, and cardiovascular disease over adulthood.
EUROPEAN HEART JOURNAL
(2023)
Article
Otorhinolaryngology
Jing Wang, Katherine Lange, Valerie Sung, Angela Morgan, Richard Saffery, Melissa Wake
Summary: Although more than 200 genes have been associated with monogenic congenital hearing loss, the polygenic contribution to hearing decline across the life course remains largely unknown. This study found an association between polygenic risk scores for self-reported hearing difficulty among adults and measured hearing and speech reception abilities in mid-childhood and early midlife.
JAMA OTOLARYNGOLOGY-HEAD & NECK SURGERY
(2023)
Correction
Clinical Neurology
Michaela-Kristina Keck, Martin Sill, Andrea Wittmann, Piyush Joshi, Damian Stichel, Pengbo Beck, Konstantin Okonechnikow, Philipp Sievers, Annika K. Wefers, Federico Roncaroli, Shivaram Avula, Martin G. McCabe, James T. Hayden, Pieter Wesseling, Ingrid Ora, Monica Nister, Mariette E. G. Kranendonk, Bastiaan B. J. Tops, Michal Zapotocky, Josef Zamecnik, Alexandre Vasiljevic, Tanguy Fenouil, David Meyronet, Katja von Hoff, Ulrich Schueller, Hugues Loiseau, Dominique Figarella-Branger, Christof M. Kramm, Dominik Sturm, David Scheie, Tuomas Rauramaa, Jouni Pesola, Johannes Gojo, Christine Haberler, Sebastian Brandner, Tom Jacques, Alexandra Sexton Oates, Richard Saffery, Ewa Koscielniak, Suzanne J. Baker, Stephen Yip, Matija Snuderl, Nasir Ud Din, David Samuel, Kathrin Schramm, Mirjam Blattner-Johnson, Florian Selt, Jonas Ecker, Till Milde, Andreas von Deimling, Andrey Korshunov, Arie Perry, Stefan M. Pfister, Felix Sahm, David A. Solomon, David T. W. Jones
ACTA NEUROPATHOLOGICA
(2023)
Article
Biotechnology & Applied Microbiology
Xi Yuan, Jiayu Huang, Li Wen, Boris Novakovic, Mark D. Kilby, Chao Tong, Hongbo Qi, Richard Saffery, Philip N. Baker
Summary: Despite being genetically identical, monozygotic (MZ) twins can have discordant congenital heart disease (CHD) due to in utero environmental factors. This study identified epigenetic variations in cord blood of discordant MZ twins that are associated with CHD. The results revealed specific DNA methylation variations that are biomarkers and potential targets for intervention in CHD.
Article
Cell Biology
Samira Imran, Melanie R. Neeland, David J. J. Martino, Stephen Peng, Jennifer Koplin, Shyamali C. Dharmage, Mimi L. K. Tang, Susan Sawyer, Thanh Dang, Vicki McWilliam, Rachel L. Peters, Susan Prescott, Kirsten P. Perrett, Boris Novakovic, Richard Saffery
Summary: Childhood is a critical period of immune development, and the epigenetic signatures associated with CD4 T cell activation during different developmental stages are yet to be described. A study investigated the DNA methylation changes associated with nCD4 T activation in infants and adolescents, and found similar extensive epigenetic reprogramming in both age groups. However, age-specific effects were identified in terms of methylation and cytokine responses, which may contribute to variation in disease risk and immune function.
IMMUNOLOGY AND CELL BIOLOGY
(2023)
Article
Nutrition & Dietetics
Yong Li, Yifan Xu, Caroline Le Roy, Jiaying Hu, Claire J. Steves, Jordana T. T. Bell, Tim D. D. Spector, Rachel Gibson, Cristina Menni, Ana Rodriguez-Mateos
Summary: This study found significant associations between phenolic acid metabolites, gut microbiome, and cardiovascular disease risk. Certain beverages and foods, especially coffee, tea, red wine, and berries, are rich in phenolic acids and negatively correlated with cardiovascular disease risk. The gut microbiome, particularly the genus 5-7N15, partially mediates the negative association between urinary (poly)phenols and cardiovascular risk.
Article
Pediatrics
Li Wen, Huijia Fu, Richard Saffery, Chao Tong, Yamin Liu, Mark D. Kilby, Hongbo Qi, Philip N. Baker
Summary: This study measured the concentrations of adiponectin and leptin in the cord blood of monochorionic twins with selective intrauterine growth restriction (IUGR). The findings showed that cord blood adiponectin concentrations were negatively associated with IUGR, while cord blood leptin concentrations were significantly lower in IUGR twins. Furthermore, adiponectin was negatively associated with height increments in the first 6 months, and leptin was inversely associated with weight and height increments in the first 6 months, as well as weight and height at 6 and 24 months. These results indicate the influence of adiponectin and leptin in cord blood on IUGR and childhood growth trajectories.
Article
Neurosciences
Elisa Weiss, Anna Schruefer, Carolina Tocantins, Mariana Simoes Diniz, Boris Novakovic, Anke S. van Bergen, Azra Kulovic-Sissawo, Richard Saffery, Reinier. A. A. Boon, Ursula Hiden
Summary: High gestational weight gain (GWG) is associated with impaired wound healing of neonatal endothelial colony forming cells (ECFCs). A specific long non-coding RNA (lncRNA), KLRK1-AS1, was found to be downregulated in neonatal ECFCs from pregnancies with higher GWG, and its knockdown resulted in further impairment of barrier recovery. These findings suggest a potential role for lncRNAs, particularly KLRK1-AS1, in regulating neonatal ECFC function and may provide insights into the link between GWG and cardiovascular risk factors.
JOURNAL OF PHYSIOLOGY-LONDON
(2023)
Article
Biochemistry & Molecular Biology
Cindy Pham, Sarah Thomson, Sung-Tong Chin, Peter Vuillermin, Martin O'Hely, David Burgner, Samuel Tanner, Richard Saffery, Toby Mansell, Sze Bong, Elaine Holmes, Peter D. Sly, Nicola Gray, Anne-Louise Ponsonby, Barwon Infant Study Invest Grp
Summary: Childhood mental disorders are becoming increasingly common, and higher maternal oxidative stress during pregnancy is linked to these disorders. Social and prenatal environmental factors contribute to maternal oxidative stress and childhood mental disorders. Future studies are needed to further understand the role of early-life oxidant damage in childhood mental disorders.
MOLECULAR PSYCHIATRY
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
E. Weiss, R. Boon, A. van Bergen, B. Novakovic, S. Cvitic, R. Saffery, U. Hiden