Articles

DNA methylation patterns of β-globin cluster in β-thalassemia patients

Reactivation of fetal hemoglobin (HbF, α₂γ₂) holds a therapeutic target for β-thalassemia and sickle cell disease. Although many HbF regulators have been identified, the methylation patterns in β-globin cluster d...

Authors: Xiuqin Bao, Yangjin Zuo, Diyu Chen and Cunyou Zhao

Epigenetic regulation of inflammation in periodontitis: cellular mechanisms and therapeutic potential

Epigenetic mechanisms, namely DNA and histone modifications, are critical regulators of immunity and inflammation which have emerged as potential targets for immunomodulating therapies. The prevalence and sign...

Authors: Krzysztof T. Jurdziński, Jan Potempa and Aleksander M. Grabiec

Developmental programming in human umbilical cord vein endothelial cells following fetal growth restriction

Fetal growth restriction (FGR) is associated with an increased susceptibility for various noncommunicable diseases in adulthood, including cardiovascular and renal disease. During FGR, reduced uteroplacental b...

Authors: Fieke Terstappen, Jorg J. A. Calis, Nina D. Paauw, Jaap A. Joles, Bas B. van Rijn, Michal Mokry, Torsten Plösch and A. Titia Lely

Whole blood DNA methylation aging markers predict colorectal cancer survival: a prospective cohort study

Blood DNA methylation-based aging algorithms predict mortality in the general population. We investigated the prognostic value of five established DNA methylation aging algorithms for patients with colorectal ...

Authors: Xīn Gào, Yan Zhang, Daniel Boakye, Xiangwei Li, Jenny Chang-Claude, Michael Hoffmeister and Hermann Brenner

Epigenetic modification mechanisms involved in keloid: current status and prospect

Keloid, a common dermal fibroproliferative disorder, is benign skin tumors characterized by the aggressive fibroblasts proliferation and excessive accumulation of extracellular matrix. However, common therapeu...

Authors: Wenchang Lv, Yuping Ren, Kai Hou, Weijie Hu, Yi Yi, Mingchen Xiong, Min Wu, Yiping Wu and Qi Zhang

Mitochondrial metabolism and DNA methylation: a review of the interaction between two genomes

Mitochondria are controlled by the coordination of two genomes: the mitochondrial and the nuclear DNA. As such, variations in nuclear gene expression as a consequence of mutations and epigenetic modifications ...

Authors: Amanda F. C. Lopes

Dynamic changes in chromatin accessibility, altered adipogenic gene expression, and total versus de novo fatty acid synthesis in subcutaneous adipose stem cells of normal-weight polycystic ovary syndrome (PCOS) women during adipogenesis: evidence of cellular programming

Normal-weight polycystic ovary syndrome (PCOS) women exhibit adipose resistance in vivo accompanied by enhanced subcutaneous (SC) abdominal adipose stem cell (ASC) development to adipocytes with accelerated li...

Authors: Karen L. Leung, Smriti Sanchita, Catherine T. Pham, Brett A. Davis, Mariam Okhovat, Xiangming Ding, Phillip Dumesic, Tristan R. Grogan, Kevin J. Williams, Marco Morselli, Feiyang Ma, Lucia Carbone, Xinmin Li, Matteo Pellegrini, Daniel A. Dumesic and Gregorio D. Chazenbalk

DNA methylation signatures to predict the cervicovaginal microbiome status

The composition of the microbiome plays an important role in human health and disease. Whether there is a direct association between the cervicovaginal microbiome and the host’s epigenome is largely unexplored.

Authors: Nuno R. Nené, James Barrett, Allison Jones, Iona Evans, Daniel Reisel, John F. Timms, Tobias Paprotka, Andreas Leimbach, Dorella Franchi, Nicoletta Colombo, Line Bjørge, Michal Zikan, David Cibula and Martin Widschwendter

High-fat diet-induced and genetically inherited obesity differentially alters DNA methylation profile in the germline of adult male rats

Paternal obesity has been associated with reduced live birth rates. It could lead to inheritance of metabolic disturbances to the offspring through epigenetic mechanisms. However, obesity is a multifactorial d...

Authors: Sharvari S. Deshpande, Harishankar Nemani, Gandhimathi Arumugam, Avinash Ravichandran and Nafisa H. Balasinor

Correction to: Combining the differentiating effect of panobinostat with the apoptotic effect of arsenic trioxide leads to significant survival benefit in a model of t(8;21) acute myeloid leukemia

An amendment to this paper has been published and can be accessed via the original article.

Authors: Jessica M. Salmon, Michael Bots, Eva Vidacs, Kym L. Stanley, Peter Atadja, Johannes Zuber and Ricky W. Johnstone

Altered immune phenotype and DNA methylation in panic disorder

Multiple studies have related psychiatric disorders and immune alterations. Panic disorder (PD) has been linked with changes in leukocytes distributions in several small studies using different methods for imm...

Authors: Curtis L. Petersen, Ji-Qing Chen, Lucas A. Salas and Brock C. Christensen

Epigenetic profiling of Italian patients identified methylation sites associated with hereditary transthyretin amyloidosis

Hereditary transthyretin (TTR) amyloidosis (hATTR) is a rare life-threatening disorder caused by amyloidogenic coding mutations located in TTR gene. To understand the high phenotypic variability observed among ca...

Authors: Antonella De Lillo, Gita A. Pathak, Flavio De Angelis, Marco Di Girolamo, Marco Luigetti, Mario Sabatelli, Federico Perfetto, Sabrina Frusconi, Dario Manfellotto, Maria Fuciarelli and Renato Polimanti

5-Hydroxymethylation highlights the heterogeneity in keratinization and cell junctions in head and neck cancers

Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent cancer worldwide, with human papillomavirus (HPV)-related HNSCC rising to concerning levels. Extensive clinical, genetic and epigenetic...

Authors: Siyu Liu, Marcell Costa de Medeiros, Evan M. Fernandez, Katie R. Zarins, Raymond G. Cavalcante, Tingting Qin, Gregory T. Wolf, Maria E. Figueroa, Nisha J. D’Silva, Laura S. Rozek and Maureen A. Sartor

Assessment of MGMT methylation status using high-performance liquid chromatography in newly diagnosed glioblastoma

The utility of O⁶-methylguanine-DNA methyltransferase (MGMT) gene promoter methylation status as a prognostic marker in patients with glioblastoma (GBM) has been established. However, the number of CpG sites that...

Authors: Mitsuto Hanihara, Kunio Miyake, Atsushi Watanabe, Yuriko Yamada, Naoki Oishi, Tomoyuki Kawataki, Takeshi Inukai, Tetsuo Kondo and Hiroyuki Kinouchi

The tumor suppressor Zinc finger protein 471 suppresses breast cancer growth and metastasis through inhibiting AKT and Wnt/β-catenin signaling

Zinc-finger protein 471 (ZNF471) is a member of the Krüppel-associated box domain zinc finger protein (KRAB-ZFP) family. ZNF471 is methylated in squamous cell carcinomas of tongue, stomach and esophageal. However...

Authors: Chunfang Tao, Juan Luo, Jun Tang, Danfeng Zhou, Shujun Feng, Zhu Qiu, Thomas C. Putti, Tingxiu Xiang, Qiao Tao, Lili Li and Guosheng Ren

Epimutations in human sperm from patients with impaired spermatogenesis

Authors: Joana Marques, Filipa Carvalho, Alberto Barros and Mário Sousa

Triage of hrHPV-positive women: comparison of two commercial methylation-specific PCR assays

High-risk human papillomavirus (hrHPV)-based screening is becoming increasingly important, either by supplementing or replacing the traditional cytology-based cervical Pap smear. However, hrHPV screening lacks...

Authors: Carolin Dippmann, Martina Schmitz, Kristina Wunsch, Stefanie Schütze, Katrin Beer, Christiane Greinke, Hans Ikenberg, Heike Hoyer, Ingo B. Runnebaum, Alfred Hansel and Matthias Dürst

BET protein inhibitor apabetalone (RVX-208) suppresses pro-inflammatory hyper-activation of monocytes from patients with cardiovascular disease and type 2 diabetes

Patients with cardiovascular disease (CVD) and type 2 diabetes (DM2) have a high residual risk for experiencing a major adverse cardiac event. Dysregulation of epigenetic mechanisms of gene transcription in in...

Authors: Sylwia Wasiak, Kim E. Dzobo, Brooke D. Rakai, Yannick Kaiser, Miranda Versloot, Mahnoush Bahjat, Stephanie C. Stotz, Li Fu, Michael Sweeney, Jan O. Johansson, Norman C. W. Wong, Erik S. G. Stroes, Jeffrey Kroon and Ewelina Kulikowski

Morphine leads to global genome changes in H3K27me3 levels via a Polycomb Repressive Complex 2 (PRC2) self-regulatory mechanism in mESCs

Environmentally induced epigenetic changes can lead to health problems or disease, but the mechanisms involved remain unclear. Morphine can pass through the placental barrier leading to abnormal embryo develop...

Authors: Iraia Muñoa-Hoyos, John A. Halsall, Manu Araolaza, Carl Ward, Idoia Garcia, Itziar Urizar-Arenaza, Marta Gianzo, Paloma Garcia, Bryan Turner and Nerea Subirán

Epigenetic alterations and advancement of treatment in peripheral T-cell lymphoma

Peripheral T-cell lymphoma (PTCL) is a rare and heterogeneous group of clinically aggressive diseases associated with poor prognosis. Except for ALK + anaplastic large-cell lymphoma (ALCL), most peripheral T-c...

Authors: Ping Zhang and Mingzhi Zhang

LncRNA STXBP5-AS1 suppresses stem cell-like properties of pancreatic cancer by epigenetically inhibiting neighboring androglobin gene expression

Previous studies suggest the tumor suppressor role of long non-coding RNA (lncRNA) STXBP5-AS1 in cervical and gastric cancer, but its expression pattern and functional mechanism are still elusive in pancreatic ca...

Authors: Shi Chen, Long Huang, Ge Li, Funan Qiu, Yaodong Wang, Can Yang, Jingjing Pan, Zhangwei Wu, Jiangzhi Chen and Yifeng Tian

Changes in DNA methylation profiles of myalgic encephalomyelitis/chronic fatigue syndrome patients reflect systemic dysfunctions

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a lifelong debilitating disease with a complex pathology not yet clearly defined. Susceptibility to ME/CFS involves genetic predisposition and exp...

Authors: A. M. Helliwell, E. C. Sweetman, P. A. Stockwell, C. D. Edgar, A. Chatterjee and W. P. Tate

Non-invasive detection of endometrial cancer by DNA methylation analysis in urine

The incidence of endometrial cancer is rising, and current diagnostics often require invasive biopsy procedures. Urine may offer an alternative sample type, which is easily accessible and allows repetitive sel...

Authors: Rianne van den Helder, Birgit M. M. Wever, Nienke E. van Trommel, Annina P. van Splunter, Constantijne H. Mom, Jenneke C. Kasius, Maaike C. G. Bleeker and Renske D. M. Steenbergen

Longitudinal analysis of healthy colon establishes aspirin as a suppressor of cancer-related epigenetic aging

Colon cancer (CC) is the third most common cancer worldwide, highlighting the importance of developing effective prevention strategies. Accumulating evidence supports that aspirin use reduces CC incidence. We ...

Authors: Faiza Noreen, Anna Chaber-Ciopinska, Jaroslaw Regula, Primo Schär and Kaspar Truninger

DNA hydroxymethylation is associated with disease severity and persists at enhancers of oncogenic regions in multiple myeloma

Multiple myeloma (MM) is a heterogeneous plasma cell malignancy that remains challenging to cure. Global hypomethylation correlates with an aggressive phenotype of the disease, while hypermethylation is observ...

Authors: Jean-Baptiste Alberge, Florence Magrangeas, Mirko Wagner, Soline Denié, Catherine Guérin-Charbonnel, Loïc Campion, Michel Attal, Hervé Avet-Loiseau, Thomas Carell, Philippe Moreau, Stéphane Minvielle and Aurélien A. Sérandour

Robust performance of a novel stool DNA test of methylated SDC2 for colorectal cancer detection: a multicenter clinical study

Stool DNA testing is an emerging and attractive option for colorectal cancer (CRC) screening. We previously evaluated the feasibility of a stool DNA (sDNA) test of methylated SDC2 for CRC detection. The aim of th...

Authors: Jianping Wang, Side Liu, Hui Wang, Lei Zheng, Changchun Zhou, Guoxin Li, Rongkang Huang, Huaiming Wang, Chujun Li, Xinjuan Fan, Xinhui Fu, Xinying Wang, Hongliang Guo, Jie Guan, Yanlai Sun, Xilin Song…

Identification of the subtypes of gastric cancer based on DNA methylation and the prediction of prognosis

Gastric cancer (GC) is a digestive system cancer with a high mortality rate globally. Previous experiences and studies have provided clinicians with ample evidence to diagnose and treat patients with reasonabl...

Authors: Tengda Li, Xin Chen, Mingli Gu, Anmei Deng and Cheng Qian

Clinical efficacy and molecular biomarkers in a phase II study of tucidinostat plus R-CHOP in elderly patients with newly diagnosed diffuse large B-cell lymphoma

Elderly patients with diffuse large B-cell lymphoma (DLBCL) present with poor clinical outcome and intolerance to intensive chemotherapy. Histone deacetylase inhibitors (HDACIs) show anti-lymphoma activities a...

Authors: Mu-Chen Zhang, Ying Fang, Li Wang, Shu Cheng, Di Fu, Yang He, Yan Zhao, Chao-Fu Wang, Xu-Feng Jiang, Qi Song, Peng-Peng Xu and Wei-Li Zhao

Genome-wide methylation analysis in Silver–Russell syndrome, Temple syndrome, and Prader–Willi syndrome

Imprinting disorders (IDs) show overlapping phenotypes, particularly in Silver–Russell syndrome (SRS), Temple syndrome (TS14), and Prader–Willi syndrome (PWS). These three IDs include fetal and postnatal growt...

Authors: Kaori Hara-Isono, Keiko Matsubara, Tomoko Fuke, Kazuki Yamazawa, Kazuhito Satou, Nobuyuki Murakami, Shinji Saitoh, Kazuhiko Nakabayashi, Kenichiro Hata, Tsutomu Ogata, Maki Fukami and Masayo Kagami

Genetic and environmental causes of variation in epigenetic aging across the lifespan

DNA methylation-based biological age (DNAm age) is an important biomarker for adult health. Studies in specific age ranges have found widely varying results about its genetic and environmental causes of variat...

Authors: Shuai Li, Tuong L. Nguyen, Ee Ming Wong, Pierre-Antoine Dugué, Gillian S. Dite, Nicola J. Armstrong, Jeffrey M. Craig, Karen A. Mather, Perminder S. Sachdev, Richard Saffery, Joohon Sung, Qihua Tan, Anbupalam Thalamuthu, Roger L. Milne, Graham G. Giles, Melissa C. Southey…

Smoking-related changes in DNA methylation and gene expression are associated with cardio-metabolic traits

Tobacco smoking is a well-known modifiable risk factor for many chronic diseases, including cardiovascular disease (CVD). One of the proposed underlying mechanism linking smoking to disease is via epigenetic m...

Authors: Silvana C. E. Maas, Michelle M. J. Mens, Brigitte Kühnel, Joyce B. J. van Meurs, André G. Uitterlinden, Annette Peters, Holger Prokisch, Christian Herder, Harald Grallert, Sonja Kunze, Melanie Waldenberger, Maryam Kavousi, Manfred Kayser and Mohsen Ghanbari

The epigenetic implication in coronavirus infection and therapy

Epigenetics is a relatively new field of science that studies the genetic and non-genetic aspects related to heritable phenotypic changes, frequently caused by environmental and metabolic factors. In the host,...

Authors: Sandra Atlante, Alessia Mongelli, Veronica Barbi, Fabio Martelli, Antonella Farsetti and Carlo Gaetano

Time course of altered DNA methylation evoked by critical illness and by early administration of parenteral nutrition in the paediatric ICU

A genome-wide study identified de novo DNA methylation alterations in leukocytes of children at paediatric intensive care unit (PICU) discharge, offering a biological basis for their impaired long-term developmen...

Authors: Ines Verlinden, Fabian Güiza, Inge Derese, Pieter J. Wouters, Koen Joosten, Sascha C. Verbruggen, Greet Van den Berghe and Ilse Vanhorebeek

Leveraging locus-specific epigenetic heterogeneity to improve the performance of blood-based DNA methylation biomarkers

Variation in intercellular methylation patterns can complicate the use of methylation biomarkers for clinical diagnostic applications such as blood-based cancer testing. Here, we describe development and valid...

Authors: Brendan F. Miller, Thomas R. Pisanic II, Gennady Margolin, Hanna M. Petrykowska, Pornpat Athamanolap, Alexander Goncearenco, Akosua Osei-Tutu, Christina M. Annunziata, Tza-Huei Wang and Laura Elnitski

Identification of fetal unmodified and 5-hydroxymethylated CG sites in maternal cell-free DNA for non-invasive prenatal testing

Massively parallel sequencing of maternal cell-free DNA (cfDNA) is widely used to test fetal genetic abnormalities in non-invasive prenatal testing (NIPT). However, sequencing-based approaches are still of hig...

Authors: Juozas Gordevičius, Milda Narmontė, Povilas Gibas, Kotryna Kvederavičiūtė, Vita Tomkutė, Priit Paluoja, Kaarel Krjutškov, Andres Salumets and Edita Kriukienė

Novel mutation points to a hot spot in CDKN1C causing Silver–Russell syndrome

Pathogenic CDKN1C gain-of-function variants on the maternal allele were initially reported as a cause of IMAGe syndrome characterized by intrauterine growth retardation, metaphyseal dysplasia, primary adrenal ins...

Authors: Gerhard Binder, Julian Ziegler, Roland Schweizer, Wisam Habhab, Tobias B. Haack, Tilman Heinrich and Thomas Eggermann

Serious neonatal morbidities are associated with differences in DNA methylation among very preterm infants

Infants born very preterm are more likely to experience neonatal morbidities compared to their term peers. Variations in DNA methylation (DNAm) associated with these morbidities may yield novel information abo...

Authors: Todd M. Everson, T. Michael O’Shea, Amber Burt, Karen Hermetz, Brian S. Carter, Jennifer Helderman, Julie A. Hofheimer, Elisabeth C. McGowan, Charles R. Neal, Steven L. Pastyrnak, Lynne M. Smith, Antoine Soliman, Sheri A. DellaGrotta, Lynne M. Dansereau, James F. Padbury, Barry M. Lester…

Epigenetic silencing of miR-342-3p in B cell lymphoma and its impact on autophagy

miR-342-3p, localized to 14q32, is a tumor suppressor miRNA implicated in carcinogenesis. Given the presence of a promotor-associated CpG island for its host gene, EVL, we hypothesized that intronic miR-342-3p is...

Authors: Min Yue Zhang, George A. Calin, Kit San Yuen, Dong Yan Jin and Chor Sang Chim

Epigenome-wide association study of Alzheimer’s disease replicates 22 differentially methylated positions and 30 differentially methylated regions

Growing evidence shows that epigenetic modifications play a role in Alzheimer’s disease (AD). We performed an epigenome-wide association study (EWAS) to evaluate the DNA methylation differences using postmorte...

Authors: Qingqin S. Li, Yu Sun and Tania Wang

The influences of DNA methylation and epigenetic clocks, on metabolic disease, in middle-aged Koreans

Considering that DNA methylation (DNAm) profiles are, in large part, modifiable by lifestyle and environmental influences, it has been proposed that epigenetic clocks provide a better estimate of biological ag...

Authors: Ho-Sun Lee and Taesung Park

Rebelled epigenome: histone H3S10 phosphorylation and H3S10 kinases in cancer biology and therapy

With the discovery that more than half of human cancers harbor mutations in chromatin proteins, deregulation of epigenetic mechanisms has been recognized a hallmark of malignant transformation. Post-translatio...

Authors: Dorota Komar and Przemyslaw Juszczynski

Clinicopathologic significance of protein lysine methyltransferases in cancer

Protein lysine methyltransferases (PKMTs) constitute a large family of approximately 50 chromatin modifiers that mono-, di- and/or tri-methylate lysine residues on histone and non-histone substrates. With the ...

Authors: Theodore Vougiouklakis, Benjamin J. Bernard, Nupur Nigam, Kyunghee Burkitt, Yusuke Nakamura and Vassiliki Saloura

TWIST1 DNA methylation is a cell marker of airway and parenchymal lung fibroblasts that are differentially methylated in asthma

Mesenchymal fibroblasts are ubiquitous cells that maintain the extracellular matrix of organs. Within the lung, airway and parenchymal fibroblasts are crucial for lung development and are altered with disease,...

Authors: Rachel L. Clifford, Chen Xi Yang, Nick Fishbane, Jamie Patel, Julia L. MacIsaac, Lisa M. McEwen, Sean T. May, Marcos Castellanos-Uribe, Parameswaran Nair, Ma’en Obeidat, Michael S. Kobor, Alan J. Knox and Tillie-Louise Hackett

Epigenetic approach in obesity: DNA methylation in a prepubertal population which underwent a lifestyle modification

Metabolically healthy obesity (MHO) is a considerably controversial concept as it is considered a transitory condition towards the development of different pathologies (type 2 diabetes, insulin resistance, or ...

Authors: Cristina Gallardo-Escribano, Verónica Buonaiuto, M. Isabel Ruiz-Moreno, Antonio Vargas-Candela, Alberto Vilches-Perez, Javier Benitez-Porres, Angel Ramon Romance-Garcia, Alejandro Ruiz-Moreno, Ricardo Gomez-Huelgas and M. Rosa Bernal-Lopez

Universal NicE-seq for high-resolution accessible chromatin profiling for formaldehyde-fixed and FFPE tissues

Accessible chromatin plays a central role in gene expression and chromatin architecture. Current accessible chromatin approaches depend on limited digestion/cutting and pasting adaptors at the accessible DNA, ...

Authors: Hang Gyeong Chin, Zhiyi Sun, Udayakumar S. Vishnu, Pengying Hao, Paloma Cejas, George Spracklin, Pierre-Olivier Estève, Shuang-yong Xu, Henry W. Long and Sriharsa Pradhan

Low-dose DNA demethylating therapy induces reprogramming of diverse cancer-related pathways at the single-cell level

Epigenetic reprogramming using DNA demethylating drugs is a promising approach for cancer therapy, but its efficacy is highly dependent on the dosing regimen. Low-dose treatment for a prolonged period shows a ...

Authors: Hideyuki Takeshima, Yukie Yoda, Mika Wakabayashi, Naoko Hattori, Satoshi Yamashita and Toshikazu Ushijima

DNA methylation of FKBP5 in South African women: associations with obesity and insulin resistance

Disruption of the hypothalamic–pituitary–adrenal (HPA) axis, a neuroendocrine system associated with the stress response, has been hypothesized to contribute to obesity development. This may be mediated throug...

Authors: Tarryn Willmer, Julia H. Goedecke, Stephanie Dias, Johan Louw and Carmen Pheiffer

DNA methylation mediates the effect of cocaine use on HIV severity

Cocaine use accelerates human immunodeficiency virus (HIV) progression and worsens HIV outcomes. We assessed whether DNA methylation in blood mediates the association between cocaine use and HIV severity in a ...

Authors: Chang Shu, Amy C. Justice, Xinyu Zhang, Zuoheng Wang, Dana B. Hancock, Eric O. Johnson and Ke Xu

Loss-of-function maternal-effect mutations of PADI6 are associated with familial and sporadic Beckwith-Wiedemann syndrome with multi-locus imprinting disturbance

PADI6 is a component of the subcortical maternal complex, a group of proteins that is abundantly expressed in the oocyte cytoplasm, but is required for the correct development of early embryo. Maternal-effect ...

Authors: Maria Vittoria Cubellis, Laura Pignata, Ankit Verma, Angela Sparago, Rosita Del Prete, Maria Monticelli, Luciano Calzari, Vincenzo Antona, Daniela Melis, Romano Tenconi, Silvia Russo, Flavia Cerrato and Andrea Riccio

Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes

Inflammation has been associated with higher rates of recurrence and mortality in head and neck cancer (HNC). While the biological mechanisms predisposing patients to heightened inflammatory states remain larg...

Authors: Laura Moody, Sylvia L. Crowder, Andrew D. Fruge, Julie L. Locher, Wendy Demark-Wahnefried, Laura Q. Rogers, Ashley Delk-Licata, William R. Carroll, Sharon A. Spencer, Molly Black, John W. Erdman Jr, Hong Chen, Yuan-Xiang Pan and Anna E. Arthur