Articles

Genome-wide DNA methylome analysis identifies methylation signatures associated with survival and drug resistance of ovarian cancers

In contrast to stable genetic events, epigenetic changes are highly plastic and play crucial roles in tumor evolution and development. Epithelial ovarian cancer (EOC) is a highly heterogeneous disease that is ...

Authors: David W. Chan, Wai-Yip Lam, Fushun Chen, Mingo M. H. Yung, Yau-Sang Chan, Wai-Sun Chan, Fangfang He, Stephanie S. Liu, Karen K. L. Chan, Benjamin Li and Hextan Y. S. Ngan

Abnormal methylation characteristics predict chemoresistance and poor prognosis in advanced high-grade serous ovarian cancer

Primary or acquired chemoresistance is a key link in the high mortality rate of ovarian cancer. There is no reliable method to predict chemoresistance in ovarian cancer. We hypothesized that specific methylati...

Authors: Li-yuan Feng, Bing-bing Yan, Yong-zhi Huang and Li Li

DNA methylation under the major depression pathway predicts pediatric quality of life four-month post-pediatric mild traumatic brain injury

Major depression has been recognized as the most commonly diagnosed psychiatric complication of mild traumatic brain injury (mTBI). Moreover, major depression is associated with poor outcomes following mTBI; h...

Authors: Kuaikuai Duan, Andrew R. Mayer, Nicholas A. Shaff, Jiayu Chen, Dongdong Lin, Vince D. Calhoun, Dawn M. Jensen and Jingyu Liu

DNA methylation analysis reveals epimutation hotspots in patients with dilated cardiomyopathy-associated laminopathies

Mutations in LMNA, encoding lamin A/C, lead to a variety of diseases known as laminopathies including dilated cardiomyopathy (DCM) and skeletal abnormalities. Though previous studies have investigated the dysregu...

Authors: Julien L. P. Morival, Halida P. Widyastuti, Cecilia H. H. Nguyen, Michael V. Zaragoza and Timothy L. Downing

The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes

Transcriptionally active chromatin is marked by tri-methylation of histone H3 at lysine 4 (H3K4me3) located after first exons and around transcription start sites. This epigenetic mark is typically restricted ...

Authors: Tasnim H. Beacon, Geneviève P. Delcuve, Camila López, Gino Nardocci, Igor Kovalchuk, Andre J. van Wijnen and James R. Davie

PRDX1 gene-related epi-cblC disease is a common type of inborn error of cobalamin metabolism with mono- or bi-allelic MMACHC epimutations

The role of epigenetics in inborn errors of metabolism (IEMs) is poorly investigated. Epigenetic changes can contribute to clinical heterogeneity of affected patients but could also be underestimated determini...

Authors: Catia Cavicchi, Abderrahim Oussalah, Silvia Falliano, Lorenzo Ferri, Alessia Gozzini, Serena Gasperini, Serena Motta, Miriam Rigoldi, Giancarlo Parenti, Albina Tummolo, Concetta Meli, Francesca Menni, Francesca Furlan, Marta Daniotti, Sabrina Malvagia, Giancarlo la Marca…

DNA methylation and behavioral dysfunction in males with 47,XXY and 49,XXXXY: a pilot study

Equal dosage of X-linked genes between males and females is maintained by the X-inactivation of the second X chromosome in females through epigenetic mechanisms. Boys with aneuploidy of the X chromosome exhibi...

Authors: Richard S. Lee, Sophia Q. Song, Henri M. Garrison-Desany, Jenny L. Carey, Patricia Lasutschinkow, Andrew Zabel, Joseph Bressler, Andrea Gropman and Carole Samango-Sprouse

Combined prenatal Lactobacillus reuteri and ω-3 supplementation synergistically modulates DNA methylation in neonatal T helper cells

Environmental exposures may alter DNA methylation patterns of T helper cells. As T helper cells are instrumental for allergy development, changes in methylation patterns may constitute a mechanism of action fo...

Authors: Johanna Huoman, David Martínez-Enguita, Elin Olsson, Jan Ernerudh, Lennart Nilsson, Karel Duchén, Mika Gustafsson and Maria C. Jenmalm

Methylation status of genes escaping from X-chromosome inactivation in patients with X-chromosome rearrangements

X-chromosome inactivation (XCI) is a mechanism in which one of two X chromosomes in females is randomly inactivated in order to compensate for imbalance of gene dosage between sexes. However, about 15% of gene...

Authors: Sayaka Kawashima, Atsushi Hattori, Erina Suzuki, Keiko Matsubara, Machiko Toki, Rika Kosaki, Yukihiro Hasegawa, Kazuhiko Nakabayashi, Maki Fukami and Masayo Kagami

A novel DNA methylation signature is associated with androgen receptor activity and patient prognosis in bone metastatic prostate cancer

Patients with metastatic prostate cancer (PC) are treated with androgen deprivation therapy (ADT) that initially reduces metastasis growth, but after some time lethal castration-resistant PC (CRPC) develops. A...

Authors: Erik Bovinder Ylitalo, Elin Thysell, Mattias Landfors, Maria Brattsand, Emma Jernberg, Sead Crnalic, Anders Widmark, Magnus Hultdin, Anders Bergh, Sofie Degerman and Pernilla Wikström

Oxygen concentration affects de novo DNA methylation and transcription in in vitro cultured oocytes

Reproductive biology methods rely on in vitro follicle cultures from mature follicles obtained by hormonal stimulation for generating metaphase II oocytes to be fertilised and developed into a healthy embryo. ...

Authors: Florence Naillat, Heba Saadeh, Joanna Nowacka-Woszuk, Lenka Gahurova, Fatima Santos, Shin-ichi Tomizawa and Gavin Kelsey

Detecting cord blood cell type-specific epigenetic associations with gestational diabetes mellitus and early childhood growth

Epigenome-wide association studies (EWAS) have provided opportunities to understand the role of epigenetic mechanisms in development and pathophysiology of many chronic diseases. However, an important limitati...

Authors: Tianyuan Lu, Andres Cardenas, Patrice Perron, Marie-France Hivert, Luigi Bouchard and Celia M. T. Greenwood

Correction to: Does the epigenetic clock GrimAge predict mortality independent of genetic influences: an 18 year follow-up study in older female twin pairs

Authors: Tiina Föhr, Katja Waller, Anne Viljanen, Riikka Sanchez, Miina Ollikainen, Taina Rantanen, Jaakko Kaprio and Elina Sillanpää

The epigenetic etiology of cardiovascular disease in a longitudinal Swedish twin study

Studies on DNA methylation have the potential to discover mechanisms of cardiovascular disease (CVD) risk. However, the role of DNA methylation in CVD etiology remains unclear.

Authors: Xueying Qin, Ida K. Karlsson, Yunzhang Wang, Xia Li, Nancy Pedersen, Chandra A. Reynolds and Sara Hägg

Does the epigenetic clock GrimAge predict mortality independent of genetic influences: an 18 year follow-up study in older female twin pairs

Epigenetic clocks are based on DNA methylation (DNAm). It has been suggested that these clocks are useable markers of biological aging and premature mortality. Because genetic factors explain variations in bot...

Authors: Tiina Föhr, Katja Waller, Anne Viljanen, Riikka Sanchez, Miina Ollikainen, Taina Rantanen, Jaakko Kaprio and Elina Sillanpää

STAT1 epigenetically regulates LCP2 and TNFAIP2 by recruiting EP300 to contribute to the pathogenesis of inflammatory bowel disease

The aetiology of inflammatory bowel disease (IBD) is related to genetics and epigenetics. Epigenetic regulation of the pathogenesis of IBD has not been well defined. Here, we investigated the role of H3K27ac e...

Authors: Ya-Li Yu, Meng Chen, Hua Zhu, Ming-Xing Zhuo, Ping Chen, Yu-Juan Mao, Lian-Yun Li, Qiu Zhao, Min Wu and Mei Ye

Identification of DNA methylation biomarkers for risk of liver metastasis in early-stage colorectal cancer

Liver metastases can occur even in CRC patients who underwent curative surgery. While evidence suggested that adjuvant chemotherapy can help to reduce the occurrence of liver metastases for certain patients, i...

Authors: Weihua Li, Lei Guo, Wanxiangfu Tang, Yutong Ma, Xiaonan Wang, Yang Shao, Hong Zhao and Jianming Ying

Epigenetic mechanisms underlying prostate cancer radioresistance

Radiotherapy (RT) is one of the mainstay treatments for prostate cancer (PCa), a highly prevalent neoplasm among males worldwide. About 30% of newly diagnosed PCa patients receive RT with a curative intent. Ho...

Authors: Catarina Macedo-Silva, Rosaria Benedetti, Fortunato Ciardiello, Salvatore Cappabianca, Carmen Jerónimo and Lucia Altucci

Altered DNA methylation pattern reveals epigenetic regulation of Hox genes in thoracic aortic dissection and serves as a biomarker in disease diagnosis

Thoracic aortic dissection (TAD) is a severe disease with limited understandings in its pathogenesis. Altered DNA methylation has been revealed to be involved in many diseases etiology. Few studies have examin...

Authors: Peiru Liu, Jing Zhang, Duo Du, Dandan Zhang, Zelin Jin, Wenqing Qiu, Xiushi Zhou, Shulong Dong, Mengyu Zhou, Heyu Zhao, Wei Zhang, Jiakang Ma, Shaoyang Sun, Weiguo Fu, Yun Liu and Lixin Wang

Genome‑wide profiling of DNA methylation and gene expression unravel the epigenetic landscape in diabetes-related hypothyroidism

Type 2 diabetes mellitus (T2DM) and hypothyroidism are two common endocrine diseases and the phenomenon that the prevalence of diabetes-related hypothyroidism shows a significant upward trend deserves further ...

Authors: Jingyi Luo, Xiaoxia Wang, Li Yuan and Lixin Guo

Chromatin accessibility changes at intergenic regions are associated with ovarian cancer drug resistance

Resistance to DNA damaging chemotherapies leads to cancer treatment failure and poor patient prognosis. We investigated how genomic distribution of accessible chromatin sites is altered during acquisition of c...

Authors: John Gallon, Erick Loomis, Edward Curry, Nicholas Martin, Leigh Brody, Ian Garner, Robert Brown and James M. Flanagan

DNAm-based signatures of accelerated aging and mortality in blood are associated with low renal function

The difference between an individual's chronological and DNA methylation predicted age (DNAmAge), termed DNAmAge acceleration (DNAmAA), can capture life-long environmental exposures and age-related physiologic...

Authors: Pamela R. Matías-García, Cavin K. Ward-Caviness, Laura M. Raffield, Xu Gao, Yan Zhang, Rory Wilson, Xīn Gào, Jana Nano, Andrew Bostom, Elena Colicino, Adolfo Correa, Brent Coull, Charles Eaton, Lifang Hou, Allan C. Just, Sonja Kunze…

Current understanding of epigenetics mechanism as a novel target in reducing cancer stem cells resistance

At present, after extensive studies in the field of cancer, cancer stem cells (CSCs) have been proposed as a major factor in tumor initiation, progression, metastasis, and recurrence. CSCs are a subpopulation ...

Authors: Saeedeh Keyvani-Ghamsari, Khatereh Khorsandi, Azhar Rasul and Muhammad Khatir Zaman

ZNF445: a homozygous truncating variant in a patient with Temple syndrome and multilocus imprinting disturbance

ZNF445, as well as ZFP57, is involved in the postfertilization methylation maintenance of multiple imprinting-associated differentially methylated regions (iDMRs). Thus, ZNF445 pathogenic variants are predicted t...

Authors: Masayo Kagami, Kaori Hara-Isono, Keiko Matsubara, Kazuhiko Nakabayashi, Satoshi Narumi, Maki Fukami, Yumiko Ohkubo, Hirotomo Saitsu, Shuji Takada and Tsutomu Ogata

Blood DNA methylation and COVID-19 outcomes

There are no prior reports that compare differentially methylated regions of DNA in blood samples from COVID-19 patients to samples collected before the SARS-CoV-2 pandemic using a shared epigenotyping platfor...

Authors: Joseph Balnis, Andy Madrid, Kirk J. Hogan, Lisa A. Drake, Hau C. Chieng, Anupama Tiwari, Catherine E. Vincent, Amit Chopra, Peter A. Vincent, Michael D. Robek, Harold A. Singer, Reid S. Alisch and Ariel Jaitovich

Clinical and epigenetic features of colorectal cancer patients with somatic POLE proofreading mutations

Mutations in the POLE gene result in an ultra-hypermutated phenotype in colorectal cancer (CRC); however, the molecular characterisation of epigenetic alterations remains unclear. We examined the genetic and epig...

Authors: Takashi Kawai, Akihiro Nyuya, Yoshiko Mori, Takehiro Tanaka, Hiroaki Tanioka, Kazuya Yasui, Toshiaki Toshima, Fumitaka Taniguchi, Kunitoshi Shigeyasu, Yuzo Umeda, Toshiyoshi Fujiwara, Makoto Okawaki, Yoshiyuki Yamaguchi, Ajay Goel and Takeshi Nagasaka

The role of epigenetic mechanisms in the regulation of gene expression in the cyclical endometrium

The human endometrium is a highly dynamic tissue whose function is mainly regulated by the ovarian steroid hormones estradiol and progesterone. The serum levels of these and other hormones are associated with ...

Authors: Alejandra Monserrat Retis-Resendiz, Ixchel Nayeli González-García, Moisés León-Juárez, Ignacio Camacho-Arroyo, Marco Cerbón and Edgar Ricardo Vázquez-Martínez

Leveraging epigenetics to enhance the efficacy of immunotherapy

Epigenetic mechanisms regulate chromatin accessibility patterns that govern interaction of transcription machinery with genes and their cis-regulatory elements. Mutations that affect epigenetic mechanisms are ...

Authors: Jonathan D. Licht and Richard L. Bennett

Increased PARylation impacts the DNA methylation process in type 2 diabetes mellitus

Epigenetic modifications, such as DNA methylation, can influence the genetic susceptibility to type 2 diabetes mellitus (T2DM) and the progression of the disease. Our previous studies demonstrated that the reg...

Authors: Michele Zampieri, Maria Giulia Bacalini, Ilaria Barchetta, Stefania Scalea, Flavia Agata Cimini, Laura Bertoccini, Stefano Tagliatesta, Giovanna De Matteis, Giuseppe Zardo, Maria Gisella Cavallo and Anna Reale

Predictive biomarkers and potential drug combinations of epi-drugs in cancer therapy

Epigenetics studies heritable genomic modifications that occur with the participation of epigenetic modifying enzymes but without alterations of the nucleotide structure. Small-molecule inhibitors of these epi...

Authors: Tianshu Yang, Yunkai Yang and Yan Wang

NEFM DNA methylation correlates with immune infiltration and survival in breast cancer

This study aims to determine whether NEFM (neurofilament medium) DNA methylation correlates with immune infiltration and prognosis in breast cancer (BRCA) and to explore NEFM-connected immune gene signature.

Authors: Dandan Li, Wenhao Zhao, Xinyu Zhang, Hanning Lv, Chunhong Li and Lichun Sun

Methylated circulating tumor DNA as a biomarker for colorectal cancer diagnosis, prognosis, and prediction

Worldwide, colorectal cancer (CRC) is a deadly disease whose death rate ranks second among cancers though its incidence ranks third. Early CRC detection is key and is associated with improved survival outcomes...

Authors: Farah J. Nassar, Zahraa S. Msheik, Rihab R. Nasr and Sally N. Temraz

Blood and skeletal muscle ageing determined by epigenetic clocks and their associations with physical activity and functioning

The aim of this study was to investigate the correspondence of different biological ageing estimates (i.e. epigenetic age) in blood and muscle tissue and their associations with physical activity (PA), physica...

Authors: Elina Sillanpää, Aino Heikkinen, Anna Kankaanpää, Aini Paavilainen, Urho M. Kujala, Tuija H. Tammelin, Vuokko Kovanen, Sarianna Sipilä, Kirsi H. Pietiläinen, Jaakko Kaprio, Miina Ollikainen and Eija K. Laakkonen

Identification of prognosis-related molecular subgroups based on DNA methylation in pancreatic cancer

Pancreatic cancer (PC) is one of the most lethal and aggressive cancer malignancies. The lethality of PC is associated with delayed diagnosis, presence of distant metastasis, and its easy relapse. It is known ...

Authors: Xiaoli Yin, Lingming Kong and Peng Liu

The role of epigenetic modifications for the pathogenesis of Crohn's disease

Epigenetics has become a promising field for finding new biomarkers and improving diagnosis, prognosis, and drug response in inflammatory bowel disease. The number of people suffering from inflammatory bowel d...

Authors: M. Hornschuh, E. Wirthgen, M. Wolfien, K. P. Singh, O. Wolkenhauer and J. Däbritz

Ultralow amounts of DNA from long-term archived serum samples produce high-quality methylomes

Long-term stored serum is considered challenging for epigenomic analyses: as there are no cells, circulating DNA is scarce, and amplification removes epigenetic signals. Additionally, pre-analytical treatments...

Authors: Marcin W. Wojewodzic, Magnus Leithaug, Marianne Lauritzen, Robert Lyle, Sofia Haglund, Carl-Johan Rubin, Philip A. Ewels, Tom Grotmol and Trine B. Rounge

High-resolution targeted bisulfite sequencing reveals blood cell type-specific DNA methylation patterns in IL13 and ORMDL3

Methylation of DNA at CpG sites is an epigenetic modification and a potential modifier of disease risk, possibly mediating environmental effects. Currently, DNA methylation is commonly assessed using specific ...

Authors: Cilla Söderhäll, Lovisa E. Reinius, Pertteli Salmenperä, Massimiliano Gentile, Nathalie Acevedo, Jon R. Konradsen, Björn Nordlund, Gunilla Hedlin, Annika Scheynius, Samuel Myllykangas and Juha Kere

Conducting epigenetics research with refugees and asylum seekers: attending to the ethical challenges

An increase in global violence has forced the displacement of more than 70 million people, including 26 million refugees and 3.5 asylum seekers. Refugees and asylum seekers face serious socioeconomic and healt...

Authors: Faten Taki and Inmaculada de Melo-Martin

Methylated markers accurately distinguish primary central nervous system lymphomas (PCNSL) from other CNS tumors

Definitive diagnosis of primary central nervous system lymphoma (PCNSL) requires invasive surgical brain biopsy, causing treatment delays. In this paper, we identified and validated tumor-specific markers that...

Authors: Bradley M. Downs, Wanjun Ding, Leslie M. Cope, Christopher B. Umbricht, Wenge Li, Huihua He, Xiaokang Ke, Matthias Holdhoff, Chetan Bettegowda, Weiping Tao and Saraswati Sukumar

Development of a prognostic risk model for clear cell renal cell carcinoma by systematic evaluation of DNA methylation markers

Current risk models for renal cell carcinoma (RCC) based on clinicopathological factors are sub-optimal in accurately identifying high-risk patients. Here, we perform a head-to-head comparison of previously pu...

Authors: S. C. Joosten, S. N. O. Odeh, A. Koch, N. Buekers, M. J. B. Aarts, M. M. L. L. Baldewijns, L. Van Neste, S. van Kuijk, L. J. Schouten, P. A. van den Brandt, V. C. Tjan-Heijnen, M. van Engeland and K. M. Smits

DNA methylation profiling for molecular classification of adult diffuse lower-grade gliomas

DNA methylation profiling has facilitated and improved the classification of a wide variety of tumors of the central nervous system. In this study, we investigated the potential utility of DNA methylation prof...

Authors: Sandra Ferreyra Vega, Thomas Olsson Bontell, Alba Corell, Anja Smits, Asgeir Store Jakola and Helena Carén

Epigenetic landscape of testis specific histone H2B variant and its influence on sperm function

Biological relevance of the major testis specific histone H2B variant (TH2B) in sperm is not fully understood. Studies in TH2A/TH2B double knockout male mice indicate its role in chromatin compaction and male ...

Authors: Aniket Patankar, Rahul Gajbhiye, Suchitra Surve and Priyanka Parte

Weight loss after Roux-En-Y gastric bypass surgery reveals skeletal muscle DNA methylation changes

The mechanisms of weight loss and metabolic improvements following bariatric surgery in skeletal muscle are not well known; however, epigenetic modifications are likely to contribute. The aim of our study was ...

Authors: Luis A. Garcia, Samantha E. Day, Richard L. Coletta, Baltazar Campos, Tonya R. Benjamin, Eleanna De Filippis, James A. Madura II, Lawrence J. Mandarino, Lori R. Roust and Dawn K. Coletta

Assessment of differentially methylated loci in individuals with end-stage kidney disease attributed to diabetic kidney disease: an exploratory study

A subset of individuals with type 1 diabetes mellitus (T1DM) are predisposed to developing diabetic kidney disease (DKD), the most common cause globally of end-stage kidney disease (ESKD). Emerging evidence su...

Authors: L. J. Smyth, J. Kilner, V. Nair, H. Liu, E. Brennan, K. Kerr, N. Sandholm, J. Cole, E. Dahlström, A. Syreeni, R. M. Salem, R. G. Nelson, H. C. Looker, C. Wooster, K. Anderson, G. J. McKay…

Estimands in epigenome-wide association studies

In DNA methylation analyses like epigenome-wide association studies, effects in differentially methylated CpG sites are assessed. Two kinds of outcomes can be used for statistical analysis: Beta-values and M-valu...

Authors: Jochen Kruppa, Miriam Sieg, Gesa Richter and Anne Pohrt

Characteristics of epigenetic aging across gestational and perinatal tissues

Epigenetic clocks have been used to indicate differences in biological states between individuals of same chronological age. However, so far, only few studies have examined epigenetic aging in newborns—especia...

Authors: Linda Dieckmann, Marius Lahti-Pulkkinen, Tuomas Kvist, Jari Lahti, Peter E. DeWitt, Cristiana Cruceanu, Hannele Laivuori, Sara Sammallahti, Pia M. Villa, Sanna Suomalainen-König, Johan G. Eriksson, Eero Kajantie, Katri Raikkönen, Elisabeth B. Binder and Darina Czamara

HDAC2 enhances esophageal squamous cell carcinoma development through down-regulating microRNA-503-5p and promoting CXCL10

Although esophageal squamous cell carcinoma (ESCC)-oriented mechanism has been widely explored, the integrated action of histone deacetylase 2 (HDAC2), microRNA (miR)-503-5p and C-X-C motif chemokine 10 (CXCL1...

Authors: Jindong Li, Chengyan Jin, Lihua Sun, Bin Wang, Peiyan Hua and Yan Zhang

Associations of circulating folate, vitamin B12 and homocysteine concentrations in early pregnancy and cord blood with epigenetic gestational age: the Generation R Study

Circulating folate, vitamin B12 and homocysteine concentrations during fetal development have been associated with health outcomes in childhood. Changes in fetal DNA methylation may be an underlying mechanism....

Authors: Giulietta S. Monasso, Leanne K. Küpers, Vincent W. V. Jaddoe, Sandra G. Heil and Janine F. Felix

Correction to: Integrative study of EZH2 mutational status, copy number, protein expression and H3K27 trimethylation in AML/MDS patients

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

Authors: Julia Stomper, Ruth Meier, Tobias Ma, Dietmar Pfeifer, Gabriele Ihorst, Nadja Blagitko-Dorfs, Gabriele Greve, Dennis Zimmer, Uwe Platzbecker, Anne Hagemeijer, Ingrid Schmitt-Graeff and Michael Lübbert

The role of DNA methylation in syndromic and non-syndromic congenital heart disease

Congenital heart disease (CHD) is a common structural birth defect worldwide, and defects typically occur in the walls and valves of the heart or enlarged blood vessels. Chromosomal abnormalities and genetic m...

Authors: Jiali Cao, Qichang Wu, Yanru Huang, Lingye Wang, Zhiying Su and Huiming Ye