Review
Chemistry, Medicinal
Zijun Geng, Meiqi Chen, Qixuan Yu, Shuoxi Guo, Tianli Chen, Da Liu
Summary: This review presents the epigenetic roles of various natural products in colorectal cancer, including their impact on cell proliferation, apoptosis, invasion, migration, and anti-chemotherapeutic resistance. The aim is to elucidate the epigenetic mechanisms of action of natural products in cancer prevention and treatment, and provide a theoretical basis for studying the role of epigenetics in influencing colorectal cancer, as well as new directions for studying the occurrence, development, and prognosis of colorectal cancer, and new targets for treating and preventing colorectal cancer.
Review
Biochemistry & Molecular Biology
Yihong Feng, Masayuki Endo, Hiroshi Sugiyama
Summary: Nucleosomes, as the fundamental building blocks of chromatin, are highly dynamic and play vital roles in the formation of higher-order chromatin structures and gene regulation. Recent advances in epigenetics research have gradually unraveled nucleosome structures, histone modifications, nucleosome-binding proteins, and their functions. With the continuous development of research methods such as cryo-EM and next-generation sequencing, our understanding of nucleosomes is becoming broader and deeper.
Article
Chemistry, Multidisciplinary
Lin Chen, Zhihui Luo, Chen Zhao, Qinglan Li, Yingjie Geng, Yong Xiao, Ming-Kai Chen, Lianyun Li, Zhen-Xia Chen, Min Wu
Summary: In this study, a systematic epigenomic study of histone modifications in an AOM-DSS-induced CRC mouse model is conducted. The dynamic landscape of chromatin states during inflammation-cancer transition is illustrated and functional gene clusters and key signaling pathways are identified. The study reveals the important role of enhancer state regions during inflammation-cancer transition and experimentally confirms OTX2 as a critical tumor suppressive transcription factor.
Article
Cell Biology
Maxime Galloy, Catherine Lachance, Xue Cheng, Felix Distefano-Gagne, Jacques Cote, Amelie Fradet-Turcotte
Summary: This article introduces experimental methods for studying the key mechanisms of chromatin modification, such as purifying native chromatin modifier complexes and producing recombinant nucleosomes. In addition, a new approach is proposed to study the functions of essential chromatin modifiers by inducing their quick depletion from the nucleus.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Yuexuan Wang, Yu Han, Yuzhen Jin, Qiang He, Zhicheng Wang
Summary: This study discusses the pathogenesis of cancer and the impact of radiotherapy on cancer. It has been found that epigenetic modification plays an important role in the occurrence and development of cancer. Radiation therapy affects the epigenetic modifications of DNA, chromatin, etc., which in turn affects the treatment outcomes. Therefore, studying the interaction between radiotherapy and epigenetic modifications can help us better understand cancer treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Futaba Inoue, Kenbun Sone, Yusuke Toyohara, Yu Takahashi, Asako Kukita, Aki Hara, Ayumi Taguchi, Michihiro Tanikawa, Tetsushi Tsuruga, Yutaka Osuga
Summary: Epigenetic changes play a crucial role in endometrial cancer, including DNA methylation and histone modification. There are currently inhibitors targeting epigenetic regulators in preclinical studies and clinical trials.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Cell Biology
Domenica Scumaci, Qingfei Zheng
Summary: Histones undergo a variety of post-translational modifications that regulate cell fate. Accumulation of epigenetic alterations is a driving force behind cancer progression. Non-enzymatic covalent modifications of histones have been recently described, which are closely related to cellular metabolism and can impair chromatin structure. Cancer cells counteract the accumulation of these modifications by overexpressing eraser enzymes. This review explores these modifications and their corresponding eraser enzymes, and proposes targeting these enzymes as a strategy for personalized medicine.
CELL COMMUNICATION AND SIGNALING
(2023)
Article
Biochemistry & Molecular Biology
Meiting Yang, Xiaorong Li, Zizi Tian, Lulu Ma, Jun Ma, Yunlong Liu, Guohui Shang, Ailing Liang, Wei Wu, Zhongzhou Chen
Summary: Recent research has discovered the MPND protein as a potential sensor for recognizing DNA 6mA modification in eukaryotes. Crystal structures of apo-MPND and MPND-DNA complex were determined, revealing dynamic assemblies. MPND was found to directly bind to histones and the interaction between MPND and histones was enhanced by DNA and the acidic regions of MPND. These findings provide structural information for further research on gene control and transcriptional regulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Dan Wu, Yunfeng Zhang, Zhiheng Tang, Xiaoxu Chen, Xinyu Ling, Longtu Li, Wenbing Cao, Wei Zheng, Jiale Wu, Hongting Tang, Xiaoyun Liu, Xiaozhou Luo, Tao Liu
Summary: This study investigates the functions and regulations of structurally diverse acylations as post-translational modifications (PTMs) on histone lysine residues. It introduces the concept of a lysine acylation analog, pyrrolysine, as a co-translational modification (CTM) through genetic encoding. By creating a model organism Saccharomyces cerevisiae with site-specific lysine CTMs at histone H3K56, the study demonstrates that acetylation of histone H3K56 provides a more favorable chromatin environment for DNA repair compared to crotonylation and crosstalk with other PTMs differently. This research provides a potentially universal approach to understanding the consequences of different histone lysine PTMs in eukaryotes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Oncology
Kenji Ohshima, Ryo Oi, Satoshi Nojima, Eiichi Morii
Summary: Mitochondria in colorectal cancer cells maintain histone acetylation, particularly H3K27ac, a surrogate marker of active super-enhancers. Mitochondrial mass and H3K27ac marks are increased in colorectal adenocarcinoma lesions, suggesting that mitochondria function as inducers of histone acetylation in human colorectal cancer cells.
JOURNAL OF PATHOLOGY
(2022)
Article
Genetics & Heredity
Wladyslaw A. Krajewski
Summary: Tight packaging of DNA in chromatin restricts DNA accessibility and dynamics, while studying the inherent dynamics and interactions of nucleosomes is crucial for understanding their functionality and diversifying epigenetic programming methods.
FRONTIERS IN GENETICS
(2022)
Review
Biochemistry & Molecular Biology
Lidia Borkiewicz
Summary: Cancer development and progression are governed by complex genetic and epigenetic changes, with histone 3 trimethylation of lysine 27 (H3K27me3) playing a significant role in silencing tumor suppressor genes in breast cancer. This review highlights the importance of H3K27me3 status in breast cancer biology and potential therapeutic implications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Pharmacology & Pharmacy
Weizheng Liang, Hongyang Yi, Chenyu Mao, Qingxue Meng, Xueliang Wu, Shanliang Li, Jun Xue
Summary: RNA methylation plays a significant role in tumor progression and metastasis, and colorectal cancer is a common malignant tumor in the digestive system with deficiencies in diagnosis and prognosis. This article highlights the various RNA chemical modifications and their functions in colorectal cancer.
FRONTIERS IN PHARMACOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Cecilia Fernandez-Ponce, Noelia Geribaldi-Doldan, Ismael Sanchez-Gomar, Roberto Navarro Quiroz, Linda Atencio Ibarra, Lorena Gomez Escorcia, Ricardo Fernandez-Cisnal, Gustavo Aroca Martinez, Francisco Garcia-Cozar, Elkin Navarro Quiroz
Summary: The dysregulation of glycosyltransferase expression in colorectal cancer affects key molecules involved in oncogenesis and metastasis, impacting functions such as cell migration, cell-cell adhesion, apoptosis, and immune system regulation. Strategies to alter oligosaccharide processing and modify glycoconjugate structures have been evaluated to control CRC progression and prevent metastasis, while immunotherapy approaches target altered glycosylation as potential neo-antigens for tumor-specific T cells or engineered CAR T cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Hui Liu, Huimin Ma, Yang Li, Hua Zhao
Summary: This article reviews the current research status of epigenetic modifications in cervical cancer, including DNA methylation, histone modification, noncoding RNA regulation, and chromatin regulation. The functions and molecular mechanisms of these modifications in the occurrence and progression of cervical cancer are also discussed. This review provides new ideas for early screening, risk assessment, molecular targeted therapy, and prognostic prediction of cervical cancer.
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER
(2023)
Article
Oncology
Necla Gurdal, Merdan Fayda, Nijat Alishev, Baris Bakir, Didem Tastekin, Faruk Aykan, Ugur Gezer, Emre Balik, Esra Kaytan Saglam, Ethem Nezih Oral, Mine Gulluoglu, Ahmet Kizir
Review
Oncology
Ebru Esin Yoruker, Stefan Holdenrieder, Ugur Gezer
TRANSLATIONAL CANCER RESEARCH
(2018)
Article
Oncology
Necla Gurdal, Merdan Fayda, Nijat Alishev, Baris Bakir, Didem Tastekin, Faruk Aykan, Ugur Gezer, Emre Balik, Esra Kaytan Saglam, Ethem Nezih Oral, Mine Gulluoglu, Ahmet Kizir
Article
Oncology
Murat Serilmez, Emre Ozgur, Sule Karaman, Ugur Gezer, Derya Duranyildiz
Article
Oncology
Emre Ozgur, Ferhat Ferhatoglu, Fatma Sen, Pinar Saip, Ugur Gezer
Article
Medical Laboratory Technology
Emre Ozgur, Zsuzsanna Mayer, Metin Keskin, Ebru E. Yoruker, Stefan Holdenrieder, Ugur Gezer
Summary: This study demonstrates that HSATII DNA levels are elevated in various cancer patients compared to controls, particularly chr10-HSATII. Digital PCR showed significantly higher levels of chr10-HSATII in breast cancer patients. Diluted plasma samples also indicated increased levels of HSATII DNA in multiple cancer types, suggesting its potential as a surrogate cancer biomarker.
CLINICA CHIMICA ACTA
(2021)
Review
Medicine, General & Internal
Ugur Gezer, Abel J. Bronkhorst, Stefan Holdenrieder
Summary: Liquid biopsy is a method of diagnosing pathological conditions by testing biomarkers in body fluids. Cell-free DNA (cfDNA) has significant potential as a biomarker in oncology, prenatal testing, and transplant monitoring. The clinical potential of repeat DNA sequences in cfDNA as an underappreciated marker in liquid biopsy for cancer is highlighted.
Review
Medicine, General & Internal
Ugur Gezer, Abel J. Bronkhorst, Stefan Holdenrieder
Summary: This review evaluates the clinical utility of Droplet digital PCR as a technique for mutational profiling in breast cancer patients, focusing on the most frequently mutated genes in breast cancer.
Article
Medicine, General & Internal
E. Ozgur, U. Gezer
BRATISLAVA MEDICAL JOURNAL-BRATISLAVSKE LEKARSKE LISTY
(2020)
Article
Medicine, Research & Experimental
Emre Ozgur, Metin Keskin, Ebru E. Yoruker, Stefan Holdenrieder, Ugur Gezer
Article
Medicine, Research & Experimental
Ebru Esin Yoruker, Metin Keskin, Cemil Burak Kulle, Stefan Holdenrieder, Ugur Gezer
BIOMEDICAL REPORTS
(2018)
Article
Medicine, Research & Experimental
Oguz Koldemir, Emre Ozgur, Ugur Gezer
BIOMEDICAL REPORTS
(2017)