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Wang B, Wang M, Lin Y, Zhao J, Gu H, Li X. Circulating tumor DNA methylation: a promising clinical tool for cancer diagnosis and management. Clin Chem Lab Med 2024; 0:cclm-2023-1327. [PMID: 38443752 DOI: 10.1515/cclm-2023-1327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/19/2024] [Indexed: 03/07/2024]
Abstract
Cancer continues to pose significant challenges to the medical community. Early detection, accurate molecular profiling, and adequate assessment of treatment response are critical factors in improving the quality of life and survival of cancer patients. Accumulating evidence shows that circulating tumor DNA (ctDNA) shed by tumors into the peripheral blood preserves the genetic and epigenetic information of primary tumors. Notably, DNA methylation, an essential and stable epigenetic modification, exhibits both cancer- and tissue-specific patterns. As a result, ctDNA methylation has emerged as a promising molecular marker for noninvasive testing in cancer clinics. In this review, we summarize the existing techniques for ctDNA methylation detection, describe the current research status of ctDNA methylation, and present the potential applications of ctDNA-based assays in the clinic. The insights presented in this article could serve as a roadmap for future research and clinical applications of ctDNA methylation.
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Affiliation(s)
- Binliang Wang
- Department of Respiratory Medicine, Huangyan Hospital Affiliated to Wenzhou Medical University, Taizhou, P.R. China
| | - Meng Wang
- Institute of Health Education, Hangzhou Center for Disease Control and Prevention, Hangzhou, P.R. China
| | - Ya Lin
- Zhejiang University of Chinese Medicine, Hangzhou, P.R. China
| | - Jinlan Zhao
- Scientific Research Department, Zhejiang Shengting Medical Company, Hangzhou, P.R. China
| | - Hongcang Gu
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, P.R. China
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, P.R. China
| | - Xiangjuan Li
- Department of Gynaecology, Hangzhou Obstetrics and Gynecology Hospital, Hangzhou, P.R. China
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Liu C, Tang H, Hu N, Li T. Methylomics and cancer: the current state of methylation profiling and marker development for clinical care. Cancer Cell Int 2023; 23:242. [PMID: 37840147 PMCID: PMC10577916 DOI: 10.1186/s12935-023-03074-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023] Open
Abstract
Epigenetic modifications have long been recognized as an essential level in transcriptional regulation linking behavior and environmental conditions or stimuli with biological processes and disease development. Among them, methylation is the most abundant of these reversible epigenetic marks, predominantly occurring on DNA, RNA, and histones. Methylation modification is intimately involved in regulating gene transcription and cell differentiation, while aberrant methylation status has been linked with cancer development in several malignancies. Early detection and precise restoration of dysregulated methylation form the basis for several epigenetics-based therapeutic strategies. In this review, we summarize the current basic understanding of the regulation and mechanisms responsible for methylation modification and cover several cutting-edge research techniques for detecting methylation across the genome and transcriptome. We then explore recent advances in clinical diagnostic applications of methylation markers of various cancers and address the current state and future prospects of methylation modifications in therapies for different diseases, especially comparing pharmacological methylase/demethylase inhibitors with the CRISPRoff/on methylation editing systems. This review thus provides a resource for understanding the emerging role of epigenetic methylation in cancer, the use of methylation-based biomarkers in cancer detection, and novel methylation-targeted drugs.
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Affiliation(s)
- Chengyin Liu
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Georgetown University, Washington, DC, USA
| | - Han Tang
- BioChain (Beijing) Science & Technology Inc., Beijing, People's Republic of China
| | - Nana Hu
- BioChain (Beijing) Science & Technology Inc., Beijing, People's Republic of China
| | - Tianbao Li
- Department of Molecular Medicine, The University of Texas Health, San Antonio, USA.
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Yavanoglu Atay F, Bozkurt O, Sahin S, Bidev D, Sari FN, Uras N. A Comparison of Slow Infusion Intermittent Feeding versus Gravity Feeding in Preterm Infants: A Randomized Controlled Trial. CHILDREN (BASEL, SWITZERLAND) 2023; 10:1389. [PMID: 37628387 PMCID: PMC10453490 DOI: 10.3390/children10081389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/01/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023]
Abstract
BACKGROUND The transition to full enteral feeding is important for ensuring adequate growth in preterm infants. AIMS The aim of this study was to investigate the effects of two different intermittent feeding methods on the transition to full enteral feeding in preterm infants. STUDY DESIGN A prospective, randomized controlled study was conducted in a neonatology and perinatology center. SUBJECTS Preterm infants with a gestational age between 24 + 0/7 and 31 + 6/7 were included in this study. They were divided into two groups: the SIF (slow infusion feeding) group and the IBF (intermittent bolus feeding) group. In the SIF group, feed volumes were administered over one hour using an infusion pump through an orogastric tube, with feeding occurring every three hours. The IBF group received enteral feeding using a gravity-based technique with a syringe through an orogastric tube, completed within 10 to 30 min. OUTCOME MEASURES The primary outcome was the achievement of full enteral feeding and the occurrence of feeding intolerance. RESULTS A total of 103 infants were enrolled in the study (50 in SIF and 53 in IBF). The time to achieve full enteral feeding did not differ significantly between the two groups (p = 0.20). The SIF group had significantly fewer occurrences in which gastric residual volume exceeded 50% (p = 0.01). Moreover, the SIF group had a significantly shorter duration of non-per-oral (NPO) status than the IBF group (p = 0.03). CONCLUSIONS It is our contention that the use of the SIF method as an alternative feeding method is appropriate for infants with feeding intolerance and those at high risk of feeding intolerance.
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Affiliation(s)
- Funda Yavanoglu Atay
- Department of Pediatrics, Division of Neonatology, Umraniye Training and Research Hospital, 34764 Istanbul, Türkiye
| | - Ozlem Bozkurt
- Department of Pediatrics, Division of Neonatology, Faculty of Medicine, Kocaeli University, 41380 Izmit, Türkiye
| | - Suzan Sahin
- Department of Pediatrics, Division of Neonatology, Buca Seyfi Demirsoy Training and Research Hospital, Izmir Democracy University, 35140 Izmir, Türkiye
| | - Duygu Bidev
- Neonatal Care Intensive Unit, Koru Sincan Hospital, 06934 Ankara, Türkiye
| | - Fatma Nur Sari
- Department of Pediatrics, Division of Neonatology, Ankara City Hospital, 06800 Ankara, Türkiye
| | - Nurdan Uras
- Department of Pediatrics, Division of Neonatology, Faculty of Medicine, Istinye University, 34517 Istanbul, Türkiye
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Sun J, Chong J, Zhang J, Ge L. Preterm pigs for preterm birth research: reasonably feasible. Front Physiol 2023; 14:1189422. [PMID: 37520824 PMCID: PMC10374951 DOI: 10.3389/fphys.2023.1189422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023] Open
Abstract
Preterm birth will disrupt the pattern and course of organ development, which may result in morbidity and mortality of newborn infants. Large animal models are crucial resources for developing novel, credible, and effective treatments for preterm infants. This review summarizes the classification, definition, and prevalence of preterm birth, and analyzes the relationship between the predicted animal days and one human year in the most widely used animal models (mice, rats, rabbits, sheep, and pigs) for preterm birth studies. After that, the physiological characteristics of preterm pig models at different gestational ages are described in more detail, including birth weight, body temperature, brain development, cardiovascular system development, respiratory, digestive, and immune system development, kidney development, and blood constituents. Studies on postnatal development and adaptation of preterm pig models of different gestational ages will help to determine the physiological basis for survival and development of very preterm, middle preterm, and late preterm newborns, and will also aid in the study and accurate optimization of feeding conditions, diet- or drug-related interventions for preterm neonates. Finally, this review summarizes several accepted pediatric applications of preterm pig models in nutritional fortification, necrotizing enterocolitis, neonatal encephalopathy and hypothermia intervention, mechanical ventilation, and oxygen therapy for preterm infants.
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Affiliation(s)
- Jing Sun
- Chongqing Academy of Animal Sciences, Chongqing, China
- National Center of Technology Innovation for Pigs, Chongqing, China
- Key Laboratory of Pig Industry Sciences, Ministry of Agriculture, Chongqing, China
| | - Jie Chong
- Chongqing Academy of Animal Sciences, Chongqing, China
- National Center of Technology Innovation for Pigs, Chongqing, China
| | - Jinwei Zhang
- Chongqing Academy of Animal Sciences, Chongqing, China
- National Center of Technology Innovation for Pigs, Chongqing, China
- Key Laboratory of Pig Industry Sciences, Ministry of Agriculture, Chongqing, China
| | - Liangpeng Ge
- Chongqing Academy of Animal Sciences, Chongqing, China
- National Center of Technology Innovation for Pigs, Chongqing, China
- Key Laboratory of Pig Industry Sciences, Ministry of Agriculture, Chongqing, China
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DNA Methylome Mapping Identifies Epigenetic Abnormalities in Intestinal Lymphocyte Regulation in Human Necrotizing Enterocolitis. Dig Dis Sci 2022; 67:4434-4443. [PMID: 34846677 DOI: 10.1007/s10620-021-07314-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 11/02/2021] [Indexed: 12/09/2022]
Abstract
BACKGROUND Epigenetic changes occur in response to environmental factors during the pathogenesis of necrotizing enterocolitis (NEC) in animal models, but the DNA methylation signature in human patients with NEC has not been examined. AIM To illustrate the signature and function of DNA methylation in the intestine of human NEC. METHODS DNA methyltransferases (DNMTs) were compared between intestinal tissue with NEC and control. Genome-wide DNA methylation was analyzed by reduced representation bisulfite sequencing (RRBS). The biological functions of the potential methylation regulated genes were analyzed by Gene Ontology. Gene methylation and expression were confirmed by bisulfite genomic sequencing (BGS) and RT-qPCR. RESULTS By screening the expression of DNMTs, we identified a marked reduction in DNMT3A at both the mRNA and protein levels in NEC. Genome-wide variation of DNA methylation was detected in NEC lesions. The CG methylation level in almost all unique regions except CpG islands (CGIs) was lower in NEC compared with control. A total of 287 differentially methylated regions (DMRs) were identified across the whole genome in NEC, 123 of them are located on the CGI in the promoter. The DMR-associated genes were linked to intestinal epithelial permeability, platelet aggregation, and lymphocyte proliferation. Four genes (ZNF335, MPL, RASAL3, and KDM6A) with roles in the regulation of lymphocytes that may predispose the intestine to imbalanced immune processes were further confirmed to be hypermethylated and transcriptionally downregulated. CONCLUSIONS These findings underscore the novel relationship between epigenetic changes and lymphocyte regulation in human NEC, which may have potential diagnostic and therapeutic relevance for NEC.
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Abstract
The intestinal tract is the entry gate for nutrients and symbiotic organisms, being in constant contact with external environment. DNA methylation is one of the keys to how environmental conditions, diet and nutritional status included, shape functionality in the gut and systemically. This review aims to summarise findings on the importance of methylation to gut development, differentiation and function. Evidence to date on how external factors such as diet, dietary supplements, nutritional status and microbiota modifications modulate intestinal function through DNA methylation is also presented.
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Buddington RK, Yakimkova T, Adebiyi A, Chizhikov VV, Iskusnykh IY, Buddington KK. Organ Growth and Intestinal Functions of Preterm Pigs Fed Low and High Protein Formulas With or Without Supplemental Leucine or Hydroxymethylbutyrate as Growth Promoters. Front Nutr 2021; 8:687703. [PMID: 34150831 PMCID: PMC8211743 DOI: 10.3389/fnut.2021.687703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/10/2021] [Indexed: 01/07/2023] Open
Abstract
The goal of enteral nutritional support for infants born preterm or small for gestational age (SGA) is to achieve normal growth and development. Yet, this is difficult to achieve because of intestinal immaturity. Our objective was to determine if birth weight, protein intake, and the growth promoters leucine (10 g/L) or calcium-ß-hydroxy-ß-methylbutryate (HMB; 1.1 g/L) would affect trajectories of intestinal growth and functions and weights of other organs. Preterm pigs were delivered at gestational day 105 (91% of term) and fed for 6 or 7 days isocaloric formulas that differed in protein content (50 g or 100 g protein/L), with and without the growth promoters leucine or HMB. For comparative purposes organ weights were measured within 12 h after delivery for six term pigs of low and six of average birth weights. The responses of intestinal growth and total intestinal brush border membrane carbohydrases to protein level and supplemental leucine were of greater magnitude for preterm pigs of lower birth weight. Forskolin stimulated chloride secretion in the proximal small intestine was lower for pigs fed the low protein milk replacers. Capacities of the entire small intestine to transport glucose (mmol/kg-day) were not responsive to protein level, leucine, or HMB, and did not differ between small and large pigs. Relative organ weights of the small and average weight term pigs were similar, but some differed from those of the preterm pigs suggesting preterm birth and the standards of care used for this study altered the trajectories of development for the intestine and other organs. Although leucine is an effective generalized growth promoter that enhances gut development of small preterm pigs, it does not mitigate compromised neurodevelopment. Our findings using preterm pigs as a relevant preclinical model indicate nutrition support strategies can influence development of some gastrointestinal tract characteristics and the growth of other organs.
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Affiliation(s)
| | - Taisiya Yakimkova
- College of Health Studies, University of Memphis, Memphis, TN, United States
| | - Adebowale Adebiyi
- Department of Physiology, University of Tennessee Health Sciences Center, Memphis, TN, United States
| | - Victor V Chizhikov
- Department of Anatomy and Neurobiology, University of Tennessee Health Sciences Center, Memphis, TN, United States
| | - Igor Y Iskusnykh
- Department of Anatomy and Neurobiology, University of Tennessee Health Sciences Center, Memphis, TN, United States
| | - Karyl K Buddington
- Department of Biological Sciences, University of Memphis, Memphis, TN, United States
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Wang M, Ibeagha-Awemu EM. Impacts of Epigenetic Processes on the Health and Productivity of Livestock. Front Genet 2021; 11:613636. [PMID: 33708235 PMCID: PMC7942785 DOI: 10.3389/fgene.2020.613636] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/21/2020] [Indexed: 12/23/2022] Open
Abstract
The dynamic changes in the epigenome resulting from the intricate interactions of genetic and environmental factors play crucial roles in individual growth and development. Numerous studies in plants, rodents, and humans have provided evidence of the regulatory roles of epigenetic processes in health and disease. There is increasing pressure to increase livestock production in light of increasing food needs of an expanding human population and environment challenges, but there is limited related epigenetic data on livestock to complement genomic information and support advances in improvement breeding and health management. This review examines the recent discoveries on epigenetic processes due to DNA methylation, histone modification, and chromatin remodeling and their impacts on health and production traits in farm animals, including bovine, swine, sheep, goat, and poultry species. Most of the reports focused on epigenome profiling at the genome-wide or specific genic regions in response to developmental processes, environmental stressors, nutrition, and disease pathogens. The bulk of available data mainly characterized the epigenetic markers in tissues/organs or in relation to traits and detection of epigenetic regulatory mechanisms underlying livestock phenotype diversity. However, available data is inadequate to support gainful exploitation of epigenetic processes for improved animal health and productivity management. Increased research effort, which is vital to elucidate how epigenetic mechanisms affect the health and productivity of livestock, is currently limited due to several factors including lack of adequate analytical tools. In this review, we (1) summarize available evidence of the impacts of epigenetic processes on livestock production and health traits, (2) discuss the application of epigenetics data in livestock production, and (3) present gaps in livestock epigenetics research. Knowledge of the epigenetic factors influencing livestock health and productivity is vital for the management and improvement of livestock productivity.
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Affiliation(s)
- Mengqi Wang
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
- Department of Animal Science, Laval University, Quebec, QC, Canada
| | - Eveline M. Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
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