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Alves VC, Carro E, Figueiro-Silva J. Unveiling DNA methylation in Alzheimer's disease: a review of array-based human brain studies. Neural Regen Res 2024; 19:2365-2376. [PMID: 38526273 PMCID: PMC11090417 DOI: 10.4103/1673-5374.393106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 12/05/2023] [Indexed: 03/26/2024] Open
Abstract
The intricacies of Alzheimer's disease pathogenesis are being increasingly illuminated by the exploration of epigenetic mechanisms, particularly DNA methylation. This review comprehensively surveys recent human-centered studies that investigate whole genome DNA methylation in Alzheimer's disease neuropathology. The examination of various brain regions reveals distinctive DNA methylation patterns that associate with the Braak stage and Alzheimer's disease progression. The entorhinal cortex emerges as a focal point due to its early histological alterations and subsequent impact on downstream regions like the hippocampus. Notably, ANK1 hypermethylation, a protein implicated in neurofibrillary tangle formation, was recurrently identified in the entorhinal cortex. Further, the middle temporal gyrus and prefrontal cortex were shown to exhibit significant hypermethylation of genes like HOXA3, RHBDF2, and MCF2L, potentially influencing neuroinflammatory processes. The complex role of BIN1 in late-onset Alzheimer's disease is underscored by its association with altered methylation patterns. Despite the disparities across studies, these findings highlight the intricate interplay between epigenetic modifications and Alzheimer's disease pathology. Future research efforts should address methodological variations, incorporate diverse cohorts, and consider environmental factors to unravel the nuanced epigenetic landscape underlying Alzheimer's disease progression.
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Affiliation(s)
- Victoria Cunha Alves
- Neurodegenerative Diseases Group, Hospital Universitario 12 de Octubre Research Institute (imas12), Madrid, Spain
- Network Center for Biomedical Research, Neurodegenerative Diseases (CIBERNED), Madrid, Spain
- PhD Program in Neuroscience, Autonoma de Madrid University, Madrid, Spain
- Neurotraumatology and Subarachnoid Hemorrhage Group, Hospital Universitario 12 de Octubre Research Institute (imas12), Madrid, Spain
| | - Eva Carro
- Network Center for Biomedical Research, Neurodegenerative Diseases (CIBERNED), Madrid, Spain
- Neurobiology of Alzheimer's Disease Unit, Functional Unit for Research Into Chronic Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Joana Figueiro-Silva
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
- Department of Molecular Life Science, University of Zurich, Zurich, Switzerland
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Pei X, Luo Y, Zeng H, Jamil M, Liu X, Jiang B. Identification and validation of key genes in gastric cancer: insights from in silico analysis, clinical samples, and functional assays. Aging (Albany NY) 2024; 16:205965. [PMID: 38913913 DOI: 10.18632/aging.205965] [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: 12/19/2023] [Accepted: 05/16/2024] [Indexed: 06/26/2024]
Abstract
INTRODUCTION The underlying mechanisms of gastric cancer (GC) remain unknown. Therefore, in this study, we employed a comprehensive approach, combining computational and experimental methods, to identify potential key genes and unveil the underlying pathogenesis and prognosis of GC. METHODS Gene expression profiles from GEO databases (GSE118916, GSE79973, and GSE29272) were analyzed to identify DEGs between GC and normal tissues. A PPI network was constructed using STRING and Cytoscape, followed by hub gene identification with CytoHubba. Investigations included expression and promoter methylation analysis, survival modeling, mutational and miRNA analysis, gene enrichment, drug prediction, and in vitro assays for cellular behaviors. RESULTS A total of 83 DEGs were identified in the three datasets, comprising 41 up-regulated genes and 42 down-regulated genes. Utilizing the degree and MCC methods, we identified four hub genes that were hypomethylated and up-regulated: COL1A1, COL1A2, COL3A1, and FN1. Subsequent validation of their expression and promoter methylation on clinical GC samples through targeted bisulfite sequencing and RT-qPCR analysis further confirmed the hypomethylation and overexpression of these genes in local GC patients. Furthermore, it was observed that these hub genes regulate tumor proliferation and metastasis in in vivo and exhibited mutations in GC patients. CONCLUSION We found four potential diagnostic and prognostic biomarkers, including COL1A1, COL1A2, COL3A1, and FN1 that may be involved in the occurrence and progression of GC.
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Affiliation(s)
- Xiaofeng Pei
- Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China
| | - Yuanling Luo
- Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China
| | - Huanwen Zeng
- Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China
| | - Muhammad Jamil
- PARC Arid Zone Research Center, Dera Ismail Khan 29050, Pakistan
| | - Xiaodong Liu
- Department of Pharmacy, The 922 Hospital of Joint Logistics Support Force, PLA, Hengyang 421002, China
| | - Bo Jiang
- Department of Emergency, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China
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Yang S, Kim SH, Yang E, Kang M, Joo JY. Molecular insights into regulatory RNAs in the cellular machinery. Exp Mol Med 2024:10.1038/s12276-024-01239-6. [PMID: 38871819 DOI: 10.1038/s12276-024-01239-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 06/15/2024] Open
Abstract
It is apparent that various functional units within the cellular machinery are derived from RNAs. The evolution of sequencing techniques has resulted in significant insights into approaches for transcriptome studies. Organisms utilize RNA to govern cellular systems, and a heterogeneous class of RNAs is involved in regulatory functions. In particular, regulatory RNAs are increasingly recognized to participate in intricately functioning machinery across almost all levels of biological systems. These systems include those mediating chromatin arrangement, transcription, suborganelle stabilization, and posttranscriptional modifications. Any class of RNA exhibiting regulatory activity can be termed a class of regulatory RNA and is typically represented by noncoding RNAs, which constitute a substantial portion of the genome. These RNAs function based on the principle of structural changes through cis and/or trans regulation to facilitate mutual RNA‒RNA, RNA‒DNA, and RNA‒protein interactions. It has not been clearly elucidated whether regulatory RNAs identified through deep sequencing actually function in the anticipated mechanisms. This review addresses the dominant properties of regulatory RNAs at various layers of the cellular machinery and covers regulatory activities, structural dynamics, modifications, associated molecules, and further challenges related to therapeutics and deep learning.
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Affiliation(s)
- Sumin Yang
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Sung-Hyun Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Eunjeong Yang
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Mingon Kang
- Department of Computer Science, University of Nevada, Las Vegas, NV, 89154, USA
| | - Jae-Yeol Joo
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea.
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Xie J, Chen P, Mao S, Zang X, Cao R, Liu W, Wang X, Dai Y. Mir-204-5p alleviates mitochondrial dysfunction by targeting IGFBP5 in diabetic cataract. Mol Biol Rep 2024; 51:755. [PMID: 38874707 DOI: 10.1007/s11033-024-09701-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 06/04/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND Cataract contributes to visual impairment worldwide, and diabetes mellitus accelerates the formation and progression of cataract. Here we found that the expression level of miR-204-5p was diminished in the lens epithelium with anterior lens capsule of cataract patients compared to normal donors, and decreased more obviously in those of diabetic cataract (DC) patients. However, the contribution and mechanism of miR-204-5p during DC development remain elusive. METHODS AND RESULT The mitochondrial membrane potential (MMP) was reduced in the lens epithelium with anterior lens capsule of DC patients and the H2O2-induced human lens epithelial cell (HLEC) cataract model, suggesting impaired mitochondrial functional capacity. Consistently, miR-204-5p knockdown by the specific inhibitor also attenuated the MMP in HLECs. Using bioinformatics and a luciferase assay, further by immunofluorescence staining and Western blot, we identified IGFBP5, an insulin-like growth factor binding protein, as a direct target of miR-204-5p in HLECs. IGFBP5 expression was upregulated in the lens epithelium with anterior lens capsule of DC patients and in the HLEC cataract model, and IGFBP5 knockdown could reverse the mitochondrial dysfunction in the HLEC cataract model. CONCLUSIONS Our results demonstrate that miR-204-5p maintains mitochondrial functional integrity through repressing IGFBP5, and reveal IGFBP5 may be a new therapeutic target and prognostic factor for DC.
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Affiliation(s)
- Jin Xie
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Peng Chen
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Qingdao University, Qingdao, China
- Institute of Stem Cell Regeneration Medicine, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Shilan Mao
- Shandong First Medical University, Jinan, China
- School of Ophthalmology, Shandong First Medical University, Qingdao, China
| | - Xinyi Zang
- Weifang Medical University, Weifang, China
| | - Rui Cao
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Wenhui Liu
- The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaolei Wang
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China.
| | - Yunhai Dai
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China.
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China.
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Dymek A, Oleksy Ł, Stolarczyk A, Bartosiewicz A. Choline-An Underappreciated Component of a Mother-to-Be's Diet. Nutrients 2024; 16:1767. [PMID: 38892700 PMCID: PMC11174651 DOI: 10.3390/nu16111767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/27/2024] [Accepted: 06/02/2024] [Indexed: 06/21/2024] Open
Abstract
The nutritional status of the mother-to-be has a key impact on the proper development of the fetus. Although all nutrients are important for the developing baby, recent research indicates the importance of adequate choline intake during the periconceptional period, pregnancy, and lactation. Choline plays a key role in the biosynthesis of cell membranes, supporting liver function, neurotransmission, brain development, and DNA and histone methylation. Choline participates in the formation of a child's nervous system, supports its cognitive development, and reduces the risk of neural tube defects. The human body is incapable of producing sufficient choline to meet its needs; therefore, it must be obtained from the diet. Current data indicate that most women in their reproductive years do not achieve the recommended daily intake of choline. The presented narrative review indicates the importance of educating mothers-to-be and thereby increasing their awareness of the effects of choline on maternal and child health, which can lead to a more aware and healthy pregnancy and proper child development.
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Affiliation(s)
- Agnieszka Dymek
- Students Scientific Club of Dietetics, Institute of Health Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | - Łukasz Oleksy
- Department of Physiotherapy, Faculty of Health Sciences, Jagiellonian University Medical College, 31-008 Kraków, Poland
| | - Artur Stolarczyk
- Department of Orthopedics and Rehabilitation, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Anna Bartosiewicz
- Institute of Health Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
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Wen B, Zhang Y, He J, Tan L, Xiao G, Wang Z, Cui W, Wu B, Wang X, He L, Li M, Zhu Z, Sang D, Zeng C, Jia P, Liu F, Liu T. Causal impact of DNA methylation on refracture in elderly individuals with osteoporosis - a prospective cohort study. BMC Musculoskelet Disord 2024; 25:432. [PMID: 38831438 PMCID: PMC11149363 DOI: 10.1186/s12891-024-07521-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/13/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND Osteoporotic vertebral compression fractures (OVCF) in the elderly increase refracture risk post-surgery, leading to higher mortality rates. Genome-wide association studies (GWAS) have identified susceptibility genes for osteoporosis, but the phenotypic variance explained by these genes has been limited, indicating the need to explore additional causal factors. Epigenetic modifications, such as DNA methylation, may influence osteoporosis and refracture risk. However, prospective cohorts for assessing epigenetic alterations in Chinese elderly patients are lacking. Here, we propose to conduct a prospective cohort study to investigate the causal network of DNA polymorphisms, DNA methylation, and environmental factors on the development of osteoporosis and the risk of refracture. METHODS We will collect vertebral and peripheral blood from 500 elderly OVCF patients undergoing surgery, extract DNA, and generate whole genome genotype data and DNA methylation data. Observation indicators will be collected and combined with one-year follow-up data. A healthy control group will be selected from a natural population cohort. Epigenome-wide association studies (EWAS) of osteoporosis and bone mineral density will be conducted. Differential methylation analysis will compare candidate gene methylation patterns in patients with and without refracture. Multi-omics prediction models using genetic variants and DNA methylation sites will be built to predict OVCF risk. DISCUSSION This study will be the first large-scale population-based study of osteoporosis and bone mineral density phenotypes based on genome-wide data, multi-time point methylation data, and phenotype data. By analyzing methylation changes related to osteoporosis and bone mineral density in OVCF patients, the study will explore the feasibility of DNA methylation in evaluating postoperative osteoporosis intervention effects. The findings may identify new molecular markers for effective anti-osteoporosis treatment and inform individualized prevention and treatment strategies. TRIAL REGISTRATION chictr.org.cn ChiCTR2200065316, 02/11/2022.
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Affiliation(s)
- Bingtao Wen
- Department of Orthopedics, Peking University International Hospital, Beijing, China
| | - Yaning Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- Institute of Biomedical Research, Henan Academy of Sciences, Zhengzhou, Henan, China
| | - Jianhua He
- Department of Orthopedics, Peking University International Hospital, Beijing, China
| | - Lei Tan
- Department of Orthopedics, Peking University International Hospital, Beijing, China
| | - Guanggui Xiao
- Department of Rehabilitation, the Second Medical Center of Chinese People's Liberation Army General Hospital, Beijing, China
| | - Zunliang Wang
- Beijing University of Posts and Telecommunications, Beijing, China
| | - Wei Cui
- Department of Orthopedics, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Bingxuan Wu
- Department of Orthopedics, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xianhai Wang
- Department of Orthopedics, Changping District Hospital, Beijing, China
| | - Lei He
- Department of Orthopedics, Changping District Hospital, Beijing, China
| | - Ming Li
- Department of Orthopedics, Tengzhou Central People's Hospital, Tengzhou, Shandong, China
| | - Zhongjiao Zhu
- Department of Orthopedics, Tengzhou Central People's Hospital, Tengzhou, Shandong, China
| | - Dacheng Sang
- Department of Orthopaedic Surgery, Yijishan Hospital, The First Affiliated Hospital of Wannan Medical College, Wannan Medical College, Wuhu, Anhui, China
| | - Changqing Zeng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- Institute of Biomedical Research, Henan Academy of Sciences, Zhengzhou, Henan, China
| | - Peilin Jia
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Fan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Tianzi Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China.
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Klokkaris A, Migdalska-Richards A. An Overview of Epigenetic Changes in the Parkinson's Disease Brain. Int J Mol Sci 2024; 25:6168. [PMID: 38892355 PMCID: PMC11172855 DOI: 10.3390/ijms25116168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Parkinson's disease is a progressive neurodegenerative disorder, predominantly of the motor system. Although some genetic components and cellular mechanisms of Parkinson's have been identified, much is still unknown. In recent years, emerging evidence has indicated that non-DNA-sequence variation (in particular epigenetic mechanisms) is likely to play a crucial role in the development and progression of the disease. Here, we present an up-to-date overview of epigenetic processes including DNA methylation, DNA hydroxymethylation, histone modifications and non-coding RNAs implicated in the brain of those with Parkinson's disease. We will also discuss the limitations of current epigenetic research in Parkinson's disease, the advantages of simultaneously studying genetics and epigenetics, and putative novel epigenetic therapies.
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Affiliation(s)
| | - Anna Migdalska-Richards
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK;
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Chen J, Wang Y, Dai W, Xu X, Ni Q, Yi X, Kang P, Ma J, Wu L, Li C, Li S. Oxidative stress-induced hypermethylation and low expression of ANXA2R: Novel insights into the dysfunction of melanocytes in vitiligo. J Dermatol Sci 2024; 114:115-123. [PMID: 38806323 DOI: 10.1016/j.jdermsci.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 01/30/2024] [Accepted: 02/27/2024] [Indexed: 05/30/2024]
Abstract
BACKGROUND Vitiligo is a skin disorder with melanocyte destruction caused by complex interplay between multiple genetic and environmental factors. Recent studies have suggested DNA methylation is involved in the melanocyte damage, but the underlying mechanism remains unknown. OBJECTIVE To explore the abnormal DNA methylation patterns in vitiligo lesional and nonlesional skin, and the mechanism of DNA methylation involved in vitiligo pathogenesis. METHODS Initially, the genome-wide aberrant DNA methylation profiles in lesional and nonlesional skin of vitiligo were detect via Illumina methylation EPIC 850k Beadchip. Subsequently, a comprehensive analysis was conduct to investigate the genomic characteristics of differentially methylated regions (DMRs). Furthermore, the effects of key aberrant methylated genes on cell apoptosis and function of both melanocytes and keratinocytes were further identified and validated by western bloting, ELISA, and immunofluorescence. RESULTS Compared with nonlesional skins, we discovered 79 significantly differentially methylated CpG sites in vitiligo lesions. These DMRs were mainly located in the gene body and the TS1500 region. Annexin A2 receptor (ANXA2R), a crucial gene in cell apoptosis, was hypermethylated in vitiligo lesions. Furthermore, we showed that ANXA2R displayed hypermethylation and low expression levels in both keratinocytes and melanocytes of vitiligo patients, and the hypermethylated-triggered downregulation of ANXA2R under oxidative stress induced melanocyte apoptosis, and inhibited the secretion of stem cell factor (SCF) from keratinocytes thus impaired the survival of melanocytes. CONCLUSIONS Our study illustrates the DNA methylation modification in vitiligo, and further demonstrates the molecular mechanism of hypermethylated ANXA2R in the dysfunction of melanocytes under oxidative stress.
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Affiliation(s)
- Jiaxi Chen
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China
| | - Yinghan Wang
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China
| | - Wei Dai
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China
| | - Xinyuan Xu
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China
| | - Qingrong Ni
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China
| | - Xiuli Yi
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China
| | - Pan Kang
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China
| | - Jingjing Ma
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China
| | - Lili Wu
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China
| | - Chunying Li
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China.
| | - Shuli Li
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China.
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Lutfi H, Kirsch-Mangu TK, Fletcher-King NM, Ruden DM, Diamond MP, Saed GM. Epigenetics: new insights into postoperative adhesion development. Minerva Obstet Gynecol 2024; 76:231-237. [PMID: 36222785 DOI: 10.23736/s2724-606x.22.05158-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
BACKGROUND The link between post-operative adhesion development and epigenetic modifications is important in understanding the mechanism behind their formation. The aim of this study was to determine whether epigenetic differences exist between primary fibroblasts of normal peritoneum and adhesion tissues isolated from the same patient(s). METHODS DNA from fibroblasts isolated from normal peritoneum and adhesion tissues was isolated using Qiagen's EZ1 Advanced Kit. Methylation patterns of genes were quantified and compared in both cell lines using the Infinium Human Methylation 27 BeadChip® system (Illumina, San Diego, CA, USA). RESULTS A total of 7364 genes had been found to manifest significantly different DNA methylation levels in adhesion fibroblasts as compared to normal peritoneal fibroblasts (P<0.01). A total of 1685 genes were found to have increased DNA methylation by 50% in adhesion compared to peritoneal fibroblasts, and were enriched in gene ontology categories, glycoprotein, and defense response. Furthermore, 1287 genes were found to have decreased DNA methylation patterns with enriched gene ontology categories, "homeobox," and transcription factor activity in adhesion fibroblasts. CONCLUSIONS Epigenetic differences in fibroblasts isolated from normal peritoneum and adhesion tissues were observed. Future studies focusing on the precise role of these genes in the development of postoperative adhesions will allow us to more fully appreciate regulatory mechanisms leading to adhesion development, thereby establishing targets for therapeutic interventions to prevent or limit adhesion development.
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Affiliation(s)
- Hala Lutfi
- School of Medicine, Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, The C.S. Mott Center for Human Growth and Development, Wayne State University, Detroit, MI, USA
| | - Thea K Kirsch-Mangu
- School of Medicine, Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, The C.S. Mott Center for Human Growth and Development, Wayne State University, Detroit, MI, USA
| | - Nicole M Fletcher-King
- School of Medicine, Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, The C.S. Mott Center for Human Growth and Development, Wayne State University, Detroit, MI, USA
| | - Douglas M Ruden
- School of Medicine, Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, The C.S. Mott Center for Human Growth and Development, Wayne State University, Detroit, MI, USA
| | - Michael P Diamond
- Department of Obstetrics and Gynecology, Medical College of Georgia Augusta University, Augusta, GA, USA
| | - Ghassan M Saed
- School of Medicine, Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, The C.S. Mott Center for Human Growth and Development, Wayne State University, Detroit, MI, USA -
- Karmanos Cancer Center, Detroit, MI, USA
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Wang Y, Liu Q, Deng L, Ma X, Gong Y, Wang Y, Zhou F. The roles of epigenetic regulation in graft-versus-host disease. Biomed Pharmacother 2024; 175:116652. [PMID: 38692061 DOI: 10.1016/j.biopha.2024.116652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/18/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024] Open
Abstract
Allogeneic hematopoietic stem cell transplantation (aHSCT) is utilized as a potential curative treatment for various hematologic malignancies. However, graft-versus-host disease (GVHD) post-aHSCT is a severe complication that significantly impacts patients' quality of life and overall survival, becoming a major cause of non-relapse mortality. In recent years, the association between epigenetics and GVHD has garnered increasing attention. Epigenetics focuses on studying mechanisms that affect gene expression without altering DNA sequences, primarily including DNA methylation, histone modifications, non-coding RNAs (ncRNAs) regulation, and RNA modifications. This review summarizes the role of epigenetic regulation in the pathogenesis of GVHD, with a focus on DNA methylation, histone modifications, ncRNA, RNA modifications and their involvement and applications in the occurrence and development of GVHD. It also highlights advancements in relevant diagnostic markers and drugs, aiming to provide new insights for the clinical diagnosis and treatment of GVHD.
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Affiliation(s)
- Yimin Wang
- The First Clinical Medical School, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Qi Liu
- The First Clinical Medical School, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Lei Deng
- Department of Hematology, the 960th Hospital of the People's Liberation Army Joint Logistics Support Force, Jinan, China
| | - Xiting Ma
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Yuling Gong
- Department of Cardiovascular, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yifei Wang
- Department of Cardiovascular, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China.
| | - Fang Zhou
- Department of Hematology, the 960th Hospital of the People's Liberation Army Joint Logistics Support Force, Jinan, China.
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11
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Gao S, Song H. Differences between psoriatic arthritis and psoriasis in multi-omics. Arch Dermatol Res 2024; 316:217. [PMID: 38787526 DOI: 10.1007/s00403-024-03018-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 04/08/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024]
Abstract
We aim to systemically review the genomics, transcriptomics, epigenetics, proteomics, metabonomics and microbiota of psoriatic arthritis and psoriasis, illustrating the differences of these two diseases, broadening our understanding of the pathogenesis of them and providing important clues for valuable biomarkers of earlier diagnosis and treatments. To our knowledge, this is the first study that combine all omics studies from genomics to microbiota and may serve as a reference for future studies to identify the key underlying pathways in psoriatic arthritis.
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Affiliation(s)
- Siming Gao
- Department of Rheumatology, Beijing Jishuitan Hospital, Guizhou Hospital, Guiyang, China
- Department of Rheumatology, Beijing Jishuitan Hospital, Capital Medical University, No.31, Xin Jie Kou East Street, Xicheng District, Beijing, 100035, China
| | - Hui Song
- Department of Rheumatology, Beijing Jishuitan Hospital, Capital Medical University, No.31, Xin Jie Kou East Street, Xicheng District, Beijing, 100035, China.
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Jiao P, Lu H, Hao L, Degen AA, Cheng J, Yin Z, Mao S, Xue Y. Nutrigenetic and Epigenetic Mechanisms of Maternal Nutrition-Induced Glucolipid Metabolism Changes in the Offspring. Nutr Rev 2024:nuae048. [PMID: 38781288 DOI: 10.1093/nutrit/nuae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024] Open
Abstract
Maternal nutrition during pregnancy regulates the offspring's metabolic homeostasis, including insulin sensitivity and the metabolism of glucose and lipids. The fetus undergoes a crucial period of plasticity in the uterus; metabolic changes in the fetus during pregnancy caused by maternal nutrition not only influence fetal growth and development but also have a long-term or even life-long impact for the offspring. Epigenetic modifications, such as DNA methylation, histone modification, and non-coding RNAs, play important roles in intergenerational and transgenerational effects. In this context, this narrative review comprehensively summarizes and analyzes the molecular mechanisms underlying how maternal nutrition, including a high-fat diet, polyunsaturated fatty acid diet, methyl donor nutrient supplementation, feed restriction, and protein restriction during pregnancy, impacts the genes involved in glucolipid metabolism in the liver, adipose tissue, hypothalamus, muscle, and oocytes of the offspring in terms of the epigenetic modifications. This will provide a foundation for the further exploration of nutrigenetic and epigenetic mechanisms for integrative mother-child nutrition and promotion of the offspring's health through the regulation of maternal nutrition during pregnancy. Note: This paper is part of the Nutrition Reviews Special Collection on Precision Nutrition.
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Affiliation(s)
- Peng Jiao
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Huizhen Lu
- Biotechnology Center, Anhui Agricultural University, Hefei, China
| | - Lizhuang Hao
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Plateau Yak Research Center, Qinghai Academy of Science and Veterinary Medicine of Qinghai University, Xining, China
| | - A Allan Degen
- Desert Animal Adaptations and Husbandry, Wyler Department of Dryland Agriculture, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Jianbo Cheng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Shengyong Mao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yanfeng Xue
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
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Yang M, Kaarbø M, Myhre V, Reims HM, Karlsen TH, Wang J, Rognes T, Halvorsen B, Fevang B, Lundin KEA, Aukrust P, Bjørås M, Jørgensen SF. Altered Genome-Wide DNA Methylation in the Duodenum of Common Variable Immunodeficiency Patients. J Clin Immunol 2024; 44:133. [PMID: 38780872 PMCID: PMC11116262 DOI: 10.1007/s10875-024-01726-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
PURPOSE A large proportion of Common variable immunodeficiency (CVID) patients has duodenal inflammation with increased intraepithelial lymphocytes (IEL) of unknown aetiology. The histologic similarities to celiac disease, lead to confusion regarding treatment (gluten-free diet) of these patients. We aimed to elucidate the role of epigenetic DNA methylation in the aetiology of duodenal inflammation in CVID and differentiate it from true celiac disease. METHODS DNA was isolated from snap-frozen pieces of duodenal biopsies and analysed for differences in genome-wide epigenetic DNA methylation between CVID patients with increased IEL (CVID_IEL; n = 5) without IEL (CVID_N; n = 3), celiac disease (n = 3) and healthy controls (n = 3). RESULTS The DNA methylation data of 5-methylcytosine in CpG sites separated CVID and celiac diseases from healthy controls. Differential methylation in promoters of genes were identified as potential novel mediators in CVID and celiac disease. There was limited overlap of methylation associated genes between CVID_IEL and Celiac disease. High frequency of differentially methylated CpG sites was detected in over 100 genes nearby transcription start site (TSS) in both CVID_IEL and celiac disease, compared to healthy controls. Differential methylation of genes involved in regulation of TNF/cytokine production were enriched in CVID_IEL, compared to healthy controls. CONCLUSION This is the first study to reveal a role of epigenetic DNA methylation in the etiology of duodenal inflammation of CVID patients, distinguishing CVID_IEL from celiac disease. We identified potential biomarkers and therapeutic targets within gene promotors and in high-frequency differentially methylated CpG regions proximal to TSS in both CVID_IEL and celiac disease.
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Affiliation(s)
- Mingyi Yang
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Medical Biochemistry, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Mari Kaarbø
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Vegard Myhre
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Henrik M Reims
- Department of Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Tom H Karlsen
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Junbai Wang
- Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital and University of Oslo, Lørenskog, Norway
| | - Torbjørn Rognes
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Bente Halvorsen
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Børre Fevang
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Knut E A Lundin
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Pål Aukrust
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
- The Proteomics and Modomics Experimental Core Facility (PROMEC) at Norwegian University of Science and Technology, Trondheim, Norway
| | - Silje F Jørgensen
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway.
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
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Viana Filho JMC, Castro Coêlho MD, Queiroz Neto JND, Souza BFD, Valença AMG, Oliveira NFPD. TNF-α promoter hypomethylation is frequent in oncopediatric patients who recovered from mucositis. Braz Oral Res 2024; 38:e042. [PMID: 38747829 DOI: 10.1590/1807-3107bor-2024.vol38.0042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/20/2023] [Indexed: 06/15/2024] Open
Abstract
The aim of this study was to investigate the DNA methylation profile in genes encoding catalase (CAT) and superoxide dismutase (SOD3) enzymes, which are involved in oxidative stress mechanisms, and in genes encoding pro-inflammatory cytokines interleukin-6 (IL6) and tumor necrosis factor-alpha (TNF-α) in the oral mucosa of oncopediatric patients treated with methotrexate (MTX®). This was a cross-sectional observational study and the population comprised healthy dental patients (n = 21) and those with hematological malignancies (n = 64) aged between 5 and 19 years. Oral conditions were evaluated using the Oral Assessment Guide and participants were divided into 4 groups: 1- healthy individuals; 2- oncopediatric patients without mucositis; 3- oncopediatric patients with mucositis; 4- oncopediatric patients who had recovered from mucositis. Methylation of DNA from oral mucosal cells was evaluated using the Methylation-Specific PCR technique (MSP). For CAT, the partially methylated profile was the most frequent and for SOD3 and IL6, the hypermethylated profile was the most frequent, with no differences between groups. For TNF-α, the hypomethylated profile was more frequent in the group of patients who had recovered from mucositis. It was concluded that the methylation profiles of CAT, SOD3, and IL6 are common profiles for oral cells of children and adolescents and have no association with oral mucositis or exposure to chemotherapy with MTX®. Hypomethylation of TNF-α is associated with oral mucosal recovery in oncopediatric patients who developed oral mucositis during chemotherapy.
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Affiliation(s)
- José Maria Chagas Viana Filho
- Universidade Federal da Paraíba - UFPB, Centro de Ciências da Saúde, Programa de Pós Graduação em Odontologia, João Pessoa, PB, Brasil
| | - Marina de Castro Coêlho
- Universidade Federal da Paraíba - UFPB, Centro de Ciências da Saúde, Programa de Pós Graduação em Odontologia, João Pessoa, PB, Brasil
| | - José Nunes de Queiroz Neto
- Universidade Federal da Paraíba - UFPB, Centro de Ciências Exatas e da Natureza, Departamento de Biologia Molecular, João Pessoa, PB, Brasil
| | - Beatriz Fernandes de Souza
- Universidade Federal da Paraíba - UFPB, Centro de Ciências da Saúde, Programa de Pós Graduação em Odontologia, João Pessoa, PB, Brasil
| | - Ana Maria Gondim Valença
- Universidade Federal da Paraíba - UFPB, Centro de Ciências da Saúde, Programa de Pós Graduação em Odontologia, João Pessoa, PB, Brasil
| | - Naila Francis Paulo de Oliveira
- Universidade Federal da Paraíba - UFPB, Centro de Ciências da Saúde, Programa de Pós Graduação em Odontologia, João Pessoa, PB, Brasil
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Verma C, Jain K, Saini A, Mani I, Singh V. Exploring the potential of drug repurposing for treating depression. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 207:79-105. [PMID: 38942546 DOI: 10.1016/bs.pmbts.2024.03.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Researchers are interested in drug repurposing or drug repositioning of existing pharmaceuticals because of rising costs and slower rates of new medication development. Other investigations that authorized these treatments used data from experimental research and off-label drug use. More research into the causes of depression could lead to more effective pharmaceutical repurposing efforts. In addition to the loss of neurotransmitters like serotonin and adrenaline, inflammation, inadequate blood flow, and neurotoxins are now thought to be plausible mechanisms. Because of these other mechanisms, repurposing drugs has resulted for treatment-resistant depression. This chapter focuses on therapeutic alternatives and their effectiveness in drug repositioning. Atypical antipsychotics, central nervous system stimulants, and neurotransmitter antagonists have investigated for possible repurposing. Nonetheless, extensive research is required to ensure their formulation, effectiveness, and regulatory compliance.
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Affiliation(s)
- Chaitenya Verma
- Department of Pathology, Ohio State University, Columbus, OH, United States
| | - Kritika Jain
- Department of Microbiology, Institute of Home Economics, University of Delhi, New Delhi, India
| | - Ashok Saini
- Department of Microbiology, Institute of Home Economics, University of Delhi, New Delhi, India
| | - Indra Mani
- Department of Microbiology, Gargi College, University of Delhi, New Delhi, India.
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, India.
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de Oliveira Melo NC, Cuevas-Sierra A, Souto VF, Martínez JA. Biological Rhythms, Chrono-Nutrition, and Gut Microbiota: Epigenomics Insights for Precision Nutrition and Metabolic Health. Biomolecules 2024; 14:559. [PMID: 38785965 PMCID: PMC11117887 DOI: 10.3390/biom14050559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Circadian rhythms integrate a finely tuned network of biological processes recurring every 24 h, intricately coordinating the machinery of all cells. This self-regulating system plays a pivotal role in synchronizing physiological and behavioral responses, ensuring an adaptive metabolism within the environmental milieu, including dietary and physical activity habits. The systemic integration of circadian homeostasis involves a balance of biological rhythms, each synchronically linked to the central circadian clock. Central to this orchestration is the temporal dimension of nutrient and food intake, an aspect closely interwoven with the neuroendocrine circuit, gut physiology, and resident microbiota. Indeed, the timing of meals exerts a profound influence on cell cycle regulation through genomic and epigenetic processes, particularly those involving gene expression, DNA methylation and repair, and non-coding RNA activity. These (epi)genomic interactions involve a dynamic interface between circadian rhythms, nutrition, and the gut microbiota, shaping the metabolic and immune landscape of the host. This research endeavors to illustrate the intricate (epi)genetic interplay that modulates the synchronization of circadian rhythms, nutritional signaling, and the gut microbiota, unravelling the repercussions on metabolic health while suggesting the potential benefits of feed circadian realignment as a non-invasive therapeutic strategy for systemic metabolic modulation via gut microbiota. This exploration delves into the interconnections that underscore the significance of temporal eating patterns, offering insights regarding circadian rhythms, gut microbiota, and chrono-nutrition interactions with (epi)genomic phenomena, thereby influencing diverse aspects of metabolic, well-being, and quality of life outcomes.
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Affiliation(s)
| | - Amanda Cuevas-Sierra
- Precision Nutrition Program, Research Institute on Food and Health Sciences IMDEA Food, CSIC-UAM, 28049 Madrid, Spain;
| | - Vitória Felício Souto
- Department of Nutrition at the Federal University of Pernambuco, Recife 50670-901, PE, Brazil; (N.C.d.O.M.); (V.F.S.)
| | - J. Alfredo Martínez
- Precision Nutrition Program, Research Institute on Food and Health Sciences IMDEA Food, CSIC-UAM, 28049 Madrid, Spain;
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Centre of Medicine and Endocrinology, University of Valladolid, 47002 Valladolid, Spain
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17
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Gerra MC, Dallabona C, Cecchi R. Epigenetic analyses in forensic medicine: future and challenges. Int J Legal Med 2024; 138:701-719. [PMID: 38242965 PMCID: PMC11003920 DOI: 10.1007/s00414-024-03165-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 01/09/2024] [Indexed: 01/21/2024]
Abstract
The possibility of using epigenetics in forensic investigation has gradually risen over the last few years. Epigenetic changes with their dynamic nature can either be inherited or accumulated throughout a lifetime and be reversible, prompting investigation of their use across various fields. In forensic sciences, multiple applications have been proposed, such as the discrimination of monozygotic twins, identifying the source of a biological trace left at a crime scene, age prediction, determination of body fluids and tissues, human behavior association, wound healing progression, and determination of the post-mortem interval (PMI). Despite all these applications, not all the studies considered the impact of PMI and post-sampling effects on the epigenetic modifications and the tissue-specificity of the epigenetic marks.This review aims to highlight the substantial forensic significance that epigenetics could support in various forensic investigations. First, basic concepts in epigenetics, describing the main epigenetic modifications and their functions, in particular, DNA methylation, histone modifications, and non-coding RNA, with a particular focus on forensic applications, were covered. For each epigenetic marker, post-mortem stability and tissue-specificity, factors that should be carefully considered in the study of epigenetic biomarkers in the forensic context, have been discussed. The advantages and limitations of using post-mortem tissues have been also addressed, proposing directions for these innovative strategies to analyze forensic specimens.
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Affiliation(s)
- Maria Carla Gerra
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 11a, Viale Delle Scienze 11a, 43124, Parma, PR, Italy
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 11a, Viale Delle Scienze 11a, 43124, Parma, PR, Italy.
| | - Rossana Cecchi
- Department of Medicine and Surgery, University of Parma, Via Antonio Gramsci 14, 43126, Parma, PR, Italy
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18
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Rey F, Esposito L, Maghraby E, Mauri A, Berardo C, Bonaventura E, Tonduti D, Carelli S, Cereda C. Role of epigenetics and alterations in RNA metabolism in leukodystrophies. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1854. [PMID: 38831585 DOI: 10.1002/wrna.1854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 06/05/2024]
Abstract
Leukodystrophies are a class of rare heterogeneous disorders which affect the white matter of the brain, ultimately leading to a disruption in brain development and a damaging effect on cognitive, motor and social-communicative development. These disorders present a great clinical heterogeneity, along with a phenotypic overlap and this could be partially due to contributions from environmental stimuli. It is in this context that there is a great need to investigate what other factors may contribute to both disease insurgence and phenotypical heterogeneity, and novel evidence are raising the attention toward the study of epigenetics and transcription mechanisms that can influence the disease phenotype beyond genetics. Modulation in the epigenetics machinery including histone modifications, DNA methylation and non-coding RNAs dysregulation, could be crucial players in the development of these disorders, and moreover an aberrant RNA maturation process has been linked to leukodystrophies. Here, we provide an overview of these mechanisms hoping to supply a closer step toward the analysis of leukodystrophies not only as genetically determined but also with an added level of complexity where epigenetic dysregulation is of key relevance. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNA RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Federica Rey
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Letizia Esposito
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Erika Maghraby
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
- Department of Biology and Biotechnology "L. Spallanzani" (DBB), University of Pavia, Pavia, Italy
| | - Alessia Mauri
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Clarissa Berardo
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Eleonora Bonaventura
- Unit of Pediatric Neurology, COALA Center for Diagnosis and Treatment of Leukodystrophies, V. Buzzi Children's Hospital, Milan, Italy
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Davide Tonduti
- Unit of Pediatric Neurology, COALA Center for Diagnosis and Treatment of Leukodystrophies, V. Buzzi Children's Hospital, Milan, Italy
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Stephana Carelli
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Cristina Cereda
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
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Kim SE, Lee J. Children's health affected by parent's behavioral characteristics: a review. Clin Exp Pediatr 2024; 67:232-239. [PMID: 37605537 PMCID: PMC11065636 DOI: 10.3345/cep.2023.00115] [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: 01/18/2023] [Revised: 04/19/2023] [Accepted: 07/19/2023] [Indexed: 08/23/2023] Open
Abstract
Exposure of an individual to occupational and environmental risk factors for a certain disease affects them and their family. Children are highly vulnerable in this setting because they are family-dependent. This review discusses diseases that occur in children according to the occupational and behavioral characteristics of their parents. Toxic agents in the home environment can affect children's health. Maternal exposure to substances during pregnancy may directly affect fetal outcomes. The Industrial Accident Compensation Insurance Act in Korea was amended in 2023 to compensate for children's adverse health effects due to their parents' occupational risks. The long working hours and smoking behaviors of parents and toxic materials in the home environment are highlighted. To control for the diverse factors affecting children's health in medical research, this review introduces directed acyclic graphs. Pediatric, occupational, and environmental medicine must collaborate to prevent childhood diseases related to environmental factors.
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Affiliation(s)
- Sung Eun Kim
- Department of Pediatrics, College of Medicine, Incheon St. Mary’s Hospital, The Catholic University of Korea, Seoul Korea
| | - Jongin Lee
- Department of Occupational and Environmental Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Zhuang S, Yang Z, Cui Z, Zhang Y, Che F. Epigenetic alterations and advancement of lymphoma treatment. Ann Hematol 2024; 103:1435-1454. [PMID: 37581713 DOI: 10.1007/s00277-023-05395-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/29/2023] [Indexed: 08/16/2023]
Abstract
Lymphomas, complex and heterogeneous malignant tumors, originate from the lymphopoietic system. These tumors are notorious for their high recurrence rates and resistance to treatment, which leads to poor prognoses. As ongoing research has shown, epigenetic modifications like DNA methylation, histone modifications, non-coding RNA regulation, and RNA modifications play crucial roles in lymphoma pathogenesis. Epigenetic modification-targeting drugs have exhibited therapeutic efficacy and tolerability in both monotherapy and combination lymphoma therapy. This review discusses pathogenic mechanisms and potential epigenetic therapeutic targets in common lymphomas, offering new avenues for lymphoma diagnosis and treatment. We also discuss the shortcomings of current lymphoma treatments, while suggesting potential areas for future research, in order to improve the prediction and prognosis of lymphoma.
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Affiliation(s)
- Shuhui Zhuang
- Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang, China
- Department of Hematology, Linyi People's Hospital, Shandong University, Linyi, 276000, Shandong, China
| | - Zhaobo Yang
- Spine Surgery, Linyi People's Hospital, Shandong University, Linyi, 276000, Shandong, China
| | - Zhuangzhuang Cui
- Department of Hematology, Linyi People's Hospital, Shandong University, Linyi, 276000, Shandong, China
| | - Yuanyuan Zhang
- Department of Hematology, Linyi People's Hospital, Shandong University, Linyi, 276000, Shandong, China.
- Department of Hematology, Shandong Key Laboratory of Immunohematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, People's Republic of China.
| | - Fengyuan Che
- Department of Neurology, Central Laboratory and Key Laboratory of Neurophysiology, Linyi People's Hospital, Shandong University, Linyi, 276000, China.
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Sui J, Guo J, Pan D, Wang Y, Xu Y, Sun G, Xia H. The Efficacy of Dietary Intake, Supplementation, and Blood Concentrations of Carotenoids in Cancer Prevention: Insights from an Umbrella Meta-Analysis. Foods 2024; 13:1321. [PMID: 38731692 PMCID: PMC11083701 DOI: 10.3390/foods13091321] [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: 04/07/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
Previous meta-analyses of multiple studies have suggested that dietary intake and blood concentrations of carotenoids, as well as dietary supplement of certain carotenoids, play a role in reducing the risk of cancer. However, the conclusions of these studies have been subject to controversy. We conducted an umbrella review of meta-analyses to comprehensively analyze and evaluate the evidence pertaining the association between carotenoids and cancer outcomes. We searched PubMed, Web of Science, Embase, and Cochrane Library databases of meta-analyses and systematic reviews up to June 2023. Our selection criteria encompassed meta-analyses of cohort and case-control studies, as well as randomized controlled clinical trials, which investigated the associations between carotenoids and cancer risk. We also determined the levels of evidence for these associations with AMSTAR 2 criteria. We included 51 eligible articles, including 198 meta-analyses for qualitative synthesis in the umbrella review. Despite the presence of moderate to high heterogeneity among the studies, dietary intake, supplementation, and blood concentrations of carotenoids were inversely associated with the risk of total cancer, and certain specific cancers of lung, digestive system, prostate, breast, head and neck, and others. Subgroup analysis also showed that individual carotenoids (α-carotene, β-carotene, β-cryptoxanthin, lutein, zeaxanthin, and lycopene) offer certain protection against specific types of cancers. However, high doses of carotenoid supplements, especially β-carotene, significantly increased the risk of total cancer, lung cancer, and bladder cancer. Our umbrella meta-analysis supported that high intake of dietary carotenoids as a whole food approach could be more beneficial in reducing cancer risk. Concurrently, the findings suggest that the efficacy of single-carotenoid supplementation in cancer prevention remains a subject of controversy.
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Affiliation(s)
- Jing Sui
- Research Institute for Environment and Health, Nanjing University of Information Science and Technology, Nanjing 210044, China; (J.S.); (J.G.); (Y.X.)
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China; (D.P.); (Y.W.); (G.S.)
| | - Jingwen Guo
- Research Institute for Environment and Health, Nanjing University of Information Science and Technology, Nanjing 210044, China; (J.S.); (J.G.); (Y.X.)
| | - Da Pan
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China; (D.P.); (Y.W.); (G.S.)
| | - Ying Wang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China; (D.P.); (Y.W.); (G.S.)
| | - Ying Xu
- Research Institute for Environment and Health, Nanjing University of Information Science and Technology, Nanjing 210044, China; (J.S.); (J.G.); (Y.X.)
| | - Guiju Sun
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China; (D.P.); (Y.W.); (G.S.)
| | - Hui Xia
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China; (D.P.); (Y.W.); (G.S.)
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Liu Y, Qin Y, Zhang Y. circRNA-PTPN4 mediated regulation of FOXO3 and ZO-1 expression: implications for blood-brain barrier integrity and cognitive function in uremic encephalopathy. Cell Biol Toxicol 2024; 40:22. [PMID: 38630149 PMCID: PMC11024022 DOI: 10.1007/s10565-024-09865-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 03/25/2024] [Indexed: 04/19/2024]
Abstract
Uremic encephalopathy (UE) poses a significant challenge in neurology, leading to the need to investigate the involvement of non-coding RNA (ncRNA) in its development. This study employed ncRNA-seq and RNA-seq approaches to identify fundamental ncRNAs, specifically circRNA and miRNA, in the pathogenesis of UE using a mouse model. In vitro and in vivo experiments were conducted to explore the circRNA-PTPN4/miR-301a-3p/FOXO3 axis and its effects on blood-brain barrier (BBB) function and cognitive abilities. The research revealed that circRNA-PTPN4 binds to and inhibits miR-301a-3p, leading to an increase in FOXO3 expression. This upregulation results in alterations in the transcriptional regulation of ZO-1, affecting the permeability of human brain microvascular endothelial cells (HBMECs). The axis also influences the growth, proliferation, and migration of HBMECs. Mice with UE exhibited cognitive deficits, which were reversed by overexpression of circRNA-PTPN4, whereas silencing FOXO3 exacerbated these deficits. Furthermore, the uremic mice showed neuronal loss, inflammation, and dysfunction in the BBB, with the expression of circRNA-PTPN4 demonstrating therapeutic effects. In conclusion, circRNA-PTPN4 plays a role in promoting FOXO3 expression by sequestering miR-301a-3p, ultimately leading to the upregulation of ZO-1 expression and restoration of BBB function in mice with UE. This process contributes to the restoration of cognitive abilities.
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Affiliation(s)
- Yuhan Liu
- Department of Nephrology, General Hospital of the Northern Theatre, No. 83, Wenhua Road, Shenhe District, Shenyang, 110000, Liaoning Province, People's Republic of China
| | - Yanling Qin
- Department of Nephrology, General Hospital of the Northern Theatre, No. 83, Wenhua Road, Shenhe District, Shenyang, 110000, Liaoning Province, People's Republic of China
| | - Yanning Zhang
- Department of Nephrology, General Hospital of the Northern Theatre, No. 83, Wenhua Road, Shenhe District, Shenyang, 110000, Liaoning Province, People's Republic of China.
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23
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Ducellier S, Demeules M, Letribot B, Gaetani M, Michaudel C, Sokol H, Hamze A, Alami M, Nascimento M, Apcher S. Dual molecule targeting HDAC6 leads to intratumoral CD4+ cytotoxic lymphocytes recruitment through MHC-II upregulation on lung cancer cells. J Immunother Cancer 2024; 12:e007588. [PMID: 38609101 PMCID: PMC11015306 DOI: 10.1136/jitc-2023-007588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Despite the current therapeutic treatments including surgery, chemotherapy, radiotherapy and more recently immunotherapy, the mortality rate of lung cancer stays high. Regarding lung cancer, epigenetic modifications altering cell cycle, angiogenesis and programmed cancer cell death are therapeutic targets to combine with immunotherapy to improve treatment success. In a recent study, we uncovered that a molecule called QAPHA ((E)-3-(5-((2-cyanoquinolin-4-yl)(methyl)amino)-2-methoxyphenyl)-N-hydroxyacrylamide) has a dual function as both a tubulin polymerization and HDAC inhibitors. Here, we investigate the impact of this novel dual inhibitor on the immune response to lung cancer. METHODS To elucidate the mechanism of action of QAPHA, we conducted a chemical proteomics analysis. Using an in vivo mouse model of lung cancer (TC-1 tumor cells), we assessed the effects of QAPHA on tumor regression. Tumor infiltrating immune cells were characterized by flow cytometry. RESULTS In this study, we first showed that QAPHA effectively inhibited histone deacetylase 6, leading to upregulation of HSP90, cytochrome C and caspases, as revealed by proteomic analysis. We confirmed that QAPHA induces immunogenic cell death (ICD) by expressing calreticulin at cell surface in vitro and demonstrated its efficacy as a vaccine in vivo. Remarkably, even at a low concentration (0.5 mg/kg), QAPHA achieved complete tumor regression in approximately 60% of mice treated intratumorally, establishing a long-lasting anticancer immune response. Additionally, QAPHA treatment promoted the infiltration of M1-polarized macrophages in treated mice, indicating the induction of a pro-inflammatory environment within the tumor. Very interestingly, our findings also revealed that QAPHA upregulated major histocompatibility complex class II (MHC-II) expression on TC-1 tumor cells both in vitro and in vivo, facilitating the recruitment of cytotoxic CD4+T cells (CD4+CTL) expressing CD4+, NKG2D+, CRTAM+, and Perforin+. Finally, we showed that tumor regression strongly correlates to MHC-II expression level on tumor cell and CD4+ CTL infiltrate. CONCLUSION Collectively, our findings shed light on the discovery of a new multitarget inhibitor able to induce ICD and MHC-II upregulation in TC-1 tumor cell. These two processes participate in enhancing a specific CD4+ cytotoxic T cell-mediated antitumor response in vivo in our model of lung cancer. This breakthrough suggests the potential of QAPHA as a promising agent for cancer treatment.
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Affiliation(s)
- Sarah Ducellier
- UMR 1015 Immunologie des tumeurs et immunothérapie contre le cancer, B2M, Gustave Roussy, Villejuif, France
| | - Mélanie Demeules
- UMR 1015 Immunologie des tumeurs et immunothérapie contre le cancer, B2M, Gustave Roussy, Villejuif, France
| | | | - Massimiliano Gaetani
- Chemical Proteomics Core Facility, Division of Chemistry I Department of Medical Biochemistry andBiophysics, Karolinska Institute, Stockholm, Sweden
- Chemical Proteomics Unit, Science for Life Laboratory (SciLifeLab), Stockholm, Sweden
- Chemical Proteomics, Swedish National Infrastructure for Biological Mass Spectrometry (BioMS), Stockholm, Sweden
| | - Chloé Michaudel
- AgroParisTech Micalis institute, INRAe Université Paris-Saclay, Jouy-en-Josas, France
| | - Harry Sokol
- Gastroenterology Department, Centre de Recherche Saint-Antoine Sorbonne Université, INSERM CRSA, AP-HP, Paris, France
- Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France
| | | | - Mouad Alami
- BioCIS, CNRS Université Paris-Saclay, Orsay, France
| | - Mégane Nascimento
- UMR 1015 Immunologie des tumeurs et immunothérapie contre le cancer, B2M, Gustave Roussy, Villejuif, France
| | - Sébastien Apcher
- UMR 1015 Immunologie des tumeurs et immunothérapie contre le cancer, B2M, Gustave Roussy, Villejuif, France
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24
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Zhang S, Yu Q, Li Z, Zhao Y, Sun Y. Protein neddylation and its role in health and diseases. Signal Transduct Target Ther 2024; 9:85. [PMID: 38575611 PMCID: PMC10995212 DOI: 10.1038/s41392-024-01800-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/22/2024] [Accepted: 03/04/2024] [Indexed: 04/06/2024] Open
Abstract
NEDD8 (Neural precursor cell expressed developmentally downregulated protein 8) is an ubiquitin-like protein that is covalently attached to a lysine residue of a protein substrate through a process known as neddylation, catalyzed by the enzyme cascade, namely NEDD8 activating enzyme (E1), NEDD8 conjugating enzyme (E2), and NEDD8 ligase (E3). The substrates of neddylation are categorized into cullins and non-cullin proteins. Neddylation of cullins activates CRLs (cullin RING ligases), the largest family of E3 ligases, whereas neddylation of non-cullin substrates alters their stability and activity, as well as subcellular localization. Significantly, the neddylation pathway and/or many neddylation substrates are abnormally activated or over-expressed in various human diseases, such as metabolic disorders, liver dysfunction, neurodegenerative disorders, and cancers, among others. Thus, targeting neddylation becomes an attractive strategy for the treatment of these diseases. In this review, we first provide a general introduction on the neddylation cascade, its biochemical process and regulation, and the crystal structures of neddylation enzymes in complex with cullin substrates; then discuss how neddylation governs various key biological processes via the modification of cullins and non-cullin substrates. We further review the literature data on dysregulated neddylation in several human diseases, particularly cancer, followed by an outline of current efforts in the discovery of small molecule inhibitors of neddylation as a promising therapeutic approach. Finally, few perspectives were proposed for extensive future investigations.
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Affiliation(s)
- Shizhen Zhang
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China
| | - Qing Yu
- Department of Thyroid Surgery, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
- Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, 310022, China
| | - Zhijian Li
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China
| | - Yongchao Zhao
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Department of Hepatobiliary and Pancreatic Surgery, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Zhejiang University Cancer Center, Hangzhou, 310029, China.
| | - Yi Sun
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Zhejiang University Cancer Center, Hangzhou, 310029, China.
- Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang, Hangzhou, 310024, China.
- Research Center for Life Science and Human Health, Binjiang Institute of Zhejiang University, Hangzhou, 310053, China.
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25
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Bekdash RA. Epigenetics, Nutrition, and the Brain: Improving Mental Health through Diet. Int J Mol Sci 2024; 25:4036. [PMID: 38612845 PMCID: PMC11012292 DOI: 10.3390/ijms25074036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 03/30/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
The relationship between nutrition and brain health is intricate. Studies suggest that nutrients during early life impact not only human physiology but also mental health. Although the exact molecular mechanisms that depict this relationship remain unclear, there are indications that environmental factors such as eating, lifestyle habits, stress, and physical activity, influence our genes and modulate their function by epigenetic mechanisms to shape mental health outcomes. Epigenetic mechanisms act as crucial link between genes and environmental influences, proving that non-genetic factors could have enduring effects on the epigenome and influence health trajectories. We review studies that demonstrated an epigenetic mechanism of action of nutrition on mental health, focusing on the role of specific micronutrients during critical stages of brain development. The methyl-donor micronutrients of the one-carbon metabolism, such as choline, betaine, methionine, folic acid, VitB6 and VitB12 play critical roles in various physiological processes, including DNA and histone methylation. These micronutrients have been shown to alter gene function and susceptibility to diseases including mental health and metabolic disorders. Understanding how micronutrients influence metabolic genes in humans can lead to the implementation of early nutritional interventions to reduce the risk of developing metabolic and mental health disorders later in life.
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Affiliation(s)
- Rola A Bekdash
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
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26
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Fang T, Liu MN, Liu MQ, Tian XY, Zhang XJ, Liu F, Hao W, Wu N, Li H, Li J. A preliminary study on the association of single nucleotide polymorphisms and methylation of dopamine system-related genes with psychotic symptoms in patients with methamphetamine use disorder. Eur J Neurosci 2024; 59:1428-1440. [PMID: 38151046 DOI: 10.1111/ejn.16238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023]
Abstract
Methamphetamine use disorder (MAUD) can substantially jeopardize public security due to its high-risk social psychology and behaviour. Given that the dopamine reward system is intimately correlated with MAUD, we investigated the association of single nucleotide polymorphisms (SNPs), as well as methylation status of dopamine receptor type 4 (DRD4), catechol-O-methyltransferase (COMT) genes, and paranoid and motor-impulsive symptoms in MAUD patients. A total of 189 MAUD patients participated in our study. Peripheral blood samples were used to detect 3 SNPs and 35 CpG units of methylation in the DRD4 gene promoter region and 5 SNPs and 39 CpG units in the COMT gene. MAUD patients with the DRD4 rs1800955 C allele have a lower percentage of paranoid symptoms than those with the rs1800955 TT allele. Individuals with paranoid symptoms exhibited a reduced methylation degree at a particular DRD4 CpG2.3 unit. The interaction of the DRD4 rs1800955 C allele and the reduced DRD4CpG2.3 methylation degree were associated with a lower occurrence of paranoid symptoms. Meanwhile, those with the COMT rs4818 CC allele had lower motor-impulsivity scores in MAUD patients but greater COMT methylation levels in the promoter region and methylation degree at the COMT CpG 51.52 unit. Therefore, based only on the COMT rs4818 CC polymorphism, there was a negative correlation between COMT methylation and motor-impulsive scores. Our preliminary results provide a clue that the combination of SNP genotype and methylation status of the DRD4 and COMT genes serve as biological indicators for the prevalence of relatively high-risk psychotic symptoms in MAUD patients.
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Affiliation(s)
- Ting Fang
- Beijing Key Laboratory of Neuropsychopharmacology, State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Meng-Nan Liu
- Beijing Key Laboratory of Neuropsychopharmacology, State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Meng-Qi Liu
- National Clinical Research Center for Mental Disorders, and Department of Psychiatry, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xiao-Yu Tian
- Beijing Key Laboratory of Neuropsychopharmacology, State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
- Medical School of Chinese PLA, Beijing, China
| | - Xiao-Jie Zhang
- National Clinical Research Center for Mental Disorders, and Department of Psychiatry, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Feng Liu
- Compulsory Detoxification Center of Changsha Public Security Bureau, Changsha, China
| | - Wei Hao
- National Clinical Research Center for Mental Disorders, and Department of Psychiatry, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Ning Wu
- Beijing Key Laboratory of Neuropsychopharmacology, State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Hong Li
- Beijing Key Laboratory of Neuropsychopharmacology, State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Jin Li
- Beijing Key Laboratory of Neuropsychopharmacology, State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
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27
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Zhang F, Liu C, Chen Z, Zhao C. A novel PDIA3/FTO/USP20 positive feedback regulatory loop induces osteogenic differentiation of preosteoblast in osteoporosis. Cell Biol Int 2024; 48:541-550. [PMID: 38321831 DOI: 10.1002/cbin.12134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/05/2023] [Accepted: 01/01/2024] [Indexed: 02/08/2024]
Abstract
Osteoporosis is a chronic skeletal disease and the major source of risk for fractures in aged people. It is urgent to investigate the mechanism regulating osteoporosis for developing potential treatment and prevention strategies. Osteogenic differentiation of preosteoblast enhances bone formation, which might be a promising strategy for treatment and prevention of osteoporosis. Protein disulfide isomerase family A, member 3 (PDIA3) could induce bone formation, yet the role of PDIA3 in osteogenic differentiation of preosteoblast remains unknown. In this study, m6 A RNA methylation was detected by methylated RNA immunoprecipitation (MeRIP), while mRNA stability was identified by RNA decay assay. Besides, protein-protein interaction and protein phosphorylation were determined using co-immunoprecipitation (Co-IP). Herein, results revealed that PDIA3 promoted osteogenic differentiation of preosteoblast MC3T3-E1. Besides, PDIA3 mRNA methylation was suppressed by FTO alpha-ketoglutarate dependent dioxygenase (FTO) as RNA methylation reduced PDIA3 mRNA stability during osteogenic differentiation of MC3T3-E1 cells. Moreover, ubiquitin specific peptidase 20 (USP20) improved FTO level through inhibiting FTO degradation while PDIA3 increased FTO level by enhancing USP20 phosphorylation during osteogenic differentiation of MC3T3-E1 cells, suggesting a positive feedback regulatory loop between PDIA3 and FTO. In summary, these findings indicated the mechanism of PDIA3 regulating osteogenic differentiation of preosteoblast and provided potential therapeutic targets for osteoporosis.
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Affiliation(s)
- Fei Zhang
- First Department of Orthopaedics, Zhongshan City People's Hospital, Zhongshan, Guangdong, China
| | - Chen Liu
- Surgery Department, Zhongshan Port Hospital, Zhongshan, Guangdong, China
| | - Zhiyong Chen
- Department of Neurosurgery, The Affiliated Hospital of Jinan University, Guangzhou, China
- Minimally Invasive Treatment Center for Pituitary Adenoma of Jinan University, Guangzhou, China
| | - Chengyi Zhao
- Second Department of Orthopaedics, Zhongshan City People's Hospital, Zhongshan, Guangdong, China
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28
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Olejnik-Wojciechowska J, Boboryko D, Bratborska AW, Rusińska K, Ostrowski P, Baranowska M, Pawlik A. The Role of Epigenetic Factors in the Pathogenesis of Psoriasis. Int J Mol Sci 2024; 25:3831. [PMID: 38612637 PMCID: PMC11011681 DOI: 10.3390/ijms25073831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/21/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Psoriasis is a chronic inflammatory skin disease, the prevalence of which is increasing. Genetic, genomic, and epigenetic changes play a significant role in the pathogenesis of psoriasis. This review summarizes the impact of epigenetics on the development of psoriasis and highlights challenges for the future. The development of epigenetics provides a basis for the search for genetic markers associated with the major histocompatibility complex. Genome-wide association studies have made it possible to link psoriasis to genes and therefore to epigenetics. The acquired knowledge may in the future serve as a solid foundation for developing newer, increasingly effective methods of treating psoriasis. In this narrative review, we discuss the role of epigenetic factors in the pathogenesis of psoriasis.
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Affiliation(s)
- Joanna Olejnik-Wojciechowska
- Department of Physiology, Pomeranian Medical University, al. Powstańców Wlkp. 72, 70-111 Szczecin, Poland; (J.O.-W.); (D.B.); (M.B.)
| | - Dominika Boboryko
- Department of Physiology, Pomeranian Medical University, al. Powstańców Wlkp. 72, 70-111 Szczecin, Poland; (J.O.-W.); (D.B.); (M.B.)
| | | | - Klaudia Rusińska
- Department of General Pathology, Pomeranian Medical University, al. Powstańców Wlkp. 72, 70-111 Szczecin, Poland;
| | - Piotr Ostrowski
- Department of Nursing, Pomeranian Medical University, Żołnierska 48, 71-210 Szczecin, Poland
| | - Magdalena Baranowska
- Department of Physiology, Pomeranian Medical University, al. Powstańców Wlkp. 72, 70-111 Szczecin, Poland; (J.O.-W.); (D.B.); (M.B.)
| | - Andrzej Pawlik
- Department of Physiology, Pomeranian Medical University, al. Powstańców Wlkp. 72, 70-111 Szczecin, Poland; (J.O.-W.); (D.B.); (M.B.)
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29
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Davydova E, Perenkov A, Vedunova M. Building Minimized Epigenetic Clock by iPlex MassARRAY Platform. Genes (Basel) 2024; 15:425. [PMID: 38674360 PMCID: PMC11049545 DOI: 10.3390/genes15040425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Epigenetic clocks are valuable tools for estimating both chronological and biological age by assessing DNA methylation levels at specific CpG dinucleotides. While conventional epigenetic clocks rely on genome-wide methylation data, targeted approaches offer a more efficient alternative. In this study, we explored the feasibility of constructing a minimized epigenetic clock utilizing data acquired through the iPlex MassARRAY technology. The study enrolled a cohort of relatively healthy individuals, and their methylation levels of eight specific CpG dinucleotides in genes SLC12A5, LDB2, FIGN, ACSS3, FHL2, and EPHX3 were evaluated using the iPlex MassARRAY system and the Illumina EPIC array. The methylation level of five studied CpG sites demonstrated significant correlations with chronological age and an acceptable convergence of data obtained by the iPlex MassARRAY and Illumina EPIC array. At the same time, the methylation level of three CpG sites showed a weak relationship with age and exhibited a low concordance between the data obtained from the two technologies. The construction of the epigenetic clock involved the utilization of different machine-learning models, including linear models, deep neural networks (DNN), and gradient-boosted decision trees (GBDT). The results obtained from these models were compared with each other and with the outcomes generated by other well-established epigenetic clocks. In our study, the TabNet architecture (deep tabular data learning architecture) exhibited the best performance (best MAE = 5.99). Although our minimized epigenetic clock yielded slightly higher age prediction errors compared to other epigenetic clocks, it still represents a viable alternative to the genome-wide epigenotyping array.
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Affiliation(s)
- Ekaterina Davydova
- Institute of Biology and Biomedicine, Lobachevsky State University, 23 Gagarin Ave., Nizhny Novgorod 603022, Russia (M.V.)
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Caldwell BA, Wu Y, Wang J, Li L. Altered DNA methylation underlies monocyte dysregulation and immune exhaustion memory in sepsis. Cell Rep 2024; 43:113894. [PMID: 38442017 DOI: 10.1016/j.celrep.2024.113894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/12/2024] [Accepted: 02/14/2024] [Indexed: 03/07/2024] Open
Abstract
Monocytes can develop an exhausted memory state characterized by reduced differentiation, pathogenic inflammation, and immune suppression that drives immune dysregulation during sepsis. Chromatin alterations, notably via histone modifications, underlie innate immune memory, but the contribution of DNA methylation remains poorly understood. Using an ex vivo sepsis model, we show altered DNA methylation throughout the genome of exhausted monocytes, including genes implicated in immune dysregulation during sepsis and COVID-19 infection (e.g., Plac8). These changes are recapitulated in septic mice induced by cecal slurry injection. Methylation profiles developed in septic mice are maintained during ex vivo culture, supporting the involvement of DNA methylation in stable monocyte exhaustion memory. Methylome reprogramming is driven in part by Wnt signaling inhibition in exhausted monocytes and can be reversed with DNA methyltransferase inhibitors, Wnt agonists, or immune training molecules. Our study demonstrates the significance of altered DNA methylation in the maintenance of stable monocyte exhaustion memory.
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Affiliation(s)
- Blake A Caldwell
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061-0910, USA
| | - Yajun Wu
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061-0910, USA
| | - Jing Wang
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061-0910, USA
| | - Liwu Li
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061-0910, USA.
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31
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Ding Y, Zhou G, Hu W. Epigenetic regulation of TGF-β pathway and its role in radiation response. Int J Radiat Biol 2024; 100:834-848. [PMID: 38506660 DOI: 10.1080/09553002.2024.2327395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/27/2024] [Indexed: 03/21/2024]
Abstract
PURPOSE Transforming growth factor (TGF-β) plays a dual role in tumor progression as well as a pivotal role in radiation response. TGF-β-related epigenetic regulations, including DNA methylation, histone modifications (including methylation, acetylation, phosphorylation, ubiquitination), chromatin remodeling and non-coding RNA regulation, have been found to affect the occurrence and development of tumors as well as their radiation response in multiple dimensions. Due to the significance of radiotherapy in tumor treatment and the essential roles of TGF-β signaling in radiation response, it is important to better understand the role of epigenetic regulation mechanisms mediated by TGF-β signaling pathways in radiation-induced targeted and non-targeted effects. CONCLUSIONS By revealing the epigenetic mechanism related to TGF-β-mediated radiation response, summarizing the existing relevant adjuvant strategies for radiotherapy based on TGF-β signaling, and discovering potential therapeutic targets, we hope to provide a new perspective for improving clinical treatment.
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Affiliation(s)
- Yunan Ding
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Guangming Zhou
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Wentao Hu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
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32
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Shan Y, Hou B, Wang J, Chen A, Liu S. Exploring the role of exosomal MicroRNAs as potential biomarkers in preeclampsia. Front Immunol 2024; 15:1385950. [PMID: 38566996 PMCID: PMC10985148 DOI: 10.3389/fimmu.2024.1385950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
The complex pathogenesis of preeclampsia (PE), a significant contributor to maternal and neonatal mortality globally, is poorly understood despite substantial research. This review explores the involvement of exosomal microRNAs (exomiRs) in PE, focusing on their impact on the protein kinase B (AKT)/hypoxia-inducible factor 1-α (HIF1α)/vascular endothelial growth factor (VEGF) signaling pathway as well as endothelial cell proliferation and migration. Specifically, this article amalgamates existing evidence to reveal the pivotal role of exomiRs in regulating mesenchymal stem cell and trophoblast function, placental angiogenesis, the renin-angiotensin system, and nitric oxide production, which may contribute to PE etiology. This review emphasizes the limited knowledge regarding the role of exomiRs in PE while underscoring the potential of exomiRs as non-invasive biomarkers for PE diagnosis, prediction, and treatment. Further, it provides valuable insights into the mechanisms of PE, highlighting exomiRs as key players with clinical implications, warranting further exploration to enhance the current understanding and the development of novel therapeutic interventions.
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Affiliation(s)
- Yuping Shan
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Bo Hou
- Department of Cardiovascular Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jingli Wang
- Department of Medical Genetics, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Aiping Chen
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Shiguo Liu
- Department of Medical Genetics, The Affiliated Hospital of Qingdao University, Qingdao, China
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Azizidoost S, Nasrolahi A, Sheykhi-Sabzehpoush M, Anbiyaiee A, Khoshnam SE, Farzaneh M, Uddin S. Signaling pathways governing the behaviors of leukemia stem cells. Genes Dis 2024; 11:830-846. [PMID: 37692500 PMCID: PMC10491880 DOI: 10.1016/j.gendis.2023.01.008] [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: 07/09/2022] [Accepted: 01/02/2023] [Indexed: 08/28/2023] Open
Abstract
Leukemia is a malignancy in the blood that develops from the lymphatic system and bone marrow. Although various treatment options have been used for different types of leukemia, understanding the molecular pathways involved in the development and progression of leukemia is necessary. Recent studies showed that leukemia stem cells (LSCs) play essential roles in the pathogenesis of leukemia by targeting several signaling pathways, including Notch, Wnt, Hedgehog, and STAT3. LSCs are highly proliferative cells that stimulate tumor initiation, migration, EMT, and drug resistance. This review summarizes cellular pathways that stimulate and prevent LSCs' self-renewal, metastasis, and tumorigenesis.
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Affiliation(s)
- Shirin Azizidoost
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 6193673111, Iran
| | - Ava Nasrolahi
- Infectious Ophthalmologic Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 6193673111, Iran
| | - Mohadeseh Sheykhi-Sabzehpoush
- Department of Laboratory, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran 2193672411, Iran
| | - Amir Anbiyaiee
- Department of Surgery, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 6193673111, Iran
| | - Seyed Esmaeil Khoshnam
- Persian Gulf Physiology Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 6193673111, Iran
| | - Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 6193673111, Iran
| | - Shahab Uddin
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar
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Das A, Giri AK, Bhattacharjee P. Targeting 'histone mark': Advanced approaches in epigenetic regulation of telomere dynamics in cancer. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195007. [PMID: 38237857 DOI: 10.1016/j.bbagrm.2024.195007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024]
Abstract
Telomere integrity is required for the maintenance of genome stability and prevention of oncogenic transformation of cells. Recent evidence suggests the presence of epigenetic modifications as an important regulator of mammalian telomeres. Telomeric and subtelomeric regions are rich in epigenetic marks that regulate telomere length majorly through DNA methylation and post-translational histone modifications. Specific histone modifying enzymes play an integral role in establishing telomeric histone codes necessary for the maintenance of structural integrity. Alterations of crucial histone moieties and histone modifiers cause deregulations in the telomeric chromatin leading to carcinogenic manifestations. This review delves into the significance of histone modifications and their influence on telomere dynamics concerning cancer. Additionally, it highlights the existing research gaps that hold the potential to drive the development of therapeutic interventions targeting the telomere epigenome.
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Affiliation(s)
- Ankita Das
- Department of Environmental Science, University of Calcutta, Kolkata 700019, India; Department of Zoology, University of Calcutta, Kolkata 700019, India
| | - Ashok K Giri
- Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Pritha Bhattacharjee
- Department of Environmental Science, University of Calcutta, Kolkata 700019, India.
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Wang J, Fu G, Wang Q, Ma G, Wang Z, Lu C, Fu L, Zhang X, Cong B, Li S. Differences of circular RNA expression profiles between monozygotic twins' blood, with the forensic application in bloodstain and saliva. Forensic Sci Int Genet 2024; 69:103001. [PMID: 38150775 DOI: 10.1016/j.fsigen.2023.103001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/26/2023] [Accepted: 12/14/2023] [Indexed: 12/29/2023]
Abstract
Monozygotic twins (MZTs) possess identical genomic DNA sequences and are usually indistinguishable through routine forensic DNA typing methods, which can be relevant in criminal and paternity cases. Recently, novel epigenetic methods involving DNA methylation and microRNA analysis have been introduced to differentiate MZTs. In this study, we explore the potential of using epigenetic markers, specifically circular RNAs (circRNAs), a type of non-coding RNA (ncRNA), to identify MZTs, and investigate the unique expression patterns of circRNAs within pairs of MZTs, enabling effective differentiation. Epigenetics regulates gene expression at the post-transcriptional level and plays a crucial role in cell growth and aging. CircRNAs, a recently characterized subclass of ncRNA, have a distinct covalent loop structure without the typical 5' cap or 3' tail. They have been reported to modulate various cellular processes and play roles in embryogenesis and eukaryotic development. To achieve this, we conducted a comprehensive circRNA sequencing analysis (circRNA-seq) using total RNA extracted from the blood samples of five pairs of MZTs. We identified a total of 15,257 circRNAs in all MZTs using circRNA-seq. Among them, 3, 21, 338, and 2967 differentially expressed circRNAs (DEcircRNAs) were shared among five, four, three, and two pairs of MZTs, respectively. Subsequently, we validated twelve selected DEcircRNAs using real-time quantitative polymerase chain reaction (RT-qPCR) assays, which included hsa_circ_0004724, hsa_circ_0054196, hsa_circ_004964, hsa_circ_0000591, hsa_circ_0005077, hsa_circ_0054853, hsa_circ_0054716, hsa_circ_0002302, hsa_circ_0004482, hsa_circ_0001103, novel_circ_0030288 and novel_circ_0056831. Among them, hsa_circ_0005077 and hsa_circ_0004482 exhibited the best performance, showing differences in 7 out of 10 pairs of MZTs. These twelve differentially expressed circRNAs also demonstrated strong discriminative power when tested on saliva samples from 10 pairs of MZTs. Notably, hsa_circ_0004724 displayed differential expression in 8 out of 10 pairs of MZTs in their saliva. Additionally, we evaluated the detection sensitivity, longitudinal temporal stability, and suitability for aged bloodstains of these twelve DEcircRNAs in forensic scenarios. Our findings highlight the potential of circRNAs as molecular markers for distinguishing MZTs, emphasizing their suitability for forensic application.
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Affiliation(s)
- Junyan Wang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China.
| | - Guangping Fu
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Qian Wang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Guanju Ma
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Zhonghua Wang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Chaolong Lu
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Lihong Fu
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Xiaojing Zhang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Bin Cong
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China.
| | - Shujin Li
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China.
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Chaaban A, Salman Z, Karam L, Kobeissy PH, Ibrahim JN. Updates on the role of epigenetics in familial mediterranean fever (FMF). Orphanet J Rare Dis 2024; 19:90. [PMID: 38409042 PMCID: PMC10898143 DOI: 10.1186/s13023-024-03098-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/21/2024] [Indexed: 02/28/2024] Open
Abstract
Familial Mediterranean Fever (FMF) is an autosomal recessive autoinflammatory disease caused by mutations in the MEFV (MEditerranean FeVer) gene that affects people originating from the Mediterranean Sea. The high variability in severity and clinical manifestations observed not only between ethnic groups but also between and within families is mainly related to MEFV allelic heterogeneity and to some modifying genes. In addition to the genetic factors underlying FMF, the environment plays a significant role in the development and manifestation of this disease through various epigenetic mechanisms, including DNA methylation, histone modification, and noncoding RNAs. Indeed, epigenetic events have been identified as an important pathophysiological determinant of FMF and co-factors shaping the clinical picture and outcome of the disease. Therefore, it is essential to better understand the contribution of epigenetic factors to autoinflammatory diseases, namely, FMF, to improve disease prognosis and potentially develop effective targeted therapies. In this review, we highlight the latest updates on the role of epigenetics in FMF.
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Affiliation(s)
- Ahlam Chaaban
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University (LAU), Beirut, Lebanon
| | - Zeina Salman
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University (LAU), Beirut, Lebanon
| | - Louna Karam
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University (LAU), Beirut, Lebanon
| | - Philippe Hussein Kobeissy
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University (LAU), Beirut, Lebanon.
| | - José-Noel Ibrahim
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University (LAU), Beirut, Lebanon.
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Krause C, Bergmann E, Schmidt SV. Epigenetic modulation of myeloid cell functions in HIV and SARS-CoV-2 infection. Mol Biol Rep 2024; 51:342. [PMID: 38400997 PMCID: PMC10894183 DOI: 10.1007/s11033-024-09266-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/18/2024] [Indexed: 02/26/2024]
Abstract
Myeloid cells play a vital role in innate immune responses as they recognize and phagocytose pathogens like viruses, present antigens, produce cytokines, recruit other immune cells to combat infections, and contribute to the attenuation of immune responses to restore homeostasis. Signal integration by pathogen recognition receptors enables myeloid cells to adapt their functions by a network of transcription factors and chromatin remodelers. This review provides a brief overview of the subtypes of myeloid cells and the main epigenetic regulation mechanisms. Special focus is placed on the epigenomic alterations in viral nucleic acids of HIV and SARS-CoV-2 along with the epigenetic changes in the host's myeloid cell compartment. These changes are important as they lead to immune suppression and promote the progression of the disease. Finally, we highlight some promising examples of 'epidrugs' that modulate the epigenome of immune cells and could be used as therapeutics for viral infections.
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Affiliation(s)
- Carolyn Krause
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127, Bonn, Germany
- Department of Microbiology and Immunology, the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Eva Bergmann
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127, Bonn, Germany
| | - Susanne Viktoria Schmidt
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127, Bonn, Germany.
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Kimura TDC, de Lima-Souza RA, Maciel TF, Kowalski LP, Coutinho-Camillo CM, Egal ESA, Altemani A, Mariano FV. Dynamic Role of miRNAs in Salivary Gland Carcinomas: From Biomarkers to Therapeutic Targets. Head Neck Pathol 2024; 18:12. [PMID: 38393615 PMCID: PMC10891027 DOI: 10.1007/s12105-023-01603-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 12/15/2023] [Indexed: 02/25/2024]
Abstract
BACKGROUND Salivary gland carcinomas (SGCs) are a rare group of malignant neoplasms of the head and neck region. MicroRNAs (miRNAs) are a class of small non-coding RNAs that have been associated with the control biological process and oncogenic mechanism by the regulation of gene expression at the post-transcriptional level. Recent evidence has suggested that miRNA expression may play a role in the tumorigenesis and carcinogenesis process in SGCs. METHODS This review provides a comprehensive literature review of the role of miRNAs expression in SGCs focusing on the diagnostic, prognostic, and therapeutic applications. RESULTS In this review, numerous dysregulated miRNAs have demonstrated an oncogenic and suppressor role in SGCs. CONCLUSION In the future, these miRNAs may eventually constitute useful diagnostic and prognostic biomarkers that may lead to a better understanding of SGCs oncogenesis. Additionally, the development of therapeutic agents based on miRNAs may be a promising target in SGC treatment.
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Affiliation(s)
- Talita de Carvalho Kimura
- Department of Oral Diagnosis, Piracicaba Dental School, State University of Campinas (UNICAMP), Piracicaba, Brazil
- Department of Pathology, School of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Reydson Alcides de Lima-Souza
- Department of Oral Diagnosis, Piracicaba Dental School, State University of Campinas (UNICAMP), Piracicaba, Brazil
- Department of Pathology, School of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Tayná Figueiredo Maciel
- Department of Oral Diagnosis, Piracicaba Dental School, State University of Campinas (UNICAMP), Piracicaba, Brazil
- Department of Pathology, School of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Luiz Paulo Kowalski
- Department of Head and Neck Surgery and Otorhinolaryngology, A.C. Camargo Cancer Center, São Paulo, Brazil
| | | | - Erika Said Abu Egal
- Department of Pathology, School of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
- Biorepository and Molecular Pathology, Huntsman Cancer Institute, University of Utah (UU), Salt Lake City, Utah, USA
| | - Albina Altemani
- Department of Pathology, School of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Fernanda Viviane Mariano
- Department of Pathology, School of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil.
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Terriaca S, Monastero R, Orlandi A, Balistreri CR. The key role of miRNA in syndromic and sporadic forms of ascending aortic aneurysms as biomarkers and targets of novel therapeutic strategies. Front Genet 2024; 15:1365711. [PMID: 38450200 PMCID: PMC10915088 DOI: 10.3389/fgene.2024.1365711] [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: 01/04/2024] [Accepted: 01/30/2024] [Indexed: 03/08/2024] Open
Abstract
Increasing evidence shows that epigenetics also plays a key role in regulating the pathogenetic mechanism of all types of aortic aneurysms. It is well-known that epigenetic factors modulate gene expression. This mechanism appears to be of interest especially knowing the relevance of genetic susceptibility and genetic factors in the complex pathophysiology of aortic aneurysms, and of sporadic forms; in fact, the latter are the result of a close interaction between genetic and modifiable lifestyle factors (i.e., nutrition, smoking, infections, use of drugs, alcohol, sedentary lifestyle, etc.). Epigenetic factors include DNA methylation, post-translational histone modifications, and non-coding RNA. Here, our attention is focused on the role of miRNA in syndromic and sporadic forms of thoracic aortic aneurysms. They could be both biomarkers and targets of novel therapeutic strategies.
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Affiliation(s)
- Sonia Terriaca
- Pathological Anatomy, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Roberto Monastero
- Section of Neurology, Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, Palermo, Italy
| | - Augusto Orlandi
- Pathological Anatomy, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Carmela Rita Balistreri
- Cellular, Molecular, and Clinical Pathological Laboratory, Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi N D), University of Palermo, Palermo, Italy
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Wang J, Kuang J, Zhang S, Liu Z, Guo Q, Li S, Qiu L, Fu G, Lin X, Wu J, Tian J, Huang J, Niu Y, Kang K, Zhang Y, Gou D. Comprehensive characterization of small noncoding RNA profiles in hypoxia-induced pulmonary hypertension (HPH) rat tissues. iScience 2024; 27:108815. [PMID: 38322991 PMCID: PMC10844824 DOI: 10.1016/j.isci.2024.108815] [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: 07/24/2023] [Revised: 11/10/2023] [Accepted: 01/02/2024] [Indexed: 02/08/2024] Open
Abstract
Hypoxia-induced pulmonary hypertension (HPH) is a fatal cardiovascular disease characterized by an elevation in pulmonary artery pressure, resulting in right ventricular dysfunction and eventual heart failure. Exploring the pathogenesis of HPH is crucial, and small noncoding RNAs (sncRNAs) are gaining recognition as potential regulators of cellular responses to hypoxia. In this study, we conducted a comprehensive analysis of sncRNA profiles in eight tissues of male HPH rats using high-throughput sequencing. Our study unveiled several sncRNAs, with the brain, kidney, and spleen exhibiting the highest abundance of microRNA (miRNA), tRNA-derived small RNA (tDR), and small nucleolar RNA (snoRNA), respectively. Moreover, we identified numerous tissue-specific and hypoxia-responsive sncRNAs, particularly miRNAs and tDRs. Interestingly, we observed arm switching in miRNAs under hypoxic conditions and a significant increase in the abundance of 5' tRNA-halves among the total tDRs during hypoxia. Overall, our study provides a comprehensive characterization of the sncRNA profiles in HPH rats.
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Affiliation(s)
- Jun Wang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Jiahao Kuang
- College of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Shasha Zhang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Zixin Liu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Qianwen Guo
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Shujin Li
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Lin Qiu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Gaohui Fu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Xinyang Lin
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Jiayu Wu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Jinglin Tian
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Jinyong Huang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen 518060, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Yanqin Niu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Kang Kang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen 518060, China
- College of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Yunhui Zhang
- Department of Pulmonary and Critical Care Medicine, The First People’s Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming 650022, China
| | - Deming Gou
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen 518060, China
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Liu J, Liu JB, Ke XY. [Research progress on the mechanism of the impact of maternal childhood trauma on intergenerational transmission]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2024; 26:207-212. [PMID: 38436321 PMCID: PMC10921875 DOI: 10.7499/j.issn.1008-8830.2309147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/05/2024] [Indexed: 03/05/2024]
Abstract
Childhood trauma refers to trauma experiences encountered during childhood and adolescence. Maternal childhood trauma experiences have a lasting impact on the next generation, affecting their physical and mental well-being. The mechanisms involved include the hypothalamic-pituitary-adrenal axis, inflammatory factors, brain structure and function, gene interactions, and parenting styles. This paper systematically reviews the mechanisms of the impact of maternal childhood trauma on intergenerational transmission, providing insights for the prevention of intergenerational transmission of childhood trauma.
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Affiliation(s)
- Juan Liu
- School of Mental Health, Jining Medical University, Jining, Shandong 272000, China (Ke X-Y, ); Department of Child Psychiatry, Shenzhen Mental Health Center/Shenzhen Kangning Hospital, Shenzhen, Guangdong 518000, China (Liu J-B, 308017398@qq. com)
| | | | - Xiao-Yin Ke
- School of Mental Health, Jining Medical University, Jining, Shandong 272000, China (Ke X-Y, ); Department of Child Psychiatry, Shenzhen Mental Health Center/Shenzhen Kangning Hospital, Shenzhen, Guangdong 518000, China (Liu J-B, 308017398@qq. com)
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Liu Y, Wu J, Chen L, Zou J, Yang Q, Tian H, Zheng D, Ji Z, Cai J, Li Z, Chen Y. ncRNAs-mediated overexpression of TET3 predicts unfavorable prognosis and correlates with immunotherapy efficacy in breast cancer. Heliyon 2024; 10:e24855. [PMID: 38318018 PMCID: PMC10838756 DOI: 10.1016/j.heliyon.2024.e24855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 01/07/2024] [Accepted: 01/16/2024] [Indexed: 02/07/2024] Open
Abstract
Breast cancer is the most frequent form of cancer in women and the primary cause of cancer-related deaths globally. DNA methylation and demethylation are important processes in human tumorigenesis. Ten-eleven translocation 3 (TET3) is a DNA demethylase. Prior research has demonstrated that TET3 is highly expressed in various human malignant tumors. However, the exact function and mechanism of TET3 in breast cancer remain unclear. In this study, we investigated TET3 expression in breast cancer and its correlation with clinicopathological characteristics of breast cancer patients. The results presented that TET3 expression was significantly increased in breast cancer and associated with the PAM50 subtype. Subsequently, we performed receiver operating characteristic, survival, and Cox hazard regression analyses. These results suggest that TET3 expression is associated with a poor prognosis and may be an indirect independent prognostic indicator in breast cancer. We also established a protein-protein interaction (PPI) network of TET3 and executed enrichment analyses of TET3 co-expressed genes, revealing their primary association with the cell cycle. Moreover, we identified noncoding RNAs (ncRNAs) contributing to TET3 overexpression using expression, correlation, and survival analyses. We identified the LINC01521/hsa-miR-29a-3p axis as the primary TET3 upstream ncRNA-related pathway in breast cancer. Furthermore, TET3 expression was positively associated with immune cell infiltration, immune cell biomarkers, and eight immune checkpoint gene expressions in breast cancer. TET3 expression also correlated with patient responses to immunotherapy. Finally, we conducted subcellular localization and immunohistochemical staining analysis of TET3 in breast cancer. We found that TET3 localized to the nucleoplasm, vesicles, and cytosol in the MCF-7 cell line, and TET3 expression was significantly upregulated in breast cancer tissues compared to para-tumor tissues. Our findings indicate that ncRNA-mediated overexpression of TET3 predicts an unfavorable prognosis and correlates with immunotherapy efficacy in breast cancer.
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Affiliation(s)
| | | | | | - Juan Zou
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Qiuping Yang
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Huiting Tian
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Daitian Zheng
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Zeqi Ji
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Jiehui Cai
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Zhiyang Li
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Yexi Chen
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
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Rinaldi S, Moroni E, Rozza R, Magistrato A. Frontiers and Challenges of Computing ncRNAs Biogenesis, Function and Modulation. J Chem Theory Comput 2024; 20:993-1018. [PMID: 38287883 DOI: 10.1021/acs.jctc.3c01239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Non-coding RNAs (ncRNAs), generated from nonprotein coding DNA sequences, constitute 98-99% of the human genome. Non-coding RNAs encompass diverse functional classes, including microRNAs, small interfering RNAs, PIWI-interacting RNAs, small nuclear RNAs, small nucleolar RNAs, and long non-coding RNAs. With critical involvement in gene expression and regulation across various biological and physiopathological contexts, such as neuronal disorders, immune responses, cardiovascular diseases, and cancer, non-coding RNAs are emerging as disease biomarkers and therapeutic targets. In this review, after providing an overview of non-coding RNAs' role in cell homeostasis, we illustrate the potential and the challenges of state-of-the-art computational methods exploited to study non-coding RNAs biogenesis, function, and modulation. This can be done by directly targeting them with small molecules or by altering their expression by targeting the cellular engines underlying their biosynthesis. Drawing from applications, also taken from our work, we showcase the significance and role of computer simulations in uncovering fundamental facets of ncRNA mechanisms and modulation. This information may set the basis to advance gene modulation tools and therapeutic strategies to address unmet medical needs.
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Affiliation(s)
- Silvia Rinaldi
- National Research Council of Italy (CNR) - Institute of Chemistry of OrganoMetallic Compounds (ICCOM), c/o Area di Ricerca CNR di Firenze Via Madonna del Piano 10, 50019 Sesto Fiorentino, Florence, Italy
| | - Elisabetta Moroni
- National Research Council of Italy (CNR) - Institute of Chemical Sciences and Technologies (SCITEC), via Mario Bianco 9, 20131 Milano, Italy
| | - Riccardo Rozza
- National Research Council of Italy (CNR) - Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
| | - Alessandra Magistrato
- National Research Council of Italy (CNR) - Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
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Yu Z, Xu Z, Li S, Tian Z, Feng Y, Zhao H, Xue G, Cui J, Yan C, Yuan J. Prophylactic vitamin C supplementation regulates DNA demethylation to protect against cisplatin-induced acute kidney injury in mice. Biochem Biophys Res Commun 2024; 695:149463. [PMID: 38176172 DOI: 10.1016/j.bbrc.2023.149463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/15/2023] [Accepted: 12/29/2023] [Indexed: 01/06/2024]
Abstract
Cisplatin-induced acute kidney injury (AKI) restricts the use of cisplatin as a first-line chemotherapeutic agent. Our previous study showed that prophylactic vitamin C supplementation may act as an epigenetic modulator in alleviating cisplatin-induced AKI in mice. However, the targets of vitamin C and the mechanisms underlying the epigenetics changes remain largely unknown. Herein, whole-genome bisulfite sequencing and bulk RNA sequencing were performed on the kidney tissues of mice treated with cisplatin with prophylactic vitamin C supplementation (treatment mice) or phosphate-buffered saline (control mice) at 24 h after cisplatin treatment. Ascorbyl phosphate magnesium (APM), an oxidation-resistant vitamin C derivative, was found that led to global hypomethylation in the kidney tissue and regulated different functional genes in the promoter region and gene body region. Integrated evidence suggested that APM enhanced renal ion transport and metabolism, and reduced apoptosis and inflammation in the kidney tissues. Strikingly, Mapk15, Slc22a6, Cxcl5, and Cd44 were the potential targets of APM that conferred protection against cisplatin-induced AKI. Moreover, APM was found to be difficult to rescue cell proliferation and apoptosis caused by cisplatin in the Slc22a6 knockdown cell line. These results elucidate the mechanism by which vitamin C as an epigenetic regulator to protects against cisplatin-induced AKI and provides a new perspective and evidence support for controlling the disease process through regulating DNA methylation.
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Affiliation(s)
- Zihui Yu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Ziying Xu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Shang Li
- Department of Orthopedics, Chinese PLA General Hospital, Fuxing Road 8th, Haidian District, Beijing, 100853, China; National Clinical Research Center for Orthopedics, Sports Medicine & Rehabilitation, Fuxing Road 8th, Haidian District, Beijing, 100853, China
| | - Ziyan Tian
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Yanling Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Hanqing Zhao
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Guanhua Xue
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Jinghua Cui
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Chao Yan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Jing Yuan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China.
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Gareev I, Beylerli O, Zhao B. MiRNAs as potential therapeutic targets and biomarkers for non-traumatic intracerebral hemorrhage. Biomark Res 2024; 12:17. [PMID: 38308370 PMCID: PMC10835919 DOI: 10.1186/s40364-024-00568-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 01/20/2024] [Indexed: 02/04/2024] Open
Abstract
Non-traumatic intracerebral hemorrhage (ICH) is the most common type of hemorrhagic stroke, most often occurring between the ages of 45 and 60. Hypertension is most often the cause of ICH. Less often, atherosclerosis, blood diseases, inflammatory changes in cerebral vessels, intoxication, vitamin deficiencies, and other reasons cause hemorrhages. Cerebral hemorrhage can occur by diapedesis or as a result of a ruptured vessel. This very dangerous disease is difficult to treat, requires surgery and can lead to disability or death. MicroRNAs (miRNAs) are a class of non-coding RNAs (about 18-22 nucleotides) that are involved in a variety of biological processes including cell differentiation, proliferation, apoptosis, etc., through gene repression. A growing number of studies have demonstrated miRNAs deregulation in various cardiovascular diseases, including ICH. In addition, given that computed tomography (CT) and/or magnetic resonance imaging (MRI) are either not available or do not show clear signs of possible vessel rupture, accurate and reliable analysis of circulating miRNAs in biological fluids can help in early diagnosis for prevention of ICH and prognosis patient outcome after hemorrhage. In this review, we highlight the up-to-date findings on the deregulated miRNAs in ICH, and the potential use of miRNAs in clinical settings, such as therapeutic targets and non-invasive diagnostic/prognostic biomarker tools.
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Affiliation(s)
- Ilgiz Gareev
- Bashkir State Medical University, Ufa, 450008, Russia
| | - Ozal Beylerli
- Bashkir State Medical University, Ufa, 450008, Russia
| | - Boxian Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, No. 23 Youzheng Street, Nangang District, Harbin, 150001, China.
- Harbin Medical University No, 157, Baojian Road, Nangang District, Harbin, 150001, China.
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Peng X, Hu Z, Zeng L, Zhang M, Xu C, Lu B, Tao C, Chen W, Hou W, Cheng K, Bi H, Pan W, Chen J. Overview of epigenetic degraders based on PROTAC, molecular glue, and hydrophobic tagging technologies. Acta Pharm Sin B 2024; 14:533-578. [PMID: 38322348 PMCID: PMC10840439 DOI: 10.1016/j.apsb.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/21/2023] [Accepted: 08/30/2023] [Indexed: 02/08/2024] Open
Abstract
Epigenetic pathways play a critical role in the initiation, progression, and metastasis of cancer. Over the past few decades, significant progress has been made in the development of targeted epigenetic modulators (e.g., inhibitors). However, epigenetic inhibitors have faced multiple challenges, including limited clinical efficacy, toxicities, lack of subtype selectivity, and drug resistance. As a result, the design of new epigenetic modulators (e.g., degraders) such as PROTACs, molecular glue, and hydrophobic tagging (HyT) degraders has garnered significant attention from both academia and pharmaceutical industry, and numerous epigenetic degraders have been discovered in the past decade. In this review, we aim to provide an in-depth illustration of new degrading strategies (2017-2023) targeting epigenetic proteins for cancer therapy, focusing on the rational design, pharmacodynamics, pharmacokinetics, clinical status, and crystal structure information of these degraders. Importantly, we also provide deep insights into the potential challenges and corresponding remedies of this approach to drug design and development. Overall, we hope this review will offer a better mechanistic understanding and serve as a useful guide for the development of emerging epigenetic-targeting degraders.
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Affiliation(s)
- Xiaopeng Peng
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Zhihao Hu
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Limei Zeng
- College of Basic Medicine, Gannan Medical University, Ganzhou 314000, China
| | - Meizhu Zhang
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Congcong Xu
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Benyan Lu
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Chengpeng Tao
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Weiming Chen
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Wen Hou
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Kui Cheng
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Huichang Bi
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Wanyi Pan
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Jianjun Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
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Zhu JX, Dun Y, Wu W, Shen J, Zhang F, Zhang L. Curcumin suppresses the Wnt/β-catenin signaling pathway by inhibiting NKD2 methylation to ameliorate intestinal ischemia/reperfusion injury. Kaohsiung J Med Sci 2024; 40:175-187. [PMID: 38010861 DOI: 10.1002/kjm2.12782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 11/29/2023] Open
Abstract
Intestinal ischemia/reperfusion (I/R) injury is a life-threatening condition with no effective treatment currently available. Curcumin (CCM), a polyphenol compound in Curcuma Longa, reportedly has positive effects against intestinal I/R injury. However, the mechanism underlying the protective effect of CCM against intestinal I/R injury has not been fully clarified. To determine whether the protective effect of CCM was mediated by epigenetic effects on Wnt/β-catenin signaling, the effect of CCM was examined in vivo and in vitro. An intestinal I/R model was established in Sprague-Dawley (SD) rats with superior mesenteric artery occlusion, and Caco-2 cells were subjected to hypoxia/reoxygenation (H/R) for in vivo simulation of I/R. The results showed that CCM significantly reduced inflammatory, cell apoptosis, and oxidative stress induced by I/R insult in vivo and in vitro. Western blot analysis showed that CCM preconditioning reduced the protein levels of β-catenin, p-GSK3β, and cyclin-D1 and increased the protein level of GSK3β compared with the I/R group. Overexpressing β-catenin aggravated H/R injury, and knocking down β-catenin relieved H/R injury by improving intestinal permeability and reducing the cell apoptosis. Moreover, Naked cuticle homolog 2(NKD2) mRNA and protein levels were upregulated in the CCM-pretreated group. 5-aza-2'-deoxycytidine (5-AZA) treatment improved intestinal epithelial barrier impairment induced by H/R. Besides, the protein levels of total β-catenin, phosphor-β-catenin and cyclin-D1 were reduced after overexpressing NKD2 in Caco-2 cells following H/R insult. In conclusion, Our study suggests that CCM could attenuate intestinal I/R injury in vitro and in vivo by suppressing the Wnt/β-catenin signaling pathway via inhibition of NKD2 methylation.
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Affiliation(s)
- Jia-Xi Zhu
- Center of Emergency and Critical Medicine, Jinshan Hospital of Fudan University, Shanghai, China
- Research Center for Chemical Injury, Emergency and Critical Medicine of Fudan University, Shanghai, China
- Key Laboratory of Chemical Injury, Emergency and Critical Medicine of Shanghai Municipal Health Commission, Shanghai, China
| | - Yu Dun
- Center of Emergency and Critical Medicine, Jinshan Hospital of Fudan University, Shanghai, China
- Research Center for Chemical Injury, Emergency and Critical Medicine of Fudan University, Shanghai, China
- Key Laboratory of Chemical Injury, Emergency and Critical Medicine of Shanghai Municipal Health Commission, Shanghai, China
| | - Wei Wu
- Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jie Shen
- Center of Emergency and Critical Medicine, Jinshan Hospital of Fudan University, Shanghai, China
- Research Center for Chemical Injury, Emergency and Critical Medicine of Fudan University, Shanghai, China
- Key Laboratory of Chemical Injury, Emergency and Critical Medicine of Shanghai Municipal Health Commission, Shanghai, China
| | - Feng Zhang
- Center of Emergency and Critical Medicine, Jinshan Hospital of Fudan University, Shanghai, China
- Research Center for Chemical Injury, Emergency and Critical Medicine of Fudan University, Shanghai, China
- Key Laboratory of Chemical Injury, Emergency and Critical Medicine of Shanghai Municipal Health Commission, Shanghai, China
| | - Lin Zhang
- Center of Emergency and Critical Medicine, Jinshan Hospital of Fudan University, Shanghai, China
- Research Center for Chemical Injury, Emergency and Critical Medicine of Fudan University, Shanghai, China
- Key Laboratory of Chemical Injury, Emergency and Critical Medicine of Shanghai Municipal Health Commission, Shanghai, China
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48
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Mathes A, Duman MB, Neumann A, Dobreva G, Schmidt T. S-adenosylmethionine treatment affects histone methylation in prostate cancer cells. Gene 2024; 893:147915. [PMID: 37866662 DOI: 10.1016/j.gene.2023.147915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 10/24/2023]
Abstract
S-adenosylmethionine (SAM) represents a potent inhibitor of cancer cell proliferation, migration, and invasionin vitro.The underlying mechanisms remain elusive. Here, we examined, if treatment with SAM may cause alterations in the methylation of the histone marks H3K4me3 and H3K27me3, which are both known to play important roles in the initiation and progression of prostate cancer. We treated PC-3 cells with 200 µmol SAM, a concentration known to cause anticancerogenic effects, followed by ChIP-sequencing for H3K4me3 and H3K27me3. We detected 236 differentially methylated regions for H3K27me3 and 560 differentially methylated regions for H3K4me3. GO Term enrichment showed upregulation of anticancerogenic, as well as downregulation of cancerogenic related biological processes, molecular functions, and pathways. Furthermore, we compared specific methylation profiles of SAM treated samples to gene expression changes (RNA-Seq). 35 upregulated and 56 downregulated genes (total: 604 differentially expressed genes) could be related to hypomethylated and hypermethylated regions. 17 upregulated genes could be identified as tumor suppressor genes, 45 downregulated genes in contrast are considered as oncogenes. As a conclusion it can be stated that SAM treatment of prostate cancer cells resulted in alterations of H3K4me3 and H3K27me3 methylation profiles. Gene to peak annotation, alignment with results of a transcriptome study as well as GO-term analysis underpinned the biological relevance of methylation changes.
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Affiliation(s)
- Arthur Mathes
- Cardiovascular Genomics and Epigenomics, European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | | | | | - Gergana Dobreva
- Cardiovascular Genomics and Epigenomics, European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Thomas Schmidt
- Anatomy and Developmental Biology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
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Arroyo Villora S, Castellanos Silva P, Zenz T, Kwon JS, Schlaudraff N, Nitaj D, Meckbach C, Dammann R, Richter AM. Biomarker RIPK3 Is Silenced by Hypermethylation in Melanoma and Epigenetic Editing Reestablishes Its Tumor Suppressor Function. Genes (Basel) 2024; 15:175. [PMID: 38397165 PMCID: PMC10888250 DOI: 10.3390/genes15020175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
For several decades, cancers have demonstrably been one of the most frequent causes of death worldwide. In addition to genetic causes, cancer can also be caused by epigenetic gene modifications. Frequently, tumor suppressor genes are epigenetically inactivated due to hypermethylation of their CpG islands, actively contributing to tumorigenesis. Since CpG islands are usually localized near promoters, hypermethylation of the promoter can have a major impact on gene expression. In this study, the potential tumor suppressor gene Receptor Interacting Serine/Threonine Protein Kinase 3 (RIPK3) was examined for an epigenetic regulation and its gene inactivation in melanomas. A hypermethylation of the RIPK3 CpG island was detected by bisulfite pyrosequencing and was accompanied by a correlated loss of its expression. In addition, an increasing RIPK3 methylation rate was observed with increasing tumor stage of melanomas. For further epigenetic characterization of RIPK3, epigenetic modulation was performed using a modified CRISPR/dCas9 (CRISPRa activation) system targeting its DNA hypermethylation. We observed a reduced fitness of melanoma cells by (re-)expression and demethylation of the RIPK3 gene using the epigenetic editing-based method. The tumor suppressive function of RIPK3 was evident by phenotypic determination using fluorescence microscopy, flow cytometry and wound healing assay. Our data highlight the function of RIPK3 as an epigenetically regulated tumor suppressor in melanoma, allowing it to be classified as a biomarker.
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Affiliation(s)
- Sarah Arroyo Villora
- Institute for Genetics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
| | | | - Tamara Zenz
- Institute for Genetics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
| | - Ji Sun Kwon
- Institute for Genetics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
- Department of Mathematics, Natural Sciences and Computer Science, University of Applied Sciences Mittelhessen, 35390 Giessen, Germany
| | - Nico Schlaudraff
- Institute for Genetics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
| | - Dafina Nitaj
- Institute for Genetics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
| | - Cornelia Meckbach
- Department of Mathematics, Natural Sciences and Computer Science, University of Applied Sciences Mittelhessen, 35390 Giessen, Germany
| | - Reinhard Dammann
- Institute for Genetics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
| | - Antje M. Richter
- Institute for Genetics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
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50
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Shen L, Wang B, Wang SP, Ji SK, Fu MJ, Wang SW, Hou WQ, Dai XJ, Liu HM. Combination Therapy and Dual-Target Inhibitors Based on LSD1: New Emerging Tools in Cancer Therapy. J Med Chem 2024; 67:922-951. [PMID: 38214982 DOI: 10.1021/acs.jmedchem.3c02133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2024]
Abstract
Lysine specific demethylase 1 (LSD1), a transcriptional modulator that represses or activates target gene expression, is overexpressed in many cancer and causes imbalance in the expression of normal gene networks. Over two decades, numerous LSD1 inhibitors have been reported, especially some of which have entered clinical trials, including eight irreversible inhibitors (TCP, ORY-1001, GSK-2879552, INCB059872, IMG-7289, ORY-2001, TAK-418, and LH-1802) and two reversible inhibitors (CC-90011 and SP-2577). Most clinical LSD1 inhibitors demonstrated enhanced efficacy in combination with other agents. LSD1 multitarget inhibitors have also been reported, exampled by clinical dual LSD1/histone deacetylases (HDACs) inhibitors 4SC-202 and JBI-802. Herein, we present a comprehensive overview of the combination of LSD1 inhibitors with various antitumor agents, as well as LSD1 multitarget inhibitors. Additionally, the challenges and future research directionsare also discussed, and we hope this review will provide new insight into the development of LSD1-targeted anticancer agents.
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Affiliation(s)
- Liang Shen
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou 450001, Henan, China
| | - Bo Wang
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou 450001, Henan, China
| | - Shao-Peng Wang
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou 450001, Henan, China
| | - Shi-Kun Ji
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou 450001, Henan, China
| | - Meng-Jie Fu
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou 450001, Henan, China
| | - Shu-Wu Wang
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou 450001, Henan, China
| | - Wen-Qing Hou
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou 450001, Henan, China
| | - Xing-Jie Dai
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou 450001, Henan, China
| | - Hong-Min Liu
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou 450001, Henan, China
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