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Rinaldi M, Pezone A, Quadrini GI, Abbadessa G, Laezza MP, Passaro ML, Porcellini A, Costagliola C. Targeting shared pathways in tauopathies and age-related macular degeneration: implications for novel therapies. Front Aging Neurosci 2024; 16:1371745. [PMID: 38633983 PMCID: PMC11021713 DOI: 10.3389/fnagi.2024.1371745] [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: 01/16/2024] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
The intricate parallels in structure and function between the human retina and the central nervous system designate the retina as a prospective avenue for understanding brain-related processes. This review extensively explores the shared physiopathological mechanisms connecting age-related macular degeneration (AMD) and proteinopathies, with a specific focus on tauopathies. The pivotal involvement of oxidative stress and cellular senescence emerges as key drivers of pathogenesis in both conditions. Uncovering these shared elements not only has the potential to enhance our understanding of intricate neurodegenerative diseases but also sets the stage for pioneering therapeutic approaches in AMD.
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Affiliation(s)
- Michele Rinaldi
- Department of Neurosciences, Reproductive Sciences and Dentistry, University of Naples Federico II, Naples, Italy
| | - Antonio Pezone
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Gaia Italia Quadrini
- Department of Neurosciences, Reproductive Sciences and Dentistry, University of Naples Federico II, Naples, Italy
| | - Gianmarco Abbadessa
- Division of Neurology, Department of Advanced Medical and Surgical Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Maria Paola Laezza
- Department of Neurosciences, Reproductive Sciences and Dentistry, University of Naples Federico II, Naples, Italy
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, Campobasso, Italy
| | - Maria Laura Passaro
- Department of Neurosciences, Reproductive Sciences and Dentistry, University of Naples Federico II, Naples, Italy
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, Campobasso, Italy
| | | | - Ciro Costagliola
- Department of Neurosciences, Reproductive Sciences and Dentistry, University of Naples Federico II, Naples, Italy
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2
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Panier S, Wang S, Schumacher B. Genome Instability and DNA Repair in Somatic and Reproductive Aging. ANNUAL REVIEW OF PATHOLOGY 2024; 19:261-290. [PMID: 37832947 DOI: 10.1146/annurev-pathmechdis-051122-093128] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Genetic material is constantly subjected to genotoxic insults and is critically dependent on DNA repair. Genome maintenance mechanisms differ in somatic and germ cells as the soma only requires maintenance during an individual's lifespan, while the germline indefinitely perpetuates its genetic information. DNA lesions are recognized and repaired by mechanistically highly diverse repair machineries. The DNA damage response impinges on a vast array of homeostatic processes and can ultimately result in cell fate changes such as apoptosis or cellular senescence. DNA damage causally contributes to the aging process and aging-associated diseases, most prominently cancer. By causing mutations, DNA damage in germ cells can lead to genetic diseases and impact the evolutionary trajectory of a species. The mechanisms ensuring tight control of germline DNA repair could be highly instructive in defining strategies for improved somatic DNA repair. They may provide future interventions to maintain health and prevent disease during aging.
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Affiliation(s)
- Stephanie Panier
- Institute for Genome Stability in Aging and Disease and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital of Cologne, Cologne, Germany;
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Siyao Wang
- Institute for Genome Stability in Aging and Disease and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital of Cologne, Cologne, Germany;
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital of Cologne, Cologne, Germany;
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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3
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Naeimi N, Mohseni Kouchesfehani H, Heidari Z, Mahmoudzadeh-Sagheb H. Effect of smoking on methylation and semen parameters. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024; 65:76-83. [PMID: 38299759 DOI: 10.1002/em.22583] [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: 08/29/2023] [Revised: 12/03/2023] [Accepted: 01/04/2024] [Indexed: 02/02/2024]
Abstract
One type of epigenetic modification is genomic DNA methylation, which is induced by smoking, and both are associated with male infertility. In this study, the relationship between smoking and CHD5 gene methylation and semen parameters in infertile men was determined. After the MS-PCR of blood in 224 samples, 103 infertile patients (62 smokers and 41 non-smokers) and 121 fertile men, methylation level changes between groups and the effect of methylation and smoking on infertility and semen parameters in infertile men were determined. The results showed that there is a significant difference in the methylation status (MM, MU, UU) of the CHD5 gene between the patient and the control group, and this correlation also exists for the semen parameters (p < .001). The average semen parameters in smokers decreased significantly compared to non-smokers and sperm concentration was (32.21 ± 5.27 vs. 55.27 ± 3.38), respectively. MM methylation status was higher in smokers (22.5%) compared to non-smokers (14.6%). Smoking components affect the methylation pattern of CHD5 gene, and smokers had higher methylation levels and lower semen parameters than non-smokers, which can be biomarkers for evaluating semen quality and infertility risk factors. Understanding the epigenetic effects of smoking on male infertility can be very useful for predicting negative consequences of smoking and providing therapeutic solutions.
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Affiliation(s)
- Nasim Naeimi
- Department of Biology, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran
| | | | - Zahra Heidari
- Department of Histology, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
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Koch Z, Li A, Evans DS, Cummings S, Ideker T. Somatic mutation as an explanation for epigenetic aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.569638. [PMID: 38106096 PMCID: PMC10723383 DOI: 10.1101/2023.12.08.569638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
DNA methylation marks have recently been used to build models known as "epigenetic clocks" which predict calendar age. As methylation of cytosine promotes C-to-T mutations, we hypothesized that the methylation changes observed with age should reflect the accrual of somatic mutations, and the two should yield analogous aging estimates. In analysis of multimodal data from 9,331 human individuals, we find that CpG mutations indeed coincide with changes in methylation, not only at the mutated site but also with pervasive remodeling of the methylome out to ±10 kilobases. This one-to-many mapping enables mutation-based predictions of age that agree with epigenetic clocks, including which individuals are aging faster or slower than expected. Moreover, genomic loci where mutations accumulate with age also tend to have methylation patterns that are especially predictive of age. These results suggest a close coupling between the accumulation of sporadic somatic mutations and the widespread changes in methylation observed over the course of life.
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Affiliation(s)
- Zane Koch
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla CA, 92093, USA
| | - Adam Li
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla CA, 92093, USA
| | - Daniel S. Evans
- California Pacific Medical Center Research Institute, San Francisco CA 94158, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, 94158
| | - Steven Cummings
- California Pacific Medical Center Research Institute, San Francisco CA 94158, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, 94158
| | - Trey Ideker
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla CA, 92093, USA
- Department of Medicine, University of California San Diego, La Jolla California, 92093, USA
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5
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Challis D, Lippis T, Wilson R, Wilkinson E, Dickinson J, Black A, Azimi I, Holloway A, Taberlay P, Brettingham-Moore K. Multiomics analysis of adaptation to repeated DNA damage in prostate cancer cells. Epigenetics 2023; 18:2214047. [PMID: 37196186 DOI: 10.1080/15592294.2023.2214047] [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: 09/28/2022] [Revised: 04/25/2023] [Accepted: 05/09/2023] [Indexed: 05/19/2023] Open
Abstract
DNA damage is frequently utilized as the basis for cancer therapies; however, resistance to DNA damage remains one of the biggest challenges for successful treatment outcomes. Critically, the molecular drivers behind resistance are poorly understood. To address this question, we created an isogenic model of prostate cancer exhibiting more aggressive characteristics to better understand the molecular signatures associated with resistance and metastasis. 22Rv1 cells were repeatedly exposed to DNA damage daily for 6 weeks, similar to patient treatment regimes. Using Illumina Methylation EPIC arrays and RNA-seq, we compared DNA methylation and transcriptional profiles between the parental 22Rv1 cell line and the lineage exposed to prolonged DNA damage. Here we show that repeated DNA damage drives the molecular evolution of cancer cells to a more aggressive phenotype and identify molecular candidates behind this process. Total DNA methylation was increased while RNA-seq demonstrated these cells had dysregulated expression of genes involved in metabolism and the unfolded protein response (UPR) with Asparagine synthetase (ASNS) identified as central to this process. Despite the limited overlap between RNA-seq and DNA methylation, oxoglutarate dehydrogenase-like (OGDHL) was identified as altered in both data sets. Utilising a second approach we profiled the proteome in 22Rv1 cells following a single dose of radiotherapy. This analysis also highlighted the UPR in response to DNA damage. Together, these analyses identified dysregulation of metabolism and the UPR and identified ASNS and OGDHL as candidates for resistance to DNA damage. This work provides critical insight into molecular changes which underpin treatment resistance and metastasis.
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Affiliation(s)
- D Challis
- Tasmanian School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - T Lippis
- Tasmanian School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - R Wilson
- Central Science Laboratory, University of Tasmania, Hobart, Tasmania, Australia
| | - E Wilkinson
- Menzies Institute of Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - J Dickinson
- Menzies Institute of Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - A Black
- Medical Oncology, Royal Hobart Hospital, Hobart, Tasmania, Australia
| | - I Azimi
- School of Pharmacy and Pharmacology, University of Tasmania, Hobart, Tasmania, Australia
| | - A Holloway
- Tasmanian School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - P Taberlay
- Tasmanian School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - K Brettingham-Moore
- Tasmanian School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
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Zhang F, Zhang X, Zhang H, Lin D, Fan H, Guo S, An F, Zhao Y, Li J, Schrodi SJ, Zhang D. Pan-precancer and cancer DNA methylation profiles revealed significant tissue specificity of interrupted biological processes in tumorigenesis. Epigenetics 2023; 18:2231222. [PMID: 37393582 DOI: 10.1080/15592294.2023.2231222] [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: 03/03/2023] [Revised: 06/13/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023] Open
Abstract
DNA methylation (DNAme) alterations are known to initiate from the precancerous stage of tumorigenesis. Herein, we investigated the global and local patterns of DNAme perturbations in tumorigenesis by analysing the genome-wide DNAme profiles of the cervix, colorectum, stomach, prostate, and liver at precancerous and cancer stages. We observed global hypomethylation in tissues of both two stages, except for the cervix, whose global DNAme level in normal tissue was lower than that of the other four tumour types. For alterations shared by both stages, there were common hyper-methylation (sHyperMethyl) and hypo-methylation (sHypoMethyl) changes, of which the latter type was more frequently identified in all tissues. Biological pathways interrupted by sHyperMethyl and sHypoMethyl alterations demonstrated significant tissue specificity. DNAme bidirectional chaos indicated by the enrichment of both sHyperMethyl and sHypoMethyl changes in the same pathway was observed in most tissues and was a common phenomenon, particularly in liver lesions. Moreover, for the same enriched pathways, different tissues may be affected by distinct DNAme types. For the PI3K-Akt signalling pathway, sHyperMethyl enrichment was observed in the prostate dataset, but sHypoMethyl enrichment was observed in the colorectum and liver datasets. Nevertheless, they did not show an increased possibility in survival prediction of patients in comparison with other DNAme types. Additionally, our study demonstrated that gene-body DNAme changes of tumour suppressor genes and oncogenes may persist from precancerous lesions to the tumour. Overall, we demonstrate the tissue specificity and commonality of cross-stage alterations in DNA methylation profiles in multi-tissue tumorigenesis.
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Affiliation(s)
- Feifan Zhang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
| | - Xin Zhang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Haikun Zhang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
| | - Dongdong Lin
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Hailang Fan
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
| | - Shicheng Guo
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Fang An
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China
| | - Yaqian Zhao
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
| | - Jun Li
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Steven J Schrodi
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
- Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Dake Zhang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
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7
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Smagulova F. [Multigenerational epigenetic inheritance in human: the past, present and perspectives]. Biol Aujourdhui 2023; 217:233-243. [PMID: 38018951 DOI: 10.1051/jbio/2023032] [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: 05/01/2023] [Indexed: 11/30/2023]
Abstract
Nowadays, a growing body of evidence suggests that the developmental programs of each individual could be modified. The acquired new phenotypic changes could be persistent throughout the individual's life and even transmitted to the next generation. While the exact mechanism for that preservation is not well understood yet, there are many evidences showing that epigenetic alterations, which are robust and dynamic in response to the influence of the environmental factors, could be responsible for that inheritance. A growing number of external factors such as social stress, environmental pollution and climate changes make adaptation to these environmental changes rather challenging. According to the Developmental Origin of Human Disease theory, formulated by David Barker, environmental conditions experienced during the first phases of development can have long term effects on later phases of life. This phenomenon is linked to the biological plasticity of development, which allows reprogramming of physiological functions in response to different stimuli. Consequently, in utero exposure to environmental pollutants can increase predisposition to different pathologies that can occur both in early and later phases of life not only in the living generation but also in subsequent ones. Here, we have summarised some findings in human epigenetic research studies performed for the past few years which address the question whether transgenerational effects observed in model organisms could also occur in humans.
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Affiliation(s)
- Fatima Smagulova
- Univ. Rennes, EHESP, Inserm, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, 9 avenue Léon Bernard, 35000 Rennes, France
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8
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Craddock J, Jiang J, Patrick SM, Mutambirwa SBA, Stricker PD, Bornman MSR, Jaratlerdsiri W, Hayes VM. Alterations in the Epigenetic Machinery Associated with Prostate Cancer Health Disparities. Cancers (Basel) 2023; 15:3462. [PMID: 37444571 DOI: 10.3390/cancers15133462] [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: 05/24/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Prostate cancer is driven by acquired genetic alterations, including those impacting the epigenetic machinery. With African ancestry as a significant risk factor for aggressive disease, we hypothesize that dysregulation among the roughly 656 epigenetic genes may contribute to prostate cancer health disparities. Investigating prostate tumor genomic data from 109 men of southern African and 56 men of European Australian ancestry, we found that African-derived tumors present with a longer tail of epigenetic driver gene candidates (72 versus 10). Biased towards African-specific drivers (63 versus 9 shared), many are novel to prostate cancer (18/63), including several putative therapeutic targets (CHD7, DPF3, POLR1B, SETD1B, UBTF, and VPS72). Through clustering of all variant types and copy number alterations, we describe two epigenetic PCa taxonomies capable of differentiating patients by ancestry and predicted clinical outcomes. We identified the top genes in African- and European-derived tumors representing a multifunctional "generic machinery", the alteration of which may be instrumental in epigenetic dysregulation and prostate tumorigenesis. In conclusion, numerous somatic alterations in the epigenetic machinery drive prostate carcinogenesis, but African-derived tumors appear to achieve this state with greater diversity among such alterations. The greater novelty observed in African-derived tumors illustrates the significant clinical benefit to be derived from a much needed African-tailored approach to prostate cancer healthcare aimed at reducing prostate cancer health disparities.
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Affiliation(s)
- Jenna Craddock
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
| | - Jue Jiang
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2006, Australia
| | - Sean M Patrick
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
| | - Shingai B A Mutambirwa
- Department of Urology, Sefako Makgatho Health Science University, Dr George Mukhari Academic Hospital, Medunsa 0208, South Africa
| | - Phillip D Stricker
- Department of Urology, St Vincent's Hospital, Darlinghurst, NSW 2010, Australia
| | - M S Riana Bornman
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
| | - Weerachai Jaratlerdsiri
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2006, Australia
| | - Vanessa M Hayes
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2006, Australia
- Manchester Cancer Research Centre, University of Manchester, Manchester M20 4GJ, UK
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Lackner M, Helmbrecht N, Pääbo S, Riesenberg S. Detection of unintended on-target effects in CRISPR genome editing by DNA donors carrying diagnostic substitutions. Nucleic Acids Res 2023; 51:e26. [PMID: 36620901 PMCID: PMC10018342 DOI: 10.1093/nar/gkac1254] [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: 08/09/2022] [Revised: 11/18/2022] [Accepted: 12/15/2022] [Indexed: 01/10/2023] Open
Abstract
CRISPR nucleases can introduce double-stranded DNA breaks in genomes at positions specified by guide RNAs. When repaired by the cell, this may result in the introduction of insertions and deletions or nucleotide substitutions provided by exogenous DNA donors. However, cellular repair can also result in unintended on-target effects, primarily larger deletions and loss of heterozygosity due to gene conversion. Here we present a strategy that allows easy and reliable detection of unintended on-target effects as well as the generation of control cells that carry wild-type alleles but have demonstratively undergone genome editing at the target site. Our 'sequence-ascertained favorable editing' (SAFE) donor approach relies on the use of DNA donor mixtures containing the desired nucleotide substitutions or the wild-type alleles together with combinations of additional 'diagnostic' substitutions unlikely to have any effects. Sequencing of the target sites then results in that two different sequences are seen when both chromosomes are edited with 'SAFE' donors containing different sets of substitutions, while a single sequence indicates unintended effects such as deletions or gene conversion. We analyzed more than 850 human embryonic stem cell clones edited with 'SAFE' donors and detect all copy number changes and almost all clones with gene conversion.
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Affiliation(s)
| | - Nelly Helmbrecht
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Sachsen 04103, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Sachsen 04103, Germany
- Okinawa Institute of Science and Technology, Onna-son, Okinawa 904-0495, Japan
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Escalona RM, Chu S, Kadife E, Kelly JK, Kannourakis G, Findlay JK, Ahmed N. Knock down of TIMP-2 by siRNA and CRISPR/Cas9 mediates diverse cellular reprogramming of metastasis and chemosensitivity in ovarian cancer. Cancer Cell Int 2022; 22:422. [PMID: 36585738 PMCID: PMC9805260 DOI: 10.1186/s12935-022-02838-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The endogenous tissue inhibitor of metalloproteinase-2 (TIMP-2), through its homeostatic action on certain metalloproteinases, plays a vital role in remodelling extracellular matrix (ECM) to facilitate cancer progression. This study investigated the role of TIMP-2 in an ovarian cancer cell line in which the expression of TIMP-2 was reduced by either siRNA or CRISPR/Cas9. METHODS OVCAR5 cells were transiently and stably transfected with either single or pooled TIMP-2 siRNAs (T2-KD cells) or by CRISPR/Cas9 under the influence of two distinct guide RNAs (gRNA1 and gRNA2 cell lines). The expression of different genes was analysed at the mRNA level by quantitative real time PCR (qRT-PCR) and at the protein level by immunofluorescence (IF) and western blot. Proliferation of cells was investigated by 5-Ethynyl-2'-deoxyuridine (EdU) assay or staining with Ki67. Cell migration/invasion was determined by xCELLigence. Cell growth in vitro was determined by 3D spheroid cultures and in vivo by a mouse xenograft model. RESULTS Approximately 70-90% knock down of TIMP-2 expression were confirmed in T2-KD, gRNA1 and gRNA2 OVCAR5 ovarian cancer cells at the protein level. T2-KD, gRNA1 and gRNA2 cells exhibited a significant downregulation of MMP-2 expression, but concurrently a significant upregulation in the expression of membrane bound MMP-14 compared to control and parental cells. Enhanced proliferation and invasion were exhibited in all TIMP-2 knocked down cells but differences in sensitivity to paclitaxel (PTX) treatment were observed, with T2-KD cells and gRNA2 cell line being sensitive, while the gRNA1 cell line was resistant to PTX treatment. In addition, significant differences in the growth of gRNA1 and gRNA2 cell lines were observed in in vitro 3D cultures as well as in an in vivo mouse xenograft model. CONCLUSIONS Our results suggest that the inhibition of TIMP-2 by siRNA and CRISPR/Cas-9 modulate the expression of MMP-2 and MMP-14 and reprogram ovarian cancer cells to facilitate proliferation and invasion. Distinct disparities in in vitro chemosensitivity and growth in 3D culture, and differences in tumour burden and invasion to proximal organs in a mouse model imply that selective suppression of TIMP-2 expression by siRNA or CRISPR/Cas-9 alters important aspects of metastasis and chemosensitivity in ovarian cancer.
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Affiliation(s)
- Ruth M. Escalona
- grid.1008.90000 0001 2179 088XDepartment of Obstetrics and Gynaecology, University of Melbourne, Melbourne, VIC 3052 Australia ,grid.1002.30000 0004 1936 7857Centre for Reproductive Health, Hudson Institute of Medical Research and Department of Translational Medicine, Monash University, Clayton, VIC 3168 Australia ,Fiona Elsey Cancer Research Institute, Suites 23, 106-110 Lydiard Street South, Ballarat Technology Park Central, Ballarat, VIC 3350 Australia
| | - Simon Chu
- grid.1002.30000 0004 1936 7857Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research and Department of Translational Medicine, Monash University, Clayton, VIC 3168 Australia
| | - Elif Kadife
- Fiona Elsey Cancer Research Institute, Suites 23, 106-110 Lydiard Street South, Ballarat Technology Park Central, Ballarat, VIC 3350 Australia
| | - Jason K. Kelly
- Fiona Elsey Cancer Research Institute, Suites 23, 106-110 Lydiard Street South, Ballarat Technology Park Central, Ballarat, VIC 3350 Australia
| | - George Kannourakis
- Fiona Elsey Cancer Research Institute, Suites 23, 106-110 Lydiard Street South, Ballarat Technology Park Central, Ballarat, VIC 3350 Australia ,grid.1040.50000 0001 1091 4859School of Science, Psychology and Sport, Federation University, Mt Helen, VIC 3350 Australia
| | - Jock K. Findlay
- grid.1008.90000 0001 2179 088XDepartment of Obstetrics and Gynaecology, University of Melbourne, Melbourne, VIC 3052 Australia ,grid.1002.30000 0004 1936 7857Centre for Reproductive Health, Hudson Institute of Medical Research and Department of Translational Medicine, Monash University, Clayton, VIC 3168 Australia
| | - Nuzhat Ahmed
- grid.1008.90000 0001 2179 088XDepartment of Obstetrics and Gynaecology, University of Melbourne, Melbourne, VIC 3052 Australia ,grid.1002.30000 0004 1936 7857Centre for Reproductive Health, Hudson Institute of Medical Research and Department of Translational Medicine, Monash University, Clayton, VIC 3168 Australia ,Fiona Elsey Cancer Research Institute, Suites 23, 106-110 Lydiard Street South, Ballarat Technology Park Central, Ballarat, VIC 3350 Australia ,grid.1040.50000 0001 1091 4859School of Science, Psychology and Sport, Federation University, Mt Helen, VIC 3350 Australia
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Pal R, Rakshit S, Shanmugam G, Paul N, Bhattacharya D, Chatterjee A, Singh A, George M, Sarkar K. Involvement of Xeroderma Pigmentosum Complementation Group G (XPG) in epigenetic regulation of T-Helper (T H) cell differentiation during breast cancer. Immunobiology 2022; 227:152259. [PMID: 36037675 DOI: 10.1016/j.imbio.2022.152259] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 08/03/2022] [Accepted: 08/13/2022] [Indexed: 11/05/2022]
Abstract
TNFα and IFN-γ secreted by CD4+T-Helper (TH) cells have antitumor activity followed by polarisation of TH1 phenotype in response to IL-12 secreted by dendritic cells, inducing expression of XPG, Nucleotide-Excision Repair (NER) complex component, which is downregulated in breast cancer. Therefore, we investigated the involvement of XPG in TH-cell differentiation in breast cancer. XPG knock-out (KO) PBMC and TH1 polarised CD4+ TH-cells isolated from breast cancer and control subjects blood samples were used to observe mRNA expressions of associated genes, % enrichment of corresponding epigenetic markers, and m6A RNA methylation levels to study the molecular mechanisms involved. Assays to investigate Cytotoxic T Lymphocyte (CTL) activity after cross-checking extracellular secretion levels. Our XPGKO results indicated upregulation of TH2 and Treg, downregulation of TH1, and negligible change for TH17; reduced expression of genes associated with tumour suppression (TP53, BRCA1) and DNA repair (H2AFX, ATM) for breast cancer TH-cells. CTCF associated TH1 specific function, reduced %enrichment of XPG, CSA, and ERCC1, increased %enrichment of γH2A.X, and altered histone modifications (methylation, deacetylation) at the IFN-γ gene locus in XPGKO breast cancer TH1-cells. Increased m6A RNA methylation mediated by XPG leads to TH1 cell specificity, further inducing CTL activity by releasing extracellular IFG-γ, which activates CD8+ CTLs. This article explores the association of the vital NER protein, XPG with the epigenetic modifications behind TH1 cell differentiation, augmenting the expressions of TH1-network genes to evoke protective immunity in breast cancer.
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Affiliation(s)
- Riasha Pal
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
| | - Sudeshna Rakshit
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
| | - Geetha Shanmugam
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
| | - Nilanjan Paul
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
| | - Deep Bhattacharya
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
| | - Arya Chatterjee
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
| | - Arunangsu Singh
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
| | - Melvin George
- Department of Clinical Pharmacology, SRM Medical College Hospital and Research Centre, Kattankulathur, Tamil Nadu 603203, India
| | - Koustav Sarkar
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India.
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12
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Anqi Y, Saina Y, Chujie C, Yanfei Y, Xiangwei T, Jiajia M, Jiaojiao X, Maoliang R, Bin C. Regulation of DNA methylation during the testicular development of Shaziling pigs. Genomics 2022; 114:110450. [PMID: 35995261 DOI: 10.1016/j.ygeno.2022.110450] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/21/2022] [Accepted: 08/16/2022] [Indexed: 11/18/2022]
Abstract
DNA methylation is one of the key epigenetic regulatory mechanisms in development and spermatogenesis. However, the dynamic regulatory mechanisms of genome-wide DNA methylation during testicular development remain largely unknown. Herein, we generated a single-base resolution DNA methylome and transcriptome atlas of precocious porcine testicular tissues across three developmental stages (1, 75, and 150 days old). The results showed that the dynamic methylation patterns were directly related to the expression of the DNMT3A gene. Conjoint analysis revealed a negative regulatory pattern between promoter methylation and the positive regulation of 3'-untranslated region (3'UTR) methylation. Mechanistically, the decrease in promoter methylation affected the upregulation of meiosis-related genes, such as HORMAD1, SPO11, and SYCE1. Demethylation in the 3'UTR induced the downregulation of the INHBA gene and knockdown of INHBA inhibited cell proliferation by reducing the synthesis of activin A. These findings contribute to exploring the regulatory mechanisms of DNA methylation in testicular development.
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Affiliation(s)
- Yang Anqi
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Yan Saina
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Chen Chujie
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Yin Yanfei
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Tang Xiangwei
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Ma Jiajia
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Xiang Jiaojiao
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Ran Maoliang
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China.
| | - Chen Bin
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China.
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13
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Abstract
Over the course of a human lifespan, genome integrity erodes, leading to an increased abundance of several types of chromatin changes. The abundance of DNA lesions (chemical perturbations to nucleotides) increases with age, as does the number of genomic mutations and transcriptional disruptions caused by replication or transcription of those lesions, respectively. At the epigenetic level, precise DNA methylation patterns degrade, likely causing increasingly stochastic variations in gene expression. Similarly, the tight regulation of histone modifications begins to unravel. The genomic instability caused by these mechanisms allows transposon element reactivation and remobilization, further mutations, gene dysregulation, and cytoplasmic chromatin fragments. This cumulative genomic instability promotes cell signaling events that drive cell fate decisions and extracellular communications known to disrupt tissue homeostasis and regeneration. In this Review, we focus on age-related epigenetic changes and their interactions with age-related genomic changes that instigate these events.
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Affiliation(s)
- Carolina Soto-Palma
- Institute on the Biology of Aging and Metabolism
- Department of Biochemistry, Molecular Biology, and Biophysics
| | - Laura J. Niedernhofer
- Institute on the Biology of Aging and Metabolism
- Department of Biochemistry, Molecular Biology, and Biophysics
| | - Christopher D. Faulk
- Institute on the Biology of Aging and Metabolism
- Department of Animal Science, and
| | - Xiao Dong
- Institute on the Biology of Aging and Metabolism
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
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14
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Michalak M, Plitta-Michalak BP, Naskręt-Barciszewska MZ, Barciszewski J, Chmielarz P. DNA Methylation as an Early Indicator of Aging in Stored Seeds of “Exceptional” Species Populus nigra L. Cells 2022; 11:cells11132080. [PMID: 35805164 PMCID: PMC9265770 DOI: 10.3390/cells11132080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 01/27/2023] Open
Abstract
Ex situ preservation of genetic resources is an essential strategy for the conservation of plant biodiversity. In this regard, seed storage is the most convenient and efficient way of preserving germplasm for future plant breeding efforts. A better understanding of the molecular changes that occur during seed desiccation and aging is necessary to improve conservation protocols, as well as real-time methods for monitoring seed quality. In the present study, we assessed changes in the level of genomic 5-methylcytosine (5mC) in seeds of Populus nigra L. by 2D-TLC. Epigenetic changes were characterized in response to several seed storage regimes. Our results demonstrate that P. nigra seeds represent an intermediate type of post-harvest behavior, falling between recalcitrant and orthodox seeds. This was also true for the epigenetic response of P. nigra seeds to external factors. A crucial question is whether aging in seeds is initiated by a decline in the level of 5mC, or if epigenetic changes induce a process that leads to deterioration. In our study, we demonstrate for the first time that 5mC levels decrease during storage and that the decline can be detected before any changes in seed germination are evident. Once P. nigra seeds reached an 8–10% reduction in the level of 5mC, a substantial decrease in germination occurred. The decline in the level of 5mC appears to be a critical parameter underlying the rapid deterioration of intermediate seeds. Thus, the measurement of 5mC can be a fast, real-time method for assessing asymptomatic aging in stored seeds.
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Affiliation(s)
- Marcin Michalak
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, M Oczapowskiego 1A, 10-721 Olsztyn, Poland;
- Correspondence: ; Tel.: +48-89-523-44-55
| | - Beata Patrycja Plitta-Michalak
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, M Oczapowskiego 1A, 10-721 Olsztyn, Poland;
- Department of Chemistry, University of Warmia and Mazury in Olsztyn, Plac Łódzki 4, 10-719 Olsztyn, Poland
| | | | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznan, Poland; (M.Z.N.-B.); (J.B.)
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland
| | - Paweł Chmielarz
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kornik, Poland;
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15
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Kciuk M, Gielecińska A, Kołat D, Kałuzińska Ż, Kontek R. Transcription factors in DNA damage response. Biochim Biophys Acta Rev Cancer 2022; 1877:188757. [PMID: 35781034 DOI: 10.1016/j.bbcan.2022.188757] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/13/2022] [Accepted: 06/25/2022] [Indexed: 10/17/2022]
Abstract
Transcription factors (TFs) constitute a wide and highly diverse group of proteins capable of controlling gene expression. Their roles in oncogenesis, tumor progression, and metastasis have been established, but recently their role in the DNA damage response pathway (DDR) has emerged. Many of them can affect elements of canonical DDR pathways, modulating their activity and deciding on the effectiveness of DNA repair. In this review, we focus on the latest reports on the effects of two TFs with dual roles in oncogenesis and metastasis (hypoxia-inducible factor-1 α (HIF1α), proto-oncogene MYC) and three epithelial-mesenchymal transition (EMT) TFs (twist-related protein 1 (TWIST), zinc-finger E-box binding homeobox 1 (ZEB1), and zinc finger protein 281 (ZNF281)) associated with control of canonical DDR pathways.
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Affiliation(s)
- Mateusz Kciuk
- Department of Molecular Biotechnology and Genetics, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland; University of Lodz, Doctoral School of Exact and Natural Sciences, Banacha Street 12/16, 90-237 Lodz, Poland.
| | - Adrianna Gielecińska
- Department of Molecular Biotechnology and Genetics, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
| | - Damian Kołat
- Department of Experimental Surgery, Faculty of Medicine, Medical University of Lodz, Narutowicza 60, 90-136 Lodz, Poland
| | - Żaneta Kałuzińska
- Department of Experimental Surgery, Faculty of Medicine, Medical University of Lodz, Narutowicza 60, 90-136 Lodz, Poland
| | - Renata Kontek
- Department of Molecular Biotechnology and Genetics, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
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16
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Laqqan MM, Yassin MM. Cigarette heavy smoking alters DNA methylation patterns and gene transcription levels in humans spermatozoa. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:26835-26849. [PMID: 34855177 DOI: 10.1007/s11356-021-17786-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/23/2021] [Indexed: 05/27/2023]
Abstract
Tobacco smoking is considered the most common reason of death and infertility around the world. This study was designed to assess the impact of tobacco heavy smoking on sperm DNA methylation patterns and to determine whether the transcription level of ALDH3B2, PTGIR, PRICKLE2, and ALS2CR12 genes is different in heavy smokers compared to non-smokers. As a screening study, the 450 K array was used to assess the alteration in DNA methylation patterns between heavy smokers (n = 15) and non-smokers (n = 15). Then, four CpGs that have the highest difference in methylation level (cg16338278, cg08408433, cg05799088, and cg07227024) were selected for validation using deep bisulfite sequencing in an independent cohort of heavy smokers (n = 200) and non-smokers (n = 100). A significant variation was found between heavy smokers and non-smokers in the methylation level at all CpGs within the PRICKLE2 and ALS2CR12 gene amplicon (P < 0.001). Similarly, a significant variation was found in the methylation level at nine out of thirteen CpGs within the ALDH3B2 gene amplicon (P < 0.01). Additionally, eighteen CpGs out of the twenty-six within the PTGIR gene amplicon have a significant difference in the methylation level between heavy smokers and non-smokers (P < 0.01). The study showed a significant difference in sperm global DNA methylation, chromatin non-condensation, and DNA fragmentation (P < 0.001) between heavy smokers and non-smokers. A significant decline was shown in the transcription level of ALDH3B2, PTGIR, PRICKLE2, and ALS2CR12 genes (P < 0.001) in heavy smokers. In conclusion, heavy smoking influences DNA methylation at several CpGs, sperm global DNA methylation, and transcription level of the PRICKLE2, ALS2CR12, ALDH3B2, and PTGIR genes, which affects negatively the semen parameters of heavy smokers.
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Affiliation(s)
- Mohammed M Laqqan
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, Islamic University, Gaza, Palestinian Territories, Palestine.
| | - Maged M Yassin
- Department of Human Physiology, Faculty of Medicine, Islamic University, Gaza, Palestinian Territories, Palestine
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17
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Fan X, Fan Z, Yang Z, Huang T, Tong Y, Yang D, Mao X, Yang M. Flavonoids-Natural Gifts to Promote Health and Longevity. Int J Mol Sci 2022; 23:ijms23042176. [PMID: 35216290 PMCID: PMC8879655 DOI: 10.3390/ijms23042176] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 02/01/2023] Open
Abstract
The aging of mammals is accompanied by the progressive atrophy of tissues and organs and the accumulation of random damage to macromolecular DNA, protein, and lipids. Flavonoids have excellent antioxidant, anti-inflammatory, and neuroprotective effects. Recent studies have shown that flavonoids can delay aging and prolong a healthy lifespan by eliminating senescent cells, inhibiting senescence-related secretion phenotypes (SASPs), and maintaining metabolic homeostasis. However, only a few systematic studies have described flavonoids in clinical treatment for anti-aging, which needs to be explored further. This review first highlights the association between aging and macromolecular damage. Then, we discuss advances in the role of flavonoid molecules in prolonging the health span and lifespan of organisms. This study may provide crucial information for drug design and developmental and clinical applications based on flavonoids.
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Affiliation(s)
- Xiaolan Fan
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China; (X.F.); (Z.F.); (Z.Y.); (T.H.); (Y.T.); (D.Y.); (X.M.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Ziqiang Fan
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China; (X.F.); (Z.F.); (Z.Y.); (T.H.); (Y.T.); (D.Y.); (X.M.)
| | - Ziyue Yang
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China; (X.F.); (Z.F.); (Z.Y.); (T.H.); (Y.T.); (D.Y.); (X.M.)
| | - Tiantian Huang
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China; (X.F.); (Z.F.); (Z.Y.); (T.H.); (Y.T.); (D.Y.); (X.M.)
| | - Yingdong Tong
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China; (X.F.); (Z.F.); (Z.Y.); (T.H.); (Y.T.); (D.Y.); (X.M.)
| | - Deying Yang
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China; (X.F.); (Z.F.); (Z.Y.); (T.H.); (Y.T.); (D.Y.); (X.M.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xueping Mao
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China; (X.F.); (Z.F.); (Z.Y.); (T.H.); (Y.T.); (D.Y.); (X.M.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingyao Yang
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China; (X.F.); (Z.F.); (Z.Y.); (T.H.); (Y.T.); (D.Y.); (X.M.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence:
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18
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Irfan J, Febrianto MR, Sharma A, Rose T, Mahmudzade Y, Di Giovanni S, Nagy I, Torres-Perez JV. DNA Methylation and Non-Coding RNAs during Tissue-Injury Associated Pain. Int J Mol Sci 2022; 23:ijms23020752. [PMID: 35054943 PMCID: PMC8775747 DOI: 10.3390/ijms23020752] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 02/01/2023] Open
Abstract
While about half of the population experience persistent pain associated with tissue damages during their lifetime, current symptom-based approaches often fail to reduce such pain to a satisfactory level. To provide better patient care, mechanism-based analgesic approaches must be developed, which necessitates a comprehensive understanding of the nociceptive mechanism leading to tissue injury-associated persistent pain. Epigenetic events leading the altered transcription in the nervous system are pivotal in the maintenance of pain in tissue injury. However, the mechanisms through which those events contribute to the persistence of pain are not fully understood. This review provides a summary and critical evaluation of two epigenetic mechanisms, DNA methylation and non-coding RNA expression, on transcriptional modulation in nociceptive pathways during the development of tissue injury-associated pain. We assess the pre-clinical data and their translational implication and evaluate the potential of controlling DNA methylation and non-coding RNA expression as novel analgesic approaches and/or biomarkers of persistent pain.
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Affiliation(s)
- Jahanzaib Irfan
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
| | - Muhammad Rizki Febrianto
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
| | - Anju Sharma
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
| | - Thomas Rose
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
| | - Yasamin Mahmudzade
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
| | - Simone Di Giovanni
- Department of Brain Sciences, Division of Neuroscience, Imperial College London, E505, Burlington Danes, Du Cane Road, London W12 ONN, UK;
| | - Istvan Nagy
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
- Correspondence: (I.N.); (J.V.T.-P.)
| | - Jose Vicente Torres-Perez
- Department of Brain Sciences, Dementia Research Institute, Imperial College London, 86 Wood Ln, London W12 0BZ, UK
- Departament de Biologia Cellular, Biologia Funcional i Antropologia Física, Facultat de Ciències Biològiques, Universitat de València, C/Dr. Moliner 50, 46100 Burjassot, Spain
- Correspondence: (I.N.); (J.V.T.-P.)
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19
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Li X, Zhang Y, Dong X, Zhou G, Sang Y, Gao L, Zhou X, Sun Z. DNA methylation changes induced by BDE-209 are related to DNA damage response and germ cell development in GC-2spd. J Environ Sci (China) 2021; 109:161-170. [PMID: 34607665 DOI: 10.1016/j.jes.2021.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 06/13/2023]
Abstract
Decabrominated diphenyl ether (BDE-209) is generally utilized in multiple polymer materials as common brominated flame retardant. BDE-209 has been listed as persistent organic pollutants (POPs), which was considered to be reproductive toxin in the environment. But it still remains unclear about the effects of BDE-209 on DNA methylation and the induced-male reproductive toxicity. Due to the extensive epigenetic regulation in germ line development, we hypothesize that BDE-209 exposure impacts the statue of DNA methylation in spermatocytes in vitro. Therefore, the mouse GC-2spd (GC-2) cells were used for the genome wide DNA methylation analysis after treated with 32 μg/mL BDE-209 for 24 hr. The results showed that BDE-209 caused genomic methylation changes with 32,083 differentially methylated CpGs in GC-2 cells, including 16,164 (50.38%) hypermethylated and 15,919 (49.62%) hypomethylated sites. With integrated analysis of DNA methylation data and functional enrichment, we found that BDE-209 might affect the functional transcription in cell growth and sperm development by differential gene methylation. qRT-PCR validation demonstrated the involvement of p53-dependent DNA damage response in the GC-2 cells after BDE-209 exposure. In general, our findings indicated that BDE-209-induced genome wide methylation changes could be interrelated with reproductive dysfunction. This study might provide new insights into the mechanisms of male reproductive toxicity under the environmental exposure to BDE-209.
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Affiliation(s)
- Xiangyang Li
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Yue Zhang
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Xiaomin Dong
- Experimental Center for basic medical teaching, Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Guiqing Zhou
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Yujian Sang
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Leqiang Gao
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Xianqing Zhou
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China.
| | - Zhiwei Sun
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
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20
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Divoux A, Eroshkin A, Erdos E, Sandor K, Osborne TF, Smith SR. DNA Methylation as a Marker of Body Shape in Premenopausal Women. Front Genet 2021; 12:709342. [PMID: 34394195 PMCID: PMC8358448 DOI: 10.3389/fgene.2021.709342] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/05/2021] [Indexed: 12/23/2022] Open
Abstract
Preferential accumulation of fat in the gluteo-femoral (GF) depot (pear shape) rather than in the abdominal (A) depot (apple shape), protects against the development of metabolic diseases but the underlying molecular mechanism is still unknown. Recent data, including our work, suggest that differential epigenetic marking is associated with regulation of genes attributed to distinct fat distribution. Here, we aimed to compare the genomic DNA methylation signatures between apple and pear-shaped premenopausal women. To investigate the contribution of upper and lower body fat, we used paired samples of A-FAT and GF-FAT, analyzed on the BeadChip Methylation Array and quantified the differentially methylated sites between the 2 groups of women. We found unique DNA methylation patterns within both fat depots that are significantly different depending on the body fat distribution. Around 60% of the body shape specific DNA methylation sites identified in adipose tissue are maintained ex vivo in cultured preadipocytes. As it has been reported before in other cell types, we found only a hand full of genes showing coordinated differential methylation and expression levels. Finally, we determined that more than 50% of the body shape specific DNA methylation sites could also be detected in whole blood derived DNA. These data reveal a strong DNA methylation program associated with adipose tissue distribution with the possibility that a simple blood test could be used as a predictive diagnostic indicator of young women who are at increased risk for progressing to the apple body shape with a higher risk of developing obesity related complications. Clinical Trial Registration:https://clinicaltrials.gov/ct2/show/NCT02728635 and https://clinicaltrials.gov/ct2/show/NCT02226640, identifiers NCT02728635 and NCT02226640.
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Affiliation(s)
- Adeline Divoux
- Translational Research Institute for Metabolism and Diabetes, AdventHealth, Orlando, FL, United States
| | | | - Edina Erdos
- Department of Medicine, Johns Hopkins University School of Medicine, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, United States
| | - Katalin Sandor
- Department of Medicine, Johns Hopkins University School of Medicine, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, United States
| | - Timothy F. Osborne
- Department of Medicine, Johns Hopkins University School of Medicine, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, United States
| | - Steven R. Smith
- Translational Research Institute for Metabolism and Diabetes, AdventHealth, Orlando, FL, United States
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21
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Mechanisms of Ataxia Telangiectasia Mutated (ATM) Control in the DNA Damage Response to Oxidative Stress, Epigenetic Regulation, and Persistent Innate Immune Suppression Following Sepsis. Antioxidants (Basel) 2021; 10:antiox10071146. [PMID: 34356379 PMCID: PMC8301080 DOI: 10.3390/antiox10071146] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 02/06/2023] Open
Abstract
Cells have evolved extensive signaling mechanisms to maintain redox homeostasis. While basal levels of oxidants are critical for normal signaling, a tipping point is reached when the level of oxidant species exceed cellular antioxidant capabilities. Myriad pathological conditions are characterized by elevated oxidative stress, which can cause alterations in cellular operations and damage to cellular components including nucleic acids. Maintenance of nuclear chromatin are critically important for host survival and eukaryotic organisms possess an elaborately orchestrated response to initiate repair of such DNA damage. Recent evidence indicates links between the cellular antioxidant response, the DNA damage response (DDR), and the epigenetic status of the cell under conditions of elevated oxidative stress. In this emerging model, the cellular response to excessive oxidants may include redox sensors that regulate both the DDR and an orchestrated change to the epigenome in a tightly controlled program that both protects and regulates the nuclear genome. Herein we use sepsis as a model of an inflammatory pathophysiological condition that results in elevated oxidative stress, upregulation of the DDR, and epigenetic reprogramming of hematopoietic stem cells (HSCs) to discuss new evidence for interplay between the antioxidant response, the DNA damage response, and epigenetic status.
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22
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Mancini M, Magnani E, Macchi F, Bonapace IM. The multi-functionality of UHRF1: epigenome maintenance and preservation of genome integrity. Nucleic Acids Res 2021; 49:6053-6068. [PMID: 33939809 PMCID: PMC8216287 DOI: 10.1093/nar/gkab293] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 04/02/2021] [Accepted: 04/12/2021] [Indexed: 12/23/2022] Open
Abstract
During S phase, the cooperation between the macromolecular complexes regulating DNA synthesis, epigenetic information maintenance and DNA repair is advantageous for cells, as they can rapidly detect DNA damage and initiate the DNA damage response (DDR). UHRF1 is a fundamental epigenetic regulator; its ability to coordinate DNA methylation and histone code is unique across proteomes of different species. Recently, UHRF1’s role in DNA damage repair has been explored and recognized to be as important as its role in maintaining the epigenome. UHRF1 is a sensor for interstrand crosslinks and a determinant for the switch towards homologous recombination in the repair of double-strand breaks; its loss results in enhanced sensitivity to DNA damage. These functions are finely regulated by specific post-translational modifications and are mediated by the SRA domain, which binds to damaged DNA, and the RING domain. Here, we review recent studies on the role of UHRF1 in DDR focusing on how it recognizes DNA damage and cooperates with other proteins in its repair. We then discuss how UHRF1’s epigenetic abilities in reading and writing histone modifications, or its interactions with ncRNAs, could interlace with its role in DDR.
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Affiliation(s)
- Monica Mancini
- Department of Biotechnology and Life Sciences, University of Insubria, Busto Arsizio, VA 21052, Italy
| | - Elena Magnani
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, PO Box 129188, United Arab Emirates
| | - Filippo Macchi
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, PO Box 129188, United Arab Emirates
| | - Ian Marc Bonapace
- Department of Biotechnology and Life Sciences, University of Insubria, Busto Arsizio, VA 21052, Italy
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23
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The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts. Nat Commun 2021; 12:4247. [PMID: 34253727 PMCID: PMC8275611 DOI: 10.1038/s41467-021-24528-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/21/2021] [Indexed: 02/06/2023] Open
Abstract
The gymnosperm Welwitschia mirabilis belongs to the ancient, enigmatic gnetophyte lineage. It is a unique desert plant with extreme longevity and two ever-elongating leaves. We present a chromosome-level assembly of its genome (6.8 Gb/1 C) together with methylome and transcriptome data to explore its astonishing biology. We also present a refined, high-quality assembly of Gnetum montanum to enhance our understanding of gnetophyte genome evolution. The Welwitschia genome has been shaped by a lineage-specific ancient, whole genome duplication (~86 million years ago) and more recently (1-2 million years) by bursts of retrotransposon activity. High levels of cytosine methylation (particularly at CHH motifs) are associated with retrotransposons, whilst long-term deamination has resulted in an exceptionally GC-poor genome. Changes in copy number and/or expression of gene families and transcription factors (e.g. R2R3MYB, SAUR) controlling cell growth, differentiation and metabolism underpin the plant's longevity and tolerance to temperature, nutrient and water stress.
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24
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Yoblinski AR, Chung S, Robinson SB, Forester KE, Strahl BD, Dronamraju R. Catalysis-dependent and redundant roles of Dma1 and Dma2 in maintenance of genome stability in Saccharomyces cerevisiae. J Biol Chem 2021; 296:100721. [PMID: 33933452 PMCID: PMC8165551 DOI: 10.1016/j.jbc.2021.100721] [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: 12/03/2020] [Revised: 04/20/2021] [Accepted: 04/27/2021] [Indexed: 10/25/2022] Open
Abstract
DNA double-strand breaks (DSBs) are among the deleterious lesions that are both endogenous and exogenous in origin and are repaired by nonhomologous end joining or homologous recombination. However, the molecular mechanisms responsible for maintaining genome stability remain incompletely understood. Here, we investigate the role of two E3 ligases, Dma1 and Dma2 (homologs of human RNF8), in the maintenance of genome stability in budding yeast. Using yeast spotting assays, chromatin immunoprecipitation and plasmid and chromosomal repair assays, we establish that Dma1 and Dma2 act in a redundant and a catalysis-dependent manner in the maintenance of genome stability, as well as localize to transcribed regions of the genome and increase in abundance upon phleomycin treatment. In addition, Dma1 and Dma2 are required for the normal kinetics of histone H4 acetylation under DNA damage conditions, genetically interact with RAD9 and SAE2, and are in a complex with Rad53 and histones. Taken together, our results demonstrate the requirement of Dma1 and Dma2 in regulating DNA repair pathway choice, preferentially affecting homologous recombination over nonhomologous end joining, and open up the possibility of using these candidates in manipulating the repair pathways toward precision genome editing.
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Affiliation(s)
- Andrew R Yoblinski
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Seoyoung Chung
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Sophie B Robinson
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Kaitlyn E Forester
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Brian D Strahl
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
| | - Raghuvar Dronamraju
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.
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25
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Epigenome Chaos: Stochastic and Deterministic DNA Methylation Events Drive Cancer Evolution. Cancers (Basel) 2021; 13:cancers13081800. [PMID: 33918773 PMCID: PMC8069666 DOI: 10.3390/cancers13081800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/04/2021] [Accepted: 04/07/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Cancer is a group of diseases characterized by abnormal cell growth with a high potential to invade other tissues. Genetic abnormalities and epigenetic alterations found in tumors can be due to high levels of DNA damage and repair. These can be transmitted to daughter cells, which assuming other alterations as well, will generate heterogeneous and complex populations. Deciphering this complexity represents a central point for understanding the molecular mechanisms of cancer and its therapy. Here, we summarize the genomic and epigenomic events that occur in cancer and discuss novel approaches to analyze the epigenetic complexity of cancer cell populations. Abstract Cancer evolution is associated with genomic instability and epigenetic alterations, which contribute to the inter and intra tumor heterogeneity, making genetic markers not accurate to monitor tumor evolution. Epigenetic changes, aberrant DNA methylation and modifications of chromatin proteins, determine the “epigenome chaos”, which means that the changes of epigenetic traits are randomly generated, but strongly selected by deterministic events. Disordered changes of DNA methylation profiles are the hallmarks of all cancer types, but it is not clear if aberrant methylation is the cause or the consequence of cancer evolution. Critical points to address are the profound epigenetic intra- and inter-tumor heterogeneity and the nature of the heterogeneity of the methylation patterns in each single cell in the tumor population. To analyze the methylation heterogeneity of tumors, new technological and informatic tools have been developed. This review discusses the state of the art of DNA methylation analysis and new approaches to reduce or solve the complexity of methylated alleles in DNA or cell populations.
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26
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Schumacher B, Pothof J, Vijg J, Hoeijmakers JH. The central role of DNA damage in the ageing process. Nature 2021; 592:695-703. [PMID: 33911272 PMCID: PMC9844150 DOI: 10.1038/s41586-021-03307-7] [Citation(s) in RCA: 310] [Impact Index Per Article: 103.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 01/28/2021] [Indexed: 01/31/2023]
Abstract
Ageing is a complex, multifaceted process leading to widespread functional decline that affects every organ and tissue, but it remains unknown whether ageing has a unifying causal mechanism or is grounded in multiple sources. Phenotypically, the ageing process is associated with a wide variety of features at the molecular, cellular and physiological level-for example, genomic and epigenomic alterations, loss of proteostasis, declining overall cellular and subcellular function and deregulation of signalling systems. However, the relative importance, mechanistic interrelationships and hierarchical order of these features of ageing have not been clarified. Here we synthesize accumulating evidence that DNA damage affects most, if not all, aspects of the ageing phenotype, making it a potentially unifying cause of ageing. Targeting DNA damage and its mechanistic links with the ageing phenotype will provide a logical rationale for developing unified interventions to counteract age-related dysfunction and disease.
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Affiliation(s)
- Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Cologne, Germany. .,Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
| | - Joris Pothof
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA,Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jan H.J. Hoeijmakers
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany,Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany,Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands,Princess Máxima Center for Pediatric Oncology, Oncode Institute, Utrecht, The Netherlands
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27
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Chen F, Zhang Y, Creighton CJ. Systematic identification of non-coding somatic single nucleotide variants associated with altered transcription and DNA methylation in adult and pediatric cancers. NAR Cancer 2021; 3:zcab001. [PMID: 33554123 PMCID: PMC7849833 DOI: 10.1093/narcan/zcab001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/09/2020] [Accepted: 01/05/2021] [Indexed: 01/12/2023] Open
Abstract
Whole-genome sequencing combined with transcriptomics can reveal impactful non-coding single nucleotide variants (SNVs) in cancer. Here, we developed an integrative analytical approach that, as a first step, identifies genes altered in expression or DNA methylation in association with nearby somatic SNVs, in contrast to alternative approaches that first identify mutational hotspots. Using genomic datasets from the Pan-Cancer Analysis of Whole Genomes (PCAWG) consortium and the Children's Brain Tumor Tissue Consortium (CBTTC), we identified hundreds of genes and associated CpG islands for which the nearby presence of a non-coding somatic SNV recurrently associated with altered expression or DNA methylation, respectively. Genomic regions upstream or downstream of genes, gene introns and gene untranslated regions were all involved. The PCAWG adult cancer cohort yielded different significant SNV-expression associations from the CBTTC pediatric brain tumor cohort. The SNV-expression associations involved a wide range of cancer types and histologies, as well as potential gain or loss of transcription factor binding sites. Notable genes with SNV-associated increased expression include TERT, COPS3, POLE2 and HDAC2—involving multiple cancer types—MYC, BCL2, PIM1 and IGLL5—involving lymphomas—and CYHR1—involving pediatric low-grade gliomas. Non-coding somatic SNVs show a major role in shaping the cancer transcriptome, not limited to mutational hotspots.
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Affiliation(s)
- Fengju Chen
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
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28
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Siametis A, Niotis G, Garinis GA. DNA Damage and the Aging Epigenome. J Invest Dermatol 2021; 141:961-967. [PMID: 33494932 DOI: 10.1016/j.jid.2020.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/28/2020] [Accepted: 10/01/2020] [Indexed: 12/29/2022]
Abstract
In mammals, genome instability and aging are intimately linked as illustrated by the growing list of patients with progeroid and animal models with inborn DNA repair defects. Until recently, DNA damage was thought to drive aging by compromising transcription or DNA replication, thereby leading to age-related cellular malfunction and somatic mutations triggering cancer. However, recent evidence suggests that DNA lesions also elicit widespread epigenetic alterations that threaten cell homeostasis as a function of age. In this review, we discuss the functional links of persistent DNA damage with the epigenome in the context of aging and age-related diseases.
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Affiliation(s)
- Athanasios Siametis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Greece; Department of Biology, University of Crete, Heraklion, Greece
| | - George Niotis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Greece; Department of Biology, University of Crete, Heraklion, Greece
| | - George A Garinis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Greece; Department of Biology, University of Crete, Heraklion, Greece.
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29
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Pezone A, Tramontano A, Scala G, Cuomo M, Riccio P, De Nicola S, Porcellini A, Chiariotti L, Avvedimento E. Tracing and tracking epiallele families in complex DNA populations. NAR Genom Bioinform 2020; 2:lqaa096. [PMID: 33575640 PMCID: PMC7671405 DOI: 10.1093/nargab/lqaa096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 09/14/2020] [Accepted: 10/28/2020] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is a stable epigenetic modification, extremely polymorphic and driven by stochastic and deterministic events. Most of the current techniques used to analyse methylated sequences identify methylated cytosines (mCpGs) at a single-nucleotide level and compute the average methylation of CpGs in the population of molecules. Stable epialleles, i.e. CpG strings with the same DNA sequence containing a discrete linear succession of phased methylated/non-methylated CpGs in the same DNA molecule, cannot be identified due to the heterogeneity of the 5'-3' ends of the molecules. Moreover, these are diluted by random unstable methylated CpGs and escape detection. We present here MethCoresProfiler, an R-based tool that provides a simple method to extract and identify combinations of methylated phased CpGs shared by all components of epiallele families in complex DNA populations. The methylated cores are stable over time, evolve by acquiring or losing new methyl sites and, ultimately, display high information content and low stochasticity. We have validated this method by identifying and tracing rare epialleles and their families in synthetic or in vivo complex cell populations derived from mouse brain areas and cells during postnatal differentiation. MethCoresProfiler is written in R language. The software is freely available at https://github.com/84AP/MethCoresProfiler/.
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Affiliation(s)
- Antonio Pezone
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II Napoli, 80131 Naples, Italy
| | - Alfonso Tramontano
- Department of Precision Medicine, University of Campania ‘L. Vanvitelli’, 80138 Naples, Italy
| | - Giovanni Scala
- Department of Biology, Università Federico II Napoli, 80126 Naples, Italy
| | - Mariella Cuomo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II Napoli, 80131 Naples, Italy
| | - Patrizia Riccio
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II Napoli, 80131 Naples, Italy
| | - Sergio De Nicola
- Department of Physics, Università Federico II Napoli, 80126 Naples, Italy
| | - Antonio Porcellini
- Department of Biology, Università Federico II Napoli, 80126 Naples, Italy
| | - Lorenzo Chiariotti
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II Napoli, 80131 Naples, Italy
| | - Enrico V Avvedimento
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II Napoli, 80131 Naples, Italy
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30
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Lou M, Li R, Lang TY, Zhang LY, Zhou Q, Li L. Aberrant methylation of GADD45A is associated with decreased radiosensitivity in cervical cancer through the PI3K/AKT signaling pathway. Oncol Lett 2020; 21:8. [PMID: 33240414 PMCID: PMC7681222 DOI: 10.3892/ol.2020.12269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 10/08/2020] [Indexed: 12/12/2022] Open
Abstract
Epigenetic inactivation of GADD45A is a common occurrence in different types of cancer. However, little is known regarding its association with radiosensitivity in cervical cancer (CC). Thus, the present study aimed to investigate the association between aberrant GADD45A methylation and radiosensitivity in CC. SiHa, HeLa and CaSki CC cells were treated with 5-azacytidine (5-azaC), with or without irradiation. The expression levels of GADD45A and AKT related molecules were detected via reverse transcription-quantitative PCR and western blot analyses. The methylation status of GADD45A was assessed via methylation-specific PCR and cell proliferation assays, while clonogenic assays and flow cytometric analysis were performed to assess the function of the genes (GADD45A and AKT) in the CC cell lines. The results demonstrated that methylation of GADD45A was significantly higher in the radioresistant tissues (63.16%) compared with the radiosensitive samples (33.33%). In addition, the surviving fraction of SiHa cells following irradiation with 2 Gy was demonstrated to be highest amongst the three CC cells (CaSki, 57±9.5%; HeLa, 70±4% and SiHa, 75±10%). The survival rate of SiHa cells following treatment with 5-azaC and ionizing radiation (IR) significantly decreased as the radiation dose increased, compared with treatment with IR alone. Following overexpression of GADD45A or treatment with 5-azaC, the radiosensitivity of SiHa cells significantly increased compared with both the control vector and PBS treated groups. In addition, the AKT inhibitor, MK-2206, increased the radiosensitivity of SiHa cells. Notably, aberrant methylation of GADD45A was associated with decreased radiosensitivity in CC, and the PI3K/AKT signaling pathway was essential for radioresistance, which was mediated through downregulation of GADD45A.
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Affiliation(s)
- Meng Lou
- Department of Gynecologic Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Rong Li
- Department of Gynecologic Oncology, Chongqing University Cancer Hospital and Chongqing Cancer Institute and Chongqing Cancer Hospital, Chongqing 400030, P.R. China
| | - Ting-Yuan Lang
- Department of Gynecologic Oncology, Chongqing University Cancer Hospital and Chongqing Cancer Institute and Chongqing Cancer Hospital, Chongqing 400030, P.R. China
| | - Li-Ying Zhang
- Department of Gynecology, The Second Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi 530000, P.R. China
| | - Qi Zhou
- Department of Gynecologic Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China.,Department of Gynecologic Oncology, Chongqing University Cancer Hospital and Chongqing Cancer Institute and Chongqing Cancer Hospital, Chongqing 400030, P.R. China.,Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital and Chongqing Cancer Institute and Chongqing Cancer Hospital, Chongqing 400030, P.R. China.,Key Laboratory for Biorheological Science and Technology of Ministry of Education, Chongqing University Cancer Hospital and Chongqing Cancer Institute and Chongqing Cancer Hospital, Chongqing 400030, P.R. China
| | - Li Li
- Department of Gynecologic Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
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31
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Eze IC, Jeong A, Schaffner E, Rezwan FI, Ghantous A, Foraster M, Vienneau D, Kronenberg F, Herceg Z, Vineis P, Brink M, Wunderli JM, Schindler C, Cajochen C, Röösli M, Holloway JW, Imboden M, Probst-Hensch N. Genome-Wide DNA Methylation in Peripheral Blood and Long-Term Exposure to Source-Specific Transportation Noise and Air Pollution: The SAPALDIA Study. ENVIRONMENTAL HEALTH PERSPECTIVES 2020; 128:67003. [PMID: 32484729 PMCID: PMC7263738 DOI: 10.1289/ehp6174] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 04/27/2020] [Accepted: 04/30/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Few epigenome-wide association studies (EWAS) on air pollutants exist, and none have been done on transportation noise exposures, which also contribute to environmental burden of disease. OBJECTIVE We performed mutually independent EWAS on transportation noise and air pollution exposures. METHODS We used data from two time points of the Swiss Cohort Study on Air Pollution and Lung and Heart Diseases in Adults (SAPALDIA) from 1,389 participants contributing 2,542 observations. We applied multiexposure linear mixed-effects regressions with participant-level random intercept to identify significant Cytosine-phosphate-Guanine (CpG) sites and differentially methylated regions (DMRs) in relation to 1-y average aircraft, railway, and road traffic day-evening-night noise (Lden); nitrogen dioxide (NO 2 ); and particulate matter (PM) with aerodynamic diameter < 2.5 μ m (PM 2.5 ). We performed candidate (CpG-based; cross-systemic phenotypes, combined into "allostatic load") and agnostic (DMR-based) pathway enrichment tests, and replicated previously reported air pollution EWAS signals. RESULTS We found no statistically significant CpGs at false discovery rate < 0.05 . However, 14, 48, 183, 8, and 71 DMRs independently associated with aircraft, railway, and road traffic Lden; NO 2 ; and PM 2.5 , respectively, with minimally overlapping signals. Transportation Lden and air pollutants tendentially associated with decreased and increased methylation, respectively. We observed significant enrichment of candidate DNA methylation related to C-reactive protein and body mass index (aircraft, road traffic Lden, and PM 2.5 ), renal function and "allostatic load" (all exposures). Agnostic functional networks related to cellular immunity, gene expression, cell growth/proliferation, cardiovascular, auditory, embryonic, and neurological systems development were enriched. We replicated increased methylation in cg08500171 (NO 2 ) and decreased methylation in cg17629796 (PM 2.5 ). CONCLUSIONS Mutually independent DNA methylation was associated with source-specific transportation noise and air pollution exposures, with distinct and shared enrichments for pathways related to inflammation, cellular development, and immune responses. These findings contribute in clarifying the pathways linking these exposures and age-related diseases but need further confirmation in the context of mediation analyses. https://doi.org/10.1289/EHP6174.
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Affiliation(s)
- Ikenna C Eze
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Ayoung Jeong
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Emmanuel Schaffner
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Faisal I Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- School of Water, Energy and Environment, Cranfield University, Cranfield, UK
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Maria Foraster
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- University Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiologia y Salud Publica, Madrid, Spain
- Blanquerna School of Health Science, Universitat Ramon Llull, Barcelona, Spain
| | - Danielle Vienneau
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, UK
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | - Mark Brink
- Federal Office for the Environment, Bern, Switzerland
| | - Jean-Marc Wunderli
- Empa Laboratory for Acoustics/Noise Control, Swiss Federal Laboratories for Material Science and Technology, Dübendorf, Switzerland
| | - Christian Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Christian Cajochen
- Center for Chronobiology, Psychiatric Hospital of the University of Basel, and Transfaculty Research Platform Molecular and Cognitive Neurosciences (MCN), Basel, Switzerland
| | - Martin Röösli
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Nicole Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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Tramontano A, Boffo FL, Russo G, De Rosa M, Iodice I, Pezone A. Methylation of the Suppressor Gene p16INK4a: Mechanism and Consequences. Biomolecules 2020; 10:biom10030446. [PMID: 32183138 PMCID: PMC7175352 DOI: 10.3390/biom10030446] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 12/15/2022] Open
Abstract
Tumor suppressor genes in the CDKN2A/B locus (p15INK4b, p16INK4a, and p14ARF) function as biological barriers to transformation and are the most frequently silenced or deleted genes in human cancers. This gene silencing frequently occurs due to DNA methylation of the promoter regions, although the underlying mechanism is currently unknown. We present evidence that methylation of p16INK4a promoter is associated with DNA damage caused by interference between transcription and replication processes. Inhibition of replication or transcription significantly reduces the DNA damage and CpGs methylation of the p16INK4a promoter. We conclude that de novo methylation of the promoter regions is dependent on local DNA damage. DNA methylation reduces the expression of p16INK4a and ultimately removes this barrier to oncogene-induced senescence.
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Affiliation(s)
- Alfonso Tramontano
- Department of Precision Medicine University of Campania “L. Vanvitelli”, 80131 Naples, Italy;
| | - Francesca Ludovica Boffo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Istituto di Endocrinologia ed Oncologia Sperimentale del C.N.R., Università Federico II, 80131 Napoli, Italy; (F.L.B.); (G.R.); (M.D.R.); (I.I.)
| | - Giusi Russo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Istituto di Endocrinologia ed Oncologia Sperimentale del C.N.R., Università Federico II, 80131 Napoli, Italy; (F.L.B.); (G.R.); (M.D.R.); (I.I.)
| | - Mariarosaria De Rosa
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Istituto di Endocrinologia ed Oncologia Sperimentale del C.N.R., Università Federico II, 80131 Napoli, Italy; (F.L.B.); (G.R.); (M.D.R.); (I.I.)
| | - Ilaria Iodice
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Istituto di Endocrinologia ed Oncologia Sperimentale del C.N.R., Università Federico II, 80131 Napoli, Italy; (F.L.B.); (G.R.); (M.D.R.); (I.I.)
| | - Antonio Pezone
- Department of Precision Medicine University of Campania “L. Vanvitelli”, 80131 Naples, Italy;
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Istituto di Endocrinologia ed Oncologia Sperimentale del C.N.R., Università Federico II, 80131 Napoli, Italy; (F.L.B.); (G.R.); (M.D.R.); (I.I.)
- Correspondence: or ; Tel.: +39-0817-463-614
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Thalheim T, Hopp L, Herberg M, Siebert S, Kerner C, Quaas M, Schweiger MR, Aust G, Galle J. Fighting Against Promoter DNA Hyper-Methylation: Protective Histone Modification Profiles of Stress-Resistant Intestinal Stem Cells. Int J Mol Sci 2020; 21:ijms21061941. [PMID: 32178409 PMCID: PMC7139626 DOI: 10.3390/ijms21061941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/27/2020] [Accepted: 03/02/2020] [Indexed: 12/13/2022] Open
Abstract
Aberrant DNA methylation in stem cells is a hallmark of aging and tumor development. Recently, we have suggested that promoter DNA hyper-methylation originates in DNA repair and that even successful DNA repair might confer this kind of epigenetic long-term change. Here, we ask for interrelations between promoter DNA methylation and histone modification changes observed in the intestine weeks after irradiation and/or following Msh2 loss. We focus on H3K4me3 recruitment to the promoter of H3K27me3 target genes. By RNA- and histone ChIP-sequencing, we demonstrate that this recruitment occurs without changes of the average gene transcription and does not involve H3K9me3. Applying a mathematical model of epigenetic regulation of transcription, we show that the recruitment can be explained by stronger DNA binding of H3K4me3 and H3K27me3 histone methyl-transferases as a consequence of lower DNA methylation. This scenario implicates stable transcription despite of H3K4me3 recruitment, in agreement with our RNA-seq data. Following several kinds of stress, including moderate irradiation, stress-sensitive intestinal stem cell (ISCs) are known to become replaced by more resistant populations. Our simulation results suggest that the stress-resistant ISCs are largely protected against promoter hyper-methylation of H3K27me3 target genes.
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Affiliation(s)
- Torsten Thalheim
- Interdisciplinary Center for Bioinformatics (IZBI), Leipzig University, 04107 Leipzig, Germany; (T.T.); (L.H.); (M.H.)
| | - Lydia Hopp
- Interdisciplinary Center for Bioinformatics (IZBI), Leipzig University, 04107 Leipzig, Germany; (T.T.); (L.H.); (M.H.)
| | - Maria Herberg
- Interdisciplinary Center for Bioinformatics (IZBI), Leipzig University, 04107 Leipzig, Germany; (T.T.); (L.H.); (M.H.)
| | - Susann Siebert
- Laboratory for Translational Epigenetics and Tumor Genetics, University Hospital Cologne, 50391 Cologne, Germany; (S.S.); (M.R.S.)
- Center for Molecular Medicine Cologne, CMMC, 50391 Cologne, Germany
| | - Christiane Kerner
- Department of Surgery, Research Laboratories, Leipzig University, 04103 Leipzig, Germany; (C.K.); (M.Q.); (G.A.)
| | - Marianne Quaas
- Department of Surgery, Research Laboratories, Leipzig University, 04103 Leipzig, Germany; (C.K.); (M.Q.); (G.A.)
| | - Michal R. Schweiger
- Laboratory for Translational Epigenetics and Tumor Genetics, University Hospital Cologne, 50391 Cologne, Germany; (S.S.); (M.R.S.)
- Center for Molecular Medicine Cologne, CMMC, 50391 Cologne, Germany
| | - Gabriela Aust
- Department of Surgery, Research Laboratories, Leipzig University, 04103 Leipzig, Germany; (C.K.); (M.Q.); (G.A.)
| | - Joerg Galle
- Interdisciplinary Center for Bioinformatics (IZBI), Leipzig University, 04107 Leipzig, Germany; (T.T.); (L.H.); (M.H.)
- Correspondence:
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TIRR: a potential front runner in HDR race−hypotheses and perspectives. Mol Biol Rep 2020; 47:2371-2379. [DOI: 10.1007/s11033-020-05285-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/27/2020] [Indexed: 01/01/2023]
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35
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Cali CP, Park DS, Lee EB. Targeted DNA methylation of neurodegenerative disease genes via homology directed repair. Nucleic Acids Res 2019; 47:11609-11622. [PMID: 31680172 PMCID: PMC7145628 DOI: 10.1093/nar/gkz979] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/18/2019] [Accepted: 10/11/2019] [Indexed: 12/13/2022] Open
Abstract
DNA methyltransferases (DNMTs) are thought to be involved in the cellular response to DNA damage, thus linking DNA repair mechanisms with DNA methylation. In this study we present Homology Assisted Repair Dependent Epigenetic eNgineering (HARDEN), a novel method of targeted DNA methylation that utilizes endogenous DNA double strand break repair pathways. This method allows for stable targeted DNA methylation through the process of homology directed repair (HDR) via an in vitro methylated exogenous repair template. We demonstrate that HARDEN can be applied to the neurodegenerative disease genes C9orf72 and APP, and methylation can be induced via HDR with both single and double stranded methylated repair templates. HARDEN allows for higher targeted DNA methylation levels than a dCas9-DNMT3a fusion protein construct at C9orf72, and genome-wide methylation analysis reveals no significant off-target methylation changes when inducing methylation via HARDEN, whereas the dCas9-DNMT3a fusion construct causes global off-target methylation. HARDEN is applied to generate a patient derived iPSC model of amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD) that recapitulates DNA methylation patterns seen in patients, demonstrating that DNA methylation of the 5' regulatory region directly reduces C9orf72 expression and increases histone H3K9 tri-methylation levels.
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Affiliation(s)
- Christopher P Cali
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel S Park
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Edward B Lee
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
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36
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Zhang Y, Yang L, Kucherlapati M, Hadjipanayis A, Pantazi A, Bristow CA, Lee EA, Mahadeshwar HS, Tang J, Zhang J, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Park PJ, Kucherlapati R, Creighton CJ. Global impact of somatic structural variation on the DNA methylome of human cancers. Genome Biol 2019; 20:209. [PMID: 31610796 PMCID: PMC6792267 DOI: 10.1186/s13059-019-1818-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 09/09/2019] [Indexed: 12/21/2022] Open
Abstract
Background Genomic rearrangements exert a heavy influence on the molecular landscape of cancer. New analytical approaches integrating somatic structural variants (SSVs) with altered gene features represent a framework by which we can assign global significance to a core set of genes, analogous to established methods that identify genes non-randomly targeted by somatic mutation or copy number alteration. While recent studies have defined broad patterns of association involving gene transcription and nearby SSV breakpoints, global alterations in DNA methylation in the context of SSVs remain largely unexplored. Results By data integration of whole genome sequencing, RNA sequencing, and DNA methylation arrays from more than 1400 human cancers, we identify hundreds of genes and associated CpG islands (CGIs) for which the nearby presence of a somatic structural variant (SSV) breakpoint is recurrently associated with altered expression or DNA methylation, respectively, independently of copy number alterations. CGIs with SSV-associated increased methylation are predominantly promoter-associated, while CGIs with SSV-associated decreased methylation are enriched for gene body CGIs. Rearrangement of genomic regions normally having higher or lower methylation is often involved in SSV-associated CGI methylation alterations. Across cancers, the overall structural variation burden is associated with a global decrease in methylation, increased expression in methyltransferase genes and DNA damage response genes, and decreased immune cell infiltration. Conclusion Genomic rearrangement appears to have a major role in shaping the cancer DNA methylome, to be considered alongside commonly accepted mechanisms including histone modifications and disruption of DNA methyltransferases.
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Affiliation(s)
- Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lixing Yang
- Ben May Department for Cancer Research and Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - Melanie Kucherlapati
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Angela Hadjipanayis
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Angeliki Pantazi
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Christopher A Bristow
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Harshad S Mahadeshwar
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jiabin Tang
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sahil Seth
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Semin Lee
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Xiaojia Ren
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Xingzhi Song
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Huandong Sun
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jonathan Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Lovelace J Luquette
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Ruibin Xi
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Lynda Chin
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,The Eli and Edythe L. Broad Institute of Massachusetts Institute Of Technology and Harvard University, Cambridge, MA, 02142, USA
| | | | - Peter J Park
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA.,Center for Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Raju Kucherlapati
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. .,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA. .,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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37
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Bhargava A, Shukla A, Bunkar N, Shandilya R, Lodhi L, Kumari R, Gupta PK, Rahman A, Chaudhury K, Tiwari R, Goryacheva IY, Mishra PK. Exposure to ultrafine particulate matter induces NF-κβ mediated epigenetic modifications. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:39-50. [PMID: 31146237 DOI: 10.1016/j.envpol.2019.05.065] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/13/2019] [Accepted: 05/13/2019] [Indexed: 06/09/2023]
Abstract
Exposure to ultrafine particulate matter (PM0.1) is positively associated with the etiology of different acute and chronic disorders; however, the in-depth biological imprints that link these submicron particles with the disturbances in the epigenomic machinery are not well defined. Earlier, we showed that exposure to these particles causes significant disturbances in the mitochondrial machinery and triggers PI-3-kinase mediated DNA damage responses. In the present study, we aimed to further understand the epigenomic insights of the ultrafine PM exposure. The higher levels of intracellular reactive oxygen species and depleted Nrf-2 in ultrafine PM exposed cells reconfirmed its potential to induce oxidative stress. Importantly, the observed increase in the levels of NF-κβ and associated cytokines among exposed cells suggested the activation of NF-κβ mediated inflammatory loop which potentially serves as a platform for initiating epigenetic insinuations. This fact was strongly supported by the altered miRNA expression profile of the ultrafine PM exposed cells. These NF-κβ induced miRNA alterations were also found to be associated with other epigenetic targets as the exposed cells showed higher expression levels of DNA methyltransferases which positively corresponded with the global changes in DNA methylation levels. Upon further analysis, significant alterations in histone code were also reported in ultrafine PM exposed cells. Conclusively our results suggested that NF-κβ acts as an inflammatory switch that possesses the potential to induce genome-wide epigenetic modification upon ultrafine PM exposure.
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Affiliation(s)
- Arpit Bhargava
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Anushi Shukla
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Neha Bunkar
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Ruchita Shandilya
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Lalit Lodhi
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Roshani Kumari
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Pushpendra Kumar Gupta
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Akhlaqur Rahman
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Koel Chaudhury
- School of Medical Science & Technology, Indian Institute of Technology, Kharagpur, India
| | - Rajnarayan Tiwari
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Irina Yu Goryacheva
- Department of General and Inorganic Chemistry, Saratov State University, Saratov, Russia
| | - Pradyumna Kumar Mishra
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
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38
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Kim JH. Chromatin Remodeling and Epigenetic Regulation in Plant DNA Damage Repair. Int J Mol Sci 2019; 20:ijms20174093. [PMID: 31443358 PMCID: PMC6747262 DOI: 10.3390/ijms20174093] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/19/2022] Open
Abstract
DNA damage response (DDR) in eukaryotic cells is initiated in the chromatin context. DNA damage and repair depend on or have influence on the chromatin dynamics associated with genome stability. Epigenetic modifiers, such as chromatin remodelers, histone modifiers, DNA (de-)methylation enzymes, and noncoding RNAs regulate DDR signaling and DNA repair by affecting chromatin dynamics. In recent years, significant progress has been made in the understanding of plant DDR and DNA repair. SUPPRESSOR OF GAMMA RESPONSE1, RETINOBLASTOMA RELATED1 (RBR1)/E2FA, and NAC103 have been proven to be key players in the mediation of DDR signaling in plants, while plant-specific chromatin remodelers, such as DECREASED DNA METHYLATION1, contribute to chromatin dynamics for DNA repair. There is accumulating evidence that plant epigenetic modifiers are involved in DDR and DNA repair. In this review, I examine how DDR and DNA repair machineries are concertedly regulated in Arabidopsis thaliana by a variety of epigenetic modifiers directing chromatin remodeling and epigenetic modification. This review will aid in updating our knowledge on DDR and DNA repair in plants.
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Affiliation(s)
- Jin-Hong Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212, Korea.
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39
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Gensous N, Bacalini MG, Franceschi C, Meskers CGM, Maier AB, Garagnani P. Age-Related DNA Methylation Changes: Potential Impact on Skeletal Muscle Aging in Humans. Front Physiol 2019; 10:996. [PMID: 31427991 PMCID: PMC6688482 DOI: 10.3389/fphys.2019.00996] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/18/2019] [Indexed: 12/27/2022] Open
Abstract
Human aging is accompanied by a decline in muscle mass and muscle function, which is commonly referred to as sarcopenia. Sarcopenia is associated with detrimental clinical outcomes, such as a reduced quality of life, frailty, an increased risk of falls, fractures, hospitalization, and mortality. The exact underlying mechanisms of sarcopenia are poorly delineated and the molecular mechanisms driving the development and progression of this disorder remain to be uncovered. Previous studies have described age-related differences in gene expression, with one study identifying an age-specific expression signature of sarcopenia, but little is known about the influence of epigenetics, and specially of DNA methylation, in its pathogenesis. In this review, we will focus on the available knowledge in literature on the characterization of DNA methylation profiles during skeletal muscle aging and the possible impact of physical activity and nutrition. We will consider the possible use of the recently developed DNA methylation-based biomarkers of aging called epigenetic clocks in the assessment of physical performance in older individuals. Finally, we will discuss limitations and future directions of this field.
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Affiliation(s)
- Noémie Gensous
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | | | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.,Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Carel G M Meskers
- Amsterdam UMC, Department of Rehabilitation Medicine, Amsterdam Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Andrea B Maier
- Department of Human Movement Sciences, @AgeAmsterdam, Faculty of Behavioural and Movement Sciences, Amsterdam Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Department of Medicine and Aged Care, @AgeMelbourne, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, VIC, Australia
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.,Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Applied Biomedical Research Center (CRBA), Policlinico S.Orsola-Malpighi Polyclinic, Bologna, Italy.,CNR Institute of Molecular Genetics, Unit of Bologna, Bologna, Italy
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40
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Verkest A, Bourout S, Debaveye J, Reynaert K, Saey B, den Brande IV, D'Halluin K. Impact of differential DNA methylation on transgene expression in cotton (Gossypium hirsutum L.) events generated by targeted sequence insertion. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1236-1247. [PMID: 30549163 PMCID: PMC6576080 DOI: 10.1111/pbi.13049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/15/2018] [Accepted: 11/23/2018] [Indexed: 05/11/2023]
Abstract
Targeted Genome Optimization (TGO) using site-specific nucleases to introduce a DNA double-strand break (DSB) at a specific target locus has broadened the options available to breeders for generation and combination of multiple traits. The use of targeted DNA cleavage in combination with homologous recombination (HR)-mediated repair, enabled the precise targeted insertion of additional trait genes (2mepsps, hppd, axmi115) at a pre-existing transgenic locus in cotton. Here we describe the expression and epigenome analyses of cotton Targeted Sequence Insertion (TSI) events over generations. In a subset of events, we observed variability in the level of transgene (hppd, axmi115) expression between independent but genetically identical TSI events. Transgene expression could also be differential within single events and variable over generations. This expression variability and silencing occurred independently of the transgene sequence and could be attributed to DNA methylation that was further linked to different DNA methylation mechanisms. The trigger(s) of transgene DNA methylation remains elusive but we hypothesize that targeted DSB induction and repair could be a potential trigger for DNA methylation.
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41
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Silva E, Ideker T. Transcriptional responses to DNA damage. DNA Repair (Amst) 2019; 79:40-49. [PMID: 31102970 PMCID: PMC6570417 DOI: 10.1016/j.dnarep.2019.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/20/2019] [Accepted: 05/04/2019] [Indexed: 12/31/2022]
Abstract
In response to the threat of DNA damage, cells exhibit a dramatic and multi-factorial response spanning from transcriptional changes to protein modifications, collectively known as the DNA damage response (DDR). Here, we review the literature surrounding the transcriptional response to DNA damage. We review differences in observed transcriptional responses as a function of cell cycle stage and emphasize the importance of experimental design in these transcriptional response studies. We additionally consider topics including structural challenges in the transcriptional response to DNA damage as well as the connection between transcription and protein abundance.
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Affiliation(s)
- Erica Silva
- Department of Medicine, University of California San Diego, La Jolla, California, USA; Biomedical Sciences Program, University of California San Diego, La Jolla, California, USA.
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, California, USA; Biomedical Sciences Program, University of California San Diego, La Jolla, California, USA; Program in Bioinformatics, University of California San Diego, La Jolla, California, USA; Department of Bioengineering, University of California San Diego, La Jolla, California, USA.
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42
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Sutton LP, Jeffreys SA, Phillips JL, Taberlay PC, Holloway AF, Ambrose M, Joo JHE, Young A, Berry R, Skala M, Brettingham-Moore KH. DNA methylation changes following DNA damage in prostate cancer cells. Epigenetics 2019; 14:989-1002. [PMID: 31208284 PMCID: PMC6691980 DOI: 10.1080/15592294.2019.1629231] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Many cancer therapies operate by inducing double-strand breaks (DSBs) in cancer cells, however treatment-resistant cells rapidly initiate mechanisms to repair damage enabling survival. While the DNA repair mechanisms responsible for cancer cell survival following DNA damaging treatments are becoming better understood, less is known about the role of the epigenome in this process. Using prostate cancer cell lines with differing sensitivities to radiation treatment, we analysed the DNA methylation profiles prior to and following a single dose of radiotherapy (RT) using the Illumina Infinium HumanMethylation450 BeadChip platform. DSB formation and repair, in the absence and presence of the DNA hypomethylating agent, 5-azacytidine (5-AzaC), were also investigated using γH2A.X immunofluorescence staining. Here we demonstrate that DNA methylation is generally stable following a single dose of RT; however, a small number of CpG sites are stably altered up to 14 d following exposure. While the radioresistant and radiosensitive cells displayed distinct basal DNA methylation profiles, their susceptibility to DNA damage appeared similar demonstrating that basal DNA methylation has a limited influence on DSB induction at the regions examined. Recovery from DSB induction was also similar between these cells. Treatment with 5-AzaC did not sensitize resistant cells to DNA damage, but rather delayed recruitment of phosphorylated BRCA1 (S1423) and repair of DSBs. These results highlight that stable epigenetic changes are possible following a single dose of RT and may have significant clinical implications for cancer treatment involving recurrent or fractionated dosing regimens.
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Affiliation(s)
- Laura P Sutton
- a School of Medicine, College of Health and Medicine, University of Tasmania , Hobart , Australia
| | - Sarah A Jeffreys
- a School of Medicine, College of Health and Medicine, University of Tasmania , Hobart , Australia
| | - Jessica L Phillips
- a School of Medicine, College of Health and Medicine, University of Tasmania , Hobart , Australia
| | - Phillippa C Taberlay
- a School of Medicine, College of Health and Medicine, University of Tasmania , Hobart , Australia
| | - Adele F Holloway
- a School of Medicine, College of Health and Medicine, University of Tasmania , Hobart , Australia
| | - Mark Ambrose
- a School of Medicine, College of Health and Medicine, University of Tasmania , Hobart , Australia
| | - Ji-Hoon E Joo
- b Colorectal Oncogenomics Group, Department of Clinical Pathology & University of Melbourne Centre for Cancer Research, The University of Melbourne , Parkville , Australia
| | - Arabella Young
- a School of Medicine, College of Health and Medicine, University of Tasmania , Hobart , Australia
| | - Rachael Berry
- a School of Medicine, College of Health and Medicine, University of Tasmania , Hobart , Australia
| | - Marketa Skala
- c Department of Radiation Oncology, Royal Hobart Hospital , Hobart , Australia
| | - Kate H Brettingham-Moore
- a School of Medicine, College of Health and Medicine, University of Tasmania , Hobart , Australia
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43
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Ma Y, Ma Y, Wen L, Lei H, Chen S, Wang X. Changes in DNA methylation and imprinting disorders in E9.5 mouse fetuses and placentas derived from vitrified eight-cell embryos. Mol Reprod Dev 2019; 86:404-415. [PMID: 30680835 DOI: 10.1002/mrd.23118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/08/2019] [Accepted: 01/20/2019] [Indexed: 01/21/2023]
Abstract
Vitrification is increasingly used in assisted reproductive technology (ART) laboratories worldwide, and potential vitrification-induced risks require further exploration. The effect of vitrification on changes in DNA methylation and imprinting disorders was investigated in E9.5 mouse fetuses and placentas. Fetus and placental tissues were collected from the natural mating (nautural conception [NC]) group, in vitro culture (IVC) group and vitrified embryo transfer (VET) group. The fetal crown-rump length at E9.5 in both the IVC (0.210 ± 0.059 mm) and VET (0.205 ± 0.048 mm) groups was significantly reduced compared with the NC group (0.288 ± 0.083 mm). The global methylation levels of fetuses were decreased in the IVC group compared with the NC group and it was increased after vitrification compared with IVC (p < 0.05), similar to what was observed in the NC group (p > 0.05). The changes could be attributed to the disorders of DNA methyltransferases and ten-eleven translocations. In the IVC and VET fetuses, a majority of maternally expressed genes were upregulated, which repressed fetal growth. Furthermore, vitrification led to a change in the methylation level of KvDMR1, which resulted in the disturbance of gene imprinting. According to our results, vitrification could contribute to increased methylation compared with IVC and contributes to a gene imprinting disorder rather than recovery. Despite the routine use of embryo vitrification in clinical settings, the effect that this procedure may have on genomic imprinting deserves much greater attention.
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Affiliation(s)
- Yuan Ma
- Department of Obstetrics and Gynecology, The Reproductive Medicine Center, Tangdu Hospital, Air Force Military Medical University, Xi'an, Shaanxi, China
| | - Yefei Ma
- Department of Obstetrics and Gynecology, The Reproductive Medicine Center, Tangdu Hospital, Air Force Military Medical University, Xi'an, Shaanxi, China
| | - Liang Wen
- Department of Obstetrics and Gynecology, The Reproductive Medicine Center, Tangdu Hospital, Air Force Military Medical University, Xi'an, Shaanxi, China
| | - Hui Lei
- Department of Obstetrics and Gynecology, The Reproductive Medicine Center, Tangdu Hospital, Air Force Military Medical University, Xi'an, Shaanxi, China
| | - Shuqiang Chen
- Department of Obstetrics and Gynecology, The Reproductive Medicine Center, Tangdu Hospital, Air Force Military Medical University, Xi'an, Shaanxi, China
| | - Xiaohong Wang
- Department of Obstetrics and Gynecology, The Reproductive Medicine Center, Tangdu Hospital, Air Force Military Medical University, Xi'an, Shaanxi, China
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44
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Adult Neural Stem Cell Multipotency and Differentiation Are Directed by the Methyl-CpG-Binding Protein MBD1. J Neurosci 2018; 37:4228-4230. [PMID: 28424299 DOI: 10.1523/jneurosci.0411-17.2017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 03/23/2017] [Accepted: 03/25/2017] [Indexed: 11/21/2022] Open
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45
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Allen B, Pezone A, Porcellini A, Muller MT, Masternak MM. Non-homologous end joining induced alterations in DNA methylation: A source of permanent epigenetic change. Oncotarget 2018; 8:40359-40372. [PMID: 28423717 PMCID: PMC5522286 DOI: 10.18632/oncotarget.16122] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/07/2017] [Indexed: 01/11/2023] Open
Abstract
In addition to genetic mutations, epigenetic revision plays a major role in the development and progression of cancer; specifically, inappropriate DNA methylation or demethylation of CpG residues may alter the expression of genes that promote tumorigenesis. We hypothesize that DNA repair, specifically the repair of DNA double strand breaks (DSB) by Non-Homologous End Joining (NHEJ) may play a role in this process. Using a GFP reporter system inserted into the genome of HeLa cells, we are able to induce targeted DNA damage that enables the cells, after successfully undergoing NHEJ repair, to express WT GFP. These GFP+ cells were segregated into two expression classes, one with robust expression (Bright) and the other with reduced expression (Dim). Using a DNA hypomethylating drug (AzadC) we demonstrated that the different GFP expression levels was due to differential methylation statuses of CpGs in regions on either side of the break site. Deep sequencing analysis of this area in sorted Bright and Dim populations revealed a collection of different epi-alleles that display patterns of DNA methylation following repair by NHEJ. These patterns differ between Bright and Dim cells which are hypo- and hypermethylated, respectively, and between the post-repair populations and the original, uncut cells. These data suggest that NHEJ repair facilitates a rewrite of the methylation landscape in repaired genes, elucidating a potential source for the altered methylation patterns seen in cancer cells, and understanding the mechanism by which this occurs could provide new therapeutic targets for preventing this process from contributing to tumorigenesis.
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Affiliation(s)
- Brittany Allen
- College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Antonio Pezone
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Istituto di Endocrinologia ed Oncologia Sperimentale del C.N.R., Università Federico II, Napoli, Italy
| | | | - Mark T Muller
- Epigenetics Division, TopoGEN, Inc., Buena Vista, CO, USA
| | - Michal M Masternak
- College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA.,Department of Head and Neck Surgery, The Greater Poland Cancer Centre, Poznan, Poland, Europe
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46
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Alessio N, Riccitiello F, Squillaro T, Capasso S, Del Gaudio S, Di Bernardo G, Cipollaro M, Melone MAB, Peluso G, Galderisi U. Neural stem cells from a mouse model of Rett syndrome are prone to senescence, show reduced capacity to cope with genotoxic stress, and are impaired in the differentiation process. Exp Mol Med 2018; 50:1. [PMID: 29563495 PMCID: PMC6118406 DOI: 10.1038/s12276-017-0005-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 10/17/2017] [Accepted: 10/20/2017] [Indexed: 02/06/2023] Open
Abstract
Several aspects of stem cell life are governed by epigenetic variations, such as DNA methylation, histone modifications, and chromatin remodeling. Epigenetic events are also connected with the impairment of stem cell functions. For example, during senescence, there are significant changes in chromatin organization that alter transcription. The MECP2 protein can bind methylated cytosines and contribute to regulating gene expression at one of the highest hierarchical levels. Researchers are particularly interested in this protein, as up to 90% of Rett syndrome patients have an MECP2 gene mutation. Nevertheless, the role of MECP2 in this disease remains poorly understood. We used a mouse model of Rett syndrome to evaluate whether residual MECP2 activity in neural stem cells (NSCs) induced the senescence phenomena that could affect stem cell function. Our study clearly demonstrated that the reduced expression of MECP2 is connected with an increase in senescence, an impairment in proliferation capacity, and an accumulation of unrepaired DNA foci. Mecp2+/− NSCs did not cope with genotoxic stress in the same way as the control cells did. Indeed, after treatment with different DNA-damaging agents, the NSCs from mice with mutated Mecp2 accumulated more DNA damage foci (γ-H2AX+) and were more prone to cell death than the controls. Senescence in Mecp2+/− NSCs decreased the number of stem cells and progenitors and gave rise to a high percentage of cells that expressed neither stem/progenitor nor differentiation markers. These cells could be senescent and dysfunctional. In Rett syndrome, neural stem cells lose some of their “stem cell like” properties, impairing brain functions. Patients with this rare neurological condition, almost exclusively girls, show impaired movement and speech beginning at 6–18 months of age. Mutations in the MECP2 gene are known to be involved, but the specifics are poorly understood. Umberto Galderisi at Temple University in Philadelphia and co-workers in Italy used a mouse model to trace how MECP2 mutations affect neural stem cells. They found that the mutated cells lost key stem cell abilities, including the capacity to renew themselves by dividing, and the ability to differentiate, or turn into other cell types. The cells were also highly susceptible to DNA damage and unable to repair it. These results improve our understanding of Rett syndrome and may help develop new treatments.
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Affiliation(s)
- Nicola Alessio
- Department of Experimental Medicine, Campania University "Luigi Vanvitelli", Naples, Italy
| | - Francesco Riccitiello
- Department of Neurosciences, Reproductive and Odontostomatologic Science, University "Federico II", Naples, Italy
| | - Tiziana Squillaro
- Department of Experimental Medicine, Campania University "Luigi Vanvitelli", Naples, Italy.,Department of Medical, Surgical, Neurological, Metabolic Sciences, and Aging, Division of Neurology and InterUniversity Center for Research in Neurosciences, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Stefania Capasso
- Department of Experimental Medicine, Campania University "Luigi Vanvitelli", Naples, Italy
| | - Stefania Del Gaudio
- Department of Experimental Medicine, Campania University "Luigi Vanvitelli", Naples, Italy
| | - Giovanni Di Bernardo
- Department of Experimental Medicine, Campania University "Luigi Vanvitelli", Naples, Italy
| | - Marilena Cipollaro
- Department of Experimental Medicine, Campania University "Luigi Vanvitelli", Naples, Italy
| | - Mariarosa A B Melone
- Department of Medical, Surgical, Neurological, Metabolic Sciences, and Aging, Division of Neurology and InterUniversity Center for Research in Neurosciences, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Gianfranco Peluso
- Institute of Agro-Environmental Biology and Forestry (IBAF), CNR, Naples, Italy
| | - Umberto Galderisi
- Department of Experimental Medicine, Campania University "Luigi Vanvitelli", Naples, Italy. .,Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Temple University, Philadelphia, PA, USA.
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47
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DNA redox modulations and global DNA methylation in bipolar disorder: Effects of sex, smoking and illness state. Psychiatry Res 2018; 261:589-596. [PMID: 29407727 DOI: 10.1016/j.psychres.2017.12.051] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 11/22/2017] [Accepted: 12/18/2017] [Indexed: 01/20/2023]
Abstract
DNA redox modulations and methylation have been associated with bipolar disorder (BD) pathophysiology. We aimed to investigate DNA redox modulation and global DNA methylation and demethylation levels in patients with BD during euthymia, mania or depression in comparison to non-psychiatric controls. The roles of sex and smoking as susceptibility factors for DNA redox modulations and global DNA methylation and demethylation were also explored. Levels of 5-methylcytosine (5-mC), 5-hydroxymethylcytosine (5-hmC) and 8-hydroxy-2'-deoxyguanosine (8-OHdG) were assessed in DNA samples of 75 patients with DSM-IV BD type I (37 euthymic, 18 manic, 20 depressive) in comparison to 60 non-psychiatric controls. Levels of 5-mC and 5-hmC were assessed using Dot Blot as a screening process, and verified using ELISA. Levels of 8-OHdG were assessed using ELISA. The levels of 8-OHdG significantly differed among non-psychiatric control, euthymia, mania and depression groups [F (3,110) = 2.771, p = 0.046], whereas there were no alterations in the levels of 5-hmC and 5-mC. Linear regression analyses revealed the significant effects of smoking (p = 0.031) and sex (p = 0.012) as well as state of illness on the levels of 8-OHdG (p = 0.025) in patients with BD. Our results suggest that levels of 8-OHdG may be affected by sex, illness states and smoking in BD.
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48
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Turgeon MO, Perry NJS, Poulogiannis G. DNA Damage, Repair, and Cancer Metabolism. Front Oncol 2018; 8:15. [PMID: 29459886 PMCID: PMC5807667 DOI: 10.3389/fonc.2018.00015] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 01/17/2018] [Indexed: 12/12/2022] Open
Abstract
Although there has been a renewed interest in the field of cancer metabolism in the last decade, the link between metabolism and DNA damage/DNA repair in cancer has yet to be appreciably explored. In this review, we examine the evidence connecting DNA damage and repair mechanisms with cell metabolism through three principal links. (1) Regulation of methyl- and acetyl-group donors through different metabolic pathways can impact DNA folding and remodeling, an essential part of accurate double strand break repair. (2) Glutamine, aspartate, and other nutrients are essential for de novo nucleotide synthesis, which dictates the availability of the nucleotide pool, and thereby influences DNA repair and replication. (3) Reactive oxygen species, which can increase oxidative DNA damage and hence the load of the DNA-repair machinery, are regulated through different metabolic pathways. Interestingly, while metabolism affects DNA repair, DNA damage can also induce metabolic rewiring. Activation of the DNA damage response (DDR) triggers an increase in nucleotide synthesis and anabolic glucose metabolism, while also reducing glutamine anaplerosis. Furthermore, mutations in genes involved in the DDR and DNA repair also lead to metabolic rewiring. Links between cancer metabolism and DNA damage/DNA repair are increasingly apparent, yielding opportunities to investigate the mechanistic basis behind potential metabolic vulnerabilities of a substantial fraction of tumors.
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Affiliation(s)
- Marc-Olivier Turgeon
- Department of Cancer Biology, Institute of Cancer Research, London, United Kingdom
| | - Nicholas J S Perry
- Department of Cancer Biology, Institute of Cancer Research, London, United Kingdom
| | - George Poulogiannis
- Department of Cancer Biology, Institute of Cancer Research, London, United Kingdom.,Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
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49
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Jenkins TG, James ER, Alonso DF, Hoidal JR, Murphy PJ, Hotaling JM, Cairns BR, Carrell DT, Aston KI. Cigarette smoking significantly alters sperm DNA methylation patterns. Andrology 2017; 5:1089-1099. [PMID: 28950428 DOI: 10.1111/andr.12416] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 06/27/2017] [Accepted: 07/18/2017] [Indexed: 12/15/2022]
Abstract
Numerous health consequences of tobacco smoke exposure have been characterized, and the effects of smoking on traditional measures of male fertility are well described. However, a growing body of data indicates that pre-conception paternal smoking also confers increased risk for a number of morbidities on offspring. The mechanism for this increased risk has not been elucidated, but it is likely mediated, at least in part, through epigenetic modifications transmitted through spermatozoa. In this study, we investigated the impact of cigarette smoke exposure on sperm DNA methylation patterns in 78 men who smoke and 78 never-smokers using the Infinium Human Methylation 450 beadchip. We investigated two models of DNA methylation alterations: (i) consistently altered methylation at specific CpGs or within specific genomic regions and (ii) stochastic DNA methylation alterations manifest as increased variability in genome-wide methylation patterns in men who smoke. We identified 141 significantly differentially methylated CpGs associated with smoking. In addition, we identified a trend toward increased variance in methylation patterns genome-wide in sperm DNA from men who smoke compared with never-smokers. These findings of widespread DNA methylation alterations are consistent with the broad range of offspring heath disparities associated with pre-conception paternal smoke exposure and warrant further investigation to identify the specific mechanism by which sperm DNA methylation perturbation confers risk to offspring health and whether these changes can be transmitted to offspring and transgenerationally.
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Affiliation(s)
- T G Jenkins
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - E R James
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - D F Alonso
- Department of Psychology, University of Utah, Salt Lake City, UT, USA
| | - J R Hoidal
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - P J Murphy
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - J M Hotaling
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - B R Cairns
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA.,Howard Hughes Medical Institute, Chevy Chase, MA, USA
| | - D T Carrell
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA.,Department of Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - K I Aston
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
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50
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High-coverage methylation data of a gene model before and after DNA damage and homologous repair. Sci Data 2017; 4:170043. [PMID: 28398335 PMCID: PMC5387920 DOI: 10.1038/sdata.2017.43] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/27/2017] [Indexed: 02/04/2023] Open
Abstract
Genome-wide methylation analysis is limited by its low coverage and the inability to detect single variants below 10%. Quantitative analysis provides accurate information on the extent of methylation of single CpG dinucleotide, but it does not measure the actual polymorphism of the methylation profiles of single molecules. To understand the polymorphism of DNA methylation and to decode the methylation signatures before and after DNA damage and repair, we have deep sequenced in bisulfite-treated DNA a reporter gene undergoing site-specific DNA damage and homologous repair. In this paper, we provide information on the data generation, the rationale for the experiments and the type of assays used, such as cytofluorimetry and immunoblot data derived during a previous work published in Scientific Reports, describing the methylation and expression changes of a model gene (GFP) before and after formation of a double-strand break and repair by homologous-recombination or non-homologous-end-joining. These data provide: 1) a reference for the analysis of methylation polymorphism at selected loci in complex cell populations; 2) a platform and the tools to compare transcription and methylation profiles.
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