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Viet CT, Zhang M, Dharmaraj N, Li GY, Pearson AT, Manon VA, Grandhi A, Xu K, Aouizerat BE, Young S. Artificial Intelligence Applications in Oral Cancer and Oral Dysplasia. Tissue Eng Part A 2024. [PMID: 39041628 DOI: 10.1089/ten.tea.2024.0096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a highly unpredictable disease with devastating mortality rates that have not changed over the past decades, in the face of advancements in treatments and biomarkers, which have improved survival for other cancers. Delays in diagnosis are frequent, leading to more disfiguring treatments and poor outcomes in patients. The clinical challenge lies in identifying those patients at highest risk for developing OSCC. Oral epithelial dysplasia (OED) is a precursor of OSCC with highly variable behavior across patients. There is no reliable clinical, pathologic, histologic or molecular biomarker to determine individual risk in OED patients. Similarly, there are no robust biomarkers to predict treatment outcomes or mortality of OSCC patients. This review aims to highlight advancements in artificial intelligence (AI)-based methods to develop predictive biomarkers of OED transformation to OSCC or predictive biomarkers of OSCC mortality and treatment response. Machine-learning based biomarkers, such as S100A7, demonstrate promising appraisal for the risk of malignant transformation of OED. Machine learning-enhanced multiplex immunohistochemistry (mIHC) workflows examine immune cell patterns and organization within the tumor immune microenvironment to generate outcome predictions in immunotherapy. Deep learning (DL) is an AI-based method using an extended neural network or related architecture with multiple "hidden" layers of simulated neurons to combine simple visual features into complex patterns. DL-based digital pathology is currently being developed to assess OED and OSCC outcomes. The integration of machine learning in epigenomics aims to examine the epigenetic modification of diseases and improve our ability to detect, classify, and predict outcomes associated with epigenetic marks. Collectively, these tools showcase promising advancements in discovery and technology, which may provide a potential solution to addressing the current limitations in predicting OED transformation and OSCC behavior, both of which are clinical challenges that must be addressed in order to improve OSCC survival.
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Affiliation(s)
- Chi Tonglien Viet
- Loma Linda University, Department of Oral and Maxillofacial Surgery, Loma Linda, California, United States;
| | - Michael Zhang
- Loma Linda University, Department of Oral and Maxillofacial Surgery, Loma Linda, California, United States;
| | - Neeraja Dharmaraj
- The University of Texas Health Science Center at Houston School of Dentistry, Bernard & Gloria Pepper Katz Department of Oral and Maxillofacial Surgery, Houston, Texas, United States;
| | - Grace Y Li
- The University of Chicago Medical Center, Department of Medicine, Section of Hematology/Oncology,, Chicago, Illinois, United States;
| | - Alexander T Pearson
- The University of Chicago Medical Center, Department of Medicine, Section of Hematology/Oncology,, Chicago, Illinois, United States;
| | - Victoria A Manon
- The University of Texas Health Science Center at Houston School of Dentistry, Bernard & Gloria Pepper Katz Department of Oral and Maxillofacial Surgery, Houston, Texas, United States;
| | - Anupama Grandhi
- Loma Linda University, Department of Oral and Maxillofacial Surgery, Loma Linda, California, United States;
| | - Ke Xu
- Yale School of Medicine, Department of Psychiatry, New Haven, Connecticut, United States
- VA Connecticut Healthcare System - West Haven Campus, West Haven, Connecticut, United States;
| | - Bradley E Aouizerat
- New York University College of Dentistry, Translational Research Center, New York, New York, United States;
| | - Simon Young
- The University of Texas Health Science Center at Houston School of Dentistry, Bernard & Gloria Pepper Katz Department of Oral and Maxillofacial Surgery, Houston, Texas, United States;
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Shelton WJ, Zandpazandi S, Nix JS, Gokden M, Bauer M, Ryan KR, Wardell CP, Vaske OM, Rodriguez A. Long-read sequencing for brain tumors. Front Oncol 2024; 14:1395985. [PMID: 38915364 PMCID: PMC11194609 DOI: 10.3389/fonc.2024.1395985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/27/2024] [Indexed: 06/26/2024] Open
Abstract
Brain tumors and genomics have a long-standing history given that glioblastoma was the first cancer studied by the cancer genome atlas. The numerous and continuous advances through the decades in sequencing technologies have aided in the advanced molecular characterization of brain tumors for diagnosis, prognosis, and treatment. Since the implementation of molecular biomarkers by the WHO CNS in 2016, the genomics of brain tumors has been integrated into diagnostic criteria. Long-read sequencing, also known as third generation sequencing, is an emerging technique that allows for the sequencing of longer DNA segments leading to improved detection of structural variants and epigenetics. These capabilities are opening a way for better characterization of brain tumors. Here, we present a comprehensive summary of the state of the art of third-generation sequencing in the application for brain tumor diagnosis, prognosis, and treatment. We discuss the advantages and potential new implementations of long-read sequencing into clinical paradigms for neuro-oncology patients.
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Affiliation(s)
- William J. Shelton
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Sara Zandpazandi
- Department of Neurosurgery, Medical University of South Carolina, Charleston, SC, United States
| | - J Stephen Nix
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Murat Gokden
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Michael Bauer
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Katie Rose Ryan
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Christopher P. Wardell
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Olena Morozova Vaske
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Analiz Rodriguez
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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Ye Z, Jiang Y, Wu J. DNMT3B attenuated the inhibition of TET3 on epithelial-mesenchymal transition in TGF-β1-induced ovarian cancer by methylating the TET3 promoter. Reprod Biol 2022; 22:100701. [DOI: 10.1016/j.repbio.2022.100701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/29/2022] [Accepted: 10/01/2022] [Indexed: 11/06/2022]
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Sung WY, Lin YZ, Hwang DY, Lin CH, Li RN, Tseng CC, Wu CC, Ou TT, Yen JH. Methylation of TET2 Promoter Is Associated with Global Hypomethylation and Hypohydroxymethylation in Peripheral Blood Mononuclear Cells of Systemic Lupus Erythematosus Patients. Diagnostics (Basel) 2022; 12:diagnostics12123006. [PMID: 36553013 PMCID: PMC9776498 DOI: 10.3390/diagnostics12123006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/28/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
(1) Background: It is widely accepted that aberrant methylation patterns contribute to the development of systemic lupus erythematosus (SLE). Ten-eleven translocation (TET) methylcytosine dioxygenase is an essential enzyme of which there are three members, TET1, 2, and 3, involved in hydroxymethylation, a newly uncovered mechanism of active DNA methylation. The epigenomes of gene transcription are regulated by 5-hydroxymethylcytocine (5-hmC) and TETs, leading to dysregulation of the immune system in SLE. The purpose of this study was to investigate the global hydroxymethylation status in SLE peripheral blood mononuclear cells (PBMCs) and to explore the role of TETs in changing the patterns of methylation. (2) Methods: We collected PBMCs from 101 SLE patients and 100 healthy donors. TaqMan real-time polymerase chain-reaction assay was performed for the detection of 5-methylcytosine (5-mC), 5-hmC, and TET2 mRNA expression and single-nucleotide polymorphism genotyping. The methylation rates in different CpG sites of TET2 promoters were examined using next-generation sequencing-based deep bisulfite sequencing. Putative transcription factors were investigated using the UCSC Genome Browser on the Human Dec. 2013 (GRCh38/hg38) Assembly. (3) Results: 5-mC and 5-hmC were both decreased in SLE. The mRNA expression level of TET2 was notably high and found to be correlated with the levels of immunologic biomarkers that are indicative of SLE disease activity. The analysis of methylation rates in the TET2 promoter revealed that SLE patients had significantly higher and lower rates of methylation in TET2 105146072-154 and TET2 105146218-331, respectively. (4) Conclusions: TET2 may play an important role in 5-mC/5-hmC dynamics in the PBMCs of SLE patients. The epigenetic modification of TET2 promoters could contribute to the pathogenesis of SLE and the intensity of the immunologic reaction.
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Affiliation(s)
- Wan-Yu Sung
- Division of Rheumatology, Department of Internal medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
- Correspondence: (W.-Y.S.); (J.-H.Y.)
| | - Yuan-Zhao Lin
- Division of Rheumatology, Department of Internal medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
| | - Daw-Yang Hwang
- National Institute of Cancer Research, National Health Research Institutes, Tainan 350401, Taiwan
- Division of Nephrology, Department of Internal medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
| | - Chia-Hui Lin
- Division of Rheumatology, Department of Internal medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
| | - Ruei-Nian Li
- Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Chia-Chun Tseng
- Division of Rheumatology, Department of Internal medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Cheng-Chin Wu
- Division of Rheumatology, Department of Internal medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
| | - Tsan-Teng Ou
- Division of Rheumatology, Department of Internal medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
| | - Jeng-Hsien Yen
- Division of Rheumatology, Department of Internal medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- College of Biological Science and Technology, National Chiao Tung University, Hsinchu 30010, Taiwan
- Institute of Medical Science and Technology, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
- Correspondence: (W.-Y.S.); (J.-H.Y.)
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Chen Z, Rasheed M, Deng Y. The epigenetic mechanisms involved in mitochondrial dysfunction: Implication for Parkinson's disease. Brain Pathol 2021; 32:e13012. [PMID: 34414627 PMCID: PMC9048811 DOI: 10.1111/bpa.13012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/21/2021] [Accepted: 07/27/2021] [Indexed: 12/18/2022] Open
Abstract
Mitochondrial dysfunction is one of the crucial factors involved in PD’s pathogenicity, which emerges from a combination of genetic and environmental factors. These factors cause differential molecular expression in neurons, such as varied transcriptional regulation of genes, elevated oxidative stress, α‐synuclein aggregation and endogenous neurotoxins release, which induces epigenetic modifications and triggers energy crisis by damaging mitochondria of the dopaminergic neurons (DN). So far, these events establish a complicated relationship with underlying mechanisms of mitochondrial anomalies in PD, which has remained unclear for years and made PD diagnosis and treatment extremely difficult. Therefore, in this review, we endeavored to discuss the complex association of epigenetic modifications and other associated vital factors in mitochondrial dysfunction. We propose a hypothesis that describes a vicious cycle in which mitochondrial dysfunction and oxidative stress act as a hub for regulating DA neuron's fate in PD. Oxidative stress triggers the release of endogenous neurotoxins (CTIQs) that lead to mitochondrial dysfunction along with abnormal α‐synuclein aggregation and epigenetic modifications. These disturbances further intensify oxidative stress and mitochondrial damage, amplifying the synthesis of CTIQs and works vice versa. This vicious cycle may result in the degeneration of DN to hallmark Parkinsonism. Furthermore, we have also highlighted various endogenous compounds and epigenetic marks (neurotoxic and neuroprotective), which may help for devising future diagnostic biomarkers and target specific drugs using novel PD management strategies.
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Affiliation(s)
- Zixuan Chen
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Madiha Rasheed
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Yulin Deng
- School of Life Science, Beijing Institute of Technology, Beijing, China
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Yang Y, Zeng C, Lu X, Song Y, Nie J, Ran R, Zhang Z, He C, Zhang W, Liu SM. 5-Hydroxymethylcytosines in Circulating Cell-Free DNA Reveal Vascular Complications of Type 2 Diabetes. Clin Chem 2019; 65:1414-1425. [PMID: 31575611 DOI: 10.1373/clinchem.2019.305508] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/06/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Long-term complications of type 2 diabetes (T2D), such as macrovascular and microvascular events, are the major causes for T2D-related disability and mortality. A clinically convenient, noninvasive approach for monitoring the development of these complications would improve the overall life quality of patients with T2D and help reduce healthcare burden through preventive interventions. METHODS A selective chemical labeling strategy for 5-hydroxymethylcytosines (5hmC-Seal) was used to profile genome-wide 5hmCs, an emerging class of epigenetic markers implicated in complex diseases including diabetes, in circulating cell-free DNA (cfDNA) from a collection of Chinese patients (n = 62). Differentially modified 5hmC markers between patients with T2D with and without macrovascular/microvascular complications were analyzed under a case-control design. RESULTS Statistically significant changes in 5hmC markers were associated with T2D-related macrovascular/microvascular complications, involving genes and pathways relevant to vascular biology and diabetes, including insulin resistance and inflammation. A 16-gene 5hmC marker panel accurately distinguished patients with vascular complications from those without [testing set: area under the curve (AUC) = 0.85; 95% CI, 0.73-0.96], outperforming conventional clinical variables such as urinary albumin. In addition, a separate 13-gene 5hmC marker panel could distinguish patients with single complications from those with multiple complications (testing set: AUC = 0.84; 95% CI, 0.68-0.99), showing superiority over conventional clinical variables. CONCLUSIONS The 5hmC markers in cfDNA reflected the epigenetic changes in patients with T2D who developed macrovascular/microvascular complications. The 5hmC-Seal assay has the potential to be a clinically convenient, noninvasive approach that can be applied in the clinic to monitor the presence and severity of diabetic vascular complications.
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Affiliation(s)
- Ying Yang
- Department of Clinical Laboratory, Center for Gene Diagnosis, and Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chang Zeng
- Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL.,Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Xingyu Lu
- Shanghai Epican Genetech Co. Ltd., Shanghai, China
| | - Yanqun Song
- Shanghai Epican Genetech Co. Ltd., Shanghai, China
| | - Ji Nie
- Department of Chemistry, The University of Chicago, Chicago, IL
| | - Ruoxi Ran
- Department of Clinical Laboratory, Center for Gene Diagnosis, and Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhou Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL; .,Department of Biochemistry and Molecular Biology; Institute for Biophysical Dynamics; and The Howard Hughes Medical Institute, The University of Chicago, Chicago, IL
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL;
| | - Song-Mei Liu
- Department of Clinical Laboratory, Center for Gene Diagnosis, and Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China;
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Moore-Morris T, van Vliet PP, Andelfinger G, Puceat M. Role of Epigenetics in Cardiac Development and Congenital Diseases. Physiol Rev 2019; 98:2453-2475. [PMID: 30156497 DOI: 10.1152/physrev.00048.2017] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The heart is the first organ to be functional in the fetus. Heart formation is a complex morphogenetic process regulated by both genetic and epigenetic mechanisms. Congenital heart diseases (CHD) are the most prominent congenital diseases. Genetics is not sufficient to explain these diseases or the impact of them on patients. Epigenetics is more and more emerging as a basis for cardiac malformations. This review brings the essential knowledge on cardiac biology of development. It further provides a broad background on epigenetics with a focus on three-dimensional conformation of chromatin. Then, we summarize the current knowledge of the impact of epigenetics on cardiac cell fate decision. We further provide an update on the epigenetic anomalies in the genesis of CHD.
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Affiliation(s)
- Thomas Moore-Morris
- Université Aix-Marseille, INSERM UMR- 1251, Marseille , France ; Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Quebec , Canada ; Université de Montréal, Montreal, Quebec , Canada ; and Laboratoire International Associé INSERM, Marseille France-CHU Ste Justine, Quebec, Canada
| | - Patrick Piet van Vliet
- Université Aix-Marseille, INSERM UMR- 1251, Marseille , France ; Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Quebec , Canada ; Université de Montréal, Montreal, Quebec , Canada ; and Laboratoire International Associé INSERM, Marseille France-CHU Ste Justine, Quebec, Canada
| | - Gregor Andelfinger
- Université Aix-Marseille, INSERM UMR- 1251, Marseille , France ; Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Quebec , Canada ; Université de Montréal, Montreal, Quebec , Canada ; and Laboratoire International Associé INSERM, Marseille France-CHU Ste Justine, Quebec, Canada
| | - Michel Puceat
- Université Aix-Marseille, INSERM UMR- 1251, Marseille , France ; Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Quebec , Canada ; Université de Montréal, Montreal, Quebec , Canada ; and Laboratoire International Associé INSERM, Marseille France-CHU Ste Justine, Quebec, Canada
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Wiehe RS, Gole B, Chatre L, Walther P, Calzia E, Ricchetti M, Wiesmüller L. Endonuclease G promotes mitochondrial genome cleavage and replication. Oncotarget 2018; 9:18309-18326. [PMID: 29719607 PMCID: PMC5915074 DOI: 10.18632/oncotarget.24822] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/12/2018] [Indexed: 12/26/2022] Open
Abstract
Endonuclease G (EndoG) is a nuclear-encoded endonuclease, mostly localised in mitochondria. In the nucleus EndoG participates in site-specific cleavage during replication stress and genome-wide DNA degradation during apoptosis. However, the impact of EndoG on mitochondrial DNA (mtDNA) metabolism is poorly understood. Here, we investigated whether EndoG is involved in the regulation of mtDNA replication and removal of aberrant copies. We applied the single-cell mitochondrial Transcription and Replication Imaging Protocol (mTRIP) and PCR-based strategies on human cells after knockdown/knockout and re-expression of EndoG. Our analysis revealed that EndoG stimulates both mtDNA replication initiation and mtDNA depletion, the two events being interlinked and dependent on EndoG's nuclease activity. Stimulation of mtDNA replication by EndoG was independent of 7S DNA processing at the replication origin. Importantly, both mtDNA-directed activities of EndoG were promoted by oxidative stress. Inhibition of base excision repair (BER) that repairs oxidative stress-induced DNA damage unveiled a pronounced effect of EndoG on mtDNA removal, reminiscent of recently discovered links between EndoG and BER in the nucleus. Altogether with the downstream effects on mitochondrial transcription, protein expression, redox status and morphology, this study demonstrates that removal of damaged mtDNA by EndoG and compensatory replication play a critical role in mitochondria homeostasis.
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Affiliation(s)
| | - Boris Gole
- Department of Obstetrics and Gynecology, Ulm University, Ulm, 89075, Germany
- Present address: Centre for Human Molecular Genetics and Pharmacogenomics, Medical Faculty, University of Maribor, Maribor, SI-2000, Slovenia
| | - Laurent Chatre
- Department of Developmental and Stem Cell Biology, Institute Pasteur, Stem Cells and Development, 75724 Cedex 15, Paris, France
- Team Stability of Nuclear and Mitochondrial DNA, Unit of Stem Cells and Development, CNRS UMR 3738, 75724 Cedex 15, Paris, France
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, Ulm, 89081, Germany
| | - Enrico Calzia
- Institute of Anesthesiological Pathophysiology and Process Engineering, Ulm University Hospital, Ulm, 89081, Germany
| | - Miria Ricchetti
- Department of Developmental and Stem Cell Biology, Institute Pasteur, Stem Cells and Development, 75724 Cedex 15, Paris, France
- Team Stability of Nuclear and Mitochondrial DNA, Unit of Stem Cells and Development, CNRS UMR 3738, 75724 Cedex 15, Paris, France
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, Ulm, 89075, Germany
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Kovalchuk A, Kolb B. Chemo brain: From discerning mechanisms to lifting the brain fog-An aging connection. Cell Cycle 2017; 16:1345-1349. [PMID: 28657421 DOI: 10.1080/15384101.2017.1334022] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Mounting evidence indicates that cancer treatments cause numerous deleterious effects, including central nervous system (CNS) toxicity. Chemotherapy-caused CNS side effects encompass changes in cognitive function, memory, and attention, to name a few. Although chemotherapy treatment-induced side effects occur in 16-75% of all patients, the mechanisms of these effects are not well understood. We have recently proposed a new epigenetic theory of chemo brain and, in a pioneer study, determined that cytotoxic chemotherapy agents induce oxidative DNA damage and affect molecular and epigenetic processes in the brain, and may be associated with brain aging processes. In this paper, we discuss the implications of chemo brain epigenetic effects and future perspectives, as well as outline potential links with brain aging and future translational research opportunities.
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Affiliation(s)
- Anna Kovalchuk
- a Department of Neuroscience , University of Lethbridge, Lethbridge, AB Canadian Institute for Advanced Research , Toronto , ON Alberta Epigenetics Network, AB
| | - Bryan Kolb
- a Department of Neuroscience , University of Lethbridge, Lethbridge, AB Canadian Institute for Advanced Research , Toronto , ON Alberta Epigenetics Network, AB
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Genome-wide 5-hydroxymethylcytosine patterns in human spermatogenesis are associated with semen quality. Oncotarget 2017; 8:88294-88307. [PMID: 29179435 PMCID: PMC5687605 DOI: 10.18632/oncotarget.18331] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 05/21/2017] [Indexed: 12/30/2022] Open
Abstract
We performed immunofluorescent analysis of DNA hydroxymethylation and methylation in human testicular spermatogenic cells from azoospermic patients and ejaculated spermatozoa from sperm donors and patients from infertile couples. In contrast to methylation which was present throughout spermatogenesis, hydroxymethylation was either high or almost undetectable in both spermatogenic cells and ejaculated spermatozoa. On testicular cytogenetic preparations, 5-hydroxymethylcytosine was undetectable in mitotic and meiotic chromosomes, and was present exclusively in interphase spermatogonia Ad and in a minor spermatid population. The proportions of hydroxymethylated and non-hydroxymethylated diploid and haploid nuclei were similar among samples, suggesting that the observed alterations of 5-hydroxymethylcytosine patterns in differentiating spermatogenic cells are programmed. In ejaculates, a few spermatozoa had high 5-hydroxymethylcytosine level, while in the other ones hydroxymethylation was almost undetectable. The percentage of highly hydroxymethylated (5-hydroxymethylcytosine-positive) spermatozoa varied strongly among individuals. In patients from infertile couples, it was higher than in sperm donors (P<0.0001) and varied in a wider range: 0.12-21.24% versus 0.02-0.46%. The percentage of highly hydroxymethylated spermatozoa correlated strongly negatively with the indicators of good semen quality – normal morphology (r=-0.567, P<0.0001) and normal head morphology (r=-0.609, P<0.0001) – and strongly positively with the indicator of poor semen quality: sperm DNA fragmentation (r=0.46, P=0.001). Thus, the immunocytochemically detected increase of 5hmC in individual spermatozoa is associated with infertility in a couple and with deterioration of sperm parameters. We hypothesize that this increase is not programmed, but represents an induced abnormality and, therefore, it can be potentially used as a novel indicator of semen quality.
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12
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Naderlinger E, Holzmann K. Epigenetic Regulation of Telomere Maintenance for Therapeutic Interventions in Gliomas. Genes (Basel) 2017; 8:E145. [PMID: 28513547 PMCID: PMC5448019 DOI: 10.3390/genes8050145] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/08/2017] [Accepted: 05/12/2017] [Indexed: 02/07/2023] Open
Abstract
High-grade astrocytoma of WHO grade 4 termed glioblastoma multiforme (GBM) is a common human brain tumor with poor patient outcome. Astrocytoma demonstrates two known telomere maintenance mechanisms (TMMs) based on telomerase activity (TA) and on alternative lengthening of telomeres (ALT). ALT is associated with lower tumor grades and better outcome. In contrast to ALT, regulation of TA in tumors by direct mutation and epigenetic activation of the hTERT promoter is well established. Here, we summarize the genetic background of TMMs in non-malignant cells and in cancer, in addition to clinical and pathological features of gliomas. Furthermore, we present new evidence for epigenetic mechanisms (EMs) involved in regulation of ALT and TA with special emphasis on human diffuse gliomas as potential therapeutic drug targets. We discuss the role of TMM associated telomeric chromatin factors such as DNA and histone modifying enzymes and non-coding RNAs including microRNAs and long telomeric TERRA transcripts.
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Affiliation(s)
- Elisabeth Naderlinger
- Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Borschkegasse 8a, Vienna 1090, Austria.
| | - Klaus Holzmann
- Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Borschkegasse 8a, Vienna 1090, Austria.
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13
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Wei H, Feng Y, Liang F, Cheng W, Wu X, Zhou R, Wang Y. Role of oxidative stress and DNA hydroxymethylation in the neurotoxicity of fine particulate matter. Toxicology 2017; 380:94-103. [PMID: 28153600 DOI: 10.1016/j.tox.2017.01.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 01/22/2017] [Accepted: 01/26/2017] [Indexed: 11/26/2022]
Abstract
Epidemiological studies have implicated fine particulate matter (PM2.5) as a risk factor for neurodegenerative diseases and neurodevelopmental disorders. However, the underlying molecular mechanisms and the influences of different components remain largely elusive. Here, we extended our previous work to investigate the role of oxidative stress and DNA hydroxymethylation in neuronal pathology of PM2.5. We found PM2.5 and its extracts (water-soluble extracts, organic extracts and carbon core component) differentially caused cell cycle arrest, cell apoptosis and the cell proliferation inhibition in neuronal cells. These effects were mechanistically related to each other and oxidative stress, suggesting PM2.5 and toxic compounds adsorbed on the particles may cause different types of brain damages. In addition, PM2.5 and its organic extracts increased global DNA hydroxymethylation and gene-specific DNA hydroxymethylation of neuronal genes, and subsequently interfered with their mRNA expression. The impairments in neuronal progression characterized with decreased length of neurite and reduced mRNA expression of neuronal markers and synaptic markers. The blocking effects of antioxidants demonstrated the involvement of oxidative stress-mediated hydroxymethylation abnormalities in PM2.5-induced defects in neurite outgrowth and synapse formation. Our results first revealed the role of oxidative stress-mediated abnormal DNA hydroxymethylation in neuronal impairments of PM2.5, and thoroughly evaluated the neurocytotoxicity of different components.
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Affiliation(s)
- Hongying Wei
- The Ninth People Hospital of Shanghai Jiao Tong University School of Medicine, No. 639 Zhizaoju Road, Shanghai 200011, China
| | - Yan Feng
- School of Public Health, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqing South Road, Shanghai 200025, China
| | - Fan Liang
- School of Public Health, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqing South Road, Shanghai 200025, China
| | - Wei Cheng
- School of Public Health, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqing South Road, Shanghai 200025, China
| | - Xiaomeng Wu
- School of Public Health, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqing South Road, Shanghai 200025, China
| | - Ren Zhou
- School of Public Health, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqing South Road, Shanghai 200025, China
| | - Yan Wang
- The Ninth People Hospital of Shanghai Jiao Tong University School of Medicine, No. 639 Zhizaoju Road, Shanghai 200011, China; School of Public Health, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqing South Road, Shanghai 200025, China; MOE-Shanghai Key Laboratory of Children's Environmental Health, No. 1665 Kongjiang Road, Shanghai, 200092, China.
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