1
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Sánchez-Ortí JV, Correa-Ghisays P, Balanzá-Martínez V, Macías Saint-Gerons D, Berenguer-Pascual E, Romá-Mateo C, Victor VM, Forés-Martos J, San-Martin C, Selva-Vera G, Tabarés-Seisdedos R. Systemic inflammation, oxidative damage and neurocognition predict telomere length in a transdiagnostic sample stratified by global DNA methylation levels. Sci Rep 2024; 14:13159. [PMID: 38849401 PMCID: PMC11161596 DOI: 10.1038/s41598-024-62980-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
Epigenetic mechanisms contribute to the maintenance of both type 2 diabetes mellitus (T2DM) and psychiatric disorders. Emerging evidence suggests that molecular pathways and neurocognitive performance regulate epigenetic dynamics in these disorders. The current combined and transdiagnostic study investigated whether inflammatory, oxidative stress, adhesion molecule, neurocognitive and functional performance are significant predictors of telomere dynamics in a sample stratified by global DNA methylation levels. Peripheral blood inflammation, oxidative stress and adhesion molecule biomarkers and neurocognitive function were assessed twice over a 1-year period in 80 individuals, including 16 with schizophrenia (SZ), 16 with bipolar disorder (BD), 16 with major depressive disorder (MDD), 15 with T2DM, and 17 healthy controls (HCs). Leukocyte telomere length (LTL) was measured by qRT-PCR using deoxyribonucleic acid (DNA) extracted from peripheral blood samples. A posteriori, individuals were classified based on their global methylation score (GMS) at baseline into two groups: the below-average methylation (BM) and above-average methylation (AM) groups. Hierarchical and k-means clustering methods, mixed one-way analysis of variance and linear regression analyses were performed. Overall, the BM group showed a significantly higher leukocyte telomere length (LTL) than the AM group at both time points (p = 0.02; η2p = 0.06). Moreover, the BM group had significantly lower levels of tumor necrosis factor alpha (TNF-α) (p = 0.03; η2p = 0.06) and C-reactive protein (CRP) (p = 0.03; η2p = 0.06) than the AM group at the 1-year follow-up. Across all participants, the regression models showed that oxidative stress (reactive oxygen species [ROS]) (p = 0.04) and global cognitive score [GCS] (p = 0.02) were significantly negatively associated with LTL, whereas inflammatory (TNF-α) (p = 0.04), adhesion molecule biomarkers (inter cellular adhesion molecule [ICAM]) (p = 0.009), and intelligence quotient [IQ] (p = 0.03) were significantly positively associated with LTL. Moreover, the model predictive power was increased when tested in both groups separately, explaining 15.8% and 28.1% of the LTL variance at the 1-year follow-up for the AM and BM groups, respectively. Heterogeneous DNA methylation in individuals with T2DM and severe mental disorders seems to support the hypothesis that epigenetic dysregulation occurs in a transdiagnostic manner. Our results may help to elucidate the interplay between epigenetics, molecular processes and neurocognitive function in these disorders. DNA methylation and LTL are potential therapeutic targets for transdiagnostic interventions to decrease the risk of comorbidities.
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Affiliation(s)
- Joan Vicent Sánchez-Ortí
- INCLIVA - Health Research Institute, Valencia, Spain
- TMAP - Evaluation Unit in Personal Autonomy, Dependency and Serious Mental Disorders, University of Valencia, Valencia, Spain
- Faculty of Psychology, University of Valencia, Valencia, Spain
- Center for Biomedical Research in Mental Health Network (CIBERSAM), Health Institute, Carlos III, Madrid, Spain
| | - Patricia Correa-Ghisays
- INCLIVA - Health Research Institute, Valencia, Spain
- TMAP - Evaluation Unit in Personal Autonomy, Dependency and Serious Mental Disorders, University of Valencia, Valencia, Spain
- Faculty of Psychology, University of Valencia, Valencia, Spain
- Center for Biomedical Research in Mental Health Network (CIBERSAM), Health Institute, Carlos III, Madrid, Spain
| | - Vicent Balanzá-Martínez
- INCLIVA - Health Research Institute, Valencia, Spain.
- TMAP - Evaluation Unit in Personal Autonomy, Dependency and Serious Mental Disorders, University of Valencia, Valencia, Spain.
- Center for Biomedical Research in Mental Health Network (CIBERSAM), Health Institute, Carlos III, Madrid, Spain.
- Teaching Unit of Psychiatry and Psychological Medicine, Department of Medicine, University of Valencia, Valencia, Spain.
- VALSME (VALencia Salut Mental i Estigma), University of Valencia, Valencia, Spain.
| | - Diego Macías Saint-Gerons
- INCLIVA - Health Research Institute, Valencia, Spain
- TMAP - Evaluation Unit in Personal Autonomy, Dependency and Serious Mental Disorders, University of Valencia, Valencia, Spain
- Center for Biomedical Research in Mental Health Network (CIBERSAM), Health Institute, Carlos III, Madrid, Spain
| | | | - Carlos Romá-Mateo
- INCLIVA - Health Research Institute, Valencia, Spain
- CIBER de Enfermedades Raras (CIBERER), Health Institute, Carlos III, Madrid, Spain
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Víctor M Victor
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
- Service of Endocrinology and Nutrition, University Hospital Dr. Peset, Valencia, Spain
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Region (FISABIO), Valencia, Spain
| | - Jaume Forés-Martos
- INCLIVA - Health Research Institute, Valencia, Spain
- TMAP - Evaluation Unit in Personal Autonomy, Dependency and Serious Mental Disorders, University of Valencia, Valencia, Spain
- Center for Biomedical Research in Mental Health Network (CIBERSAM), Health Institute, Carlos III, Madrid, Spain
| | - Constanza San-Martin
- INCLIVA - Health Research Institute, Valencia, Spain
- TMAP - Evaluation Unit in Personal Autonomy, Dependency and Serious Mental Disorders, University of Valencia, Valencia, Spain
- Center for Biomedical Research in Mental Health Network (CIBERSAM), Health Institute, Carlos III, Madrid, Spain
- Department of Physiotherapy, University of Valencia, Valencia, Spain
| | - Gabriel Selva-Vera
- INCLIVA - Health Research Institute, Valencia, Spain
- TMAP - Evaluation Unit in Personal Autonomy, Dependency and Serious Mental Disorders, University of Valencia, Valencia, Spain
- Center for Biomedical Research in Mental Health Network (CIBERSAM), Health Institute, Carlos III, Madrid, Spain
- Teaching Unit of Psychiatry and Psychological Medicine, Department of Medicine, University of Valencia, Valencia, Spain
| | - Rafael Tabarés-Seisdedos
- INCLIVA - Health Research Institute, Valencia, Spain.
- TMAP - Evaluation Unit in Personal Autonomy, Dependency and Serious Mental Disorders, University of Valencia, Valencia, Spain.
- Center for Biomedical Research in Mental Health Network (CIBERSAM), Health Institute, Carlos III, Madrid, Spain.
- Teaching Unit of Psychiatry and Psychological Medicine, Department of Medicine, University of Valencia, Valencia, Spain.
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2
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Karimian K, Groot A, Huso V, Kahidi R, Tan KT, Sholes S, Keener R, McDyer JF, Alder JK, Li H, Rechtsteiner A, Greider CW. Human telomere length is chromosome end-specific and conserved across individuals. Science 2024; 384:533-539. [PMID: 38603523 DOI: 10.1126/science.ado0431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 03/30/2024] [Indexed: 04/13/2024]
Abstract
Short telomeres cause age-related disease, and long telomeres contribute to cancer; however, the mechanisms regulating telomere length are unclear. We developed a nanopore-based method, which we call Telomere Profiling, to determine telomere length at nearly single-nucleotide resolution. Mapping telomere reads to chromosome ends showed chromosome end-specific length distributions that could differ by more than six kilobases. Examination of telomere lengths in 147 individuals revealed that certain chromosome ends were consistently longer or shorter. The same rank order was found in newborn cord blood, suggesting that telomere length is determined at birth and that chromosome end-specific telomere length differences are maintained as telomeres shorten with age. Telomere Profiling makes precision investigation of telomere length widely accessible for laboratory, clinical, and drug discovery efforts and will allow deeper insights into telomere biology.
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Affiliation(s)
- Kayarash Karimian
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aljona Groot
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Vienna Huso
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ramin Kahidi
- Health Sciences Program, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Kar-Tong Tan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, The Broad Institute, Cambridge, MA, USA
| | - Samantha Sholes
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rebecca Keener
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - John F McDyer
- Pulmonary, Allergy, Critical Care, and Sleep Medicine Division, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jonathan K Alder
- Pulmonary, Allergy, Critical Care, and Sleep Medicine Division, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Andreas Rechtsteiner
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Carol W Greider
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
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3
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Das A, Giri AK, Bhattacharjee P. Targeting 'histone mark': Advanced approaches in epigenetic regulation of telomere dynamics in cancer. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195007. [PMID: 38237857 DOI: 10.1016/j.bbagrm.2024.195007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024]
Abstract
Telomere integrity is required for the maintenance of genome stability and prevention of oncogenic transformation of cells. Recent evidence suggests the presence of epigenetic modifications as an important regulator of mammalian telomeres. Telomeric and subtelomeric regions are rich in epigenetic marks that regulate telomere length majorly through DNA methylation and post-translational histone modifications. Specific histone modifying enzymes play an integral role in establishing telomeric histone codes necessary for the maintenance of structural integrity. Alterations of crucial histone moieties and histone modifiers cause deregulations in the telomeric chromatin leading to carcinogenic manifestations. This review delves into the significance of histone modifications and their influence on telomere dynamics concerning cancer. Additionally, it highlights the existing research gaps that hold the potential to drive the development of therapeutic interventions targeting the telomere epigenome.
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Affiliation(s)
- Ankita Das
- Department of Environmental Science, University of Calcutta, Kolkata 700019, India; Department of Zoology, University of Calcutta, Kolkata 700019, India
| | - Ashok K Giri
- Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Pritha Bhattacharjee
- Department of Environmental Science, University of Calcutta, Kolkata 700019, India.
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4
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Margiana R, Gupta R, Al-Jewari WM, Hjazi A, Alsaab HO, Mustafa YF, Singh R, Thaibt R, Alkhayyat S, Ibrahim AJ. Evaluation of telomere length, reactive oxygen species, and apoptosis in spermatozoa of patients with oligospermia. Cell Biochem Funct 2024; 42:e3935. [PMID: 38379260 DOI: 10.1002/cbf.3935] [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: 07/16/2023] [Revised: 01/04/2024] [Accepted: 01/09/2024] [Indexed: 02/22/2024]
Abstract
50% of cases of infertility are caused by male factor, which acquired or congenital problems may bring on. Male infertility can be caused by oligospermia and asthenozoospermia, which are common. Since the same mutations that cause azoospermia in some people also cause oligozoospermia in others, oligozoospermia may be thought of as a less severe form of azoospermia. Studies have demonstrated telomere length, catalase activity, super oxide dismutase (SOD), and DNA fragmentation can be influential factors for male infertility. The amount of apoptosis, oxidative stress factors, telomere length, and DNA fragmentation were some aspects of healthy sperm that we chose to look into in this study and compare to oligospermia individuals. Oligospermia patients (n = 24) and fertile men (n = 27) semen samples were collected, and the apoptosis rate of sperms in both groups was analyzed (Flow cytometry). Also, gene expression of apoptotic and antiapoptotic markers and telomere length were examined (real-time polymerase chain reaction). The sperm DNA fragmentation kit was used to determine DNA fragmentation and to evaluate catalase and SOD activity; the specific kits and methods were utilized. Higher expression levels of caspase3 (p = .0042), caspase8 (p = .0145), caspase9 (p = .0275), and BAX (p = .0202) mRNA were observed in patients who had oligospermia. In contrast, lower mRNA expression of BCL-2 (p = .0009) was detected in this group. In addition, telomere length was decreased in the oligospermia group (p < .0001) compared to the health group. Moreover, the frequency of apoptosis is induced in patients (p = .0026). The catalase activity is low (p = .0008), but the SOD activity is high (p = .0015) in the patient group. As a result of our findings, we may list the sperm cell apoptosis rate, telomere length, the degree of sperm DNA fragmentation, and lastly, the measurement of significant and efficient oxidative stress markers like SOD and catalase in semen plasma among the principal diagnostic characteristics for oligospermia. Future studies will be better able to treat oligospermia by showing whether these indicators are rising or falling.
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Affiliation(s)
- Ria Margiana
- Department of Anatomy, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Master's Programme Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Andrology Program, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
- Dr. Soetomo General Academic Hospital, Surabaya, Indonesia
| | - Reena Gupta
- Institute of Pharmaceutical Research, GLA University, Bharthia, India
| | | | - Ahmed Hjazi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Hashem O Alsaab
- Pharmaceutics and Pharmaceutical Technology, Taif University, Taif, Saudi Arabia
| | | | - Rajesh Singh
- Uttaranchal Institute of Technology, Uttaranchal University, Dehradun, India
| | - Ruiscul Thaibt
- Medical Technical College, Al-Farahidi University, Baghdad, Iraq
| | - Safa Alkhayyat
- College of Pharmacy, The Islamic University, Najaf, Iraq
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5
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Karimian K, Groot A, Huso V, Kahidi R, Tan KT, Sholes S, Keener R, McDyer JF, Alder JK, Li H, Rechtsteiner A, Greider CW. Human telomere length is chromosome specific and conserved across individuals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.21.572870. [PMID: 38187739 PMCID: PMC10769321 DOI: 10.1101/2023.12.21.572870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Short telomeres cause age-related disease and long telomeres predispose to cancer; however, the mechanisms regulating telomere length are unclear. To probe these mechanisms, we developed a nanopore sequencing method, Telomere Profiling, that is easy to implement, precise, and cost effective with broad applications in research and the clinic. We sequenced telomeres from individuals with short telomere syndromes and found similar telomere lengths to the clinical FlowFISH assay. We mapped telomere reads to specific chromosome end and identified both chromosome end-specific and haplotype-specific telomere length distributions. In the T2T HG002 genome, where the average telomere length is 5kb, we found a remarkable 6kb difference in lengths between some telomeres. Further, we found that specific chromosome ends were consistently shorter or longer than the average length across 147 individuals. The presence of conserved chromosome end-specific telomere lengths suggests there are new paradigms in telomere biology that are yet to be explored. Understanding the mechanisms regulating length will allow deeper insights into telomere biology that can lead to new approaches to disease.
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Affiliation(s)
- Kayarash Karimian
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Aljona Groot
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz
| | - Vienna Huso
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | | | - Kar-Tong Tan
- Harvard Medical School, Department of Genetics, Boston, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute, Cancer Program, Cambridge, MA
| | - Samantha Sholes
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Present address Merck & Co., 770 Sumneytown Pike, West Point, PA 19486
| | - Rebecca Keener
- Department of Biomedical Engineering, Johns Hopkins University
| | - John F. McDyer
- Pulmonary, Allergy, Critical Care, and Sleep Medicine Division, Department of Medicine, University of Pittsburgh
| | - Jonathan K. Alder
- Pulmonary, Allergy, Critical Care, and Sleep Medicine Division, Department of Medicine, University of Pittsburgh
| | - Heng Li
- Dana-Farber Cancer Institute, Department of Data Sciences, Boston, MA
- Harvard Medical School, Department of Biomedical Informatics, Boston, MA
| | - Andreas Rechtsteiner
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz
| | - Carol W. Greider
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz
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Catto LFB, Zanelatto LC, Donaires FS, de Carvalho VS, Santana BA, Pinto AL, Fantacini D, de Souza LEB, Fonseca NP, Telho BS, Ayrosa Madeira MI, Barbosa Pagnano KB, Firmato AB, Fagundes EM, Higashi M, Nunes EC, Traina F, Lobo de F. Pontes L, Rego EM, Calado RT. Telomeric repeat-containing RNA is dysregulated in acute myeloid leukemia. Blood Adv 2023; 7:7067-7078. [PMID: 37773887 PMCID: PMC10694524 DOI: 10.1182/bloodadvances.2023010658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 09/11/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023] Open
Abstract
TERRA (telomeric repeat-containing RNA) is a class of long noncoding RNAs transcribed from subtelomeric and telomeric regions. TERRA binds to the subtelomeric and telomeric DNA-forming R-loops (DNA-RNA hybrids), which are involved in telomere maintenance and telomerase function, but the role of TERRA in human cells is not well characterized. Here, we comprehensively investigated for the first time TERRA expression in primary human hematopoietic cells from an exploratory cohort of patients with acute myeloid leukemia (AML), patients with acute lymphoblastic leukemia (ALL), patients with telomere biology disorder (TBD), and healthy subjects. TERRA expression was repressed in primary human hematopoietic cells, including healthy donors, patients with ALL, and patients with TBD, irrespective of their telomere length, except for AML. A second cohort comprising 88 patients with AML showed that TERRA was overexpressed in an AML subgroup also characterized by higher R-loop formation, low TERT and RNAseH2 expression, and a paucity of somatic splicing factor mutations. Telomere length did not correlate with TERRA expression levels. To assess the role of TERRA R-loops in AML, we induced R-loop depletion by increasing RNAseH1 expression in 2 AML cell lines. Decreased TERRA R-loops in AML cell lines resulted in increased chemosensitivity to cytarabine. Our findings indicate that TERRA is uniformly repressed in primary human hematopoietic cells but abnormally expressed in an AML subset with low telomerase.
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Affiliation(s)
- Luiz Fernando B. Catto
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Leonardo C. Zanelatto
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Flavia S. Donaires
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Vinicius S. de Carvalho
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Bárbara A. Santana
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - André L. Pinto
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Daianne Fantacini
- Regional Blood Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Lucas Eduardo B. de Souza
- Regional Blood Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Natasha P. Fonseca
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Bruno S. Telho
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Maria Isabel Ayrosa Madeira
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | | | | | | | | | | | - Fabiola Traina
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Lorena Lobo de F. Pontes
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Eduardo M. Rego
- Department of Internal Medicine, University of São Paulo Medical School, São Paulo, Brazil
| | - Rodrigo T. Calado
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- Regional Blood Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
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Rivosecchi J, Cusanelli E. TERRA beyond cancer: the biology of telomeric repeat-containing RNAs in somatic and germ cells. FRONTIERS IN AGING 2023; 4:1224225. [PMID: 37636218 PMCID: PMC10448526 DOI: 10.3389/fragi.2023.1224225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/31/2023] [Indexed: 08/29/2023]
Abstract
The telomeric noncoding RNA TERRA is a key component of telomeres and it is widely expressed in normal as well as cancer cells. In the last 15 years, several publications have shed light on the role of TERRA in telomere homeostasis and cell survival in cancer cells. However, only few studies have investigated the regulation or the functions of TERRA in normal tissues. A better understanding of the biology of TERRA in non-cancer cells may provide unexpected insights into how these lncRNAs are transcribed and operate in cells, and their potential role in physiological processes, such as aging, age-related pathologies, inflammatory processes and human genetic diseases. In this review we aim to discuss the findings that have advanced our understanding of the biology of TERRA using non-cancer mammalian cells as a model system.
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Affiliation(s)
- Julieta Rivosecchi
- Laboratory of Cell Biology and Molecular Genetics, Department of Cellular, Computational and Integrative Biology—CIBIO, University of Trento, Trento, Italy
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8
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Kuan XY, Fauzi NSA, Ng KY, Bakhtiar A. Exploring the Causal Relationship Between Telomere Biology and Alzheimer's Disease. Mol Neurobiol 2023; 60:4169-4183. [PMID: 37046137 PMCID: PMC10293431 DOI: 10.1007/s12035-023-03337-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/03/2023] [Indexed: 04/14/2023]
Abstract
Telomeres, also known as the "protective caps" of our chromosomes, shorten with each cell cycle due to the end replication problem. This process, termed telomere attrition, is associated with many age-related disorders, such as Alzheimer's disease (AD). Despite the numerous studies conducted in this field, the role of telomere attrition in the onset of the disease remains unclear. To investigate the causal relationship between short telomeres and AD, this review aims to highlight the primary factors that regulate telomere length and maintain its integrity, with an additional outlook on the role of oxidative stress, which is commonly associated with aging and molecular damage. Although some findings thus far might be contradictory, telomere attrition likely plays a crucial role in the progression of AD due to its close association with oxidative stress. The currently available treatments for AD are only symptomatic without affecting the progression of the disease. The components of telomere biology discussed in this paper have previously been studied as an alternative treatment option for several diseases and have exhibited promising in vitro and in vivo results. Hence, this should provide a basis for future research to develop a potential therapeutic strategy for AD. (Created with BioRender.com).
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Affiliation(s)
- Xi-Yuen Kuan
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Nurul Syahira Ahmad Fauzi
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Khuen Yen Ng
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Athirah Bakhtiar
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.
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9
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Gong Y, Liu Y. R-Loops at Chromosome Ends: From Formation, Regulation, and Cellular Consequence. Cancers (Basel) 2023; 15:cancers15072178. [PMID: 37046839 PMCID: PMC10093737 DOI: 10.3390/cancers15072178] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/14/2023] Open
Abstract
Telomeric repeat containing RNA (TERRA) is transcribed from subtelomeric regions to telomeres. TERRA RNA can invade telomeric dsDNA and form telomeric R-loop structures. A growing body of evidence suggests that TERRA-mediated R-loops are critical players in telomere length homeostasis. Here, we will review current knowledge on the regulation of R-loop levels at telomeres. In particular, we will discuss how the central player TERRA and its binding proteins modulate R-loop levels through various mechanisms. We will further provide an overview of the consequences of TERRA-mediated persistent or unscheduled R-loops at telomeres in human ALT cancers and other organisms, with a focus on telomere length regulation after replication interference-induced damage and DNA homologous recombination-mediated repair.
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Affiliation(s)
- Yi Gong
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Yie Liu
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
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10
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Extra-hematopoietic immunomodulatory role of the guanine-exchange factor DOCK2. Commun Biol 2022; 5:1246. [DOI: 10.1038/s42003-022-04078-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 10/06/2022] [Indexed: 11/16/2022] Open
Abstract
AbstractStromal cells interact with immune cells during initiation and resolution of immune responses, though the precise underlying mechanisms remain to be resolved. Lessons learned from stromal cell-based therapies indicate that environmental signals instruct their immunomodulatory action contributing to immune response control. Here, to the best of our knowledge, we show a novel function for the guanine-exchange factor DOCK2 in regulating immunosuppressive function in three human stromal cell models and by siRNA-mediated DOCK2 knockdown. To identify immune function-related stromal cell molecular signatures, we first reprogrammed mesenchymal stem/progenitor cells (MSPCs) into induced pluripotent stem cells (iPSCs) before differentiating these iPSCs in a back-loop into MSPCs. The iPSCs and immature iPS-MSPCs lacked immunosuppressive potential. Successive maturation facilitated immunomodulation, while maintaining clonogenicity, comparable to their parental MSPCs. Sequential transcriptomics and methylomics displayed time-dependent immune-related gene expression trajectories, including DOCK2, eventually resembling parental MSPCs. Severe combined immunodeficiency (SCID) patient-derived fibroblasts harboring bi-allelic DOCK2 mutations showed significantly reduced immunomodulatory capacity compared to non-mutated fibroblasts. Conditional DOCK2 siRNA knockdown in iPS-MSPCs and fibroblasts also immediately reduced immunomodulatory capacity. Conclusively, CRISPR/Cas9-mediated DOCK2 knockout in iPS-MSPCs also resulted in significantly reduced immunomodulation, reduced CDC42 Rho family GTPase activation and blunted filopodia formation. These data identify G protein signaling as key element devising stromal cell immunomodulation.
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11
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Seddon AR, Das AB, Hampton MB, Stevens AJ. Site-specific decreases in DNA methylation in replicating cells following exposure to oxidative stress. Hum Mol Genet 2022; 32:632-648. [PMID: 36106794 PMCID: PMC9896486 DOI: 10.1093/hmg/ddac232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/01/2022] [Accepted: 09/03/2022] [Indexed: 02/07/2023] Open
Abstract
Oxidative stress is a common feature of inflammation-driven cancers, and it promotes genomic instability and aggressive tumour phenotypes. It is known that oxidative stress transiently modulates gene expression through the oxidation of transcription factors and associated regulatory proteins. Neutrophils are our most abundant white blood cells and accumulate at sites of infection and inflammation. Activated neutrophils produce hypochlorous acid and chloramines, which can disrupt DNA methylation by oxidizing methionine. The goal of the current study was to determine whether chloramine exposure results in sequence-specific modifications in DNA methylation that enable long-term alterations in transcriptional output. Proliferating Jurkat T-lymphoma cells were exposed to sublethal doses of glycine chloramine and differential methylation patterns were compared using Illumina EPIC 850 K bead chip arrays. There was a substantial genome-wide decrease in methylation 4 h after exposure that correlated with altered RNA expression for 24 and 48 h, indicating sustained impacts on exposed cells. A large proportion of the most significant differentially methylated CpG sites were situated towards chromosomal ends, suggesting that these regions are most susceptible to inhibition of maintenance DNA methylation. This may contribute to epigenetic instability of chromosomal ends in rapidly dividing cells, with potential implications for the regulation of telomere length and cellular longevity.
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Affiliation(s)
- Annika R Seddon
- University of Otago, Christchurch, Department of Pathology and Biomedical Science, Christchurch, 8011, New Zealand
| | - Andrew B Das
- University of Otago, Christchurch, Department of Pathology and Biomedical Science, Christchurch, 8011, New Zealand,Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Australia
| | - Mark B Hampton
- University of Otago, Christchurch, Department of Pathology and Biomedical Science, Christchurch, 8011, New Zealand
| | - Aaron J Stevens
- To whom correspondence should be addressed at: Department of Pathology, University of Otago, Wellington, 23 Mein St, Newtown, Wellington 6021, New Zealand. Tel: +64 43855541; Fax: +64 4 389 5725;
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12
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Farrell C, Vaquero-Sedas MI, Cubiles MD, Thompson M, Vega-Vaquero A, Pellegrini M, Vega-Palas MA. A complex network of interactions governs DNA methylation at telomeric regions. Nucleic Acids Res 2022; 50:1449-1464. [PMID: 35061900 PMCID: PMC8860613 DOI: 10.1093/nar/gkac012] [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: 12/17/2021] [Accepted: 01/10/2022] [Indexed: 12/13/2022] Open
Abstract
DNA methylation modulates telomere function. In Arabidopsis thaliana, telomeric regions have a bimodal chromatin organization with unmethylated telomeres and methylated subtelomeres. To gain insight into this organization we have generated TAIR10-Tel, a modified version of the Arabidopsis reference genome with additional sequences at most chromosome ends. TAIR10-Tel has allowed us to analyse DNA methylation at nucleotide resolution level in telomeric regions. We have analysed the wild-type strain and mutants that encode inactive versions of all currently known relevant methyltransferases involved in cytosine methylation. These analyses have revealed that subtelomeric DNA methylation extends 1 to 2 kbp from Interstitial Telomeric Sequences (ITSs) that abut or are very near to telomeres. However, DNA methylation drops at the telomeric side of the telomere-subtelomere boundaries and disappears at the inner part of telomeres. We present a comprehensive and integrative model for subtelomeric DNA methylation that should help to decipher the mechanisms that govern the epigenetic regulation of telomeres. This model involves a complex network of interactions between methyltransferases and subtelomeric DNA sequences.
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Affiliation(s)
- Colin Farrell
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA90095, USA
| | - María I Vaquero-Sedas
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, IBVF (CSIC-US), Seville, E41092, Spain
| | - María D Cubiles
- Departamento de Estadística e Investigación Operativa, Facultad de Matemáticas, Universidad de Sevilla, Seville, E41012, Spain
| | - Michael Thompson
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA90095, USA
| | - Alejandro Vega-Vaquero
- Escuela Técnica Superior de Ingeniería Informática, Universidad de Sevilla, Seville, E41012, Spain
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA90095, USA.,Institute of Genomics and Proteomics, Los Angeles, CA90095, USA
| | - Miguel A Vega-Palas
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, IBVF (CSIC-US), Seville, E41092, Spain
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13
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Desaulniers D, Vasseur P, Jacobs A, Aguila MC, Ertych N, Jacobs MN. Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. Int J Mol Sci 2021; 22:10969. [PMID: 34681626 PMCID: PMC8535778 DOI: 10.3390/ijms222010969] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Sciences and Research Bureau, Hazard Identification Division, Health Canada, AL:2203B, Ottawa, ON K1A 0K9, Canada
| | - Paule Vasseur
- CNRS, LIEC, Université de Lorraine, 57070 Metz, France;
| | - Abigail Jacobs
- Independent at the Time of Publication, Previously US Food and Drug Administration, Rockville, MD 20852, USA;
| | - M. Cecilia Aguila
- Toxicology Team, Division of Human Food Safety, Center for Veterinary Medicine, US Food and Drug Administration, Department of Health and Human Services, Rockville, MD 20852, USA;
| | - Norman Ertych
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany;
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OX11 0RQ, UK;
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14
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Delbarre E, Janicki SM. Modulation of H3.3 chromatin assembly by PML: A way to regulate epigenetic inheritance. Bioessays 2021; 43:e2100038. [PMID: 34423467 DOI: 10.1002/bies.202100038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/15/2022]
Abstract
Although the promyelocytic leukemia (PML) protein is renowned for regulating a wide range of cellular processes and as an essential component of PML nuclear bodies (PML-NBs), the mechanisms through which it exerts its broad physiological impact are far from fully elucidated. Here, we review recent studies supporting an emerging view that PML's pleiotropic effects derive, at least partially, from its role in regulating histone H3.3 chromatin assembly, a critical epigenetic mechanism. These studies suggest that PML maintains heterochromatin organization by restraining H3.3 incorporation. Examination of PML's contribution to H3.3 chromatin assembly in the context of the cell cycle and PML-NB assembly suggests that PML represses heterochromatic H3.3 deposition during S phase and that transcription and SUMOylation regulate PML's recruitment to heterochromatin. Elucidating PML' s contributions to H3.3-mediated epigenetic regulation will provide insight into PML's expansive influence on cellular physiology and open new avenues for studying oncogenesis linked to PML malfunction.
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Affiliation(s)
- Erwan Delbarre
- Faculty of Health Sciences, OsloMet-Oslo Metropolitan University, Oslo, Norway
| | - Susan M Janicki
- Drexel University Thomas R. Kline School of Law, Philadelphia, Pennsylvania, USA
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15
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Samra N, Toubiana S, Yttervik H, Tzur-Gilat A, Morani I, Itzkovich C, Giladi L, Abu Jabal K, Cao JZ, Godley LA, Mory A, Baris Feldman H, Tveten K, Selig S, Weiss K. RBL2 bi-allelic truncating variants cause severe motor and cognitive impairment without evidence for abnormalities in DNA methylation or telomeric function. J Hum Genet 2021; 66:1101-1112. [PMID: 33980986 DOI: 10.1038/s10038-021-00931-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 02/01/2023]
Abstract
RBL2/p130, a member of the retinoblastoma family of proteins, is a key regulator of cell division and propagates irreversible senescence. RBL2/p130 is also involved in neuronal differentiation and survival, and eliminating Rbl2 in certain mouse strains leads to embryonic lethality accompanied by an abnormal central nervous system (CNS) phenotype. Conflicting reports exist regarding a role of RBL2/p130 in transcriptional regulation of DNA methyltransferases (DNMTs), as well as the control of telomere length. Here we describe the phenotype of three patients carrying bi-allelic RBL2-truncating variants. All presented with infantile hypotonia, severe developmental delay and microcephaly. Malignancies were not reported in carriers or patients. Previous studies carried out on mice and human cultured cells, associated RBL2 loss to DNA methylation and telomere length dysregulation. Here, we investigated whether patient cells lacking RBL2 display related abnormalities. The study of primary patient fibroblasts did not detect abnormalities in expression of DNMTs. Furthermore, methylation levels of whole genome DNA, and specifically of pericentromeric repeats and subtelomeric regions, were unperturbed. RBL2-null fibroblasts show no evidence for abnormal elongation by telomeric recombination. Finally, gradual telomere shortening, and normal onset of senescence were observed following continuous culturing of RBL2-mutated fibroblasts. Thus, this study resolves uncertainties regarding a potential non-redundant role for RBL2 in DNA methylation and telomere length regulation, and indicates that loss of function variants in RBL2 cause a severe autosomal recessive neurodevelopmental disorder in humans.
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Affiliation(s)
- Nadra Samra
- Genetic Unit, Ziv Medical Center, Tzfat, Israel.,Faculty of Medicine, Bar Ilan University, Tzfat, Israel
| | - Shir Toubiana
- Department of Genetics and Developmental Biology, The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Hilde Yttervik
- Department of Medical Genetics, University Hospital of North Norway, Tromsø, Norway
| | - Aya Tzur-Gilat
- Department of Genetics and Developmental Biology, The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | | | - Chen Itzkovich
- The Clinical Research Institute at Rambam Health Care Campus, Haifa, Israel
| | - Liran Giladi
- Department of Genetics and Developmental Biology, The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | | | - John Z Cao
- Section of Hematology Oncology, Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Lucy A Godley
- Section of Hematology Oncology, Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Adi Mory
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel.,The Genetics Institute, Tel Aviv Sourasky Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hagit Baris Feldman
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel.,The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.,The Genetics Institute, Tel Aviv Sourasky Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Sara Selig
- Department of Genetics and Developmental Biology, The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel. .,Laboratory of Molecular Medicine, Rambam Health Care Campus, Haifa, Israel.
| | - Karin Weiss
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel.,The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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16
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Toubiana S, Tzur-Gilat A, Selig S. Epigenetic Characteristics of Human Subtelomeres Vary in Cells Utilizing the Alternative Lengthening of Telomeres (ALT) Pathway. Life (Basel) 2021; 11:life11040278. [PMID: 33810393 PMCID: PMC8065733 DOI: 10.3390/life11040278] [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: 03/01/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/26/2022] Open
Abstract
Most human cancers circumvent senescence by activating a telomere length maintenance mechanism, most commonly involving telomerase activation. A minority of cancers utilize the recombination-based alternative lengthening of telomeres (ALT) pathway. The exact requirements for unleashing normally repressed recombination at telomeres are yet unclear. Epigenetic modifications at telomeric regions were suggested to be pivotal for activating ALT; however, conflicting data exist regarding their exact nature and necessity. To uncover common ALT-positive epigenetic characteristics, we performed a comprehensive analysis of subtelomeric DNA methylation, histone modifications, and TERRA expression in several ALT-positive and ALT-negative cell lines. We found that subtelomeric DNA methylation does not differentiate between the ALT-positive and ALT-negative groups, and most of the analyzed subtelomeres within each group do not share common DNA methylation patterns. Additionally, similar TERRA levels were measured in the ALT-positive and ALT-negative groups, and TERRA levels varied significantly among the members of the ALT-positive group. Subtelomeric H3K4 and H3K9 trimethylation also differed significantly between samples in the ALT-positive group. Our findings do not support a common route by which epigenetic modifications activate telomeric recombination in ALT-positive cells, and thus, different therapeutic approaches will be necessary to overcome ALT-dependent cellular immortalization.
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Affiliation(s)
- Shir Toubiana
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel; (S.T.); (A.T.-G.)
| | - Aya Tzur-Gilat
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel; (S.T.); (A.T.-G.)
| | - Sara Selig
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel; (S.T.); (A.T.-G.)
- Laboratory of Molecular Medicine, Rambam Health Care Campus, Haifa 31096, Israel
- Correspondence:
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17
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Evidence for divergence of DNA methylation maintenance and a conserved inhibitory mechanism from DNA demethylation in chickens and mammals. Genes Genomics 2021; 43:269-280. [PMID: 33555502 PMCID: PMC7966644 DOI: 10.1007/s13258-021-01046-7] [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: 12/17/2020] [Accepted: 01/06/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND DNA methylation is a significant epigenetic modification that is evolutionarily conserved in various species and often serves as a repressive mark for transcription. DNA methylation levels and patterns are regulated by a balance of opposing enzyme functions, DNA methyltransferases, DNMT1/3A/3B and methylcytosine dioxygenases, TET1/2/3. In mice, the TET enzyme converts DNA cytosine methylation (5mC) to 5-hydroxymethylcytosine (5hmC) at the beginning of fertilisation and gastrulation and initiates a global loss of 5mC, while the 5mC level is increased on the onset of cell differentiation during early embryonic development. OBJECTIVE Global loss and gain of DNA methylation may be differently regulated in diverged species. METHODS Chicken B-cell lymphoma DT40 cells were used as an avian model to compare differences in the overall regulation of DNA modification with mammals. RESULTS We found that DNA methylation is maintained at high levels in DT40 cells through compact chromatin formation, which inhibits TET-mediated demethylation. Human and mouse chromosomes introduced into DT40 cells by cell fusion lost the majority of 5mC, except for human subtelomeric repeats. CONCLUSION Our attempt to elucidate the differences in the epigenetic regulatory mechanisms between birds and mammals explored the evidence that they share a common chromatin-based regulation of TET-DNA access, while chicken DNMT1 is involved in different target sequence recognition systems, suggesting that factors inducing DNMT-DNA association have already diverged.
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18
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Toubiana S, Larom G, Smoom R, Duszynski RJ, Godley LA, Francastel C, Velasco G, Selig S. Regulation of telomeric function by DNA methylation differs between humans and mice. Hum Mol Genet 2020; 29:3197-3210. [PMID: 32916696 DOI: 10.1093/hmg/ddaa206] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/02/2020] [Accepted: 09/04/2020] [Indexed: 11/13/2022] Open
Abstract
The most distal 2 kb region in the majority of human subtelomeres contains CpG-rich promoters for TERRA, a long non-coding RNA. When the function of the de novo DNA methyltransferase DNMT3B is disrupted, as in ICF1 syndrome, subtelomeres are abnormally hypomethylated, subtelomeric heterochromatin acquires open chromatin characteristics, TERRA is highly expressed, and telomeres shorten rapidly. In this study, we explored whether the regulation of subtelomeric epigenetic characteristics by DNMT3B is conserved between humans and mice. Studying the DNA sequence of the distal 30 kb of the majority of murine q-arm subtelomeres indicated that these regions are relatively CpG-poor and do not contain TERRA promoters similar to those present in humans. Despite the lack of human-like TERRA promoters, we clearly detected TERRA expression originating from at least seven q-arm subtelomeres, and at higher levels in mouse pluripotent stem cells in comparison with mouse embryonic fibroblasts (MEFs). However, these differences in TERRA expression could not be explained by differential methylation of CpG islands present in the TERRA-expressing murine subtelomeres. To determine whether Dnmt3b regulates the expression of TERRA in mice, we characterized subtelomeric methylation and associated telomeric functions in cells derived from ICF1 model mice. Littermate-derived WT and ICF1 MEFs demonstrated no significant differences in subtelomeric DNA methylation, chromatin modifications, TERRA expression levels, telomere sister chromatid exchange or telomere length. We conclude that the epigenetic characteristics of murine subtelomeres differ substantially from their human counterparts and that TERRA transcription in mice is regulated by factors others than Dnmt3b.
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Affiliation(s)
- Shir Toubiana
- Department of Genetics, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel
| | - Gal Larom
- Department of Genetics, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel
| | - Riham Smoom
- Department of Genetics, The Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Robert J Duszynski
- Department of Medicine, Section of Hematology Oncology, The University of Chicago, Chicago 60637, USA
| | - Lucy A Godley
- Department of Medicine, Section of Hematology Oncology, The University of Chicago, Chicago 60637, USA
| | - Claire Francastel
- Université de Paris, Epigénétique et Destin Cellulaire, CNRS, Paris 75013, France
| | - Guillaume Velasco
- Université de Paris, Epigénétique et Destin Cellulaire, CNRS, Paris 75013, France
| | - Sara Selig
- Department of Genetics, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel
- Laboratory of Molecular Medicine, Rambam Health Care Campus, Haifa 31096, Israel
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Polettini J, da Silva MG. Telomere-Related Disorders in Fetal Membranes Associated With Birth and Adverse Pregnancy Outcomes. Front Physiol 2020; 11:561771. [PMID: 33123024 PMCID: PMC7573552 DOI: 10.3389/fphys.2020.561771] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 09/14/2020] [Indexed: 12/22/2022] Open
Abstract
Telomere disorders have been associated with aging-related diseases, including diabetes, vascular, and neurodegenerative diseases. The main consequence of altered telomere is the induction of the state of irreversible cell cycle arrest. Though several mechanisms responsible for the activation of senescence have been identified, it is still unclear how a cell is indeed induced to become irreversibly arrested. Most tissues in the body will experience senescence throughout its lifespan, but intrinsic and extrinsic stressors, such as chemicals, pollution, oxidative stress (OS), and inflammation accelerate the process. Pregnancy is a state of OS, as the higher metabolic demand of the growing fetus results in increased reactive oxygen species production. As a temporary organ in the mother, senescence in fetal membranes and placenta is expected and linked to term parturition (>37 weeks of gestation). However, a persistent, overwhelming, or premature OS affects placental antioxidant capacity, with consequent accumulation of OS causing damage to lipids, proteins, and DNA in the placental tissues. Therefore, senescence and its main inducer, telomere length (TL) reduction, have been associated with pregnancy complications, including stillbirth, preeclampsia, intrauterine growth restriction, and prematurity. Fetal membranes have a notable role in preterm births, which continue to be a major health issue associated with increased risk of neo and perinatal adverse outcomes and/or predisposition to disease in later life; however, the ability to mediate a delay in parturition during such cases is limited, because the pathophysiology of preterm births and physiological mechanisms of term births are not yet fully elucidated. Here, we review the current knowledge regarding the regulation of telomere-related senescence mechanisms in fetal membranes, highlighting the role of inflammation, methylation, and telomerase activity. Moreover, we present the evidences of TL reduction and senescence in gestational tissues by the time of term parturition. In conclusion, we verified that telomere regulation in fetal membranes requires a more complete understanding, in order to support the development of successful effective interventions of the molecular mechanisms that triggers parturition, including telomere signals, which may vary throughout placental tissues.
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Affiliation(s)
- Jossimara Polettini
- Universidade Federal da Fronteira Sul (UFFS), Programa de Pós Graduação em Ciências Biomédicas, Faculdade de Medicina, Campus Passo Fundo, Brazil
| | - Marcia Guimarães da Silva
- Universidade Estadual Paulista (UNESP), Faculdade de Medicina, Departamento de Patologia, Botucatu, Brazil
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