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Amiard S, Feit L, Vanrobays E, Simon L, Le Goff S, Loizeau L, Wolff L, Butter F, Bourbousse C, Barneche F, Tatout C, Probst AV. The TELOMERE REPEAT BINDING proteins TRB4 and TRB5 function as transcriptional activators of PRC2-controlled genes to regulate plant development. PLANT COMMUNICATIONS 2024; 5:100890. [PMID: 38566416 DOI: 10.1016/j.xplc.2024.100890] [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: 08/06/2023] [Revised: 02/07/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Plant-specific transcriptional regulators called TELOMERE REPEAT BINDING proteins (TRBs) combine two DNA-binding domains, the GH1 domain, which binds to linker DNA and is shared with H1 histones, and the Myb/SANT domain, which specifically recognizes the telobox DNA-binding site motif. TRB1, TRB2, and TRB3 proteins recruit Polycomb group complex 2 (PRC2) to deposit H3K27me3 and JMJ14 to remove H3K4me3 at gene promoters containing telobox motifs to repress transcription. Here, we demonstrate that TRB4 and TRB5, two related paralogs belonging to a separate TRB clade conserved in spermatophytes, regulate the transcription of several hundred genes involved in developmental responses to environmental cues. TRB4 binds to several thousand sites in the genome, mainly at transcription start sites and promoter regions of transcriptionally active and H3K4me3-marked genes, but, unlike TRB1, it is not enriched at H3K27me3-marked gene bodies. However, TRB4 can physically interact with the catalytic components of PRC2, SWINGER, and CURLY LEAF (CLF). Unexpectedly, we show that TRB4 and TRB5 are required for distinctive phenotypic traits observed in clf mutant plants and thus function as transcriptional activators of several hundred CLF-controlled genes, including key flowering genes. We further demonstrate that TRB4 shares multiple target genes with TRB1 and physically and genetically interacts with members of both TRB clades. Collectively, these results reveal that TRB proteins engage in both positive and negative interactions with other members of the family to regulate plant development through both PRC2-dependent and -independent mechanisms.
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Affiliation(s)
- Simon Amiard
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France.
| | - Léa Feit
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Emmanuel Vanrobays
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Lauriane Simon
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Samuel Le Goff
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Loriane Loizeau
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Léa Wolff
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Falk Butter
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Clara Bourbousse
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Fredy Barneche
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Christophe Tatout
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Aline V Probst
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France.
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Ng YB, Akincilar SC. Shaping DNA damage responses: Therapeutic potential of targeting telomeric proteins and DNA repair factors in cancer. Curr Opin Pharmacol 2024; 76:102460. [PMID: 38776747 DOI: 10.1016/j.coph.2024.102460] [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: 12/10/2022] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 05/25/2024]
Abstract
Shelterin proteins regulate genomic stability by preventing inappropriate DNA damage responses (DDRs) at telomeres. Unprotected telomeres lead to persistent DDR causing cell cycle inhibition, growth arrest, and apoptosis. Cancer cells rely on DDR to protect themselves from DNA lesions and exogenous DNA-damaging agents such as chemotherapy and radiotherapy. Therefore, targeting DDR machinery is a promising strategy to increase the sensitivity of cancer cells to existing cancer therapies. However, the success of these DDR inhibitors depends on other mutations, and over time, patients develop resistance to these therapies. This suggests the need for alternative approaches. One promising strategy is co-inhibiting shelterin proteins with DDR molecules, which would offset cellular fitness in DNA repair in a mutation-independent manner. This review highlights the associations and dependencies of the shelterin complex with the DDR proteins and discusses potential co-inhibition strategies that might improve the therapeutic potential of current inhibitors.
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Affiliation(s)
- Yu Bin Ng
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
| | - Semih Can Akincilar
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore.
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Siametis A, Stratigi K, Giamaki D, Chatzinikolaou G, Akalestou-Clocher A, Goulielmaki E, Luke B, Schumacher B, Garinis GA. Transcription stress at telomeres leads to cytosolic DNA release and paracrine senescence. Nat Commun 2024; 15:4061. [PMID: 38744897 PMCID: PMC11094137 DOI: 10.1038/s41467-024-48443-6] [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: 08/24/2023] [Accepted: 04/30/2024] [Indexed: 05/16/2024] Open
Abstract
Transcription stress has been linked to DNA damage -driven aging, yet the underlying mechanism remains unclear. Here, we demonstrate that Tcea1-/- cells, which harbor a TFIIS defect in transcription elongation, exhibit RNAPII stalling at oxidative DNA damage sites, impaired transcription, accumulation of R-loops, telomere uncapping, chromatin bridges, and genome instability, ultimately resulting in cellular senescence. We found that R-loops at telomeres causally contribute to the release of telomeric DNA fragments in the cytoplasm of Tcea1-/- cells and primary cells derived from naturally aged animals triggering a viral-like immune response. TFIIS-defective cells release extracellular vesicles laden with telomeric DNA fragments that target neighboring cells, which consequently undergo cellular senescence. Thus, transcription stress elicits paracrine signals leading to cellular senescence, promoting aging.
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Affiliation(s)
- Athanasios Siametis
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Kalliopi Stratigi
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Despoina Giamaki
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology (IMB), Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland
| | - Georgia Chatzinikolaou
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Alexia Akalestou-Clocher
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Evi Goulielmaki
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Brian Luke
- Institute of Molecular Biology (IMB), Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - George A Garinis
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece.
- Department of Biology, University of Crete, Heraklion, Crete, Greece.
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Wolf SE, Woodruff MJ, Chang van Oordt DA, Clotfelter ED, Cristol DA, Derryberry EP, Ferguson SM, Stanback MT, Taff CC, Vitousek MN, Westneat DF, Rosvall KA. Among-population variation in telomere regulatory proteins and their potential role as hidden drivers of intraspecific variation in life history. J Anim Ecol 2024. [PMID: 38509838 DOI: 10.1111/1365-2656.14071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/14/2024] [Indexed: 03/22/2024]
Abstract
Biologists aim to explain patterns of growth, reproduction and ageing that characterize life histories, yet we are just beginning to understand the proximate mechanisms that generate this diversity. Existing research in this area has focused on telomeres but has generally overlooked the telomere's most direct mediator, the shelterin protein complex. Shelterin proteins physically interact with the telomere to shape its shortening and repair. They also regulate metabolism and immune function, suggesting a potential role in life history variation in the wild. However, research on shelterin proteins is uncommon outside of biomolecular work. Intraspecific analyses can play an important role in resolving these unknowns because they reveal subtle variation in life history within and among populations. Here, we assessed ecogeographic variation in shelterin protein abundance across eight populations of tree swallow (Tachycineta bicolor) with previously documented variation in environmental and life history traits. Using the blood gene expression of four shelterin proteins in 12-day-old nestlings, we tested the hypothesis that shelterin protein gene expression varies latitudinally and in relation to both telomere length and life history. Shelterin protein gene expression differed among populations and tracked non-linear variation in latitude: nestlings from mid-latitudes expressed nearly double the shelterin mRNA on average than those at more northern and southern sites. However, telomere length was not significantly related to latitude. We next assessed whether telomere length and shelterin protein gene expression correlate with 12-day-old body mass and wing length, two proxies of nestling growth linked to future fecundity and survival. We found that body mass and wing length correlated more strongly (and significantly) with shelterin protein gene expression than with telomere length. These results highlight telomere regulatory shelterin proteins as potential mediators of life history variation among populations. Together with existing research linking shelterin proteins and life history variation within populations, these ecogeographic patterns underscore the need for continued integration of ecology, evolution and telomere biology, which together will advance understanding of the drivers of life history variation in nature.
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Affiliation(s)
- Sarah E Wolf
- Department of Biology, Indiana University, Bloomington, Indiana, USA
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Mary J Woodruff
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - David A Chang van Oordt
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
- Cornell Lab of Ornithology, Ithaca, New York, USA
| | | | - Daniel A Cristol
- Department of Biology, William & Mary, Williamsburg, Virginia, USA
| | - Elizabeth P Derryberry
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Stephen M Ferguson
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA
- Department of Biology, University of Richmond, Richmond, Virginia, USA
| | - Mark T Stanback
- Department of Biology, Davidson College, Davidson, North Carolina, USA
| | - Conor C Taff
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
- Cornell Lab of Ornithology, Ithaca, New York, USA
| | - Maren N Vitousek
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
- Cornell Lab of Ornithology, Ithaca, New York, USA
| | - David F Westneat
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA
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Wolf SE, Shalev I. The shelterin protein expansion of telomere dynamics: Linking early life adversity, life history, and the hallmarks of aging. Neurosci Biobehav Rev 2023; 152:105261. [PMID: 37268182 PMCID: PMC10527177 DOI: 10.1016/j.neubiorev.2023.105261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/10/2023] [Accepted: 05/30/2023] [Indexed: 06/04/2023]
Abstract
Aging is characterized by functional decline occurring alongside changes to several hallmarks of aging. One of the hallmarks includes attrition of repeated DNA sequences found at the ends of chromosomes called telomeres. While telomere attrition is linked to morbidity and mortality, whether and how it causally contributes to lifelong rates of functional decline is unclear. In this review, we propose the shelterin-telomere hypothesis of life history, in which telomere-binding shelterin proteins translate telomere attrition into a range of physiological outcomes, the extent of which may be modulated by currently understudied variation in shelterin protein levels. Shelterin proteins may expand the breadth and timing of consequences of telomere attrition, e.g., by translating early life adversity into acceleration of the aging process. We consider how the pleiotropic roles of shelterin proteins provide novel insights into natural variation in physiology, life history, and lifespan. We highlight key open questions that encourage the integrative, organismal study of shelterin proteins that enhances our understanding of the contribution of the telomere system to aging.
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Affiliation(s)
- Sarah E Wolf
- Department of Biobehavioral Health, Penn State University, University Park, PA 16802, USA.
| | - Idan Shalev
- Department of Biobehavioral Health, Penn State University, University Park, PA 16802, USA
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Teng Y, Huang DQ, Li RX, Yi C, Zhan YQ. Association Between Telomere Length and Risk of Lung Cancer in an Asian Population: A Mendelian Randomization Study. World J Oncol 2023; 14:277-284. [PMID: 37560336 PMCID: PMC10409562 DOI: 10.14740/wjon1624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/19/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND Several traditional observational studies and Mendelian randomization (MR) studies have indicated an association between leukocyte telomere length (LTL) and the risk of lung cancer in the European population. However, the results in the Asian population are still unclear. The objective was to reveal the genetic causal association between LTL and the risk of lung cancer in the Asian population. METHODS We conducted a two-sample MR analysis using summary statistics. Instrumental variables (IVs) were obtained from the genome-wide association studies (GWAS) of LTL (n = 23,096) and lung cancer (n = 212,453) of Asian ancestry. We applied the random-effects inverse-variance weighted (IVW) model as the main method. As well, several other models were performed as complementary methods to assess the impact of potential MR assumption violations, including MR-Egger regression, weighted median, and weighted mode models. RESULTS We included eight single-nucleotide polymorphisms (SNPs) as IVs for LTL and found that LTL was significantly associated with the risk of lung cancer in the IVW model (odds ratio (OR): 1.60; 95% confidence interval (CI): 1.31 - 1.97; P = 5.96 × 10-6), which was in line with the results in the weighted median and weighted mode models. However, the relationship was not statistically significant in the MR-Egger regression model (OR: 1.44; 95% CI: 0.92 - 2.26; P = 0.160). Sensitivity analyses indicated the robustness of the results. CONCLUSIONS This two-sample MR study confirmed that longer telomere length significantly increased the risk of lung cancer in the Asian population, which was in accord with findings in the Western population.
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Affiliation(s)
- Yi Teng
- Department of Epidemiology, School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen, China
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- These authors contributed equally to this work
| | - Dan Qi Huang
- Department of Epidemiology, School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen, China
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- These authors contributed equally to this work
| | - Rui Xi Li
- Department of Hepatobiliary and Pancreatic Surgery, The Eighth Affiliated Hospital, Sun Yat-Sen University, China
- These authors contributed equally to this work
| | - Chao Yi
- Guangming Center for Disease Control and Prevention, Shenzhen, China
| | - Yi Qiang Zhan
- Department of Epidemiology, School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen, China
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
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Chang DG, Kim JW, Kim HJ, Kim YH, Kim SI, Ha KY. The neuro-protective role of telomerase via TERT/TERF-2 in the acute phase of spinal cord injury. EUROPEAN SPINE JOURNAL : OFFICIAL PUBLICATION OF THE EUROPEAN SPINE SOCIETY, THE EUROPEAN SPINAL DEFORMITY SOCIETY, AND THE EUROPEAN SECTION OF THE CERVICAL SPINE RESEARCH SOCIETY 2023; 32:2431-2440. [PMID: 37165116 DOI: 10.1007/s00586-023-07561-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/04/2023] [Accepted: 01/22/2023] [Indexed: 05/12/2023]
Abstract
PURPOSE To investigate the interaction of telomerase activity and telomere length on neuro-protection or neuro-degeneration effects after spinal cord injury (SCI). METHODS A contusive SCI model was developed using 56 Sprague-Dawley rats. Seven rats were allocated into acute injury phase groups (1, 3, 8, 24, and 48 h), and sub-acute and chronic injury phase groups (1, 2, and 4 weeks). Telomerase activity was assessed by telomerase reverse transcriptase (TERT) and telomeric repeat binding factor-2 (TERF-2). Differentiation of activated neural stem cells was investigated by co-expression of neuronal/glial cell markers. Apoptosis expression was also investigated by caspase-3, 8, and 9 using terminal deoxynucleotidyl transferase dUTP nick end labelling staining. Immunofluorescence staining and western blotting were performed for quantitative analyses. RESULTS Expression of TERT increased gradually until 24 h post-injury, and was decreased following SCI (P < 0.05). TERF-2 also was increased following SCI until 24 h post-injury and then decreased with time (P < 0.05). Co-localization of TERT and TERF-2 was higher at 24 h post-injury. High expression of TERT was seen in neurons (Neu N Ab), however, expression of TERT was relatively lower in astrocytes and oligodendrocytes. Apoptosis analysis showed persistent high expression of caspases-3, -9, and -8 during the observation period. CONCLUSIONS Increased TERT and TERF-2 activity were noted 24 h post-injury in the acute phase of SCI with TERF-2 maintaining telomeric-repeat length. Our results suggest that increased activity of telomere maintenance may be related to neuro-protective mechanisms against subsequent apoptosis resulting from DNA damage after acute SCI.
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Affiliation(s)
- Dong-Gune Chang
- Department of Orthopaedic Surgery, Inje University Sanggye Paik Hospital, College of Medicine, Inje University, Seoul, Korea
| | - Jang-Woon Kim
- Department of Orthopaedic Surgery, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hong Jin Kim
- Department of Orthopaedic Surgery, Inje University Sanggye Paik Hospital, College of Medicine, Inje University, Seoul, Korea
| | - Young-Hoon Kim
- Department of Orthopaedic Surgery, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sang-Il Kim
- Department of Orthopaedic Surgery, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kee-Yong Ha
- Department of Orthopaedic Surgery, College of Medicine, Kyung Hee University at Gangdong, Dongnam-ro, Gangdong-Gu, 892, Seoul, Republic of Korea.
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Zhao N, Yin G, Liu C, Zhang W, Shen Y, Wang D, Lin Z, Yang J, Mao J, Guo R, Zhang Y, Wang F, Liu Z, Lu X, Liu L. Critically short telomeres derepress retrotransposons to promote genome instability in embryonic stem cells. Cell Discov 2023; 9:45. [PMID: 37130870 PMCID: PMC10154409 DOI: 10.1038/s41421-023-00538-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/08/2023] [Indexed: 05/04/2023] Open
Abstract
Telomeres, at the ends of chromosomes, protect chromosomes from fusion and preserve genomic stability. However, the molecular mechanisms underlying telomere attrition-induced genome instability remain to be understood. We systematically analyzed the expression of retrotransposons and performed genomic sequencing of different cell and tissue types with telomeres of varying lengths due to telomerase deficiency. We found that critically short telomeres altered retrotransposon activity to promote genomic instability in mouse embryonic stem cells, as evidenced by elevated numbers of single nucleotide variants, indels and copy number variations (CNVs). Transpositions of retrotransposons such as LINE1 resulting from the short telomeres can also be found in these genomes with elevated number of mutations and CNVs. Retrotransposon activation is linked to increased chromatin accessibility, and reduced heterochromatin abundance correlates with short telomeres. Re-elongation of telomeres upon recovery of telomerase partly represses retrotransposons and heterochromatin accumulation. Together, our findings suggest a potential mechanism by which telomeres maintain genomic stability by suppressing chromatin accessibility and retrotransposon activity.
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Affiliation(s)
- Nannan Zhao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Guoxing Yin
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Chun Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Weiyu Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- College of Pharmacy, Nankai University, Tianjin, China
| | - Yang Shen
- Genome Institute of Singapore, Singapore, Singapore
| | - Dan Wang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Immunology, Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhenzhen Lin
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Immunology, Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jiao Yang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Jian Mao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Renpeng Guo
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Yongwang Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- College of Pharmacy, Nankai University, Tianjin, China
| | - Feng Wang
- Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhe Liu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Immunology, Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China.
- College of Pharmacy, Nankai University, Tianjin, China.
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China.
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China.
- Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.
- Institute of Translational Medicine, Tianjin Union Medical Center, Nankai University, Tianjin, China.
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Chromatin modifiers: A new class of pollutants with potential epigenetic effects revealed by in vitro assays and transcriptomic analyses. Toxicology 2023; 484:153413. [PMID: 36581016 DOI: 10.1016/j.tox.2022.153413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/14/2022] [Accepted: 12/24/2022] [Indexed: 12/27/2022]
Abstract
A great variety of endocrine-disrupting chemicals (EDCs) have been used extensively and become widespread in the environment nowadays. Limited mammalian studies have shown that certain EDCs may target chromosome and epigenome of the germline, leading to adverse effects in subsequent generations, despite these progenies having never been exposed to the EDC before. However, the underlying mechanisms of chromosomal changes induced by these pollutants remain poorly known. Using the human ovarian granulosa tumor cell line COV434 as a model, we investigated and compared the transcriptomic changes induced by nine EDCs with diverse chemical structures (i.e. BDE-47, BPA, BP-3, DEHP, DHP, EE2, TCS, TDCPP and NP), to inquire if there is any common epigenetic modification associated with reproductive functions induced by these EDCs. Our results showed that COV434 cells were more responsive to BP-3, NP, DEHP and EE2, and more importantly, these four EDCs altered the expression of gene clusters related to DNA damage response, cell cycle, proliferation, and chromatin remodeling, which can potentially lead to epigenetic modifications and transgenerational inheritance. Furthermore, dysregulation of similar gene clusters was common in DEHP and NP treatments. Bioinformatics analysis further revealed that BP-3 disturbed signaling pathways associated with reproductive functions, whereas alterations in telomere-related pathways were highlighted upon EE2 exposure. Overall, this study highlighted chromatin modifications caused by a class of chemicals which that may potentially lead to epigenetic changes and transgenerational reproductive impairments.
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Vinayagamurthy S, Bagri S, Mergny JL, Chowdhury S. Telomeres expand sphere of influence: emerging molecular impact of telomeres in non-telomeric functions. Trends Genet 2023; 39:59-73. [PMID: 36404192 PMCID: PMC7614491 DOI: 10.1016/j.tig.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 09/12/2022] [Accepted: 10/26/2022] [Indexed: 11/18/2022]
Abstract
Although the impact of telomeres on physiology stands well established, a question remains: how do telomeres impact cellular functions at a molecular level? This is because current understanding limits the influence of telomeres to adjacent subtelomeric regions despite the wide-ranging impact of telomeres. Emerging work in two distinct aspects offers opportunities to bridge this gap. First, telomere-binding factors were found with non-telomeric functions. Second, locally induced DNA secondary structures called G-quadruplexes are notably abundant in telomeres, and gene regulatory regions genome wide. Many telomeric factors bind to G-quadruplexes for non-telomeric functions. Here we discuss a more general model of how telomeres impact the non-telomeric genome - through factors that associate at telomeres and genome wide - and influence cell-intrinsic functions, particularly aging, cancer, and pluripotency.
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Affiliation(s)
- Soujanya Vinayagamurthy
- Integrative and Functional Biology Unit, CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sulochana Bagri
- Integrative and Functional Biology Unit, CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Jean-Louis Mergny
- Institute of Biophysics of the CAS, v.v.i. Královopolská 135, 612 65 Brno, Czech Republic; Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Shantanu Chowdhury
- Integrative and Functional Biology Unit, CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; GNR Knowledge Centre for Genome and Informatics, CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India.
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11
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Zhuang Z, Pan X, Zhang M, Liu Y, Huang C, Li Y, Hao L, Wang S. Set2 family regulates mycotoxin metabolism and virulence via H3K36 methylation in pathogenic fungus Aspergillus flavus. Virulence 2022; 13:1358-1378. [PMID: 35943142 PMCID: PMC9364737 DOI: 10.1080/21505594.2022.2101218] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Aspergillus flavus infects various crops with aflatoxins, and leads to aspergillosis opportunistically. Though H3K36 methylation plays an important role in fungal toxin metabolism and virulence, no data about the biological function of H3K36 methylation in A. flavus virulence has been reported. Our study showed that the Set2 histone methyltransferase family, AshA and SetB, involves in morphogenesis and mycotoxin anabolism by regulating related transcriptional factors, and they are important for fungal virulence to crops and animals. Western-blotting and double deletion analysis revealed that AshA mainly regulates H3K36me2, whereas SetB is mainly responsible for H3K36me3 in the nucleus. By construction of domain deletion A. flavus strain and point mutation strains by homologous recombination, the study revealed that SET domain is indispensable in mycotoxin anabolism and virulence of A. flavus, and N455 and V457 in it are the key amino acid residues. ChIP analysis inferred that the methyltransferase family controls fungal reproduction and regulates the production of AFB1 by directly regulating the production of the transcriptional factor genes, including wetA, steA, aflR and amylase, through H3K36 trimethylation in their chromatin fragments, based on which this study proposed that, by H3K36 trimethylation, this methyltransferase family controls AFB1 anabolism through transcriptional level and substrate utilization level. This study illuminates the epigenetic mechanism of the Set2 family in regulating fungal virulence and mycotoxin production, and provides new targets for controlling the virulence of the fungus A. flavus.
AUTHOR SUMMARY
The methylation of H3K36 plays an important role in the fungal secondary metabolism and virulence, but no data about the regulatory mechanism of H3K36 methylation in the virulence of A. flavus have been reported. Our study revealed that, in the histone methyltransferase Set2 family, AshA mainly catalyzes H3K36me2, and involves in the methylation of H3K36me1, and SetB mainly catalyzes H3K36me3 and H3K36me1. Through domain deletion and point mutation analysis, this study also revealed that the SET domain was critical for the normal biological function of the Set2 family and that N455 and V457 in the domain were critical for AshA. By ChIP-seq and ChIP-qPCR analysis, H3K36 was found to be trimethylation modified in the promotors and ORF positions of wetA, steA, aflR and the amylase gene (AFLA_084340), and further qRT-PCR results showed that these methylation modifications regulate the expression levels of these genes. According to the results of ChIP-seq analysis, we proposed that, by H3K36 trimethylation, this methyltransferase family controls the metabolism of mycotoxin through transcriptional level and substrate utilization level. All the results from this study showed that Set2 family is essential for fungal secondary metabolism and virulence, which lays a theoretical groundwork in the early prevention and treatment of A. flavus pollution, and also provides an effective strategy to fight against other pathogenic fungi.
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Affiliation(s)
- Zhenhong Zhuang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaohua Pan
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Key Laboratory of Propagated Sensation along Meridian, Fujian Academy of Chinese Medical Sciences, Fuzhou, China
| | - Mengjuan Zhang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yaju Liu
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chuanzhong Huang
- Immuno-Oncology Laboratory of Fujian Cancer Hospital, Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fujian Medical University Cancer Hospital, Fuzhou, China
| | - Yu Li
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ling Hao
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shihua Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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12
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Guo Z, Zou K, Li X, Duan X, Fan Y, Liu X, Wang W. Relationship between miRNAs polymorphisms and peripheral blood leukocyte DNA telomere length in coke oven workers: A cross-sectional study. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2022; 95:103941. [PMID: 35931358 DOI: 10.1016/j.etap.2022.103941] [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: 03/03/2022] [Revised: 07/23/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVE The purpose of this study was to investigate the factors affecting telomere length (TL) in coke oven workers by analyzing the interaction between miRNAs polymorphisms and coke oven emissions (COEs) exposure. METHODS A total of 544 coke oven workers and 238 healthy controls were recruited. Peripheral blood was collected from the subjects, genomic DNA was extracted, leukocyte TL was detected by real-time quantitative polymerase chain reaction, and fifteen polymorphisms of eight miRNAs were genotyped by flight mass spectrometry. RESULTS Statistical analysis showed that the peripheral blood DNA TL in the exposure group was shorter than that in the control group (P < 0.001). Generalized linear model found that COEs-exposure [β (95%CI) = -0.427 (-0.556, -0.299), P < 0.001], genotype CC+CT for miR-612 rs1144925 [β (95%CI) = -0.367 (-0.630, -0.104), P = 0.006], and the interaction of miR-181B1 rs12039395 TT genotype and COEs-exposure [β (95% CI) = 0.564 (0.108, 1.020), P = 0.015] were associated with the shortened TL. CONCLUSION COEs-exposure and miR-612 rs1144925 TT could promote telomere shortening in coke oven workers. The interaction of miR-181B1 rs12039395 TT genotype and COEs-exposure could protect telomere. This provides clues for further mechanistic studies between miRNA and telomere damage.
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Affiliation(s)
- Zhifeng Guo
- Department of Occupational Health and Occupational Diseases, College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan, China; The Key Laboratory of Nanomedicine and Health Inspection of Zhengzhou, Zhengzhou 450001, Henan, China
| | - Kaili Zou
- Department of Occupational Health and Occupational Diseases, College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan, China; The Key Laboratory of Nanomedicine and Health Inspection of Zhengzhou, Zhengzhou 450001, Henan, China
| | - Xinling Li
- Department of Occupational Health and Occupational Diseases, College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan, China; The Key Laboratory of Nanomedicine and Health Inspection of Zhengzhou, Zhengzhou 450001, Henan, China
| | - Xiaoran Duan
- Department of Occupational Health and Occupational Diseases, College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan, China; Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Yahui Fan
- Department of Occupational Health and Occupational Diseases, College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan, China; The Key Laboratory of Nanomedicine and Health Inspection of Zhengzhou, Zhengzhou 450001, Henan, China
| | - Xiaohua Liu
- Department of Occupational Health and Occupational Diseases, College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan, China; The Key Laboratory of Nanomedicine and Health Inspection of Zhengzhou, Zhengzhou 450001, Henan, China
| | - Wei Wang
- Department of Occupational Health and Occupational Diseases, College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan, China; The Key Laboratory of Nanomedicine and Health Inspection of Zhengzhou, Zhengzhou 450001, Henan, China.
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13
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Emerging mechanisms of telomerase reactivation in cancer. Trends Cancer 2022; 8:632-641. [PMID: 35568649 PMCID: PMC7614490 DOI: 10.1016/j.trecan.2022.03.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 12/17/2022]
Abstract
Mutations in the promoter of human telomerase reverse transcriptase (hTERT) result in hyperactivation of hTERT. Notably, all mutations are G>A transitions, frequently found in a wide range of cancer types, and causally associated with cancer progression. Initially, the mutations were understood to reactivate hTERT by generating novel E26 transformation-specific (ETS) binding sites. Recent work reveals the role of DNA secondary structure G-quadruplexes, telomere binding factor(s), and chromatin looping in hTERT regulation. Here, we discuss these emerging findings in relation to the clinically significant promoter mutations to provide a broader understanding of the context-dependent outcomes that result in hTERT activation in normal and pathogenic conditions.
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14
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Lee KH, Kim DY, Kim W. Regulation of Gene Expression by Telomere Position Effect. Int J Mol Sci 2021; 22:ijms222312807. [PMID: 34884608 PMCID: PMC8657463 DOI: 10.3390/ijms222312807] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022] Open
Abstract
Many diseases that involve malignant tumors in the elderly affect the quality of human life; therefore, the relationship between aging and pathogenesis in geriatric diseases must be under-stood to develop appropriate treatments for these diseases. Recent reports have shown that epigenetic regulation caused by changes in the local chromatin structure plays an essential role in aging. This review provides an overview of the roles of telomere shortening on genomic structural changes during an age-dependent shift in gene expression. Telomere shortening is one of the most prominent events that is involved in cellular aging and it affects global gene expression through genome rearrangement. This review provides novel insights into the roles of telomere shortening in disease-affected cells during pathogenesis and suggests novel therapeutic approaches.
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Affiliation(s)
- Kyung-Ha Lee
- Division of Cosmetic Science and Technology, Daegu Haany University, Gyeongsan 38610, Korea;
| | - Do-Yeon Kim
- Department of Pharmacology, School of Dentistry, Kyungpook National University, Daegu 41940, Korea
- Correspondence: (D.-Y.K.); (W.K.)
| | - Wanil Kim
- Department of Biochemistry, Department of Convergence Medical Science, Institute of Health Sciences, School of Medicine, Gyeongsang National University, Jinju 52727, Korea
- Correspondence: (D.-Y.K.); (W.K.)
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15
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Mojiri A, Walther BK, Jiang C, Matrone G, Holgate R, Xu Q, Morales E, Wang G, Gu J, Wang R, Cooke JP. Telomerase therapy reverses vascular senescence and extends lifespan in progeria mice. Eur Heart J 2021; 42:4352-4369. [PMID: 34389865 PMCID: PMC8603239 DOI: 10.1093/eurheartj/ehab547] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 03/29/2021] [Accepted: 08/12/2021] [Indexed: 12/28/2022] Open
Abstract
AIMS Hutchinson-Gilford progeria syndrome (HGPS) is an accelerated ageing syndrome associated with premature vascular disease and death due to heart attack and stroke. In HGPS a mutation in lamin A (progerin) alters nuclear morphology and gene expression. Current therapy increases the lifespan of these children only modestly. Thus, greater understanding of the underlying mechanisms of HGPS is required to improve therapy. Endothelial cells (ECs) differentiated from induced pluripotent stem cells (iPSCs) derived from these patients exhibit hallmarks of senescence including replication arrest, increased expression of inflammatory markers, DNA damage, and telomere erosion. We hypothesized that correction of shortened telomeres may reverse these measures of vascular ageing. METHODS AND RESULTS We generated ECs from iPSCs belonging to children with HGPS and their unaffected parents. Telomerase mRNA (hTERT) was used to treat HGPS ECs. Endothelial morphology and functions were assessed, as well as proteomic and transcriptional profiles with attention to inflammatory markers, DNA damage, and EC identity genes. In a mouse model of HGPS, we assessed the effects of lentiviral transfection of mTERT on measures of senescence, focusing on the EC phenotype in various organs. hTERT treatment of human HGPS ECs improved replicative capacity; restored endothelial functions such as nitric oxide generation, acetylated low-density lipoprotein uptake and angiogenesis; and reduced the elaboration of inflammatory cytokines. In addition, hTERT treatment improved cellular and nuclear morphology, in association with a normalization of the transcriptional profile, effects that may be mediated in part by a reduction in progerin expression and an increase in sirtuin 1 (SIRT1). Progeria mice treated with mTERT lentivirus manifested similar improvements, with a reduction in inflammatory and DNA damage markers and increased SIRT1 in their vasculature and other organs. Furthermore, mTERT therapy increased the lifespan of HGPS mice. CONCLUSION Vascular rejuvenation using telomerase mRNA is a promising approach for progeria and other age-related diseases.
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Affiliation(s)
- Anahita Mojiri
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Ave., R10-South, Houston, TX 77030, USA
| | - Brandon K Walther
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Ave., R10-South, Houston, TX 77030, USA
- Department of Biomedical Engineering, Texas A&M University, 101 Bizzell St., College Station, TX 77840, USA
| | - Chongming Jiang
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gianfranco Matrone
- British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute, The University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Rhonda Holgate
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Ave., R10-South, Houston, TX 77030, USA
| | - Qiu Xu
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Ave., R10-South, Houston, TX 77030, USA
| | - Elisa Morales
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Ave., R10-South, Houston, TX 77030, USA
| | - Guangyu Wang
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Ave., R10-South, Houston, TX 77030, USA
- Center for Bioinformatics and Computational Biology, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Jianhua Gu
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Ave., R10-South, Houston, TX 77030, USA
| | - Rongfu Wang
- Department of Medicine, and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - John P Cooke
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Ave., R10-South, Houston, TX 77030, USA
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16
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Forsyth RG, Krenács T, Athanasou N, Hogendoorn PCW. Cell Biology of Giant Cell Tumour of Bone: Crosstalk between m/wt Nucleosome H3.3, Telomeres and Osteoclastogenesis. Cancers (Basel) 2021; 13:5119. [PMID: 34680268 PMCID: PMC8534144 DOI: 10.3390/cancers13205119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022] Open
Abstract
Giant cell tumour of bone (GCTB) is a rare and intriguing primary bone neoplasm. Worrisome clinical features are its local destructive behaviour, its high tendency to recur after surgical therapy and its ability to create so-called benign lung metastases (lung 'plugs'). GCTB displays a complex and difficult-to-understand cell biological behaviour because of its heterogenous morphology. Recently, a driver mutation in histone H3.3 was found. This mutation is highly conserved in GCTB but can also be detected in glioblastoma. Denosumab was recently introduced as an extra option of medical treatment next to traditional surgical and in rare cases, radiotherapy. Despite these new insights, many 'old' questions about the key features of GCTB remain unanswered, such as the presence of telomeric associations (TAs), the reactivation of hTERT, and its slight genomic instability. This review summarises the recent relevant literature of histone H3.3 in relation to the GCTB-specific G34W mutation and pays specific attention to the G34W mutation in relation to the development of TAs, genomic instability, and the characteristic morphology of GCTB. As pieces of an etiogenetic puzzle, this review tries fitting all these molecular features and the unique H3.3 G34W mutation together in GCTB.
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Affiliation(s)
- Ramses G. Forsyth
- Department of Pathology, University Hospital Brussels (UZB), Laarbeeklaan 101, 1090 Brussels, Belgium;
- Labaratorium for Experimental Pathology (EXPA), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Tibor Krenács
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllöi ut 26, 1085 Budapest, Hungary;
| | - Nicholas Athanasou
- Department of Histopathology, Nuffield Orthopaedic Centre, University of Oxford, NDORMS, Oxford OX3 7HE, UK;
| | - Pancras C. W. Hogendoorn
- Department of Pathology, University Hospital Brussels (UZB), Laarbeeklaan 101, 1090 Brussels, Belgium;
- Labaratorium for Experimental Pathology (EXPA), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllöi ut 26, 1085 Budapest, Hungary;
- Department of Histopathology, Nuffield Orthopaedic Centre, University of Oxford, NDORMS, Oxford OX3 7HE, UK;
- Department of Pathology, Leiden University Medical Center (LUMC), Albinusdreef 2, 2300 RC Leiden, The Netherlands
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17
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Leung CT, Yang Y, Yu KN, Tam N, Chan TF, Lin X, Kong RYC, Chiu JMY, Wong AST, Lui WY, Yuen KWY, Lai KP, Wu RSS. Low-Dose Radiation Can Cause Epigenetic Alterations Associated With Impairments in Both Male and Female Reproductive Cells. Front Genet 2021; 12:710143. [PMID: 34408775 PMCID: PMC8365519 DOI: 10.3389/fgene.2021.710143] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/07/2021] [Indexed: 12/13/2022] Open
Abstract
Humans are regularly and continuously exposed to ionizing radiation from both natural and artificial sources. Cumulating evidence shows adverse effects of ionizing radiation on both male and female reproductive systems, including reduction of testis weight and sperm count and reduction of female germ cells and premature ovarian failure. While most of the observed effects were caused by DNA damage and disturbance of DNA repairment, ionizing radiation may also alter DNA methylation, histone, and chromatin modification, leading to epigenetic changes and transgenerational effects. However, the molecular mechanisms underlying the epigenetic changes and transgenerational reproductive impairment induced by low-dose radiation remain largely unknown. In this study, two different types of human ovarian cells and two different types of testicular cells were exposed to low dose of ionizing radiation, followed by bioinformatics analysis (including gene ontology functional analysis and Ingenuity Pathway Analysis), to unravel and compare epigenetic effects and pathway changes in male and female reproductive cells induced by ionizing radiation. Our findings showed that the radiation could alter the expression of gene cluster related to DNA damage responses through the control of MYC. Furthermore, ionizing radiation could lead to gender-specific reproductive impairment through deregulation of different gene networks. More importantly, the observed epigenetic modifications induced by ionizing radiation are mediated through the alteration of chromatin remodeling and telomere function. This study, for the first time, demonstrated that ionizing radiation may alter the epigenome of germ cells, leading to transgenerational reproductive impairments, and correspondingly call for research in this new emerging area which remains almost unknown.
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Affiliation(s)
- Chi Tim Leung
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, Hong Kong, China.,Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Yi Yang
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, Hong Kong, China.,School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Kwan Ngok Yu
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong.,Department of Physics, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Nathan Tam
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Ting Fung Chan
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Xiao Lin
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Richard Yuen Chong Kong
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, Hong Kong, China.,Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong.,State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Jill Man Ying Chiu
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, Hong Kong, China.,Department of Biology, Hong Kong Baptist University, Kowloon Tsai, Hong Kong
| | - Alice Sze Tsai Wong
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, Hong Kong, China.,School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Wing Yee Lui
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Karen Wing Yee Yuen
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Keng Po Lai
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, Hong Kong, China.,Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong.,State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong.,Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Guilin, China
| | - Rudolf Shiu Sun Wu
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, Hong Kong, China.,State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong.,Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong
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18
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Wang Z, Wu X. Abnormal function of telomere protein TRF2 induces cell mutation and the effects of environmental tumor‑promoting factors (Review). Oncol Rep 2021; 46:184. [PMID: 34278498 PMCID: PMC8273685 DOI: 10.3892/or.2021.8135] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/14/2021] [Indexed: 01/30/2023] Open
Abstract
Recent studies have found that somatic gene mutations and environmental tumor-promoting factors are both indispensable for tumor formation. Telomeric repeat-binding factor (TRF)2 is the core component of the telomere shelterin complex, which plays an important role in chromosome stability and the maintenance of normal cell physiological states. In recent years, TRF2 and its role in tumor formation have gradually become a research hot topic, which has promoted in-depth discussions into tumorigenesis and treatment strategies, and has achieved promising results. Some cells bypass elimination, due to either aging, apoptosis via mutations or abnormal prolongation of the mitotic cycle, and enter the telomere crisis period, where large-scale DNA reorganization occurs repeatedly, which manifests as the precancerous cell cycle. Finally, at the end of the crisis cycle, the mutation activates either the expression level of telomerase or activates the alternative lengthening of telomere mechanism to extend the local telomeres. Under the protection of TRF2, chromosomes are gradually stabilized, immortal cells are formed and the stagewise mutation-driven transformation of normal cells to cancer cells is completed. In addition, TRF2 also shares the characteristics of environmental tumor-promoting factors. It acts on multiple signal transduction pathway-related proteins associated with cell proliferation, and affects peripheral angiogenesis, inhibits the immune recognition and killing ability of the microenvironment, and maintains the stemness characteristics of tumor cells. TRF2 levels are abnormally elevated by a variety of tumor control proteins, which are more conducive to the protection of telomeres and the survival of tumor cells. In brief, the various regulatory mechanisms which tumor cells rely on to survive are organically integrated around TRF2, forming a regulatory network, which is conducive to the optimization of the survival direction of heterogeneous tumor cells, and promotes their survival and adaptability. In terms of clinical application, TRF2 is expected to become a new type of cancer prognostic marker and a new tumor treatment target. Inhibition of TRF2 overexpression could effectively cut off the core network regulating tumor cell survival, reduce drug resistance, or bypass the mutation under the pressure of tumor treatment selection, which may represent a promising therapeutic strategy for the complete eradication of tumors in the clinical setting. Based on recent research, the aim of the present review was to systematically elaborate on the basic structure and functional characteristics of TRF2 and its role in tumor formation, and to analyze the findings indicating that TRF2 deficiency or overexpression could cause severe damage to telomere function and telomere shortening, and induce DNA damage response and chromosomal instability.
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Affiliation(s)
- Zhengyi Wang
- Good Clinical Practice Center, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan 610071, P.R. China
| | - Xiaoying Wu
- Ministry of Education and Training, Chengdu Second People's Hospital, Chengdu, Sichuan 610000, P.R. China
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19
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Krapivin MI, Tikhonov AV, Efimova OA, Pendina AA, Smirnova AA, Chiryaeva OG, Talantova OE, Petrova LI, Dudkina VS, Baranov VS. Telomere Length in Chromosomally Normal and Abnormal Miscarriages and Ongoing Pregnancies and Its Association with 5-hydroxymethylcytosine Patterns. Int J Mol Sci 2021; 22:ijms22126622. [PMID: 34205622 PMCID: PMC8234291 DOI: 10.3390/ijms22126622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/06/2021] [Accepted: 06/18/2021] [Indexed: 12/15/2022] Open
Abstract
The present study investigates telomere length (TL) in dividing chorionic cytotrophoblast cells from karyotypically normal and abnormal first trimester miscarriages and ongoing pregnancies. Using Q-FISH, we measured relative TLs in the metaphase chromosomes of 61 chorionic villous samples. Relative TLs did not differ between karyotypically normal samples from miscarriages and those from ongoing pregnancies (p = 0.3739). However, among the karyotypically abnormal samples, relative TLs were significantly higher in ongoing pregnancies than in miscarriages (p < 0.0001). Relative TLs were also significantly higher in chorion samples from karyotypically abnormal ongoing pregnancies than in those from karyotypically normal ones (p = 0.0018) in contrast to miscarriages, where relative TL values were higher in the karyotypically normal samples (p = 0.002). In the karyotypically abnormal chorionic cytotrophoblast, the TL variance was significantly lower than in any other group (p < 0.05). Assessed by TL ratios between sister chromatids, interchromatid TL asymmetry demonstrated similar patterns across all of the chorion samples (p = 0.22) but significantly exceeded that in PHA-stimulated lymphocytes (p < 0.0001, p = 0.0003). The longer telomere was predominantly present in the hydroxymethylated sister chromatid in chromosomes featuring hemihydroxymethylation (containing 5-hydroxymethylcytosine in only one sister chromatid)-a typical sign of chorionic cytotrophoblast cells. Our results suggest that the phenomena of interchromatid TL asymmetry and its association to 5hmC patterns in chorionic cytotrophoblast, which are potentially linked to telomere lengthening through recombination, are inherent to the development programme. The TL differences in chorionic cytotrophoblast that are associated with karyotype and embryo viability seem to be determined by heredity rather than telomere elongation mechanisms. The inheritance of long telomeres by a karyotypically abnormal embryo promotes his development, whereas TL in karyotypically normal first-trimester embryos does not seem to have a considerable impact on developmental capacity.
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Affiliation(s)
- Mikhail I. Krapivin
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.I.K.); (A.V.T.); (A.A.P.); (O.G.C.); (O.E.T.); (L.I.P.); (V.S.D.); (V.S.B.)
| | - Andrei V. Tikhonov
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.I.K.); (A.V.T.); (A.A.P.); (O.G.C.); (O.E.T.); (L.I.P.); (V.S.D.); (V.S.B.)
| | - Olga A. Efimova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.I.K.); (A.V.T.); (A.A.P.); (O.G.C.); (O.E.T.); (L.I.P.); (V.S.D.); (V.S.B.)
- Correspondence:
| | - Anna A. Pendina
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.I.K.); (A.V.T.); (A.A.P.); (O.G.C.); (O.E.T.); (L.I.P.); (V.S.D.); (V.S.B.)
| | - Anna A. Smirnova
- Department of Medical Biophysics, Saint Petersburg State Pediatric Medical University, Litovskaya Street 2, 194100 Saint Petersburg, Russia;
| | - Olga G. Chiryaeva
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.I.K.); (A.V.T.); (A.A.P.); (O.G.C.); (O.E.T.); (L.I.P.); (V.S.D.); (V.S.B.)
| | - Olga E. Talantova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.I.K.); (A.V.T.); (A.A.P.); (O.G.C.); (O.E.T.); (L.I.P.); (V.S.D.); (V.S.B.)
| | - Lubov’ I. Petrova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.I.K.); (A.V.T.); (A.A.P.); (O.G.C.); (O.E.T.); (L.I.P.); (V.S.D.); (V.S.B.)
| | - Vera S. Dudkina
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.I.K.); (A.V.T.); (A.A.P.); (O.G.C.); (O.E.T.); (L.I.P.); (V.S.D.); (V.S.B.)
| | - Vladislav S. Baranov
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.I.K.); (A.V.T.); (A.A.P.); (O.G.C.); (O.E.T.); (L.I.P.); (V.S.D.); (V.S.B.)
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Dong X, Sun S, Zhang L, Kim S, Tu Z, Montagna C, Maslov AY, Suh Y, Wang T, Campisi J, Vijg J. Age-related telomere attrition causes aberrant gene expression in sub-telomeric regions. Aging Cell 2021; 20:e13357. [PMID: 34018656 PMCID: PMC8208793 DOI: 10.1111/acel.13357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 03/01/2021] [Accepted: 03/07/2021] [Indexed: 12/13/2022] Open
Abstract
Telomere attrition has been proposed as a biomarker and causal factor in aging. In addition to causing cellular senescence and apoptosis, telomere shortening has been found to affect gene expression in subtelomeric regions. Here, we analyzed the distribution of age-related differentially expressed genes from the GTEx RNA sequencing database of 54 tissue types from 979 human subjects and found significantly more upregulated than downregulated genes in subtelomeric regions as compared to the genome-wide average. Our data demonstrate spatial relationships between telomeres and gene expression in aging.
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Affiliation(s)
- Xiao Dong
- Department of GeneticsAlbert Einstein College of MedicineBronxNYUSA
- Institute on the Biology of Aging and MetabolismDepartment of Genetics, Cell Biology and DevelopmentUniversity of MinnesotaMinneapolisMNUSA
| | - Shixiang Sun
- Department of GeneticsAlbert Einstein College of MedicineBronxNYUSA
| | - Lei Zhang
- Department of GeneticsAlbert Einstein College of MedicineBronxNYUSA
- Institute on the Biology of Aging and MetabolismDepartment of Genetics, Cell Biology and DevelopmentUniversity of MinnesotaMinneapolisMNUSA
| | - Seungsoo Kim
- Department of Obstetrics and GynecologyColumbia University Irving Medical CenterNew YorkNYUSA
| | - Zhidong Tu
- Department of Genetics and Genomic SciencesIcahn Institute for Genomics and Multiscale BiologyIcahn School of Medicine Mount SinaiNew YorkNYUSA
| | | | - Alexander Y. Maslov
- Department of GeneticsAlbert Einstein College of MedicineBronxNYUSA
- Laboratory of Applied Genomic TechnologiesVoronezh State University of Engineering TechnologyVoronezhRussia
| | - Yousin Suh
- Department of Obstetrics and GynecologyColumbia University Irving Medical CenterNew YorkNYUSA
- Department of Genetics and DevelopmentColumbia University Irving Medical CenterNew YorkNYUSA
| | - Tao Wang
- Department of Epidemiology & Population HealthAlbert Einstein College of MedicineBronxNYUSA
| | | | - Jan Vijg
- Department of GeneticsAlbert Einstein College of MedicineBronxNYUSA
- School of Public HealthCenter for Single‐Cell OmicsShanghai Jiao Tong University School of MedicineShanghaiChina
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21
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Sharma S, Mukherjee AK, Roy SS, Bagri S, Lier S, Verma M, Sengupta A, Kumar M, Nesse G, Pandey DP, Chowdhury S. Human telomerase is directly regulated by non-telomeric TRF2-G-quadruplex interaction. Cell Rep 2021; 35:109154. [PMID: 34010660 PMCID: PMC7611063 DOI: 10.1016/j.celrep.2021.109154] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/15/2021] [Accepted: 04/28/2021] [Indexed: 12/16/2022] Open
Abstract
Human telomerase reverse transcriptase (hTERT) remains suppressed in most normal somatic cells. Resulting erosion of telomeres leads eventually to replicative senescence. Reactivation of hTERT maintains telomeres and triggers progression of >90% of cancers. However, any direct causal link between telomeres and telomerase regulation remains unclear. Here, we show that the telomere-repeat-binding-factor 2 (TRF2) binds hTERT promoter G-quadruplexes and recruits the polycomb-repressor EZH2/PRC2 complex. This is causal for H3K27 trimethylation at the hTERT promoter and represses hTERT in cancer as well as normal cells. Two highly recurrent hTERT promoter mutations found in many cancers, including ∼83% glioblastoma multiforme, that are known to destabilize hTERT promoter G-quadruplexes, showed loss of TRF2 binding in patient-derived primary glioblastoma multiforme cells. Ligand-induced G-quadruplex stabilization restored TRF2 binding, H3K27-trimethylation, and hTERT re-suppression. These results uncover a mechanism of hTERT regulation through a telomeric factor, implicating telomere-telomerase molecular links important in neoplastic transformation, aging, and regenerative therapy.
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Affiliation(s)
- Shalu Sharma
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Ananda Kishore Mukherjee
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Shuvra Shekhar Roy
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Sulochana Bagri
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Silje Lier
- Department of Microbiology, Oslo University Hospital, Oslo, Norway; Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Meenakshi Verma
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Antara Sengupta
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Manish Kumar
- Imaging Facility, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Gaute Nesse
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | | | - Shantanu Chowdhury
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; GNR Knowledge Centre for Genome and Informatics, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India.
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22
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Ogrodnik M. Cellular aging beyond cellular senescence: Markers of senescence prior to cell cycle arrest in vitro and in vivo. Aging Cell 2021; 20:e13338. [PMID: 33711211 PMCID: PMC8045927 DOI: 10.1111/acel.13338] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/09/2021] [Accepted: 02/19/2021] [Indexed: 12/14/2022] Open
Abstract
The field of research on cellular senescence experienced a rapid expansion from being primarily focused on in vitro aspects of aging to the vast territories of animal and clinical research. Cellular senescence is defined by a set of markers, many of which are present and accumulate in a gradual manner prior to senescence induction or are found outside of the context of cellular senescence. These markers are now used to measure the impact of cellular senescence on aging and disease as well as outcomes of anti-senescence interventions, many of which are at the stage of clinical trials. It is thus of primary importance to discuss their specificity as well as their role in the establishment of senescence. Here, the presence and role of senescence markers are described in cells prior to cell cycle arrest, especially in the context of replicative aging and in vivo conditions. Specifically, this review article seeks to describe the process of "cellular aging": the progression of internal changes occurring in primary cells leading to the induction of cellular senescence and culminating in cell death. Phenotypic changes associated with aging prior to senescence induction will be characterized, as well as their effect on the induction of cell senescence and the final fate of cells reviewed. Using published datasets on assessments of senescence markers in vivo, it will be described how disparities between quantifications can be explained by the concept of cellular aging. Finally, throughout the article the applicational value of broadening cellular senescence paradigm will be discussed.
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Affiliation(s)
- Mikolaj Ogrodnik
- Ludwig Boltzmann Research Group Senescence and Healing of Wounds Vienna Austria
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology in AUVA Research Center Vienna Austria
- Austrian Cluster for Tissue Regeneration Vienna Austria
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Emerging Molecular Connections between NM23 Proteins, Telomeres and Telomere-Associated Factors: Implications in Cancer Metastasis and Ageing. Int J Mol Sci 2021; 22:ijms22073457. [PMID: 33801585 PMCID: PMC8036570 DOI: 10.3390/ijms22073457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 11/20/2022] Open
Abstract
The metastasis suppressor function of NM23 proteins is widely understood. Multiple enzymatic activities of NM23 proteins have also been identified. However, relatively less known interesting aspects are being revealed from recent developments that corroborate the telomeric interactions of NM23 proteins. Telomeres are known to regulate essential physiological events such as metastasis, ageing, and cellular differentiation via inter-connected signalling pathways. Here, we review the literature on the association of NM23 proteins with telomeres or telomere-related factors, and discuss the potential implications of emerging telomeric functions of NM23 proteins. Further understanding of these aspects might be instrumental in better understanding the metastasis suppressor functions of NM23 proteins.
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24
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Arantes Dos Santos G, Viana NI, Pimenta R, Reis ST, Ramos Moreira Leite K, Srougi M. Hypothesis: The triad androgen receptor, zinc finger proteins and telomeres modulates the global gene expression pattern during prostate cancer progression. Med Hypotheses 2021; 150:110566. [PMID: 33799157 DOI: 10.1016/j.mehy.2021.110566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/19/2021] [Accepted: 03/09/2021] [Indexed: 01/11/2023]
Abstract
Currently, the biggest challenge for prostate cancer (PCa) is to understand the mechanism by which the disease acquires the castration-resistant phenotype and progresses to a fatal disease. PCa has a high genetic heterogeneity, and cannot be separated into well-defined molecular subtypes. Despite this, there is consensus about the role of the androgen receptor (AR) in all stages of the disease, including the transition to the castration-resistant phenotype. Since AR is a transcription factor, we investigated the possibility of PCa presenting a pattern of global gene expression during disease progression. By analyzing the TCGA and CCLE datasets, we were able to find a pattern of waves of genes being expressed during each stage of disease progression. This phenomenon suggests the existence of a mechanism that globally regulates gene expression, being AR, telomeres, and zinc finger proteins (ZNF), three important players. The AR modulates the telomere biology, and its transcription is regulated by ZNF. Recently, a study suggested that the telomere length might influence the expression of ZNF. Thus, we hypothesized that changes in the triad AR, telomeres, and ZNF control gene expression during the progression of PCa.
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Affiliation(s)
- Gabriel Arantes Dos Santos
- Urology Department, Laboratory of Medical Investigation (LIM55), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil; D'Or Institute for Research and Education (IDOR), Sao Paulo, SP, Brazil.
| | - Nayara Izabel Viana
- Urology Department, Laboratory of Medical Investigation (LIM55), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Ruan Pimenta
- Urology Department, Laboratory of Medical Investigation (LIM55), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil; D'Or Institute for Research and Education (IDOR), Sao Paulo, SP, Brazil
| | - Sabrina T Reis
- Urology Department, Laboratory of Medical Investigation (LIM55), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil; Athens University Center (UniAtenas), Passos, MG, Brazil; Minas Gerais State University (UEMG), Passos, MG, Brazil
| | - Katia Ramos Moreira Leite
- Urology Department, Laboratory of Medical Investigation (LIM55), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Miguel Srougi
- Urology Department, Laboratory of Medical Investigation (LIM55), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil; D'Or Institute for Research and Education (IDOR), Sao Paulo, SP, Brazil
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25
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Zhang N, Li Y, Lai TP, Shay JW, Danuser G. Imaging assay to probe the role of telomere length shortening on telomere-gene interactions in single cells. Chromosoma 2021; 130:61-73. [PMID: 33555479 PMCID: PMC7889534 DOI: 10.1007/s00412-020-00747-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/23/2020] [Accepted: 11/30/2020] [Indexed: 12/20/2022]
Abstract
Telomeres are repetitive non-coding nucleotide sequences (TTAGGGn) capping the ends of chromosomes. Progressive telomere shortening with increasing age has been associated with shifts in gene expression through models such as the telomere position effect (TPE), which suggests reduced interference of the telomere with transcriptional activity of increasingly more distant genes. A modification of the TPE model, referred to as Telomere Position Effects over Long Distance (TPE-OLD), explains why some genes 1-10 MB from a telomere are still affected by TPE, but genes closer to the telomere are not. Here, we describe an imaging approach to systematically examine the occurrence of TPE-OLD at the single cell level. Compared to existing methods, the pipeline allows rapid analysis of hundreds to thousands of cells, which is necessary to establish TPE-OLD as an acceptable mechanism of gene expression regulation. We examined two human genes, ISG15 and TERT, for which TPE-OLD has been described before. For both genes, we found less interaction with the telomere on the same chromosome in old cells compared to young cells; and experimentally elongated telomeres in old cells rescued the level of telomere interaction for both genes. However, the dependency of the interactions on the age progression from young to old cells varied. One model for the differences between ISG15 and TERT may relate to the markedly distinct interstitial telomeric sequence arrangement in the two genes. Overall, this provides a strong rationale for the role of telomere length shortening in the regulation of gene expression.
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Affiliation(s)
- Ning Zhang
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yanhui Li
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Tsung-Po Lai
- Center of Human Development and Aging, Rutgers New Jersey Medical School, The State University of New Jersey, Newark, NJ, USA
| | - Jerry W Shay
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA.
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA.
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26
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Bhari VK, Kumar D, Kumar S, Mishra R. Shelterin complex gene: Prognosis and therapeutic vulnerability in cancer. Biochem Biophys Rep 2021; 26:100937. [PMID: 33553693 PMCID: PMC7859307 DOI: 10.1016/j.bbrep.2021.100937] [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: 09/03/2020] [Revised: 01/08/2021] [Accepted: 01/25/2021] [Indexed: 02/06/2023] Open
Abstract
Telomere encompasses a (TTAGGG)n tandem repeats, and its dysfunction has emerged as the epicenter of driving carcinogenesis by promoting genetic instability. Indeed, they play an essential role in stabilizing chromosomes and therefore protecting them from end-to-end fusion and DNA degradation. Telomere length homeostasis is regulated by several key players including shelterin complex genes, telomerase, and various other regulators. Targeting these regulatory players can be a good approach to combat cancer as telomere length is increasingly correlated with cancer initiation and progression. In this review, we have aimed to describe the telomere length regulator's role in prognostic significance and important drug targets in breast cancer. Moreover, we also assessed alteration in telomeric function by various telomere length regulators and compares this to the regulatory mechanisms that can be associated with clinical biomarkers in cancer. Using publicly available software we summarized mutational and CpG island prediction analysis of the TERT gene breast cancer patient database. Studies have reported that the TERT gene has prognostic significance in breast cancer progression however mechanistic approaches are not defined yet. Interestingly, we reported using the UCSC Xena web-based tool, we confirmed a positive correlation of shelterin complex genes TERF1 and TERF2 in recurrent free survival, indicating the critical role of these genes in breast cancer prognosis. Moreover, the epigenetic landscape of DNA damage repair genes in different breast cancer subtypes also being analyzed using the UCSC Xena database. Together, these datasets provide a comprehensive resource for shelterin complex gene profiles and define epigenetic landscapes of DNA damage repair genes which reveals the key role of shelterin complex genes in breast cancer with the potential to identify novel and actionable targets for treatment.
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Affiliation(s)
- Vikas Kumar Bhari
- Department of Biosciences, Manipal University Jaipur, Rajasthan, India
| | - Durgesh Kumar
- Department of Physiology, Government Medical College, Kannauj, Uttar Pradesh, India
| | - Surendra Kumar
- Department of Neurology, Rajendra Institute of Medical Sciences, Ranchi, Jharkhand, India
| | - Rajeev Mishra
- Department of Biosciences, Manipal University Jaipur, Rajasthan, India
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Sengupta A, Roy SS, Chowdhury S. Non-duplex G-Quadruplex DNA Structure: A Developing Story from Predicted Sequences to DNA Structure-Dependent Epigenetics and Beyond. Acc Chem Res 2021; 54:46-56. [PMID: 33347280 DOI: 10.1021/acs.accounts.0c00431] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The story of the non-duplex DNA form known as the G-quadruplex (G4) has traversed a winding path. From initial skepticism followed by debate to a surge in interest, the G4 story intertwines many threads. Starting with computational predictions of a gene regulatory role, which now include epigenetic functions, our group was involved in many of these advances along with many other laboratories. Following a brief background, set in the latter half of the last century when the concept of the G4 as a structure took ground, here we account the developments. This is through a lens that though focused on our groups' research presents work from many other groups that played significant roles. Together these provide a broad perspective to the G4 story. Initially we were intrigued on seeing potential G4 (pG4)-forming sequences, then known to be found primarily at the telomeres and immunoglobin switch regions, occurring throughout the genome and being particularly prevalent in promoters of bacteria. We further observed that pG4s were not only prevalent but also conserved through evolution in promoters of human, chimpanzee, mouse and rat genomes. This was between 2005 and 2007. Encouraged by these partly and partly in response to the view held by many that genome-wide presence of G4s were genomic "accidents", the focus shifted to seeking experimental evidence.In the next year, 2008, two independent findings showed promise. First, on treating human cancer cells with G4-binding ligands, we observed widespread change in gene expression. Second, our search for the missing G4-specific transcription factor, without which, importantly, G4s in promoters posed only half the story, yielded results. We determined how NM23-H2 (also known as NME2 or NDPK-B) interacts with G4s and how interaction of NM23-H2 with a G4 in the promoter of the oncogene c-myc was important for regulation of c-myc transcription. NM23-H2, and subsequently many other similar factors discovered by multiple groups, is possibly giving shape to what might be the "G4-transcriptome". Later, a close look at NM23-H2-G4 interaction in regulation of the human reverse transcriptase gene (hTERT) revealed the role of G4s in local epigenetic modifications. Meanwhile work from others showed how G4s impact histone modifications following replication. Together these show the intrinsic role of DNA sequence, through formation of DNA structure, in epigenetics.More recent work, however, was waiting to reveal aspects that tend to bring forth a completely new understanding of G4s. We observed that the telomere-repeat-binding-factor-2 (TRF2), known canonically to be telomere-associated, binds extensively outside telomeres throughout the genome. Moreover, a large fraction of the non-telomeric TRF2 sites comprise G4s. Second, the extent of non-telomeric TRF2 binding at promoters was dependent on telomere length. Thereby TRF2-induced epigenetic gene regulation was telomere-dependent. Together these implicate underlying connections that show signs of addressing an intriguing unanswered question that takes us back to the beginning: Why are G4s prevalent in two distinct regions, the telomeres and gene promoters?
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Affiliation(s)
- Antara Sengupta
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shuvra Shekhar Roy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shantanu Chowdhury
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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28
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More than Meets the ISG15: Emerging Roles in the DNA Damage Response and Beyond. Biomolecules 2020; 10:biom10111557. [PMID: 33203188 PMCID: PMC7698331 DOI: 10.3390/biom10111557] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/13/2022] Open
Abstract
Maintenance of genome stability is a crucial priority for any organism. To meet this priority, robust signalling networks exist to facilitate error-free DNA replication and repair. These signalling cascades are subject to various regulatory post-translational modifications that range from simple additions of chemical moieties to the conjugation of ubiquitin-like proteins (UBLs). Interferon Stimulated Gene 15 (ISG15) is one such UBL. While classically thought of as a component of antiviral immunity, ISG15 has recently emerged as a regulator of genome stability, with key roles in the DNA damage response (DDR) to modulate p53 signalling and error-free DNA replication. Additional proteomic analyses and cancer-focused studies hint at wider-reaching, uncharacterised functions for ISG15 in genome stability. We review these recent discoveries and highlight future perspectives to increase our understanding of this multifaceted UBL in health and disease.
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Mukherjee AK, Sharma S, Sengupta S, Saha D, Kumar P, Hussain T, Srivastava V, Roy SD, Shay JW, Chowdhury S. Correction: Telomere length-dependent transcription and epigenetic modifications in promoters remote from telomere ends. PLoS Genet 2020; 16:e1009152. [PMID: 33091002 PMCID: PMC7580915 DOI: 10.1371/journal.pgen.1009152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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30
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Abstract
Several decades elapsed between the first descriptions of G-quadruplex nucleic acid structures (G4s) assembled in vitro and the emergence of experimental findings indicating that such structures can form and function in living systems. A large body of evidence now supports roles for G4s in many aspects of nucleic acid biology, spanning processes from transcription and chromatin structure, mRNA processing, protein translation, DNA replication and genome stability, and telomere and mitochondrial function. Nonetheless, it must be acknowledged that some of this evidence is tentative, which is not surprising given the technical challenges associated with demonstrating G4s in biology. Here I provide an overview of evidence for G4 biology, focusing particularly on the many potential pitfalls that can be encountered in its investigation, and briefly discuss some of broader biological processes that may be impacted by G4s including cancer.
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Affiliation(s)
- F. Brad Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
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31
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Vinayagamurthy S, Ganguly A, Chowdhury S. Extra-telomeric impact of telomeres: Emerging molecular connections in pluripotency or stemness. J Biol Chem 2020; 295:10245-10254. [PMID: 32444498 DOI: 10.1074/jbc.rev119.009710] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/21/2020] [Indexed: 12/26/2022] Open
Abstract
Telomeres comprise specialized nucleic acid-protein complexes that help protect chromosome ends from DNA damage. Moreover, telomeres associate with subtelomeric regions through looping. This results in altered expression of subtelomeric genes. Recent observations further reveal telomere length-dependent gene regulation and epigenetic modifications at sites spread across the genome and distant from telomeres. This regulation is mediated through the telomere-binding protein telomeric repeat-binding factor 2 (TRF2). These observations suggest a role of telomeres in extra-telomeric functions. Most notably, telomeres have a broad impact on pluripotency and differentiation. For example, cardiomyocytes differentiate with higher efficacy from induced pluripotent stem cells having long telomeres, and differentiated cells obtained from human embryonic stem cells with relatively long telomeres have a longer lifespan. Here, we first highlight reports on these two seemingly distinct research areas: the extra-telomeric role of telomere-binding factors and the role of telomeres in pluripotency/stemness. On the basis of the observations reported in these studies, we draw attention to potential molecular connections between extra-telomeric biology and pluripotency. Finally, in the context of the nonlocal influence of telomeres on pluripotency and stemness, we discuss major opportunities for progress in molecular understanding of aging-related disorders and neurodegenerative diseases.
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Affiliation(s)
- Soujanya Vinayagamurthy
- Integrative and Functional Biology Unit, CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Akansha Ganguly
- Integrative and Functional Biology Unit, CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Shantanu Chowdhury
- Integrative and Functional Biology Unit, CSIR Institute of Genomics and Integrative Biology, New Delhi, India .,Academy of Scientific and Innovative Research (AcSIR), CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,G.N.R. Knowledge Centre for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, New Delhi, India
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32
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Yudin NS, Belyavskaya VA, Maksimov VN, Ivanoshchuk DE, Orlov PS, Voevoda MI. Association between leukocyte telomere length and specific antibody levels after vaccination against tick-borne encephalitis. Vavilovskii Zhurnal Genet Selektsii 2020. [DOI: 10.18699/vj19.580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- N. S. Yudin
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University; Research Institute of Internal and Preventive Medicine
| | - V. A. Belyavskaya
- State Research Center of Virology and Biotechnology “Vector” of the Federal Service for Surveillance in Consumer Rights Protection and Human Well-being
| | - V. N. Maksimov
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University; Research Institute of Internal and Preventive Medicine
| | - D. E. Ivanoshchuk
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University; Research Institute of Internal and Preventive Medicine
| | - P. S. Orlov
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University; Research Institute of Internal and Preventive Medicine
| | - M. I. Voevoda
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University; Research Institute of Internal and Preventive Medicine
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33
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Abstract
Telomere-binding protein TRF2 protects the linear chromosome ends, telomeres, from being recognized as damaged DNA. TRF2 also regulates gene expression outside telomeres, but the detailed mechanism has not been fully understood. Mukherjee and colleagues have employed ChIP-Seq and biochemical analyses to identify G-quadruplexes at gene promoters across the genome as nontelomeric TRF2-binding sites. TRF2 occupancy on such target sites leads to epigenetic gene repression, implicating TRF2-G-quadruplex interaction as a sophisticated regulator of gene expression.
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Affiliation(s)
- Keiji Okamoto
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Hiroyuki Seimiya
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
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34
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Mukherjee AK, Sharma S, Bagri S, Kutum R, Kumar P, Hussain A, Singh P, Saha D, Kar A, Dash D, Chowdhury S. Telomere repeat-binding factor 2 binds extensively to extra-telomeric G-quadruplexes and regulates the epigenetic status of several gene promoters. J Biol Chem 2019; 294:17709-17722. [PMID: 31575660 PMCID: PMC6879327 DOI: 10.1074/jbc.ra119.008687] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 09/18/2019] [Indexed: 12/22/2022] Open
Abstract
The role of the telomere repeat-binding factor 2 (TRF2) in telomere maintenance is well-established. However, recent findings suggest that TRF2 also functions outside telomeres, but relatively little is known about this function. Herein, using genome-wide ChIP-Seq assays of TRF2-bound chromatin from HT1080 fibrosarcoma cells, we identified thousands of TRF2-binding sites within the extra-telomeric genome. In light of this observation, we asked how TRF2 occupancy is organized within the genome. Interestingly, we found that extra-telomeric TRF2 sites throughout the genome are enriched in potential G-quadruplex-forming DNA sequences. Furthermore, we validated TRF2 occupancy at several promoter G-quadruplex motifs, which did adopt quadruplex forms in solution. TRF2 binding altered expression and the epigenetic state of several target promoters, indicated by histone modifications resulting in transcriptional repression of eight of nine genes investigated here. Furthermore, TRF2 occupancy and target gene expression were also sensitive to the well-known intracellular G-quadruplex-binding ligand 360A. Together, these results reveal an extensive genome-wide association of TRF2 outside telomeres and that it regulates gene expression in a G-quadruplex-dependent fashion.
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Affiliation(s)
- Ananda Kishore Mukherjee
- Integrative and Functional Biology Unit, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| | - Shalu Sharma
- Integrative and Functional Biology Unit, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| | - Sulochana Bagri
- Integrative and Functional Biology Unit, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| | - Rintu Kutum
- Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India.,G.N.R. Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India.,CSIR Ayurgenomics Unit-TRISUTRA, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| | - Pankaj Kumar
- Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India.,G.N.R. Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| | - Asgar Hussain
- Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India.,G.N.R. Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| | - Prateek Singh
- Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India.,G.N.R. Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| | - Dhurjhoti Saha
- Integrative and Functional Biology Unit, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| | - Anirban Kar
- Integrative and Functional Biology Unit, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| | - Debasis Dash
- Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India.,G.N.R. Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India.,CSIR Ayurgenomics Unit-TRISUTRA, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| | - Shantanu Chowdhury
- Integrative and Functional Biology Unit, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India .,Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India.,G.N.R. Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
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35
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Histone Modifications and the Maintenance of Telomere Integrity. Cells 2019; 8:cells8020199. [PMID: 30823596 PMCID: PMC6407025 DOI: 10.3390/cells8020199] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 02/09/2019] [Accepted: 02/20/2019] [Indexed: 12/20/2022] Open
Abstract
Telomeres, the nucleoprotein structures at the ends of eukaryotic chromosomes, play an integral role in protecting linear DNA from degradation. Dysregulation of telomeres can result in genomic instability and has been implicated in increased rates of cellular senescence and many diseases, including cancer. The integrity of telomeres is maintained by a coordinated network of proteins and RNAs, such as the telomerase holoenzyme and protective proteins that prevent the recognition of the telomere ends as a DNA double-strand breaks. The structure of chromatin at telomeres and within adjacent subtelomeres has been implicated in telomere maintenance pathways in model systems and humans. Specific post-translational modifications of histones, including methylation, acetylation, and ubiquitination, have been shown to be necessary for maintaining a chromatin environment that promotes telomere integrity. Here we review the current knowledge regarding the role of histone modifications in maintaining telomeric and subtelomeric chromatin, discuss the implications of histone modification marks as they relate to human disease, and highlight key areas for future research.
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36
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Sengupta A, Ganguly A, Chowdhury S. Promise of G-Quadruplex Structure Binding Ligands as Epigenetic Modifiers with Anti-Cancer Effects. Molecules 2019; 24:E582. [PMID: 30736345 PMCID: PMC6384772 DOI: 10.3390/molecules24030582] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 11/16/2022] Open
Abstract
Evidences from more than three decades of work support the function of non-duplex DNA structures called G-quadruplex (G4) in important processes like transcription and replication. In addition, G4 structures have been studied in connection with DNA base modifications and chromatin/nucleosome arrangements. Recent work, interestingly, shows promise of G4 structures, through interaction with G4 structure-interacting proteins, in epigenetics-in both DNA and histone modification. Epigenetic changes are found to be intricately associated with initiation as well as progression of cancer. Multiple oncogenes have been reported to harbor the G4 structure at regulatory regions. In this context, G4 structure-binding ligands attain significance as molecules with potential to modify the epigenetic state of chromatin. Here, using examples from recent studies we discuss the emerging role of G4 structures in epigenetic modifications and, therefore, the promise of G4 structure-binding ligands in epigenetic therapy.
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Affiliation(s)
- Antara Sengupta
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi-110025, India.
- Academy of Scientific and Innovative Research, Rafi Marg, New Delhi-110001, India.
| | - Akansha Ganguly
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi-110025, India.
| | - Shantanu Chowdhury
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi-110025, India.
- Academy of Scientific and Innovative Research, Rafi Marg, New Delhi-110001, India.
- GNR Knowledge Centre for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi-110025, India.
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37
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Aksenova AY, Mirkin SM. At the Beginning of the End and in the Middle of the Beginning: Structure and Maintenance of Telomeric DNA Repeats and Interstitial Telomeric Sequences. Genes (Basel) 2019; 10:genes10020118. [PMID: 30764567 PMCID: PMC6410037 DOI: 10.3390/genes10020118] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 02/07/2023] Open
Abstract
Tandem DNA repeats derived from the ancestral (TTAGGG)n run were first detected at chromosome ends of the majority of living organisms, hence the name telomeric DNA repeats. Subsequently, it has become clear that telomeric motifs are also present within chromosomes, and they were suitably called interstitial telomeric sequences (ITSs). It is well known that telomeric DNA repeats play a key role in chromosome stability, preventing end-to-end fusions and precluding the recurrent DNA loss during replication. Recent data suggest that ITSs are also important genomic elements as they confer its karyotype plasticity. In fact, ITSs appeared to be among the most unstable microsatellite sequences as they are highly length polymorphic and can trigger chromosomal fragility and gross chromosomal rearrangements. Importantly, mechanisms responsible for their instability appear to be similar to the mechanisms that maintain the length of genuine telomeres. This review compares the mechanisms of maintenance and dynamic properties of telomeric repeats and ITSs and discusses the implications of these dynamics on genome stability.
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Affiliation(s)
- Anna Y Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02421, USA.
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38
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Okamoto K, Seimiya H. Revisiting Telomere Shortening in Cancer. Cells 2019; 8:cells8020107. [PMID: 30709063 PMCID: PMC6406355 DOI: 10.3390/cells8020107] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 01/28/2019] [Accepted: 01/28/2019] [Indexed: 12/21/2022] Open
Abstract
Telomeres, the protective structures of chromosome ends are gradually shortened by each cell division, eventually leading to senescence or apoptosis. Cancer cells maintain the telomere length for unlimited growth by telomerase reactivation or a recombination-based mechanism. Recent genome-wide analyses have unveiled genetic and epigenetic alterations of the telomere maintenance machinery in cancer. While telomerase inhibition reveals that longer telomeres are more advantageous for cell survival, cancer cells often have paradoxically shorter telomeres compared with those found in the normal tissues. In this review, we summarize the latest knowledge about telomere length alterations in cancer and revisit its rationality. Finally, we discuss the potential utility of telomere length as a prognostic biomarker.
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Affiliation(s)
- Keiji Okamoto
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, Japan.
| | - Hiroyuki Seimiya
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, Japan.
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39
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Cacchione S, Biroccio A, Rizzo A. Emerging roles of telomeric chromatin alterations in cancer. J Exp Clin Cancer Res 2019; 38:21. [PMID: 30654820 PMCID: PMC6337846 DOI: 10.1186/s13046-019-1030-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 01/07/2019] [Indexed: 12/26/2022] Open
Abstract
Telomeres, the nucleoprotein structures that cap the ends of eukaryotic chromosomes, play important and multiple roles in tumorigenesis. Functional telomeres need the establishment of a protective chromatin structure based on the interplay between the specific complex named shelterin and a tight nucleosomal organization. Telomere shortening in duplicating somatic cells leads eventually to the destabilization of the telomere capping structure and to the activation of a DNA damage response (DDR) signaling. The final outcome of this process is cell replicative senescence, which constitute a protective barrier against unlimited proliferation. Cells that can bypass senescence checkpoint continue to divide until a second replicative checkpoint, crisis, characterized by chromosome fusions and rearrangements leading to massive cell death by apoptosis. During crisis telomere dysfunctions can either inhibit cell replication or favor tumorigenesis by the accumulation of chromosomal rearrangements and neoplastic mutations. The acquirement of a telomere maintenance mechanism allows fixing the aberrant phenotype, and gives the neoplastic cell unlimited replicative potential, one of the main hallmarks of cancer.Despite the crucial role that telomeres play in cancer development, little is known about the epigenetic alterations of telomeric chromatin that affect telomere protection and are associated with tumorigenesis. Here we discuss the current knowledge on the role of telomeric chromatin in neoplastic transformation, with a particular focus on H3.3 mutations in alternative lengthening of telomeres (ALT) cancers and sirtuin deacetylases dysfunctions.
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Affiliation(s)
- Stefano Cacchione
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy.
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic Unit, IRCCS-Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Angela Rizzo
- Oncogenomic and Epigenetic Unit, IRCCS-Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy.
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40
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Laberthonnière C, Magdinier F, Robin JD. Bring It to an End: Does Telomeres Size Matter? Cells 2019; 8:E30. [PMID: 30626097 PMCID: PMC6356554 DOI: 10.3390/cells8010030] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/01/2019] [Accepted: 01/04/2019] [Indexed: 12/22/2022] Open
Abstract
Telomeres are unique nucleoprotein structures. Found at the edge of each chromosome, their main purpose is to mask DNA ends from the DNA-repair machinery by formation of protective loops. Through life and cell divisions, telomeres shorten and bring cells closer to either cell proliferation crisis or senescence. Beyond this mitotic clock role attributed to the need for telomere to be maintained over a critical length, the very tip of our DNA has been shown to impact transcription by position effect. TPE and a long-reach counterpart, TPE-OLD, are mechanisms recently described in human biology. Still in infancy, the mechanism of action of these processes and their respective genome wide impact remain to be resolved. In this review, we will discuss recent findings on telomere dynamics, TPE, TPE-OLD, and lessons learnt from model organisms.
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Affiliation(s)
| | - Frédérique Magdinier
- Aix Marseille Univ, MMG, Marseille Medical Genetics U1251, 13385 Marseille, France.
| | - Jérôme D Robin
- Aix Marseille Univ, MMG, Marseille Medical Genetics U1251, 13385 Marseille, France.
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41
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Non-duplex G-Quadruplex Structures Emerge as Mediators of Epigenetic Modifications. Trends Genet 2018; 35:129-144. [PMID: 30527765 DOI: 10.1016/j.tig.2018.11.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/10/2018] [Accepted: 11/02/2018] [Indexed: 12/16/2022]
Abstract
The role of non-duplex DNA, the guanine-quadruplex structure in particular, is becoming widely appreciated. Increasing evidence in the last decade implicates quadruplexes in important processes such as transcription and replication. Interestingly, more recent work suggests roles for quadruplexes, in association with quadruplex-interacting proteins, in epigenetics through both DNA and histone modifications. Here, we review the effect of the quadruplex structure on post-replication epigenetic memory and quadruplex-induced promoter DNA/histone modifications. Furthermore, we highlight the epigenetic state of the telomerase promoter where quadruplexes could play a key regulatory role. Finally, we discuss the possibility that DNA structures such as quadruplexes, within a largely duplex DNA background, could act as molecular anchors for locally induced epigenetic modifications.
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