1
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Tan KT, Slevin MK, Leibowitz ML, Garrity-Janger M, Shan J, Li H, Meyerson M. Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing. CELL GENOMICS 2024; 4:100588. [PMID: 38917803 DOI: 10.1016/j.xgen.2024.100588] [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: 12/14/2022] [Revised: 11/09/2023] [Accepted: 05/30/2024] [Indexed: 06/27/2024]
Abstract
Alterations in the structure and location of telomeres are pivotal in cancer genome evolution. Here, we applied both long-read and short-read genome sequencing to assess telomere repeat-containing structures in cancers and cancer cell lines. Using long-read genome sequences that span telomeric repeats, we defined four types of telomere repeat variations in cancer cells: neotelomeres where telomere addition heals chromosome breaks, chromosomal arm fusions spanning telomere repeats, fusions of neotelomeres, and peri-centromeric fusions with adjoined telomere and centromere repeats. These results provide a framework for the systematic study of telomeric repeats in cancer genomes, which could serve as a model for understanding the somatic evolution of other repetitive genomic elements.
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Affiliation(s)
- Kar-Tong Tan
- Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA
| | | | - Mitchell L Leibowitz
- Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Max Garrity-Janger
- Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Jidong Shan
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Heng Li
- Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02215, USA.
| | - Matthew Meyerson
- Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA.
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2
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Hinchie AM, Sanford SL, Loughridge KE, Sutton RM, Parikh AH, Gil Silva AA, Sullivan DI, Chun-On P, Morrell MR, McDyer JF, Opresko PL, Alder JK. A persistent variant telomere sequence in a human pedigree. Nat Commun 2024; 15:4681. [PMID: 38824190 PMCID: PMC11144197 DOI: 10.1038/s41467-024-49072-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 05/22/2024] [Indexed: 06/03/2024] Open
Abstract
The telomere sequence, TTAGGG, is conserved across all vertebrates and plays an essential role in suppressing the DNA damage response by binding a set of proteins termed shelterin. Changes in the telomere sequence impair shelterin binding, initiate a DNA damage response, and are toxic to cells. Here we identify a family with a variant in the telomere template sequence of telomerase, the enzyme responsible for telomere elongation, that led to a non-canonical telomere sequence. The variant is inherited across at least one generation and one family member reports no significant medical concerns despite ~9% of their telomeres converting to the novel sequence. The variant template disrupts telomerase repeat addition processivity and decreased the binding of the telomere-binding protein POT1. Despite these disruptions, the sequence is readily incorporated into cellular chromosomes. Incorporation of a variant sequence prevents POT1-mediated inhibition of telomerase suggesting that incorporation of a variant sequence may influence telomere addition. These findings demonstrate that telomeres can tolerate substantial degeneracy while remaining functional and provide insights as to how incorporation of a non-canonical telomere sequence might alter telomere length dynamics.
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Affiliation(s)
- Angela M Hinchie
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Samantha L Sanford
- Environmental and Occupational Health Department, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA, USA
| | - Kelly E Loughridge
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Rachel M Sutton
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anishka H Parikh
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Agustin A Gil Silva
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel I Sullivan
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Pattra Chun-On
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew R Morrell
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - John F McDyer
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Patricia L Opresko
- Environmental and Occupational Health Department, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA, USA
- Pharmacology and Chemical Biology Department, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jonathan K Alder
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA.
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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3
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Stephens Z, Kocher JP. Characterization of telomere variant repeats using long reads enables allele-specific telomere length estimation. BMC Bioinformatics 2024; 25:194. [PMID: 38755561 PMCID: PMC11100205 DOI: 10.1186/s12859-024-05807-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/09/2024] [Indexed: 05/18/2024] Open
Abstract
Telomeres are regions of repetitive DNA at the ends of linear chromosomes which protect chromosome ends from degradation. Telomere lengths have been extensively studied in the context of aging and disease, though most studies use average telomere lengths which are of limited utility. We present a method for identifying all 92 telomere alleles from long read sequencing data. Individual telomeres are identified using variant repeats proximal to telomere regions, which are unique across alleles. This high-throughput and high-resolution characterization of telomeres could be foundational to future studies investigating the roles of specific telomeres in aging and disease.
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4
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Ertunc O, Smearman E, Zheng Q, Hicks JL, Brosnan-Cashman JA, Jones T, Gomes-Alexandre C, Trabzonlu L, Meeker AK, De Marzo AM, Heaphy CM. Chromogenic detection of telomere lengths in situ aids the identification of precancerous lesions in the prostate. Prostate 2024; 84:148-157. [PMID: 37849074 PMCID: PMC10843147 DOI: 10.1002/pros.24633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/05/2023] [Accepted: 09/19/2023] [Indexed: 10/19/2023]
Abstract
BACKGROUND Telomeres are terminal chromosomal elements that are essential for the maintenance of genomic integrity. The measurement of telomere content provides useful diagnostic and prognostic information, and fluorescent methods have been developed for this purpose. However, fluorescent-based tissue assays are cumbersome for investigators to undertake, both in research and clinical settings. METHODS A robust chromogenic in situ hybridization (CISH) approach was developed to visualize and quantify telomere content at single cell resolution in human prostate tissues, both frozen and formalin-fixed, paraffin-embedded (FFPE). RESULTS This new assay (telomere chromogenic in situ hybridization ["Telo-CISH"]) produces permanently stained slides that are viewable with a standard light microscope, thus avoiding the need for specialized equipment and storage. The assay is compatible with standard immunohistochemistry, thereby allowing simultaneous assessment of histomorphology, identification of specific cell types, and assessment of telomere status. In addition, Telo-CISH eliminates the problem of autofluorescent interference that frequently occurs with fluorescent-based methods. Using this new assay, we demonstrate successful application of Telo-CISH to help identify precancerous lesions in the prostate by the presence of markedly short telomeres specifically in the luminal epithelial cells. CONCLUSIONS In summary, with fewer restrictions on the types of tissues that can be tested, and increased histologic information provided, the advantages presented by this novel chromogenic assay should extend the applicability of tissue-based telomere length assessment in research and clinical settings.
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Affiliation(s)
- Onur Ertunc
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Erica Smearman
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Qizhi Zheng
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jessica L. Hicks
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Tracy Jones
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Levent Trabzonlu
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alan K. Meeker
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Sidney Kimmel Comprehensive Cancer Institute at Johns Hopkins, Baltimore, Maryland
| | - Angelo M. De Marzo
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Sidney Kimmel Comprehensive Cancer Institute at Johns Hopkins, Baltimore, Maryland
| | - Christopher M. Heaphy
- Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts
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5
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Valle-Orero J, Rieu M, Allemand JF, Bujaa D, Joubert A, Tran PLT, Croquette V, Boulé JB. Observing G4 formation and its resolution by Pif1 in real time by manipulation under magnetic tweezers. Methods Enzymol 2024; 695:119-158. [PMID: 38521583 DOI: 10.1016/bs.mie.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
G-quadruplexes (G4s) are nucleic acids secondary structures that may form in guanine-rich sequences, either intra or inter-molecularly. Ability of a primary sequence to form a G4 can be predicted computationally with an improving accuracy as well as tested in bulk using biophysical measurements. As a result, G4 density maps have been devised for a large number of genomes from all life kingdoms. Experimental validation of the formation of G4s in vivo however remains indirect and relies on their stabilization with small molecules, antibodies or proteins, or mutational studies, in order to measure downstream effects on gene expression or genome stability for example. Although numerous techniques exist to observe spontaneous formation of G4s in single-stranded DNA, observing G4 formation in double-stranded DNA (dsDNA) is more challenging. However, it is particularly relevant to understand if a given G4 sequence forms stably in a dsDNA context, if it is stable enough to dock proteins or pose a challenge to molecular motors such as helicases or polymerases. In essence, G4s can be a threat to genomic stability but carry as well as the potential to be elements of a structural language in the non-replicating genome. To study quantitatively the formation dynamics and stability of single intramolecular G4s embedded in dsDNA, we have adapted techniques of DNA manipulation under magnetic tweezers. This technique also allows to study encounters of molecular motors with G4 at a single molecule resolution, in order to gain insight into the specificity of G4 resolution by molecular motors, and its efficiency. The procedures described here include the design of the G4 substrate, the study of G4 formation probability and lifetime in dsDNA, as well as procedures to characterize the encounter between the Pif1 helicase and a G4 until G4 resolution. The procedures that we described here can easily be extended to the study of other G4s or molecular motors.
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Affiliation(s)
- Jessica Valle-Orero
- Physics Laboratory of the École Normale Supérieure, CNRS, ENS, PSL University, Sorbonne University, Paris-Cité University, Paris, France; Biology Institute of the École Normale Supérieure (IBENS), ENS, CNRS, INSERM, PSL University, Paris, France; Department of Computer Science, Mathematics and Environmental Sciences, The American University of Paris, Paris, France.
| | - Martin Rieu
- Physics Laboratory of the École Normale Supérieure, CNRS, ENS, PSL University, Sorbonne University, Paris-Cité University, Paris, France; Biology Institute of the École Normale Supérieure (IBENS), ENS, CNRS, INSERM, PSL University, Paris, France; Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Jean-François Allemand
- Physics Laboratory of the École Normale Supérieure, CNRS, ENS, PSL University, Sorbonne University, Paris-Cité University, Paris, France; Biology Institute of the École Normale Supérieure (IBENS), ENS, CNRS, INSERM, PSL University, Paris, France
| | - Dulamkhuu Bujaa
- Physics Laboratory of the École Normale Supérieure, CNRS, ENS, PSL University, Sorbonne University, Paris-Cité University, Paris, France; Biology Institute of the École Normale Supérieure (IBENS), ENS, CNRS, INSERM, PSL University, Paris, France
| | - Alexandra Joubert
- Genome Structure and Instability Laboratory, National Museum of Natural History, CNRS, INSERM, Sorbonne University Alliance, Paris, France
| | - Phong Lan Thao Tran
- Genome Structure and Instability Laboratory, National Museum of Natural History, CNRS, INSERM, Sorbonne University Alliance, Paris, France; Depixus SAS, 3-5 impasse Reille, Paris, France
| | - Vincent Croquette
- Physics Laboratory of the École Normale Supérieure, CNRS, ENS, PSL University, Sorbonne University, Paris-Cité University, Paris, France; Biology Institute of the École Normale Supérieure (IBENS), ENS, CNRS, INSERM, PSL University, Paris, France; ESPCI Paris, PSL University, Paris, France.
| | - Jean-Baptiste Boulé
- Genome Structure and Instability Laboratory, National Museum of Natural History, CNRS, INSERM, Sorbonne University Alliance, Paris, France.
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Mano J, Sushida H, Tanaka T, Naito K, Ono H, Ike M, Tokuyasu K, Kitaoka M. Extracellular oil production by Rhodotorula paludigena BS15 for biorefinery without complex downstream processes. Appl Microbiol Biotechnol 2023; 107:6799-6809. [PMID: 37725141 DOI: 10.1007/s00253-023-12762-3] [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: 04/04/2023] [Revised: 07/12/2023] [Accepted: 08/30/2023] [Indexed: 09/21/2023]
Abstract
To realize biomass refinery without complex downstream processes, we extensively screened for microbial strains that efficiently produce extracellular oil from sugars. Rhodotorula paludigena (formerly Rhodosporidium paludigenum) BS15 was found to efficiently produce polyol esters of fatty acids (PEFAs), which mainly comprised of 3-acetoxypalmitic acid and partially acetylated mannitol/arabinitol. To evaluate the performance of this strain, fed-batch fermentation was demonstrated on a flask scale, and 110 g/L PEFA and 103 g/L dry cells were produced in 12 days. To the best of our knowledge, the strain BS15 exhibited the highest PEFA titer (g/L) ever to be reported so far. Because the PEFA precipitated at the bottom of the culture broth, it could be easily recovered by simply discarding the upper phase. Various carbon sources can be utilized for cell growth and/or PEFA production, which signifies the potential for converting diverse biomass sources. Two different types of next-generation sequencers, Illumina HiSeq and Oxford Nanopore PromethION, were used to analyze the whole-genome sequence of the strain BS15. The integrative data analysis generated a high-quality and reliable reference genome for PEFA-producing R. paludigena. The 22.5-M base genome sequence and the estimated genes were registered in Genbank (accession numbers BQKY01000001-BQKY01000019). KEY POINTS: • R. paludigena BS15 was isolated after an extensive screening of extracellular oil producers from natural sources. • Fed-batch fermentation of R. paludigena BS15 yielded 110 g/L of PEFA, which is the highest titer ever reported to date. • Combined analysis using Illumina and Oxford Nanopore sequencers produced the near-complete genome sequence.
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Affiliation(s)
- Junichi Mano
- Institute of Food Research, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan.
| | - Hirotoshi Sushida
- Institute of Food Research, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
| | - Tsuyoshi Tanaka
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Ken Naito
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Hiroshi Ono
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Masakazu Ike
- Institute of Food Research, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
| | - Ken Tokuyasu
- Institute of Food Research, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
| | - Motomitsu Kitaoka
- Institute of Food Research, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
- Faculty of Agriculture, Niigata University, Niigata, 950-2181, Japan
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7
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Ertunc O, Smearman E, Zheng Q, Hicks JL, Brosnan-Cashman JA, Jones T, Gomes-Alexandre C, Trabzonlu L, Meeker AK, De Marzo AM, Heaphy CM. Chromogenic detection of telomere lengths in situ aids the identification of precancerous lesions in the prostate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.04.535575. [PMID: 37066381 PMCID: PMC10104079 DOI: 10.1101/2023.04.04.535575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Telomeres are terminal chromosomal elements that are essential for the maintenance of genomic integrity. The measurement of telomere content provides useful diagnostic and prognostic information, and fluorescent methods have been developed for this purpose. However, fluorescent-based tissue assays are cumbersome for investigators to undertake, both in research and clinical settings. Here, a robust chromogenic in situ hybridization (CISH) approach was developed to visualize and quantify telomere content at single cell resolution in human prostate tissues, both frozen and formalin-fixed, paraffin-embedded (FFPE). This new assay ("Telo-CISH") produces permanently stained slides that are viewable with a standard light microscope, thus avoiding the need for specialized equipment and storage. The assay is compatible with standard immunohistochemistry, thereby allowing simultaneous assessment of histomorphology, identification of specific cell types, and assessment of telomere status. In addition, Telo-CISH eliminates the problem of autofluorescent interference that frequently occurs with fluorescent-based methods. Using this new assay, we demonstrate successful application of Telo-CISH to help identify precancerous lesions in the prostate by the presence of markedly short telomeres specifically in the luminal epithelial cells. In summary, with fewer restrictions on the types of tissues that can be tested, and increased histologic information provided, the advantages presented by this novel chromogenic assay should extend the applicability of tissue-based telomere length assessment in research and clinical settings.
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Affiliation(s)
- Onur Ertunc
- The Department of Pathology, The Johns Hopkins University School of Medicine
| | - Erica Smearman
- The Department of Pathology, The Johns Hopkins University School of Medicine
| | - Qizhi Zheng
- The Department of Pathology, The Johns Hopkins University School of Medicine
| | - Jessica L. Hicks
- The Department of Pathology, The Johns Hopkins University School of Medicine
| | | | - Tracy Jones
- The Department of Pathology, The Johns Hopkins University School of Medicine
| | | | - Levent Trabzonlu
- The Department of Pathology, The Johns Hopkins University School of Medicine
| | - Alan K. Meeker
- The Department of Pathology, The Johns Hopkins University School of Medicine
- The Department of Urology, The Johns Hopkins University School of Medicine
- The Department of Oncology, The Johns Hopkins University School of Medicine
- The Sidney Kimmel Comprehensive Cancer Institute at Johns Hopkins, Baltimore, Maryland
| | - Angelo M. De Marzo
- The Department of Pathology, The Johns Hopkins University School of Medicine
- The Department of Urology, The Johns Hopkins University School of Medicine
- The Department of Oncology, The Johns Hopkins University School of Medicine
- The Sidney Kimmel Comprehensive Cancer Institute at Johns Hopkins, Baltimore, Maryland
| | - Christopher M. Heaphy
- The Department of Medicine, Boston University, School of Medicine and Boston Medical Center, Boston, Massachusetts
- The Department Pathology and Laboratory Medicine, Boston University, School of Medicine and Boston Medical Center, Boston, Massachusetts
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8
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Telomere Length Changes in Cancer: Insights on Carcinogenesis and Potential for Non-Invasive Diagnostic Strategies. Genes (Basel) 2023; 14:genes14030715. [PMID: 36980987 PMCID: PMC10047978 DOI: 10.3390/genes14030715] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Telomere dynamics play a crucial role in the maintenance of chromosome integrity; changes in telomere length may thus contribute to the development of various diseases including cancer. Understanding the role of telomeric DNA in carcinogenesis and detecting the presence of cell-free telomeric DNA (cf-telDNA) in body fluids offer a potential biomarker for novel cancer screening and diagnostic strategies. Liquid biopsy is becoming increasingly popular due to its undeniable benefits over conventional invasive methods. However, the organization and function of cf-telDNA in the extracellular milieu are understudied. This paper provides a review based on 3,398,017 cancer patients, patients with other conditions, and control individuals with the aim to shed more light on the inconsistent nature of telomere lengthening/shortening in oncological contexts. To gain a better understanding of biological factors (e.g., telomerase activation, alternative lengthening of telomeres) affecting telomere homeostasis across different types of cancer, we summarize mechanisms responsible for telomere length maintenance. In conclusion, we compare tissue- and liquid biopsy-based approaches in cancer assessment and provide a brief outlook on the methodology used for telomere length evaluation, highlighting the advances of state-of-the-art approaches in the field.
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9
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Lyčka M, Fajkus P, Jenner LP, Sýkorová E, Fojtová M, Peska V. Identification of the Sequence and the Length of Telomere DNA. Methods Mol Biol 2023; 2672:285-302. [PMID: 37335484 DOI: 10.1007/978-1-0716-3226-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Telomeres are essential nucleoprotein structures at the very ends of linear eukaryote chromosomes. They shelter the terminal genome territories against degradation and prevent the natural chromosome ends from being recognized by repair mechanisms as double-strand DNA breaks.There are two basic characteristics of telomeric DNA, its sequence and its length. The telomere sequence is important as a "landing area" for specific telomere-binding proteins, which function as signals and moderate the interactions required for correct telomere function. While the sequence forms the proper "landing surface" of telomeric DNA, its length is similarly important. Too short or exceptionally long telomere DNA cannot perform its function properly. In this chapter, methods for the investigation of these two basic telomere DNA characteristics are described, namely, telomere motif identification and telomere length measurement.
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Affiliation(s)
- Martin Lyčka
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petr Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Leon P Jenner
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Eva Sýkorová
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Vratislav Peska
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
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10
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Geiller HEB, Harvey A, Jones RE, Grimstead JW, Cleal K, Hendrickson EA, Baird DM. ATRX modulates the escape from a telomere crisis. PLoS Genet 2022; 18:e1010485. [PMID: 36350851 PMCID: PMC9678338 DOI: 10.1371/journal.pgen.1010485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/21/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022] Open
Abstract
Telomerase activity is the principal telomere maintenance mechanism in human cancers, however 15% of cancers utilise a recombination-based mechanism referred to as alternative lengthening of telomeres (ALT) that leads to long and heterogenous telomere length distributions. Loss-of-function mutations in the Alpha Thalassemia/Mental Retardation Syndrome X-Linked (ATRX) gene are frequently found in ALT cancers. Here, we demonstrate that the loss of ATRX, coupled with telomere dysfunction during crisis, is sufficient to initiate activation of the ALT pathway and that it confers replicative immortality in human fibroblasts. Additionally, loss of ATRX combined with a telomere-driven crisis in HCT116 epithelial cancer cells led to the initiation of an ALT-like pathway. In these cells, a rapid and precise telomeric elongation and the induction of C-circles was observed; however, this process was transient and the telomeres ultimately continued to erode such that the cells either died or the escape from crisis was associated with telomerase activation. In both of these instances, telomere sequencing revealed that all alleles, irrespective of whether they were elongated, were enriched in variant repeat types, that appeared to be cell-line specific. Thus, our data show that the loss of ATRX combined with telomere dysfunction during crisis induces the ALT pathway in fibroblasts and enables a transient activation of ALT in epithelial cells.
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Affiliation(s)
- Helene E. B. Geiller
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
| | - Adam Harvey
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Rhiannon E. Jones
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
| | - Julia W. Grimstead
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
| | - Kez Cleal
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
| | - Eric A. Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Duncan M. Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
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11
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Telomeres and Their Neighbors. Genes (Basel) 2022; 13:genes13091663. [PMID: 36140830 PMCID: PMC9498494 DOI: 10.3390/genes13091663] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/21/2022] Open
Abstract
Telomeres are essential structures formed from satellite DNA repeats at the ends of chromosomes in most eukaryotes. Satellite DNA repeat sequences are useful markers for karyotyping, but have a more enigmatic role in the eukaryotic cell. Much work has been done to investigate the structure and arrangement of repetitive DNA elements in classical models with implications for species evolution. Still more is needed until there is a complete picture of the biological function of DNA satellite sequences, particularly when considering non-model organisms. Celebrating Gregor Mendel’s anniversary by going to the roots, this review is designed to inspire and aid new research into telomeres and satellites with a particular focus on non-model organisms and accessible experimental and in silico methods that do not require specialized equipment or expensive materials. We describe how to identify telomere (and satellite) repeats giving many examples of published (and some unpublished) data from these techniques to illustrate the principles behind the experiments. We also present advice on how to perform and analyse such experiments, including details of common pitfalls. Our examples are a selection of recent developments and underexplored areas of research from the past. As a nod to Mendel’s early work, we use many examples from plants and insects, especially as much recent work has expanded beyond the human and yeast models traditional in telomere research. We give a general introduction to the accepted knowledge of telomere and satellite systems and include references to specialized reviews for the interested reader.
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12
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Akinnibosun OA, Maier MC, Eales J, Tomaszewski M, Charchar FJ. Telomere therapy for chronic kidney disease. Epigenomics 2022; 14:1039-1054. [PMID: 36177720 DOI: 10.2217/epi-2022-0073] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Chronic kidney disease (CKD) is estimated to affect almost 10% of individuals worldwide and is one of the leading causes of morbidity and mortality. Renal fibrosis, a central pathway in CKD progression (irrespective of etiology), is associated with shortened or dysfunctional telomeres in animal studies. Telomeres are specialized nucleoprotein structures located at the chromosome end that maintain genomic integrity. The mechanisms of associations between telomere length and CKD have not yet been fully elucidated, however, CKD patients with shorter telomere length may have decreased renal function and a higher mortality rate. A plethora of ongoing research has focused on possible therapeutic applications of telomeres with the overall goal to preserve telomere length as a therapy to treat CKD.
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Affiliation(s)
| | - Michelle C Maier
- Health Innovation and Transformation Centre, Federation University Australia, Ballarat, Victoria, Australia
| | - James Eales
- Division of Cardiovascular Sciences, University of Manchester, Manchester, UK
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, University of Manchester, Manchester, UK.,Manchester Heart Centre and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Fadi J Charchar
- Health Innovation and Transformation Centre, Federation University Australia, Ballarat, Victoria, Australia.,Department of Cardiovascular Sciences, University of Leicester, Leicester, UK.,Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria, Australia
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13
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Lee J, Sung K, Joo SY, Jeong JH, Kim SK, Lee H. Dynamic interaction of BRCA2 with telomeric G-quadruplexes underlies telomere replication homeostasis. Nat Commun 2022; 13:3396. [PMID: 35697743 PMCID: PMC9192595 DOI: 10.1038/s41467-022-31156-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 05/31/2022] [Indexed: 12/02/2022] Open
Abstract
BRCA2-deficient cells precipitate telomere shortening upon collapse of stalled replication forks. Here, we report that the dynamic interaction between BRCA2 and telomeric G-quadruplex (G4), the non-canonical four-stranded secondary structure, underlies telomere replication homeostasis. We find that the OB-folds of BRCA2 binds to telomeric G4, which can be an obstacle during replication. We further demonstrate that BRCA2 associates with G-triplex (G3)-derived intermediates, which are likely to form during direct interconversion between parallel and non-parallel G4. Intriguingly, BRCA2 binding to G3 intermediates promoted RAD51 recruitment to the telomere G4. Furthermore, MRE11 resected G4-telomere, which was inhibited by BRCA2. Pathogenic mutations at the OB-folds abrogated the binding with telomere G4, indicating that the way BRCA2 associates with telomere is innate to its tumor suppressor activity. Collectively, we propose that BRCA2 binding to telomeric G4 remodels it and allows RAD51-mediated restart of the G4-driven replication fork stalling, simultaneously preventing MRE11-mediated breakdown of telomere. G-quadruplex (G4) can be formed in telomeric DNA. Here the authors show that BRCA2 interacts with telomere G4 structure generated during telomere replication, protecting telomere from nuclease attack.
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Affiliation(s)
- Junyeop Lee
- Department of Biological Sciences & IMBG, Seoul National University, Seoul, 08826, South Korea
| | - Keewon Sung
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - So Young Joo
- Department of Biological Sciences & IMBG, Seoul National University, Seoul, 08826, South Korea
| | - Jun-Hyeon Jeong
- Department of Biological Sciences & IMBG, Seoul National University, Seoul, 08826, South Korea
| | - Seong Keun Kim
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea.
| | - Hyunsook Lee
- Department of Biological Sciences & IMBG, Seoul National University, Seoul, 08826, South Korea.
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14
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Lu R, Pickett HA. Telomeric replication stress: the beginning and the end for alternative lengthening of telomeres cancers. Open Biol 2022; 12:220011. [PMID: 35259951 PMCID: PMC8905155 DOI: 10.1098/rsob.220011] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Telomeres are nucleoprotein structures that cap the ends of linear chromosomes. Telomeric DNA comprises terminal tracts of G-rich tandem repeats, which are inherently difficult for the replication machinery to navigate. Structural aberrations that promote activation of the alternative lengthening of telomeres (ALT) pathway of telomere maintenance exacerbate replication stress at ALT telomeres, driving fork stalling and fork collapse. This form of telomeric DNA damage perpetuates recombination-mediated repair pathways and break-induced telomere synthesis. The relationship between replication stress and DNA repair is tightly coordinated for the purpose of regulating telomere length in ALT cells, but has been shown to be experimentally manipulatable. This raises the intriguing possibility that induction of replication stress can be used as a means to cause toxic levels of DNA damage at ALT telomeres, thereby selectively disrupting the viability of ALT cancers.
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Affiliation(s)
- Robert Lu
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Hilda A. Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
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15
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Xiong F, Frasch WD. ΩqPCR measures telomere length from single-cells in base pair units. Nucleic Acids Res 2021; 49:e120. [PMID: 34534325 PMCID: PMC8599887 DOI: 10.1093/nar/gkab753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 08/13/2021] [Accepted: 09/07/2021] [Indexed: 12/25/2022] Open
Abstract
ΩqPCR determines absolute telomere length in kb units from single cells. Accuracy and precision of ΩqPCR were assessed using 800 bp and 1600 bp synthetic telomeres inserted into plasmids, which were measured to be 819 ± 19.6 and 1590 ± 42.3 bp, respectively. This is the first telomere length measuring method verified in this way. The approach uses Ω-probes, a DNA strand containing sequence information that enables: (i) hybridization with the telomere via the 3' and 5' ends that become opposed; (ii) ligation of the hybridized probes to circularize the Ω-probes and (iii) circularized-dependent qPCR due to sequence information for a forward primer, and for a reverse primer binding site, and qPCR hydrolysis probe binding. Read through of the polymerase during qPCR occurs only in circularized Ω-probes, which quantifies their number that is directly proportional to telomere length. When used in concert with information about the cell cycle stage from a single-copy gene, and ploidy, the MTL of single cells measured by ΩqPCR was consistent with that obtained from large sample sizes by TRF.
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Affiliation(s)
- Fusheng Xiong
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ 85287-4501, USA
| | - Wayne D Frasch
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ 85287-4501, USA
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16
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Sellami M, Bragazzi N, Prince MS, Denham J, Elrayess M. Regular, Intense Exercise Training as a Healthy Aging Lifestyle Strategy: Preventing DNA Damage, Telomere Shortening and Adverse DNA Methylation Changes Over a Lifetime. Front Genet 2021; 12:652497. [PMID: 34421981 PMCID: PMC8379006 DOI: 10.3389/fgene.2021.652497] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/30/2021] [Indexed: 12/13/2022] Open
Abstract
Exercise training is one of the few therapeutic interventions that improves health span by delaying the onset of age-related diseases and preventing early death. The length of telomeres, the 5'-TTAGGG n -3' tandem repeats at the ends of mammalian chromosomes, is one of the main indicators of biological age. Telomeres undergo shortening with each cellular division. This subsequently leads to alterations in the expression of several genes that encode vital proteins with critical functions in many tissues throughout the body, and ultimately impacts cardiovascular, immune and muscle physiology. The sub-telomeric DNA is comprised of heavily methylated, heterochromatin. Methylation and histone acetylation are two of the most well-studied examples of the epigenetic modifications that occur on histone proteins. DNA methylation is the type of epigenetic modification that alters gene expression without modifying gene sequence. Although diet, genetic predisposition and a healthy lifestyle seem to alter DNA methylation and telomere length (TL), recent evidence suggests that training status or physical fitness are some of the major factors that control DNA structural modifications. In fact, TL is positively associated with cardiorespiratory fitness, physical activity level (sedentary, active, moderately trained, or elite) and training intensity, but is shorter in over-trained athletes. Similarly, somatic cells are vulnerable to exercise-induced epigenetic modification, including DNA methylation. Exercise-training load, however, depends on intensity and volume (duration and frequency). Training load-dependent responses in genomic profiles could underpin the discordant physiological and physical responses to exercise. In the current review, we will discuss the role of various forms of exercise training in the regulation of DNA damage, TL and DNA methylation status in humans, to provide an update on the influence exercise training has on biological aging.
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Affiliation(s)
- Maha Sellami
- Physical Education Department (PE), College of Education (CEdu), Qatar University, Doha, Qatar
| | - Nicola Bragazzi
- Department of Health Sciences (DISSAL), Postgraduate School of Public Health, University of Genoa, Genoa, Italy
| | - Mohammad Shoaib Prince
- Physical Education Department (PE), College of Education (CEdu), Qatar University, Doha, Qatar
- Division of Sports and Wellness, Department of Students Affairs, College of North Atlantic Qatar (CNAQ), Doha, Qatar
| | - Joshua Denham
- School of Health and Biomedical Sciences, RMIT University, Melbourne, VIC, Australia
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17
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Chatain J, Blond A, Phan AT, Saintomé C, Alberti P. GGGCTA repeats can fold into hairpins poorly unfolded by replication protein A: a possible origin of the length-dependent instability of GGGCTA variant repeats in human telomeres. Nucleic Acids Res 2021; 49:7588-7601. [PMID: 34214172 PMCID: PMC8287962 DOI: 10.1093/nar/gkab518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 06/01/2021] [Accepted: 06/30/2021] [Indexed: 11/19/2022] Open
Abstract
Human telomeres are composed of GGGTTA repeats and interspersed with variant repeats. The GGGCTA variant motif was identified in the proximal regions of human telomeres about 10 years ago and was shown to display a length-dependent instability. In parallel, a structural study showed that four GGGCTA repeats folded into a non-canonical G-quadruplex (G4) comprising a Watson-Crick GCGC tetrad. It was proposed that this non-canonical G4 might be an additional obstacle for telomere replication. In the present study, we demonstrate that longer GGGCTA arrays fold into G4 and into hairpins. We also demonstrate that replication protein A (RPA) efficiently binds to GGGCTA repeats structured into G4 but poorly binds to GGGCTA repeats structured into hairpins. Our results (along with results obtained with a more stable variant motif) suggest that GGGCTA hairpins are at the origin of GGGCTA length-dependent instability. They also suggest, as working hypothesis, that failure of efficient binding of RPA to GGGCTA structured into hairpins might be involved in the mechanism of GGGCTA array instability. On the basis of our present and past studies about telomeric G4 and their interaction with RPA, we propose an original point of view about telomeric G4 and the evolution of telomeric motifs.
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Affiliation(s)
- Jean Chatain
- Laboratoire Structure et Instabilité des Génomes (StrInG), Muséum national d’Histoire naturelle, CNRS, Inserm, Paris 75005, France
| | - Alain Blond
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum national d’Histoire naturelle, CNRS, Paris 75005, France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
| | - Carole Saintomé
- Laboratoire Structure et Instabilité des Génomes (StrInG), Muséum national d’Histoire naturelle, CNRS, Inserm, Paris 75005, France
- Sorbonne Université, UFR927, Paris 75005, France
| | - Patrizia Alberti
- Laboratoire Structure et Instabilité des Génomes (StrInG), Muséum national d’Histoire naturelle, CNRS, Inserm, Paris 75005, France
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18
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Tran PLT, Rieu M, Hodeib S, Joubert A, Ouellet J, Alberti P, Bugaut A, Allemand JF, Boulé JB, Croquette V. Folding and persistence times of intramolecular G-quadruplexes transiently embedded in a DNA duplex. Nucleic Acids Res 2021; 49:5189-5201. [PMID: 34009328 PMCID: PMC8136832 DOI: 10.1093/nar/gkab306] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 04/09/2021] [Accepted: 04/14/2021] [Indexed: 12/19/2022] Open
Abstract
G-quadruplex (G4) DNA structures have emerged as important regulatory elements during DNA metabolic transactions. While many in vitro studies have focused on the kinetics of G4 formation within DNA single-strands, G4 are found in vivo in double-stranded DNA regions, where their formation is challenged by the complementary strand. Since the energy of hybridization of Watson-Crick structures dominates the energy of G4 folding, this competition should play a critical role on G4 persistence. To address this, we designed a single-molecule assay allowing to measure G4 folding and persistence times in the presence of the complementary strand. We quantified both folding and unfolding rates of biologically relevant G4 sequences, such as the cMYC and cKIT oncogene promoters, human telomeres and an avian replication origin. We confirmed that G4s are found much more stable in tested replication origin and promoters than in human telomere repeats. In addition, we characterized how G4 dynamics was affected by G4 ligands and showed that both folding rate and persistence time increased. Our assay opens new perspectives for the measurement of G4 dynamics in double-stranded DNA mimicking a replication fork, which is important to understand their role in DNA replication and gene regulation at a mechanistic level.
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Affiliation(s)
- Phong Lan Thao Tran
- Structure et Instabilité des Génomes, Museum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France
| | - Martin Rieu
- Laboratoire de physique de L'École Normale Supérieure de Paris, CNRS, ENS, Université PSL, Sorbonne Université, Université de Paris, 75005 Paris, France.,Institut de Biologie de l'École Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Samar Hodeib
- Laboratoire de physique de L'École Normale Supérieure de Paris, CNRS, ENS, Université PSL, Sorbonne Université, Université de Paris, 75005 Paris, France.,Institut de Biologie de l'École Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Alexandra Joubert
- Structure et Instabilité des Génomes, Museum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France
| | - Jimmy Ouellet
- Depixus SAS, 3-5 Impasse Reille, 75014 Paris, France
| | - Patrizia Alberti
- Structure et Instabilité des Génomes, Museum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France
| | - Anthony Bugaut
- Structure et Instabilité des Génomes, Museum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France
| | - Jean-François Allemand
- Laboratoire de physique de L'École Normale Supérieure de Paris, CNRS, ENS, Université PSL, Sorbonne Université, Université de Paris, 75005 Paris, France.,Institut de Biologie de l'École Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Jean-Baptiste Boulé
- Structure et Instabilité des Génomes, Museum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France
| | - Vincent Croquette
- Laboratoire de physique de L'École Normale Supérieure de Paris, CNRS, ENS, Université PSL, Sorbonne Université, Université de Paris, 75005 Paris, France.,Institut de Biologie de l'École Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France.,ESPCI Paris, Université PSL, 75005 Paris, France
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19
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Grigorev K, Foox J, Bezdan D, Butler D, Luxton JJ, Reed J, McKenna MJ, Taylor L, George KA, Meydan C, Bailey SM, Mason CE. Haplotype diversity and sequence heterogeneity of human telomeres. Genome Res 2021; 31:1269-1279. [PMID: 34162698 PMCID: PMC8256856 DOI: 10.1101/gr.274639.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 05/04/2021] [Indexed: 12/11/2022]
Abstract
Telomeres are regions of repetitive nucleotide sequences capping the ends of eukaryotic chromosomes that protect against deterioration, and whose lengths can be correlated with age and adverse health risk factors. Yet, given their length and repetitive nature, telomeric regions are not easily reconstructed from short-read sequencing, thus making telomere sequencing, mapping, and variant resolution challenging problems. Recently, long-read sequencing, with read lengths measuring in hundreds of kilobase pairs, has made it possible to routinely read into telomeric regions and inspect their sequence structure. Here, we describe a framework for extracting telomeric reads from whole-genome single-molecule sequencing experiments, including de novo identification of telomere repeat motifs and repeat types, and also describe their sequence variation. We find that long, complex telomeric stretches and repeats can be accurately captured with long-read sequencing, observe extensive sequence heterogeneity of human telomeres, discover and localize noncanonical telomere sequence motifs (both previously reported, as well as novel), and validate them in short-read sequence data. These data reveal extensive intra- and inter-population diversity of repeats in telomeric haplotypes, reveal higher paternal inheritance of telomeric variants, and represent the first motif composition maps of multi-kilobase-pair human telomeric haplotypes across three distinct ancestries (Ashkenazi, Chinese, and Utah), which can aid in future studies of genetic variation, aging, and genome biology.
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Affiliation(s)
- Kirill Grigorev
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York 10021, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York 10021, USA
- The Feil Family Brain and Mind Research Institute, New York, New York 10065, USA
| | - Daniela Bezdan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York 10021, USA
- The Feil Family Brain and Mind Research Institute, New York, New York 10065, USA
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- NGS Competence Center Tübingen, University of Tübingen, 72076 Tübingen, Germany
| | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York 10065, USA
| | - Jared J Luxton
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Jake Reed
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York 10065, USA
| | - Miles J McKenna
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Lynn Taylor
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
| | | | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York 10021, USA
- The Feil Family Brain and Mind Research Institute, New York, New York 10065, USA
| | - Susan M Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York 10021, USA
- The Feil Family Brain and Mind Research Institute, New York, New York 10065, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, New York 10065, USA
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20
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Shen M, Young A, Autexier C. PCNA, a focus on replication stress and the alternative lengthening of telomeres pathway. DNA Repair (Amst) 2021; 100:103055. [PMID: 33581499 DOI: 10.1016/j.dnarep.2021.103055] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/25/2021] [Indexed: 12/16/2022]
Abstract
The maintenance of telomeres, which are specialized stretches of DNA found at the ends of linear chromosomes, is a crucial step for the immortalization of cancer cells. Approximately 10-15 % of cancer cells use a homologous recombination-based mechanism known as the Alternative Lengthening of Telomeres (ALT) pathway to maintain their telomeres. Telomeres in general pose a challenge to DNA replication owing to their repetitive nature and potential for forming secondary structures. Telomeres in ALT+ cells especially are subject to elevated levels of replication stress compared to telomeres that are maintained by the enzyme telomerase, in part due to the incorporation of telomeric variant repeats at ALT+ telomeres, their on average longer lengths, and their modified chromatin states. Many DNA metabolic strategies exist to counter replication stress and to protect stalled replication forks. The role of proliferating cell nuclear antigen (PCNA) as a platform for recruiting protein partners that participate in several of these DNA replication and repair pathways has been well-documented. We propose that many of these pathways may be active at ALT+ telomeres, either to facilitate DNA replication, to manage replication stress, or during telomere extension. Here, we summarize recent evidence detailing the role of PCNA in pathways including DNA secondary structure resolution, DNA damage bypass, replication fork restart, and DNA damage synthesis. We propose that an examination of PCNA and its post-translational modifications (PTMs) may offer a unique lens by which we might gain insight into the DNA metabolic landscape that is distinctively present at ALT+ telomeres.
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Affiliation(s)
- Michelle Shen
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada; Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada
| | - Adrian Young
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada; Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada
| | - Chantal Autexier
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada; Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada.
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21
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Li D, Pan S, Zhang H, Fu Y, Peng Z, Zhang L, Peng S, Xu F, Huang H, Shi R, Zheng H, Peng Y, Tan Z. A comprehensive microsatellite landscape of human Y-DNA at kilobase resolution. BMC Genomics 2021; 22:76. [PMID: 33482734 PMCID: PMC7821415 DOI: 10.1186/s12864-021-07389-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/13/2021] [Indexed: 12/12/2022] Open
Abstract
Background Though interest in human simple sequence repeats (SSRs) is increasing, little is known about the exact distributional features of numerous SSRs in human Y-DNA at chromosomal level. Herein, totally 540 maps were established, which could clearly display SSR landscape in every bin of 1 k base pairs (Kbp) along the sequenced part of human reference Y-DNA (NC_000024.10), by our developed differential method for improving the existing method to reveal SSR distributional characteristics in large genomic sequences. Results The maps show that SSRs accumulate significantly with forming density peaks in at least 2040 bins of 1 Kbp, which involve different coding, noncoding and intergenic regions of the Y-DNA, and 10 especially high density peaks were reported to associate with biological significances, suggesting that the other hundreds of especially high density peaks might also be biologically significant and worth further analyzing. In contrast, the maps also show that SSRs are extremely sparse in at least 207 bins of 1 Kbp, including many noncoding and intergenic regions of the Y-DNA, which is inconsistent with the widely accepted view that SSRs are mostly rich in these regions, and these sparse distributions are possibly due to powerfully regional selection. Additionally, many regions harbor SSR clusters with same or similar motif in the Y-DNA. Conclusions These 540 maps may provide the important information of clearly position-related SSR distributional features along the human reference Y-DNA for better understanding the genome structures of the Y-DNA. This study may contribute to further exploring the biological significance and distribution law of the huge numbers of SSRs in human Y-DNA. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07389-5.
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Affiliation(s)
- Douyue Li
- Bioinformatics Center, College of Biology, Hunan University, Changsha, 410082, China
| | - Saichao Pan
- Bioinformatics Center, College of Biology, Hunan University, Changsha, 410082, China
| | - Hongxi Zhang
- Bioinformatics Center, College of Biology, Hunan University, Changsha, 410082, China
| | - Yongzhuo Fu
- Bioinformatics Center, College of Biology, Hunan University, Changsha, 410082, China
| | - Zhuli Peng
- Bioinformatics Center, College of Biology, Hunan University, Changsha, 410082, China
| | - Liang Zhang
- Bioinformatics Center, College of Biology, Hunan University, Changsha, 410082, China
| | - Shan Peng
- Bioinformatics Center, College of Biology, Hunan University, Changsha, 410082, China
| | - Fei Xu
- Department of Mathematics, Wilfrid Laurier University, Waterloo, Ontario, N2L 3C5, Canada
| | - Hanrou Huang
- Bioinformatics Center, College of Biology, Hunan University, Changsha, 410082, China
| | - Ruixue Shi
- Bioinformatics Center, College of Biology, Hunan University, Changsha, 410082, China
| | - Heping Zheng
- Bioinformatics Center, College of Biology, Hunan University, Changsha, 410082, China
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan University, Changsha, 410082, China
| | - Zhongyang Tan
- Bioinformatics Center, College of Biology, Hunan University, Changsha, 410082, China.
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22
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Lindrose AR, McLester-Davis LWY, Tristano RI, Kataria L, Gadalla SM, Eisenberg DTA, Verhulst S, Drury S. Method comparison studies of telomere length measurement using qPCR approaches: A critical appraisal of the literature. PLoS One 2021; 16:e0245582. [PMID: 33471860 PMCID: PMC7817045 DOI: 10.1371/journal.pone.0245582] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/05/2021] [Indexed: 12/16/2022] Open
Abstract
Use of telomere length (TL) as a biomarker for various environmental exposures and diseases has increased in recent years. Various methods have been developed to measure telomere length. Polymerase chain reaction (PCR)-based methods remain wide-spread for population-based studies due to the high-throughput capability. While several studies have evaluated the repeatability and reproducibility of different TL measurement methods, the results have been variable. We conducted a literature review of TL measurement cross-method comparison studies that included a PCR-based method published between January 1, 2002 and May 25, 2020. A total of 25 articles were found that matched the inclusion criteria. Papers were reviewed for quality of methodologic reporting of sample and DNA quality, PCR assay characteristics, sample blinding, and analytic approaches to determine final TL. Overall, methodologic reporting was low as assessed by two different reporting guidelines for qPCR-based TL measurement. There was a wide range in the reported correlation between methods (as assessed by Pearson’s r) and few studies utilized the recommended intra-class correlation coefficient (ICC) for assessment of assay repeatability and methodologic comparisons. The sample size for nearly all studies was less than 100, raising concerns about statistical power. Overall, this review found that the current literature on the relation between TL measurement methods is lacking in validity and scientific rigor. In light of these findings, we present reporting guidelines for PCR-based TL measurement methods and results of analyses of the effect of assay repeatability (ICC) on statistical power of cross-sectional and longitudinal studies. Additional cross-laboratory studies with rigorous methodologic and statistical reporting, adequate sample size, and blinding are essential to accurately determine assay repeatability and replicability as well as the relation between TL measurement methods.
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Affiliation(s)
- Alyssa R. Lindrose
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
- * E-mail: (ARL); (SD)
| | | | - Renee I. Tristano
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Leila Kataria
- School of Science and Engineering, Tulane University, New Orleans, Louisiana, United States of America
| | - Shahinaz M. Gadalla
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Dan T. A. Eisenberg
- Department of Anthropology, Department of Biology, Center for Studies in Demography and Ecology, University of Washington, Seattle, Washington, United States of America
| | - Simon Verhulst
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Stacy Drury
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
- Tulane Brain Institute, Tulane University, New Orleans, Louisiana, United States of America
- Department of Pediatrics, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
- * E-mail: (ARL); (SD)
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23
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Jebaraj BMC, Stilgenbauer S. Telomere Dysfunction in Chronic Lymphocytic Leukemia. Front Oncol 2021; 10:612665. [PMID: 33520723 PMCID: PMC7844343 DOI: 10.3389/fonc.2020.612665] [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: 09/30/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022] Open
Abstract
Telomeres are nucleprotein structures that cap the chromosomal ends, conferring genomic stability. Alterations in telomere maintenance and function are associated with tumorigenesis. In chronic lymphocytic leukemia (CLL), telomere length is an independent prognostic factor and short telomeres are associated with adverse outcome. Though telomere length associations have been suggested to be only a passive reflection of the cell’s replication history, here, based on published findings, we suggest a more dynamic role of telomere dysfunction in shaping the disease course. Different members of the shelterin complex, which form the telomere structure have deregulated expression and POT1 is recurrently mutated in about 3.5% of CLL. In addition, cases with short telomeres have higher telomerase (TERT) expression and activity. TERT activation and shelterin deregulation thus may be pivotal in maintaining the minimal telomere length necessary to sustain survival and proliferation of CLL cells. On the other hand, activation of DNA damage response and repair signaling at dysfunctional telomeres coupled with checkpoint deregulation, leads to terminal fusions and genomic complexity. In summary, multiple components of the telomere system are affected and they play an important role in CLL pathogenesis, progression, and clonal evolution. However, processes leading to shelterin deregulation as well as cell intrinsic and microenvironmental factors underlying TERT activation are poorly understood. The present review comprehensively summarizes the complex interplay of telomere dysfunction in CLL and underline the mechanisms that are yet to be deciphered.
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Affiliation(s)
| | - Stephan Stilgenbauer
- Department of Internal Medicine III, University of Ulm, Ulm, Germany.,Klinik für Innere Medizin I, Universitätsklinikum des Saarlandes, Homburg, Germany
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24
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Alhendi ASN, Royle NJ. The absence of (TCAGGG) n repeats in some telomeres, combined with variable responses to NR2F2 depletion, suggest that this nuclear receptor plays an indirect role in the alternative lengthening of telomeres. Sci Rep 2020; 10:20597. [PMID: 33244044 PMCID: PMC7691514 DOI: 10.1038/s41598-020-77606-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 11/04/2020] [Indexed: 12/26/2022] Open
Abstract
The alternative lengthening of telomeres (ALT) facilitates telomere lengthening by a DNA strand invasion and copying mechanism. The nuclear receptors (NRs), NR2F2 and NR2C2, can bind to (TCAGGG)n variant repeats within telomeres and it has been proposed that this facilitates telomere interactions in ALT+ cells. Here we show that the frequency of cells with detectable NR2F2 and NR2C2 nuclear foci varies considerably between ALT+ cell lines and does not correlate with the level of protein expression. In addition, four of five ALT+ cell lines lack (TCAGGG)n repeats in some telomeres, indicating that direct NR binding does not play a role in ALT at these telomeres. NR2F2-depletion altered the abundance of C-circles and APBs but the direction of the response was inconsistent between three ALT+ cell lines. Moreover, transcriptome analysis following NR2F2-depletion in the ALT+ cell lines revealed different very responses. For example, NR2F2-depletion down-regulated many genes in U2OS cells, consistent with the cell cycle arrest and changes to ALT markers, but these features were not shared by the other two ALT+ cell lines. Among 86 ALT-associated genes, only MND1 showed consistent down-regulation across three NR2F2-depleted ALT+ cell lines. Altogether our data suggest that NR2F2 does not play a direct role in ALT and we speculate about an alternative role for this NR in a DNA damage response at telomeres.
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Affiliation(s)
- Ahmed S N Alhendi
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 3HE, UK
| | - Nicola J Royle
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 3HE, UK.
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25
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Abstract
Next-generation sequencing technologies allowed sequencing of thousands of genomes. However, there are genomic regions that remain difficult to characterize, including telomeres, centromeres, and other low-complexity regions, as well as transposable elements and endogenous viruses. Human herpesvirus 6A and 6B (HHV-6A and HHV-6B) are closely related viruses that infect most humans and can integrate their genomes into the telomeres of infected cells. Integration also occurs in germ cells, meaning that the virus can be inherited and result in individuals harboring the virus in every cell of their body. The integrated virus can reactivate and cause disease in humans. While it is well established that the virus resides in the telomere region, the integration locus is poorly defined due to the low sequence complexity (TTAGGG)n of telomeres that cannot be easily resolved through sequencing. We therefore employed genome imaging of the integrated HHV-6A and HHV-6B genomes using whole-genome optical site mapping technology. Using this technology, we identified which chromosome arm harbors the virus genome and obtained a high-resolution map of the integration loci of multiple patients. Surprisingly, this revealed long telomere sequences at the virus-subtelomere junction that were previously missed using PCR-based approaches. Contrary to what was previously thought, our technique revealed that the telomere lengths of chromosomes harboring the integrated virus genome were comparable to the other chromosomes. Taken together, our data shed light on the genetic structure of the HHV-6A and HHV-6B integration locus, demonstrating the utility of optical mapping for the analysis of genomic regions that are difficult to sequence.
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26
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Nguyen TQN, Lim KW, Phan AT. Folding Kinetics of G-Quadruplexes: Duplex Stem Loops Drive and Accelerate G-Quadruplex Folding. J Phys Chem B 2020; 124:5122-5130. [DOI: 10.1021/acs.jpcb.0c02548] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Thi Quynh Ngoc Nguyen
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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27
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Bajaj S, Kumar MS, Peters GJ, Mayur YC. Targeting telomerase for its advent in cancer therapeutics. Med Res Rev 2020; 40:1871-1919. [PMID: 32391613 DOI: 10.1002/med.21674] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 12/24/2022]
Abstract
Telomerase has emerged as an important primary target in anticancer therapy. It is a distinctive reverse transcriptase enzyme, which extends the length of telomere at the 3' chromosomal end, and uses telomerase reverse transcriptase (TERT) and telomerase RNA template-containing domains. Telomerase has a vital role and is a contributing factor in human health, mainly affecting cell aging and cell proliferation. Due to its unique feature, it ensures unrestricted cell proliferation in malignancy and plays a major role in cancer disease. The development of telomerase inhibitors with increased specificity and better pharmacokinetics is being considered to design and develop newer potent anticancer agents. Use of natural and synthetic compounds for the inhibition of telomerase activity can lead to an opening of new vistas in cancer treatment. This review details about the telomerase biochemistry, use of natural and synthetic compounds; vaccines and oncolytic virus in therapy that suppress the telomerase activity. We have discussed structure-activity relationships of various natural and synthetic telomerase inhibitors to help medicinal chemists and chemical biology researchers with a ready reference and updated status of their clinical trials. Suppression of human TERT (hTERT) activity through inhibition of hTERT promoter is an important approach for telomerase inhibition.
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Affiliation(s)
| | | | - G J Peters
- Department of Medical Oncology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Y C Mayur
- SPPSPTM, SVKM's NMIMS, Mumbai, India
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28
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Alaguponniah S, Velayudhan Krishna D, Paul S, Christyraj JRSS, Nallaperumal K, Sivasubramaniam S. Finding of novel telomeric repeats and their distribution in the human genome. Genomics 2020; 112:3565-3570. [PMID: 32320819 DOI: 10.1016/j.ygeno.2020.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 02/15/2020] [Accepted: 04/15/2020] [Indexed: 11/16/2022]
Abstract
Telomeres, the nucleoprotein structures, located at the end of the chromosomes are correlated with cancer and aging. The accelerated telomere attrition can accelerate human aging and leads to the progression of several cancers. Our work describes the finding of two novel telomeric repeats "CACAGA" and "TCTCTGCGCCTGCGCCGGCGCGGCGCGCC" and demonstrates their distribution in human chromosomes compare to the reported telomeric repeat TTAGGG. Simultaneously, the distance between the adjacent telomeric repeats (loop) was determined and the presence of shorter loops in the telomeric regions might address the correlation between the telomere attrition and senescence condition in human.
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Affiliation(s)
- Sathyalakshmi Alaguponniah
- Centre for Information Technology & Engineering, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu 627012, India
| | - Deepa Velayudhan Krishna
- Centre for Information Technology & Engineering, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu 627012, India
| | - Sayan Paul
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu 627012, India
| | - Johnson Retnaraj Samuel Selvan Christyraj
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu 627012, India; Centre for Nanoscience and Nanotechnology, Sathyabama Institute of Science and Technology, Chennai, Tamilnadu 600 119, India
| | - Krishnan Nallaperumal
- Centre for Information Technology & Engineering, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu 627012, India
| | - Sudhakar Sivasubramaniam
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu 627012, India.
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29
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Sieverling L, Hong C, Koser SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortés-Ciriano I, Xi R, Kabbe R, Park PJ, Eils R, Schlesner M, Brors B, Rippe K, Jones DTW, Feuerbach L. Genomic footprints of activated telomere maintenance mechanisms in cancer. Nat Commun 2020; 11:733. [PMID: 32024817 PMCID: PMC7002710 DOI: 10.1038/s41467-019-13824-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 11/26/2019] [Indexed: 12/14/2022] Open
Abstract
Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the telomere content of tumors with ATRX or DAXX mutations (ATRX/DAXXtrunc) is increased, tumors with TERT modifications show a moderate decrease of telomere content. One quarter of all tumor samples contain somatic integrations of telomeric sequences into non-telomeric DNA. This fraction is increased to 80% prevalence in ATRX/DAXXtrunc tumors, which carry an aberrant telomere variant repeat (TVR) distribution as another genomic marker. The latter feature includes enrichment or depletion of the previously undescribed singleton TVRs TTCGGG and TTTGGG, respectively. Our systematic analysis provides new insight into the recurrent genomic alterations associated with telomere maintenance mechanisms in cancer.
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Affiliation(s)
- Lina Sieverling
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Chen Hong
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Sandra D Koser
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Philip Ginsbach
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Kortine Kleinheinz
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, 69120, Heidelberg, Germany
| | - Barbara Hutter
- German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Delia M Braun
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, 69120, Heidelberg, Germany
| | - Isidro Cortés-Ciriano
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Department of Chemistry, Centre for Molecular Science Informatics, University of Cambridge, Cambridge, CB2 1EW, UK
- Ludwig Center at Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Ruibin Xi
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing, 100871, China
| | - Rolf Kabbe
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Ludwig Center at Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, 69120, Heidelberg, Germany
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, 69120, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lars Feuerbach
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
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30
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Sommer A, Royle NJ. ALT: A Multi-Faceted Phenomenon. Genes (Basel) 2020; 11:E133. [PMID: 32012790 PMCID: PMC7073516 DOI: 10.3390/genes11020133] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/17/2020] [Accepted: 01/22/2020] [Indexed: 01/13/2023] Open
Abstract
One of the hallmarks of cancer cells is their indefinite replicative potential, made possible by the activation of a telomere maintenance mechanism (TMM). The majority of cancers reactivate the reverse transcriptase, telomerase, to maintain their telomere length but a minority (10% to 15%) utilize an alternative lengthening of telomeres (ALT) pathway. Here, we review the phenotypes and molecular markers specific to ALT, and investigate the significance of telomere mutations and sequence variation in ALT cell lines. We also look at the recent advancements in understanding the different mechanisms behind ALT telomere elongation and finally, the progress made in identifying potential ALT-targeted therapies, including those already in use for the treatment of both hematological and solid tumors.
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Affiliation(s)
| | - Nicola J. Royle
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK;
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31
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Nersisyan L, Hopp L, Loeffler-Wirth H, Galle J, Loeffler M, Arakelyan A, Binder H. Telomere Length Maintenance and Its Transcriptional Regulation in Lynch Syndrome and Sporadic Colorectal Carcinoma. Front Oncol 2019; 9:1172. [PMID: 31750255 PMCID: PMC6848383 DOI: 10.3389/fonc.2019.01172] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 10/18/2019] [Indexed: 12/14/2022] Open
Abstract
Background: Activation of telomere maintenance mechanisms (TMMs) is a hallmark of most cancers, and is required to prevent genome instability and to establish cellular immortality through reconstitution of capping of chromosome ends. TMM depends on the cancer type. Comparative studies linking tumor biology and TMM have potential impact for evaluating cancer onset and development. Methods: We have studied alterations of telomere length, their sequence composition and transcriptional regulation in mismatch repair deficient colorectal cancers arising in Lynch syndrome (LS-CRC) and microsatellite instable (MSI) sporadic CRC (MSI s-CRC), and for comparison, in microsatellite stable (MSS) s-CRC and in benign colon mucosa. Our study applied bioinformatics analysis of whole genome DNA and RNA sequencing data and a pathway model to study telomere length alterations and the potential effect of the "classical" telomerase (TEL-) and alternative (ALT-) TMM using transcriptomic signatures. Results: We have found progressive decrease of mean telomere length in all cancer subtypes compared with reference systems. Our results support the view that telomere attrition is an early event in tumorigenesis. TMM gets activated in all tumors studied due to concerted overexpression of a large fraction of genes with direct relation to telomere function, where only a very small fraction of them showed recurrent mutations. TEL-related transcriptional state was dominating in all CRC subtypes, showing, however, subtype-specific activation patterns; while contribution of the ALT-TMM was slightly more prominent in the hypermutated MSI s-CRC and LS-CRC. TEL-TMM is mainly activated by over-expression of DKC1 and/or TERT genes and their interaction partners, where DKC1 is more prominent in MSS than in MSI s-CRC and can serve as a transcriptomic marker of TMM activity. Conclusions: Our results suggest that transcriptional patterns are indicative for TMM pathway activation with subtle differences between TEL and ALT mechanisms in a CRC subtype-specific fashion. Sequencing data potentially provide a suited measure to study alterations of telomere length and of underlying transcriptional regulation. Further studies are needed to improve this method.
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Affiliation(s)
- Lilit Nersisyan
- Group of Bioinformatics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | - Lydia Hopp
- Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Henry Loeffler-Wirth
- Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Jörg Galle
- Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Markus Loeffler
- Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany.,Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany
| | - Arsen Arakelyan
- Group of Bioinformatics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | - Hans Binder
- Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany
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32
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Lee M, Teber ET, Holmes O, Nones K, Patch AM, Dagg RA, Lau LMS, Lee JH, Napier CE, Arthur JW, Grimmond SM, Hayward NK, Johansson PA, Mann GJ, Scolyer RA, Wilmott JS, Reddel RR, Pearson JV, Waddell N, Pickett HA. Telomere sequence content can be used to determine ALT activity in tumours. Nucleic Acids Res 2019; 46:4903-4918. [PMID: 29718321 PMCID: PMC6007693 DOI: 10.1093/nar/gky297] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 04/10/2018] [Indexed: 01/16/2023] Open
Abstract
The replicative immortality of human cancer cells is achieved by activation of a telomere maintenance mechanism (TMM). To achieve this, cancer cells utilise either the enzyme telomerase, or the Alternative Lengthening of Telomeres (ALT) pathway. These distinct molecular pathways are incompletely understood with respect to activation and propagation, as well as their associations with clinical outcomes. We have identified significant differences in the telomere repeat composition of tumours that use ALT compared to tumours that do not. We then employed a machine learning approach to stratify tumours according to telomere repeat content with an accuracy of 91.6%. Importantly, this classification approach is applicable across all tumour types. Analysis of pathway mutations that were under-represented in ALT tumours, across 1,075 tumour samples, revealed that the autophagy, cell cycle control of chromosomal replication, and transcriptional regulatory network in embryonic stem cells pathways are involved in the survival of ALT tumours. Overall, our approach demonstrates that telomere sequence content can be used to stratify ALT activity in cancers, and begin to define the molecular pathways involved in ALT activation.
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Affiliation(s)
- Michael Lee
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Erdahl T Teber
- Bioinformatics Unit, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Oliver Holmes
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Katia Nones
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Ann-Marie Patch
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Rebecca A Dagg
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Loretta M S Lau
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Joyce H Lee
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Christine E Napier
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Jonathan W Arthur
- Bioinformatics Unit, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Sean M Grimmond
- University of Melbourne Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Nicholas K Hayward
- Melanoma Institute Australia, University of Sydney, North Sydney, New South Wales, Australia.,Oncogenomics Group, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Peter A Johansson
- Oncogenomics Group, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Graham J Mann
- Melanoma Institute Australia, University of Sydney, North Sydney, New South Wales, Australia.,Centre for Cancer Research, Westmead Institute for Medical Research, University of Sydney, Westmead, New South Wales, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, University of Sydney, North Sydney, New South Wales, Australia.,Discipline of Pathology, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia.,Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, New South Wales, Australia
| | - James S Wilmott
- Melanoma Institute Australia, University of Sydney, North Sydney, New South Wales, Australia.,Discipline of Pathology, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Roger R Reddel
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - John V Pearson
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Nicola Waddell
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
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33
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Abstract
Many recent advances have emerged in the telomere and telomerase fields. This Timeline article highlights the key advances that have expanded our views on the mechanistic underpinnings of telomeres and telomerase and their roles in ageing and disease. Three decades ago, the classic view was that telomeres protected the natural ends of linear chromosomes and that telomerase was a specific telomere-terminal transferase necessary for the replication of chromosome ends in single-celled organisms. While this concept is still correct, many diverse fields associated with telomeres and telomerase have substantially matured. These areas include the discovery of most of the key molecular components of telomerase, implications for limits to cellular replication, identification and characterization of human genetic disorders that result in premature telomere shortening, the concept that inhibiting telomerase might be a successful therapeutic strategy and roles for telomeres in regulating gene expression. We discuss progress in these areas and conclude with challenges and unanswered questions in the field.
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Affiliation(s)
- Jerry W Shay
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Woodring E Wright
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA
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Ediriweera MK, Tennekoon KH, Samarakoon SR. In vitro assays and techniques utilized in anticancer drug discovery. J Appl Toxicol 2018; 39:38-71. [DOI: 10.1002/jat.3658] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/01/2018] [Accepted: 06/04/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Meran Keshawa Ediriweera
- Institute of Biochemistry, Molecular Biology and Biotechnology; University of Colombo; Colombo 03 Sri Lanka
| | - Kamani Hemamala Tennekoon
- Institute of Biochemistry, Molecular Biology and Biotechnology; University of Colombo; Colombo 03 Sri Lanka
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Lorenzi M, Bonassi S, Lorenzi T, Giovannini S, Bernabei R, Onder G. A review of telomere length in sarcopenia and frailty. Biogerontology 2018; 19:209-221. [PMID: 29549539 DOI: 10.1007/s10522-018-9749-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/23/2018] [Indexed: 12/16/2022]
Abstract
Sarcopenia and frailty are associated with several important health-related adverse events, including disability, loss of independence, institutionalization and mortality. Sarcopenia can be considered a biological substrate of frailty, and the prevalence of both these conditions progressively increases with age. Telomeres are nucleoprotein structures located at the end of linear chromosomes and implicated in cellular ageing, shorten with age, and are associated with various age-related diseases. In addition, telomere length (TL) is widely considered a molecular/cellular hallmark of the ageing process. This narrative review summarizes the knowledge about telomeres and analyzes for the first time a possible association of TL with sarcopenia and frailty. The overview provided by the present review suggests that leukocyte TL as single measurement, calculated by quantitative real-time polymerase chain reaction (qRT-PCR), cannot be considered a meaningful biological marker for complex, multidimensional age-related conditions, such as sarcopenia and frailty. Panels of biomarkers, including TL, may provide more accurate assessment and prediction of outcomes in these geriatric syndromes in elderly people.
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Affiliation(s)
- Maria Lorenzi
- Laboratory of Biogerontology, Department of Geriatrics, Neurosciences and Orthopedics, A. Gemelli Foundation, Catholic University of the Sacred Heart, School of Medicine, L.go F. Vito 1, 00168, Rome, Italy.
| | - Stefano Bonassi
- Unit of Clinical and Molecular Epidemiology, IRCCS San Raffaele Pisana, Via di Val Cannuta 247, 00166, Rome, Italy
| | - Teresa Lorenzi
- Department of Experimental and Clinical Medicine, Section of Neuroscience and Cell Biology, School of Medicine, Università Politecnica delle Marche, Via Tronto 10/A, 60020, Ancona, Italy
| | - Silvia Giovannini
- Laboratory of Biogerontology, Department of Geriatrics, Neurosciences and Orthopedics, A. Gemelli Foundation, Catholic University of the Sacred Heart, School of Medicine, L.go F. Vito 1, 00168, Rome, Italy
| | - Roberto Bernabei
- Department of Geriatrics, Neurosciences and Orthopedics, A. Gemelli Foundation, Catholic University of the Sacred Heart, School of Medicine, L.go F. Vito 1, 00168, Rome, Italy
| | - Graziano Onder
- Department of Geriatrics, Neurosciences and Orthopedics, A. Gemelli Foundation, Catholic University of the Sacred Heart, School of Medicine, L.go F. Vito 1, 00168, Rome, Italy
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Hastings WJ, Shalev I, Belsky DW. Translating Measures of Biological Aging to Test Effectiveness of Geroprotective Interventions: What Can We Learn from Research on Telomeres? Front Genet 2017; 8:164. [PMID: 29213278 PMCID: PMC5702647 DOI: 10.3389/fgene.2017.00164] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 10/16/2017] [Indexed: 11/13/2022] Open
Abstract
Intervention studies in animals suggest molecular changes underlying age-related disease and disability can be slowed or reversed. To speed translation of these so-called "geroprotective" therapies to prevent age-related disease and disability in humans, biomarkers are needed that can track changes in the rate of human aging over the course of intervention trials. Algorithm methods that measure biological processes of aging from combinations of DNA methylation marks or clinical biomarkers show promise. To identify next steps for establishing utility of these algorithm-based measures of biological aging for geroprotector trials, we considered the history a candidate biomarker of aging that has received substantial research attention, telomere length. Although telomere length possesses compelling biology to recommend it as a biomarker of aging, mixed research findings have impeded clinical and epidemiologic translation. Strengths of telomeres that should be established for algorithm biomarkers of aging are correlation with chronological age across the lifespan, prediction of disease, disability, and early death, and responsiveness to risk and protective exposures. Key challenges in telomere research that algorithm biomarkers of aging must address are measurement precision and reliability, establishing links between longitudinal rates of change across repeated measurements and aging outcomes, and clarity over whether the biomarker is a causal mechanism of aging. These strengths and challenges suggest a research agenda to advance translation of algorithm-based aging biomarkers: establish validity in young-adult and midlife individuals; test responsiveness to exposures that shorten or extend healthy lifespan; and conduct repeated-measures longitudinal studies to test differential rates of change.
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Affiliation(s)
- Waylon J Hastings
- Department of Biobehavioral Health, Pennsylvania State University, State College, PA, United States
| | - Idan Shalev
- Department of Biobehavioral Health, Pennsylvania State University, State College, PA, United States
| | - Daniel W Belsky
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, United States.,Center for the Study of Aging and Human Development, Duke University, Durham, NC, United States
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Abstract
Aberrations in telomere biology are among the earliest events in prostate cancer tumorigenesis and continue during tumour progression. Substantial telomere shortening occurs in prostate cancer cells and high-grade prostatic intraepithelial neoplasia. Not all mechanisms of telomere shortening are understood, but oxidative stress from local inflammation might accelerate prostatic telomere loss. Critically short telomeres can drive the accumulation of tumour-promoting genomic alterations; however, continued telomere erosion is unsustainable and must be mitigated to ensure cancer cell survival and unlimited replication potential. Prostate cancers predominantly maintain telomeres by activating telomerase, but alternative mechanisms of telomere extension can occur in metastatic disease. Telomerase activity and telomere length assessment might be useful in prostate cancer diagnosis and prognosis. Telomere shortening in normal stromal cells has been associated with prostate cancer, whereas variable telomere lengths in prostate cancer cells and telomere shortening in cancer-associated stromal cells correlated with lethal disease. Single-agent telomerase-targeted treatments for solid cancers were ineffective in clinical trials but have not been investigated in prostate cancer and might be useful in combination with established regimens. Telomere-directed strategies have not been explored as extensively. Telomere deprotection strategies have the advantage of being effective in both telomerase-dependent and telomerase-independent cancers. Disruption of androgen receptor function in prostate cancer cells results in telomere dysfunction, indicating telomeres and telomerase as potential therapeutic targets in prostate cancer.
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Erlendson AA, Friedman S, Freitag M. A Matter of Scale and Dimensions: Chromatin of Chromosome Landmarks in the Fungi. Microbiol Spectr 2017; 5:10.1128/microbiolspec.FUNK-0054-2017. [PMID: 28752814 PMCID: PMC5536859 DOI: 10.1128/microbiolspec.funk-0054-2017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Indexed: 02/06/2023] Open
Abstract
Chromatin and chromosomes of fungi are highly diverse and dynamic, even within species. Much of what we know about histone modification enzymes, RNA interference, DNA methylation, and cell cycle control was first addressed in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Aspergillus nidulans, and Neurospora crassa. Here, we examine the three landmark regions that are required for maintenance of stable chromosomes and their faithful inheritance, namely, origins of DNA replication, telomeres and centromeres. We summarize the state of recent chromatin research that explains what is required for normal function of these specialized chromosomal regions in different fungi, with an emphasis on the silencing mechanism associated with subtelomeric regions, initiated by sirtuin histone deacetylases and histone H3 lysine 27 (H3K27) methyltransferases. We explore mechanisms for the appearance of "accessory" or "conditionally dispensable" chromosomes and contrast what has been learned from studies on genome-wide chromosome conformation capture in S. cerevisiae, S. pombe, N. crassa, and Trichoderma reesei. While most of the current knowledge is based on work in a handful of genetically and biochemically tractable model organisms, we suggest where major knowledge gaps remain to be closed. Fungi will continue to serve as facile organisms to uncover the basic processes of life because they make excellent model organisms for genetics, biochemistry, cell biology, and evolutionary biology.
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Affiliation(s)
- Allyson A. Erlendson
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
| | - Steven Friedman
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
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Jahn A, Rane G, Paszkowski-Rogacz M, Sayols S, Bluhm A, Han CT, Draškovič I, Londoño-Vallejo JA, Kumar AP, Buchholz F, Butter F, Kappei D. ZBTB48 is both a vertebrate telomere-binding protein and a transcriptional activator. EMBO Rep 2017; 18:929-946. [PMID: 28500257 PMCID: PMC5452029 DOI: 10.15252/embr.201744095] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 03/31/2017] [Accepted: 04/18/2017] [Indexed: 11/09/2022] Open
Abstract
Telomeres constitute the ends of linear chromosomes and together with the shelterin complex form a structure essential for genome maintenance and stability. In addition to the constitutive binding of the shelterin complex, other direct, yet more transient interactions are mediated by the CST complex and HOT1/HMBOX1, while subtelomeric variant repeats are recognized by NR2C/F transcription factors. Recently, the Kruppel-like zinc finger protein ZBTB48/HKR3/TZAP has been described as a novel telomere-associated factor in the vertebrate lineage. Here, we show that ZBTB48 binds directly both to telomeric and to subtelomeric variant repeat sequences. ZBTB48 is found at telomeres of human cancer cells regardless of the mode of telomere maintenance and it acts as a negative regulator of telomere length. In addition to its telomeric function, we demonstrate through a combination of RNAseq, ChIPseq and expression proteomics experiments that ZBTB48 acts as a transcriptional activator on a small set of target genes, including mitochondrial fission process 1 (MTFP1). This discovery places ZBTB48 at the interface of telomere length regulation, transcriptional control and mitochondrial metabolism.
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Affiliation(s)
- Arne Jahn
- Medical Systems Biology, UCC, University Hospital and Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany.,Institute for Clinical Genetics, Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Grishma Rane
- Cancer Science Institute of Singapore, National University of Singapore, Singapore City, Singapore
| | - Maciej Paszkowski-Rogacz
- Medical Systems Biology, UCC, University Hospital and Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Sergi Sayols
- Institute of Molecular Biology (IMB) gGmbH, Mainz, Germany
| | - Alina Bluhm
- Institute of Molecular Biology (IMB) gGmbH, Mainz, Germany
| | - Chung-Ting Han
- Institute of Molecular Biology (IMB) gGmbH, Mainz, Germany
| | - Irena Draškovič
- Telomeres & Cancer Laboratory, UMR3244, Institut Curie-CNRS-UPMC, Paris Cedex 05, France
| | | | - Alan Prem Kumar
- Cancer Science Institute of Singapore, National University of Singapore, Singapore City, Singapore.,Department of Pharmacology, Yong Loo Lin School of Medicine National University of Singapore, Singapore City, Singapore.,Curtin Medical School, Faculty of Health Sciences Curtin University, Perth, Australia
| | - Frank Buchholz
- Medical Systems Biology, UCC, University Hospital and Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany .,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK) Partner Site Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB) gGmbH, Mainz, Germany
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore City, Singapore
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Márquez-Ruiz AB, González-Herrera L, Valenzuela A. Usefulness of telomere length in DNA from human teeth for age estimation. Int J Legal Med 2017; 132:353-359. [DOI: 10.1007/s00414-017-1595-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 04/19/2017] [Indexed: 01/03/2023]
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Bhaumik P, Bhattacharya M, Ghosh P, Ghosh S, Kumar Dey S. Telomere length analysis in Down syndrome birth. Mech Ageing Dev 2017; 164:20-26. [PMID: 28327364 DOI: 10.1016/j.mad.2017.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 02/27/2017] [Accepted: 03/14/2017] [Indexed: 11/19/2022]
Abstract
Human reproductive fitness depends upon telomere chemistry. Maternal age, meiotic nondisjunction error and telomere length of mother of trisomic child are someway associated. Reports exhibiting maternal inheritance of telomere length in Down syndrome child are very scanty. To investigate this, we collected peripheral blood from 170 mothers of Down syndrome child and 186 age matched mothers of euploid child with their newly born babies. Telomere length was measured by restriction digestion - southern blotting technique. Meiotic nondisjunction error was detected by STR genotyping. Subjects are classified by age (old >35 years and young ˂35 years) and by meiotic error (MI and MII). Linear regression was run to explore the age - telomere length relationship in each maternal groups. The study reveals that with age, telomere erodes in length. Old MII mothers carry the shortest (p˂0.001), control mothers have the longest telomere and MI lies in between. Babies from older mother have longer telomere (p˂0.001) moreover; telomeres are longer in Down syndrome babies than control babies (p˂0.001). To conclude, this study represents not only the relation between maternal aging and telomere length but also explore the maternal heritability of telomere length in families with Down syndrome child.
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Affiliation(s)
- Pranami Bhaumik
- Department of Biotechnology, School of Biotechnology and Biological Sciences. Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly known as West Bengal University of Technology) BF-142, Salt Lake City, Sector I, Kolkata, West Bengal, 700064, India
| | - Mandar Bhattacharya
- Department of Biotechnology, School of Biotechnology and Biological Sciences. Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly known as West Bengal University of Technology) BF-142, Salt Lake City, Sector I, Kolkata, West Bengal, 700064, India
| | - Priyanka Ghosh
- Department of Biotechnology, School of Biotechnology and Biological Sciences. Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly known as West Bengal University of Technology) BF-142, Salt Lake City, Sector I, Kolkata, West Bengal, 700064, India
| | - Sujay Ghosh
- Cytogenetics and Genomics Research Unit, Department of Zoology, University of Calcutta,(Ballygunge Science college campus), 35 Ballygunge Circular Road., Kolkata, West Bengal, 700019, India
| | - Subrata Kumar Dey
- Department of Biotechnology, School of Biotechnology and Biological Sciences. Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly known as West Bengal University of Technology) BF-142, Salt Lake City, Sector I, Kolkata, West Bengal, 700064, India.
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42
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Bondarev IE, Khavinson VK. Suppression of alternative telomere lengthening in cancer cells with reverse transcriptase inhibitors. ADVANCES IN GERONTOLOGY 2016. [DOI: 10.1134/s2079057016040020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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43
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Menyhárt O, Harami-Papp H, Sukumar S, Schäfer R, Magnani L, de Barrios O, Győrffy B. Guidelines for the selection of functional assays to evaluate the hallmarks of cancer. Biochim Biophys Acta Rev Cancer 2016; 1866:300-319. [PMID: 27742530 DOI: 10.1016/j.bbcan.2016.10.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/06/2016] [Accepted: 10/08/2016] [Indexed: 01/05/2023]
Abstract
The hallmarks of cancer capture the most essential phenotypic characteristics of malignant transformation and progression. Although numerous factors involved in this multi-step process are still unknown to date, an ever-increasing number of mutated/altered candidate genes are being identified within large-scale cancer genomic projects. Therefore, investigators need to be aware of available and appropriate techniques capable of determining characteristic features of each hallmark. We review the methods tailored to experimental cancer researchers to evaluate cell proliferation, programmed cell death, replicative immortality, induction of angiogenesis, invasion and metastasis, genome instability, and reprogramming of energy metabolism. Selecting the ideal method is based on the investigator's goals, available equipment and also on financial constraints. Multiplexing strategies enable a more in-depth data collection from a single experiment - obtaining several results from a single procedure reduces variability and saves time and relative cost, leading to more robust conclusions compared to a single end point measurement. Each hallmark possesses characteristics that can be analyzed by immunoblot, RT-PCR, immunocytochemistry, immunoprecipitation, RNA microarray or RNA-seq. In general, flow cytometry, fluorescence microscopy, and multiwell readers are extremely versatile tools and, with proper sample preparation, allow the detection of a vast number of hallmark features. Finally, we also provide a list of hallmark-specific genes to be measured in transcriptome-level studies. Although our list is not exhaustive, we provide a snapshot of the most widely used methods, with an emphasis on methods enabling the simultaneous evaluation of multiple hallmark features.
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Affiliation(s)
- Otília Menyhárt
- MTA TTK Lendület Cancer Biomarker Research Group, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
| | | | - Saraswati Sukumar
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Reinhold Schäfer
- German Cancer Consortium (DKTK), DKFZ, Im Neuenheimer Feld 280, D-69120 Heidelberg and Charité Comprehensive Cancer Center, Invalidenstr. 80, D-10115 Berlin, Germany
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Oriol de Barrios
- Group of Transcriptional Regulation of Gene Expression, Department of Oncology and Hematology, IDIBAPS, Barcelona, Spain
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Magyar tudósok körútja 2, H-1117 Budapest, Hungary; 2nd Department of Pediatrics, Semmelweis University, H-1094 Budapest, Hungary.
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Jha NS, Mishra S, Mamidi AS, Mishra A, Jha SK, Surolia A. Targeting human telomeric G-quadruplex DNA with curcumin and its synthesized analogues under molecular crowding conditions. RSC Adv 2016. [DOI: 10.1039/c5ra17390f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The formation of telomeric G-quadruplexes has been shown to inhibit telomerase activity.
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Affiliation(s)
- Niki S. Jha
- Department of Chemistry
- National Institute of Technology
- Patna-800005
- India
| | | | | | - Archita Mishra
- Molecular Biophysics Unit
- Indian Institute of Science
- Bangalore 560012
- India
| | | | - Avadhesha Surolia
- Molecular Biophysics Unit
- Indian Institute of Science
- Bangalore 560012
- India
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Karasawa K, Arakawa H. Detection of telomerase activity using microchip electrophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 993-994:14-9. [DOI: 10.1016/j.jchromb.2015.04.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 04/17/2015] [Accepted: 04/20/2015] [Indexed: 10/23/2022]
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47
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Reddel RR. Telomere maintenance mechanisms in cancer: clinical implications. Curr Pharm Des 2015; 20:6361-74. [PMID: 24975603 PMCID: PMC4262939 DOI: 10.2174/1381612820666140630101047] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 06/26/2014] [Indexed: 01/20/2023]
Abstract
The presence of immortal cell populations with an up-regulated telomere maintenance mechanism (TMM) is an almost universal characteristic of cancers, whereas normal somatic cells are unable to prevent proliferation-associated telomere shortening and have a limited proliferative potential. TMMs and related aspects of telomere structure and function therefore appear to be ideal targets for the development of anticancer therapeutics. Such treatments would be targeted to a specific cancer-related molecular abnormality, and also be broad-spectrum in that they would be expected to be potentially applicable to most cancers. However, the telomere biology of normal and malignant human cells is a relatively young research field with large numbers of unanswered questions, so the optimal design of TMM-targeted therapeutic approaches remains unclear. This review outlines the opportunities and challenges presented by telomeres and TMMs for clinical management of cancer.
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Affiliation(s)
- Roger R Reddel
- Children's Medical Research Institute, 214 Hawkesbury Road, Westmead, New South Wales 2145, Australia.
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48
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Nuclear-receptor-mediated telomere insertion leads to genome instability in ALT cancers. Cell 2015; 160:913-927. [PMID: 25723166 DOI: 10.1016/j.cell.2015.01.044] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 11/18/2014] [Accepted: 01/27/2015] [Indexed: 01/26/2023]
Abstract
The breakage-fusion-bridge cycle is a classical mechanism of telomere-driven genome instability in which dysfunctional telomeres are fused to other chromosomal extremities, creating dicentric chromosomes that eventually break at mitosis. Here, we uncover a distinct pathway of telomere-driven genome instability, specifically occurring in cells that maintain telomeres with the alternative lengthening of telomeres mechanism. We show that, in these cells, telomeric DNA is added to multiple discrete sites throughout the genome, corresponding to regions regulated by NR2C/F transcription factors. These proteins drive local telomere DNA addition by recruiting telomeric chromatin. This mechanism, which we name targeted telomere insertion (TTI), generates potential common fragile sites that destabilize the genome. We propose that TTI driven by NR2C/F proteins contributes to the formation of complex karyotypes in ALT tumors.
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49
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Koroleva AG, Evtushenko EV, Maximova NV, Vershinin AV, Sitnikova TY, Kirilchik SV. Length and structure of telomeric DNA in three species of Baikal gastropods (Caenogastropoda: Hydrobioidea: Benedictiidae). RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415030060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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50
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Abstract
Telomeres form protective caps at the ends of linear chromosomes to prevent nucleolytic degradation, end-to-end fusion, irregular recombination, and chromosomal instability. Telomeres are composed of repetitive DNA sequences (TTAGGG)n in humans, that are bound by specialized telomere binding proteins. Telomeres lose capping function in response to telomere shortening, which occurs during each division of cells that lack telomerase activity-the enzyme that can synthesize telomeres de novo. Telomeres have a dual role in cancer: telomere shortening can lead to induction of chromosomal instability and to the initiation of tumors, however, initiated tumors need to reactivate telomerase in order to stabilize chromosomes and to gain immortal growth capacity. In this review, we summarize current knowledge on the role of telomeres in the maintenance of chromosomal stability and carcinogenesis.
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