1
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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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2
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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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3
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Muyas F, Rodriguez MJG, Cascão R, Afonso A, Sauer CM, Faria CC, Cortés-Ciriano I, Flores I. The ALT pathway generates telomere fusions that can be detected in the blood of cancer patients. Nat Commun 2024; 15:82. [PMID: 38167290 PMCID: PMC10762111 DOI: 10.1038/s41467-023-44287-8] [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: 01/28/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
Telomere fusions (TFs) can trigger the accumulation of oncogenic alterations leading to malignant transformation and drug resistance. Despite their relevance in tumour evolution, our understanding of the patterns and consequences of TFs in human cancers remains limited. Here, we characterize the rates and spectrum of somatic TFs across >30 cancer types using whole-genome sequencing data. TFs are pervasive in human tumours with rates varying markedly across and within cancer types. In addition to end-to-end fusions, we find patterns of TFs that we mechanistically link to the activity of the alternative lengthening of telomeres (ALT) pathway. We show that TFs can be detected in the blood of cancer patients, which enables cancer detection with high specificity and sensitivity even for early-stage tumours and cancers of high unmet clinical need. Overall, we report a genomic footprint that enables characterization of the telomere maintenance mechanism of tumours and liquid biopsy analysis.
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Affiliation(s)
- Francesc Muyas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Rita Cascão
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Angela Afonso
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Carolin M Sauer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Claudia C Faria
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Department of Neurosurgery, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisboa, Portugal
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK.
| | - Ignacio Flores
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, 28029, Spain.
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, Madrid, 28049, Spain.
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4
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Stundon JL, Ijaz H, Gaonkar KS, Kaufman RS, Jin R, Karras A, Vaksman Z, Kim J, Corbett RJ, Lueder MR, Miller DP, Guo Y, Santi M, Li M, Lopez G, Storm PB, Resnick AC, Waanders AJ, MacFarland SP, Stewart DR, Diskin SJ, Rokita JL, Cole KA. Alternative lengthening of telomeres (ALT) in pediatric high-grade gliomas can occur without ATRX mutation and is enriched in patients with pathogenic germline mismatch repair (MMR) variants. Neuro Oncol 2023; 25:1331-1342. [PMID: 36541551 PMCID: PMC10326481 DOI: 10.1093/neuonc/noac278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND To achieve replicative immortality, most cancers develop a telomere maintenance mechanism, such as reactivation of telomerase or alternative lengthening of telomeres (ALT). There are limited data on the prevalence and clinical significance of ALT in pediatric brain tumors, and ALT-directed therapy is not available. METHODS We performed C-circle analysis (CCA) on 579 pediatric brain tumors that had corresponding tumor/normal whole genome sequencing through the Open Pediatric Brain Tumor Atlas (OpenPBTA). We detected ALT in 6.9% (n = 40/579) of these tumors and completed additional validation by ultrabright telomeric foci in situ on a subset of these tumors. We used CCA to validate TelomereHunter for computational prediction of ALT status and focus subsequent analyses on pediatric high-grade gliomas (pHGGs) Finally, we examined whether ALT is associated with recurrent somatic or germline alterations. RESULTS ALT is common in pHGGs (n = 24/63, 38.1%), but occurs infrequently in other pediatric brain tumors (<3%). Somatic ATRX mutations occur in 50% of ALT+ pHGGs and in 30% of ALT- pHGGs. Rare pathogenic germline variants in mismatch repair (MMR) genes are significantly associated with an increased occurrence of ALT. CONCLUSIONS We demonstrate that ATRX is mutated in only a subset of ALT+ pHGGs, suggesting other mechanisms of ATRX loss of function or alterations in other genes may be associated with the development of ALT in these patients. We show that germline variants in MMR are associated with the development of ALT in patients with pHGG.
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Affiliation(s)
- Jennifer L Stundon
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania,USA
| | - Heba Ijaz
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania,USA
| | - Krutika S Gaonkar
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Rebecca S Kaufman
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Run Jin
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Anastasios Karras
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Zalman Vaksman
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Jung Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland,USA
| | - Ryan J Corbett
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Matthew R Lueder
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Daniel P Miller
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Yiran Guo
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Marilyn Li
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Gonzalo Lopez
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Phillip B Storm
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Adam C Resnick
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Angela J Waanders
- Division of Hematology, Oncology, NeuroOncology, and Stem Cell Transplant, Ann & Robert H Lurie Children’s Hospital of Chicago, Illinois,USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,USA
| | - Suzanne P MacFarland
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania,USA
| | - Douglas R Stewart
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland,USA
| | - Sharon J Diskin
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania,USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania,USA
| | - Jo Lynne Rokita
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Kristina A Cole
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania,USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania,USA
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5
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Raseley K, Jinwala Z, Zhang D, Xiao M. Single-Molecule Telomere Assay via Optical Mapping (SMTA-OM) Can Potentially Define the ALT Positivity of Cancer. Genes (Basel) 2023; 14:1278. [PMID: 37372458 DOI: 10.3390/genes14061278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Telomeres play an essential role in protecting the ends of linear chromosomes and maintaining the integrity of the human genome. One of the key hallmarks of cancers is their replicative immortality. As many as 85-90% of cancers activate the expression of telomerase (TEL+) as the telomere maintenance mechanism (TMM), and 10-15% of cancers utilize the homology-dependent repair (HDR)-based Alternative Lengthening of Telomere (ALT+) pathway. Here, we performed statistical analysis of our previously reported telomere profiling results from Single Molecule Telomere Assay via Optical Mapping (SMTA-OM), which is capable of quantifying individual telomeres from single molecules across all chromosomes. By comparing the telomeric features from SMTA-OM in TEL+ and ALT+ cancer cells, we demonstrated that ALT+ cancer cells display certain unique telomeric profiles, including increased fusions/internal telomere-like sequence (ITS+), fusions/internal telomere-like sequence loss (ITS-), telomere-free ends (TFE), super-long telomeres, and telomere length heterogeneity, compared to TEL+ cancer cells. Therefore, we propose that ALT+ cancer cells can be differentiated from TEL+ cancer cells using the SMTA-OM readouts as biomarkers. In addition, we observed variations in SMTA-OM readouts between different ALT+ cell lines that may potentially be used as biomarkers for discerning subtypes of ALT+ cancer and monitoring the response to cancer therapy.
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Affiliation(s)
- Kaitlin Raseley
- School of Biomedical Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Zeal Jinwala
- School of Biomedical Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Dong Zhang
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA
- Center for Cancer Research, New York Institute of Technology, Old Westbury, NY 11568, USA
| | - Ming Xiao
- School of Biomedical Engineering, Drexel University, Philadelphia, PA 19104, USA
- Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
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6
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Sohn EJ, Goralsky JA, Shay JW, Min J. The Molecular Mechanisms and Therapeutic Prospects of Alternative Lengthening of Telomeres (ALT). Cancers (Basel) 2023; 15:cancers15071945. [PMID: 37046606 PMCID: PMC10093677 DOI: 10.3390/cancers15071945] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 04/14/2023] Open
Abstract
As detailed by the end replication problem, the linear ends of a cell's chromosomes, known as telomeres, shorten with each successive round of replication until a cell enters into a state of growth arrest referred to as senescence. To maintain their immortal proliferation capacity, cancer cells must employ a telomere maintenance mechanism, such as telomerase activation or the Alternative Lengthening of Telomeres pathway (ALT). With only 10-15% of cancers utilizing the ALT mechanism, progress towards understanding its molecular components and associated hallmarks has only recently been made. This review analyzes the advances towards understanding the ALT pathway by: (1) detailing the mechanisms associated with engaging the ALT pathway as well as (2) identifying potential therapeutic targets of ALT that may lead to novel cancer therapeutic treatments. Collectively, these studies indicate that the ALT molecular mechanisms involve at least two distinct pathways induced by replication stress and damage at telomeres. We suggest exploiting tumor dependency on ALT is a promising field of study because it suggests new approaches to ALT-specific therapies for cancers with poorer prognosis. While substantial progress has been made in the ALT research field, additional progress will be required to realize these advances into clinical practices to treat ALT cancers and improve patient prognoses.
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Affiliation(s)
- Eric J Sohn
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Julia A Goralsky
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Jaewon Min
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
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7
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Sun H, Chen G, Guo B, Lv S, Yuan G. Potential clinical treatment prospects behind the molecular mechanism of alternative lengthening of telomeres (ALT). J Cancer 2023; 14:417-433. [PMID: 36860927 PMCID: PMC9969575 DOI: 10.7150/jca.80097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 12/25/2022] [Indexed: 02/04/2023] Open
Abstract
Normal somatic cells inevitably experience replicative stress and senescence during proliferation. Somatic cell carcinogenesis can be prevented in part by limiting the reproduction of damaged or old cells and removing them from the cell cycle [1, 2]. However, Cancer cells must overcome the issues of replication pressure and senescence as well as preserve telomere length in order to achieve immortality, in contrast to normal somatic cells [1, 2]. Although telomerase accounts for the bulk of telomere lengthening methods in human cancer cells, there is a non-negligible portion of telomere lengthening pathways that depend on alternative lengthening of telomeres (ALT) [3]. For the selection of novel possible therapeutic targets for ALT-related disorders, a thorough understanding of the molecular biology of these diseases is crucial [4]. The roles of ALT, typical ALT tumor cell traits, the pathophysiology and molecular mechanisms of ALT tumor disorders, such as adrenocortical carcinoma (ACC), are all summarized in this work. Additionally, this research compiles as many of its hypothetically viable but unproven treatment targets as it can (ALT-associated PML bodies (APB), etc.). This review is intended to contribute as much as possible to the development of research, while also trying to provide a partial information for prospective investigations on ALT pathways and associated diseases.
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Affiliation(s)
- Haolu Sun
- Department of Pathophysiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230011, China
| | - Guijuan Chen
- School of Environment and Chemical Engineering, Anhui Vocational and Technical College, Hefei, 230011, China
| | - Baochang Guo
- Rehabilitation Department of Traditional Chinese Medicine, 969 Hospital of the Joint Support Force of the Chinese People's Liberation Army, Hohhot, 010000, China
| | - Shushu Lv
- Department of Pathology, The First Affiliated Hospital of Huzhou University, Huzhou 313000, China
| | - Guojun Yuan
- School of Environment and Chemical Engineering, Anhui Vocational and Technical College, Hefei, 230011, China
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8
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Ballinger ML, Pattnaik S, Mundra PA, Zaheed M, Rath E, Priestley P, Baber J, Ray-Coquard I, Isambert N, Causeret S, van der Graaf WTA, Puri A, Duffaud F, Le Cesne A, Seddon B, Chandrasekar C, Schiffman JD, Brohl AS, James PA, Kurtz JE, Penel N, Myklebost O, Meza-Zepeda LA, Pickett H, Kansara M, Waddell N, Kondrashova O, Pearson JV, Barbour AP, Li S, Nguyen TL, Fatkin D, Graham RM, Giannoulatou E, Green MJ, Kaplan W, Ravishankar S, Copty J, Powell JE, Cuppen E, van Eijk K, Veldink J, Ahn JH, Kim JE, Randall RL, Tucker K, Judson I, Sarin R, Ludwig T, Genin E, Deleuze JF, Haber M, Marshall G, Cairns MJ, Blay JY, Thomas DM, Tattersall M, Neuhaus S, Lewis C, Tucker K, Carey-Smith R, Wood D, Porceddu S, Dickinson I, Thorne H, James P, Ray-Coquard I, Blay JY, Cassier P, Le Cesne A, Duffaud F, Penel N, Isambert N, Kurtz JE, Puri A, Sarin R, Ahn JH, Kim JE, Ward I, Judson I, van der Graaf W, Seddon B, Chandrasekar C, Rickar R, Hennig I, Schiffman J, Randall RL, Silvestri A, Zaratzian A, Tayao M, Walwyn K, Niedermayr E, Mang D, Clark R, Thorpe T, MacDonald J, Riddell K, Mar J, Fennelly V, Wicht A, Zielony B, Galligan E, Glavich G, Stoeckert J, Williams L, Djandjgava L, Buettner I, Osinki C, Stephens S, Rogasik M, Bouclier L, Girodet M, Charreton A, Fayet Y, Crasto S, Sandupatla B, Yoon Y, Je N, Thompson L, Fowler T, Johnson B, Petrikova G, Hambridge T, Hutchins A, Bottero D, Scanlon D, Stokes-Denson J, Génin E, Campion D, Dartigues JF, Deleuze JF, Lambert JC, Redon R, Ludwig T, Grenier-Boley B, Letort S, Lindenbaum P, Meyer V, Quenez O, Dina C, Bellenguez C, Le Clézio CC, Giemza J, Chatel S, Férec C, Le Marec H, Letenneur L, Nicolas G, Rouault K. Heritable defects in telomere and mitotic function selectively predispose to sarcomas. Science 2023; 379:253-260. [PMID: 36656928 DOI: 10.1126/science.abj4784] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 11/16/2022] [Indexed: 01/20/2023]
Abstract
Cancer genetics has to date focused on epithelial malignancies, identifying multiple histotype-specific pathways underlying cancer susceptibility. Sarcomas are rare malignancies predominantly derived from embryonic mesoderm. To identify pathways specific to mesenchymal cancers, we performed whole-genome germline sequencing on 1644 sporadic cases and 3205 matched healthy elderly controls. Using an extreme phenotype design, a combined rare-variant burden and ontologic analysis identified two sarcoma-specific pathways involved in mitotic and telomere functions. Variants in centrosome genes are linked to malignant peripheral nerve sheath and gastrointestinal stromal tumors, whereas heritable defects in the shelterin complex link susceptibility to sarcoma, melanoma, and thyroid cancers. These studies indicate a specific role for heritable defects in mitotic and telomere biology in risk of sarcomas.
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Affiliation(s)
- Mandy L Ballinger
- Garvan Institute of Medical Research, Sydney 2010, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney 2010, Australia
| | - Swetansu Pattnaik
- Garvan Institute of Medical Research, Sydney 2010, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney 2010, Australia
| | - Piyushkumar A Mundra
- Garvan Institute of Medical Research, Sydney 2010, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney 2010, Australia
| | - Milita Zaheed
- Hereditary Cancer Centre, Prince of Wales Hospital, Sydney 2031, Australia
| | - Emma Rath
- Garvan Institute of Medical Research, Sydney 2010, Australia
| | - Peter Priestley
- Hartwig Medical Foundation, 1098 XH Amsterdam, Netherlands
- Hartwig Medical Foundation Australia, Sydney 2000, Australia
| | - Jonathan Baber
- Hartwig Medical Foundation, 1098 XH Amsterdam, Netherlands
- Hartwig Medical Foundation Australia, Sydney 2000, Australia
| | - Isabelle Ray-Coquard
- Department of Adult Medical Oncology, Centre Leon Berard, University Claude Bernard, 69373 Lyon, France
| | | | | | | | - Ajay Puri
- Department of Orthopedic Oncology, Tata Memorial Hospital, Mumbai, Maharashtra 400012, India
| | | | | | - Beatrice Seddon
- Sarcoma Unit, University College Hospital, London NW1 2BU, UK
| | | | - Joshua D Schiffman
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Andrew S Brohl
- Sarcoma Department, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Paul A James
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne 3010, Australia
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne 3000, Australia
| | | | | | - Ola Myklebost
- Western Norway Familial Cancer Centre, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Science, University of Bergen, 5007 Bergen, Norway
- Institute for Cancer Research, Oslo University Hospital, N-0424 Oslo, Norway
| | | | - Hilda Pickett
- Children's Medical Research Institute, The University of Sydney, Westmead 2145, Australia
| | - Maya Kansara
- Garvan Institute of Medical Research, Sydney 2010, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney 2010, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane 4006, Australia
| | - Olga Kondrashova
- QIMR Berghofer Medical Research Institute, Brisbane 4006, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, Brisbane 4006, Australia
| | - Andrew P Barbour
- Faculty of Medicine. The University of Queensland, Brisbane 4072, Australia
| | - Shuai Li
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne 3010, Australia
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton 3800, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville 3051, Australia
| | - Tuong L Nguyen
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne 3010, Australia
| | - Diane Fatkin
- St Vincent's Clinical School, University of New South Wales, Sydney 2010, Australia
- Molecular Cardiology Division, Victor Chang Cardiac Research Institute, Darlinghurst 2010, Australia
- Cardiology Department, St Vincent's Hospital, Sydney 2010, Australia
| | - Robert M Graham
- St Vincent's Clinical School, University of New South Wales, Sydney 2010, Australia
- Molecular Cardiology Division, Victor Chang Cardiac Research Institute, Darlinghurst 2010, Australia
| | - Eleni Giannoulatou
- St Vincent's Clinical School, University of New South Wales, Sydney 2010, Australia
- Computational Genomics Division, Victor Chang Cardiac Research Institute, Sydney 2010, Australia
| | - Melissa J Green
- School of Psychiatry, University of New South Wales, Sydney 2052, Australia
- Neuorscience Research Australia, Sydney 2031, Australia
| | - Warren Kaplan
- Garvan Institute of Medical Research, Sydney 2010, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney 2010, Australia
| | | | - Joseph Copty
- Garvan Institute of Medical Research, Sydney 2010, Australia
| | - Joseph E Powell
- Garvan Institute of Medical Research, Sydney 2010, Australia
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney 2052, Australia
| | - Edwin Cuppen
- Hartwig Medical Foundation, 1098 XH Amsterdam, Netherlands
| | - Kristel van Eijk
- Department of Neurology, University Medical Centre Utrecht Brain Center, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Jan Veldink
- Department of Neurology, University Medical Centre Utrecht Brain Center, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Jin-Hee Ahn
- Department of Oncology, Asan Medical Centre, Seoul 05505, South Korea
| | - Jeong Eun Kim
- Department of Oncology, Asan Medical Centre, Seoul 05505, South Korea
| | - R Lor Randall
- Department of Orthopaedic Surgery, University of California, Davis Health, Sacramento, CA 95817, USA
| | - Kathy Tucker
- Hereditary Cancer Centre, Prince of Wales Hospital, Sydney 2031, Australia
| | - Ian Judson
- Sarcoma Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Rajiv Sarin
- Cancer Genetics Unit, ACTREC, Tata Memorial Centre, Mumbai, Maharashtra 410210, India
| | - Thomas Ludwig
- Université de Brest, Inserm, EFS, UMR 1078, GGB, CHU de Brest, 29200 Brest, France
| | - Emmanuelle Genin
- Université de Brest, Inserm, EFS, UMR 1078, GGB, CHU de Brest, 29200 Brest, France
| | - Jean-Francois Deleuze
- Centre National de Recherche en Génomique Humaine, Institut de Génomique, 91057 Evry, France
| | - Michelle Haber
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Kensington 2033, Australia
| | - Glenn Marshall
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Kensington 2033, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick 2031, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan 2308, Australia
- Centre for Brain and Mental Health Research, The Hunter Medical Research Institute, Newcastle 2305, Australia
| | - Jean-Yves Blay
- Department of Adult Medical Oncology, Centre Leon Berard, University Claude Bernard, 69373 Lyon, France
| | - David M Thomas
- Garvan Institute of Medical Research, Sydney 2010, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney 2010, Australia
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9
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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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10
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Gao J, Pickett HA. Targeting telomeres: advances in telomere maintenance mechanism-specific cancer therapies. Nat Rev Cancer 2022; 22:515-532. [PMID: 35790854 DOI: 10.1038/s41568-022-00490-1] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 12/31/2022]
Abstract
Cancer cells establish replicative immortality by activating a telomere-maintenance mechanism (TMM), be it telomerase or the alternative lengthening of telomeres (ALT) pathway. Targeting telomere maintenance represents an intriguing opportunity to treat the vast majority of all cancer types. Whilst telomerase inhibitors have historically been heralded as promising anticancer agents, the reality has been more challenging, and there are currently no therapeutic options for cancer types that use ALT despite their aggressive nature and poor prognosis. In this Review, we discuss the mechanistic differences between telomere maintenance by telomerase and ALT, the current methods used to detect each mechanism, the utility of these tests for clinical diagnosis, and recent developments in the therapeutic strategies being employed to target both telomerase and ALT. We present notable developments in repurposing established therapeutic agents and new avenues that are emerging to target cancer types according to which TMM they employ. These opportunities extend beyond inhibition of telomere maintenance, by finding and exploiting inherent weaknesses in the telomeres themselves to trigger rapid cellular effects that lead to cell death.
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Affiliation(s)
- Jixuan Gao
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia.
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11
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Alessandrini I, Percio S, Naghshineh E, Zuco V, Stacchiotti S, Gronchi A, Pasquali S, Zaffaroni N, Folini M. Telomere as a Therapeutic Target in Dedifferentiated Liposarcoma. Cancers (Basel) 2022; 14:2624. [PMID: 35681604 PMCID: PMC9179266 DOI: 10.3390/cancers14112624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Well-differentiated (WD)/dedifferentiated (DD) liposarcoma (LPS) accounts for ~60% of retroperitoneal sarcomas. WDLPS and DDLPS divergently evolve from a common precursor and are both marked by the amplification of the 12q13-q15 region, leading to the abnormal expression of MDM2, CDK4, and HMGA2 genes. DDLPS is a non-lipogenic disease associated with aggressive clinical behavior. Patients have limited therapeutic options, especially for advanced disease, and their outcome remains largely unsatisfactory. This evidence underlines the need for identifying and validating DDLPS-specific actionable targets to design novel biology-driven therapies. METHODS Following gene expression profiling of DDLPS clinical specimens, we observed the up-regulation of "telomere maintenance" (TMM) pathways in paired DD and WD components of DDLPS. Considering the relevance of TMM for LPS onset and progression, the activity of a telomeric G-quadruplex binder (RHPS4) was assessed in DDLPS patient-derived cell lines. RESULTS Equitoxic concentrations of RHPS4 in DDLPS cells altered telomeric c-circle levels, induced DNA damage, and resulted in the accumulation of γ-H2AX-stained micronuclei. This evidence was paralleled by an RHPS4-mediated reduction of in vitro cell migration and induction of apoptosis/autophagy. CONCLUSIONS Our findings support telomere as an intriguing therapeutic target in DDLPS and suggest G-quadruplex binders as innovative therapeutic agents.
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Affiliation(s)
- Irene Alessandrini
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G.A. Amadeo 42, 20133 Milan, Italy; (I.A.); (S.P.); (E.N.); (V.Z.); (S.P.)
| | - Stefano Percio
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G.A. Amadeo 42, 20133 Milan, Italy; (I.A.); (S.P.); (E.N.); (V.Z.); (S.P.)
| | - Eisa Naghshineh
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G.A. Amadeo 42, 20133 Milan, Italy; (I.A.); (S.P.); (E.N.); (V.Z.); (S.P.)
| | - Valentina Zuco
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G.A. Amadeo 42, 20133 Milan, Italy; (I.A.); (S.P.); (E.N.); (V.Z.); (S.P.)
| | - Silvia Stacchiotti
- Adult Mesenchymal Tumor and Rare Cancer Unit, Department of Cancer Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via Venezian 1, 20133 Milan, Italy;
| | - Alessandro Gronchi
- Sarcoma Service, Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via Venezian 1, 20133 Milan, Italy;
| | - Sandro Pasquali
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G.A. Amadeo 42, 20133 Milan, Italy; (I.A.); (S.P.); (E.N.); (V.Z.); (S.P.)
- Sarcoma Service, Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via Venezian 1, 20133 Milan, Italy;
| | - Nadia Zaffaroni
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G.A. Amadeo 42, 20133 Milan, Italy; (I.A.); (S.P.); (E.N.); (V.Z.); (S.P.)
| | - Marco Folini
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via G.A. Amadeo 42, 20133 Milan, Italy; (I.A.); (S.P.); (E.N.); (V.Z.); (S.P.)
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12
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Barroso-González J, García-Expósito L, Galaviz P, Lynskey ML, Allen JAM, Hoang S, Watkins SC, Pickett HA, O'Sullivan RJ. Anti-recombination function of MutSα restricts telomere extension by ALT-associated homology-directed repair. Cell Rep 2021; 37:110088. [PMID: 34879271 PMCID: PMC8724847 DOI: 10.1016/j.celrep.2021.110088] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/13/2021] [Accepted: 11/10/2021] [Indexed: 01/02/2023] Open
Abstract
Alternative lengthening of telomeres (ALT) is a telomere-elongation mechanism observed in ~15% of cancer subtypes. Current models indicate that ALT is mediated by homology-directed repair mechanisms. By disrupting MSH6 gene expression, we show that the deficiency of MutSα (MSH2/MSH6) DNA mismatch repair complex causes striking telomere hyperextension. Mechanistically, we show MutSα is specifically recruited to telomeres in ALT cells by associating with the proliferating-cell nuclear antigen (PCNA) subunit of the ALT telomere replisome. We also provide evidence that MutSα counteracts Bloom (BLM) helicase, which adopts a crucial role in stabilizing hyper-extended telomeres and maintaining the survival of MutSα-deficient ALT cancer cells. Lastly, we propose a model in which MutSα deficiency impairs heteroduplex rejection, leading to premature initiation of telomere DNA synthesis that coincides with an accumulation of telomere variant repeats (TVRs). These findings provide evidence that the MutSα DNA mismatch repair complex acts to restrain unwarranted ALT. Barroso-Gonzalez et al. show that the mismatch repair complex MutSα restricts the alternative lengthening of telomeres (ALT) pathway in cancer cells. MutSα has an anti-recombination function and limits recombination between heteroduplex sequences at telomeres, in part by counteracting the Bloom helicase (BLM).
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Affiliation(s)
- Jonathan Barroso-González
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Laura García-Expósito
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Pablo Galaviz
- Bioinformatics Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Michelle Lee Lynskey
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Joshua A M Allen
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - SongMy Hoang
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Simon C Watkins
- Department of Cell Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
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13
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Fontanilles M, Sanson M, Touat M. Liquid biopsy in neuro-oncology: are we finally there? Ann Oncol 2021; 32:1472-1474. [PMID: 34815016 DOI: 10.1016/j.annonc.2021.10.215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 11/30/2022] Open
Affiliation(s)
- M Fontanilles
- Cancer Centre Henri Becquerel, Département d'oncologie médicale, Rouen, France; Normandie Université, Rouen University Hospital, UNIROUEN, IRON group, Normandy Centre for Genomic and Personalized Medicine, Inserm U1245, Rouen, France
| | - M Sanson
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - M Touat
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France.
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14
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Billard P, Guerriau C, Carpentier C, Juillard F, Grandin N, Lomonte P, Kantapareddy P, Dufay N, Barritault M, Rimokh R, Verrelle P, Maucort-Boulch D, Figarella-Branger D, Ducray F, Dehais C, Charbonneau M, Meyronet D, Poncet DA. The TeloDIAG: how telomeric parameters can help in glioma rapid diagnosis and liquid biopsy approaches. Ann Oncol 2021; 32:1608-1617. [PMID: 34690007 DOI: 10.1016/j.annonc.2021.09.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/22/2021] [Accepted: 09/05/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In glioma, TERT promoter mutation and loss of ATRX (ATRX loss) are associated with reactivation of telomerase or alternative lengthening of telomeres (ALT), respectively, i.e. the two telomere maintenance mechanisms (TMM). Strangely, 25% of gliomas have been reported to display neither or both of these alterations. MATERIALS AND METHODS The C-circle (CC) assay was adapted to tumor (formalin-fixed paraffin-embedded and frozen) and blood samples to investigate the TMM. RESULTS We constructed a CC-based algorithm able to identify the TMM and reported a sensitivity of 100% and a specificity of 97.3% (n = 284 gliomas). By combining the TMM, the mutational status of the isocitrate dehydrogenase 1/2 (IDH) gene (IDHmt), and the histological grading, we propose a new classification tool: TeloDIAG. This classification defined five subtypes: tOD, tLGA, tGBM_IDHmt, tGBM, and tAIV, corresponding to oligodendroglioma, IDHmt low-grade astrocytoma, IDHmt glioblastoma, and IDHwt glioblastoma (GBM), respectively; the last class gathers ALT+ IDHwt gliomas that tend to be related to longer survival (21.2 months) than tGBM (16.5 months). The TeloDIAG was 99% concordant with the World Health Organization classification (n = 312), and further modified the classification of 55 of 144 (38%) gliomas with atypical molecular characteristics. As an example, 14 of 69 (20%) of TERTwt, ATRXwt, and IDHwt GBM were actually tAIV. Outstandingly, CC in blood sampled from IDHmt astrocytoma patients was detected with a sensitivity of 56% and a specificity of 97% (n = 206 gliomas and 30 healthy donors). CONCLUSION The TeloDIAG is a new, simple, and effective tool helping in glioma diagnosis and a promising option for liquid biopsy.
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Affiliation(s)
- P Billard
- Institut de Pathologie Est, Hospices Civils de Lyon, Lyon, France; Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène (INMG), Neuron-Muscle Interaction Team, Lyon, France
| | - C Guerriau
- Institut de Pathologie Est, Hospices Civils de Lyon, Lyon, France
| | - C Carpentier
- Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, Paris, France
| | - F Juillard
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France
| | - N Grandin
- GReD Institute, CNRS UMR6293, INSERM U1103, University Clermont Auvergne, Faculty of Medicine, Clermont-Ferrand, France
| | - P Lomonte
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France
| | | | - N Dufay
- Hospices Civils de Lyon, Lyon, France
| | - M Barritault
- Institut de Pathologie Est, Hospices Civils de Lyon, Lyon, France
| | - R Rimokh
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - P Verrelle
- GReD Institute, CNRS UMR6293, INSERM U1103, University Clermont Auvergne, Faculty of Medicine, Clermont-Ferrand, France
| | - D Maucort-Boulch
- Biostatistics and Bioinformatics Department of the Hospices Civils de Lyon, Lyon, France
| | - D Figarella-Branger
- Aix-Marseille Univ, CNRS, INP, Inst. Neurophysiopathol, Marseille, France; AP-HM, CHU Timone, Service d'Anatomie Pathologique et de Neuropathologie, Centre de Ressources Biologiques CRB-TBM, Marseille, France
| | - F Ducray
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France; Hospices Civils de Lyon, Hôpital Neurologique, Bron, France
| | - C Dehais
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière-Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - M Charbonneau
- GReD Institute, CNRS UMR6293, INSERM U1103, University Clermont Auvergne, Faculty of Medicine, Clermont-Ferrand, France
| | - D Meyronet
- Institut de Pathologie Est, Hospices Civils de Lyon, Lyon, France; Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - D A Poncet
- Institut de Pathologie Est, Hospices Civils de Lyon, Lyon, France; Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène (INMG), Neuron-Muscle Interaction Team, Lyon, France.
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15
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Hu K, Ghandi M, Huang FW. Integrated evaluation of telomerase activation and telomere maintenance across cancer cell lines. eLife 2021; 10:e66198. [PMID: 34486523 PMCID: PMC8530513 DOI: 10.7554/elife.66198] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
In cancer, telomere maintenance is critical for the development of replicative immortality. Using genome sequences from the Cancer Cell Line Encyclopedia and Genomics of Drug Sensitivity in Cancer Project, we calculated telomere content across 1299 cancer cell lines. We find that telomerase reverse transcriptase (TERT) expression correlates with telomere content in lung, central nervous system, and leukemia cell lines. Using CRISPR/Cas9 screening data, we show that lower telomeric content is associated with dependency of CST telomere maintenance genes. Increased dependencies of shelterin members are associated with wild-type TP53 status. Investigating the epigenetic regulation of TERT, we find widespread allele-specific expression in promoter-wildtype contexts. TERT promoter-mutant cell lines exhibit hypomethylation at PRC2-repressed regions, suggesting a cooperative global epigenetic state in the reactivation of telomerase. By incorporating telomere content with genomic features across comprehensively characterized cell lines, we provide further insights into the role of telomere regulation in cancer immortality.
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Affiliation(s)
- Kevin Hu
- Broad Institute of MIT and HarvardCambridgeUnited States
- Division of Hematology/Oncology, Department of Medicine; Bakar Computational Health Sciences Institute; Institute for Human Genetics; University of California, San FranciscoSan FranciscoUnited States
- Helen Diller Family Comprehensive Cancer CenterSan FranciscoUnited States
| | - Mahmoud Ghandi
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Franklin W Huang
- Broad Institute of MIT and HarvardCambridgeUnited States
- Division of Hematology/Oncology, Department of Medicine; Bakar Computational Health Sciences Institute; Institute for Human Genetics; University of California, San FranciscoSan FranciscoUnited States
- Helen Diller Family Comprehensive Cancer CenterSan FranciscoUnited States
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16
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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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17
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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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18
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Robinson NJ, Miyagi M, Scarborough JA, Scott JG, Taylor DJ, Schiemann WP. SLX4IP promotes RAP1 SUMOylation by PIAS1 to coordinate telomere maintenance through NF-κB and Notch signaling. Sci Signal 2021; 14:eabe9613. [PMID: 34187905 PMCID: PMC8353884 DOI: 10.1126/scisignal.abe9613] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The maintenance of telomere length supports repetitive cell division and therefore plays a central role in cancer development and progression. Telomeres are extended by either the enzyme telomerase or the alternative lengthening of telomeres (ALT) pathway. Here, we found that the telomere-associated protein SLX4IP dictates telomere proteome composition by recruiting and activating the E3 SUMO ligase PIAS1 to the SLX4 complex. PIAS1 SUMOylated the telomere-binding protein RAP1, which disrupted its interaction with the telomere-binding protein TRF2 and facilitated its nucleocytoplasmic shuttling. In the cytosol, RAP1 bound to IκB kinase (IKK), resulting in activation of the transcription factor NF-κB and its induction of Jagged-1 expression, which promoted Notch signaling and the institution of ALT. This axis could be targeted therapeutically in ALT-driven cancers and in tumor cells that develop resistance to antitelomerase therapies. Our results illuminate the mechanisms underlying SLX4IP-dependent telomere plasticity and demonstrate the role of telomere proteins in directly coordinating intracellular signaling and telomere maintenance dynamics.
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Affiliation(s)
- Nathaniel J Robinson
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Masaru Miyagi
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Jessica A Scarborough
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jacob G Scott
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - William P Schiemann
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA.
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19
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MacKenzie D, Watters AK, To JT, Young MW, Muratori J, Wilkoff MH, Abraham RG, Plummer MM, Zhang D. ALT Positivity in Human Cancers: Prevalence and Clinical Insights. Cancers (Basel) 2021; 13:2384. [PMID: 34069193 PMCID: PMC8156225 DOI: 10.3390/cancers13102384] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 02/08/2023] Open
Abstract
Many exciting advances in cancer-related telomere biology have been made in the past decade. Of these recent advances, great progress has also been made with respect to the Alternative Lengthening of Telomeres (ALT) pathway. Along with a better understanding of the molecular mechanism of this unique telomere maintenance pathway, many studies have also evaluated ALT activity in various cancer subtypes. We first briefly review and assess a variety of commonly used ALT biomarkers. Then, we provide both an update on ALT-positive (ALT+) tumor prevalence as well as a systematic clinical assessment of the presently studied ALT+ malignancies. Additionally, we discuss the pathogenetic alterations in ALT+ cancers, for example, the mutation status of ATRX and DAXX, and their correlations with the activation of the ALT pathway. Finally, we highlight important ALT+ clinical associations within each cancer subtype and subdivisions within, as well as their prognoses. We hope this alternative perspective will allow scientists, clinicians, and drug developers to have greater insight into the ALT cancers so that together, we may develop more efficacious treatments and improved management strategies to meet the urgent needs of cancer patients.
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Affiliation(s)
| | | | | | | | | | | | | | - Maria M. Plummer
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA; (D.M.J.); (A.K.W.); (J.T.T.); (M.W.Y.); (J.M.); (M.H.W.); (R.G.A.)
| | - Dong Zhang
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA; (D.M.J.); (A.K.W.); (J.T.T.); (M.W.Y.); (J.M.); (M.H.W.); (R.G.A.)
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20
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Segura-Bayona S, Villamor-Payà M, Attolini CSO, Koenig LM, Sanchiz-Calvo M, Boulton SJ, Stracker TH. Tousled-Like Kinases Suppress Innate Immune Signaling Triggered by Alternative Lengthening of Telomeres. Cell Rep 2021; 32:107983. [PMID: 32755577 PMCID: PMC7408502 DOI: 10.1016/j.celrep.2020.107983] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/30/2020] [Accepted: 07/09/2020] [Indexed: 12/11/2022] Open
Abstract
The Tousled-like kinases 1 and 2 (TLK1/2) control histone deposition through the ASF1 histone chaperone and influence cell cycle progression and genome maintenance, yet the mechanisms underlying TLK-mediated genome stability remain uncertain. Here, we show that TLK loss results in severe chromatin decompaction and altered genome accessibility, particularly affecting heterochromatic regions. Failure to maintain heterochromatin increases spurious transcription of repetitive elements and induces features of alternative lengthening of telomeres (ALT). TLK depletion culminates in a cGAS-STING-TBK1-mediated innate immune response that is independent of replication-stress signaling and attenuated by the depletion of factors required to produce extra-telomeric DNA. Analysis of human cancers reveals that chromosomal instability correlates with high TLK2 and low STING levels in many cohorts. Based on these findings, we propose that high TLK levels contribute to immune evasion in chromosomally unstable and ALT+ cancers. TLK-deficient cells have increased accessibility at heterochromatin regions TLK1/2 suppress spurious transcription and telomere hyper-recombination Extra-telomeric DNA generated upon TLK loss promotes innate immune signaling cGAS-STING-TBK1 signaling in TLK-deficient cells is independent of replication stress
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Affiliation(s)
- Sandra Segura-Bayona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Marina Villamor-Payà
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Camille Stephan-Otto Attolini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Lars M Koenig
- Division of Clinical Pharmacology, University Hospital, LMU Munich, 80337 Munich, Germany
| | - Maria Sanchiz-Calvo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Travis H Stracker
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain.
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21
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Feuerbach L. Formal reply to "Alternative lengthening of telomeres is not synonymous with mutations in ATRX/DAXX". Nat Commun 2021; 12:1551. [PMID: 33692348 PMCID: PMC7946925 DOI: 10.1038/s41467-021-21796-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 02/11/2021] [Indexed: 11/26/2022] Open
Affiliation(s)
- Lars Feuerbach
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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22
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de Nonneville A, Reddel RR. Alternative lengthening of telomeres is not synonymous with mutations in ATRX/DAXX. Nat Commun 2021; 12:1552. [PMID: 33692341 PMCID: PMC7946928 DOI: 10.1038/s41467-021-21794-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 02/02/2021] [Indexed: 01/01/2023] Open
Affiliation(s)
- Alexandre de Nonneville
- Cancer Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia. .,Aix-Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France.
| | - Roger R Reddel
- Cancer Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia.
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23
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da Silva GG, Morais KS, Arcanjo DS, de Oliveira DM. Clinical Relevance of Alternative Lengthening of Telomeres in Cancer. Curr Top Med Chem 2020; 20:485-497. [PMID: 31924155 DOI: 10.2174/1568026620666200110112854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 11/22/2022]
Abstract
The alternative lengthening of telomere (ALT) is a pathway responsible for cell immortalization in some kinds of tumors. Since the first description of ALT is relatively recent in the oncology field, its mechanism remains elusive, but recent works address ALT-related proteins or cellular structures as potential druggable targets for more specific and efficient antitumor therapies. Moreover, some new generation compounds for antitelomerase therapy in cancer were able to provoke acquisition of ALT phenotype in treated tumors, enhancing the importance of studies on this alternative lengthening of the telomere. However, ALT has been implicated in different - sometimes opposite - outcomes, according to the tumor type studied. Then, in order to design and develop new drugs for ALT+ cancer in an effective way, it is crucial to understand its clinical implications. In this review, we gathered works published in the last two decades to highlight the clinical relevance of ALT on oncology.
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Affiliation(s)
- Guilherme G da Silva
- Department of Biological Basis of Health Sciences, University of Brasilia, Ceilandia Campus, Federal District, Brazil
| | - Karollyne S Morais
- Laboratory of Molecular Pathology of Cancer, University of Brasilia, Federal District, Brazil
| | - Daniel S Arcanjo
- Department of Biological Basis of Health Sciences, University of Brasilia, Ceilandia Campus, Federal District, Brazil
| | - Diêgo M de Oliveira
- Department of Biological Basis of Health Sciences, University of Brasilia, Ceilandia Campus, Federal District, Brazil.,Laboratory of Molecular Pathology of Cancer, University of Brasilia, Federal District, Brazil
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24
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Li ZQ, Shen H, Shu KX, Li JJ, Tang Y, Su JJ, Yan J, Yang J, Wang ZQ, Qiu Y, Yang Y, Liu Y, Zhou Y. Transplantation of a Novel Recombinant Adeno-Associated Virus (pAAV-HE1B19K-TE1A) Demonstrates Higher Anti-Tumor Effects in Tumor Cells. Ann Transplant 2020; 25:e925013. [PMID: 32883945 PMCID: PMC7493455 DOI: 10.12659/aot.925013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Oncolytic viruses (OVs) can specifically infect and kill tumor cells. Adeno-associated virus (AAV) is a widely-studied OV. This study aimed to construct a tumor-targeted recombinant AAV using genetic engineering technology. MATERIAL AND METHODS The transgene plasmid pAAV-HE1B19K-TE1A was constructed with 4 genes (hTERT, E1A, HKII, and E1B19K) and co-transfected with pAAV-RC and pHelper to tumor cells (HepG2, A549, BGC-803) and normal cells (HUVEC). rAAV was verified with fluorescence microscopy. Quantitative PCR (qPCR) assay was used to test the titer of rAAV in each cell line. Apoptosis was analyzed using qPCR and Western blot assay. MTT was used to detect the effect of rAAV on cell viability. RESULTS The pAAV-HE1B19K-TE1A transgene plasmid was successfully structured. pAAV-HE1B19K-TE1A was highly expressed in all tumor cells. The titers of pAAV-HE1B19K-TE1A in HepG2, A549, and BGC-803 were 7.4×10⁷, 1.4×10⁸, and 1.1×10⁸ gc/μl, respectively. pAAV-HE1B19K-TE1A significantly decreased cell viability of tumor cells compared to that in HUVEC (p<0.05). pAAV-HE1B19K-TE1A remarkably triggered cleaved caspase 3 (C-caspase 3) activity in tumor cells compared to that in untransfected tumor cells (p<0.05). pAAV-HE1B19K-TE1A significantly induced release of cytochrome C (Cyto C) in tumor cells compared to that in untransfected tumor cells (p<0.05). pAAV-HE1B19K-TE1A demonstrated no toxicity to vital tissues of animals. CONCLUSIONS Tumor-targeted rAAV was successfully produced using the Helper-free system with recombinant plasmid, demonstrating high efficacy in decreasing viability of tumor cells without adverse effects on normal cells.
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Affiliation(s)
- Zhuo-Qing Li
- Chongqing Gaosheng Pharma Co., Ltd., Chongqing, China (mainland)
| | - Hong Shen
- Chongqing HYGEIA Cancer Hospital, Chongqing, China (mainland)
| | - Kun-Xian Shu
- Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China (mainland)
| | - Jian-Jun Li
- Chongqing Gaosheng Pharma Co., Ltd., Chongqing, China (mainland)
| | - Yin Tang
- Chongqing Western Biomedical Technology Co., Ltd., Chongqing, China (mainland)
| | - Jing-Jing Su
- Chongqing Western Biomedical Technology Co., Ltd., Chongqing, China (mainland)
| | - Jun Yan
- Chongqing Gaosheng Pharma Co., Ltd., Chongqing, China (mainland)
| | - Jie Yang
- Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China (mainland)
| | - Ze-Qing Wang
- Chongqing Gaosheng Pharma Co., Ltd., Chongqing, China (mainland)
| | - Yan Qiu
- Chongqing Western Biomedical Technology Co., Ltd., Chongqing, China (mainland)
| | - Yong Yang
- Chongqing Gaosheng Pharma Co., Ltd., Chongqing, China (mainland)
| | - Yang Liu
- Chongqing Western Biomedical Technology Co., Ltd., Chongqing, China (mainland)
| | - Yong Zhou
- Chongqing Western Biopharma Technology Co., Ltd., Chongqing, China (mainland)
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25
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TCGA Pan-Cancer Genomic Analysis of Alternative Lengthening of Telomeres (ALT) Related Genes. Genes (Basel) 2020; 11:genes11070834. [PMID: 32708340 PMCID: PMC7397314 DOI: 10.3390/genes11070834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/15/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023] Open
Abstract
Telomere maintenance mechanisms (TMM) are used by cancer cells to avoid apoptosis, 85–90% reactivate telomerase, while 10–15% use the alternative lengthening of telomeres (ALT). Due to anti-telomerase-based treatments, some tumors switch from a telomerase-dependent mechanism to ALT; in fact, the co-existence between both mechanisms has been observed in some cancers. Although different elements in the ALT pathway are uncovered, some molecular mechanisms are still poorly understood. Therefore, with the aim to identify potential molecular markers for the study of ALT, we combined in silico approaches in a 411 telomere maintenance gene set. As a consequence, we conducted a genomic analysis of these genes in 31 Pan-Cancer Atlas studies from The Cancer Genome Atlas and found 325,936 genomic alterations; from which, we identified 20 genes highly mutated in the cancer studies. Finally, we made a protein-protein interaction network and enrichment analysis to observe the main pathways of these genes and discuss their role in ALT-related processes, like homologous recombination and homology directed repair. Overall, due to the lack of understanding of the molecular mechanisms of ALT cancers, we proposed a group of genes, which after ex vivo validations, could represent new potential therapeutic markers in the study of ALT.
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26
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Schaich MA, Sanford SL, Welfer GA, Johnson SA, Khoang TH, Opresko PL, Freudenthal BD. Mechanisms of nucleotide selection by telomerase. eLife 2020; 9:55438. [PMID: 32501800 PMCID: PMC7274783 DOI: 10.7554/elife.55438] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/18/2020] [Indexed: 01/31/2023] Open
Abstract
Telomerase extends telomere sequences at chromosomal ends to protect genomic DNA. During this process it must select the correct nucleotide from a pool of nucleotides with various sugars and base pairing properties, which is critically important for the proper capping of telomeric sequences by shelterin. Unfortunately, how telomerase selects correct nucleotides is unknown. Here, we determined structures of Tribolium castaneum telomerase reverse transcriptase (TERT) throughout its catalytic cycle and mapped the active site residues responsible for nucleoside selection, metal coordination, triphosphate binding, and RNA template stabilization. We found that TERT inserts a mismatch or ribonucleotide ~1 in 10,000 and ~1 in 14,000 insertion events, respectively. At biological ribonucleotide concentrations, these rates translate to ~40 ribonucleotides inserted per 10 kilobases. Human telomerase assays determined a conserved tyrosine steric gate regulates ribonucleotide insertion into telomeres. Cumulatively, our work provides insight into how telomerase selects the proper nucleotide to maintain telomere integrity.
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Affiliation(s)
- Matthew A Schaich
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, United States
| | - Samantha L Sanford
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and UPMC Hillman Cancer Center, Pittsburgh, United States
| | - Griffin A Welfer
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, United States
| | - Samuel A Johnson
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and UPMC Hillman Cancer Center, Pittsburgh, United States
| | - Thu H Khoang
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, United States
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and UPMC Hillman Cancer Center, Pittsburgh, United States
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, United States.,Department of Cancer Biology, University of Kansas Medical Center, Kansas City, United States
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27
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The Role of Alternative Lengthening of Telomeres Mechanism in Cancer: Translational and Therapeutic Implications. Cancers (Basel) 2020; 12:cancers12040949. [PMID: 32290440 PMCID: PMC7226354 DOI: 10.3390/cancers12040949] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 12/17/2022] Open
Abstract
Telomere maintenance mechanisms (i.e., telomerase activity (TA) and the alternative lengthening of telomere (ALT) mechanism) contribute to tumorigenesis by providing unlimited proliferative capacity to cancer cells. Although the role of either telomere maintenance mechanisms seems to be equivalent in providing a limitless proliferative ability to tumor cells, the contribution of TA and ALT to the clinical outcome of patients may differ prominently. In addition, several strategies have been developed to interfere with TA in cancer, including Imetelstat that has been the first telomerase inhibitor tested in clinical trials. Conversely, the limited information available on the molecular underpinnings of ALT has hindered thus far the development of genuine ALT-targeting agents. Moreover, whether anti-telomerase therapies may be hampered or not by possible adaptive responses is still debatable. Nonetheless, it is plausible hypothesizing that treatment with telomerase inhibitors may exert selective pressure for the emergence of cancer cells that become resistant to treatment by activating the ALT mechanism. This notion, together with the evidence that both telomere maintenance mechanisms may coexist within the same tumor and may distinctly impinge on patients' outcomes, suggests that ALT may exert an unexpected role in tumor biology that still needs to be fully elucidated.
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28
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Mechanisms that drive telomere maintenance and recombination in human cancers. Curr Opin Genet Dev 2020; 60:25-30. [PMID: 32119936 DOI: 10.1016/j.gde.2020.02.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/22/2020] [Accepted: 02/02/2020] [Indexed: 12/19/2022]
Abstract
Telomere maintenance is essential for the continued proliferation of mitotically active cells. Alternative Lengthening of Telomeres (ALT) is a recombination-dependent pathway of telomere maintenance analogous to break-induced replication (BIR) [1] that becomes activated in approximately 10-15% of human cancers. ALT is prevalent in tumours of mesenchymal or neuroepithelial origin, and typically confers a poor prognosis. The aggressiveness and lack of effective strategies to treat these cancers make the ALT pathway a compelling potential therapeutic target to prevent tumour formation and/or the appearance of secondary malignancies after conventional chemotherapy [2]. While the precise initiator of ALT during tumourigenesis remains elusive, substantial progress has been made in interrogating the underlying homology-directed repair mechanisms that converge at telomeres to enable telomere length maintenance. Here, we describe recent advances in our understanding of the ALT mechanism and highlight potential therapeutic targets that may offer future promise in the treatment of ALT cancers.
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29
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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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30
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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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Telomerase and Telomeres Biology in Thyroid Cancer. Int J Mol Sci 2019; 20:ijms20122887. [PMID: 31200515 PMCID: PMC6627113 DOI: 10.3390/ijms20122887] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/03/2019] [Accepted: 06/11/2019] [Indexed: 02/06/2023] Open
Abstract
Telomere and telomerase regulation contributes to the onset and evolution of several tumors, including highly aggressive thyroid cancers (TCs). TCs are the most common endocrine malignancies and are generally characterized by a high rate of curability. However, a small but significant percentage develops distant metastasis or progresses into undifferentiated forms associated with bad prognosis and for which poor therapeutic options are available. Mutations in telomerase reverse transcriptase (TERT) promoter are among the most credited prognostic marker of aggressiveness in TCs. Indeed, their frequency progressively increases passing from indolent lesions to aggressive and anaplastic forms. TERT promoter mutations create binding sites for transcription factors, increasing TERT expression and telomerase activity. Furthermore, aggressiveness of TCs is associated with TERT locus amplification. These data encourage investigating telomerase regulating pathways as relevant drivers of TC development and progression to foster the identification of new therapeutics targets. Here, we summarize the current knowledge about telomere regulation and TCs, exploring both canonical and less conventional pathways. We discuss the possible role of telomere homeostasis in mediating response to cancer therapies and the possibility of using epigenetic drugs to re-evaluate the use of telomerase inhibitors. Combined treatments could be of support to currently used therapies still presenting weaknesses.
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32
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Feuerbach L, Sieverling L, Deeg KI, Ginsbach P, Hutter B, Buchhalter I, Northcott PA, Mughal SS, Chudasama P, Glimm H, Scholl C, Lichter P, Fröhling S, Pfister SM, Jones DTW, Rippe K, Brors B. TelomereHunter - in silico estimation of telomere content and composition from cancer genomes. BMC Bioinformatics 2019; 20:272. [PMID: 31138115 PMCID: PMC6540518 DOI: 10.1186/s12859-019-2851-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 04/26/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Establishment of telomere maintenance mechanisms is a universal step in tumor development to achieve replicative immortality. These processes leave molecular footprints in cancer genomes in the form of altered telomere content and aberrations in telomere composition. To retrieve these telomere characteristics from high-throughput sequencing data the available computational approaches need to be extended and optimized to fully exploit the information provided by large scale cancer genome data sets. RESULTS We here present TelomereHunter, a software for the detailed characterization of telomere maintenance mechanism footprints in the genome. The tool is implemented for the analysis of large cancer genome cohorts and provides a variety of diagnostic diagrams as well as machine-readable output for subsequent analysis. A novel key feature is the extraction of singleton telomere variant repeats, which improves the identification and subclassification of the alternative lengthening of telomeres phenotype. We find that whole genome sequencing-derived telomere content estimates strongly correlate with telomere qPCR measurements (r = 0.94). For the first time, we determine the correlation of in silico telomere content quantification from whole genome sequencing and whole genome bisulfite sequencing data derived from the same tumor sample (r = 0.78). An analogous comparison of whole exome sequencing data and whole genome sequencing data measured slightly lower correlation (r = 0.79). However, this is considerably improved by normalization with matched controls (r = 0.91). CONCLUSIONS TelomereHunter provides new functionality for the analysis of the footprints of telomere maintenance mechanisms in cancer genomes. Besides whole genome sequencing, whole exome sequencing and whole genome bisulfite sequencing are suited for in silico telomere content quantification, especially if matched control samples are available. The software runs under a GPL license and is available at https://www.dkfz.de/en/applied-bioinformatics/telomerehunter/telomerehunter.html .
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Affiliation(s)
- Lars Feuerbach
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Lina Sieverling
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Katharina I. Deeg
- Research Group Genome Organization & Function/Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant Center, 69120 Heidelberg, Germany
| | - Philip Ginsbach
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Barbara Hutter
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Ivo Buchhalter
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Paul A. Northcott
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sadaf S. Mughal
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Priya Chudasama
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Hanno Glimm
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden, University Hospital Carl Gustav Carus, Dresden and DKFZ, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Claudia Scholl
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Division of Applied Functional Genomics, DKFZ, 69120 Heidelberg, Germany
| | - Peter Lichter
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Stefan M. Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - David T. W. Jones
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Karsten Rippe
- Research Group Genome Organization & Function/Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant Center, 69120 Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
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