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Bertrand A, Ba I, Kermasson L, Pirabakaran V, Chable N, Lainey E, Ménard C, Kallel F, Picard C, Hadiji S, Coolen-Allou N, Blanchard E, de Villartay JP, Moshous D, Roelens M, Callebaut I, Kannengiesser C, Revy P. Characterization of novel mutations in the TEL-patch domain of the telomeric factor TPP1 associated with telomere biology disorders. Hum Mol Genet 2024; 33:612-623. [PMID: 38176734 DOI: 10.1093/hmg/ddad210] [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: 07/11/2023] [Revised: 12/04/2023] [Accepted: 12/13/2023] [Indexed: 01/06/2024] Open
Abstract
Telomeres are nucleoprotein structures that protect the chromosome ends from degradation and fusion. Telomerase is a ribonucleoprotein complex essential to maintain the length of telomeres. Germline defects that lead to short and/or dysfunctional telomeres cause telomere biology disorders (TBDs), a group of rare and heterogeneous Mendelian diseases including pulmonary fibrosis, dyskeratosis congenita, and Høyeraal-Hreidarsson syndrome. TPP1, a telomeric factor encoded by the gene ACD, recruits telomerase at telomere and stimulates its activity via its TEL-patch domain that directly interacts with TERT, the catalytic subunit of telomerase. TBDs due to TPP1 deficiency have been reported only in 11 individuals. We here report four unrelated individuals with a wide spectrum of TBD manifestations carrying either heterozygous or homozygous ACD variants consisting in the recurrent and previously described in-frame deletion of K170 (K170∆) and three novel missense mutations G179D, L184R, and E215V. Structural and functional analyses demonstrated that the four variants affect the TEL-patch domain of TPP1 and impair telomerase activity. In addition, we identified in the ACD gene several motifs associated with small deletion hotspots that could explain the recurrence of the K170∆ mutation. Finally, we detected in a subset of blood cells from one patient, a somatic TERT promoter-activating mutation that likely provides a selective advantage over non-modified cells, a phenomenon known as indirect somatic genetic rescue. Together, our results broaden the genetic and clinical spectrum of TPP1 deficiency and specify new residues in the TEL-patch domain that are crucial for length maintenance and stability of human telomeres in vivo.
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Affiliation(s)
- Alexis Bertrand
- Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer, INSERM UMR 1163, Imagine Institute, 24 boulevard du Montparnasse, Paris 75015, France
- Université Paris Cité, Imagine Institute, Paris 75015, France
| | - Ibrahima Ba
- Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer, INSERM UMR 1163, Imagine Institute, 24 boulevard du Montparnasse, Paris 75015, France
- Université Paris Cité, Imagine Institute, Paris 75015, France
- Assistance Publique des Hôpitaux de Paris, Hôpital Bichat, Service de Génétique, Université Paris Diderot, Paris 75018, France
| | - Laëtitia Kermasson
- Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer, INSERM UMR 1163, Imagine Institute, 24 boulevard du Montparnasse, Paris 75015, France
- Université Paris Cité, Imagine Institute, Paris 75015, France
| | - Vithura Pirabakaran
- Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer, INSERM UMR 1163, Imagine Institute, 24 boulevard du Montparnasse, Paris 75015, France
- Université Paris Cité, Imagine Institute, Paris 75015, France
| | - Noémie Chable
- Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer, INSERM UMR 1163, Imagine Institute, 24 boulevard du Montparnasse, Paris 75015, France
- Université Paris Cité, Imagine Institute, Paris 75015, France
| | - Elodie Lainey
- Hematology Laboratory, Robert Debré Hospital-AssistancePublique-Hôpitaux de Paris (APHP), INSERM UMR 1131-Hematology University Institute-Denis Diderot School of Medicine, Paris 75019, France
| | - Christelle Ménard
- Assistance Publique des Hôpitaux de Paris, Hôpital Bichat, Service de Génétique, Université Paris Diderot, Paris 75018, France
| | - Faten Kallel
- Hematology Department, Hedi Chaker Hospital, 3029, Sfax, Tunisia
| | - Capucine Picard
- Université Paris Cité, Imagine Institute, Paris 75015, France
- Department of Pediatric Immunology, Hematology and Rheumatology, Necker-Enfants Malades Hospital, (APHP), Paris 75015, France
- Centre de références des déficits immunitaires Héréditaires (CEREDIH), Necker-Enfants Malades Hospital APHP, Paris 75015, France
- Laboratory of Lymphocyte Activation and Susceptibility to EBV infection, Inserm UMR 1163, Institut Imagine, Paris 75015, France
| | - Sondes Hadiji
- Hematology Department, Hedi Chaker Hospital, 3029, Sfax, Tunisia
| | - Nathalie Coolen-Allou
- Service de Pneumologie, Hôpital Félix Guyon, CHU Réunion, Saint-Denis de la Réunion 97400, France
| | - Elodie Blanchard
- Service de Pneumologie, Hôpital Haut-Lévêque, CHU Bordeaux, Bordeaux 33604, France
| | - Jean-Pierre de Villartay
- Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer, INSERM UMR 1163, Imagine Institute, 24 boulevard du Montparnasse, Paris 75015, France
- Université Paris Cité, Imagine Institute, Paris 75015, France
| | - Despina Moshous
- Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer, INSERM UMR 1163, Imagine Institute, 24 boulevard du Montparnasse, Paris 75015, France
- Université Paris Cité, Imagine Institute, Paris 75015, France
- Department of Pediatric Immunology, Hematology and Rheumatology, Necker-Enfants Malades Hospital, (APHP), Paris 75015, France
| | - Marie Roelens
- Université Paris Cité, Imagine Institute, Paris 75015, France
- Centre de références des déficits immunitaires Héréditaires (CEREDIH), Necker-Enfants Malades Hospital APHP, Paris 75015, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris 75005, France
| | - Caroline Kannengiesser
- Assistance Publique des Hôpitaux de Paris, Hôpital Bichat, Service de Génétique, Université Paris Diderot, Paris 75018, France
| | - Patrick Revy
- Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer, INSERM UMR 1163, Imagine Institute, 24 boulevard du Montparnasse, Paris 75015, France
- Université Paris Cité, Imagine Institute, Paris 75015, France
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Aureli S, Cardenas VB, Raniolo S, Limongelli V. Conformational plasticity and allosteric communication networks explain Shelterin protein TPP1 binding to human telomerase. Commun Chem 2023; 6:242. [PMID: 37935941 PMCID: PMC10630336 DOI: 10.1038/s42004-023-01040-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 10/24/2023] [Indexed: 11/09/2023] Open
Abstract
The Shelterin complex protein TPP1 interacts with human telomerase (TERT) by means of the TEL-patch region, controlling telomere homeostasis. Aberrations in the TPP1-TERT heterodimer formation might lead to short telomeres and severe diseases like dyskeratosis congenita and Hoyeraal-Hreidarsson syndrome. In the present study, we provide a thorough characterization of the structural properties of the TPP1's OB-domain by combining data coming from microsecond-long molecular dynamics calculations, time-series analyses, and graph-based networks. Our results show that the TEL-patch conformational freedom is influenced by a network of long-range amino acid communications that together determine the proper TPP1-TERT binding. Furthermore, we reveal that in TPP1 pathological variants Glu169Δ, Lys170Δ and Leu95Gln, the TEL-patch plasticity is reduced, affecting the correct binding to TERT and, in turn, telomere processivity, which eventually leads to accelerated aging of affected cells. Our study provides a structural basis for the design of TPP1-targeting ligands with therapeutic potential against cancer and telomeropathies.
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Affiliation(s)
- Simone Aureli
- Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera italiana (USI), via G. Buffi 13, Lugano, CH-6900, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneve, Rue Michel-Servet 1, Geneva, CH-1211, Switzerland
- Swiss Institute of Bioinformatics, University of Geneve, Geneva, CH-1206, Switzerland
| | - Vince Bart Cardenas
- Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera italiana (USI), via G. Buffi 13, Lugano, CH-6900, Switzerland
| | - Stefano Raniolo
- Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera italiana (USI), via G. Buffi 13, Lugano, CH-6900, Switzerland
| | - Vittorio Limongelli
- Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera italiana (USI), via G. Buffi 13, Lugano, CH-6900, Switzerland.
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Nelson N, Feurstein S, Niaz A, Truong J, Holien JK, Lucas S, Fairfax K, Dickinson J, Bryan TM. Functional genomics for curation of variants in telomere biology disorder associated genes: A systematic review. Genet Med 2023; 25:100354. [PMID: 36496180 DOI: 10.1016/j.gim.2022.11.021] [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: 06/28/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Patients with an underlying telomere biology disorder (TBD) have variable clinical presentations, and they can be challenging to diagnose clinically. A genomic diagnosis for patients presenting with TBD is vital for optimal treatment. Unfortunately, many variants identified during diagnostic testing are variants of uncertain significance. This complicates management decisions, delays treatment, and risks nonuptake of potentially curative therapies. Improved application of functional genomic evidence may reduce variants of uncertain significance classifications. METHODS We systematically searched the literature for published functional assays interrogating TBD gene variants. When possible, established likely benign/benign and likely pathogenic/pathogenic variants were used to estimate the assay sensitivity, specificity, positive predictive value, negative predictive value, and odds of pathogenicity. RESULTS In total, 3131 articles were screened and 151 met inclusion criteria. Sufficient data to enable a PS3/BS3 recommendation were available for TERT variants only. We recommend that PS3 and BS3 can be applied at a moderate and supportive level, respectively. PS3/BS3 application was limited by a lack of assay standardization and limited inclusion of benign variants. CONCLUSION Further assay standardization and assessment of benign variants are required for optimal use of the PS3/BS3 criterion for TBD gene variant classification.
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Affiliation(s)
- Niles Nelson
- The Menzies Institute for Medical Research, College of Health and Medicine, The University of Tasmania, Hobart, Tasmania, Australia; Department of Molecular Medicine, The Royal Hobart Hospital, Hobart, Tasmania, Australia; Department of Molecular Haematology, The Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
| | - Simone Feurstein
- Section of Hematology, Oncology, and Rheumatology, Department of Internal Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Aram Niaz
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales, Australia
| | - Jia Truong
- School of Science, STEM College, RMIT University, Bundoora, Victoria, Australia
| | - Jessica K Holien
- School of Science, STEM College, RMIT University, Bundoora, Victoria, Australia
| | - Sionne Lucas
- The Menzies Institute for Medical Research, College of Health and Medicine, The University of Tasmania, Hobart, Tasmania, Australia
| | - Kirsten Fairfax
- The Menzies Institute for Medical Research, College of Health and Medicine, The University of Tasmania, Hobart, Tasmania, Australia
| | - Joanne Dickinson
- The Menzies Institute for Medical Research, College of Health and Medicine, The University of Tasmania, Hobart, Tasmania, Australia
| | - Tracy M Bryan
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales, Australia
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Revy P, Kannengiesser C, Bertuch AA. Genetics of human telomere biology disorders. Nat Rev Genet 2023; 24:86-108. [PMID: 36151328 DOI: 10.1038/s41576-022-00527-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2022] [Indexed: 01/24/2023]
Abstract
Telomeres are specialized nucleoprotein structures at the ends of linear chromosomes that prevent the activation of DNA damage response and repair pathways. Numerous factors localize at telomeres to regulate their length, structure and function, to avert replicative senescence or genome instability and cell death. In humans, Mendelian defects in several of these factors can result in abnormally short or dysfunctional telomeres, causing a group of rare heterogeneous premature-ageing diseases, termed telomeropathies, short-telomere syndromes or telomere biology disorders (TBDs). Here, we review the TBD-causing genes identified so far and describe their main functions associated with telomere biology. We present molecular aspects of TBDs, including genetic anticipation, phenocopy, incomplete penetrance and somatic genetic rescue, which underlie the complexity of these diseases. We also discuss the implications of phenotypic and genetic features of TBDs on fundamental aspects related to human telomere biology, ageing and cancer, as well as on diagnostic, therapeutic and clinical approaches.
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Affiliation(s)
- Patrick Revy
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue Nationale contre le Cancer, Paris, France.
- Université Paris Cité, Imagine Institute, Paris, France.
| | - Caroline Kannengiesser
- APHP Service de Génétique, Hôpital Bichat, Paris, France
- Inserm U1152, Université Paris Cité, Paris, France
| | - Alison A Bertuch
- Departments of Paediatrics and Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
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