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Chaudhari S, Acharya LP, Jasti DB, Ware AP, Gorthi SP, Satyamoorthy K. Discovery of a Novel Shared Variant Among RTEL1 Gene and RTEL1-TNFRSF6B lncRNA at Chromosome 20q13.33 in Familial Progressive Myoclonus Epilepsy. Int J Genomics 2024; 2024:7518528. [PMID: 39156922 PMCID: PMC11330336 DOI: 10.1155/2024/7518528] [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: 11/23/2023] [Revised: 04/17/2024] [Accepted: 07/20/2024] [Indexed: 08/20/2024] Open
Abstract
Background: Progressive myoclonus epilepsy (PME) is a neurodegenerative disorder marked by recurrent seizures and progressive myoclonus. To date, based on the phenotypes and causal genes, more than 40 subtypes of PMEs have been identified, and more remain to be characterized. Our study is aimed at identifying the aberrant gene(s) possibly associated with PMEs in two siblings born to asymptomatic parents, in the absence of known genetic mutations. Methods: Clinical assessments and molecular analyses, such as the repeat expansion test for CSTB; SCA1, 2, 3, 6, and 7; whole exome sequencing (WES); and mitochondrial genome sequencing coupled with computational analysis, were performed. Results: A family-based segregation analysis of WES data was performed to identify novel genes associated with PMEs. The potassium channel, KCNH8 [c.298T>C; (p.Tyr100His)], a DNA repair gene, regulator of telomere elongation helicase 1 (RTEL1) [c.691G>T; (p.Asp231Tyr)] and long noncoding RNA, RTEL1-TNFRSF6B [chr20:62298898_G>T; NR_037882.1, hg19] were among the candidate genes that were found to be associated with PMEs. These homozygous variations in siblings belong to genes with a loss-of-function intolerant (pLI) score of ≤ 0.86, expected to be detrimental by multiple computational analyses, and were heterozygous in parents. Additionally, computational analysis and the expression of RTEL1 and RTEL1-TNFRSF6B revealed that RTEL1-TNFRSF6B may modulate RTEL1 via hsa-miR-3529-3p. In the patient with the severe phenotype, a further deleterious mutation in SLC22A17 was identified. No de novo variants specific to these probands were identified in the mitochondrial genome. Conclusions: Our study is the first to report variants in KCNH8, RTEL1, and RTEL1-TNFRSF6B among PME cases. These genes when characterized fully may shed light on pathogenicity and have the potential to be used in the diagnosis of PME.
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Affiliation(s)
- Sima Chaudhari
- Department of Cell and Molecular BiologyManipal School of Life SciencesManipal Academy of Higher Education 576104, Manipal, Karnataka, India
| | - Lavanya Prakash Acharya
- Department of Cell and Molecular BiologyManipal School of Life SciencesManipal Academy of Higher Education 576104, Manipal, Karnataka, India
| | - Dushyanth Babu Jasti
- Department of NeurologyKasturba Medical College 576104, Manipal, Karnataka, India
| | - Akshay Pramod Ware
- Department of BioinformaticsManipal School of Life SciencesManipal Academy of Higher Education 576104, Manipal, Karnataka, India
| | - Sankar Prasad Gorthi
- Department of NeurologyKasturba Medical College 576104, Manipal, Karnataka, India
- Department of NeurologyBharati Hospital and Research CenterBharati Vidyapeeth (Deemed to Be University) Medical College and Hospital, Dhankawadi 411043, Pune, Maharashtra, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular BiologyManipal School of Life SciencesManipal Academy of Higher Education 576104, Manipal, Karnataka, India
- SDM College of Medical Sciences and HospitalShri Dharmasthala Manjunatheshwara (SDM) University, Manjushree Nagar, Sattur 580009, Dharwad, Karnataka, India
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Fioredda F, Beccaria A, Casartelli P, Turrini E, Contratto C, Giarratana MC, Bagnasco F, Saettini F, Pillon M, Marzollo A, Zanardi S, Civino A, Onofrillo D, Lanciotti M, Ceccherini I, Grossi A, Coviello D, Terranova P, Lupia M, Del Borrello G, Uva P, Cangelosi D, Cavalca G, Miano M, Dufour C. Late-onset and long-lasting neutropenias in the young: A new entity anticipating immune-dysregulation disorders. Am J Hematol 2024; 99:534-542. [PMID: 38282561 DOI: 10.1002/ajh.27221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/09/2023] [Accepted: 01/01/2024] [Indexed: 01/30/2024]
Abstract
This study identifies a new chronic form of immune neutropenia in the young with or without detectable indirect anti-neutrophil antibodies, characterized by mild/moderate neutropenia low risk of severe infection (14%), tendency to develop autoimmune phenomena over the course of the disease (cumulative incidence of 58.6% after 20 years of disease duration), leukopenia, progressive reduction of absolute lymphocyte count and a T- and B-cell profile similar to autoimmune disorders like Sjogren syndrome, rheumatoid arthritis, and systemic lupus erythematosus (increased HLADR+ and CD3 + TCRγδ cells, reduced T regulatory cells, increased double-negative B and a tendency to reduced B memory cells). In a minority of patients, P/LP variants related to primary immuno-regulatory disorders were found. This new form may fit the group of "Likely acquired neutropenia," a provisional category included in the recent International Guidelines on Diagnosis and Management of Neutropenia of EHA and EUNET INNOCHRON ACTION 18233. The early recognition of this form of neutropenia would help clinicians to delineate better specific monitoring plans, genetic counseling, and potentially targeted therapies.
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Affiliation(s)
- F Fioredda
- Haematology Unit-IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - A Beccaria
- Epidemiology and Biostatistics Unit and DOPO Clinic-IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - P Casartelli
- Haematology Unit-IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - E Turrini
- Unit of Pediatric and OncoHematology, Department of Mother and Child, Azienda Ospedaliera Universitaria, Parma, Italy
| | - C Contratto
- Haematology Unit-IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - M C Giarratana
- Haematology Unit-IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - F Bagnasco
- Biostatistics Unit, Scientific Directorate, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - F Saettini
- Department of Pediatric Onco-Hematology, San Gerardo Hospital, Fondazione MBBM, Università degli Studi di Milano-Bicocca, Monza, Italy
| | - M Pillon
- Pediatric Hematology-Oncology Unit, Department of Women's and Children's Health, AziendaOspedaliera-University of Padova, Padua, Italy
| | - A Marzollo
- Pediatric Hematology-Oncology Unit, Department of Women's and Children's Health, AziendaOspedaliera-University of Padova, Padua, Italy
| | - S Zanardi
- Haematology Unit-IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - A Civino
- Unit of Rheumathology and Immunology-ospedale Vito Fazzi, Lecce, Italy
| | - D Onofrillo
- Pediatric Hematology and Oncology Unit, Department of Hematology, Spirito Santo Hospital, Pescara, Italy
| | - M Lanciotti
- Haematology Unit-IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - I Ceccherini
- Laboratory of Genetics and Genomics of Rare Diseases, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - A Grossi
- Laboratory of Genetics and Genomics of Rare Diseases, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - D Coviello
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - P Terranova
- Haematology Unit-IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - M Lupia
- Haematology Unit-IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - G Del Borrello
- Haematology Unit-IRCCS Istituto Giannina Gaslini, Genova, Italy
- Pediatric OncoHematology, Pediatrics Department, Hospital Città Della Salute e Della Scienza, University of Turin, Turin, Italy
| | - P Uva
- Clinical Bioinformatics Unit, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - D Cangelosi
- Clinical Bioinformatics Unit, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - G Cavalca
- Clinical Bioinformatics Unit, IRCCS Istituto Giannina Gaslini, Genova, Italy
- University of Bologna, Bologna, Italy
| | - M Miano
- Haematology Unit-IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - C Dufour
- Haematology Unit-IRCCS Istituto Giannina Gaslini, Genova, Italy
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Smoom R, May CL, Skordalakes E, Kaestner KH, Tzfati Y. Separation of telomere protection from length regulation by two different point mutations at amino acid 492 of RTEL1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582005. [PMID: 38464183 PMCID: PMC10925190 DOI: 10.1101/2024.02.26.582005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
RTEL1 is an essential DNA helicase that plays multiple roles in genome stability and telomere length regulation. A variant of RTEL1 with a lysine at position 492 is associated with short telomeres in Mus spretus , while a conserved methionine at this position is found in M. musculus, which has ultra-long telomeres. In humans, a missense mutation at this position ( RTEL1 M492I ) causes a fatal telomere biology disease termed Hoyeraal-Hreidarsson syndrome (HHS). We previously described a M. musculus mouse model termed 'Telomouse', in which changing methionine 492 to a lysine (M492K) shortened the telomeres to their length in humans. Here, we report on the derivation of a mouse strain carrying the M492I mutation, termed 'HHS mouse'. The HHS mouse telomeres are not as short as those of Telomice but nevertheless they display higher levels of telomeric DNA damage, fragility and recombination, associated with anaphase bridges and micronuclei. These observations indicate that the two mutations separate critical functions of RTEL1: M492K mainly reduces the telomere length setpoint, while M492I predominantly disrupts telomere protection. The two mouse models enable dissecting the mechanistic roles of RTEL1 and the different contributions of short telomeres and DNA damage to telomere biology diseases, genomic instability, cancer, and aging.
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Hourvitz N, Awad A, Tzfati Y. The many faces of the helicase RTEL1 at telomeres and beyond. Trends Cell Biol 2024; 34:109-121. [PMID: 37532653 DOI: 10.1016/j.tcb.2023.07.002] [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: 04/13/2023] [Revised: 07/01/2023] [Accepted: 07/05/2023] [Indexed: 08/04/2023]
Abstract
Regulator of telomere elongation 1 (RTEL1) is known as a DNA helicase that is important for telomeres and genome integrity. However, the diverse phenotypes of RTEL1 dysfunction, the wide spectrum of symptoms caused by germline RTEL1 mutations, and the association of RTEL1 mutations with cancers suggest that RTEL1 is a complex machine that interacts with DNA, RNA, and proteins, and functions in diverse cellular pathways. We summarize the proposed functions of RTEL1 and discuss their implications for telomere maintenance. Studying RTEL1 is crucial for understanding the complex interplay between telomere maintenance and other nuclear pathways, and how compromising these pathways causes telomere biology diseases, various aging-associated pathologies, and cancer.
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Affiliation(s)
- Noa Hourvitz
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Safra Campus, Jerusalem 91904, Israel
| | - Aya Awad
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Safra Campus, Jerusalem 91904, Israel
| | - Yehuda Tzfati
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Safra Campus, Jerusalem 91904, Israel.
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Schmit MM, Baxley RM, Wang L, Hinderlie P, Kaufman M, Simon E, Raju A, Miller JS, Bielinsky AK. A critical threshold of MCM10 is required to maintain genome stability during differentiation of induced pluripotent stem cells into natural killer cells. Open Biol 2024; 14:230407. [PMID: 38262603 PMCID: PMC10805602 DOI: 10.1098/rsob.230407] [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: 11/01/2023] [Accepted: 11/23/2023] [Indexed: 01/25/2024] Open
Abstract
Natural killer (NK) cell deficiency (NKD) is a rare disease in which NK cell function is reduced, leaving affected individuals susceptible to repeated viral infections and cancer. Recently, a patient with NKD was identified carrying compound heterozygous variants of MCM10 (minichromosome maintenance protein 10), an essential gene required for DNA replication, that caused a significant decrease in the amount of functional MCM10. NKD in this patient presented as loss of functionally mature late-stage NK cells. To understand how MCM10 deficiency affects NK cell development, we generated MCM10 heterozygous (MCM10+/-) induced pluripotent stem cell (iPSC) lines. Analyses of these cell lines demonstrated that MCM10 was haploinsufficient, similar to results in other human cell lines. Reduced levels of MCM10 in mutant iPSCs was associated with impaired clonogenic survival and increased genomic instability, including micronuclei formation and telomere erosion. The severity of these phenotypes correlated with the extent of MCM10 depletion. Significantly, MCM10+/- iPSCs displayed defects in NK cell differentiation, exhibiting reduced yields of hematopoietic stem cells (HSCs). Although MCM10+/- HSCs were able to give rise to lymphoid progenitors, these did not generate mature NK cells. The lack of mature NK cells coincided with telomere erosion, suggesting that NKD caused by these MCM10 variants arose from the accumulation of genomic instability including degradation of chromosome ends.
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Affiliation(s)
- Megan M. Schmit
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Ryan M. Baxley
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Liangjun Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Peter Hinderlie
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Marissa Kaufman
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Emily Simon
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Anjali Raju
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Jeffrey S. Miller
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
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Schertzer M, Jullien L, Pinto AL, Calado RT, Revy P, Londoño-Vallejo A. Human RTEL1 Interacts with KPNB1 (Importin β) and NUP153 and Connects Nuclear Import to Nuclear Envelope Stability in S-Phase. Cells 2023; 12:2798. [PMID: 38132118 PMCID: PMC10741959 DOI: 10.3390/cells12242798] [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: 11/07/2023] [Revised: 11/29/2023] [Accepted: 12/03/2023] [Indexed: 12/23/2023] Open
Abstract
Regulator of TElomere Length Helicase 1 (RTEL1) is a helicase required for telomere maintenance and genome replication and repair. RTEL1 has been previously shown to participate in the nuclear export of small nuclear RNAs. Here we show that RTEL1 deficiency leads to a nuclear envelope destabilization exclusively in cells entering S-phase and in direct connection to origin firing. We discovered that inhibiting protein import also leads to similar, albeit non-cell cycle-related, nuclear envelope disruptions. Remarkably, overexpression of wild-type RTEL1, or of its C-terminal part lacking the helicase domain, protects cells against nuclear envelope anomalies mediated by protein import inhibition. We identified distinct domains in the C-terminus of RTEL1 essential for the interaction with KPNB1 (importin β) and NUP153, respectively, and we demonstrated that, on its own, the latter domain can promote the dynamic nuclear internalization of peptides that freely diffuse through the nuclear pore. Consistent with putative functions exerted in protein import, RTEL1 can be visualized on both sides of the nuclear pore using high-resolution microscopy. In all, our work points to an unanticipated, helicase-independent, role of RTEL1 in connecting both nucleocytoplasmic trafficking and nuclear envelope integrity to genome replication initiation in S-phase.
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Affiliation(s)
- Michael Schertzer
- Institut Curie, PSL Research University, CNRS, UMR3244, F-75005 Paris, France;
- Sorbonne Universités, CNRS, UMR3244, F-75005 Paris, France
| | - Laurent Jullien
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue Contre le Cancer, F-75006 Paris, France; (L.J.); (P.R.)
- Paris Descartes–Sorbonne Paris Cité University, Imagine Institute, F-75015 Paris, France
| | - André L. Pinto
- Department of Medical Imaging, Hematology, and Oncology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto 14049-900, Brazil; (A.L.P.); (R.T.C.)
| | - Rodrigo T. Calado
- Department of Medical Imaging, Hematology, and Oncology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto 14049-900, Brazil; (A.L.P.); (R.T.C.)
| | - Patrick Revy
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue Contre le Cancer, F-75006 Paris, France; (L.J.); (P.R.)
- Paris Descartes–Sorbonne Paris Cité University, Imagine Institute, F-75015 Paris, France
| | - Arturo Londoño-Vallejo
- Institut Curie, PSL Research University, CNRS, UMR3244, F-75005 Paris, France;
- Sorbonne Universités, CNRS, UMR3244, F-75005 Paris, France
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Banaszak LG, Smith-Simmer K, Shoger K, Lovrien L, Malik A, Sandbo N, Sultan S, Guzy R, Lowery EM, Churpek JE. Implementation of a prospective screening strategy to identify adults with a telomere biology disorder among those undergoing lung transplant evaluation for interstitial lung disease. Respir Med 2023; 220:107464. [PMID: 37951311 DOI: 10.1016/j.rmed.2023.107464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 11/13/2023]
Abstract
INTRODUCTION Patients with interstitial lung disease (ILD) secondary to telomere biology disorders (TBD) experience increased morbidity after lung transplantation. Identifying patients with TBD may allow for personalized management to facilitate better outcomes. However, establishing a TBD diagnosis in adults is challenging. METHODS A TBD screening questionnaire was introduced prospectively into the lung transplant evaluation. Patients with ILD screening positive were referred for comprehensive TBD phenotyping and concurrent telomere length measurement and germline genetic testing. RESULTS Of 98 patients, 32 (33%) screened positive. Eight patients (8% of total; 25% of patients with a positive screen) met strict TBD diagnostic criteria, requiring either critically short lymphocyte telomeres (<1st percentile) (n = 4), a pathogenic variant in a TBD-associated gene (n = 1), or both (n = 3) along with a TBD clinical phenotype. Additional patients not meeting strict diagnostic criteria had histories consistent with TBD along with telomere lengths <10th percentile and/or rare variants in TBD-associated genes, highlighting a critical need to refine TBD diagnostic criteria for this patient population. CONCLUSION A TBD phenotype screening questionnaire in patients with ILD undergoing lung transplant evaluation has a diagnostic yield of 25%. Additional gene discovery, rare variant functional testing, and refined TBD diagnostic criteria are needed to realize the maximum benefit of testing for TBD in patients undergoing lung transplantation.
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Affiliation(s)
- Lauren G Banaszak
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA.
| | - Kelcy Smith-Simmer
- Oncology Genetics, University of Wisconsin Carbone Cancer Center, UW Health, Madison, WI, 53705, USA
| | - Kyle Shoger
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Lauren Lovrien
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Amy Malik
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Nathan Sandbo
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Samir Sultan
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Robert Guzy
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Erin M Lowery
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Jane E Churpek
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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Sharma R, Oak N, Chen W, Gogal R, Kirschner M, Beier F, Schnieders MJ, Spies M, Nichols KE, Wlodarski M. Germline landscape of RPA1, RPA2 and RPA3 variants in pediatric malignancies: identification of RPA1 as a novel cancer predisposition candidate gene. Front Oncol 2023; 13:1229507. [PMID: 37869077 PMCID: PMC10588448 DOI: 10.3389/fonc.2023.1229507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/18/2023] [Indexed: 10/24/2023] Open
Abstract
Replication Protein A (RPA) is single-strand DNA binding protein that plays a key role in the replication and repair of DNA. RPA is a heterotrimer made of 3 subunits - RPA1, RPA2, and RPA3. Germline pathogenic variants affecting RPA1 were recently described in patients with Telomere Biology Disorders (TBD), also known as dyskeratosis congenita or short telomere syndrome. Premature telomere shortening is a hallmark of TBD and results in bone marrow failure and predisposition to hematologic malignancies. Building on the finding that somatic mutations in RPA subunit genes occur in ~1% of cancers, we hypothesized that germline RPA alterations might be enriched in human cancers. Because germline RPA1 mutations are linked to early onset TBD with predisposition to myelodysplastic syndromes, we interrogated pediatric cancer cohorts to define the prevalence and spectrum of rare/novel and putative damaging germline RPA1, RPA2, and RPA3 variants. In this study of 5,993 children with cancer, 75 (1.25%) harbored heterozygous rare (non-cancer population allele frequency (AF) < 0.1%) variants in the RPA heterotrimer genes, of which 51 cases (0.85%) had ultra-rare (AF < 0.005%) or novel variants. Compared with Genome Aggregation Database (gnomAD) non-cancer controls, there was significant enrichment of ultra-rare and novel RPA1, but not RPA2 or RPA3, germline variants in our cohort (adjusted p-value < 0.05). Taken together, these findings suggest that germline putative damaging variants affecting RPA1 are found in excess in children with cancer, warranting further investigation into the functional role of these variants in oncogenesis.
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Affiliation(s)
- Richa Sharma
- Department of Hematology, St. Jude Children´s Research Hospital, Memphis, TN, United States
| | - Ninad Oak
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Wenan Chen
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Rose Gogal
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Martin Kirschner
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Bonn, Germany
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Bonn, Germany
| | - Michael J. Schnieders
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Maria Spies
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Kim E. Nichols
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Marcin Wlodarski
- Department of Hematology, St. Jude Children´s Research Hospital, Memphis, TN, United States
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Shin U, Lee Y. Unraveling DNA Repair Processes In Vivo: Insights from Zebrafish Studies. Int J Mol Sci 2023; 24:13120. [PMID: 37685935 PMCID: PMC10487404 DOI: 10.3390/ijms241713120] [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: 07/21/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
The critical role of the DNA repair system in preserving the health and survival of living organisms is widely recognized as dysfunction within this system can result in a broad range of severe conditions, including neurodegenerative diseases, blood disorders, infertility, and cancer. Despite comprehensive research on the molecular and cellular mechanisms of DNA repair pathways, there remains a significant knowledge gap concerning these processes at an organismal level. The teleost zebrafish has emerged as a powerful model organism for investigating these intricate DNA repair mechanisms. Their utility arises from a combination of their well-characterized genomic information, the ability to visualize specific phenotype outcomes in distinct cells and tissues, and the availability of diverse genetic experimental approaches. In this review, we provide an in-depth overview of recent advancements in our understanding of the in vivo roles of DNA repair pathways. We cover a variety of critical biological processes including neurogenesis, hematopoiesis, germ cell development, tumorigenesis, and aging, with a specific emphasis on findings obtained from the use of zebrafish as a model system. Our comprehensive review highlights the importance of zebrafish in enhancing our understanding of the functions of DNA repair systems at the organismal level and paves the way for future investigations in this field.
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Affiliation(s)
- Unbeom Shin
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yoonsung Lee
- Clinical Research Institute, Kyung Hee University Hospital at Gangdong, School of Medicine, Kyung Hee University, Seoul 05278, Republic of Korea
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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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11
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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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12
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Hassani MA, Murid J, Yan J. Regulator of telomere elongation helicase 1 gene and its association with malignancy. Cancer Rep (Hoboken) 2022; 6:e1735. [PMID: 36253342 PMCID: PMC9875622 DOI: 10.1002/cnr2.1735] [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: 06/14/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND With the progression of next-generation sequencing technologies, researchers have identified numerous variants of the regulator of telomere elongation helicase 1 (RTEL1) gene that are associated with a broad spectrum of phenotypic manifestations, including malignancies. At the molecular level, RTEL1 is involved in the regulation of the repair, replication, and transcription of deoxyribonucleic acid (DNA) and the maintenance of telomere length. RTEL1 can act both as a promotor and inhibitor of tumorigenesis. Here, we review the potential mechanisms implicated in the malignant transformation of tissues under conditions of RTEL1 deficiency or its aberrant overexpression. RECENT FINDINGS A major hemostatic challenge during RTEL1 dysfunction could arise from its unbalanced activity for unwinding guanine-rich quadruplex DNA (G4-DNA) structures. In contrast, RTEL1 deficiency leads to alterations in telomeric and genome-wide DNA maintenance mechanisms, ribonucleoprotein metabolism, and the creation of an inflammatory and immune-deficient microenvironment, all promoting malignancy. Additionally, we hypothesize that functionally similar molecules could act to compensate for the deteriorated functions of RTEL1, thereby facilitating the survival of malignant cells. On the contrary, RTEL1 over-expression was directed toward G4-unwinding, by promoting replication fork progression and maintaining intact telomeres, may facilitate malignant transformation and proliferation of various pre-malignant cellular compartments. CONCLUSIONS Therefore, restoring the equilibrium of RTEL1 functions could serve as a therapeutic approach for preventing and treating malignancies.
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Affiliation(s)
- Mohammad Arian Hassani
- Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Dalian Key Laboratory of HematologySecond Hospital of Dalian Medical UniversityDalianChina,Department of Hematology, Endocrinology and Rheumatology, Ali Abad Teaching HospitalKabul University of Medical SciencesJamal menaKabulAfghanistan
| | - Jamshid Murid
- Department of Hematology, Endocrinology and Rheumatology, Ali Abad Teaching HospitalKabul University of Medical SciencesJamal menaKabulAfghanistan
| | - Jinsong Yan
- Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Dalian Key Laboratory of HematologySecond Hospital of Dalian Medical UniversityDalianChina,Diamond Bay Institute of HematologySecond Hospital of Dalian Medical UniversityDalianChina
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13
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Milardi G, Di Lorenzo B, Gerosa J, Barzaghi F, Di Matteo G, Omrani M, Jofra T, Merelli I, Barcella M, Filippini M, Conti A, Ferrua F, Pozzo Giuffrida F, Dionisio F, Rovere‐Querini P, Marktel S, Assanelli A, Piemontese S, Brigida I, Zoccolillo M, Cirillo E, Giardino G, Danieli MG, Specchia F, Pacillo L, Di Cesare S, Giancotta C, Romano F, Matarese A, Chetta AA, Trimarchi M, Laurenzi A, De Pellegrin M, Darin S, Montin D, Marinoni M, Dellepiane RM, Sordi V, Lougaris V, Vacca A, Melzi R, Nano R, Azzari C, Bongiovanni L, Pignata C, Cancrini C, Plebani A, Piemonti L, Petrovas C, Di Micco R, Ponzoni M, Aiuti A, Cicalese MP, Fousteri G. Follicular helper T cell signature of replicative exhaustion, apoptosis, and senescence in common variable immunodeficiency. Eur J Immunol 2022; 52:1171-1189. [PMID: 35562849 PMCID: PMC9542315 DOI: 10.1002/eji.202149480] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 02/08/2022] [Accepted: 05/09/2022] [Indexed: 11/06/2022]
Abstract
Common variable immunodeficiency (CVID) is the most frequent primary antibody deficiency whereby follicular helper T (Tfh) cells fail to establish productive responses with B cells in germinal centers. Here, we analyzed the frequency, phenotype, transcriptome, and function of circulating Tfh (cTfh) cells in CVID patients displaying autoimmunity as an additional phenotype. A group of patients showed a high frequency of cTfh1 cells and a prominent expression of PD-1 and ICOS as well as a cTfh mRNA signature consistent with highly activated, but exhausted, senescent, and apoptotic cells. Plasmatic CXCL13 levels were elevated in this group and positively correlated with cTfh1 cell frequency and PD-1 levels. Monoallelic variants in RTEL1, a telomere length- and DNA repair-related gene, were identified in four patients belonging to this group. Their blood lymphocytes showed shortened telomeres, while their cTfh were more prone to apoptosis. These data point toward a novel pathogenetic mechanism in CVID, whereby alterations in DNA repair and telomere elongation might predispose to antibody deficiency. A Th1, highly activated but exhausted and apoptotic cTfh phenotype was associated with this form of CVID.
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Affiliation(s)
- Giulia Milardi
- Division of Immunology, Transplantation, and Infectious DiseasesDiabetes Research InstituteIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Biagio Di Lorenzo
- Division of Immunology, Transplantation, and Infectious DiseasesDiabetes Research InstituteIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Jolanda Gerosa
- Division of Immunology, Transplantation, and Infectious DiseasesDiabetes Research InstituteIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Federica Barzaghi
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
- Pathogenesis and therapy of primary immunodeficiencies UnitSan Raffaele Telethon Institute for Gene TherapySr‐TIGETIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Gigliola Di Matteo
- Department of Systems Medicine, University of Rome Tor VergataVia Cracovia 50Rome00133Italy
- Immune and Infectious Diseases Division, Research Unit of Primary Immunodeficiencies, Academic Department of PediatricsBambino Gesù Children's HospitalIRCCSPiazza di Sant'Onofrio 4Rome00165Italy
| | - Maryam Omrani
- Pathogenesis and therapy of primary immunodeficiencies UnitSan Raffaele Telethon Institute for Gene TherapySr‐TIGETIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
- Department of Computer Science, Systems and Communication, University of Milano‐BicoccaPiazza dell'Ateneo Nuovo 1Milan20126Italy
| | - Tatiana Jofra
- Division of Immunology, Transplantation, and Infectious DiseasesDiabetes Research InstituteIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Ivan Merelli
- Pathogenesis and therapy of primary immunodeficiencies UnitSan Raffaele Telethon Institute for Gene TherapySr‐TIGETIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
- Department of BioinformaticsInstitute for Biomedical TechnologiesNational Research CouncilVia Fratelli Cervi 93Segrate20090Italy
| | - Matteo Barcella
- Pathogenesis and therapy of primary immunodeficiencies UnitSan Raffaele Telethon Institute for Gene TherapySr‐TIGETIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Matteo Filippini
- Division of Immunology, Transplantation, and Infectious DiseasesDiabetes Research InstituteIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Anastasia Conti
- Pathogenesis and therapy of primary immunodeficiencies UnitSan Raffaele Telethon Institute for Gene TherapySr‐TIGETIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Francesca Ferrua
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
- Pathogenesis and therapy of primary immunodeficiencies UnitSan Raffaele Telethon Institute for Gene TherapySr‐TIGETIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Francesco Pozzo Giuffrida
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
- Pathogenesis and therapy of primary immunodeficiencies UnitSan Raffaele Telethon Institute for Gene TherapySr‐TIGETIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Francesca Dionisio
- Pathogenesis and therapy of primary immunodeficiencies UnitSan Raffaele Telethon Institute for Gene TherapySr‐TIGETIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Patrizia Rovere‐Querini
- Department of ImmunologyTransplantation and Infectious DiseasesIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Sarah Marktel
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Andrea Assanelli
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Simona Piemontese
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Immacolata Brigida
- Pathogenesis and therapy of primary immunodeficiencies UnitSan Raffaele Telethon Institute for Gene TherapySr‐TIGETIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Matteo Zoccolillo
- Pathogenesis and therapy of primary immunodeficiencies UnitSan Raffaele Telethon Institute for Gene TherapySr‐TIGETIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Emilia Cirillo
- Department of Translational Medical SciencesSection of PediatricsFederico II University of NaplesCorso Umberto I, 40, 80138Italy
| | - Giuliana Giardino
- Department of Translational Medical SciencesSection of PediatricsFederico II University of NaplesCorso Umberto I, 40, 80138Italy
| | - Maria Giovanna Danieli
- Department of Clinical and Molecular SciencesMarche Polytechnic University of AnconaClinica MedicaVia Tronto 10/aAncona60126Italy
| | - Fernando Specchia
- Department of PediatricsS. Orsola‐Malpighi HospitalUniversity of BolognaVia Giuseppe Massarenti 9Bologna40138Italy
| | - Lucia Pacillo
- Department of Systems Medicine, University of Rome Tor VergataVia Cracovia 50Rome00133Italy
- Immune and Infectious Diseases Division, Research Unit of Primary Immunodeficiencies, Academic Department of PediatricsBambino Gesù Children's HospitalIRCCSPiazza di Sant'Onofrio 4Rome00165Italy
| | - Silvia Di Cesare
- Department of Systems Medicine, University of Rome Tor VergataVia Cracovia 50Rome00133Italy
- Immune and Infectious Diseases Division, Research Unit of Primary Immunodeficiencies, Academic Department of PediatricsBambino Gesù Children's HospitalIRCCSPiazza di Sant'Onofrio 4Rome00165Italy
| | - Carmela Giancotta
- Department of Systems Medicine, University of Rome Tor VergataVia Cracovia 50Rome00133Italy
- Immune and Infectious Diseases Division, Research Unit of Primary Immunodeficiencies, Academic Department of PediatricsBambino Gesù Children's HospitalIRCCSPiazza di Sant'Onofrio 4Rome00165Italy
| | - Francesca Romano
- Pediatric Immunology DivisionDepartment of PediatricsAnna Meyer Children's University HospitalViale Gaetano Pieraccini 24Florence50139Italy
| | - Alessandro Matarese
- Department of Respiratory MedicineSanti AntonioBiagio and Cesare Arrigo HospitalVia Venezia 16Alessandria15121Italy
| | - Alfredo Antonio Chetta
- Department of Medicine and SurgeryRespiratory Disease and Lung Function UnitUniversity of ParmaStr. dell'Università 12Parma43121Italy
| | - Matteo Trimarchi
- Otorhinolaryngology Unit, Head and Neck Department, IRCCS San Raffaele Scientific InstituteVia Olgettina 60Milan20132Italy
- Pathology UnitIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Andrea Laurenzi
- Division of Immunology, Transplantation, and Infectious DiseasesDiabetes Research InstituteIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Maurizio De Pellegrin
- Unit of Orthopaedics, IRCCS San Raffaele Scientific InstituteVia Olgettina 60Milan20132Italy
| | - Silvia Darin
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Davide Montin
- Department of Pediatrics and Public HealthRegina Margherita HospitalPiazza Polonia 94Turin10126Italy
| | - Maddalena Marinoni
- Pediatric UnitOspedale “F. Del Ponte”Via Filippo del Ponte 19Varese21100Italy
| | - Rosa Maria Dellepiane
- Department of PediatricsFondazione IRCCS Cà Granda Ospedale Maggiore PoliclinicoUniversity of MilanVia Francesco Sforza 35Milan20122Italy
| | - Valeria Sordi
- Division of Immunology, Transplantation, and Infectious DiseasesDiabetes Research InstituteIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Vassilios Lougaris
- Department of Clinical and Experimental SciencesPediatrics Clinic and Institute for Molecular Medicine A. NocivelliUniversity of BresciaPiazza del Mercato 15Brescia25121Italy
| | - Angelo Vacca
- Department of Biomedical Sciences and Human OncologyUniversity of Bari Medical SchoolPiazza Umberto I, 1Bari70121Italy
| | - Raffaella Melzi
- Division of Immunology, Transplantation, and Infectious DiseasesDiabetes Research InstituteIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Rita Nano
- Division of Immunology, Transplantation, and Infectious DiseasesDiabetes Research InstituteIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Chiara Azzari
- Pediatric Immunology DivisionDepartment of PediatricsAnna Meyer Children's University HospitalViale Gaetano Pieraccini 24Florence50139Italy
| | - Lucia Bongiovanni
- Pathology UnitIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Claudio Pignata
- Department of Translational Medical SciencesSection of PediatricsFederico II University of NaplesCorso Umberto I, 40, 80138Italy
| | - Caterina Cancrini
- Department of Systems Medicine, University of Rome Tor VergataVia Cracovia 50Rome00133Italy
- Immune and Infectious Diseases Division, Research Unit of Primary Immunodeficiencies, Academic Department of PediatricsBambino Gesù Children's HospitalIRCCSPiazza di Sant'Onofrio 4Rome00165Italy
| | - Alessandro Plebani
- Department of Clinical and Experimental SciencesPediatrics Clinic and Institute for Molecular Medicine A. NocivelliUniversity of BresciaPiazza del Mercato 15Brescia25121Italy
| | - Lorenzo Piemonti
- Division of Immunology, Transplantation, and Infectious DiseasesDiabetes Research InstituteIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
- Faculty of MedicineUniversity Vita‐Salute San RaffaeleVia Olgettina 60Milan20132Italy
| | - Constantinos Petrovas
- Tissue Analysis Core, Immunology LaboratoryVaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of Health9000 Rockville PikeBethesdaMD20892USA
| | - Raffaella Di Micco
- Pathogenesis and therapy of primary immunodeficiencies UnitSan Raffaele Telethon Institute for Gene TherapySr‐TIGETIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Maurilio Ponzoni
- Pathology UnitIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
- Faculty of MedicineUniversity Vita‐Salute San RaffaeleVia Olgettina 60Milan20132Italy
| | - Alessandro Aiuti
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
- Pathogenesis and therapy of primary immunodeficiencies UnitSan Raffaele Telethon Institute for Gene TherapySr‐TIGETIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
- Faculty of MedicineUniversity Vita‐Salute San RaffaeleVia Olgettina 60Milan20132Italy
| | - Maria Pia Cicalese
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
- Pathogenesis and therapy of primary immunodeficiencies UnitSan Raffaele Telethon Institute for Gene TherapySr‐TIGETIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
| | - Georgia Fousteri
- Division of Immunology, Transplantation, and Infectious DiseasesDiabetes Research InstituteIRCCS San Raffaele HospitalVia Olgettina 60Milan20132Italy
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14
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Murdock HM, Kim HT, Denlinger N, Vachhani P, Hambley B, Manning BS, Gier S, Cho C, Tsai HK, McCurdy S, Ho VT, Koreth J, Soiffer RJ, Ritz J, Carroll MP, Vasu S, Perales MA, Wang ES, Gondek LP, Devine S, Alyea EP, Lindsley RC, Gibson CJ. Impact of diagnostic genetics on remission MRD and transplantation outcomes in older patients with AML. Blood 2022; 139:3546-3557. [PMID: 35286378 PMCID: PMC9203701 DOI: 10.1182/blood.2021014520] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/01/2022] [Indexed: 11/20/2022] Open
Abstract
Older patients with acute myeloid leukemia (AML) have high relapse risk and poor survival after allogeneic hematopoietic cell transplantation (HCT). Younger patients may receive myeloablative conditioning to mitigate relapse risk associated with high-risk genetics or measurable residual disease (MRD), but older adults typically receive reduced-intensity conditioning (RIC) to limit toxicity. To identify factors that drive HCT outcomes in older patients, we performed targeted mutational analysis (variant allele fraction ≥2%) on diagnostic samples from 295 patients with AML aged ≥60 years who underwent HCT in first complete remission, 91% of whom received RIC, and targeted duplex sequencing at remission in a subset comprising 192 patients. In a multivariable model for leukemia-free survival (LFS) including baseline genetic and clinical variables, we defined patients with low (3-year LFS, 85%), intermediate (55%), high (35%), and very high (7%) risk. Before HCT, 79.7% of patients had persistent baseline mutations, including 18.3% with only DNMT3A or TET2 (DT) mutations and 61.4% with other mutations (MRD positive). In univariable analysis, MRD positivity was associated with increased relapse and inferior LFS, compared with DT and MRD-negative mutations. However, in a multivariable model accounting for baseline risk, MRD positivity had no independent impact on LFS, most likely because of its significant association with diagnostic genetic characteristics, including MDS-associated gene mutations, TP53 mutations, and high-risk karyotype. In summary, molecular associations with MRD positivity and transplant outcomes in older patients with AML are driven primarily by baseline genetics, not by mutations present in remission. In this group of patients, where high-intensity conditioning carries substantial risk of toxicity, alternative approaches to mitigating MRD-associated relapse risk are needed.
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Affiliation(s)
- H Moses Murdock
- Division of Hematologic Neoplasia, Department of Medical Oncology, and
| | - Haesook T Kim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Nathan Denlinger
- Division of Hematology, The Ohio State University James Cancer Hospital, Columbus, OH
| | - Pankit Vachhani
- Division of Hematology and Oncology, University of Alabama at Birmingham School of Medicine, Birmingham, AL
| | - Bryan Hambley
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH
| | - Bryan S Manning
- Department of Medicine, Perelman Cancer Center, University of Pennsylvania, Philadelphia, PA
| | - Shannon Gier
- Department of Medicine, Perelman Cancer Center, University of Pennsylvania, Philadelphia, PA
| | - Christina Cho
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Harrison K Tsai
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Shannon McCurdy
- Department of Medicine, Perelman Cancer Center, University of Pennsylvania, Philadelphia, PA
| | - Vincent T Ho
- Division of Hematologic Malignancies, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - John Koreth
- Division of Hematologic Malignancies, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Robert J Soiffer
- Division of Hematologic Malignancies, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Jerome Ritz
- Division of Hematologic Neoplasia, Department of Medical Oncology, and
| | - Martin P Carroll
- Department of Medicine, Perelman Cancer Center, University of Pennsylvania, Philadelphia, PA
| | - Sumithira Vasu
- Division of Hematology, The Ohio State University James Cancer Hospital, Columbus, OH
| | | | - Eunice S Wang
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Lukasz P Gondek
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | | | - Edwin P Alyea
- Duke Cancer Institute, Duke University Medical Center, Durham, NC
| | | | - Christopher J Gibson
- Division of Hematologic Malignancies, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
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15
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Deshpande A, Chu LF, Stewart R, Gitter A. Network inference with Granger causality ensembles on single-cell transcriptomics. Cell Rep 2022; 38:110333. [PMID: 35139376 PMCID: PMC9093087 DOI: 10.1016/j.celrep.2022.110333] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 02/19/2021] [Accepted: 01/12/2022] [Indexed: 12/20/2022] Open
Abstract
Cellular gene expression changes throughout a dynamic biological process, such as differentiation. Pseudotimes estimate cells' progress along a dynamic process based on their individual gene expression states. Ordering the expression data by pseudotime provides information about the underlying regulator-gene interactions. Because the pseudotime distribution is not uniform, many standard mathematical methods are inapplicable for analyzing the ordered gene expression states. Here we present single-cell inference of networks using Granger ensembles (SINGE), an algorithm for gene regulatory network inference from ordered single-cell gene expression data. SINGE uses kernel-based Granger causality regression to smooth irregular pseudotimes and missing expression values. It aggregates predictions from an ensemble of regression analyses to compile a ranked list of candidate interactions between transcriptional regulators and target genes. In two mouse embryonic stem cell differentiation datasets, SINGE outperforms other contemporary algorithms. However, a more detailed examination reveals caveats about poor performance for individual regulators and uninformative pseudotimes.
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Affiliation(s)
- Atul Deshpande
- Department of Electrical and Computer Engineering, University of Wisconsin - Madison, Madison, WI 53706, USA; Morgridge Institute for Research, Madison, WI 53715, USA
| | - Li-Fang Chu
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Anthony Gitter
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin - Madison, Madison, WI 53792, USA.
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16
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Votavova H, Belickova M. Hypoplastic myelodysplastic syndrome and acquired aplastic anemia: Immune‑mediated bone marrow failure syndromes (Review). Int J Oncol 2021; 60:7. [PMID: 34958107 PMCID: PMC8727136 DOI: 10.3892/ijo.2021.5297] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/01/2021] [Indexed: 11/06/2022] Open
Abstract
Hypoplastic myelodysplastic syndrome (hMDS) and aplastic anemia (AA) are rare hematopoietic disorders characterized by pancytopenia with hypoplastic bone marrow (BM). hMDS and idiopathic AA share overlapping clinicopathological features, making a diagnosis very difficult. The differential diagnosis is mainly based on the presence of dysgranulopoiesis, dysmegakaryocytopoiesis, an increased percentage of blasts, and abnormal karyotype, all favouring the diagnosis of hMDS. An accurate diagnosis has important clinical implications, as the prognosis and treatment can be quite different for these diseases. Patients with hMDS have a greater risk of neoplastic progression, a shorter survival time and a lower response to immunosuppressive therapy compared with patients with AA. There is compelling evidence that these distinct clinical entities share a common pathophysiology based on the damage of hematopoietic stem and progenitor cells (HSPCs) by cytotoxic T cells. Expanded T cells overproduce proinflammatory cytokines (interferon-γ and tumor necrosis factor-α), resulting in decreased proliferation and increased apoptosis of HSPCs. The antigens that trigger this abnormal immune response are not known, but potential candidates have been suggested, including Wilms tumor protein 1 and human leukocyte antigen class I molecules. Our understanding of the molecular pathogenesis of these BM failure syndromes has been improved by next-generation sequencing, which has enabled the identification of a large spectrum of mutations. It has also brought new challenges, such as the interpretation of variants of uncertain significance and clonal hematopoiesis of indeterminate potential. The present review discusses the main clinicopathological differences between hMDS and acquired AA, focuses on the molecular background and highlights the importance of molecular testing.
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Affiliation(s)
- Hana Votavova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague 128 00, Czech Republic
| | - Monika Belickova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague 128 00, Czech Republic
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17
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Shin U, Nakhro K, Oh CK, Carrington B, Song H, Varshney GK, Kim Y, Song H, Jeon S, Robbins G, Kim S, Yoon S, Choi YJ, Kim YJ, Burgess S, Kang S, Sood R, Lee Y, Myung K. Large-scale generation and phenotypic characterization of zebrafish CRISPR mutants of DNA repair genes. DNA Repair (Amst) 2021; 107:103173. [PMID: 34390914 DOI: 10.1016/j.dnarep.2021.103173] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/06/2021] [Indexed: 11/20/2022]
Abstract
A systematic knowledge of the roles of DNA repair genes at the level of the organism has been limited due to the lack of appropriate experimental approaches using animal model systems. Zebrafish has become a powerful vertebrate genetic model system with availability due to the ease of genome editing and large-scale phenotype screening. Here, we generated zebrafish mutants for 32 DNA repair and replication genes through multiplexed CRISPR/Cas9-mediated mutagenesis. Large-scale phenotypic characterization of our mutant collection revealed that three genes (atad5a, ddb1, pcna) are essential for proper embryonic development and hematopoiesis; seven genes (apex1, atrip, ino80, mre11a, shfm1, telo2, wrn) are required for growth and development during juvenile stage and six genes (blm, brca2, fanci, rad51, rad54l, rtel1) play critical roles in sex development. Furthermore, mutation in six genes (atad5a, brca2, polk, rad51, shfm1, xrcc1) displayed hypersensitivity to DNA damage agents. Our zebrafish mutant collection provides a unique resource for understanding of the roles of DNA repair genes at the organismal level.
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Affiliation(s)
- Unbeom Shin
- School of Life Sciences, Ulsan National Institute for Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Khriezhanuo Nakhro
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Chang-Kyu Oh
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea; Department of Anatomy, School of Medicine, Inje University, Busan, 47392, Republic of Korea
| | - Blake Carrington
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - HeaIn Song
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Gaurav K Varshney
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA; Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Yeongjae Kim
- School of Life Sciences, Ulsan National Institute for Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Hyemin Song
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Sangeun Jeon
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Gabrielle Robbins
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sangin Kim
- School of Life Sciences, Ulsan National Institute for Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Suhyeon Yoon
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Yong Jun Choi
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Yoo Jung Kim
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Shawn Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Raman Sood
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yoonsung Lee
- School of Life Sciences, Ulsan National Institute for Science and Technology (UNIST), Ulsan, 44919, Republic of Korea; Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea; Department of Biomedical Engineering, Ulsan National Institute for Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
| | - Kyungjae Myung
- School of Life Sciences, Ulsan National Institute for Science and Technology (UNIST), Ulsan, 44919, Republic of Korea; Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea; Department of Biomedical Engineering, Ulsan National Institute for Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
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18
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Reilly CR, Myllymäki M, Redd R, Padmanaban S, Karunakaran D, Tesmer V, Tsai FD, Gibson CJ, Rana HQ, Zhong L, Saber W, Spellman SR, Hu ZH, Orr EH, Chen MM, De Vivo I, DeAngelo DJ, Cutler C, Antin JH, Neuberg D, Garber JE, Nandakumar J, Agarwal S, Lindsley RC. The clinical and functional effects of TERT variants in myelodysplastic syndrome. Blood 2021; 138:898-911. [PMID: 34019641 PMCID: PMC8432045 DOI: 10.1182/blood.2021011075] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/20/2021] [Indexed: 11/20/2022] Open
Abstract
Germline pathogenic TERT variants are associated with short telomeres and an increased risk of developing myelodysplastic syndrome (MDS) among patients with a telomere biology disorder. We identified TERT rare variants in 41 of 1514 MDS patients (2.7%) without a clinical diagnosis of a telomere biology disorder who underwent allogeneic transplantation. Patients with a TERT rare variant had shorter telomere length (P < .001) and younger age at MDS diagnosis (52 vs 59 years, P = .03) than patients without a TERT rare variant. In multivariable models, TERT rare variants were associated with inferior overall survival (P = .034) driven by an increased incidence of nonrelapse mortality (NRM; P = .015). Death from a noninfectious pulmonary cause was more frequent among patients with a TERT rare variant. Most variants were missense substitutions and classified as variants of unknown significance. Therefore, we cloned all rare missense variants and quantified their impact on telomere elongation in a cell-based assay. We found that 90% of TERT rare variants had severe or intermediate impairment in their capacity to elongate telomeres. Using a homology model of human TERT bound to the shelterin protein TPP1, we inferred that TERT rare variants disrupt domain-specific functions, including catalysis, protein-RNA interactions, and recruitment to telomeres. Our results indicate that the contribution of TERT rare variants to MDS pathogenesis and NRM risk is underrecognized. Routine screening for TERT rare variants in MDS patients regardless of age or clinical suspicion may identify clinically inapparent telomere biology disorders and improve transplant outcomes through risk-adapted approaches.
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Affiliation(s)
| | - Mikko Myllymäki
- Division of Hematological Malignancies, Department of Medical Oncology, and
| | - Robert Redd
- Department of Data Sciences, Dana Farber Cancer Institute, Boston MA
| | - Shilpa Padmanaban
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Druha Karunakaran
- Division of Hematological Malignancies, Department of Medical Oncology, and
| | - Valerie Tesmer
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Frederick D Tsai
- Division of Hematological Malignancies, Department of Medical Oncology, and
| | | | - Huma Q Rana
- Division of Population Sciences, Center for Cancer Genetics and Prevention, and
| | - Liang Zhong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston MA
- Harvard Stem Cell Institute, Boston MA
| | - Wael Saber
- Center for International Blood andMarrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Zhen-Huan Hu
- Center for International Blood andMarrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI
| | - Esther H Orr
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA; and
| | - Maxine M Chen
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA; and
| | - Immaculata De Vivo
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA; and
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Daniel J DeAngelo
- Division of Hematological Malignancies, Department of Medical Oncology, and
| | - Corey Cutler
- Division of Hematological Malignancies, Department of Medical Oncology, and
| | - Joseph H Antin
- Division of Hematological Malignancies, Department of Medical Oncology, and
| | - Donna Neuberg
- Department of Data Sciences, Dana Farber Cancer Institute, Boston MA
| | - Judy E Garber
- Division of Population Sciences, Center for Cancer Genetics and Prevention, and
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Suneet Agarwal
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston MA
- Harvard Stem Cell Institute, Boston MA
| | - R Coleman Lindsley
- Division of Hematological Malignancies, Department of Medical Oncology, and
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19
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Benyelles M, O'Donohue MF, Kermasson L, Lainey E, Borie R, Lagresle-Peyrou C, Nunes H, Cazelles C, Fourrage C, Ollivier E, Marcais A, Gamez AS, Morice-Picard F, Caillaud D, Pottier N, Ménard C, Ba I, Fernandes A, Crestani B, de Villartay JP, Gleizes PE, Callebaut I, Kannengiesser C, Revy P. NHP2 deficiency impairs rRNA biogenesis and causes pulmonary fibrosis and Høyeraal-Hreidarsson syndrome. Hum Mol Genet 2021; 29:907-922. [PMID: 31985013 DOI: 10.1093/hmg/ddaa011] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 01/14/2020] [Accepted: 01/17/2020] [Indexed: 12/18/2022] Open
Abstract
Telomeres are nucleoprotein structures at the end of chromosomes. The telomerase complex, constituted of the catalytic subunit TERT, the RNA matrix hTR and several cofactors, including the H/ACA box ribonucleoproteins Dyskerin, NOP10, GAR1, NAF1 and NHP2, regulates telomere length. In humans, inherited defects in telomere length maintenance are responsible for a wide spectrum of clinical premature aging manifestations including pulmonary fibrosis (PF), dyskeratosis congenita (DC), bone marrow failure and predisposition to cancer. NHP2 mutations have been so far reported only in two patients with DC. Here, we report the first case of Høyeraal-Hreidarsson syndrome, the severe form of DC, caused by biallelic missense mutations in NHP2. Additionally, we identified three unrelated patients with PF carrying NHP2 heterozygous mutations. Strikingly, one of these patients acquired a somatic mutation in the promoter of TERT that likely conferred a selective advantage in a subset of blood cells. Finally, we demonstrate that a functional deficit of human NHP2 affects ribosomal RNA biogenesis. Together, our results broaden the functional consequences and clinical spectrum of NHP2 deficiency.
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Affiliation(s)
- Maname Benyelles
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée La Ligue contre le Cancer, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Marie-Françoise O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Laëtitia Kermasson
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée La Ligue contre le Cancer, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Elodie Lainey
- Hematology Laboratory, Robert DEBRE Hospital-APHP and INSERM UMR 1131-Hematology University Institute-Denis Diderot School of Medicine, Paris, France
| | - Raphael Borie
- APHP, Hôpital Bichat, Service de Pneumologie A, DHU FIRE, Paris, France.,INSERM, Unité 1152, Paris, France.,Université Paris Diderot, Paris, France
| | - Chantal Lagresle-Peyrou
- Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Imagine Institute, Paris, France.,University of Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Hilario Nunes
- Service de Pneumologie, Centre de Référence des Maladies Pulmonaires rares, Hôpital Avicenne, AP-HP, INSERM 1272, Université Paris 13, Bobigny, France
| | - Clarisse Cazelles
- Service d'hématologie adulte, Hôpital Necker- Enfants malades, Paris, France
| | - Cécile Fourrage
- INSERM UMR 1163, Genomics platform, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France.,Genomic Core Facility, Imagine Institute-Structure Fédérative de Recherche Necker, INSERM U1163, Paris, France
| | - Emmanuelle Ollivier
- INSERM UMR 1163, Genomics platform, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France.,Genomic Core Facility, Imagine Institute-Structure Fédérative de Recherche Necker, INSERM U1163, Paris, France
| | - Ambroise Marcais
- Service d'hématologie Adultes, Hôpital Necker-Enfants Malades, Assistance publique hôpitaux de Paris, Paris, France, Laboratoire d'onco-hématologie, Institut Necker-Enfants Malades, INSERM U1151, Université Paris Descartes, Paris, France
| | | | - Fanny Morice-Picard
- Service de Dermatologie Pédiatrique, Centre de Reference des Maladies Rares de la Peau, CHU de Bordeaux, Bordeaux F-33076, France
| | - Denis Caillaud
- Service de Pneumologie-Allergologie, Hôpital Gabriel Montpied, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Nicolas Pottier
- Univ. Lille, CHU Lille, Institut Pasteur de Lille, EA4483-IMPECS, Lille, France
| | - Christelle Ménard
- APHP Service de Génétique, Hôpital Bichat, Paris, France Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Ibrahima Ba
- APHP Service de Génétique, Hôpital Bichat, Paris, France Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Alicia Fernandes
- Biological Resources Center, Structure Fédérative de Recherche Necker, INSERM US24, CNRS UMS3633, Assistance Publique des Hôpitaux de Paris and Institut Imagine, Paris, France
| | - Bruno Crestani
- APHP, Hôpital Bichat, Service de Pneumologie A, DHU FIRE, Paris, France
| | - Jean-Pierre de Villartay
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée La Ligue contre le Cancer, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005 Paris, France
| | - Caroline Kannengiesser
- APHP Service de Génétique, Hôpital Bichat, Paris, France Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Patrick Revy
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée La Ligue contre le Cancer, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
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20
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Carver A, Zhang X. Rad51 filament dynamics and its antagonistic modulators. Semin Cell Dev Biol 2021; 113:3-13. [PMID: 32631783 DOI: 10.1016/j.semcdb.2020.06.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/10/2020] [Accepted: 06/20/2020] [Indexed: 02/07/2023]
Abstract
Rad51 recombinase is the central player in homologous recombination, the faithful repair pathway for double-strand breaks and key event during meiosis. Rad51 forms nucleoprotein filaments on single-stranded DNA, exposed by a double-strand break. These filaments are responsible for homology search and strand invasion, which lead to homology-directed repair. Due to its central roles in DNA repair and genome stability, Rad51 is modulated by multiple factors and post-translational modifications. In this review, we summarize our current understanding of the dynamics of Rad51 filaments, the roles of other factors and their modes of action in modulating key stages of Rad51 filaments: formation, stability and disassembly.
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Affiliation(s)
- Alexander Carver
- Section of Structural Biology, Department of Infectious Diseases, Sir Alexander Fleming Building, Imperial College London, SW7 2AZ, UK
| | - Xiaodong Zhang
- Section of Structural Biology, Department of Infectious Diseases, Sir Alexander Fleming Building, Imperial College London, SW7 2AZ, UK.
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21
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Hypoplastic Myelodysplastic Syndromes: Just an Overlap Syndrome? Cancers (Basel) 2021; 13:cancers13010132. [PMID: 33401595 PMCID: PMC7795441 DOI: 10.3390/cancers13010132] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/29/2020] [Accepted: 12/29/2020] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Hypoplastic myelodysplastic syndromes (hMDS) represent a diagnostic conundrum. They share morphologic and clinical features of both MDS (dysplasia, genetic lesions and cytopenias) and aplastic anemia (AA; i.e., hypocellularity and autoimmunity) and are not comprised in the last WHO classification. In this review we recapitulate the main clinical, pathogenic and therapeutic aspects of hypo-MDS and discuss why they deserve to be distinguished from normo/hypercellular MDS and AA. We conclude that hMDS may present in two phenotypes: one more proinflammatory and autoimmune, more similar to AA, responding to immunosuppression; and one MDS-like dominated by genetic lesions, suppression of immune surveillance, and tumor escape, more prone to leukemic evolution. Abstract Myelodysplasias with hypocellular bone marrow (hMDS) represent about 10–15% of MDS and are defined by reduced bone marrow cellularity (i.e., <25% or an inappropriately reduced cellularity for their age in young patients). Their diagnosis is still an object of debate and has not been clearly established in the recent WHO classification. Clinical and morphological overlaps with both normo/hypercellular MDS and aplastic anemia include cytopenias, the presence of marrow hypocellularity and dysplasia, and cytogenetic and molecular alterations. Activation of the immune system against the hematopoietic precursors, typical of aplastic anemia, is reckoned even in hMDS and may account for the response to immunosuppressive treatment. Finally, the hMDS outcome seems more favorable than that of normo/hypercellular MDS patients. In this review, we analyze the available literature on hMDS, focusing on clinical, immunological, and molecular features. We show that hMDS pathogenesis and clinical presentation are peculiar, albeit in-between aplastic anemia (AA) and normo/hypercellular MDS. Two different hMDS phenotypes may be encountered: one featured by inflammation and immune activation, with increased cytotoxic T cells, increased T and B regulatory cells, and better response to immunosuppression; and the other, resembling MDS, where T and B regulatory/suppressor cells prevail, leading to genetic clonal selection and an increased risk of leukemic evolution. The identification of the prevailing hMDS phenotype might assist treatment choice, inform prognosis, and suggest personalized monitoring.
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22
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Trottier AM, Godley LA. Inherited predisposition to haematopoietic malignancies: overcoming barriers and exploring opportunities. Br J Haematol 2020; 194:663-676. [PMID: 33615436 DOI: 10.1111/bjh.17247] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 11/02/2020] [Indexed: 12/14/2022]
Abstract
Inherited predisposition to haematopoietic malignancies, due to deleterious germline variants in a variety of genes, is an important clinical entity with implications for the health and management of patients and their family members. Unfortunately, there remain several common misconceptions in this field that can result in patients going unrecognised and/or having incomplete or improper testing including: the impression that inherited haematological malignancy syndromes are rare, that myeloid and lymphoid malignancy predisposition syndromes are mutually exclusive, and that solid tumour predisposition syndromes are unique and distinct from haematopoietic malignancy predisposition syndromes. In the present review, we challenge these ideas with our insights into germline genetic testing for these conditions with the hope that increased awareness and knowledge will overcome barriers and lead to improved diagnosis and management.
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Affiliation(s)
- Amy M Trottier
- Division of Hematology, Department of Medicine, QEII Health Sciences Centre/Dalhousie University, Halifax, NS, Canada
| | - Lucy A Godley
- Section of Hematology/Oncology, Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL, USA
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23
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Human mutational constraint as a tool to understand biology of rare and emerging bone marrow failure syndromes. Blood Adv 2020; 4:5232-5245. [PMID: 33104793 DOI: 10.1182/bloodadvances.2020002687] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/16/2020] [Indexed: 12/17/2022] Open
Abstract
Inherited bone marrow failure (IBMF) syndromes are rare blood disorders characterized by hematopoietic cell dysfunction and predisposition to hematologic malignancies. Despite advances in the understanding of molecular pathogenesis of these heterogeneous diseases, genetic variant interpretation, genotype-phenotype correlation, and outcome prognostication remain difficult. As new IBMF and other myelodysplastic syndrome (MDS) predisposition genes continue to be discovered (frequently in small kindred studies), there is an increasing need for a systematic framework to evaluate penetrance and prevalence of mutations in genes associated with IBMF phenotypes. To address this need, we analyzed population-based genomic data from >125 000 individuals in the Genome Aggregation Database for loss-of-function (LoF) variants in 100 genes associated with IBMF. LoF variants in genes associated with IBMF/MDS were present in 0.426% of individuals. Heterozygous LoF variants in genes in which haploinsufficiency is associated with IBMF/MDS were identified in 0.422% of the population; homozygous LoF variants associated with autosomal recessive IBMF/MDS diseases were identified in only .004% of the cohort. Using age distribution of LoF variants and 2 measures of mutational constraint, LOEUF ("loss-of-function observed/expected upper bound fraction") and pLI ("probability of being loss-of-function intolerance"), we evaluated the pathogenicity, tolerance, and age-related penetrance of LoF mutations in specific genes associated with IBMF syndromes. This analysis led to insights into rare IBMF diseases, including syndromes associated with DHX34, MDM4, RAD51, SRP54, and WIPF1. Our results provide an important population-based framework for the interpretation of LoF variant pathogenicity in rare and emerging IBMF syndromes.
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24
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Ziv A, Werner L, Konnikova L, Awad A, Jeske T, Hastreiter M, Mitsialis V, Stauber T, Wall S, Kotlarz D, Klein C, Snapper SB, Tzfati Y, Weiss B, Somech R, Shouval DS. An RTEL1 Mutation Links to Infantile-Onset Ulcerative Colitis and Severe Immunodeficiency. J Clin Immunol 2020; 40:1010-1019. [PMID: 32710398 DOI: 10.1007/s10875-020-00829-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 07/16/2020] [Indexed: 12/27/2022]
Abstract
PURPOSE More than 50 different monogenic disorders causing inflammatory bowel disease (IBD) have been identified. Our goal was to characterize the clinical phenotype, genetic workup, and immunologic alterations in an Ashkenazi Jewish patient that presented during infancy with ulcerative colitis and unique clinical manifestations. METHODS Immune workup and whole-exome sequencing were performed, along with Sanger sequencing for confirmation. Next-generation sequencing of the TCRB and IgH was conducted for immune repertoire analysis. Telomere length was evaluated by in-gel hybridization assay. Mass cytometry was performed on patient's peripheral blood mononuclear cells, and compared with control subjects and patients with UC. RESULTS The patient presented in infancy with failure to thrive and dysmorphic features, consistent with a diagnosis of dyskeratosis congenita and Hoyeraal-Hreidarsson syndrome. Severe ulcerative colitis manifested in the first year of life and proceeded to the development of a primary immunodeficiency, presenting as Pneumocystis jiroveci pneumonia and hypogammaglobulinemia. Genetic studies identified a deleterious homozygous C.3791G>A missense mutation in the helicase regulator of telomere elongation 1 (RTEL1), leading to short telomeres in the index patient. Immune repertoire studies showed polyclonal T and B cell receptor distribution, while mass cytometry analysis demonstrated marked immunological alterations, including a predominance of naïve T cells, paucity of B cells, and a decrease in various innate immune subsets. CONCLUSIONS RTEL1 mutations are associated with significant alterations in immune landscape and can manifest with infantile-onset IBD. A high index of suspicion is required in Ashkenazi Jewish families where the carriage rate of the C.3791G>A variant is high.
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Affiliation(s)
- Alma Ziv
- Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lael Werner
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Liza Konnikova
- Division of Newborn Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Aya Awad
- Department of Genetics, The Silberman Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tim Jeske
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Maximilian Hastreiter
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Vanessa Mitsialis
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Tali Stauber
- Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Sarah Wall
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - Daniel Kotlarz
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Yehuda Tzfati
- Department of Genetics, The Silberman Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Batia Weiss
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Raz Somech
- Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Dror S Shouval
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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25
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Awad A, Glousker G, Lamm N, Tawil S, Hourvitz N, Smoom R, Revy P, Tzfati Y. Full length RTEL1 is required for the elongation of the single-stranded telomeric overhang by telomerase. Nucleic Acids Res 2020; 48:7239-7251. [PMID: 32542379 PMCID: PMC7367169 DOI: 10.1093/nar/gkaa503] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 12/17/2022] Open
Abstract
Telomeres cap the ends of eukaryotic chromosomes and distinguish them from broken DNA ends to suppress DNA damage response, cell cycle arrest and genomic instability. Telomeres are elongated by telomerase to compensate for incomplete replication and nuclease degradation and to extend the proliferation potential of germ and stem cells and most cancers. However, telomeres in somatic cells gradually shorten with age, ultimately leading to cellular senescence. Hoyeraal-Hreidarsson syndrome (HHS) is characterized by accelerated telomere shortening and diverse symptoms including bone marrow failure, immunodeficiency, and neurodevelopmental defects. HHS is caused by germline mutations in telomerase subunits, factors essential for its biogenesis and recruitment to telomeres, and in the helicase RTEL1. While diverse phenotypes were associated with RTEL1 deficiency, the telomeric role of RTEL1 affected in HHS is yet unknown. Inducible ectopic expression of wild-type RTEL1 in patient fibroblasts rescued the cells, enabled telomerase-dependent telomere elongation and suppressed the abnormal cellular phenotypes, while silencing its expression resulted in gradual telomere shortening. Our observations reveal an essential role of the RTEL1 C-terminus in facilitating telomerase action at the telomeric 3' overhang. Thus, the common etiology for HHS is the compromised telomerase action, resulting in telomere shortening and reduced lifespan of telomerase positive cells.
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Affiliation(s)
- Aya Awad
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Galina Glousker
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Noa Lamm
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Shadi Tawil
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Noa Hourvitz
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Riham Smoom
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Patrick Revy
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer and Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Yehuda Tzfati
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
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26
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Mangaonkar AA, Patnaik MM. Hereditary Predisposition to Hematopoietic Neoplasms: When Bloodline Matters for Blood Cancers. Mayo Clin Proc 2020; 95:1482-1498. [PMID: 32571604 DOI: 10.1016/j.mayocp.2019.12.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/23/2019] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
With the advent of precision genomics, hereditary predisposition to hematopoietic neoplasms- collectively known as hereditary predisposition syndromes (HPS)-are being increasingly recognized in clinical practice. Familial clustering was first observed in patients with leukemia, which led to the identification of several germline variants, such as RUNX1, CEBPA, GATA2, ANKRD26, DDX41, and ETV6, among others, now established as HPS, with tendency to develop myeloid neoplasms. However, evidence for hereditary predisposition is also apparent in lymphoid and plasma--cell neoplasms, with recent discoveries of germline variants in genes such as IKZF1, SH2B3, PAX5 (familial acute lymphoblastic leukemia), and KDM1A/LSD1 (familial multiple myeloma). Specific inherited bone marrow failure syndromes-such as GATA2 haploinsufficiency syndromes, short telomere syndromes, Shwachman-Diamond syndrome, Diamond-Blackfan anemia, severe congenital neutropenia, and familial thrombocytopenias-also have an increased predisposition to develop myeloid neoplasms, whereas inherited immune deficiency syndromes, such as ataxia-telangiectasia, Bloom syndrome, Wiskott Aldrich syndrome, and Bruton agammaglobulinemia, are associated with an increased risk for lymphoid neoplasms. Timely recognition of HPS is critical to ensure safe choice of donors and/or conditioning-regimen intensity for allogeneic hematopoietic stem-cell transplantation and to enable direction of appropriate genomics-driven personalized therapies. The purpose of this review is to provide a comprehensive overview of HPS and serve as a useful reference for clinicians to recognize relevant signs and symptoms among patients to enable timely screening and referrals to pursue germline assessment. In addition, we also discuss our institutional approach toward identification of HPS and offer a stepwise diagnostic and management algorithm.
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Affiliation(s)
| | - Mrinal M Patnaik
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN.
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27
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Brzeźniakiewicz-Janus K, Rupa-Matysek J, Gil L. Acquired Aplastic Anemia as a Clonal Disorder of Hematopoietic Stem Cells. Stem Cell Rev Rep 2020; 16:472-481. [PMID: 32270433 PMCID: PMC7253510 DOI: 10.1007/s12015-020-09971-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aplastic anemia is rare disorder presenting with bone marrow failure syndrome due to autoimmune destruction of early hematopoietic stem cells (HSCs) and stem cell progenitors. Recent advances in newer genomic sequencing and other molecular techniques have contributed to a better understanding of the pathogenesis of aplastic anemia with respect to the inflammaging, somatic mutations, cytogenetic abnormalities and defective telomerase functions of HSCs. These have been summarized in this review and may be helpful in differentiating aplastic anemia from hypocellular myelodysplastic syndrome. Furthermore, responses to immunosuppressive therapy and outcomes may be determined by molecular pathogenesis of HSCs autoimmune destruction, as well as treatment personalization in the future.
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Affiliation(s)
- Katarzyna Brzeźniakiewicz-Janus
- Department of Hematology, Multi-Specialist Hospital Gorzów Wielkopolski, Faculty of Medicine and Health Science, University of Zielona Góra, Gorzów Wielkopolski, Poland.
| | - Joanna Rupa-Matysek
- Department of Hematology and Bone Marrow Transplantation, Poznań University of Medical Sciences, Poznań, Poland
| | - Lidia Gil
- Department of Hematology and Bone Marrow Transplantation, Poznań University of Medical Sciences, Poznań, Poland
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28
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Winer P, Muskens IS, Walsh KM, Vora A, Moorman AV, Wiemels JL, Roberts I, Roy A, de Smith AJ. Germline variants in predisposition genes in children with Down syndrome and acute lymphoblastic leukemia. Blood Adv 2020; 4:672-675. [PMID: 32084258 PMCID: PMC7042982 DOI: 10.1182/bloodadvances.2019001216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/27/2020] [Indexed: 11/20/2022] Open
Abstract
Rare and pathogenic germline variants, including in IKZF1 , contribute to acute lymphoblastic leukemia in children with Down syndrome.
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Affiliation(s)
- Peleg Winer
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA
| | - Ivo S Muskens
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA
| | - Kyle M Walsh
- Department of Neurosurgery, Duke University, Durham, NC
| | - Ajay Vora
- Great Ormond Street Hospital for Children National Health Service Trust, London, United Kingdom
| | - Anthony V Moorman
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA
| | - Irene Roberts
- Department of Paediatrics and
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, United Kingdom; and
- Biomedical Research Centre Blood Theme, National Institute for Health Research Oxford Biomedical Centre, Oxford, United Kingdom
| | - Anindita Roy
- Department of Paediatrics and
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, United Kingdom; and
- Biomedical Research Centre Blood Theme, National Institute for Health Research Oxford Biomedical Centre, Oxford, United Kingdom
| | - Adam J de Smith
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA
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29
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Gutierrez‑Rodrigues F, Masri N, Chouery E, Diamond C, Jalkh N, Vicente A, Kajigaya S, Abillama F, Bejjani N, Serhal W, Calado RT, Young NS, Farhat H, Coussa ML. A novel homozygous RTEL1 variant in a consanguineous Lebanese family: phenotypic heterogeneity and disease anticipation. Hum Genet 2019; 138:1323-1330. [PMID: 31677132 PMCID: PMC9809984 DOI: 10.1007/s00439-019-02076-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 10/22/2019] [Indexed: 01/06/2023]
Abstract
Phenotypic heterogeneity is often observed in patients with telomeropathies caused by pathogenic variants in telomere biology genes. However, the roles of recessive variants in these different phenotypes are not fully characterized. Our goal is to describe the biological roles of a novel homozygous RTEL1 variant identified in a consanguineous Lebanese family with unusual presentation of telomeropathies. A proband was screened for germline variants in telomere biology genes by whole exome sequencing. Leukocytes' telomere length was measured in the proband and eight relatives. We identified a novel homozygous p.E665K RTEL1 variant in the proband, his mother, and seven siblings that associated with telomere shortening and a broad spectrum of clinical manifestations, ranging from mild unspecific findings to severe phenotypes. Consanguinity in at least three family generations led to increased frequency of the homozygous p.E665K variant in the youngest generation and progressive telomere shortening. The increased frequency of the homozygous RTEL1 variant due to consanguinity in this Lebanese family allowed us to infer novel behaviors of recessive RTEL1 variants, as the expressivity and penetrance of this gene are very heterogenous between inter- and intra-generations. Progressive telomere shortening was associated with disease anticipation, first reported in recessive autosomal telomeropathies. Both genetic testing and telomere length measurement were critical for the clinical diagnosis of this family with telomere diseases marked by phenotypic heterogeneity.
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Affiliation(s)
| | - Nohad Masri
- LAU Gilbert and Rose-Marie Chagoury School of Medicine, LAUMC/RH, Zahar Street, Achrafieh, Beirut 1110, Lebanon
| | - Eliane Chouery
- Unité de Génétique Médicale, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Carrie Diamond
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD 20892-1202, USA
| | - Nadine Jalkh
- Unité de Génétique Médicale, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Alana Vicente
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD 20892-1202, USA
| | - Sachiko Kajigaya
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD 20892-1202, USA
| | - Fayez Abillama
- LAU Gilbert and Rose-Marie Chagoury School of Medicine, LAUMC/RH, Zahar Street, Achrafieh, Beirut 1110, Lebanon
| | - Noha Bejjani
- LAU Gilbert and Rose-Marie Chagoury School of Medicine, LAUMC/RH, Zahar Street, Achrafieh, Beirut 1110, Lebanon
| | - Wassim Serhal
- LAU Gilbert and Rose-Marie Chagoury School of Medicine, LAUMC/RH, Zahar Street, Achrafieh, Beirut 1110, Lebanon
| | - Rodrigo T. Calado
- Department of Medical Imaging, Hematology, and Clinical Oncology, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Neal S. Young
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD 20892-1202, USA
| | - Hussein Farhat
- LAU Gilbert and Rose-Marie Chagoury School of Medicine, LAUMC/RH, Zahar Street, Achrafieh, Beirut 1110, Lebanon
| | - Marie Louise Coussa
- LAU Gilbert and Rose-Marie Chagoury School of Medicine, LAUMC/RH, Zahar Street, Achrafieh, Beirut 1110, Lebanon
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30
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Arunachalam AK, Suresh H, Edison ES, Korula A, Aboobacker FN, George B, Shaji RV, Mathews V, Balasubramanian P. Screening of genetic variants in ELANE mutation negative congenital neutropenia by next generation sequencing. J Clin Pathol 2019; 73:322-327. [PMID: 31732620 DOI: 10.1136/jclinpath-2019-206306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 10/31/2019] [Accepted: 11/01/2019] [Indexed: 12/16/2022]
Abstract
AIMS Congenital neutropenia (CN) is a rare inherited disease that results in recurrent, life-threatening bacterial infections due to a deficiency of mature neutrophils. They are usually caused by heterozygous ELANE mutations although mutations in other genes like HAX-1, G6PC3 and GFI1 have also been reported. Identifying the causative mutation aids in the establishment of diagnosis and rules out other secondary causes of neutropenia like autoimmune cytopenia and evolving aplasia. We aimed to identify the molecular defects in CN patients who had no mutations in ELANE gene, by next generation sequencing (NGS) targeting a customised panel of genes. METHODS DNA samples were sequenced with an Illumina NextSeq sequencer using an in-house customised panel of genes at ≥100× depth. Bioinformatics analysis was carried out and the pathogenic variants were identified using a stepwise filtering and analysis strategy. Specific mutations identified were subsequently validated by Sanger sequencing. RESULTS The pathogenic variants identified in the study includes previously reported variants in SBDS (compound heterozygous c.258+2T>C and c.1A>T), GATA2 (heterozygous c.1186C>T) and novel variants in WAS (hemizygous c.812T>C), JAGN1 (homozygous c.70G>A) and RTEL1 (heterozygous c.2893G>C) genes. CONCLUSION This study highlights that the absence of ELANE mutations does not rule out the diagnosis of CN and this NGS based approach with a customised panel will help in diagnostic confirmation in such patients. The early onset of the disease, clinical severity and associated high risk of malignant transformation in CN strongly suggests the need for early diagnosis and therapeutic intervention.
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Affiliation(s)
| | | | | | - Anu Korula
- Clinical Haematology, Christian Medical College, Vellore, India
| | | | - Biju George
- Clinical Haematology, Christian Medical College, Vellore, India
| | | | - Vikram Mathews
- Clinical Haematology, Christian Medical College, Vellore, India
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31
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Porreca RM, Glousker G, Awad A, Matilla Fernandez MI, Gibaud A, Naucke C, Cohen SB, Bryan TM, Tzfati Y, Draskovic I, Londoño-Vallejo A. Human RTEL1 stabilizes long G-overhangs allowing telomerase-dependent over-extension. Nucleic Acids Res 2019. [PMID: 29522136 PMCID: PMC5961080 DOI: 10.1093/nar/gky173] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Telomere maintenance protects the cell against genome instability and senescence. Accelerated telomere attrition is a characteristic of premature aging syndromes including Dyskeratosis congenita (DC). Mutations in hRTEL1 are associated with a severe form of DC called Hoyeraal-Hreidarsson syndrome (HHS). HHS patients carry short telomeres and HHS cells display telomere damage. Here we investigated how hRTEL1 contributes to telomere maintenance in human primary as well as tumor cells. Transient depletion of hRTEL1 resulted in rapid telomere shortening only in the context of telomerase-positive cells with very long telomeres and high levels of telomerase. The effect of hRTEL1 on telomere length is telomerase dependent without impacting telomerase biogenesis or targeting of the enzyme to telomeres. Instead, RTEL1 depletion led to a decrease in both G-overhang content and POT1 association with telomeres with limited telomere uncapping. Strikingly, overexpression of POT1 restored telomere length but not the overhang, demonstrating that G-overhang loss is the primary defect caused by RTEL1 depletion. We propose that hRTEL1 contributes to the maintenance of long telomeres by preserving long G-overhangs, thereby facilitating POT1 binding and elongation by telomerase.
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Affiliation(s)
- Rosa M Porreca
- Institut Curie, PSL Research University, Sorbonne Universités, CNRS UMR3244 Telomere and cancer lab, 75005 Paris, France
| | - Galina Glousker
- Department of Genetics, The Silberman Institute of Life Science, The Hebrew University of Jerusalem, Safra Campus-Givat Ram, Jerusalem 91904, Israel
| | - Aya Awad
- Department of Genetics, The Silberman Institute of Life Science, The Hebrew University of Jerusalem, Safra Campus-Givat Ram, Jerusalem 91904, Israel
| | | | - Anne Gibaud
- Institut Curie, PSL Research University, Sorbonne Universités, CNRS UMR3244 Telomere and cancer lab, 75005 Paris, France
| | - Christian Naucke
- Institut Curie, PSL Research University, Sorbonne Universités, CNRS UMR3244 Telomere and cancer lab, 75005 Paris, France
| | - Scott B Cohen
- Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Tracy M Bryan
- Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Yehuda Tzfati
- Department of Genetics, The Silberman Institute of Life Science, The Hebrew University of Jerusalem, Safra Campus-Givat Ram, Jerusalem 91904, Israel
| | - Irena Draskovic
- Institut Curie, PSL Research University, Sorbonne Universités, CNRS UMR3244 Telomere and cancer lab, 75005 Paris, France
| | - Arturo Londoño-Vallejo
- Institut Curie, PSL Research University, Sorbonne Universités, CNRS UMR3244 Telomere and cancer lab, 75005 Paris, France
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32
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Chiu V, Hogen R, Sher L, Wadé N, Conti D, Martynova A, Li H, Liang G, O'Connell C. Telomerase Variants in Patients with Cirrhosis Awaiting Liver Transplantation. Hepatology 2019; 69:2652-2663. [PMID: 30964210 PMCID: PMC6594079 DOI: 10.1002/hep.30557] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 01/27/2019] [Indexed: 12/16/2022]
Abstract
Telomeres are repetitive DNA sequences that protect the ends of linear chromosomes, and they are maintained by a ribonucleoprotein complex called telomerase. Variants in genes encoding for telomerase components have been associated with a spectrum of disease in the lung, skin, bone marrow, and liver. Mutations in the telomerase reverse transcriptase and telomerase RNA component genes have been observed at a higher prevalence in patients with liver disease compared with the general population; however, the presence of variants in other components of the telomerase complex and their impact on clinical outcomes has not been explored. We evaluated 86 patients with end-stage liver disease for variants in an expanded panel of eight genes, and found that 17 patients (20%) had likely deleterious variants by in silico analysis. Seven unique likely deleterious variants were identified in the regulator of telomere elongation helicase 1 (RTEL1) gene that encodes for a DNA helicase important in telomere maintenance and genomic stability. In gene burden association analysis of their clinical data, the presence of any RTEL1 variant was associated with a 29% lower baseline white blood cell count (95% confidence interval [CI], -7% to -46%; P Value = 0.01) compared with patients without RTEL1 variants, and the presence of any exonic missense RTEL1 variant was associated with a 42% lower baseline platelet count (95% CI, -5% to -65%: P Value = 0.03). The presence of any telomerase variant was associated with an increased number of readmissions within 1 year after transplantation demonstrated by an incident rate ratio (IRR) of 3.15 (95% CI, 1.22 to 8.57). No association with survival was observed. Conclusion: Among patients who underwent liver transplantation, the presence of any exonic missense variant was associated with a longer postoperative length of stay with an IRR of 2.16 (95% CI, 1.31 to 3.68).
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Affiliation(s)
- Victor Chiu
- Norris Comprehensive Cancer Center and Hospital, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA,Division of Hematology, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA
| | - Rachel Hogen
- Department of Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA
| | - Linda Sher
- Department of Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA
| | - Niquelle Wadé
- Department of Preventive Medicine, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA
| | - David Conti
- Department of Preventive Medicine, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA
| | - Anastasia Martynova
- Norris Comprehensive Cancer Center and Hospital, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA,Division of Hematology, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA
| | - Hongtao Li
- Department of Urology, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA
| | - Gangning Liang
- Norris Comprehensive Cancer Center and Hospital, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA,Department of Urology, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA
| | - Casey O'Connell
- Norris Comprehensive Cancer Center and Hospital, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA,Division of Hematology, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA
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33
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Shen W, Kerr CM, Przychozen B, Mahfouz RZ, LaFramboise T, Nagata Y, Hanna R, Radivoyevitch T, Nazha A, Sekeres MA, Maciejewski JP. Impact of germline CTC1 alterations on telomere length in acquired bone marrow failure. Br J Haematol 2019; 185:935-939. [PMID: 30891747 DOI: 10.1111/bjh.15862] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/25/2019] [Indexed: 11/30/2022]
Abstract
Compound heterozygous germline mutations in CTC1 gene have been found in patients with atypical dyskeratosis congenita (DC), whereas heterozygous carriers are unaffected. Through screening of a large cohort of adult patients with acquired bone marrow failure syndromes, in addition to a DC case, we have also found extremely rare or novel heterozygous deleterious germline variants of CTC1 in patients with aplastic anaemia (AA; n = 5), paroxysmal nocturnal haemoglobinuria (PNH; n = 3) and myelodysplastic syndrome (MDS; n = 2). A compound heterozygous case of AA showed clonal evolution. Our results suggest that some of the inherited CTC1 variants may represent predisposition factors for acquired bone marrow failure.
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Affiliation(s)
- Wenyi Shen
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.,Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, P.R. China
| | - Cassandra M Kerr
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Bartlomiej Przychozen
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Reda Z Mahfouz
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Yasunobu Nagata
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Rabi Hanna
- Department of Pediatric Oncology, Cleveland Clinic, Cleveland, OH, USA
| | - Tomas Radivoyevitch
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Aziz Nazha
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mikkael A Sekeres
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
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34
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Borie R, Bouvry D, Cottin V, Gauvain C, Cazes A, Debray MP, Cadranel J, Dieude P, Degot T, Dominique S, Gamez AS, Jaillet M, Juge PA, Londono-Vallejo A, Mailleux A, Mal H, Boileau C, Menard C, Nunes H, Prevot G, Quetant S, Revy P, Traclet J, Wemeau-Stervinou L, Wislez M, Kannengiesser C, Crestani B. Regulator of telomere length 1 ( RTEL1) mutations are associated with heterogeneous pulmonary and extra-pulmonary phenotypes. Eur Respir J 2019; 53:13993003.00508-2018. [PMID: 30523160 DOI: 10.1183/13993003.00508-2018] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 11/06/2018] [Indexed: 01/10/2023]
Abstract
Regulator of telomere length 1 (RTEL1) mutations have been evidenced in 5-9% of familial pulmonary fibrosis; however, the phenotype of patients with interstitial lung disease (ILD) and RTEL1 mutations is poorly understood.Whole exome sequencing was performed in 252 probands with ILD and we included all patients with ILD and RTEL1 mutation. RTEL1 expression was evaluated by immunochemistry in the lungs of controls, as well as in RTEL1 and telomerase reverse transcriptase (TERT) mutation carriers.We identified 35 subjects from 17 families. Median age at diagnosis of ILD was 53.1 years (range 28.0-80.6). The most frequent pulmonary diagnoses were idiopathic pulmonary fibrosis (n=20, 57%), secondary ILD (n=7, 20%) and unclassifiable fibrosis or interstitial pneumonia with autoimmune features (n=7, 20%). The median transplant-free and overall survival periods were 39.2 months and 45.3 months, respectively. Forced vital capacity at diagnosis was the only factor associated with decreased transplant-free survival. Extra-pulmonary manifestations were less frequent as compared to other telomere-related gene mutation carriers. A systematic analysis of the literature identified 110 patients with ILD and RTEL1 mutations (including this series) and confirmed the heterogeneity of the pulmonary phenotype, the prevalence of non-idiopathic diseases and the low prevalence of extra-pulmonary manifestations.Immunohistochemistry showed that RTEL1 was expressed by bronchial and alveolar epithelial cells, as well as by alveolar macrophages and lymphocytes, but not by fibroblasts.
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Affiliation(s)
- Raphael Borie
- Service de Pneumologie A, Hôpital Bichat, AP-HP, DHU FIRE, Paris, France.,Unité 1152, INSERM, Université Paris Diderot, Paris, France
| | - Diane Bouvry
- Service de Pneumologie, Hôpital Avicenne, AP-HP, Bobigny, France
| | - Vincent Cottin
- Service de Pneumologie, Hôpital Louis Pradel, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Aurélie Cazes
- Unité 1152, INSERM, Université Paris Diderot, Paris, France.,Service d'Anatomopathologie, Hôpital Bichat, AP-HP, Paris, France
| | - Marie-Pierre Debray
- Unité 1152, INSERM, Université Paris Diderot, Paris, France.,Service de Radiologie, Hôpital Bichat, AP-HP, Paris, France
| | | | - Philippe Dieude
- Unité 1152, INSERM, Université Paris Diderot, Paris, France.,Service de Rhumatologie, Hôpital Bichat, AP-HP, Paris, France.,Université Paris Diderot, Paris, France
| | - Tristan Degot
- Service de Pneumologie, CHU Strasbourg, Strasbourg, France
| | | | | | | | | | - Arturo Londono-Vallejo
- UMR 3244 (Telomere and Cancer Lab), CNRS, Institut Curie, PSL Research University, Sorbonne Universités, Paris, France
| | | | - Hervé Mal
- Unité 1152, INSERM, Université Paris Diderot, Paris, France.,Service de Pneumologie B, Hôpital Bichat, AP-HP, Paris, France
| | - Catherine Boileau
- Université Paris Diderot, Paris, France.,Laboratoire de Génétique, Hôpital Bichat, AP-HP, Paris, France
| | | | - Hilario Nunes
- Service de Pneumologie, Hôpital Avicenne, AP-HP, Bobigny, France
| | | | | | - Patrick Revy
- UMR 1163 (Laboratory of Genome Dynamics in the Immune System), INSERM, Imagine Institute, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Julie Traclet
- Service de Pneumologie, Hôpital Tenon, AP-HP, Paris, France
| | - Lidwine Wemeau-Stervinou
- Service de Pneumologie, Centre de Compétence des Maladies Pulmonaires Rares, CHRU de Lille, Lille, France
| | - Marie Wislez
- Service de Pneumologie, Unité d'Oncologie Thoracique, Hôpital Cochin, Hôpitaux Universitaires Paris Centre, AP-HP, Paris, France
| | - Caroline Kannengiesser
- Unité 1152, INSERM, Université Paris Diderot, Paris, France.,Université Paris Diderot, Paris, France.,Laboratoire de Génétique, Hôpital Bichat, AP-HP, Paris, France
| | - Bruno Crestani
- Service de Pneumologie A, Hôpital Bichat, AP-HP, DHU FIRE, Paris, France.,Unité 1152, INSERM, Université Paris Diderot, Paris, France.,Université Paris Diderot, Paris, France
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35
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Abstract
Purpose The acquisition of pathogenic variants in the TERT promoter (TERTp) region is a mechanism of tumorigenesis. In nonmalignant diseases, TERTp variants have been reported only in patients with idiopathic pulmonary fibrosis (IPF) due to germline variants in telomere biology genes. Methods We screened patients with a broad spectrum of telomeropathies (n = 136), their relatives (n = 52), and controls (n = 195) for TERTp variants using a customized massively parallel amplicon-based sequencing assay. Results Pathogenic −124 and −146 TERTp variants were identified in nine (7%) unrelated patients diagnosed with IPF (28%) or moderate aplastic anemia (4.6%); five of them also presented cirrhosis. Five (10%) relatives were also found with these variants, all harboring a pathogenic germline variant in telomere biology genes. TERTp clone selection did not associate with peripheral blood counts, telomere length, and response to danazol treatment. However, it was specific for patients with telomeropathies, more frequently co-occurring with TERT germline variants and associated with aging. Conclusion We extend the spectrum of nonmalignant diseases associated with pathogenic TERTp variants to marrow failure and liver disease due to inherited telomerase deficiency. Specificity of pathogenic TERTp variants for telomerase dysfunction may help to assess the pathogenicity of unclear constitutional variants in the telomere diseases.
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36
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Shallis RM, Ahmad R, Zeidan AM. Aplastic anemia: Etiology, molecular pathogenesis, and emerging concepts. Eur J Haematol 2018; 101:711-720. [PMID: 30055055 DOI: 10.1111/ejh.13153] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 12/12/2022]
Abstract
Aplastic anemia (AA) is rare disorder of bone marrow failure which if severe and not appropriately treated is highly fatal. AA is characterized by morphologic marrow features, namely hypocellularity, and resultant peripheral cytopenias. The molecular pathogenesis of AA is not fully understood, and a uniform process may not be the culprit across all cases. An antigen-driven and likely autoimmune dysregulated T-cell homeostasis is implicated in the hematopoietic stem cell injury which ultimately founds the pathologic features of the disease. Defective telomerase function and repair may also play a role in some cases as evidenced by recurring mutations in related telomerase complex genes such as TERT and TERC. In addition, recurring mutations in BCOR/BCORL, PIGA, DNMT3A, and ASXL1 as well as cytogenetic abnormalities, namely monosomy 7, trisomy 8, and uniparental disomy of the 6p arm seem to be intimately related to AA pathogenesis. The increased incidence of late clonal disease has also provided clues to accurately describe plausible predispositions to the development of AA. The emergence of newer genomic sequencing and other techniques is incrementally improving the understanding of the pathogenic mechanisms of AA, the detection of the disease, and ultimately offers the potential to improve patient outcomes. In this comprehensive review, we discuss the current understanding of the immunobiology, molecular pathogenesis, and future directions of such for AA.
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Affiliation(s)
- Rory M Shallis
- Division of Hematology/Medical Oncology, Department of Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Rami Ahmad
- Division of Hematology/Medical Oncology, Department of Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Amer M Zeidan
- Division of Hematology/Medical Oncology, Department of Medicine, Yale University School of Medicine, New Haven, Connecticut.,Cancer Outcomes, Public Policy, and Effectiveness Research (COPPER) Center, Yale University, New Haven, Connecticut
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37
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Clonal hematopoiesis in patients with multiple myeloma undergoing autologous stem cell transplantation. Leukemia 2018; 32:2020-2024. [PMID: 30026569 DOI: 10.1038/s41375-018-0208-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/09/2018] [Accepted: 06/20/2018] [Indexed: 12/26/2022]
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38
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Mangaonkar AA, Ferrer A, Pinto E Vairo F, Cousin MA, Kuisle RJ, Klee EW, Kennedy CC, Peters SG, Scott JP, Utz JP, Baqir M, Sekiguchi H, Khan SP, Rodriguez V, Simonetto DA, Kamath PS, Abraham RS, Wylam ME, Patnaik MM. Clinical Correlates and Treatment Outcomes for Patients With Short Telomere Syndromes. Mayo Clin Proc 2018; 93:834-839. [PMID: 29976374 PMCID: PMC7646091 DOI: 10.1016/j.mayocp.2018.05.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/11/2018] [Accepted: 05/18/2018] [Indexed: 10/28/2022]
Abstract
Short telomere syndromes (STSs) are accelerated aging syndromes with multisystemic manifestations that present complex management challenges. In this article, we discuss a single-institution experience in diagnosing and managing patients with inherited STSs. In total, we identified 17 patients with short telomeres, defined by flow-fluorescence in-situ hybridization telomere lengths of less than first centile in granulocytes/lymphocytes OR the presence of a characteristic germline pathogenic variant in the context of a highly suggestive clinical phenotype. Genetic variations in the telomere complex were identified in 6 (35%) patients, with 4 being known pathogenic variants involving TERT (n=2), TERC (n=1), and DKC1 (n=1) genes, while 2 were variants of uncertain significance in TERT and RTEL1 genes. Idiopathic interstitial pneumonia (IIP) (n=12 [71%]), unexplained cytopenias (n=5 [29%]), and cirrhosis (n=2 [12%]) were most frequent clinical phenotypes at diagnosis. At median follow-up of 48 (range, 0-316) months, Kaplan-Meier estimate of overall survival, median (95% CI), was 182 (113, not reached) months. Treatment modalities included lung transplantation for IIP (n=5 [29%]), with 3 patients developing signs of acute cellular rejection (2, grade A2; 1, grade A1); danazol therapy for cytopenias (n=4 [24%]), with only 1 out of 4 patients showing a partial hematologic response; and allogeneic hematopoietic stem cell transplant for progressive bone marrow failure (n=2), with 1 patient dying from transplant-related complications. In summary, patients with STSs present with diverse clinical manifestations and require a multidisciplinary approach to management, with organ-specific transplantation capable of providing clinical benefit.
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Affiliation(s)
| | - Alejandro Ferrer
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Filippo Pinto E Vairo
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Margot A Cousin
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Ryan J Kuisle
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Eric W Klee
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Cassie C Kennedy
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - Steve G Peters
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - J P Scott
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - James P Utz
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - Misbah Baqir
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - Hiroshi Sekiguchi
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - Shakila P Khan
- Division of Pediatric Hematology/Oncology, Mayo Clinic, Rochester, MN
| | | | | | | | - Roshini S Abraham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Mark E Wylam
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN.
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39
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Diagnostic algorithm for lower-risk myelodysplastic syndromes. Leukemia 2018; 32:1679-1696. [PMID: 29946191 DOI: 10.1038/s41375-018-0173-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/20/2018] [Accepted: 04/05/2018] [Indexed: 01/01/2023]
Abstract
Rapid advances over the past decade have uncovered the heterogeneous genomic and immunologic landscape of myelodysplastic syndromes (MDS). This has led to notable improvements in the accuracy and timing of diagnosis and prognostication of MDS, as well as the identification of possible novel targets for therapeutic intervention. For the practicing clinician, however, this increase in genomic, epigenomic, and immunologic knowledge needs consideration in a "real-world" context to aid diagnostic specificity. Although the 2016 revision to the World Health Organization classification for MDS is comprehensive and timely, certain limitations still exist for day-to-day clinical practice. In this review, we describe an up-to-date diagnostic approach to patients with suspected lower-risk MDS, including hypoplastic MDS, and demonstrate the requirement for an "integrated" diagnostic approach. Moreover, in the era of rapid access to massive parallel sequencing platforms for mutational screening, we suggest which patients should undergo such analyses, when such screening should be performed, and how those data should be interpreted. This is particularly relevant given the recent findings describing age-related clonal hematopoiesis.
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40
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Scheinberg P. Recent Advances and Long-Term Results of Medical Treatment of Acquired Aplastic Anemia: Are Patients Cured? Hematol Oncol Clin North Am 2018; 32:609-618. [PMID: 30047414 DOI: 10.1016/j.hoc.2018.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Horse antithymocyte globulin plus cyclosporine remains standard immunosuppressive therapy in severe aplastic anemia, with hematologic response rates of 60% to 70%. In those refractory to this regimen, a second course of therapy with rabbit antithymocyte globulin plus cyclosporine or alemtuzumab produces responses in 30% to 40%. Eltrombopag, a thrombopoietin receptor agonist, showed activity as a single agent in those refractory to initial immunosuppression with hematologic response rates of 40% to 50%. When combined with immunosuppression as frontline therapy, eltrombopag increased the rate of overall and complete response rates. Longer follow-up is needed to better define these outcomes.
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Affiliation(s)
- Phillip Scheinberg
- Division of Hematology, Hospital A Beneficência Portuguesa, Rua Martiniano de Carvalho, 951, São Paulo 01321-001, Brazil.
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