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Muiño E, Carcel-Marquez J, Llucià-Carol L, Gallego-Fabrega C, Cullell N, Lledós M, Martín-Campos JM, Villatoro-González P, Sierra-Marcos A, Ros-Castelló V, Aguilera-Simón A, Marti-Fabregas J, Fernandez-Cadenas I. Identification of Genetic Loci Associated With Intracerebral Hemorrhage Using a Multitrait Analysis Approach. Neurology 2024; 103:e209666. [PMID: 39298701 DOI: 10.1212/wnl.0000000000209666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024] Open
Abstract
BACKGROUND AND OBJECTIVES Genome-wide association studies (GWASs) have only 2 loci associated with spontaneous intracerebral hemorrhage (ICH): APOE for lobar and 1q22 for nonlobar ICH. We aimed to discover new loci through an analysis that combines correlated traits (multi-trait analysis of GWAS [MTAG]) and explore a gene-based analysis, transcriptome-wide association study (TWAS), and proteome-wide association study (PWAS) to understand the biological mechanisms of spontaneous ICH providing potential therapeutic targets. METHODS We use the published MTAG of ICH (patients with spontaneous intraparenchymal bleeding) and small-vessel ischemic stroke. For all ICH, lobar ICH, and nonlobar ICH, a pairwise MTAG combined ICH with traits related to cardiovascular risk factors, cerebrovascular diseases, or Alzheimer disease (AD). For the analysis, we assembled those traits with a genetic correlation ≥0.3. A new MTAG combining multiple traits was performed with those traits whose pairwise MTAG yielded new GWAS-significant single nucleotide polymorphisms (SNPs), with a posterior-probability of model 3 (GWAS-pairwise) ≥0.6. We perform TWAS and PWAS that correlate the genetic component of expression or protein levels with the genetic component of a trait. We use the ICH cohort from UK Biobank as replication. RESULTS For all ICH (1,543 ICH, 1,711 controls), the mean age was 72 ± 2 in cases and 70 ± 2 in controls, and half of them were women. Replication cohort: 700 ICH and 399,717 controls. Novel loci were found only for all ICH (the trait containing lobar and nonlobar ICH), combining data of ICH and small vessel stroke, white matter hyperintensities volume, fractional anisotropy, mean diffusivity, and AD. We replicated 6 SNPs belonging to 2q33.2 (ICA1L, β = 0.20, SE = 0.03, p value = 8.91 × 10-12), 10q24.33 (OBFC1, β = -0.12, SE = 0.02, p value = 1.67 × 10-8), 13q34 (COL4A2, β = 0.02, SE = 0.02, p value = 2.34 × 10-11), and 19q13.32 (APOC1, β = -0.19, SE = 0.03, p value = 1.38 × 10-12; APOE, β = 0.21, SE = 0.03, p value = 2.70 × 10-11; PVRL2:CTB-129P6.4, β = 0.15, SE = 0.03, p value = 1.38 × 10-8); 2 genes (SH3PXD2A, Z-score = 4.83, p value = 6.67 × 10-7; and APOC1, Z-score: = 5.11, p value = 1.60 × 10-7); and ICA1L transcript (Z-score = 6.8, p value = 9.1 × 10-12) and protein levels (Z-score = -5.8, p value = 6.7 × 10-9). DISCUSSION Our results reinforce the role of APOE in ICH risk, replicate previous ICH-associated loci (2q33 and 13q34), and point to new ICH associations with OBFC1, PVRL2:CTB-129P6.4, APOC1, and SH3PXD2A. Our study used data from European subjects, our main limitation. These molecules could be potential targets for future studies for modulating ICH risk.
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Affiliation(s)
- Elena Muiño
- From the Stroke Pharmacogenomics and Genetics Group (E.M., J.C.-M., L.L.-C., C.G.-F., N.C., M.L.L., J.M.M.-C., P.V.-G., I.F.-C.), Biomedical Research Institute Sant Pau (IIB SANT PAU); Epilepsy Unit (E.M., A.S.-M., V.R.-C.), Neurology Service, Hospital de la Santa Creu i Sant Pau, Barcelona; Stroke Pharmacogenomics and Genetics (N.C.), Fundació MútuaTerrassa per la Docència i la Recerca; and Department of Neurology (C.G.-F., A.A.-S., J.M.-F.), Hospital de la Santa Creu i Sant Pau, IIB SANT PAU, Barcelona, Spain
| | - Jara Carcel-Marquez
- From the Stroke Pharmacogenomics and Genetics Group (E.M., J.C.-M., L.L.-C., C.G.-F., N.C., M.L.L., J.M.M.-C., P.V.-G., I.F.-C.), Biomedical Research Institute Sant Pau (IIB SANT PAU); Epilepsy Unit (E.M., A.S.-M., V.R.-C.), Neurology Service, Hospital de la Santa Creu i Sant Pau, Barcelona; Stroke Pharmacogenomics and Genetics (N.C.), Fundació MútuaTerrassa per la Docència i la Recerca; and Department of Neurology (C.G.-F., A.A.-S., J.M.-F.), Hospital de la Santa Creu i Sant Pau, IIB SANT PAU, Barcelona, Spain
| | - Laia Llucià-Carol
- From the Stroke Pharmacogenomics and Genetics Group (E.M., J.C.-M., L.L.-C., C.G.-F., N.C., M.L.L., J.M.M.-C., P.V.-G., I.F.-C.), Biomedical Research Institute Sant Pau (IIB SANT PAU); Epilepsy Unit (E.M., A.S.-M., V.R.-C.), Neurology Service, Hospital de la Santa Creu i Sant Pau, Barcelona; Stroke Pharmacogenomics and Genetics (N.C.), Fundació MútuaTerrassa per la Docència i la Recerca; and Department of Neurology (C.G.-F., A.A.-S., J.M.-F.), Hospital de la Santa Creu i Sant Pau, IIB SANT PAU, Barcelona, Spain
| | - Cristina Gallego-Fabrega
- From the Stroke Pharmacogenomics and Genetics Group (E.M., J.C.-M., L.L.-C., C.G.-F., N.C., M.L.L., J.M.M.-C., P.V.-G., I.F.-C.), Biomedical Research Institute Sant Pau (IIB SANT PAU); Epilepsy Unit (E.M., A.S.-M., V.R.-C.), Neurology Service, Hospital de la Santa Creu i Sant Pau, Barcelona; Stroke Pharmacogenomics and Genetics (N.C.), Fundació MútuaTerrassa per la Docència i la Recerca; and Department of Neurology (C.G.-F., A.A.-S., J.M.-F.), Hospital de la Santa Creu i Sant Pau, IIB SANT PAU, Barcelona, Spain
| | - Natalia Cullell
- From the Stroke Pharmacogenomics and Genetics Group (E.M., J.C.-M., L.L.-C., C.G.-F., N.C., M.L.L., J.M.M.-C., P.V.-G., I.F.-C.), Biomedical Research Institute Sant Pau (IIB SANT PAU); Epilepsy Unit (E.M., A.S.-M., V.R.-C.), Neurology Service, Hospital de la Santa Creu i Sant Pau, Barcelona; Stroke Pharmacogenomics and Genetics (N.C.), Fundació MútuaTerrassa per la Docència i la Recerca; and Department of Neurology (C.G.-F., A.A.-S., J.M.-F.), Hospital de la Santa Creu i Sant Pau, IIB SANT PAU, Barcelona, Spain
| | - Miquel Lledós
- From the Stroke Pharmacogenomics and Genetics Group (E.M., J.C.-M., L.L.-C., C.G.-F., N.C., M.L.L., J.M.M.-C., P.V.-G., I.F.-C.), Biomedical Research Institute Sant Pau (IIB SANT PAU); Epilepsy Unit (E.M., A.S.-M., V.R.-C.), Neurology Service, Hospital de la Santa Creu i Sant Pau, Barcelona; Stroke Pharmacogenomics and Genetics (N.C.), Fundació MútuaTerrassa per la Docència i la Recerca; and Department of Neurology (C.G.-F., A.A.-S., J.M.-F.), Hospital de la Santa Creu i Sant Pau, IIB SANT PAU, Barcelona, Spain
| | - Jesús M Martín-Campos
- From the Stroke Pharmacogenomics and Genetics Group (E.M., J.C.-M., L.L.-C., C.G.-F., N.C., M.L.L., J.M.M.-C., P.V.-G., I.F.-C.), Biomedical Research Institute Sant Pau (IIB SANT PAU); Epilepsy Unit (E.M., A.S.-M., V.R.-C.), Neurology Service, Hospital de la Santa Creu i Sant Pau, Barcelona; Stroke Pharmacogenomics and Genetics (N.C.), Fundació MútuaTerrassa per la Docència i la Recerca; and Department of Neurology (C.G.-F., A.A.-S., J.M.-F.), Hospital de la Santa Creu i Sant Pau, IIB SANT PAU, Barcelona, Spain
| | - Paula Villatoro-González
- From the Stroke Pharmacogenomics and Genetics Group (E.M., J.C.-M., L.L.-C., C.G.-F., N.C., M.L.L., J.M.M.-C., P.V.-G., I.F.-C.), Biomedical Research Institute Sant Pau (IIB SANT PAU); Epilepsy Unit (E.M., A.S.-M., V.R.-C.), Neurology Service, Hospital de la Santa Creu i Sant Pau, Barcelona; Stroke Pharmacogenomics and Genetics (N.C.), Fundació MútuaTerrassa per la Docència i la Recerca; and Department of Neurology (C.G.-F., A.A.-S., J.M.-F.), Hospital de la Santa Creu i Sant Pau, IIB SANT PAU, Barcelona, Spain
| | - Alba Sierra-Marcos
- From the Stroke Pharmacogenomics and Genetics Group (E.M., J.C.-M., L.L.-C., C.G.-F., N.C., M.L.L., J.M.M.-C., P.V.-G., I.F.-C.), Biomedical Research Institute Sant Pau (IIB SANT PAU); Epilepsy Unit (E.M., A.S.-M., V.R.-C.), Neurology Service, Hospital de la Santa Creu i Sant Pau, Barcelona; Stroke Pharmacogenomics and Genetics (N.C.), Fundació MútuaTerrassa per la Docència i la Recerca; and Department of Neurology (C.G.-F., A.A.-S., J.M.-F.), Hospital de la Santa Creu i Sant Pau, IIB SANT PAU, Barcelona, Spain
| | - Victoria Ros-Castelló
- From the Stroke Pharmacogenomics and Genetics Group (E.M., J.C.-M., L.L.-C., C.G.-F., N.C., M.L.L., J.M.M.-C., P.V.-G., I.F.-C.), Biomedical Research Institute Sant Pau (IIB SANT PAU); Epilepsy Unit (E.M., A.S.-M., V.R.-C.), Neurology Service, Hospital de la Santa Creu i Sant Pau, Barcelona; Stroke Pharmacogenomics and Genetics (N.C.), Fundació MútuaTerrassa per la Docència i la Recerca; and Department of Neurology (C.G.-F., A.A.-S., J.M.-F.), Hospital de la Santa Creu i Sant Pau, IIB SANT PAU, Barcelona, Spain
| | - Ana Aguilera-Simón
- From the Stroke Pharmacogenomics and Genetics Group (E.M., J.C.-M., L.L.-C., C.G.-F., N.C., M.L.L., J.M.M.-C., P.V.-G., I.F.-C.), Biomedical Research Institute Sant Pau (IIB SANT PAU); Epilepsy Unit (E.M., A.S.-M., V.R.-C.), Neurology Service, Hospital de la Santa Creu i Sant Pau, Barcelona; Stroke Pharmacogenomics and Genetics (N.C.), Fundació MútuaTerrassa per la Docència i la Recerca; and Department of Neurology (C.G.-F., A.A.-S., J.M.-F.), Hospital de la Santa Creu i Sant Pau, IIB SANT PAU, Barcelona, Spain
| | - Joan Marti-Fabregas
- From the Stroke Pharmacogenomics and Genetics Group (E.M., J.C.-M., L.L.-C., C.G.-F., N.C., M.L.L., J.M.M.-C., P.V.-G., I.F.-C.), Biomedical Research Institute Sant Pau (IIB SANT PAU); Epilepsy Unit (E.M., A.S.-M., V.R.-C.), Neurology Service, Hospital de la Santa Creu i Sant Pau, Barcelona; Stroke Pharmacogenomics and Genetics (N.C.), Fundació MútuaTerrassa per la Docència i la Recerca; and Department of Neurology (C.G.-F., A.A.-S., J.M.-F.), Hospital de la Santa Creu i Sant Pau, IIB SANT PAU, Barcelona, Spain
| | - Israel Fernandez-Cadenas
- From the Stroke Pharmacogenomics and Genetics Group (E.M., J.C.-M., L.L.-C., C.G.-F., N.C., M.L.L., J.M.M.-C., P.V.-G., I.F.-C.), Biomedical Research Institute Sant Pau (IIB SANT PAU); Epilepsy Unit (E.M., A.S.-M., V.R.-C.), Neurology Service, Hospital de la Santa Creu i Sant Pau, Barcelona; Stroke Pharmacogenomics and Genetics (N.C.), Fundació MútuaTerrassa per la Docència i la Recerca; and Department of Neurology (C.G.-F., A.A.-S., J.M.-F.), Hospital de la Santa Creu i Sant Pau, IIB SANT PAU, Barcelona, Spain
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Zhao J, Yang K, Lu Y, Zhou L, Fu H, Feng J, Wu J. Proteomic Mendelian randomization to identify protein biomarkers of telomere length. Sci Rep 2024; 14:21594. [PMID: 39284832 PMCID: PMC11405721 DOI: 10.1038/s41598-024-72281-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 09/05/2024] [Indexed: 09/20/2024] Open
Abstract
Shortening of telomere length (TL) is correlated with many age-related disorders and is a hallmark of biological aging. This study used proteome-wide Mendelian randomization to identify the protein biomarkers associated with telomere length. Protein quantitative trait loci (pQTL) were derived from two studies, the deCODE Health study (4907 plasma proteins) and the UK Biobank Pharma Proteomics Project (2923 plasma proteins). Summary data from genome-wide association studies (GWAS) for TL were obtained from the UK Biobank (472,174 cases) and GWAS Catalog (418,401 cases). The association between proteins and TL was further assessed using colocalization and summary data-based Mendelian randomization (SMR) analyses. The protein-protein network, druggability assessment, and phenome-wide MR were used to further evaluate the potential biological effects, druggability, and safety of the target proteins. Proteome-wide MR analysis identified 22 plasma proteins that were causally associated with telomere length. Five of these proteins (APOE, SPRED2, MAX, RALY, and PSMB1) had the highest evidence of association with TL and should be prioritized. This study revealed telomere length-related protein biomarkers, providing new insights into the development of new treatment targets for chronic diseases and anti-aging intervention strategies.
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Affiliation(s)
- Jiaxuan Zhao
- Department of Clinical Laboratory, North China University of Science and Technology Affiliated Tangshan Maternal and Child Health Care Hospital, Tangshan, China
- Key Laboratory of Molecular Medicine for Abnormal Development and Related Diseases in Tangshan City, Tangshan, China
| | - Kun Yang
- Department of Clinical Laboratory, North China University of Science and Technology Affiliated Tangshan Maternal and Child Health Care Hospital, Tangshan, China
- Key Laboratory of Molecular Medicine for Abnormal Development and Related Diseases in Tangshan City, Tangshan, China
| | - Yunfei Lu
- Department of Clinical Laboratory, North China University of Science and Technology Affiliated Tangshan Maternal and Child Health Care Hospital, Tangshan, China
- Key Laboratory of Molecular Medicine for Abnormal Development and Related Diseases in Tangshan City, Tangshan, China
| | - Linfeng Zhou
- Department of Clinical Laboratory, North China University of Science and Technology Affiliated Tangshan Maternal and Child Health Care Hospital, Tangshan, China
- Key Laboratory of Molecular Medicine for Abnormal Development and Related Diseases in Tangshan City, Tangshan, China
| | - Haoran Fu
- Department of Clinical Laboratory, North China University of Science and Technology Affiliated Tangshan Maternal and Child Health Care Hospital, Tangshan, China
- Key Laboratory of Molecular Medicine for Abnormal Development and Related Diseases in Tangshan City, Tangshan, China
| | - Jingbo Feng
- The 982th Hospital of the People's Liberation Army Joint Logistics Support Force, Tangshan, China
| | - Jinghua Wu
- Department of Clinical Laboratory, North China University of Science and Technology Affiliated Tangshan Maternal and Child Health Care Hospital, Tangshan, China.
- Key Laboratory of Molecular Medicine for Abnormal Development and Related Diseases in Tangshan City, Tangshan, China.
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Feng Y, Guo X, Luo M, Sun Y, Sun L, Zhang H, Zou Y, Liu D, Lu H. GbHSP90 act as a dual functional role regulated in telomere stability in Ginkgo biloba. Int J Biol Macromol 2024; 279:135240. [PMID: 39250995 DOI: 10.1016/j.ijbiomac.2024.135240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 08/12/2024] [Accepted: 08/29/2024] [Indexed: 09/11/2024]
Abstract
The heat shock protein 90 (HSP90) family members are not only widely involved in animal cellular immune response and signal transduction pathway regulation, but also play an important role in plant development and environmental stress response. Here,we identified a HSP90 family member in Ginkgo biloba, designated as GbHSP90, which performs a dual functional role to regulate telomere stability. GbHSP90 was screened by a yeast one-hybrid library using the Ginkgo biloba telomeric DNA (TTTAGGG)5. Fluorescence polarization, surface plasmon resonance(SPR) and EMSA technologyies revealed a specific interaction between GbHSP90 and the double-stranded telomeric DNA via its N-CR region, with no affinity for the single-stranded telomeric DNA or human double-stranded telomeric DNA. Furthermore, yeast two-hybrid system and Split-LUC assay demonstrated that GbHSP90 can interacts with two telomere end-binding proteins:the ginkgo telomerase reverse transcriptase (GbTERT) and the ginkgo Structural Maintenance of Chromosomes protein 1 (GbSMC1). Overexpression of GbHSP90 in human 293 T and HeLa cells increased cell growth rate, the content of telomerase reverse transcriptase (TERT), and promote cell division and inhibit cell apoptosis. Our results indicated GbHSP90 have dually functions: as a telomere-binding protein that binds specifically to double-stranded telomeric DNA and as a molecular chaperone that modulates cell differentiation and apoptosis by binding to telomere protein complexes in Ginkgo biloba. This study contributes to a significantly understanding of the unique telomere complex structure and regulatory mechanisms in Ginkgo biloba, a long-lived tree species.
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Affiliation(s)
- Yuping Feng
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xueqin Guo
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Mei Luo
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; School of Biology and Engineering (School of Modern Industry for Health and Medicine), Guizhou Medical University, Guiyang 561113, China
| | - Yu Sun
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Leiqian Sun
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Huimin Zhang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yirong Zou
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Di Liu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Hai Lu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
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Wang P, Jiang W, Lai T, Liu Q, Shen Y, Ye B, Wu D. Germline variants in acquired aplastic anemia: current knowledge and future perspectives. Haematologica 2024; 109:2778-2789. [PMID: 38988263 PMCID: PMC11367197 DOI: 10.3324/haematol.2023.284312] [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: 09/16/2023] [Accepted: 04/09/2024] [Indexed: 07/12/2024] Open
Abstract
Aplastic anemia (AA) is a disease characterized by failure of hematopoiesis, bone marrow aplasia, and pancytopenia. It can be inherited or acquired. Although acquired AA is believed to be immune-mediated and random, new evidence suggests an underlying genetic predisposition. Besides confirmed genomic mutations that contribute to inherited AA (such as pathogenic mutations of TERT and TERC), germline variants, often in heterozygous states, also play a not negligible role in the onset and progression of acquired AA. These variants, associated with inherited bone marrow failure syndromes and inborn errors of immunity, contribute to the disease, possibly through mechanisms including gene homeostasis, DNA repair, and immune injury. This article explores the nuanced association between acquired AA and germline variants, detailing the clinical significance of germline variants in diagnosing and managing this condition. More work is encouraged to better understand the role of immunogenic pathogenic variants and whether somatic mutations participate as secondary "hits" in the development of bone marrow failure.
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Affiliation(s)
- Peicheng Wang
- Department of Hematology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China; The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang
| | - Wanzhi Jiang
- Department of Hematology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China; The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang
| | - Tianyi Lai
- Department of Hematology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China; The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang
| | - Qi Liu
- Department of Hematology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China; The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang
| | - Yingying Shen
- Department of Hematology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China; The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China; National Traditional Chinese Medicine Clinical Research Base (Hematology), Hangzhou, Zhejiang
| | - Baodong Ye
- Department of Hematology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China; The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China; National Traditional Chinese Medicine Clinical Research Base (Hematology), Hangzhou, Zhejiang.
| | - Dijiong Wu
- Department of Hematology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China; The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China; National Traditional Chinese Medicine Clinical Research Base (Hematology), Hangzhou, Zhejiang, China; Department of Oncology and Hematology, Wenzhou Hospital of Integrated Traditional Chinese and Western Medicine affiliated to Zhejiang Chinese Medicine University, Wenzhou, Zhejiang.
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Ghosh S, Nguyen MT, Choi HE, Stahl M, Kühn AL, Van der Auwera S, Grabe HJ, Völzke H, Homuth G, Myers SA, Hogaboam CM, Noth I, Martinez FJ, Petsko GA, Glimcher LH. RIOK2 transcriptionally regulates TRiC and dyskerin complexes to prevent telomere shortening. Nat Commun 2024; 15:7138. [PMID: 39164231 PMCID: PMC11335878 DOI: 10.1038/s41467-024-51336-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 08/02/2024] [Indexed: 08/22/2024] Open
Abstract
Telomere shortening is a prominent hallmark of aging and is emerging as a characteristic feature of Myelodysplastic Syndromes (MDS) and Idiopathic Pulmonary Fibrosis (IPF). Optimal telomerase activity prevents progressive shortening of telomeres that triggers DNA damage responses. However, the upstream regulation of telomerase holoenzyme components remains poorly defined. Here, we identify RIOK2, a master regulator of human blood cell development, as a critical transcription factor for telomere maintenance. Mechanistically, loss of RIOK2 or its DNA-binding/transactivation properties downregulates mRNA expression of both TRiC and dyskerin complex subunits that impairs telomerase activity, thereby causing telomere shortening. We further show that RIOK2 expression is diminished in aged individuals and IPF patients, and it strongly correlates with shortened telomeres in MDS patient-derived bone marrow cells. Importantly, ectopic expression of RIOK2 alleviates telomere shortening in IPF patient-derived primary lung fibroblasts. Hence, increasing RIOK2 levels prevents telomere shortening, thus offering therapeutic strategies for telomere biology disorders.
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Affiliation(s)
- Shrestha Ghosh
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Department of Immunology, Harvard Medical School, Boston, MA, USA.
| | - Mileena T Nguyen
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Yale University, New Haven, CT, USA
| | - Ha Eun Choi
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Maximilian Stahl
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Annemarie Luise Kühn
- Department for Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Sandra Van der Auwera
- Department for Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
- German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, Greifswald, Germany
| | - Hans J Grabe
- Department for Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
- German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | | | - Cory M Hogaboam
- Women's Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Imre Noth
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, VA, USA
| | - Fernando J Martinez
- Division of Pulmonary and Critical Care Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Gregory A Petsko
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Laurie H Glimcher
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Department of Immunology, Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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6
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Boccardi V, Marano L. Aging, Cancer, and Inflammation: The Telomerase Connection. Int J Mol Sci 2024; 25:8542. [PMID: 39126110 PMCID: PMC11313618 DOI: 10.3390/ijms25158542] [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: 07/24/2024] [Revised: 07/31/2024] [Accepted: 08/04/2024] [Indexed: 08/12/2024] Open
Abstract
Understanding the complex dynamics of telomere biology is important in the strong link between aging and cancer. Telomeres, the protective caps at the end of chromosomes, are central players in this connection. While their gradual shortening due to replication limits tumors expansion by triggering DNA repair mechanisms, it also promotes oncogenic changes within chromosomes, thus sustaining tumorigenesis. The enzyme telomerase, responsible for maintaining telomere length, emerges as a central player in this context. Its expression in cancer cells facilitates the preservation of telomeres, allowing them to circumvent the growth-limiting effects of short telomeres. Interestingly, the influence of telomerase extends beyond telomere maintenance, as evidenced by its involvement in promoting cell growth through alternative pathways. In this context, inflammation accelerates telomere shortening, resulting in telomere dysfunction, while telomere elements also play a role in modulating the inflammatory response. The recognition of this interplay has promoted the development of novel therapeutic approaches centered around telomerase inhibition. This review provides a comprehensive overview of the field, emphasizing recent progress in knowledge and the implications in understanding of cancer biology.
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Affiliation(s)
- Virginia Boccardi
- Division of Gerontology and Geriatrics, Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy
| | - Luigi Marano
- Department of Medicine, Academy of Applied Medical and Social Sciences—AMiSNS: Akademia Medycznych I Spolecznych Nauk Stosowanych, 82-300 Elbląg, Poland;
- Department of General Surgery and Surgical Oncology, “Saint Wojciech” Hospital, “Nicolaus Copernicus” Health Center, 80-462 Gdańsk, Poland
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7
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Nickens DG, Feng Z, Shen J, Gray SJ, Simmons R, Niu H, Bochman M. Cdc13 exhibits dynamic DNA strand exchange in the presence of telomeric DNA. Nucleic Acids Res 2024; 52:6317-6332. [PMID: 38613387 PMCID: PMC11194072 DOI: 10.1093/nar/gkae265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/22/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024] Open
Abstract
Telomerase is the enzyme that lengthens telomeres and is tightly regulated by a variety of means to maintain genome integrity. Several DNA helicases function at telomeres, and we previously found that the Saccharomyces cerevisiae helicases Hrq1 and Pif1 directly regulate telomerase. To extend these findings, we are investigating the interplay between helicases, single-stranded DNA (ssDNA) binding proteins (ssBPs), and telomerase. The yeast ssBPs Cdc13 and RPA differentially affect Hrq1 and Pif1 helicase activity, and experiments to measure helicase disruption of Cdc13/ssDNA complexes instead revealed that Cdc13 can exchange between substrates. Although other ssBPs display dynamic binding, this was unexpected with Cdc13 due to the reported in vitro stability of the Cdc13/telomeric ssDNA complex. We found that the DNA exchange by Cdc13 occurs rapidly at physiological temperatures, requires telomeric repeat sequence DNA, and is affected by ssDNA length. Cdc13 truncations revealed that the low-affinity binding site (OB1), which is distal from the high-affinity binding site (OB3), is required for this intermolecular dynamic DNA exchange (DDE). We hypothesize that DDE by Cdc13 is the basis for how Cdc13 'moves' at telomeres to alternate between modes where it regulates telomerase activity and assists in telomere replication.
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Affiliation(s)
- David G Nickens
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Zhitong Feng
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Jiangchuan Shen
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Spencer J Gray
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Robert H Simmons
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Hengyao Niu
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Matthew L Bochman
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
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8
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Dos Santos GA, Viana NI, Pimenta R, de Camargo JA, Guimaraes VR, Romão P, Candido P, Dos Santos VG, Ghazarian V, Reis ST, Leite KRM, Srougi M. Upregulation of shelterin and CST genes and longer telomeres are associated with unfavorable prognostic characteristics in prostate cancer. Cancer Genet 2024; 284-285:20-29. [PMID: 38503134 DOI: 10.1016/j.cancergen.2024.03.006] [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: 10/04/2023] [Revised: 02/20/2024] [Accepted: 03/14/2024] [Indexed: 03/21/2024]
Abstract
INTRODUCTION Search for new clinical biomarkers targets in prostate cancer (PC) is urgent. Telomeres might be one of these targets. Telomeres are the extremities of linear chromosomes, essential for genome stability and control of cell divisions. Telomere homeostasis relies on the proper functioning of shelterin and CST complexes. Telomeric dysfunction and abnormal expression of its components are reported in most cancers and are associated with PC. Despite this, there are only a few studies about the expression of the main telomere complexes and their relationship with PC progression. We aimed to evaluate the role of shelterin (POT1, TRF2, TPP1, TIN2, and RAP1) and CST (CTC1, STN1, and TEN1) genes and telomere length in the progression of PC. METHODS We evaluated genetic alterations of shelterin and CST by bioinformatics in samples of localized (n = 499) and metastatic castration-resistant PC (n = 444). We also analyzed the expression of the genes using TCGA (localized PC n = 497 and control n = 152) and experimental approaches, with surgical specimens (localized PC n = 81 and BPH n = 10) and metastatic cell lines (LNCaP, DU145, PC3 and PNT2 as control) by real-time PCR. Real-time PCR also determined the telomere length in the same experimental samples. All acquired data were associated with clinical parameters. RESULTS Genetic alterations are uncommon in PC, but POT1, TIN2, and TEN1 showed significantly more amplifications in the metastatic cancer. Except for CTC1 and TEN1, which are differentially expressed in localized PC samples, we did not detect an expression pattern relative to control and cell lines. Nevertheless, except for TEN1, the upregulation of all genes is associated with a worse prognosis in localized PC. We also found that increased telomere length is associated with disease aggressiveness in localized PC. CONCLUSION The upregulation of shelterin and CST genes creates an environment that favors telomere elongation, giving selective advantages for localized PC cells to progress to more aggressive stages of the disease.
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Affiliation(s)
- Gabriel Arantes Dos Santos
- Laboratory of Medical Investigation (LIM55), Urology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil.
| | - Nayara I Viana
- Laboratory of Medical Investigation (LIM55), Urology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil; Minas Gerais State University (UEMG), Passos, Minas Gerais, Brazil
| | - Ruan Pimenta
- Laboratory of Medical Investigation (LIM55), Urology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil; D'Or Institute for Research and Education (IDOR), Sao Paulo, Brazil
| | - Juliana Alves de Camargo
- Laboratory of Medical Investigation (LIM55), Urology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Vanessa R Guimaraes
- Laboratory of Medical Investigation (LIM55), Urology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Poliana Romão
- Laboratory of Medical Investigation (LIM55), Urology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Patrícia Candido
- Laboratory of Medical Investigation (LIM55), Urology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Vinicius Genuino Dos Santos
- Laboratory of Medical Investigation (LIM55), Urology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Vitória Ghazarian
- Laboratory of Medical Investigation (LIM55), Urology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Sabrina T Reis
- Laboratory of Medical Investigation (LIM55), Urology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil; Minas Gerais State University (UEMG), Passos, Minas Gerais, Brazil
| | - Katia Ramos Moreira Leite
- Laboratory of Medical Investigation (LIM55), Urology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Miguel Srougi
- Laboratory of Medical Investigation (LIM55), Urology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil; D'Or Institute for Research and Education (IDOR), Sao Paulo, Brazil
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9
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Sang PB, Jaiswal RK, Lyu X, Chai W. Human CST complex restricts excessive PrimPol repriming upon UV induced replication stress by suppressing p21. Nucleic Acids Res 2024; 52:3778-3793. [PMID: 38348929 DOI: 10.1093/nar/gkae078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 04/25/2024] Open
Abstract
DNA replication stress, caused by various endogenous and exogenous agents, halt or stall DNA replication progression. Cells have developed diverse mechanisms to tolerate and overcome replication stress, enabling them to continue replication. One effective strategy to overcome stalled replication involves skipping the DNA lesion using a specialized polymerase known as PrimPol, which reinitiates DNA synthesis downstream of the damage. However, the mechanism regulating PrimPol repriming is largely unclear. In this study, we observe that knockdown of STN1 or CTC1, components of the CTC1/STN1/TEN1 complex, leads to enhanced replication progression following UV exposure. We find that such increased replication is dependent on PrimPol, and PrimPol recruitment to stalled forks increases upon CST depletion. Moreover, we find that p21 is upregulated in STN1-depleted cells in a p53-independent manner, and p21 depletion restores normal replication rates caused by STN1 deficiency. We identify that p21 interacts with PrimPol, and STN1 depletion stimulates p21-PrimPol interaction and facilitates PrimPol recruitment to stalled forks. Our findings reveal a previously undescribed interplay between CST, PrimPol and p21 in promoting repriming in response to stalled replication, and shed light on the regulation of PrimPol repriming at stalled forks.
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Affiliation(s)
- Pau Biak Sang
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Rishi K Jaiswal
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
| | - Xinxing Lyu
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Weihang Chai
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
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10
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Kordowitzki P, Graczyk S, Mechsner S, Sehouli J. Shedding Light on the Interaction Between Rif1 and Telomeres in Ovarian Cancer. Aging Dis 2024; 15:535-545. [PMID: 37548940 PMCID: PMC10917528 DOI: 10.14336/ad.2023.0716] [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: 06/14/2023] [Accepted: 07/16/2023] [Indexed: 08/08/2023] Open
Abstract
Ovarian cancer, more precisely high-grade serous ovarian cancer, is one of the most lethal age-independent gynecologic malignancies in women worldwide, regardless of age. There is mounting evidence that there is a link between telomeres and the RIF1 protein and the proliferation of cancer cells. Telomeres are hexameric (TTAGGG) tandem repeats at the tip of chromosomes that shorten as somatic cells divide, limiting cell proliferation and serving as an important barrier in preventing cancer. RIF1 (Replication Time Regulation Factor 1) plays, among other factors, an important role in the regulation of telomere length. Interestingly, RIF1 appears to influence the DNA double-strand break (DSB) repair pathway. However, detailed knowledge regarding the interplay between RIF1 and telomeres and their degree of engagement in epithelial ovarian cancer (EOC) is still elusive, despite the fact that such knowledge could be of relevance in clinical practice to find novel biomarkers. In this review, we provide an update of recent literature to elucidate the relation between telomere biology and the RIF1 protein during the development of ovarian cancer in women.
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Affiliation(s)
- Paweł Kordowitzki
- Department of Preclinical and Basic Sciences, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Torun, Poland.
- Department of Gynecology including Center of oncological surgery (CVK) and Department of Gynaecology (CBF), European Competence Center for Ovarian Cancer, Charite, Berlin, Germany.
| | - Szymon Graczyk
- Department of Preclinical and Basic Sciences, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Torun, Poland.
| | - Sylvia Mechsner
- Department of Gynecology including Center of oncological surgery (CVK) and Department of Gynaecology (CBF), European Competence Center for Ovarian Cancer, Charite, Berlin, Germany.
| | - Jalid Sehouli
- Department of Gynecology including Center of oncological surgery (CVK) and Department of Gynaecology (CBF), European Competence Center for Ovarian Cancer, Charite, Berlin, Germany.
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11
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Nickens DG, Feng Z, Shen J, Gray SJ, Simmons RH, Niu H, Bochman ML. Cdc13 exhibits dynamic DNA strand exchange in the presence of telomeric DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.04.569902. [PMID: 38105973 PMCID: PMC10723391 DOI: 10.1101/2023.12.04.569902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Telomerase is the enzyme that lengthens telomeres and is tightly regulated by a variety of means to maintain genome integrity. Several DNA helicases function at telomeres, and we previously found that the Saccharomyces cerevisiae helicases Hrq1 and Pif1 directly regulate telomerase. To extend these findings, we are investigating the interplay between helicases, single-stranded DNA (ssDNA) binding proteins (ssBPs), and telomerase. The yeast ssBPs Cdc13 and RPA differentially affect Hrq1 and Pif1 helicase activity, and experiments to measure helicase disruption of Cdc13/ssDNA complexes instead revealed that Cdc13 can exchange between substrates. Although other ssBPs display dynamic binding, this was unexpected with Cdc13 due to the reported in vitro stability of the Cdc13/telomeric ssDNA complex. We found that the DNA exchange by Cdc13 occurs rapidly at physiological temperatures, requires telomeric repeat sequence DNA, and is affected by ssDNA length. Cdc13 truncations revealed that the low-affinity binding site (OB1), which is distal from the high-affinity binding site (OB3), is required for this intermolecular dynamic DNA exchange (DDE). We hypothesize that DDE by Cdc13 is the basis for how Cdc13 'moves' at telomeres to alternate between modes where it regulates telomerase activity and assists in telomere replication.
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12
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Gedvilaite G, Kriauciuniene L, Tamasauskas A, Liutkeviciene R. The Influence of Telomere-Related Gene Variants, Serum Levels, and Relative Leukocyte Telomere Length in Pituitary Adenoma Occurrence and Recurrence. Cancers (Basel) 2024; 16:643. [PMID: 38339395 PMCID: PMC10854692 DOI: 10.3390/cancers16030643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
In this study, we examined 130 patients with pituitary adenomas (PAs) and 320 healthy subjects, using DNA samples from peripheral blood leukocytes purified through the DNA salting-out method. Real-time polymerase chain reaction (RT-PCR) was used to assess single nucleotide polymorphisms (SNPs) and relative leukocyte telomere lengths (RLTLs), while enzyme-linked immunosorbent assay (ELISA) was used to determine the levels of TERF1, TERF2, TNKS2, CTC1, and ZNF676 in blood serum. Our findings reveal several significant associations. Genetic associations with pituitary adenoma occurrence: the TERF1 rs1545827 CT + TT genotypes were linked to 2.9-fold decreased odds of PA occurrence. Conversely, the TNKS2 rs10509637 GG genotype showed 6.5-fold increased odds of PA occurrence. Gender-specific genetic associations with PA occurrence: in females, the TERF1 rs1545827 CC + TT genotypes indicated 3.1-fold decreased odds of PA occurrence, while the TNKS2 rs10509637 AA genotype was associated with 4.6-fold increased odds. In males, the presence of the TERF1 rs1545827 T allele was associated with 2.2-fold decreased odds of PA occurrence, while the TNKS2 rs10509637 AA genotype was linked to a substantial 10.6-fold increase in odds. Associations with pituitary adenoma recurrence: the TNKS2 rs10509637 AA genotype was associated with 4.2-fold increased odds of PA recurrence. On the other hand, the TERF1 rs1545827 CT + TT genotypes were linked to 3.5-fold decreased odds of PA without recurrence, while the TNKS2 rs10509637 AA genotype was associated with 6.4-fold increased odds of PA without recurrence. Serum TERF2 and TERF1 levels: patients with PA exhibited elevated serum TERF2 levels compared to the reference group. Conversely, patients with PA had decreased TERF1 serum levels compared to the reference group. Relative leukocyte telomere length (RLTL): a significant difference in RLTL between the PA group and the reference group was observed, with PA patients having longer telomeres. Genetic associations with telomere shortening: the TERF1 rs1545827 T allele was associated with 1.4-fold decreased odds of telomere shortening. In contrast, the CTC1 rs3027234 TT genotype was linked to 4.8-fold increased odds of telomere shortening. These findings suggest a complex interplay between genetic factors, telomere length, and pituitary adenoma occurrence and recurrence, with potential gender-specific effects. Furthermore, variations in TERF1 and TNKS2 genes may play crucial roles in telomere length regulation and disease susceptibility.
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Affiliation(s)
- Greta Gedvilaite
- Laboratory of Ophthalmology, Neuroscience Institute, Lithuanian University of Health Sciences, Medical Academy, Eiveniu 2, LT-50161 Kaunas, Lithuania; (L.K.); (R.L.)
| | - Loresa Kriauciuniene
- Laboratory of Ophthalmology, Neuroscience Institute, Lithuanian University of Health Sciences, Medical Academy, Eiveniu 2, LT-50161 Kaunas, Lithuania; (L.K.); (R.L.)
| | - Arimantas Tamasauskas
- Department of Neurosurgery, Lithuanian University of Health Sciences, Medical Academy, Eiveniu 2, LT-50161 Kaunas, Lithuania;
| | - Rasa Liutkeviciene
- Laboratory of Ophthalmology, Neuroscience Institute, Lithuanian University of Health Sciences, Medical Academy, Eiveniu 2, LT-50161 Kaunas, Lithuania; (L.K.); (R.L.)
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13
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Li B. Unwrap RAP1's Mystery at Kinetoplastid Telomeres. Biomolecules 2024; 14:67. [PMID: 38254667 PMCID: PMC10813129 DOI: 10.3390/biom14010067] [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: 12/06/2023] [Revised: 12/27/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Although located at the chromosome end, telomeres are an essential chromosome component that helps maintain genome integrity and chromosome stability from protozoa to mammals. The role of telomere proteins in chromosome end protection is conserved, where they suppress various DNA damage response machineries and block nucleolytic degradation of the natural chromosome ends, although the detailed underlying mechanisms are not identical. In addition, the specialized telomere structure exerts a repressive epigenetic effect on expression of genes located at subtelomeres in a number of eukaryotic organisms. This so-called telomeric silencing also affects virulence of a number of microbial pathogens that undergo antigenic variation/phenotypic switching. Telomere proteins, particularly the RAP1 homologs, have been shown to be a key player for telomeric silencing. RAP1 homologs also suppress the expression of Telomere Repeat-containing RNA (TERRA), which is linked to their roles in telomere stability maintenance. The functions of RAP1s in suppressing telomere recombination are largely conserved from kinetoplastids to mammals. However, the underlying mechanisms of RAP1-mediated telomeric silencing have many species-specific features. In this review, I will focus on Trypanosoma brucei RAP1's functions in suppressing telomeric/subtelomeric DNA recombination and in the regulation of monoallelic expression of subtelomere-located major surface antigen genes. Common and unique mechanisms will be compared among RAP1 homologs, and their implications will be discussed.
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Affiliation(s)
- Bibo Li
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Arts and Sciences, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA;
- Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
- Center for RNA Science and Therapeutics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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14
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Lim CJ. Telomere C-Strand Fill-In Machinery: New Insights into the Human CST-DNA Polymerase Alpha-Primase Structures and Functions. Subcell Biochem 2024; 104:73-100. [PMID: 38963484 DOI: 10.1007/978-3-031-58843-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Telomeres at the end of eukaryotic chromosomes are extended by a specialized set of enzymes and telomere-associated proteins, collectively termed here the telomere "replisome." The telomere replisome acts on a unique replicon at each chromosomal end of the telomeres, the 3' DNA overhang. This telomere replication process is distinct from the replisome mechanism deployed to duplicate the human genome. The G-rich overhang is first extended before the complementary C-strand is filled in. This overhang is extended by telomerase, a specialized ribonucleoprotein and reverse transcriptase. The overhang extension process is terminated when telomerase is displaced by CTC1-STN1-TEN1 (CST), a single-stranded DNA-binding protein complex. CST then recruits DNA polymerase α-primase to complete the telomere replication process by filling in the complementary C-strand. In this chapter, the recent structure-function insights into the human telomere C-strand fill-in machinery (DNA polymerase α-primase and CST) will be discussed.
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Affiliation(s)
- Ci Ji Lim
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, WI, USA.
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15
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Li B. Telomere maintenance in African trypanosomes. Front Mol Biosci 2023; 10:1302557. [PMID: 38074093 PMCID: PMC10704157 DOI: 10.3389/fmolb.2023.1302557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/15/2023] [Indexed: 02/12/2024] Open
Abstract
Telomere maintenance is essential for genome integrity and chromosome stability in eukaryotic cells harboring linear chromosomes, as telomere forms a specialized structure to mask the natural chromosome ends from DNA damage repair machineries and to prevent nucleolytic degradation of the telomeric DNA. In Trypanosoma brucei and several other microbial pathogens, virulence genes involved in antigenic variation, a key pathogenesis mechanism essential for host immune evasion and long-term infections, are located at subtelomeres, and expression and switching of these major surface antigens are regulated by telomere proteins and the telomere structure. Therefore, understanding telomere maintenance mechanisms and how these pathogens achieve a balance between stability and plasticity at telomere/subtelomere will help develop better means to eradicate human diseases caused by these pathogens. Telomere replication faces several challenges, and the "end replication problem" is a key obstacle that can cause progressive telomere shortening in proliferating cells. To overcome this challenge, most eukaryotes use telomerase to extend the G-rich telomere strand. In addition, a number of telomere proteins use sophisticated mechanisms to coordinate the telomerase-mediated de novo telomere G-strand synthesis and the telomere C-strand fill-in, which has been extensively studied in mammalian cells. However, we recently discovered that trypanosomes lack many telomere proteins identified in its mammalian host that are critical for telomere end processing. Rather, T. brucei uses a unique DNA polymerase, PolIE that belongs to the DNA polymerase A family (E. coli DNA PolI family), to coordinate the telomere G- and C-strand syntheses. In this review, I will first briefly summarize current understanding of telomere end processing in mammals. Subsequently, I will describe PolIE-mediated coordination of telomere G- and C-strand synthesis in T. brucei and implication of this recent discovery.
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Affiliation(s)
- Bibo Li
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Arts and Sciences, Cleveland State University, Cleveland, OH, United States
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, United States
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH, United States
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16
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Gold NM, Okeke MN, He Y. Involvement of Inheritance in Determining Telomere Length beyond Environmental and Lifestyle Factors. Aging Dis 2023:AD.2023.1023. [PMID: 37962459 DOI: 10.14336/ad.2023.1023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
All linear chromosomal ends have specific DNA-protein complexes called telomeres. Telomeres serve as a "molecular clock" to estimate the potential length of cell replication. Shortening of telomere length (TL) is associated with cellular senescence, aging, and various age-related diseases in humans. Here we reviewed the structure, function, and regulation of telomeres and the age-related diseases associated with telomere attrition. Among the various determinants of TL, we highlight the connection between TL and heredity to provide a new overview of genetic determinants for TL. Studies across multiple species have shown that maternal and paternal TL influence the TL of their offspring, and this may affect life span and their susceptibility to age-related diseases. Hence, we reviewed the linkage between TL and parental influences and the proposed mechanisms involved. More in-depth studies on the genetic mechanism for TL attrition are needed due to the potential application of this knowledge in human medicine to prevent premature frailty at its earliest stage, as well as promote health and longevity.
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Affiliation(s)
- Naheemat Modupeola Gold
- Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- State Key Laboratory of Genetic, Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Michael Ngozi Okeke
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Nanomedical Technology Research, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yonghan He
- Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- State Key Laboratory of Genetic, Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Herken BW, Wong GT, Norman TM, Gilbert LA. Environmental challenge rewires functional connections among human genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.09.552346. [PMID: 37609173 PMCID: PMC10441384 DOI: 10.1101/2023.08.09.552346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
A fundamental question in biology is how a limited number of genes combinatorially govern cellular responses to environmental changes. While the prevailing hypothesis is that relationships between genes, processes, and ontologies could be plastic to achieve this adaptability, quantitatively comparing human gene functional connections between specific environmental conditions at scale is very challenging. Therefore, it remains unclear whether and how human genetic interaction networks are rewired in response to changing environmental conditions. Here, we developed a framework for mapping context-specific genetic interactions, enabling us to measure the plasticity of human genetic architecture upon environmental challenge for ~250,000 interactions, using cell cycle interruption, genotoxic perturbation, and nutrient deprivation as archetypes. We discover large-scale rewiring of human gene relationships across conditions, highlighted by dramatic shifts in the functional connections of epigenetic regulators (TIP60), cell cycle regulators (PP2A), and glycolysis metabolism. Our study demonstrates that upon environmental perturbation, intra-complex genetic rewiring is rare while inter-complex rewiring is common, suggesting a modular and flexible evolutionary genetic strategy that allows a limited number of human genes to enable adaptation to a large number of environmental conditions.
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Affiliation(s)
- Benjamin W. Herken
- Tetrad Graduate Program, University of California, San Francisco; San Francisco 94518, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco 94518, USA
| | - Garrett T. Wong
- Biological and Medical Informatics Graduate Program, University of California, San Francisco; San Francisco 94518, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco 94518, USA
| | | | - Luke A. Gilbert
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco 94518, USA
- Department of Urology, University of California, San Francisco, San Francisco 94518, USA
- Innovative Genomics Institute, University of California, San Francisco, San Francisco 94518, USA
- Arc Institute, Palo Alto 94305, USA
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18
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Singh P, Gazy I, Kupiec M. Control of telomere length in yeast by SUMOylated PCNA and the Elg1 PCNA unloader. eLife 2023; 12:RP86990. [PMID: 37530521 PMCID: PMC10396338 DOI: 10.7554/elife.86990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023] Open
Abstract
Telomeres cap and protect the linear eukaryotic chromosomes. Telomere length is determined by an equilibrium between positive and negative regulators of telomerase activity. A systematic screen for yeast mutants that affect telomere length maintenance in the yeast Saccharomyces cerevisiae revealed that mutations in any of ~500 genes affects telomere length. One of the genes that, when mutated, causes telomere elongation is ELG1, which encodes an unloader of PCNA, the processivity factor for replicative DNA polymerases. PCNA can undergo SUMOylation on two conserved residues, K164 and K127, or ubiquitination at lysine 164. These modifications have already been implicated in genome stability processes. We report that SUMOylated PCNA acts as a signal that positively regulates telomerase activity. We also uncovered physical interactions between Elg1 and the CST (Cdc13-Stn1-Ten) complex and addressed the mechanism by which Elg1 and Stn1 negatively regulates telomere elongation, coordinated by SUMO. We discuss these results with respect to how chromosomal replication and telomere elongation are coordinated.
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Affiliation(s)
- Pragyan Singh
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Inbal Gazy
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Martin Kupiec
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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19
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Mukherjee A, Hossain Z, Erben E, Ma S, Choi JY, Kim HS. Identification of a small-molecule inhibitor that selectively blocks DNA-binding by Trypanosoma brucei replication protein A1. Nat Commun 2023; 14:4390. [PMID: 37474515 PMCID: PMC10359466 DOI: 10.1038/s41467-023-39839-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 06/30/2023] [Indexed: 07/22/2023] Open
Abstract
Replication Protein A (RPA) is a broadly conserved complex comprised of the RPA1, 2 and 3 subunits. RPA protects the exposed single-stranded DNA (ssDNA) during DNA replication and repair. Using structural modeling, we discover an inhibitor, JC-229, that targets RPA1 in Trypanosoma brucei, the causative parasite of African trypanosomiasis. The inhibitor is highly toxic to T. brucei cells, while mildly toxic to human cells. JC-229 treatment mimics the effects of TbRPA1 depletion, including DNA replication inhibition and DNA damage accumulation. In-vitro ssDNA-binding assays demonstrate that JC-229 inhibits the activity of TbRPA1, but not the human ortholog. Indeed, despite the high sequence identity with T. cruzi and Leishmania RPA1, JC-229 only impacts the ssDNA-binding activity of TbRPA1. Site-directed mutagenesis confirms that the DNA-Binding Domain A (DBD-A) in TbRPA1 contains a JC-229 binding pocket. Residue Serine 105 determines specific binding and inhibition of TbRPA1 but not T. cruzi and Leishmania RPA1. Our data suggest a path toward developing and testing highly specific inhibitors for the treatment of African trypanosomiasis.
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Affiliation(s)
- Aditi Mukherjee
- Public Health Research Institute, Rutgers Biomedical Health Sciences, Newark, NJ, 07103, USA
| | - Zakir Hossain
- Department of Chemistry and Biochemistry, Queens College, New York, NY, 11367, USA
| | - Esteban Erben
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Provincia de Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, San Martín, Provincia de Buenos Aires, Argentina
| | - Shuai Ma
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Jun Yong Choi
- Department of Chemistry and Biochemistry, Queens College, New York, NY, 11367, USA.
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
| | - Hee-Sook Kim
- Public Health Research Institute, Rutgers Biomedical Health Sciences, Newark, NJ, 07103, USA.
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical Health Sciences, Newark, NJ, 07103, USA.
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20
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Abstract
It has been known for decades that telomerase extends the 3' end of linear eukaryotic chromosomes and dictates the telomeric repeat sequence based on the template in its RNA. However, telomerase does not mitigate sequence loss at the 5' ends of chromosomes, which results from lagging strand DNA synthesis and nucleolytic processing. Therefore, a second enzyme is needed to keep telomeres intact: DNA polymerase α/Primase bound to Ctc1-Stn1-Ten1 (CST). CST-Polα/Primase maintains telomeres through a fill-in reaction that replenishes the lost sequences at the 5' ends. CST not only serves to maintain telomeres but also determines their length by keeping telomerase from overelongating telomeres. Here we discuss recent data on the evolution, structure, function, and recruitment of mammalian CST-Polα/Primase, highlighting the role of this complex and telomere length control in human disease.
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Affiliation(s)
- Sarah W Cai
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, New York 10065, USA
| | - Titia de Lange
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, New York 10065, USA
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21
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Zade NH, Khattar E. POT1 mutations cause differential effects on telomere length leading to opposing disease phenotypes. J Cell Physiol 2023; 238:1237-1255. [PMID: 37183325 DOI: 10.1002/jcp.31034] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/28/2023] [Accepted: 04/17/2023] [Indexed: 05/16/2023]
Abstract
The protection of telomere protein (POT1) is a telomere-binding protein and is an essential component of the six-membered shelterin complex, which is associated with the telomeres. POT1 directly binds to the 3' single-stranded telomeric overhang and prevents the activation of DNA damage response at telomeres thus preventing the telomere-telomere fusions and genomic instability. POT1 also plays a pivotal role in maintaining telomere length by regulating telomerase-mediated telomere elongation. Mutations in POT1 proteins result in three different telomere phenotypes, which include long, short, or aberrant telomere length. Long telomeres predispose individuals to cancer, while short or aberrant telomere phenotypes result in pro-aging diseases referred to as telomeropathies. Here, we review the function of POT1 proteins in telomere length hemostasis and how the spectrum of mutations reported in POT1 can be segregated toward developing very distinct disease phenotypes of cancer and telomeropathies.
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Affiliation(s)
- Nikita Harish Zade
- Sunandan Divatia School of Science, SVKM's NMIMS (Deemed to be) University, Mumbai, India
| | - Ekta Khattar
- Sunandan Divatia School of Science, SVKM's NMIMS (Deemed to be) University, Mumbai, India
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22
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Ngo K, Gittens TH, Gonzalez DI, Hatmaker EA, Plotkin S, Engle M, Friedman GA, Goldin M, Hoerr RE, Eichman BF, Rokas A, Benton ML, Friedman KL. A comprehensive map of hotspots of de novo telomere addition in Saccharomyces cerevisiae. Genetics 2023; 224:iyad076. [PMID: 37119805 PMCID: PMC10474931 DOI: 10.1093/genetics/iyad076] [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: 03/20/2023] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 05/01/2023] Open
Abstract
Telomere healing occurs when telomerase, normally restricted to chromosome ends, acts upon a double-strand break to create a new, functional telomere. De novo telomere addition (dnTA) on the centromere-proximal side of a break truncates the chromosome but, by blocking resection, may allow the cell to survive an otherwise lethal event. We previously identified several sequences in the baker's yeast, Saccharomyces cerevisiae, that act as hotspots of dnTA [termed Sites of Repair-associated Telomere Addition (SiRTAs)], but the distribution and functional relevance of SiRTAs is unclear. Here, we describe a high-throughput sequencing method to measure the frequency and location of telomere addition within sequences of interest. Combining this methodology with a computational algorithm that identifies SiRTA sequence motifs, we generate the first comprehensive map of telomere-addition hotspots in yeast. Putative SiRTAs are strongly enriched in subtelomeric regions where they may facilitate formation of a new telomere following catastrophic telomere loss. In contrast, outside of subtelomeres, the distribution and orientation of SiRTAs appears random. Since truncating the chromosome at most SiRTAs would be lethal, this observation argues against selection for these sequences as sites of telomere addition per se. We find, however, that sequences predicted to function as SiRTAs are significantly more prevalent across the genome than expected by chance. Sequences identified by the algorithm bind the telomeric protein Cdc13, raising the possibility that association of Cdc13 with single-stranded regions generated during the response to DNA damage may facilitate DNA repair more generally.
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Affiliation(s)
- Katrina Ngo
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
| | - Tristen H Gittens
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
| | - David I Gonzalez
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
| | - E Anne Hatmaker
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37232 USA
| | - Simcha Plotkin
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
| | - Mason Engle
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
| | - Geofrey A Friedman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
| | - Melissa Goldin
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
| | - Remington E Hoerr
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232 USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37232 USA
| | | | - Katherine L Friedman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
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23
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Harmak H, Redouane S, Charoute H, Aniq Filali O, Barakat A, Rouba H. In silico exploration and molecular dynamics of deleterious SNPs on the human TERF1 protein triggering male infertility. J Biomol Struct Dyn 2023; 41:14665-14688. [PMID: 36995171 DOI: 10.1080/07391102.2023.2193995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 02/18/2023] [Indexed: 03/31/2023]
Abstract
By limiting chromosome erosion and end-to-end fusions, telomere integrity is critical for chromosome stability and cell survival. During mitotic cycles or due to environmental stresses, telomeres become progressively shorter and dysfunctional, thus triggering cellular senescence, genomic instability and cell death. To avoid such consequences, the telomerase action, as well as the Shelterin and CST complexes, assure the telomere's protection. Telomeric repeat binding factor 1 (TERF1), which is one of the primary components of the Shelterin complex, binds directly to the telomere and controls its length and function by regulating the telomerase activity. Several reports about TERF1 gene variations have been associated with different diseases, and some of them have linked these variations to male infertility. Hence, this paper can be advantageous to investigate the association between the missense variants of the TERF1 gene and the susceptibility to male infertility. The stepwise prediction of SNPs pathogenicity followed in this study was based on stability and conservation analysis, post-translational modification, secondary structure, functional interaction prediction, binding energy evaluation and finally molecular dynamic simulation. Prediction matching among the tools revealed that out of 18 SNPs, only four (rs1486407144, rs1259659354, rs1257022048 and rs1320180267) were predicted as the most damaging and highly deleterious SNPs affecting the TERF1 protein and its molecular dynamics when interacting with the TERB1 protein by influencing the function, structural stability, flexibility and compaction of the overall complex. Interestingly, these polymorphisms should be considered during genetic screening so they can be used effectively as genetic biomarkers for male infertility diagnosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Houda Harmak
- Laboratory of Genomics and Human Genetics, 1, Place Louis Pasteur, Institut Pasteur du Maroc, Casablanca, Morocco
- Laboratory of Physiopathology, Molecular Genetics and Biotechnology, Department of Biology, Faculty of Sciences Ain Chock, Hassan II University, Casablanca, Morocco
| | - Salaheddine Redouane
- Laboratory of Genomics and Human Genetics, 1, Place Louis Pasteur, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Hicham Charoute
- Research Unit of Epidemiology, Biostatistics and Bioinformatics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Ouafaa Aniq Filali
- Laboratory of Physiopathology, Molecular Genetics and Biotechnology, Department of Biology, Faculty of Sciences Ain Chock, Hassan II University, Casablanca, Morocco
| | - Abdelhamid Barakat
- Laboratory of Genomics and Human Genetics, 1, Place Louis Pasteur, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Hassan Rouba
- Laboratory of Genomics and Human Genetics, 1, Place Louis Pasteur, Institut Pasteur du Maroc, Casablanca, Morocco
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24
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Ngo K, Gittens TH, Gonzalez DI, Hatmaker EA, Plotkin S, Engle M, Friedman GA, Goldin M, Hoerr RE, Eichman BF, Rokas A, Benton ML, Friedman KL. A comprehensive map of hotspots of de novo telomere addition in Saccharomyces cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533556. [PMID: 36993206 PMCID: PMC10055226 DOI: 10.1101/2023.03.20.533556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Telomere healing occurs when telomerase, normally restricted to chromosome ends, acts upon a double-strand break to create a new, functional telomere. De novo telomere addition on the centromere-proximal side of a break truncates the chromosome but, by blocking resection, may allow the cell to survive an otherwise lethal event. We previously identified several sequences in the baker’s yeast, Saccharomyces cerevisiae , that act as hotspots of de novo telomere addition (termed Sites of Repair-associated Telomere Addition or SiRTAs), but the distribution and functional relevance of SiRTAs is unclear. Here, we describe a high-throughput sequencing method to measure the frequency and location of telomere addition within sequences of interest. Combining this methodology with a computational algorithm that identifies SiRTA sequence motifs, we generate the first comprehensive map of telomere-addition hotspots in yeast. Putative SiRTAs are strongly enriched in subtelomeric regions where they may facilitate formation of a new telomere following catastrophic telomere loss. In contrast, outside of subtelomeres, the distribution and orientation of SiRTAs appears random. Since truncating the chromosome at most SiRTAs would be lethal, this observation argues against selection for these sequences as sites of telomere addition per se. We find, however, that sequences predicted to function as SiRTAs are significantly more prevalent across the genome than expected by chance. Sequences identified by the algorithm bind the telomeric protein Cdc13, raising the possibility that association of Cdc13 with single-stranded regions generated during the response to DNA damage may facilitate DNA repair more generally.
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Affiliation(s)
- Katrina Ngo
- Department of Biological Sciences, Vanderbilt University
| | | | | | - E. Anne Hatmaker
- Department of Biological Sciences, Vanderbilt University
- Evolutionary Studies Initiative, Vanderbilt University
| | - Simcha Plotkin
- Department of Biological Sciences, Vanderbilt University
| | - Mason Engle
- Department of Biological Sciences, Vanderbilt University
| | | | - Melissa Goldin
- Department of Biological Sciences, Vanderbilt University
| | | | - Brandt F. Eichman
- Department of Biological Sciences, Vanderbilt University
- Department of Biochemistry, Vanderbilt University
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University
- Evolutionary Studies Initiative, Vanderbilt University
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25
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Ueno M. Exploring Genetic Interactions with Telomere Protection Gene pot1 in Fission Yeast. Biomolecules 2023; 13:biom13020370. [PMID: 36830739 PMCID: PMC9953254 DOI: 10.3390/biom13020370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
The regulation of telomere length has a significant impact on cancer risk and aging in humans. Circular chromosomes are found in humans and are often unstable during mitosis, resulting in genome instability. Some types of cancer have a high frequency of a circular chromosome. Fission yeast is a good model for studying the formation and stability of circular chromosomes as deletion of pot1 (encoding a telomere protection protein) results in rapid telomere degradation and chromosome fusion. Pot1 binds to single-stranded telomere DNA and is conserved from fission yeast to humans. Loss of pot1 leads to viable strains in which all three fission yeast chromosomes become circular. In this review, I will introduce pot1 genetic interactions as these inform on processes such as the degradation of uncapped telomeres, chromosome fusion, and maintenance of circular chromosomes. Therefore, exploring genes that genetically interact with pot1 contributes to finding new genes and/or new functions of genes related to the maintenance of telomeres and/or circular chromosomes.
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Affiliation(s)
- Masaru Ueno
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8530, Japan; ; Tel.: +81-82-424-7768
- Hiroshima Research Center for Healthy Aging (HiHA), Hiroshima University, Higashi-Hiroshima 739-8530, Japan
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26
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Doubková M, Vrzalová Z, Štefániková M, Červinek L, Kozubík KS, Blaháková I, Pospíšilová Š, Doubek M. Germline variant of CTC1 gene in a patient with pulmonary fibrosis and myelodysplastic syndrome. Multidiscip Respir Med 2023; 18:909. [PMID: 37404458 PMCID: PMC10316942 DOI: 10.4081/mrm.2023.909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/02/2023] [Indexed: 07/06/2023] Open
Abstract
Introduction Telomeropathies are associated with a wide range of diseases and less common combinations of various pulmonary and extrapulmonary disorders. Case presentation In proband with high-risk myelodysplastic syndrome and interstitial pulmonary fibrosis, whole exome sequencing revealed a germline heterozygous variant of CTC1 gene (c.1360delG). This "frameshift" variant results in a premature stop codon and is classified as likely pathogenic/pathogenic. So far, this gene variant has been described in a heterozygous state in adult patients with hematological diseases such as idiopathic aplastic anemia or paroxysmal nocturnal hemoglobinuria, but also in interstitial pulmonary fibrosis. Described CTC1 gene variant affects telomere length and leads to telomeropathies. Conclusions In our case report, we describe a rare case of coincidence of pulmonary fibrosis and hematological malignancy caused by a germline gene mutation in CTC1. Lung diseases and hematologic malignancies associated with short telomeres do not respond well to standard treatment.
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Affiliation(s)
- Martina Doubková
- Department of Pulmonary Diseases and Tuberculosis, University Hospital and Faculty of Medicine, Brno
| | - Zuzana Vrzalová
- Central European Institute of Technology, Masaryk University, Brno
- Department of Internal Medicine - Hematology and Oncology, University Hospital and Faculty of Medicine, Brno
| | - Marianna Štefániková
- Department of Pulmonary Diseases and Tuberculosis, University Hospital and Faculty of Medicine, Brno
| | - Libor Červinek
- Department of Internal Medicine - Hematology and Oncology, University Hospital and Faculty of Medicine, Brno
| | - Kateřina Staňo Kozubík
- Central European Institute of Technology, Masaryk University, Brno
- Department of Internal Medicine - Hematology and Oncology, University Hospital and Faculty of Medicine, Brno
| | - Ivona Blaháková
- Central European Institute of Technology, Masaryk University, Brno
- Department of Internal Medicine - Hematology and Oncology, University Hospital and Faculty of Medicine, Brno
| | - Šárka Pospíšilová
- Central European Institute of Technology, Masaryk University, Brno
- Department of Internal Medicine - Hematology and Oncology, University Hospital and Faculty of Medicine, Brno
- Department of Medical Genetics and Genomics, University Hospital and Faculty of Medicine, Brno, Czech Republic
| | - Michael Doubek
- Central European Institute of Technology, Masaryk University, Brno
- Department of Internal Medicine - Hematology and Oncology, University Hospital and Faculty of Medicine, Brno
- Department of Medical Genetics and Genomics, University Hospital and Faculty of Medicine, Brno, Czech Republic
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27
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Biological Functions of the DNA Glycosylase NEIL3 and Its Role in Disease Progression Including Cancer. Cancers (Basel) 2022; 14:cancers14235722. [PMID: 36497204 PMCID: PMC9737245 DOI: 10.3390/cancers14235722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
The accumulation of oxidative DNA base damage can severely disrupt the integrity of the genome and is strongly associated with the development of cancer. DNA glycosylase is the critical enzyme that initiates the base excision repair (BER) pathway, recognizing and excising damaged bases. The Nei endonuclease VIII-like 3 (NEIL3) is an emerging DNA glycosylase essential in maintaining genome stability. With an in-depth study of the structure and function of NEIL3, we found that it has properties related to the process of base damage repair. For example, it not only prefers the base damage of single-stranded DNA (ssDNA), G-quadruplex and DNA interstrand crosslinks (ICLs), but also participates in the maintenance of replication fork stability and telomere integrity. In addition, NEIL3 is strongly associated with the progression of cancers and cardiovascular and neurological diseases, is incredibly significantly overexpressed in cancers, and may become an independent prognostic marker for cancer patients. Interestingly, circNEIL3, a circular RNA of exon-encoded origin by NEIL3, also promotes the development of multiple cancers. In this review, we have summarized the structure and the characteristics of NEIL3 to repair base damage. We have focused on NEIL3 and circNEIL3 in cancer development, progression and prognosis.
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28
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Zia S, Khan N, Tehreem K, Rehman N, Sami R, Baty RS, Tayeb FJ, Almashjary MN, Alsubhi NH, Alrefaei GI, Shahid R. Transcriptomic Analysis of Conserved Telomere Maintenance Component 1 (CTC1) and Its Association with Leukemia. J Clin Med 2022; 11:jcm11195780. [PMID: 36233645 PMCID: PMC9571731 DOI: 10.3390/jcm11195780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Telomere length (TEL) regulation is important for genome stability and is governed by the coordinated role of shelterin proteins, telomerase (TERT), and CST (CTC1/OBFC1/TEN1) complex. Previous studies have shown the association of telomerase expression with the risk of acute lymphoblastic leukemia (ALL). However, no data are available for CST association with the ALL. The current pilot study was designed to evaluate the CST expression levels in ALL. In total, 350 subjects were recruited, including 250 ALL cases and 100 controls. The subjects were stratified by age and categorized into pediatrics (1–18 years) and adults (19–54 years). TEL and expression patterns of CTC1, OBFC1, and TERT genes were determined by qPCR. The univariable logistic regression analysis was performed to determine the association of gene expression with ALL, and the results were adjusted for age and sex in multivariable analyses. Pediatric and adult cases did not reflect any change in telomere lengths relative to controls. However, expression of CTC1, OBFC1, and TERT genes were induced among ALL cases. Multivariable logistic regression analyses showed association of CTC1 with ALL in pediatric [β estimate (standard error (SE)= −0.013 (0.007), p = 0.049, and adults [0.053 (0.023), p = 0.025]. The association of CTC1 remained significant when taken together with OBFC1 and TERT in a multivariable model. Furthermore, CTC1 showed significant association with B-cell ALL [−0.057(0.017), p = 0.002) and T-cell ALL [−0.050 (0.018), p = 0.008] in pediatric group while no such association was noted in adults. Together, our findings demonstrated that telomere modulating genes, particularly CTC1, are strongly associated with ALL. Therefore, CTC1 can potentially be used as a risk biomarker for the identification of ALL in both pediatrics and adults.
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Affiliation(s)
- Saadiya Zia
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad 45550, Pakistan
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Netasha Khan
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad 45550, Pakistan
| | - Komal Tehreem
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad 45550, Pakistan
| | - Nazia Rehman
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad 45550, Pakistan
| | - Rokayya Sami
- Department of Food Science and Nutrition, College of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Roua S. Baty
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Faris J. Tayeb
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 47713, Saudi Arabia
| | - Majed N. Almashjary
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 22254, Saudi Arabia
- Hematology Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 22254, Saudi Arabia
| | - Nouf H. Alsubhi
- Biological Sciences Department, College of Science and Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia
| | - Ghadeer I. Alrefaei
- Department of Biology, College of Science, University of Jeddah, P.O. Box 80327, Jeddah 21589, Saudi Arabia
| | - Ramla Shahid
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad 45550, Pakistan
- Correspondence:
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Telomeres and Their Neighbors. Genes (Basel) 2022; 13:genes13091663. [PMID: 36140830 PMCID: PMC9498494 DOI: 10.3390/genes13091663] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/21/2022] Open
Abstract
Telomeres are essential structures formed from satellite DNA repeats at the ends of chromosomes in most eukaryotes. Satellite DNA repeat sequences are useful markers for karyotyping, but have a more enigmatic role in the eukaryotic cell. Much work has been done to investigate the structure and arrangement of repetitive DNA elements in classical models with implications for species evolution. Still more is needed until there is a complete picture of the biological function of DNA satellite sequences, particularly when considering non-model organisms. Celebrating Gregor Mendel’s anniversary by going to the roots, this review is designed to inspire and aid new research into telomeres and satellites with a particular focus on non-model organisms and accessible experimental and in silico methods that do not require specialized equipment or expensive materials. We describe how to identify telomere (and satellite) repeats giving many examples of published (and some unpublished) data from these techniques to illustrate the principles behind the experiments. We also present advice on how to perform and analyse such experiments, including details of common pitfalls. Our examples are a selection of recent developments and underexplored areas of research from the past. As a nod to Mendel’s early work, we use many examples from plants and insects, especially as much recent work has expanded beyond the human and yeast models traditional in telomere research. We give a general introduction to the accepted knowledge of telomere and satellite systems and include references to specialized reviews for the interested reader.
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30
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Gao X, Yu X, Zhang C, Wang Y, Sun Y, Sun H, Zhang H, Shi Y, He X. Telomeres and Mitochondrial Metabolism: Implications for Cellular Senescence and Age-related Diseases. Stem Cell Rev Rep 2022; 18:2315-2327. [PMID: 35460064 PMCID: PMC9033418 DOI: 10.1007/s12015-022-10370-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2022] [Indexed: 02/06/2023]
Abstract
Cellular senescence is an irreversible cell arrest process, which is determined by a variety of complicated mechanisms, including telomere attrition, mitochondrial dysfunction, metabolic disorders, loss of protein homeostasis, epigenetic changes, etc. Cellular senescence is causally related to the occurrence and development of age-related disease. The elderly is liable to suffer from disorders such as neurodegenerative diseases, cancer, and diabetes. Therefore, it is increasingly imperative to explore specific countermeasures for the treatment of age-related diseases. Numerous studies on humans and mice emphasize the significance of metabolic imbalance caused by short telomeres and mitochondrial damages in the onset of age-related diseases. Although the experimental data are relatively independent, more and more evidences have shown that there is mutual crosstalk between telomeres and mitochondrial metabolism in the process of cellular senescence. This review systematically discusses the relationship between telomere length, mitochondrial metabolic disorder, as well as their underlying mechanisms for cellular senescence and age-related diseases. Future studies on telomere and mitochondrial metabolism may shed light on potential therapeutic strategies for age-related diseases. Graphical Abstract The characteristics of cellular senescence mainly include mitochondrial dysfunction and telomere attrition. Mitochondrial dysfunction will cause mitochondrial metabolic disorders, including decreased ATP production, increased ROS production, as well as enhanced cellular apoptosis. While oxidative stress reaction to produce ROS, leads to DNA damage, and eventually influences telomere length. Under the stimulation of oxidative stress, telomerase catalytic subunit TERT mainly plays an inhibitory role on oxidative stress, reduces the production of ROS and protects telomere function. Concurrently, mitochondrial dysfunction and telomere attrition eventually induce a range of age-related diseases, such as T2DM, osteoporosis, AD, etc. :increase; :reduce;⟝:inhibition.
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Affiliation(s)
- Xingyu Gao
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, 126 Xinmin Street, Changchun, 130021, China
| | - Xiao Yu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, 126 Xinmin Street, Changchun, 130021, China
| | - Chang Zhang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, 126 Xinmin Street, Changchun, 130021, China
| | - Yiming Wang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, 126 Xinmin Street, Changchun, 130021, China
| | - Yanan Sun
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, 126 Xinmin Street, Changchun, 130021, China
| | - Hui Sun
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, 126 Xinmin Street, Changchun, 130021, China
| | - Haiying Zhang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, 126 Xinmin Street, Changchun, 130021, China
| | - Yingai Shi
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, 126 Xinmin Street, Changchun, 130021, China
| | - Xu He
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, 126 Xinmin Street, Changchun, 130021, China.
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Pan-cancer analysis reveals that CTC1-STN1-TEN1 (CST) complex may have a key position in oncology. Cancer Genet 2022; 262-263:80-90. [DOI: 10.1016/j.cancergen.2022.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/07/2022] [Accepted: 01/30/2022] [Indexed: 12/14/2022]
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Yeast Stn1 promotes MCM to circumvent Rad53 control of the S phase checkpoint. Curr Genet 2022; 68:165-179. [PMID: 35150303 PMCID: PMC8976814 DOI: 10.1007/s00294-022-01228-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/06/2021] [Accepted: 12/16/2021] [Indexed: 11/17/2022]
Abstract
Treating yeast cells with the replication inhibitor hydroxyurea activates the S phase checkpoint kinase Rad53, eliciting responses that block DNA replication origin firing, stabilize replication forks, and prevent premature extension of the mitotic spindle. We previously found overproduction of Stn1, a subunit of the telomere-binding Cdc13–Stn1–Ten1 complex, circumvents Rad53 checkpoint functions in hydroxyurea, inducing late origin firing and premature spindle extension even though Rad53 is activated normally. Here, we show Stn1 overproduction acts through remarkably similar pathways compared to loss of RAD53, converging on the MCM complex that initiates origin firing and forms the catalytic core of the replicative DNA helicase. First, mutations affecting Mcm2 and Mcm5 block the ability of Stn1 overproduction to disrupt the S phase checkpoint. Second, loss of function stn1 mutations compensate rad53 S phase checkpoint defects. Third Stn1 overproduction suppresses a mutation in Mcm7. Fourth, stn1 mutants accumulate single-stranded DNA at non-telomeric genome locations, imposing a requirement for post-replication DNA repair. We discuss these interactions in terms of a model in which Stn1 acts as an accessory replication factor that facilitates MCM activation at ORIs and potentially also maintains MCM activity at replication forks advancing through challenging templates.
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33
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Vicari MR, Bruschi DP, Cabral-de-Mello DC, Nogaroto V. Telomere organization and the interstitial telomeric sites involvement in insects and vertebrates chromosome evolution. Genet Mol Biol 2022; 45:e20220071. [DOI: 10.1590/1678-4685-gmb-2022-0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 09/24/2022] [Indexed: 11/16/2022] Open
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34
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Telomeres and Cancer. Life (Basel) 2021; 11:life11121405. [PMID: 34947936 PMCID: PMC8704776 DOI: 10.3390/life11121405] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 12/18/2022] Open
Abstract
Telomeres cap the ends of eukaryotic chromosomes and are indispensable chromatin structures for genome protection and replication. Telomere length maintenance has been attributed to several functional modulators, including telomerase, the shelterin complex, and the CST complex, synergizing with DNA replication, repair, and the RNA metabolism pathway components. As dysfunctional telomere maintenance and telomerase activation are associated with several human diseases, including cancer, the molecular mechanisms behind telomere length regulation and protection need particular emphasis. Cancer cells exhibit telomerase activation, enabling replicative immortality. Telomerase reverse transcriptase (TERT) activation is involved in cancer development through diverse activities other than mediating telomere elongation. This review describes the telomere functions, the role of functional modulators, the implications in cancer development, and the future therapeutic opportunities.
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35
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Biegała Ł, Gajek A, Marczak A, Rogalska A. PARP inhibitor resistance in ovarian cancer: Underlying mechanisms and therapeutic approaches targeting the ATR/CHK1 pathway. Biochim Biophys Acta Rev Cancer 2021; 1876:188633. [PMID: 34619333 DOI: 10.1016/j.bbcan.2021.188633] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/14/2021] [Accepted: 10/01/2021] [Indexed: 01/01/2023]
Abstract
Ovarian cancer (OC) constitutes the most common cause of gynecologic cancer-related death in women worldwide. Despite consistent developments in treatment strategies for OC, the management of advanced-stage disease remains a significant challenge. Recent improvements in targeted treatments based on poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) have provided invaluable benefits to patients with OC. Unfortunately, numerous patients do not respond to PARPi due to intrinsic resistance or acquisition of resistance. Here, we discuss mechanisms of resistance to PARPi that have specifically emerged in OC including increased drug efflux, restoration of HR repair, re-establishment of replication fork stability, reduced PARP1 trapping, abnormalities in PARP signaling, and less common pathways associated with alternative DNA sensing and repair pathways. Elucidation of the precise mechanisms is essential for the development of novel strategies to re-sensitize OC cells to PARPi agents. Additionally, novel potential concepts for preventing and combating resistance to PARPi under development and relevant clinical reports on treatment strategies have been reviewed, with emphasis on the exploitation of the ATR/CHK1 kinase pathway in sensitization to PARPi to overcome resistance-induced vulnerability in ovarian cancer.
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Affiliation(s)
- Łukasz Biegała
- Department of Medical Biophysics, Institute of Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland.
| | - Arkadiusz Gajek
- Department of Medical Biophysics, Institute of Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland.
| | - Agnieszka Marczak
- Department of Medical Biophysics, Institute of Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland.
| | - Aneta Rogalska
- Department of Medical Biophysics, Institute of Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland.
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36
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Paiano J, Zolnerowich N, Wu W, Pavani R, Wang C, Li H, Zheng L, Shen B, Sleckman BP, Chen BR, Nussenzweig A. Role of 53BP1 in end protection and DNA synthesis at DNA breaks. Genes Dev 2021; 35:1356-1367. [PMID: 34503990 DOI: 10.1101/gad.348667.121] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/17/2021] [Indexed: 12/20/2022]
Abstract
Double-strand break (DSB) repair choice is greatly influenced by the initial processing of DNA ends. 53BP1 limits the formation of recombinogenic single-strand DNA (ssDNA) in BRCA1-deficient cells, leading to defects in homologous recombination (HR). However, the exact mechanisms by which 53BP1 inhibits DSB resection remain unclear. Previous studies have identified two potential pathways: protection against DNA2/EXO1 exonucleases presumably through the Shieldin (SHLD) complex binding to ssDNA, and localized DNA synthesis through the CTC1-STN1-TEN1 (CST) and DNA polymerase α (Polα) to counteract resection. Using a combinatorial approach of END-seq, SAR-seq, and RPA ChIP-seq, we directly assessed the extent of resection, DNA synthesis, and ssDNA, respectively, at restriction enzyme-induced DSBs. We show that, in the presence of 53BP1, Polα-dependent DNA synthesis reduces the fraction of resected DSBs and the resection lengths in G0/G1, supporting a previous model that fill-in synthesis can limit the extent of resection. However, in the absence of 53BP1, Polα activity is sustained on ssDNA yet does not substantially counter resection. In contrast, EXO1 nuclease activity is essential for hyperresection in the absence of 53BP1. Thus, Polα-mediated fill-in partially limits resection in the presence of 53BP1 but cannot counter extensive hyperresection due to the loss of 53BP1 exonuclease blockade. These data provide the first nucleotide mapping of DNA synthesis at resected DSBs and provide insight into the relationship between fill-in polymerases and resection exonucleases.
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Affiliation(s)
- Jacob Paiano
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Nicholas Zolnerowich
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Wei Wu
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Raphael Pavani
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Chen Wang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
| | - Hongzhi Li
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, California 91010, USA.,Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, California 91010, USA.,Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, California 91010, USA.,Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
| | - Barry P Sleckman
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA.,O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Bo-Ruei Chen
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA.,O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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37
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Li B, Zhao Y. Regulation of Antigenic Variation by Trypanosoma brucei Telomere Proteins Depends on Their Unique DNA Binding Activities. Pathogens 2021; 10:pathogens10080967. [PMID: 34451431 PMCID: PMC8402208 DOI: 10.3390/pathogens10080967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 01/17/2023] Open
Abstract
Trypanosoma brucei causes human African trypanosomiasis and regularly switches its major surface antigen, Variant Surface Glycoprotein (VSG), to evade the host immune response. Such antigenic variation is a key pathogenesis mechanism that enables T. brucei to establish long-term infections. VSG is expressed exclusively from subtelomere loci in a strictly monoallelic manner, and DNA recombination is an important VSG switching pathway. The integrity of telomere and subtelomere structure, maintained by multiple telomere proteins, is essential for T. brucei viability and for regulating the monoallelic VSG expression and VSG switching. Here we will focus on T. brucei TRF and RAP1, two telomere proteins with unique nucleic acid binding activities, and summarize their functions in telomere integrity and stability, VSG switching, and monoallelic VSG expression. Targeting the unique features of TbTRF and TbRAP1′s nucleic acid binding activities to perturb the integrity of telomere structure and disrupt VSG monoallelic expression may serve as potential therapeutic strategy against T. brucei.
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Affiliation(s)
- Bibo Li
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Sciences and Health Professions, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
- Center for RNA Science and Therapeutics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Correspondence: (B.L.); (Y.Z.)
| | - Yanxiang Zhao
- Shenzhen Research Institute, The Hong Kong Polytechnic University, Shenzhen, China
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China
- Correspondence: (B.L.); (Y.Z.)
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38
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Eigenfeld M, Kerpes R, Becker T. Understanding the Impact of Industrial Stress Conditions on Replicative Aging in Saccharomyces cerevisiae. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:665490. [PMID: 37744109 PMCID: PMC10512339 DOI: 10.3389/ffunb.2021.665490] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/30/2021] [Indexed: 09/26/2023]
Abstract
In yeast, aging is widely understood as the decline of physiological function and the decreasing ability to adapt to environmental changes. Saccharomyces cerevisiae has become an important model organism for the investigation of these processes. Yeast is used in industrial processes (beer and wine production), and several stress conditions can influence its intracellular aging processes. The aim of this review is to summarize the current knowledge on applied stress conditions, such as osmotic pressure, primary metabolites (e.g., ethanol), low pH, oxidative stress, heat on aging indicators, age-related physiological changes, and yeast longevity. There is clear evidence that yeast cells are exposed to many stressors influencing viability and vitality, leading to an age-related shift in age distribution. Currently, there is a lack of rapid, non-invasive methods allowing the investigation of aspects of yeast aging in real time on a single-cell basis using the high-throughput approach. Methods such as micromanipulation, centrifugal elutriator, or biotinylation do not provide real-time information on age distributions in industrial processes. In contrast, innovative approaches, such as non-invasive fluorescence coupled flow cytometry intended for high-throughput measurements, could be promising for determining the replicative age of yeast cells in fermentation and its impact on industrial stress conditions.
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Affiliation(s)
| | - Roland Kerpes
- Research Group Beverage and Cereal Biotechnology, Institute of Brewing and Beverage Technology, Technical University of Munich, Freising, Germany
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39
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Lyu X, Sang PB, Chai W. CST in maintaining genome stability: Beyond telomeres. DNA Repair (Amst) 2021; 102:103104. [PMID: 33780718 PMCID: PMC8081025 DOI: 10.1016/j.dnarep.2021.103104] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/12/2022]
Abstract
The human CST (CTC1-STN1-TEN1) complex is an RPA-like single-stranded DNA binding protein complex. While its telomeric functions have been well investigated, numerous studies have revealed that hCST also plays important roles in maintaining genome stability beyond telomeres. Here, we review and discuss recent discoveries on CST in various global genome maintenance pathways, including findings on the CST supercomplex structure, its functions in unperturbed DNA replication, stalled replication, double-strand break repair, and the ATR-CHK1 activation pathway. By summarizing these recent discoveries, we hope to offer new insights into genome maintenance mechanisms and the pathogenesis of CST mutation-associated diseases.
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Affiliation(s)
- Xinxing Lyu
- Institute of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250062, China; Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, 60153, United States
| | - Pau Biak Sang
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, 60153, United States
| | - Weihang Chai
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, 60153, United States.
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40
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Choudhury A, Mohammad T, Samarth N, Hussain A, Rehman MT, Islam A, Alajmi MF, Singh S, Hassan MI. Structural genomics approach to investigate deleterious impact of nsSNPs in conserved telomere maintenance component 1. Sci Rep 2021; 11:10202. [PMID: 33986331 PMCID: PMC8119478 DOI: 10.1038/s41598-021-89450-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/14/2021] [Indexed: 02/07/2023] Open
Abstract
Conserved telomere maintenance component 1 (CTC1) is an important component of the CST (CTC1-STN1-TEN1) complex, involved in maintaining the stability of telomeric DNA. Several non-synonymous single-nucleotide polymorphisms (nsSNPs) in CTC1 have been reported to cause Coats plus syndrome and Dyskeratosis congenital diseases. Here, we have performed sequence and structure analyses of nsSNPs of CTC1 using state-of-the-art computational methods. The structure-based study focuses on the C-terminal OB-fold region of CTC1. There are 11 pathogenic mutations identified, and detailed structural analyses were performed. These mutations cause a significant disruption of noncovalent interactions, which may be a possible reason for CTC1 instability and consequent diseases. To see the impact of such mutations on the protein conformation, all-atom molecular dynamics (MD) simulations of CTC1-wild-type (WT) and two of the selected mutations, R806C and R806L for 200 ns, were carried out. A significant conformational change in the structure of the R806C mutant was observed. This study provides a valuable direction to understand the molecular basis of CTC1 dysfunction in disease progression, including Coats plus syndrome.
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Affiliation(s)
- Arunabh Choudhury
- Department of Computer Science, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Nikhil Samarth
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SP Pune University, Campus, Pune, 411007, India
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mohamed F Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Shailza Singh
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SP Pune University, Campus, Pune, 411007, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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41
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Galli M, Frigerio C, Longhese MP, Clerici M. The regulation of the DNA damage response at telomeres: focus on kinases. Biochem Soc Trans 2021; 49:933-943. [PMID: 33769480 DOI: 10.1042/bst20200856] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 11/17/2022]
Abstract
The natural ends of linear chromosomes resemble those of accidental double-strand breaks (DSBs). DSBs induce a multifaceted cellular response that promotes the repair of lesions and slows down cell cycle progression. This response is not elicited at chromosome ends, which are organized in nucleoprotein structures called telomeres. Besides counteracting DSB response through specialized telomere-binding proteins, telomeres also prevent chromosome shortening. Despite of the different fate of telomeres and DSBs, many proteins involved in the DSB response also localize at telomeres and participate in telomere homeostasis. In particular, the DSB master regulators Tel1/ATM and Mec1/ATR contribute to telomere length maintenance and arrest cell cycle progression when chromosome ends shorten, thus promoting a tumor-suppressive process known as replicative senescence. During senescence, the actions of both these apical kinases and telomere-binding proteins allow checkpoint activation while bulk DNA repair activities at telomeres are still inhibited. Checkpoint-mediated cell cycle arrest also prevents further telomere erosion and deprotection that would favor chromosome rearrangements, which are known to increase cancer-associated genome instability. This review summarizes recent insights into functions and regulation of Tel1/ATM and Mec1/ATR at telomeres both in the presence and in the absence of telomerase, focusing mainly on discoveries in budding yeast.
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Affiliation(s)
- Michela Galli
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Chiara Frigerio
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Michela Clerici
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
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42
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Nersisyan L, Simonyan A, Binder H, Arakelyan A. Telomere Maintenance Pathway Activity Analysis Enables Tissue- and Gene-Level Inferences. Front Genet 2021; 12:662464. [PMID: 33897770 PMCID: PMC8058386 DOI: 10.3389/fgene.2021.662464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/16/2021] [Indexed: 12/31/2022] Open
Abstract
Telomere maintenance is one of the mechanisms ensuring indefinite divisions of cancer and stem cells. Good understanding of telomere maintenance mechanisms (TMM) is important for studying cancers and designing therapies. However, molecular factors triggering selective activation of either the telomerase dependent (TEL) or the alternative lengthening of telomeres (ALT) pathway are poorly understood. In addition, more accurate and easy-to-use methodologies are required for TMM phenotyping. In this study, we have performed literature based reconstruction of signaling pathways for the ALT and TEL TMMs. Gene expression data were used for computational assessment of TMM pathway activities and compared with experimental assays for TEL and ALT. Explicit consideration of pathway topology makes bioinformatics analysis more informative compared to computational methods based on simple summary measures of gene expression. Application to healthy human tissues showed high ALT and TEL pathway activities in testis, and identified genes and pathways that may trigger TMM activation. Our approach offers a novel option for systematic investigation of TMM activation patterns across cancers and healthy tissues for dissecting pathway-based molecular markers with diagnostic impact.
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Affiliation(s)
- Lilit Nersisyan
- Bioinformatics Group, Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia.,Pathverse, Yerevan, Armenia
| | - Arman Simonyan
- Bioinformatics Group, Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | - Hans Binder
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Arsen Arakelyan
- Bioinformatics Group, Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia.,Pathverse, Yerevan, Armenia
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43
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Pol α-primase dependent nuclear localization of the mammalian CST complex. Commun Biol 2021; 4:349. [PMID: 33731801 PMCID: PMC7969954 DOI: 10.1038/s42003-021-01845-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 02/11/2021] [Indexed: 01/31/2023] Open
Abstract
The human CST complex composed of CTC1, STN1, and TEN1 is critically involved in telomere maintenance and homeostasis. Specifically, CST terminates telomere extension by inhibiting telomerase access to the telomeric overhang and facilitates lagging strand fill in by recruiting DNA Polymerase alpha primase (Pol α-primase) to the telomeric C-strand. Here we reveal that CST has a dynamic intracellular localization that is cell cycle dependent. We report an increase in nuclear CST several hours after the initiation of DNA replication, followed by exit from the nucleus prior to mitosis. We identify amino acids of CTC1 involved in Pol α-primase binding and nuclear localization. We conclude, the CST complex does not contain a nuclear localization signal (NLS) and suggest that its nuclear localization is reliant on Pol α-primase. Hypomorphic mutations affecting CST nuclear import are associated with telomere syndromes and cancer, emphasizing the important role of this process in health.
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44
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Lim CJ, Cech TR. Shaping human telomeres: from shelterin and CST complexes to telomeric chromatin organization. Nat Rev Mol Cell Biol 2021; 22:283-298. [PMID: 33564154 DOI: 10.1038/s41580-021-00328-y] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2021] [Indexed: 01/14/2023]
Abstract
The regulation of telomere length in mammals is crucial for chromosome end-capping and thus for maintaining genome stability and cellular lifespan. This process requires coordination between telomeric protein complexes and the ribonucleoprotein telomerase, which extends the telomeric DNA. Telomeric proteins modulate telomere architecture, recruit telomerase to accessible telomeres and orchestrate the conversion of the newly synthesized telomeric single-stranded DNA tail into double-stranded DNA. Dysfunctional telomere maintenance leads to telomere shortening, which causes human diseases including bone marrow failure, premature ageing and cancer. Recent studies provide new insights into telomerase-related interactions (the 'telomere replisome') and reveal new challenges for future telomere structural biology endeavours owing to the dynamic nature of telomere architecture and the great number of structures that telomeres form. In this Review, we discuss recently determined structures of the shelterin and CTC1-STN1-TEN1 (CST) complexes, how they may participate in the regulation of telomere replication and chromosome end-capping, and how disease-causing mutations in their encoding genes may affect specific functions. Major outstanding questions in the field include how all of the telomere components assemble relative to each other and how the switching between different telomere structures is achieved.
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Affiliation(s)
- Ci Ji Lim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA. .,BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA.
| | - Thomas R Cech
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA. .,BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA. .,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA.
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45
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Grill S, Nandakumar J. Molecular mechanisms of telomere biology disorders. J Biol Chem 2021; 296:100064. [PMID: 33482595 PMCID: PMC7948428 DOI: 10.1074/jbc.rev120.014017] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/20/2022] Open
Abstract
Genetic mutations that affect telomerase function or telomere maintenance result in a variety of diseases collectively called telomeropathies. This wide spectrum of disorders, which include dyskeratosis congenita, pulmonary fibrosis, and aplastic anemia, is characterized by severely short telomeres, often resulting in hematopoietic stem cell failure in the most severe cases. Recent work has focused on understanding the molecular basis of these diseases. Mutations in the catalytic TERT and TR subunits of telomerase compromise activity, while others, such as those found in the telomeric protein TPP1, reduce the recruitment of telomerase to the telomere. Mutant telomerase-associated proteins TCAB1 and dyskerin and the telomerase RNA maturation component poly(A)-specific ribonuclease affect the maturation and stability of telomerase. In contrast, disease-associated mutations in either CTC1 or RTEL1 are more broadly associated with telomere replication defects. Yet even with the recent surge in studies decoding the mechanisms underlying these diseases, a significant proportion of dyskeratosis congenita mutations remain uncharacterized or poorly understood. Here we review the current understanding of the molecular basis of telomeropathies and highlight experimental data that illustrate how genetic mutations drive telomere shortening and dysfunction in these patients. This review connects insights from both clinical and molecular studies to create a comprehensive view of the underlying mechanisms that drive these diseases. Through this, we emphasize recent advances in therapeutics and pinpoint disease-associated variants that remain poorly defined in their mechanism of action. Finally, we suggest future avenues of research that will deepen our understanding of telomere biology and telomere-related disease.
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Affiliation(s)
- Sherilyn Grill
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
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46
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Fernandes CAH, Morea EGO, Cano MIN. RPA-1 from Leishmania sp.: Recombinant Protein Expression and Purification, Molecular Modeling, and Molecular Dynamics Simulations Protocols. Methods Mol Biol 2021; 2281:169-191. [PMID: 33847958 DOI: 10.1007/978-1-0716-1290-3_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
RPA is a conserved heterotrimeric complex and the major single-stranded DNA (ssDNA)-binding protein heterotrimeric complex, which in eukaryotes is formed by the RPA-1, RPA-2, and RPA-3 subunits. The main structural feature of RPA is the presence of the oligonucleotide/oligosaccharide-binding fold (OB-fold) domains, responsible for ssDNA binding and protein:protein interactions. Among the RPA subunits, RPA-1 bears three of the four OB folds involved with RPA-ssDNA binding, although in some organisms RPA-2 can also bind ssDNA. The OB-fold domains are also present in telomere end-binding proteins (TEBP), essential for chromosome end protection. RPA-1 from Leishmania sp., as well as RPA-1 from trypanosomatids, a group of early-divergent protozoa, shows some structural differences compared to higher eukaryote RPA-1. Also, RPA-1 from Leishmania sp., similar to TEBPs, may exert telomeric protective functions. Remarkably, different pieces of evidence have pointed out that trypanosomatids may not have OB fold-containing TEBPs. Moreover, recent data indicate that trypanosomatid RPA-1 may be considered a TEBP since it shares with TEBPs conserved functional and structural features. However, it is still unknown whether the RPA-1 protective telomeric role is exclusive to trypanosomatids or is also present in other primitive eukaryotes. Here, we describe a protocol to obtain highly purified and biologically active Leishmania amazonensis recombinant RPA-1, and to perform molecular modeling and molecular dynamics simulations methods which could be probably applied to functional and structural studies of homologous proteins in other primitive eukaryotes.
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Affiliation(s)
- Carlos A H Fernandes
- Department of Biophysics and Pharmacology, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Edna G O Morea
- Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Maria Isabel N Cano
- Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil.
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47
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Zhao F, Kim W, Kloeber JA, Lou Z. DNA end resection and its role in DNA replication and DSB repair choice in mammalian cells. Exp Mol Med 2020; 52:1705-1714. [PMID: 33122806 PMCID: PMC8080561 DOI: 10.1038/s12276-020-00519-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/29/2020] [Accepted: 09/09/2020] [Indexed: 12/19/2022] Open
Abstract
DNA end resection has a key role in double-strand break repair and DNA replication. Defective DNA end resection can cause malfunctions in DNA repair and replication, leading to greater genomic instability. DNA end resection is initiated by MRN-CtIP generating short, 3′-single-stranded DNA (ssDNA). This newly generated ssDNA is further elongated by multiple nucleases and DNA helicases, such as EXO1, DNA2, and BLM. Effective DNA end resection is essential for error-free homologous recombination DNA repair, the degradation of incorrectly replicated DNA and double-strand break repair choice. Because of its importance in DNA repair, DNA end resection is strictly regulated. Numerous mechanisms have been reported to regulate the initiation, extension, and termination of DNA end resection. Here, we review the general process of DNA end resection and its role in DNA replication and repair pathway choice. Carefully regulated enzymatic processing of the ends of DNA strands is essential for efficient replication and damage repair while also minimizing the risk of genomic instability. Replication and repair depend on a mechanism known as DNA resection, in which enzymes trim back double-stranded DNA ends to leave single-stranded overhangs. Zhenkun Lou and colleagues at the Mayo Clinic in Rochester, USA, have reviewed the various steps involved in the initiation and control of DNA resection. There are multiple different DNA repair processes, and the manner in which resection occurs can determine which of these processes subsequently takes place. The authors note that cancer cells rely heavily on these repair pathways to survive radiotherapy and chemotherapy, and highlight research opportunities that might reveal therapeutically useful vulnerabilities in the resection mechanism.
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Affiliation(s)
- Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Wootae Kim
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.,Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.
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48
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Nguyen DD, Kim EY, Sang PB, Chai W. Roles of OB-Fold Proteins in Replication Stress. Front Cell Dev Biol 2020; 8:574466. [PMID: 33043007 PMCID: PMC7517361 DOI: 10.3389/fcell.2020.574466] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/25/2020] [Indexed: 12/20/2022] Open
Abstract
Accurate DNA replication is essential for maintaining genome stability. However, this stability becomes vulnerable when replication fork progression is stalled or slowed - a condition known as replication stress. Prolonged fork stalling can cause DNA damage, leading to genome instabilities. Thus, cells have developed several pathways and a complex set of proteins to overcome the challenge at stalled replication forks. Oligonucleotide/oligosaccharide binding (OB)-fold containing proteins are a group of proteins that play a crucial role in fork protection and fork restart. These proteins bind to single-stranded DNA with high affinity and prevent premature annealing and unwanted nuclease digestion. Among these OB-fold containing proteins, the best studied in eukaryotic cells are replication protein A (RPA) and breast cancer susceptibility protein 2 (BRCA2). Recently, another RPA-like protein complex CTC1-STN1-TEN1 (CST) complex has been found to counter replication perturbation. In this review, we discuss the latest findings on how these OB-fold containing proteins (RPA, BRCA2, CST) cooperate to safeguard DNA replication and maintain genome stability.
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Affiliation(s)
| | | | | | - Weihang Chai
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, United States
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49
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Giaccherini M, Macauda A, Sgherza N, Sainz J, Gemignani F, Maldonado JMS, Jurado M, Tavano F, Mazur G, Jerez A, Góra-Tybor J, Gołos A, Mohedo FH, Lopez JM, Várkonyi J, Spadano R, Butrym A, Canzian F, Campa D. Genetic polymorphisms associated with telomere length and risk of developing myeloproliferative neoplasms. Blood Cancer J 2020; 10:89. [PMID: 32873778 PMCID: PMC7463014 DOI: 10.1038/s41408-020-00356-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/07/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
Telomere length measured in leukocyte (LTL) has been found to be associated with the risk of developing several cancer types, including myeloproliferative neoplasms (MPNs). LTL is genetically determined by, at least, 11 SNPs previously shown to influence LTL. Their combination in a score has been used as a genetic instrument to measure LTL and evaluate the causative association between LTL and the risk of several cancer types. We tested, for the first time, the “teloscore” in 480 MPN patients and 909 healthy controls in a European multi-center case–control study. We found an increased risk to develop MPNs with longer genetically determined telomeres (OR = 1.82, 95% CI 1.24–2.68, P = 2.21 × 10−3, comparing the highest with the lowest quintile of the teloscore distribution). Analyzing the SNPs individually we confirm the association between TERT-rs2736100-C allele and increased risk of developing MPNs and we report a novel association of the OBFC1-rs9420907-C variant with higher MPN risk (ORallelic = 1.43; 95% CI 1.15–1.77; P = 1.35 × 10−3). Consistently with the results obtained with the teloscore, both risk alleles are also associated with longer LTL. In conclusion, our results suggest that genetically determined longer telomeres could be a risk marker for MPN development.
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Affiliation(s)
- Matteo Giaccherini
- Department of Biology, University of Pisa, Pisa, Italy.,Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angelica Macauda
- Department of Biology, University of Pisa, Pisa, Italy.,Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nicola Sgherza
- Division of Hematology, Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy.,U.O.C. Ematologia con Trapianto, Azienda Ospedaliero-Universitaria Consorzionale, Policlinico di Bari, Bari, Italy
| | - Juan Sainz
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada, Granada, Spain.,Monoclonal Gammopathies Unit, University Hospital Virgen de las Nieves, Granada, Spain.,Pharmacogenetics Unit, Instituto de Investigación Biosanitaria de Granada (Ibs. Granada), Hospitales Universitarios de Granada/Universidad de Granada, Granada, Spain.,Department of Medicine, University of Granada, Granada, Spain
| | | | - Josè Manuel Sanchez Maldonado
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada, Granada, Spain.,Monoclonal Gammopathies Unit, University Hospital Virgen de las Nieves, Granada, Spain.,Pharmacogenetics Unit, Instituto de Investigación Biosanitaria de Granada (Ibs. Granada), Hospitales Universitarios de Granada/Universidad de Granada, Granada, Spain
| | - Manuel Jurado
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada, Granada, Spain.,Monoclonal Gammopathies Unit, University Hospital Virgen de las Nieves, Granada, Spain.,Pharmacogenetics Unit, Instituto de Investigación Biosanitaria de Granada (Ibs. Granada), Hospitales Universitarios de Granada/Universidad de Granada, Granada, Spain
| | - Francesca Tavano
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Grzegorz Mazur
- Department of Internal Medicine, Occupational Diseases, Hypertension and Clinical Oncology, Wroclaw Medical University, Wroclaw, Poland
| | - Andrés Jerez
- Hematology and Medical Oncology Department, University Hospital Morales Meseguer-IMIB, CIBERER, Murcia, Spain
| | | | - Aleksandra Gołos
- Department of Clinical Oncology and Chemotherapy, Magodent Hospital, Warsaw, Poland
| | - Francisca Hernández Mohedo
- Monoclonal Gammopathies Unit, University Hospital Virgen de las Nieves, Granada, Spain.,Pharmacogenetics Unit, Instituto de Investigación Biosanitaria de Granada (Ibs. Granada), Hospitales Universitarios de Granada/Universidad de Granada, Granada, Spain
| | - Joaquin Martinez Lopez
- Hospital 12 de Octubre, H12O-CNIO Hematological Malignancies Clinical Research Unitc Compluntense University, CIBERONC, Madrid, Spain
| | - Judit Várkonyi
- Third Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Raffaele Spadano
- Division of Hematology, Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Aleksandra Butrym
- Department of Cancer Prevention and Therapy, Wroclaw Medical University, Wroclaw, Poland
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
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50
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Aramburu T, Plucinsky S, Skordalakes E. POT1-TPP1 telomere length regulation and disease. Comput Struct Biotechnol J 2020; 18:1939-1946. [PMID: 32774788 PMCID: PMC7385035 DOI: 10.1016/j.csbj.2020.06.040] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/24/2020] [Accepted: 06/27/2020] [Indexed: 12/27/2022] Open
Abstract
Telomeres are DNA repeats at the ends of linear chromosomes and are replicated by telomerase, a ribonucleoprotein reverse transcriptase. Telomere length regulation and chromosome end capping are essential for genome stability and are mediated primarily by the shelterin and CST complexes. POT1-TPP1, a subunit of shelterin, binds the telomeric overhang, suppresses ATR-dependent DNA damage response, and recruits telomerase to telomeres for DNA replication. POT1 localization to telomeres and chromosome end protection requires its interaction with TPP1. Therefore, the POT1-TPP1 complex is critical to telomere maintenance and full telomerase processivity. The aim of this mini-review is to summarize recent POT1-TPP1 structural studies and discuss how the complex contributes to telomere length regulation. In addition, we review how disruption of POT1-TPP1 function leads to human disease.
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Key Words
- ATM, Ataxia Telangiectasia Mutated protein
- ATR, Ataxia Telangiectasia and Rad3-related Protein
- CST, CTC1, Stn1 and Ten1
- CTC1, Conserved Telomere Capping Protein 1
- POT1
- POT1, Protection of telomere 1
- RAP1, Repressor/Activator Protein 1
- RPA, Replication Protein A
- SMCHD1, Structural Maintenance Of Chromosomes Flexible Hinge Domain Containing 1
- Shelterin
- Stn1, Suppressor of Cdc Thirteen
- TERC, Telomerase RNA
- TERT, Telomerase Reverse Transcriptase
- TIN2, TRF1- and TRF2-Interacting Nuclear Protein 2
- TPP1
- TPP1 also known as ACD, Adrenocortical Dysplasia Protein Homolog
- TRF1, Telomere Repeat binding Factor 1
- TRF2, Telomere Repeat binding Factor 2
- TSPYL5, Testis-specific Y-encoded-like protein 5
- Telomerase
- Telomeres
- Ten1, Telomere Length Regulation Protein
- USP7, ubiquitin-specific-processing protease 7
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