1
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Lee RS, Twarowski JM, Malkova A. Stressed? Break-induced replication comes to the rescue! DNA Repair (Amst) 2024; 142:103759. [PMID: 39241677 DOI: 10.1016/j.dnarep.2024.103759] [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: 05/23/2024] [Revised: 08/22/2024] [Accepted: 08/26/2024] [Indexed: 09/09/2024]
Abstract
Break-induced replication (BIR) is a homologous recombination (HR) pathway that repairs one-ended DNA double-strand breaks (DSBs), which can result from replication fork collapse, telomere erosion, and other events. Eukaryotic BIR has been mainly investigated in yeast, where it is initiated by invasion of the broken DNA end into a homologous sequence, followed by extensive replication synthesis proceeding to the chromosome end. Multiple recent studies have described BIR in mammalian cells, the properties of which show many similarities to yeast BIR. While HR is considered as "error-free" mechanism, BIR is highly mutagenic and frequently leads to chromosomal rearrangements-genetic instabilities known to promote human disease. In addition, it is now recognized that BIR is highly stimulated by replication stress (RS), including RS constantly present in cancer cells, implicating BIR as a contributor to cancer genesis and progression. Here, we discuss the past and current findings related to the mechanism of BIR, the association of BIR with replication stress, and the destabilizing effects of BIR on the eukaryotic genome. Finally, we consider the potential for exploiting the BIR machinery to develop anti-cancer therapeutics.
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Affiliation(s)
- Rosemary S Lee
- Department of Biochemistry & Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | | | - Anna Malkova
- Department of Biochemistry & Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA.
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2
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Alcock LJ, Sudhakar HK, Young R, Lau YH. Fluorescence polarization assay for screening FANCM-RMI inhibitors to target the alternative lengthening of telomeres. Methods Enzymol 2024; 698:361-378. [PMID: 38886039 DOI: 10.1016/bs.mie.2024.04.014] [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: 06/20/2024]
Abstract
Alternative Lengthening of Telomeres (ALT) is a mechanism used by 10-15% of all cancers to achieve replicative immortality, bypassing the DNA damage checkpoint associated with short telomeres that leads to cellular senescence or apoptosis. ALT does not occur in non-cancerous cells, presenting a potential therapeutic window for cancers where this mechanism is active. Disrupting the FANCM-RMI interaction has emerged as a promising therapeutic strategy that induces synthetic ALT lethality in genetic studies on cancer cell lines. There are currently no chemical inhibitors reported in the literature, in part due to the lack of reliable biophysical or biochemical assays to screen for FANCM-RMI disruption. Here we describe the development of a robust competitive fluorescence polarization (FP) assay that quantifies target binding at the FANCM-RMI interface. The assay employs a labeled peptide tracer TMR-RaMM2 derived from the native MM2 binding motif, which binds to recombinant RMI1-RMI2 and can be displaced by competitive inhibitors. We report the methods for recombinant production of RMI1-RMI2, design and evaluation of the tracer TMR-RaMM2, along with unlabeled peptide inhibitor controls to enable ALT-targeted drug discovery.
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Affiliation(s)
- Lisa J Alcock
- School of Chemistry, The University of Sydney, Camperdown, NSW, Australia.
| | | | - Reginald Young
- School of Chemistry, The University of Sydney, Camperdown, NSW, Australia
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, NSW, Australia.
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3
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Alanazi AR, Parkinson GN, Haider S. Structural Motifs at the Telomeres and Their Role in Regulatory Pathways. Biochemistry 2024; 63:827-842. [PMID: 38481135 PMCID: PMC10993422 DOI: 10.1021/acs.biochem.4c00023] [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: 01/11/2024] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024]
Abstract
Telomeres are specialized structures, found at the ends of linear chromosomes in eukaryotic cells, that play a crucial role in maintaining the stability and integrity of genomes. They are composed of repetitive DNA sequences, ssDNA overhangs, and several associated proteins. The length of telomeres is linked to cellular aging in humans, and deficiencies in their maintenance are associated with various diseases. Key structural motifs at the telomeres serve to protect vulnerable chromosomal ends. Telomeric DNA also has the ability to form diverse complex DNA higher-order structures, including T-loops, D-loops, R-loops, G-loops, G-quadruplexes, and i-motifs, in the complementary C-rich strand. While many essential proteins at telomeres have been identified, the intricacies of their interactions and structural details are still not fully understood. This Perspective highlights recent advancements in comprehending the structures associated with human telomeres. It emphasizes the significance of telomeres, explores various telomeric structural motifs, and delves into the structural biology surrounding telomeres and telomerase. Furthermore, telomeric loops, their topologies, and the associated proteins that contribute to the safeguarding of telomeres are discussed.
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Affiliation(s)
- Abeer
F R Alanazi
- UCL
School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Gary N Parkinson
- UCL
School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Shozeb Haider
- UCL
School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
- UCL
Centre for Advanced Research Computing, University College London, London WC1H 9RN, United
Kingdom
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4
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Rai R, Sodeinde T, Boston A, Chang S. Telomeres cooperate with the nuclear envelope to maintain genome stability. Bioessays 2024; 46:e2300184. [PMID: 38047499 DOI: 10.1002/bies.202300184] [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: 09/25/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 12/05/2023]
Abstract
Mammalian telomeres have evolved safeguards to prevent their recognition as DNA double-stranded breaks by suppressing the activation of various DNA sensing and repair proteins. We have shown that the telomere-binding proteins TRF2 and RAP1 cooperate to prevent telomeres from undergoing aberrant homology-directed recombination by mediating t-loop protection. Our recent findings also suggest that mammalian telomere-binding proteins interact with the nuclear envelope to maintain chromosome stability. RAP1 interacts with nuclear lamins through KU70/KU80, and disruption of RAP1 and TRF2 function result in nuclear envelope rupture, promoting telomere-telomere recombination to form structures termed ultrabright telomeres. In this review, we discuss the importance of the interactions between shelterin components and the nuclear envelope to maintain telomere homeostasis and genome stability.
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Affiliation(s)
- Rekha Rai
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Tori Sodeinde
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ava Boston
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sandy Chang
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, USA
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5
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Thosar SA, Barnes RP, Detwiler A, Bhargava R, Wondisford A, O'Sullivan RJ, Opresko PL. Oxidative guanine base damage plays a dual role in regulating productive ALT-associated homology-directed repair. Cell Rep 2024; 43:113656. [PMID: 38194346 PMCID: PMC10851105 DOI: 10.1016/j.celrep.2023.113656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/06/2023] [Accepted: 12/20/2023] [Indexed: 01/10/2024] Open
Abstract
Cancer cells maintain telomeres by upregulating telomerase or alternative lengthening of telomeres (ALT) via homology-directed repair at telomeric DNA breaks. 8-Oxoguanine (8oxoG) is a highly prevalent endogenous DNA lesion in telomeric sequences, altering telomere structure and telomerase activity, but its impact on ALT is unclear. Here, we demonstrate that targeted 8oxoG formation at telomeres stimulates ALT activity and homologous recombination specifically in ALT cancer cells. Mechanistically, an acute 8oxoG induction increases replication stress, as evidenced by increased telomere fragility and ATR kinase activation at ALT telomeres. Furthermore, ALT cells are more sensitive to chronic telomeric 8oxoG damage than telomerase-positive cancer cells, consistent with increased 8oxoG-induced replication stress. However, telomeric 8oxoG production in G2 phase, when ALT telomere elongation occurs, impairs telomeric DNA synthesis. Our study demonstrates that a common oxidative base lesion has a dual role in regulating ALT depending on when the damage arises in the cell cycle.
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Affiliation(s)
- Sanjana A Thosar
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA; UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Ryan P Barnes
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA; UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Ariana Detwiler
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA; UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Ragini Bhargava
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Anne Wondisford
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Roderick J O'Sullivan
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA; UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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6
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Udutha S, Taglang C, Batsios G, Gillespie AM, Tran M, Ronen SM, Ten Hoeve J, Graeber TG, Viswanath P. Telomerase reverse transcriptase induces targetable alterations in glutathione and nucleotide biosynthesis in glioblastomas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.566937. [PMID: 38014170 PMCID: PMC10680720 DOI: 10.1101/2023.11.14.566937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Telomerase reverse transcriptase (TERT) is essential for glioblastoma (GBM) proliferation. Delineating metabolic vulnerabilities induced by TERT can lead to novel GBM therapies. We previously showed that TERT upregulates glutathione (GSH) pool size in GBMs. Here, we show that TERT acts via the FOXO1 transcription factor to upregulate expression of the catalytic subunit of glutamate-cysteine ligase (GCLC), the rate-limiting enzyme of de novo GSH synthesis. Inhibiting GCLC using siRNA or buthionine sulfoximine (BSO) reduces synthesis of 13 C-GSH from [U- 13 C]-glutamine and inhibits clonogenicity. However, GCLC inhibition does not induce cell death, an effect that is associated with elevated [U- 13 C]-glutamine metabolism to glutamate and pyrimidine nucleotide biosynthesis. Mechanistically, GCLC inhibition activates MYC and leads to compensatory upregulation of two key glutamine-utilizing enzymes i.e., glutaminase (GLS), which generates glutamate from glutamine, and CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamoylase, dihydroorotatase), the enzyme that converts glutamine to the pyrimidine nucleotide precursor dihydroorotate. We then examined the therapeutic potential of inhibiting GLS and CAD in combination with GCLC. 6-diazo-5-oxy-L-norleucin (DON) is a potent inhibitor of glutamine-utilizing enzymes including GLS and CAD. The combination of BSO and DON suppresses GSH and pyrimidine nucleotide biosynthesis and is synergistically lethal in GBM cells. Importantly, in vivo stable isotope tracing indicates that combined treatment with JHU-083 (a brain-penetrant prodrug of DON) and BSO abrogates synthesis of GSH and pyrimidine nucleotides from [U- 13 C]-glutamine and induces tumor shrinkage in mice bearing intracranial GBM xenografts. Collectively, our studies exploit a mechanistic understanding of TERT biology to identify synthetically lethal metabolic vulnerabilities in GBMs. SIGNIFICANCE Using in vivo stable isotope tracing, metabolomics, and loss-of-function studies, we demonstrate that TERT expression is associated with metabolic alterations that can be synergistically targeted for therapy in glioblastomas.
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7
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Rosso I, Jones-Weinert C, Rossiello F, Cabrini M, Brambillasca S, Munoz-Sagredo L, Lavagnino Z, Martini E, Tedone E, Garre' M, Aguado J, Parazzoli D, Mione M, Shay JW, Mercurio C, d'Adda di Fagagna F. Alternative lengthening of telomeres (ALT) cells viability is dependent on C-rich telomeric RNAs. Nat Commun 2023; 14:7086. [PMID: 37925537 PMCID: PMC10625592 DOI: 10.1038/s41467-023-42831-0] [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: 03/24/2022] [Accepted: 10/23/2023] [Indexed: 11/06/2023] Open
Abstract
Alternative lengthening of telomeres (ALT) is a telomere maintenance mechanism activated in ~10-15% of cancers, characterized by telomeric damage. Telomeric damage-induced long non-coding RNAs (dilncRNAs) are transcribed at dysfunctional telomeres and contribute to telomeric DNA damage response (DDR) activation and repair. Here we observed that telomeric dilncRNAs are preferentially elevated in ALT cells. Inhibition of C-rich (teloC) dilncRNAs with antisense oligonucleotides leads to DNA replication stress responses, increased genomic instability, and apoptosis induction selectively in ALT cells. Cell death is dependent on DNA replication and is increased by DNA replication stress. Mechanistically, teloC dilncRNA inhibition reduces RAD51 and 53BP1 recruitment to telomeres, boosts the engagement of BIR machinery, and increases C-circles and telomeric sister chromatid exchanges, without increasing telomeric non-S phase synthesis. These results indicate that teloC dilncRNA is necessary for a coordinated recruitment of DDR factors to ALT telomeres and it is essential for ALT cancer cells survival.
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Affiliation(s)
- Ilaria Rosso
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Corey Jones-Weinert
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Matteo Cabrini
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Silvia Brambillasca
- IFOM ETS - The AIRC Institute of Molecular Oncology (Experimental Therapeutics Program), Milan, Italy
| | - Leonel Munoz-Sagredo
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
- School of Medicine, Universidad de Valparaiso, Valparaiso, Chile
| | - Zeno Lavagnino
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Emanuele Martini
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
- Dipartimento di Oncologia ed Emato-Oncologia, Università degli Studi di Milano, Milan, Italy
| | - Enzo Tedone
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Massimiliano Garre'
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
- RCSI, Royal College of Surgeons in Ireland, Department of Chemistry, Dublin, Ireland
| | - Julio Aguado
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Dario Parazzoli
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Marina Mione
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ciro Mercurio
- IFOM ETS - The AIRC Institute of Molecular Oncology (Experimental Therapeutics Program), Milan, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy.
- Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza", Pavia, Italy.
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8
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Loe TK, Lazzerini Denchi E, Tricola GM, Azeroglu B. ALTercations at telomeres: stress, recombination and extrachromosomal affairs. Biochem Soc Trans 2023; 51:1935-1946. [PMID: 37767563 DOI: 10.1042/bst20230265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
Approximately 15% of human cancers depend on the alternative lengthening of telomeres (ALT) pathway to maintain telomeres and proliferate. Telomeres that are elongated using ALT display unique features raising the exciting prospect of tailored cancer therapies. ALT-mediated telomere elongation shares several features with recombination-based DNA repair. Strikingly, cells that use the ALT pathway display abnormal levels of replication stress at telomeres and accumulate abundant extrachromosomal telomeric DNA. In this review, we examine recent findings that shed light on the ALT mechanisms and the strategies currently available to suppress this telomere elongation mechanism.
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Affiliation(s)
- Taylor K Loe
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, U.S.A
| | - Eros Lazzerini Denchi
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, U.S.A
| | - Gianna M Tricola
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, U.S.A
| | - Benura Azeroglu
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, U.S.A
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9
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Wang X, Jin Z, Tang S, Huang X, Wang S, Ren X, Xu M. ATRX loss suppresses the type I interferon response in sarcoma cells through chromatin remodeling. Am J Cancer Res 2023; 13:3547-3558. [PMID: 37693131 PMCID: PMC10492102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/30/2023] [Indexed: 09/12/2023] Open
Abstract
Sarcomas constitute a heterogeneous group of mesenchymal cancers and are particularly common in children and adolescents, leading to significant lethality. Therefore, it is necessary to understand the underlying mechanisms by which genetic alterations promote sarcoma progression. Here, we demonstrate that loss-of-function of ATRX, a member of the SWI/SNF DNA-remodeling family, represses the interferon (IFN)-β response by inducing chromatin remodeling in sarcoma cells. We show that ATRX mutations are associated with worse prognosis and attenuate IFN-α/β response in patients with specific types of sarcomas. Using poly(I:C) as a stimulation model, we show that natural ATRX mutation or ATRX depletion via CRISPR/Cas9 or siRNA significantly suppresses the expression of IFNB1 and other cytokines in sarcoma cells. Moreover, RNA-seq data reveal that ATRX ablation globally influences the expression pattern of poly(I:C)-stimulated genes (PSGs). Through ATAC-seq, we show that ATRX loss enhance chromatin accessibility generally, which consistent with the heterochromatin modulating function of ATRX. However, a set of PSGs display a decrease of chromatin accessibility after ATRX depletion, indicating that ATRX promote the transcription of these genes through chromatin remodeling. Thus, we highlight that ATRX mutation plays critical roles in blocking Type I IFN signaling in sarcoma cells and point out the clinical importance of this effect on sarcoma treatment.
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Affiliation(s)
- Xinrui Wang
- Department of Cell Biology, School of Life Sciences, Anhui Medical University Hefei 230032, Anhui, China
| | - Zige Jin
- Department of Cell Biology, School of Life Sciences, Anhui Medical University Hefei 230032, Anhui, China
| | - Shanshan Tang
- Department of Cell Biology, School of Life Sciences, Anhui Medical University Hefei 230032, Anhui, China
| | - Xiyu Huang
- Department of Cell Biology, School of Life Sciences, Anhui Medical University Hefei 230032, Anhui, China
| | - Shanshan Wang
- Department of Cell Biology, School of Life Sciences, Anhui Medical University Hefei 230032, Anhui, China
| | - Xiaohe Ren
- Department of Cell Biology, School of Life Sciences, Anhui Medical University Hefei 230032, Anhui, China
| | - Mafei Xu
- Department of Cell Biology, School of Life Sciences, Anhui Medical University Hefei 230032, Anhui, China
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10
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van Gerven MR, Schild L, van Arkel J, Koopmans B, Broeils LA, Meijs LAM, van Oosterhout R, van Noesel MM, Koster J, van Hooff SR, Molenaar JJ, van den Boogaard ML. Two opposing gene expression patterns within ATRX aberrant neuroblastoma. PLoS One 2023; 18:e0289084. [PMID: 37540673 PMCID: PMC10403137 DOI: 10.1371/journal.pone.0289084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/02/2023] [Indexed: 08/06/2023] Open
Abstract
Neuroblastoma is the most common extracranial solid tumor in children. A subgroup of high-risk patients is characterized by aberrations in the chromatin remodeller ATRX that is encoded by 35 exons. In contrast to other pediatric cancer where ATRX point mutations are most frequent, multi-exon deletions (MEDs) are the most frequent type of ATRX aberrations in neuroblastoma. 75% of these MEDs are predicted to produce in-frame fusion proteins, suggesting a potential gain-of-function effect compared to nonsense mutations. For neuroblastoma there are only a few patient-derived ATRX aberrant models. Therefore, we created isogenic ATRX aberrant models using CRISPR-Cas9 in several neuroblastoma cell lines and one tumoroid and performed total RNA-sequencing on these and the patient-derived models. Gene set enrichment analysis (GSEA) showed decreased expression of genes related to both ribosome biogenesis and several metabolic processes in our isogenic ATRX exon 2-10 MED model systems, the patient-derived MED models and in tumor data containing two patients with an ATRX exon 2-10 MED. In sharp contrast, these same processes showed an increased expression in our isogenic ATRX knock-out and exon 2-13 MED models. Our validations confirmed a role of ATRX in the regulation of ribosome homeostasis. The two distinct molecular expression patterns within ATRX aberrant neuroblastomas that we identified imply that there might be a need for distinct treatment regimens.
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Affiliation(s)
- Michael R van Gerven
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Linda Schild
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Jennemiek van Arkel
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Bianca Koopmans
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Luuk A Broeils
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Loes A M Meijs
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Romy van Oosterhout
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Max M van Noesel
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
- Department of Cancer and Imaging, University Medical Center Utrecht, Utrecht, Utrecht, The Netherlands
| | - Jan Koster
- Department of Oncogenomics, University Medical Center Amsterdam, Amsterdam, North-Holland, The Netherlands
| | - Sander R van Hooff
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Jan J Molenaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
- Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Utrecht, The Netherlands
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11
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Comaills V, Castellano-Pozo M. Chromosomal Instability in Genome Evolution: From Cancer to Macroevolution. BIOLOGY 2023; 12:671. [PMID: 37237485 PMCID: PMC10215859 DOI: 10.3390/biology12050671] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023]
Abstract
The integrity of the genome is crucial for the survival of all living organisms. However, genomes need to adapt to survive certain pressures, and for this purpose use several mechanisms to diversify. Chromosomal instability (CIN) is one of the main mechanisms leading to the creation of genomic heterogeneity by altering the number of chromosomes and changing their structures. In this review, we will discuss the different chromosomal patterns and changes observed in speciation, in evolutional biology as well as during tumor progression. By nature, the human genome shows an induction of diversity during gametogenesis but as well during tumorigenesis that can conclude in drastic changes such as the whole genome doubling to more discrete changes as the complex chromosomal rearrangement chromothripsis. More importantly, changes observed during speciation are strikingly similar to the genomic evolution observed during tumor progression and resistance to therapy. The different origins of CIN will be treated as the importance of double-strand breaks (DSBs) or the consequences of micronuclei. We will also explain the mechanisms behind the controlled DSBs, and recombination of homologous chromosomes observed during meiosis, to explain how errors lead to similar patterns observed during tumorigenesis. Then, we will also list several diseases associated with CIN, resulting in fertility issues, miscarriage, rare genetic diseases, and cancer. Understanding better chromosomal instability as a whole is primordial for the understanding of mechanisms leading to tumor progression.
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Affiliation(s)
- Valentine Comaills
- Andalusian Center for Molecular Biology and Regenerative Medicine—CABIMER, University of Pablo de Olavide—University of Seville—CSIC, Junta de Andalucía, 41092 Seville, Spain
| | - Maikel Castellano-Pozo
- Andalusian Center for Molecular Biology and Regenerative Medicine—CABIMER, University of Pablo de Olavide—University of Seville—CSIC, Junta de Andalucía, 41092 Seville, Spain
- Genetic Department, Faculty of Biology, University of Seville, 41080 Seville, Spain
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12
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Rai R, Biju K, Sun W, Sodeinde T, Al-Hiyasat A, Morgan J, Ye X, Li X, Chen Y, Chang S. Homology directed telomere clustering, ultrabright telomere formation and nuclear envelope rupture in cells lacking TRF2 B and RAP1. Nat Commun 2023; 14:2144. [PMID: 37059728 PMCID: PMC10104862 DOI: 10.1038/s41467-023-37761-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 03/30/2023] [Indexed: 04/16/2023] Open
Abstract
Double-strand breaks (DSBs) due to genotoxic stress represent potential threats to genome stability. Dysfunctional telomeres are recognized as DSBs and are repaired by distinct DNA repair mechanisms. RAP1 and TRF2 are telomere binding proteins essential to protect telomeres from engaging in homology directed repair (HDR), but how this occurs remains unclear. In this study, we examined how the basic domain of TRF2 (TRF2B) and RAP1 cooperate to repress HDR at telomeres. Telomeres lacking TRF2B and RAP1 cluster into structures termed ultrabright telomeres (UTs). HDR factors localize to UTs, and UT formation is abolished by RNaseH1, DDX21 and ADAR1p110, suggesting that they contain DNA-RNA hybrids. Interaction between the BRCT domain of RAP1 and KU70/KU80 is also required to repress UT formation. Expressing TRF2∆B in Rap1-/- cells resulted in aberrant lamin A localization in the nuclear envelope and dramatically increased UT formation. Expressing lamin A phosphomimetic mutants induced nuclear envelope rupturing and aberrant HDR-mediated UT formation. Our results highlight the importance of shelterin and proteins in the nuclear envelope in repressing aberrant telomere-telomere recombination to maintain telomere homeostasis.
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Affiliation(s)
- Rekha Rai
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA.
| | - Kevin Biju
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Wenqi Sun
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Tori Sodeinde
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA
| | - Amer Al-Hiyasat
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA
| | - Jaida Morgan
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA
| | - Xianwen Ye
- University of Chinese Academy of Sciences, 100049, Beijing, China
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai, 201210, China
| | - Xueqing Li
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yong Chen
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai, 201210, China
| | - Sandy Chang
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA.
- Department of Pathology, Yale University School of Medicine, 330 Cedar Street, New Haven, CT, 06520, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 330 Cedar Street, New Haven, CT, 06520, USA.
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13
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Phase separation properties of RPA combine high-affinity ssDNA binding with dynamic condensate functions at telomeres. Nat Struct Mol Biol 2023; 30:451-462. [PMID: 36894693 PMCID: PMC10113159 DOI: 10.1038/s41594-023-00932-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 01/27/2023] [Indexed: 03/11/2023]
Abstract
RPA has been shown to protect single-stranded DNA (ssDNA) intermediates from instability and breakage. RPA binds ssDNA with sub-nanomolar affinity, yet dynamic turnover is required for downstream ssDNA transactions. How ultrahigh-affinity binding and dynamic turnover are achieved simultaneously is not well understood. Here we reveal that RPA has a strong propensity to assemble into dynamic condensates. In solution, purified RPA phase separates into liquid droplets with fusion and surface wetting behavior. Phase separation is stimulated by sub-stoichiometric amounts of ssDNA, but not RNA or double-stranded DNA, and ssDNA gets selectively enriched in RPA condensates. We find the RPA2 subunit required for condensation and multi-site phosphorylation of the RPA2 N-terminal intrinsically disordered region to regulate RPA self-interaction. Functionally, quantitative proximity proteomics links RPA condensation to telomere clustering and integrity in cancer cells. Collectively, our results suggest that RPA-coated ssDNA is contained in dynamic RPA condensates whose properties are important for genome organization and stability.
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14
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Sun H, Chen G, Guo B, Lv S, Yuan G. Potential clinical treatment prospects behind the molecular mechanism of alternative lengthening of telomeres (ALT). J Cancer 2023; 14:417-433. [PMID: 36860927 PMCID: PMC9969575 DOI: 10.7150/jca.80097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 12/25/2022] [Indexed: 02/04/2023] Open
Abstract
Normal somatic cells inevitably experience replicative stress and senescence during proliferation. Somatic cell carcinogenesis can be prevented in part by limiting the reproduction of damaged or old cells and removing them from the cell cycle [1, 2]. However, Cancer cells must overcome the issues of replication pressure and senescence as well as preserve telomere length in order to achieve immortality, in contrast to normal somatic cells [1, 2]. Although telomerase accounts for the bulk of telomere lengthening methods in human cancer cells, there is a non-negligible portion of telomere lengthening pathways that depend on alternative lengthening of telomeres (ALT) [3]. For the selection of novel possible therapeutic targets for ALT-related disorders, a thorough understanding of the molecular biology of these diseases is crucial [4]. The roles of ALT, typical ALT tumor cell traits, the pathophysiology and molecular mechanisms of ALT tumor disorders, such as adrenocortical carcinoma (ACC), are all summarized in this work. Additionally, this research compiles as many of its hypothetically viable but unproven treatment targets as it can (ALT-associated PML bodies (APB), etc.). This review is intended to contribute as much as possible to the development of research, while also trying to provide a partial information for prospective investigations on ALT pathways and associated diseases.
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Affiliation(s)
- Haolu Sun
- Department of Pathophysiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230011, China
| | - Guijuan Chen
- School of Environment and Chemical Engineering, Anhui Vocational and Technical College, Hefei, 230011, China
| | - Baochang Guo
- Rehabilitation Department of Traditional Chinese Medicine, 969 Hospital of the Joint Support Force of the Chinese People's Liberation Army, Hohhot, 010000, China
| | - Shushu Lv
- Department of Pathology, The First Affiliated Hospital of Huzhou University, Huzhou 313000, China
| | - Guojun Yuan
- School of Environment and Chemical Engineering, Anhui Vocational and Technical College, Hefei, 230011, China
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15
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Mulye M, Singh MI, Jain V. From Processivity to Genome Maintenance: The Many Roles of Sliding Clamps. Genes (Basel) 2022; 13:2058. [PMID: 36360296 PMCID: PMC9690074 DOI: 10.3390/genes13112058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 07/30/2023] Open
Abstract
Sliding clamps play a pivotal role in the process of replication by increasing the processivity of the replicative polymerase. They also serve as an interacting platform for a plethora of other proteins, which have an important role in other DNA metabolic processes, including DNA repair. In other words, clamps have evolved, as has been correctly referred to, into a mobile "tool-belt" on the DNA, and provide a platform for several proteins that are involved in maintaining genome integrity. Because of the central role played by the sliding clamp in various processes, its study becomes essential and relevant in understanding these processes and exploring the protein as an important drug target. In this review, we provide an updated report on the functioning, interactions, and moonlighting roles of the sliding clamps in various organisms and its utilization as a drug target.
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Affiliation(s)
- Meenakshi Mulye
- Correspondence: (M.M.); (V.J.); Tel.: +91-755-269-1425 (V.J.); Fax: +91-755-269-2392 (V.J.)
| | | | - Vikas Jain
- Correspondence: (M.M.); (V.J.); Tel.: +91-755-269-1425 (V.J.); Fax: +91-755-269-2392 (V.J.)
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16
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Yadav T, Zhang JM, Ouyang J, Leung W, Simoneau A, Zou L. TERRA and RAD51AP1 promote alternative lengthening of telomeres through an R- to D-loop switch. Mol Cell 2022; 82:3985-4000.e4. [PMID: 36265486 PMCID: PMC9637728 DOI: 10.1016/j.molcel.2022.09.026] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 08/08/2022] [Accepted: 09/23/2022] [Indexed: 11/05/2022]
Abstract
Alternative lengthening of telomeres (ALT), a telomerase-independent process maintaining telomeres, is mediated by break-induced replication (BIR). RAD52 promotes ALT by facilitating D-loop formation, but ALT also occurs through a RAD52-independent BIR pathway. Here, we show that the telomere non-coding RNA TERRA forms dynamic telomeric R-loops and contributes to ALT activity in RAD52 knockout cells. TERRA forms R-loops in vitro and at telomeres in a RAD51AP1-dependent manner. The formation of R-loops by TERRA increases G-quadruplexes (G4s) at telomeres. G4 stabilization enhances ALT even when TERRA is depleted, suggesting that G4s act downstream of R-loops to promote BIR. In vitro, the telomeric R-loops assembled by TERRA and RAD51AP1 generate G4s, which persist after R-loop resolution and allow formation of telomeric D-loops without RAD52. Thus, the dynamic telomeric R-loops formed by TERRA and RAD51AP1 enable the RAD52-independent ALT pathway, and G4s orchestrate an R- to D-loop switch at telomeres to stimulate BIR.
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Affiliation(s)
- Tribhuwan Yadav
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jia-Min Zhang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jian Ouyang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Wendy Leung
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Antoine Simoneau
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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17
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Identification of the Telomere elongation Mutation in Drosophila. Cells 2022; 11:cells11213484. [DOI: 10.3390/cells11213484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Telomeres in Drosophila melanogaster, which have inspired a large part of Sergio Pimpinelli work, are similar to those of other eukaryotes in terms of their function. Yet, their length maintenance relies on the transposition of the specialized retrotransposons Het-A, TART, and TAHRE, rather than on the activity of the enzyme telomerase as it occurs in most other eukaryotic organisms. The length of the telomeres in Drosophila thus depends on the number of copies of these transposable elements. Our previous work has led to the isolation of a dominant mutation, Tel1, that caused a several-fold elongation of telomeres. In this study, we molecularly identified the Tel1 mutation by a combination of transposon-induced, site-specific recombination and next-generation sequencing. Recombination located Tel1 to a 15 kb region in 92A. Comparison of the DNA sequence in this region with the Drosophila Genetic Reference Panel of wild-type genomic sequences delimited Tel1 to a 3 bp deletion inside intron 8 of Ino80. Furthermore, CRISPR/Cas9-induced deletions surrounding the same region exhibited the Tel1 telomere phenotype, confirming a strict requirement of this intron 8 gene sequence for a proper regulation of Drosophila telomere length.
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18
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Gulve N, Su C, Deng Z, Soldan SS, Vladimirova O, Wickramasinghe J, Zheng H, Kossenkov AV, Lieberman PM. DAXX-ATRX regulation of p53 chromatin binding and DNA damage response. Nat Commun 2022; 13:5033. [PMID: 36028493 PMCID: PMC9418176 DOI: 10.1038/s41467-022-32680-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 08/11/2022] [Indexed: 11/18/2022] Open
Abstract
DAXX and ATRX are tumor suppressor proteins that form a histone H3.3 chaperone complex and are frequently mutated in cancers with the alternative lengthening of telomeres (ALT). Here, we show that DAXX and ATRX knock-out (KO) U87-T cells that have acquired ALT-like features have defects in p53 chromatin binding and DNA damage response. RNA-seq analysis revealed that p53 pathway is among the most perturbed. ChIP-seq and ATAC-seq revealed a genome-wide reduction in p53 DNA-binding and corresponding loss of chromatin accessibility at many p53 response elements across the genome. Both DAXX and ATRX null cells showed a depletion of histone H3.3 and accumulation of γH2AX at many p53 sites, including subtelomeres. These findings indicate that loss of DAXX or ATRX can compromise p53 chromatin binding and p53 DNA damage response in ALT-like cells, providing a link between histone composition, chromatin accessibility and tumor suppressor function of p53.
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Affiliation(s)
- Nitish Gulve
- The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Chenhe Su
- The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Zhong Deng
- The Wistar Institute, Philadelphia, PA, 19104, USA
| | | | | | | | - Hongwu Zheng
- Weill School of Medicine, Cornell University, New York, NY, USA
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19
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de Nonneville A, Salas S, Bertucci F, Sobinoff AP, Adélaïde J, Guille A, Finetti P, Noble JR, Churikov D, Chaffanet M, Lavit E, Pickett HA, Bouvier C, Birnbaum D, Reddel RR, Géli V. TOP3A amplification and ATRX inactivation are mutually exclusive events in pediatric osteosarcomas using ALT. EMBO Mol Med 2022; 14:e15859. [PMID: 35920001 PMCID: PMC9549729 DOI: 10.15252/emmm.202215859] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 02/05/2023] Open
Abstract
In some types of cancer, telomere length is maintained by the alternative lengthening of telomeres (ALT) mechanism. In many ALT cancers, the α-thalassemia/mental retardation syndrome X-linked (ATRX) gene is mutated leading to the conclusion that the ATRX complex represses ALT. Here, we report that most high-grade pediatric osteosarcomas maintain their telomeres by ALT, and that the majority of these ALT tumors are ATRX wild-type (wt) and instead carry an amplified 17p11.2 chromosomal region containing TOP3A. We found that TOP3A was overexpressed in the ALT-positive ATRX-wt tumors consistent with its amplification. We demonstrated the functional significance of these results by showing that TOP3A overexpression in ALT cancer cells countered ATRX-mediated ALT inhibition and that TOP3A knockdown disrupted the ALT phenotype in ATRX-wt cells. Moreover, we report that TOP3A is required for proper BLM localization and promotes ALT DNA synthesis in ALT cell lines. Collectively, our results identify TOP3A as a major ALT player and potential therapeutic target.
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Affiliation(s)
- Alexandre de Nonneville
- Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐Calmettes, Team « Telomere and Chromatin ». Equipe labellisée Ligue Nationale Contre Le CancerAix‐Marseille UnivMarseilleFrance,Cancer Research Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia,Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance,Department of Medical Oncology, CRCM, CNRS, INSERM, Institut Paoli‐CalmettesAix‐Marseille UnivMarseilleFrance
| | - Sébastien Salas
- Department of Medical OncologyAssistance Publique Hôpitaux de Marseille ‐ Timone HospitalMarseilleFrance
| | - François Bertucci
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance,Department of Medical Oncology, CRCM, CNRS, INSERM, Institut Paoli‐CalmettesAix‐Marseille UnivMarseilleFrance
| | - Alexander P Sobinoff
- Telomere Length Regulation Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia
| | - José Adélaïde
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Arnaud Guille
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Pascal Finetti
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Jane R Noble
- Cancer Research Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia
| | - Dimitri Churikov
- Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐Calmettes, Team « Telomere and Chromatin ». Equipe labellisée Ligue Nationale Contre Le CancerAix‐Marseille UnivMarseilleFrance
| | - Max Chaffanet
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Elise Lavit
- Department of Medical OncologyAssistance Publique Hôpitaux de Marseille ‐ Timone HospitalMarseilleFrance
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia
| | - Corinne Bouvier
- Department of PathologyAssistance Publique Hôpitaux de Marseille ‐ Timone HospitalMarseilleFrance
| | - Daniel Birnbaum
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Roger R Reddel
- Cancer Research Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia
| | - Vincent Géli
- Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐Calmettes, Team « Telomere and Chromatin ». Equipe labellisée Ligue Nationale Contre Le CancerAix‐Marseille UnivMarseilleFrance
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20
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Lou X, Gao H, Xu X, Ye Z, Zhang W, Wang F, Chen J, Zhang Y, Chen X, Qin Y, Yu X, Ji S. The Interplay of Four Main Pathways Recomposes Immune Landscape in Primary and Metastatic Gastroenteropancreatic Neuroendocrine Tumors. Front Oncol 2022; 12:808448. [PMID: 35664743 PMCID: PMC9158120 DOI: 10.3389/fonc.2022.808448] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/08/2022] [Indexed: 11/29/2022] Open
Abstract
Background The four major pathways in gastroenteropancreatic neuroendocrine neoplasms (GEP-NENs) including chromatin remodeling, DNA damage repair, activation of mTOR signaling, and telomere maintenance were mediated by some critical molecules and constituted critical processes of regulation in cancer-causing processes. However, the interplay and potential role of these pathway-related molecules in the tumor microenvironment of the primary and metastatic site remained unknown. Methods We systematically evaluated the mRNA expression of 34 molecules associated with the four pathways in 227 GEP−NEN samples from 5 datasets. We assigned the samples into two expression patterns of pathway-related molecules by an unsupervised clustering method. Subsequently, we explored the specific cell-related molecules, especially immune and stromal cells using the WGCNA method, based on differentially expressed genes (DEGs) responsible for the different patterns of pathway-related molecules, which provided a new method to qualify the pathway-related subtypes of individual tumors, then the PC_Score and PI_Score scoring systems were also constructed using obtained specific cell-related molecules. Furthermore, we performed the association of pathway-related subtypes with characteristics of immune landscape in primary and metastatic GEP-NENs. Results We demonstrated that the specific pathway-related molecules (SMARCA4, MLH1, TSC1, ATRX, and ATR) were associated with cytolytic activity. Then we identified the two distinct patterns of pathway-related molecules, which were characteristic with a significantly distinct immune landscape. Using WGCNA, we also identified the fibroblast-related molecules, including ASPN, COL10A1, COL3A1, EDNRA, MYL9, PRELP, RAB31, SPARC, and THBS2, and immune-related molecules including CASP1, CCL5, CTSS, CYBRD1, PMP22, and TFEC. Based on these specific markers, we identified four distinct pathway-related subtypes, characterized by immune and fibrotic enriched (I/FE), immune enriched (IE), fibrotic enriched (FE), and immune and fibrotic desert (I/FD), of which I/FE was characteristic with the highest PC_Score and PI_Score whereas I/FD presents the opposite trend. I/FE was positively correlated with immune landscape of T-cell activation and immunosuppression. Furthermore, the I/FE marked GEP-NENs with increased immune activation scores (T-cell costimulation, MHC I presentation, and APC costimulation). Importantly, the four distinct pathway-related subtypes were not conserved in different tumor sites, because I/FE was lacking in the liver metastatic site even though IE, FE, and I/FD also could be observed in the metastatic site. Conclusions This study was the first to perform a comprehensive analysis of the four major pathways in GEP-NENs. We demonstrated the potential function of these pathway-related molecules in immune landscapes. Our findings indicated that the primary and metastatic GEP-NENs had distinct antitumor phenotypes. This work highlighted the interplay and potential clinical utility of these pathway-related molecules in GEP-NENs.
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Affiliation(s)
- Xin Lou
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Heli Gao
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xiaowu Xu
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Zeng Ye
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Wuhu Zhang
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Fei Wang
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Jie Chen
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Yue Zhang
- Department of Hepatopancreatobiliary Surgery, the Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Xuemin Chen
- Department of Hepatopancreatobiliary Surgery, the Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Yi Qin
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xianjun Yu
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Shunrong Ji
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
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21
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van Gerven MR, Bozsaky E, Matser YAH, Vosseberg J, Taschner-Mandl S, Koster J, Tytgat GAM, Molenaar JJ, van den Boogaard M. The mutational spectrum of ATRX aberrations in neuroblastoma and the associated patient and tumor characteristics. Cancer Sci 2022; 113:2167-2178. [PMID: 35384159 PMCID: PMC9207354 DOI: 10.1111/cas.15363] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/18/2022] [Accepted: 04/02/2022] [Indexed: 11/30/2022] Open
Abstract
Neuroblastoma is the most common extracranial solid tumor in children. The chromatin remodeler ATRX is frequently mutated in high‐risk patients with a poor prognosis. Although many studies have reported ATRX aberrations and the associated clinical characteristics in neuroblastoma, a comprehensive overview is currently lacking. In this study, we extensively characterize the mutational spectrum of ATRX aberrations in neuroblastoma tumors reported in previous studies and present an overview of patient and tumor characteristics. We collected the data of a total of 127 neuroblastoma patients and three cell lines with ATRX aberrations originating from 20 papers. We subdivide the ATRX aberrations into nonsense, missense, and multiexon deletions (MEDs) and show that 68% of them are MEDs. Of these MEDs, 75% are predicted to be in‐frame. Furthermore, we identify a missense mutational hotspot region in the helicase domain. We also confirm that all three ATRX mutation types are more often identified in patients diagnosed at an older age, but still approximately 40% of the patients are aged 5 years or younger at diagnosis. Surprisingly, we found that 11q deletions are enriched in neuroblastomas with ATRX deletions compared to a reference cohort, but not in neuroblastomas with ATRX point mutations. Taken together, our data emphasizes a distinct ATRX mutation spectrum in neuroblastoma, which should be considered when studying molecular phenotypes and therapeutic strategies.
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Affiliation(s)
| | - Eva Bozsaky
- Tumor biology group, St Anna Children's Cancer Research Institute, Vienna, Austria
| | - Yvette A H Matser
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Julian Vosseberg
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | | | - Jan Koster
- Department of Oncogenomics, Amsterdam UMC, location AMC, Amsterdam, the Netherlands
| | | | - Jan J Molenaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands
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22
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Lu R, Pickett HA. Telomeric replication stress: the beginning and the end for alternative lengthening of telomeres cancers. Open Biol 2022; 12:220011. [PMID: 35259951 PMCID: PMC8905155 DOI: 10.1098/rsob.220011] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Telomeres are nucleoprotein structures that cap the ends of linear chromosomes. Telomeric DNA comprises terminal tracts of G-rich tandem repeats, which are inherently difficult for the replication machinery to navigate. Structural aberrations that promote activation of the alternative lengthening of telomeres (ALT) pathway of telomere maintenance exacerbate replication stress at ALT telomeres, driving fork stalling and fork collapse. This form of telomeric DNA damage perpetuates recombination-mediated repair pathways and break-induced telomere synthesis. The relationship between replication stress and DNA repair is tightly coordinated for the purpose of regulating telomere length in ALT cells, but has been shown to be experimentally manipulatable. This raises the intriguing possibility that induction of replication stress can be used as a means to cause toxic levels of DNA damage at ALT telomeres, thereby selectively disrupting the viability of ALT cancers.
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Affiliation(s)
- Robert Lu
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Hilda A. Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
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23
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Marín-Gual L, González-Rodelas L, Pujol G, Vara C, Martín-Ruiz M, Berríos S, Fernández-Donoso R, Pask A, Renfree MB, Page J, Waters PD, Ruiz-Herrera A. Strategies for meiotic sex chromosome dynamics and telomeric elongation in Marsupials. PLoS Genet 2022; 18:e1010040. [PMID: 35130272 PMCID: PMC8853506 DOI: 10.1371/journal.pgen.1010040] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 02/17/2022] [Accepted: 01/14/2022] [Indexed: 01/30/2023] Open
Abstract
During meiotic prophase I, homologous chromosomes pair, synapse and recombine in a tightly regulated process that ensures the generation of genetically variable haploid gametes. Although the mechanisms underlying meiotic cell division have been well studied in model species, our understanding of the dynamics of meiotic prophase I in non-traditional model mammals remains in its infancy. Here, we reveal key meiotic features in previously uncharacterised marsupial species (the tammar wallaby and the fat-tailed dunnart), plus the fat-tailed mouse opossum, with a focus on sex chromosome pairing strategies, recombination and meiotic telomere homeostasis. We uncovered differences between phylogroups with important functional and evolutionary implications. First, sex chromosomes, which lack a pseudo-autosomal region in marsupials, had species specific pairing and silencing strategies, with implications for sex chromosome evolution. Second, we detected two waves of γH2AX accumulation during prophase I. The first wave was accompanied by low γH2AX levels on autosomes, which correlated with the low recombination rates that distinguish marsupials from eutherian mammals. In the second wave, γH2AX was restricted to sex chromosomes in all three species, which correlated with transcription from the X in tammar wallaby. This suggests non-canonical functions of γH2AX on meiotic sex chromosomes. Finally, we uncover evidence for telomere elongation in primary spermatocytes of the fat-tailed dunnart, a unique strategy within mammals. Our results provide new insights into meiotic progression and telomere homeostasis in marsupials, highlighting the importance of capturing the diversity of meiotic strategies within mammals. The generation of haploid gametes is a hallmark of sexual reproduction. And this is accomplished by a complex, albeit tightly regulated, reductional cell division called meiosis. Although meiosis has been extensively studied in eutherian mammal model species, our understanding of the mechanisms regulating chromosome synapsis, recombination and segregation during meiosis progression is still incomplete especially in non-eutherian mammals. To fill this gap and capture the diversity of meiotic strategies among mammals, we study previously uncharacterised representative marsupial species, an evolutionary assemblage that last shared a common ancestry more than 80 million years ago. We uncover novel, hence non-canonical, strategies for sex chromosome pairing, DNA repair, recombination and transcription. Most importantly, we reveal the uniqueness of marsupial meiosis, which includes the unprecedented detection of alternative mechanism (ALT) for the paternal control of telomere length during prophase I. Our findings suggest that ALT (previously only associated to cancer cells) could play a role in telomere homeostasis in mammalian germ cells.
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Affiliation(s)
- Laia Marín-Gual
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Laura González-Rodelas
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Gala Pujol
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Covadonga Vara
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Marta Martín-Ruiz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Soledad Berríos
- Programa de Genética Humana, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Raúl Fernández-Donoso
- Programa de Genética Humana, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Andrew Pask
- School of BioSciences, The University of Melbourne, Melbourne, Australia
| | - Marilyn B. Renfree
- School of BioSciences, The University of Melbourne, Melbourne, Australia
| | - Jesús Page
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Paul D. Waters
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Australia
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- * E-mail:
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24
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Barroso-González J, García-Expósito L, Galaviz P, Lynskey ML, Allen JAM, Hoang S, Watkins SC, Pickett HA, O'Sullivan RJ. Anti-recombination function of MutSα restricts telomere extension by ALT-associated homology-directed repair. Cell Rep 2021; 37:110088. [PMID: 34879271 PMCID: PMC8724847 DOI: 10.1016/j.celrep.2021.110088] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/13/2021] [Accepted: 11/10/2021] [Indexed: 01/02/2023] Open
Abstract
Alternative lengthening of telomeres (ALT) is a telomere-elongation mechanism observed in ~15% of cancer subtypes. Current models indicate that ALT is mediated by homology-directed repair mechanisms. By disrupting MSH6 gene expression, we show that the deficiency of MutSα (MSH2/MSH6) DNA mismatch repair complex causes striking telomere hyperextension. Mechanistically, we show MutSα is specifically recruited to telomeres in ALT cells by associating with the proliferating-cell nuclear antigen (PCNA) subunit of the ALT telomere replisome. We also provide evidence that MutSα counteracts Bloom (BLM) helicase, which adopts a crucial role in stabilizing hyper-extended telomeres and maintaining the survival of MutSα-deficient ALT cancer cells. Lastly, we propose a model in which MutSα deficiency impairs heteroduplex rejection, leading to premature initiation of telomere DNA synthesis that coincides with an accumulation of telomere variant repeats (TVRs). These findings provide evidence that the MutSα DNA mismatch repair complex acts to restrain unwarranted ALT. Barroso-Gonzalez et al. show that the mismatch repair complex MutSα restricts the alternative lengthening of telomeres (ALT) pathway in cancer cells. MutSα has an anti-recombination function and limits recombination between heteroduplex sequences at telomeres, in part by counteracting the Bloom helicase (BLM).
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Affiliation(s)
- Jonathan Barroso-González
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Laura García-Expósito
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Pablo Galaviz
- Bioinformatics Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Michelle Lee Lynskey
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Joshua A M Allen
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - SongMy Hoang
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Simon C Watkins
- Department of Cell Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
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25
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De Rosa M, Johnson SA, Opresko PL. Roles for the 8-Oxoguanine DNA Repair System in Protecting Telomeres From Oxidative Stress. Front Cell Dev Biol 2021; 9:758402. [PMID: 34869348 PMCID: PMC8640134 DOI: 10.3389/fcell.2021.758402] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/27/2021] [Indexed: 11/27/2022] Open
Abstract
Telomeres are protective nucleoprotein structures that cap linear chromosome ends and safeguard genome stability. Progressive telomere shortening at each somatic cell division eventually leads to critically short and dysfunctional telomeres, which can contribute to either cellular senescence and aging, or tumorigenesis. Human reproductive cells, some stem cells, and most cancer cells, express the enzyme telomerase to restore telomeric DNA. Numerous studies have shown that oxidative stress caused by excess reactive oxygen species is associated with accelerated telomere shortening and dysfunction. Telomeric repeat sequences are remarkably susceptible to oxidative damage and are preferred sites for the production of the mutagenic base lesion 8-oxoguanine, which can alter telomere length homeostasis and integrity. Therefore, knowledge of the repair pathways involved in the processing of 8-oxoguanine at telomeres is important for advancing understanding of the pathogenesis of degenerative diseases and cancer associated with telomere instability. The highly conserved guanine oxidation (GO) system involves three specialized enzymes that initiate distinct pathways to specifically mitigate the adverse effects of 8-oxoguanine. Here we introduce the GO system and review the studies focused on investigating how telomeric 8-oxoguanine processing affects telomere integrity and overall genome stability. We also discuss newly developed technologies that target oxidative damage selectively to telomeres to investigate roles for the GO system in telomere stability.
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Affiliation(s)
- Mariarosaria De Rosa
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health and UPMC Hillman Cancer Center, Pittsburgh, PA, United States
| | - Samuel A Johnson
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health and UPMC Hillman Cancer Center, Pittsburgh, PA, United States
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health and UPMC Hillman Cancer Center, Pittsburgh, PA, United States
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26
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ATRX proximal protein associations boast roles beyond histone deposition. PLoS Genet 2021; 17:e1009909. [PMID: 34780483 PMCID: PMC8629390 DOI: 10.1371/journal.pgen.1009909] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/29/2021] [Accepted: 10/23/2021] [Indexed: 12/31/2022] Open
Abstract
The ATRX ATP-dependent chromatin remodelling/helicase protein associates with the DAXX histone chaperone to deposit histone H3.3 over repetitive DNA regions. Because ATRX-protein interactions impart functions, such as histone deposition, we used proximity-dependent biotinylation (BioID) to identify proximal associations for ATRX. The proteomic screen captured known interactors, such as DAXX, NBS1, and PML, but also identified a range of new associating proteins. To gauge the scope of their roles, we examined three novel ATRX-associating proteins that likely differed in function, and for which little data were available. We found CCDC71 to associate with ATRX, but also HP1 and NAP1, suggesting a role in chromatin maintenance. Contrastingly, FAM207A associated with proteins involved in ribosome biosynthesis and localized to the nucleolus. ATRX proximal associations with the SLF2 DNA damage response factor help inhibit telomere exchanges. We further screened for the proteomic changes at telomeres when ATRX, SLF2, or both proteins were deleted. The loss caused important changes in the abundance of chromatin remodelling, DNA replication, and DNA repair factors at telomeres. Interestingly, several of these have previously been implicated in alternative lengthening of telomeres. Altogether, this study expands the repertoire of ATRX-associating proteins and functions. ATRX is a protein that is needed to keep repetitive DNA regions organized. It does so in part by binding the DAXX histone chaperone to deposit histone proteins on DNA and assemble structures known as nucleosomes. While important, ATRX has additional functions that remain understudied. To better understand its various biological roles, we first identified the other proteins that are found in its proximity. ATRX-associating proteins were implicated in a range of functions, in addition to histone deposition. Our results suggest that ATRX-associating proteins likely help compact DNA after it is assembled into nucleosomes, and also promote its stability. We then examined the effect of ATRX on telomeres (repetitive DNA regions at the end of chromosomes). ATRX and at least one of its associating proteins suppressed spurious DNA exchanges at telomeres. To understand why, we then identified proteomic changes that occur at telomeres when ATRX was deleted. Loss of ATRX altered the enrichment of a surprising number of proteins at telomeres, including several DNA damage response and chromatin remodelling proteins.
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27
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Impact of Chromatin Dynamics and DNA Repair on Genomic Stability and Treatment Resistance in Pediatric High-Grade Gliomas. Cancers (Basel) 2021; 13:cancers13225678. [PMID: 34830833 PMCID: PMC8616465 DOI: 10.3390/cancers13225678] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Pediatric high-grade gliomas (pHGGs) are the leading cause of mortality in pediatric neuro-oncology, due in great part to treatment resistance driven by complex DNA repair mechanisms. pHGGs have recently been divided into molecular subtypes based on mutations affecting the N-terminal tail of the histone variant H3.3 and the ATRX/DAXX histone chaperone that deposits H3.3 at repetitive heterochromatin loci that are of paramount importance to the stability of our genome. This review addresses the functions of H3.3 and ATRX/DAXX in chromatin dynamics and DNA repair, as well as the impact of mutations affecting H3.3/ATRX/DAXX on treatment resistance and how the vulnerabilities they expose could foster novel therapeutic strategies. Abstract Despite their low incidence, pediatric high-grade gliomas (pHGGs), including diffuse intrinsic pontine gliomas (DIPGs), are the leading cause of mortality in pediatric neuro-oncology. Recurrent, mutually exclusive mutations affecting K27 (K27M) and G34 (G34R/V) in the N-terminal tail of histones H3.3 and H3.1 act as key biological drivers of pHGGs. Notably, mutations in H3.3 are frequently associated with mutations affecting ATRX and DAXX, which encode a chaperone complex that deposits H3.3 into heterochromatic regions, including telomeres. The K27M and G34R/V mutations lead to distinct epigenetic reprogramming, telomere maintenance mechanisms, and oncogenesis scenarios, resulting in distinct subgroups of patients characterized by differences in tumor localization, clinical outcome, as well as concurrent epigenetic and genetic alterations. Contrasting with our understanding of the molecular biology of pHGGs, there has been little improvement in the treatment of pHGGs, with the current mainstays of therapy—genotoxic chemotherapy and ionizing radiation (IR)—facing the development of tumor resistance driven by complex DNA repair pathways. Chromatin and nucleosome dynamics constitute important modulators of the DNA damage response (DDR). Here, we summarize the major DNA repair pathways that contribute to resistance to current DNA damaging agent-based therapeutic strategies and describe the telomere maintenance mechanisms encountered in pHGGs. We then review the functions of H3.3 and its chaperones in chromatin dynamics and DNA repair, as well as examining the impact of their mutation/alteration on these processes. Finally, we discuss potential strategies targeting DNA repair and epigenetic mechanisms as well as telomere maintenance mechanisms, to improve the treatment of pHGGs.
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28
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Spegg V, Altmeyer M. Biomolecular condensates at sites of DNA damage: More than just a phase. DNA Repair (Amst) 2021; 106:103179. [PMID: 34311273 PMCID: PMC7612016 DOI: 10.1016/j.dnarep.2021.103179] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 12/12/2022]
Abstract
Protein recruitment to DNA break sites is an integral part of the DNA damage response (DDR). Elucidation of the hierarchy and temporal order with which DNA damage sensors as well as repair and signaling factors assemble around chromosome breaks has painted a complex picture of tightly regulated macromolecular interactions that build specialized compartments to facilitate repair and maintenance of genome integrity. While many of the underlying interactions, e.g. between repair factors and damage-induced histone marks, can be explained by lock-and-key or induced fit binding models assuming fixed stoichiometries, structurally less well defined interactions, such as the highly dynamic multivalent interactions implicated in phase separation, also participate in the formation of multi-protein assemblies in response to genotoxic stress. Although much remains to be learned about these types of cooperative and highly dynamic interactions and their functional roles, the rapidly growing interest in material properties of biomolecular condensates and in concepts from polymer chemistry and soft matter physics to understand biological processes at different scales holds great promises. Here, we discuss nuclear condensates in the context of genome integrity maintenance, highlighting the cooperative potential between clustered stoichiometric binding and phase separation. Rather than viewing them as opposing scenarios, their combined effects can balance structural specificity with favorable physicochemical properties relevant for the regulation and function of multilayered nuclear condensates.
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Affiliation(s)
- Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
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29
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Peng Q, Zhou M, Zuo S, Liu Y, Li X, Yang Y, He Q, Yu X, Zhou J, He Z, He Q. Nuclear Factor Related to KappaB Binding Protein ( NFRKB) Is a Telomere-Associated Protein and Involved in Liver Cancer Development. DNA Cell Biol 2021; 40:1298-1307. [PMID: 34591601 DOI: 10.1089/dna.2021.0486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Alternative lengthening of telomeres (ALT) is a homologous recombination-based telomere maintenance mechanism activated in 10-15% of human cancers. Although significant progress has been made, the key regulators of the ALT pathway and its role in cancer development remain elusive. Bioinformatics methods were used to predict novel telomere-associated proteins (TAPs) by analysis of large-scale ChIP-Seq data. Immunostaining and fluorescence in situ hybridization experiments were applied to detect the subcellular location of target genes and telomeres. Western blot and reverse transcription-polymerase chain reaction (RT-PCR) were used to examine the expression of targeting genes. Overall survival (OS) analyses were used to evaluate the relationship between gene expression and survival time; immunohistochemistry was used to detect the distribution of target genes in liver cancer tissues. We found that nuclear factor related to kappaB binding protein (NFRKB), a metazoan-specific subunit of the INO80 complex, can associate with telomeres in human ALT cells. Loss of NFRKB induces dysfunction of telomeres and less PML bodies in U2OS cells. In addition, NFRKB is low/moderately expressed in cytoplasm of normal hepatocytes but heavily accumulating in the nucleus of liver cancer cells. Finally, the high expression of NFRKB is associated with short OS time and poor prognosis. NFRKB is a TAP and protects telomeres from DNA damage in ALT cells. It is highly expressed in hepatocellular carcinoma (HCC) cells and predicts a poor prognosis. NFRKB may be a promising prognostic biomarker for the treatment of HCC in the future.
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Affiliation(s)
- Qiyao Peng
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, China
| | - Mingqing Zhou
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, China
| | - Shanru Zuo
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, China
| | - Yucong Liu
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, China
| | - Xueguang Li
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, China
| | - Yide Yang
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, China
| | - Quanze He
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Xing Yu
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, China
| | - Junhua Zhou
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, China
| | - Zuping He
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, China
| | - Quanyuan He
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, China
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30
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Kang HJ, Oh JH, Kim YW, Kim W, An J, Sung CO, Kim J, Shim JH, Hwang S, Yu E, Heaphy CM, Hong SM. Clinicopathological and molecular characterization of chromophobe hepatocellular carcinoma. Liver Int 2021; 41:2499-2510. [PMID: 34036718 DOI: 10.1111/liv.14975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/04/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Chromophobe hepatocellular carcinoma (HCC) is a newly included subtype of HCC in the 5th edition of the WHO classification with distinctive histological features (chromophobic cytoplasm with anaplastic nuclei and pseudocyst formation) and is strongly associated with the alternative lengthening of telomeres (ALT) phenotype. However, the clinicopathologic characterization and molecular features of chromophobe HCC are unknown. METHODS To comprehensively characterize chromophobe HCC, whole exome sequencing, copy number variation, and transcriptomic analyses were performed in 224 surgically resected HCC cases. Additionally, telomere-specific fluorescence in situ hybridization was used to assess ALT. These genomic profiles and ALT status were compared with clinicopathological features among subtypes of HCC, particularly chromophobe HCC and conventional HCC. RESULTS Chromophobe HCC was observed in 10.3% (23/224) cases and, compared to conventional HCC, was more frequent in females (P = .023). The overall and recurrence-free survival outcomes were similar between patients with chromophobe HCC and conventional HCC. However, chromophobe HCC displayed significantly more upregulated genes involving cell cycle progression and DNA repair. Additionally, ALT was significantly enriched in chromophobe HCC (87%; 20/23) compared to conventional HCC (2.2%, 4/178; P < .001). Somatic mutations in ALT-associated genes, including ATRX, SMARCAL1, FANCG, FANCM, SP100, TSPYL5, and RAD52 were more frequent in chromophobe HCC (30.4%, 7/23 cases) compared to conventional HCC (11.8%, 21/178 cases; P = .024). CONCLUSIONS Chromophobe HCC is a unique subtype of HCC with a prevalence of ~10%. Compared to conventional HCC, chromophobe HCC is associated with female predominance and ALT, although overall and recurrence-free outcomes are similar to conventional HCC.
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Affiliation(s)
- Hyo Jeong Kang
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.,Asan Liver Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Ji-Hye Oh
- Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yeon Wook Kim
- Asan Institute for Life Science, Asan Medical Center, Seoul, Republic of Korea
| | - Wonkyung Kim
- Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jihyun An
- Department of Gastroenterology and Hepatology, Hanyang University of Medicine, Guri, Republic of Korea
| | - Chang Ohk Sung
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jihun Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.,Asan Liver Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Ju Hyun Shim
- Asan Liver Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.,Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Shin Hwang
- Asan Liver Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.,Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Eunsil Yu
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.,Asan Liver Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Christopher M Heaphy
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA.,Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Seung-Mo Hong
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.,Asan Institute for Life Science, Asan Medical Center, Seoul, Republic of Korea
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31
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Chen J, Jin X, Mei Y, Shen Z, Zhu J, Shi H, Wang M, Zheng X, Liang G. The different biological effects of TMPyP4 and cisplatin in the inflammatory microenvironment of osteosarcoma are attributed to G-quadruplex. Cell Prolif 2021; 54:e13101. [PMID: 34296479 PMCID: PMC8450119 DOI: 10.1111/cpr.13101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/08/2021] [Accepted: 07/09/2021] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVE Osteosarcoma (OS) is characterized by high levels of the tumour-associated inflammatory microenvironment. Moreover, in approximately 60% of OS, telomere length is maintained by alternative lengthening of telomeres (ALT) pathway. Whether the ALT pathway can be exploited for OS therapeutic treatment and how the OS inflammatory microenvironment influences the anti-cancer drug effect remains unknown. Here, we examined the biological effects of TMPyP4 and cisplatin in the inflammatory microenvironment of OS cells. MATERIALS AND METHODS Immunofluorescence in situ hybridization (IF-FISH) and C-circle experiments were used to detect the G-quadruplex and ALT activity. The redox potential of single guanine, G-quadruplex and G-quadruplex/TMPyP4 was evaluated by the lowest unoccupied molecular orbital energy (LUMO), zeta potential and cyclic voltammetry. Cell viability, flow cytometry and apoptosis, Western blot, comet assay, adhesion, transwell and scratch experiments were performed to compare the anti-tumour proliferation and migration effects of TMPyP4 and cisplatin in the inflammatory microenvironment. RESULTS This study indicated that compared with cisplatin, TMPyP4 could induce the formation of human telomeres and FAK G-quadruplex in vitro and in vivo, and TMPyP4-treated OS cells showed fewer extrachromosomal C-circles and fewer ALT-associated promyelocytic leukaemia bodies. Consequently, the ALT activity and FAK-related cell migration were suppressed by TMPyP4. Mechanistically, the formation of G-quadruplex resulted in both lower redox potential than G within the genome and FAK transcription inhibition, and TMPyP4 could enhance this phenomenon, especially in the inflammatory microenvironment. CONCLUSIONS Our results reveal that TMPyP4 is more suitable for OS treatment than cisplatin.
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Affiliation(s)
- Jianqiang Chen
- Chemical Biology Research CenterSchool of Pharmaceutical SciencesWenzhou Medical UniversityWenzhouChina
| | - Xiangxiang Jin
- Chemical Biology Research CenterSchool of Pharmaceutical SciencesWenzhou Medical UniversityWenzhouChina
| | - Yanan Mei
- Chemical Biology Research CenterSchool of Pharmaceutical SciencesWenzhou Medical UniversityWenzhouChina
| | - Zhe Shen
- Chemical Biology Research CenterSchool of Pharmaceutical SciencesWenzhou Medical UniversityWenzhouChina
| | - Jufan Zhu
- Chemical Biology Research CenterSchool of Pharmaceutical SciencesWenzhou Medical UniversityWenzhouChina
| | - Hongyi Shi
- Chemical Biology Research CenterSchool of Pharmaceutical SciencesWenzhou Medical UniversityWenzhouChina
| | - Minshan Wang
- The Affiliated Xiangshan HospitalWenzhou Medical UniversityNingboChina
- Hospital of Chinese Medicine of Haishu DistrictNingboChina
| | - Xiaohui Zheng
- Chemical Biology Research CenterSchool of Pharmaceutical SciencesWenzhou Medical UniversityWenzhouChina
| | - Guang Liang
- Chemical Biology Research CenterSchool of Pharmaceutical SciencesWenzhou Medical UniversityWenzhouChina
- School of Pharmaceutical SciencesHangzhou Medical CollegeHangzhouChina
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32
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Bolzán AD. Mutagen-induced telomere instability in human cells. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2021; 868-869:503387. [PMID: 34454696 DOI: 10.1016/j.mrgentox.2021.503387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/13/2021] [Accepted: 07/18/2021] [Indexed: 11/27/2022]
Abstract
Telomere instability is one of the main sources of genome instability and may result from chromosome end loss (due to chromosome breakage at one or both ends) or, more frequently, telomere dysfunction. Dysfunctional telomeres arise when they lose their end-capping function or become critically short, which causes chromosomal termini to behave like a DNA double-strand break. Telomere instability may occur at the chromosomal or at the molecular level, giving rise, respectively, to telomere-related chromosomal aberrations or the loss or modification of any of the components of the telomere (telomere DNA, telomere-associated proteins, or telomere RNA). Since telomeres play a fundamental role in maintaining genome stability, the study of telomere instability in cells exposed to mutagens is of great importance to understand the telomere-driven genomic instability present in those cells. In the present review, we will focus on the current knowledge about telomere instability induced by physical, chemical, and biological mutagens in human cells.
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Affiliation(s)
- Alejandro D Bolzán
- Laboratorio de Citogenética y Mutagénesis, Instituto Multidisciplinario de Biología Celular (IMBICE, CONICET-CICPBA-UNLP), calle 526 y Camino General Belgrano, B1906APO La Plata, Buenos Aires, Argentina; Universidad Nacional de La Plata, Facultad de Ciencias Naturales y Museo, calle 60 y 122, La Plata, Buenos Aires, Argentina.
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33
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Ackerson SM, Romney C, Schuck PL, Stewart JA. To Join or Not to Join: Decision Points Along the Pathway to Double-Strand Break Repair vs. Chromosome End Protection. Front Cell Dev Biol 2021; 9:708763. [PMID: 34322492 PMCID: PMC8311741 DOI: 10.3389/fcell.2021.708763] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/17/2021] [Indexed: 01/01/2023] Open
Abstract
The regulation of DNA double-strand breaks (DSBs) and telomeres are diametrically opposed in the cell. DSBs are considered one of the most deleterious forms of DNA damage and must be quickly recognized and repaired. Telomeres, on the other hand, are specialized, stable DNA ends that must be protected from recognition as DSBs to inhibit unwanted chromosome fusions. Decisions to join DNA ends, or not, are therefore critical to genome stability. Yet, the processing of telomeres and DSBs share many commonalities. Accordingly, key decision points are used to shift DNA ends toward DSB repair vs. end protection. Additionally, DSBs can be repaired by two major pathways, namely homologous recombination (HR) and non-homologous end joining (NHEJ). The choice of which repair pathway is employed is also dictated by a series of decision points that shift the break toward HR or NHEJ. In this review, we will focus on these decision points and the mechanisms that dictate end protection vs. DSB repair and DSB repair choice.
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Affiliation(s)
- Stephanie M Ackerson
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - Carlan Romney
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - P Logan Schuck
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - Jason A Stewart
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
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34
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Lezaja A, Panagopoulos A, Wen Y, Carvalho E, Imhof R, Altmeyer M. RPA shields inherited DNA lesions for post-mitotic DNA synthesis. Nat Commun 2021; 12:3827. [PMID: 34158486 PMCID: PMC8219667 DOI: 10.1038/s41467-021-23806-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 05/11/2021] [Indexed: 02/05/2023] Open
Abstract
The paradigm that checkpoints halt cell cycle progression for genome repair has been challenged by the recent discovery of heritable DNA lesions escaping checkpoint control. How such inherited lesions affect genome function and integrity is not well understood. Here, we identify a new class of heritable DNA lesions, which is marked by replication protein A (RPA), a protein primarily known for shielding single-stranded DNA in S/G2. We demonstrate that post-mitotic RPA foci occur at low frequency during unperturbed cell cycle progression, originate from the previous cell cycle, and are exacerbated upon replication stress. RPA-marked inherited ssDNA lesions are found at telomeres, particularly of ALT-positive cancer cells. We reveal that RPA protects these replication remnants in G1 to allow for post-mitotic DNA synthesis (post-MiDAS). Given that ALT-positive cancer cells exhibit high levels of replication stress and telomere fragility, targeting post-MiDAS might be a new therapeutic opportunity.
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Affiliation(s)
- Aleksandra Lezaja
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Andreas Panagopoulos
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Yanlin Wen
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Edison Carvalho
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Ralph Imhof
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Matthias Altmeyer
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
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35
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Prokhorova E, Agnew T, Wondisford AR, Tellier M, Kaminski N, Beijer D, Holder J, Groslambert J, Suskiewicz MJ, Zhu K, Reber JM, Krassnig SC, Palazzo L, Murphy S, Nielsen ML, Mangerich A, Ahel D, Baets J, O'Sullivan RJ, Ahel I. Unrestrained poly-ADP-ribosylation provides insights into chromatin regulation and human disease. Mol Cell 2021; 81:2640-2655.e8. [PMID: 34019811 PMCID: PMC8221567 DOI: 10.1016/j.molcel.2021.04.028] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 02/25/2021] [Accepted: 04/29/2021] [Indexed: 12/26/2022]
Abstract
ARH3/ADPRHL2 and PARG are the primary enzymes reversing ADP-ribosylation in vertebrates, yet their functions in vivo remain unclear. ARH3 is the only hydrolase able to remove serine-linked mono(ADP-ribose) (MAR) but is much less efficient than PARG against poly(ADP-ribose) (PAR) chains in vitro. Here, by using ARH3-deficient cells, we demonstrate that endogenous MARylation persists on chromatin throughout the cell cycle, including mitosis, and is surprisingly well tolerated. Conversely, persistent PARylation is highly toxic and has distinct physiological effects, in particular on active transcription histone marks such as H3K9ac and H3K27ac. Furthermore, we reveal a synthetic lethal interaction between ARH3 and PARG and identify loss of ARH3 as a mechanism of PARP inhibitor resistance, both of which can be exploited in cancer therapy. Finally, we extend our findings to neurodegeneration, suggesting that patients with inherited ARH3 deficiency suffer from stress-induced pathogenic increase in PARylation that can be mitigated by PARP inhibition.
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Affiliation(s)
- Evgeniia Prokhorova
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Thomas Agnew
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Anne R Wondisford
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Nicole Kaminski
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Danique Beijer
- Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - James Holder
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | | | - Marcin J Suskiewicz
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Julia M Reber
- Molecular Toxicology Group, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Sarah C Krassnig
- Molecular Toxicology Group, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Luca Palazzo
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Aswin Mangerich
- Molecular Toxicology Group, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Jonathan Baets
- Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium; Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
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36
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Segura-Bayona S, Villamor-Payà M, Attolini CSO, Koenig LM, Sanchiz-Calvo M, Boulton SJ, Stracker TH. Tousled-Like Kinases Suppress Innate Immune Signaling Triggered by Alternative Lengthening of Telomeres. Cell Rep 2021; 32:107983. [PMID: 32755577 PMCID: PMC7408502 DOI: 10.1016/j.celrep.2020.107983] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/30/2020] [Accepted: 07/09/2020] [Indexed: 12/11/2022] Open
Abstract
The Tousled-like kinases 1 and 2 (TLK1/2) control histone deposition through the ASF1 histone chaperone and influence cell cycle progression and genome maintenance, yet the mechanisms underlying TLK-mediated genome stability remain uncertain. Here, we show that TLK loss results in severe chromatin decompaction and altered genome accessibility, particularly affecting heterochromatic regions. Failure to maintain heterochromatin increases spurious transcription of repetitive elements and induces features of alternative lengthening of telomeres (ALT). TLK depletion culminates in a cGAS-STING-TBK1-mediated innate immune response that is independent of replication-stress signaling and attenuated by the depletion of factors required to produce extra-telomeric DNA. Analysis of human cancers reveals that chromosomal instability correlates with high TLK2 and low STING levels in many cohorts. Based on these findings, we propose that high TLK levels contribute to immune evasion in chromosomally unstable and ALT+ cancers. TLK-deficient cells have increased accessibility at heterochromatin regions TLK1/2 suppress spurious transcription and telomere hyper-recombination Extra-telomeric DNA generated upon TLK loss promotes innate immune signaling cGAS-STING-TBK1 signaling in TLK-deficient cells is independent of replication stress
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Affiliation(s)
- Sandra Segura-Bayona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Marina Villamor-Payà
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Camille Stephan-Otto Attolini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Lars M Koenig
- Division of Clinical Pharmacology, University Hospital, LMU Munich, 80337 Munich, Germany
| | - Maria Sanchiz-Calvo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Travis H Stracker
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain.
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37
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Zhang JM, Genois MM, Ouyang J, Lan L, Zou L. Alternative lengthening of telomeres is a self-perpetuating process in ALT-associated PML bodies. Mol Cell 2021; 81:1027-1042.e4. [PMID: 33453166 PMCID: PMC8245000 DOI: 10.1016/j.molcel.2020.12.030] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/03/2020] [Accepted: 12/15/2020] [Indexed: 01/16/2023]
Abstract
Alternative lengthening of telomeres (ALT) is mediated by break-induced replication (BIR), but how BIR is regulated at telomeres is poorly understood. Here, we show that telomeric BIR is a self-perpetuating process. By tethering PML-IV to telomeres, we induced telomere clustering in ALT-associated PML bodies (APBs) and a POLD3-dependent ATR response at telomeres, showing that BIR generates replication stress. Ablation of BLM helicase activity in APBs abolishes telomere synthesis but causes multiple chromosome bridges between telomeres, revealing a function of BLM in processing inter-telomere BIR intermediates. Interestingly, the accumulation of BLM in APBs requires its own helicase activity and POLD3, suggesting that BIR triggers a feedforward loop to further recruit BLM. Enhancing BIR induces PIAS4-mediated TRF2 SUMOylation, and PIAS4 loss deprives APBs of repair proteins and compromises ALT telomere synthesis. Thus, a BLM-driven and PIAS4-mediated feedforward loop operates in APBs to perpetuate BIR, providing a critical mechanism to extend ALT telomeres.
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Affiliation(s)
- Jia-Min Zhang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Marie-Michelle Genois
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jian Ouyang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Li Lan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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38
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Abstract
Decades of study on cell cycle regulation have provided great insight into human cellular life span barriers, as well as their dysregulation during tumorigenesis. Telomeres, the extremities of linear chromosomes, perform an essential role in implementing these proliferative boundaries and preventing the propagation of potentially cancerous cells. The tumor-suppressive function of telomeres relies on their ability to initiate DNA damage signaling pathways and downstream cellular events, ranging from cell cycle perturbation to inflammation and cell death. While the tumor-suppressor role of telomeres is undoubtable, recent advances have pointed to telomeres as a major source of many of the genomic aberrations found in both early- and late-stage cancers, including the most recently discovered mutational phenomenon of chromothripsis. Telomere shortening appears as a double-edged sword that can function in opposing directions in carcinogenesis. This review focuses on the current knowledge of the dual role of telomeres in cancer and suggests a new perspective to reconcile the paradox of telomeres and their implications in cancer etiology.
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Affiliation(s)
- Joe Nassour
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Tobias T Schmidt
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Jan Karlseder
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
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39
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Shen M, Young A, Autexier C. PCNA, a focus on replication stress and the alternative lengthening of telomeres pathway. DNA Repair (Amst) 2021; 100:103055. [PMID: 33581499 DOI: 10.1016/j.dnarep.2021.103055] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/25/2021] [Indexed: 12/16/2022]
Abstract
The maintenance of telomeres, which are specialized stretches of DNA found at the ends of linear chromosomes, is a crucial step for the immortalization of cancer cells. Approximately 10-15 % of cancer cells use a homologous recombination-based mechanism known as the Alternative Lengthening of Telomeres (ALT) pathway to maintain their telomeres. Telomeres in general pose a challenge to DNA replication owing to their repetitive nature and potential for forming secondary structures. Telomeres in ALT+ cells especially are subject to elevated levels of replication stress compared to telomeres that are maintained by the enzyme telomerase, in part due to the incorporation of telomeric variant repeats at ALT+ telomeres, their on average longer lengths, and their modified chromatin states. Many DNA metabolic strategies exist to counter replication stress and to protect stalled replication forks. The role of proliferating cell nuclear antigen (PCNA) as a platform for recruiting protein partners that participate in several of these DNA replication and repair pathways has been well-documented. We propose that many of these pathways may be active at ALT+ telomeres, either to facilitate DNA replication, to manage replication stress, or during telomere extension. Here, we summarize recent evidence detailing the role of PCNA in pathways including DNA secondary structure resolution, DNA damage bypass, replication fork restart, and DNA damage synthesis. We propose that an examination of PCNA and its post-translational modifications (PTMs) may offer a unique lens by which we might gain insight into the DNA metabolic landscape that is distinctively present at ALT+ telomeres.
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Affiliation(s)
- Michelle Shen
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada; Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada
| | - Adrian Young
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada; Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada
| | - Chantal Autexier
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada; Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada.
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40
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Lezaja A, Altmeyer M. Dealing with DNA lesions: When one cell cycle is not enough. Curr Opin Cell Biol 2020; 70:27-36. [PMID: 33310228 DOI: 10.1016/j.ceb.2020.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023]
Abstract
Subversion of genome integrity fuels cellular adaptation and is a prerequisite for organismal evolution, yet genomic lesions are also the harmful driving force of cancer and other age-related human diseases. Genome integrity maintenance is inherently linked to genome organization and nuclear architecture, which are substantially remodeled during the cell cycle. Here we discuss recent findings on how actively dividing cells cope with endogenous genomic lesions that occur frequently at repetitive, heterochromatic, and late replicating regions as byproducts of genome duplication. We discuss how such lesions, rather than being resolved immediately when they occur, are dealt with in subsequent cell cycle phases, and even after mitotic cell division, and how this in turn affects genome organization, stability, and function.
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Affiliation(s)
- Aleksandra Lezaja
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
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41
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Using telomeric chromosomal aberrations to evaluate clastogen-induced genomic instability in mammalian cells. Chromosome Res 2020; 28:259-276. [DOI: 10.1007/s10577-020-09641-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/06/2020] [Accepted: 09/06/2020] [Indexed: 12/13/2022]
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Sung JY, Lim HW, Joung JG, Park WY. Pan-Cancer Analysis of Alternative Lengthening of Telomere Activity. Cancers (Basel) 2020; 12:cancers12082207. [PMID: 32784588 PMCID: PMC7465155 DOI: 10.3390/cancers12082207] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/01/2020] [Accepted: 08/05/2020] [Indexed: 02/06/2023] Open
Abstract
Alternative lengthening of telomeres (ALT) is a telomerase-independent mechanism that extends telomeres in cancer cells. It influences tumorigenesis and patient survival. Despite the clinical significance of ALT in tumors, the manner in which ALT is activated and influences prognostic outcomes in distinct cancer types is unclear. In this work, we profiled distinct telomere maintenance mechanisms (TMMs) using 8953 transcriptomes of 31 different cancer types from The Cancer Genome Atlas (TCGA). Our results demonstrated that approximately 29% of cancer types display high ALT activity with low telomerase activity in the telomere-lengthening group. Among the distinct ALT mechanisms, homologous recombination was frequently observed in sarcoma, adrenocortical carcinoma, and kidney chromophobe. Five cancer types showed a significant difference in survival in the presence of high ALT activity. Sarcoma patients with elevated ALT had unfavorable risks (p < 0.038) coupled with a high expression of TOP2A, suggesting this as a potential drug target. On the contrary, glioblastoma patients had favorable risks (p < 0.02), and showed low levels of antigen-presenting cells. Together, our analyses highlight cancer type-dependent TMM activities and ALT-associated genes as potential therapeutic targets.
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Affiliation(s)
- Ji-Yong Sung
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea;
- Department of Health Science and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul 06351, Korea
| | - Hee-Woong Lim
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA;
| | - Je-Gun Joung
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea;
- Correspondence: (J.-G.J.); (W.-Y.P.); Tel.: +82-2-3410-1706 (J.-G.J.); +82-2-3410-6128 (W.-Y.P.); Fax: +82-2-2148-9819 (W.-Y.P.)
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea;
- Department of Health Science and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul 06351, Korea
- Department of Molecular Cell Biology, School of Medicine, Sungkyunkwan University, Seoul 06351, Korea
- Correspondence: (J.-G.J.); (W.-Y.P.); Tel.: +82-2-3410-1706 (J.-G.J.); +82-2-3410-6128 (W.-Y.P.); Fax: +82-2-2148-9819 (W.-Y.P.)
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43
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TCGA Pan-Cancer Genomic Analysis of Alternative Lengthening of Telomeres (ALT) Related Genes. Genes (Basel) 2020; 11:genes11070834. [PMID: 32708340 PMCID: PMC7397314 DOI: 10.3390/genes11070834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/15/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023] Open
Abstract
Telomere maintenance mechanisms (TMM) are used by cancer cells to avoid apoptosis, 85–90% reactivate telomerase, while 10–15% use the alternative lengthening of telomeres (ALT). Due to anti-telomerase-based treatments, some tumors switch from a telomerase-dependent mechanism to ALT; in fact, the co-existence between both mechanisms has been observed in some cancers. Although different elements in the ALT pathway are uncovered, some molecular mechanisms are still poorly understood. Therefore, with the aim to identify potential molecular markers for the study of ALT, we combined in silico approaches in a 411 telomere maintenance gene set. As a consequence, we conducted a genomic analysis of these genes in 31 Pan-Cancer Atlas studies from The Cancer Genome Atlas and found 325,936 genomic alterations; from which, we identified 20 genes highly mutated in the cancer studies. Finally, we made a protein-protein interaction network and enrichment analysis to observe the main pathways of these genes and discuss their role in ALT-related processes, like homologous recombination and homology directed repair. Overall, due to the lack of understanding of the molecular mechanisms of ALT cancers, we proposed a group of genes, which after ex vivo validations, could represent new potential therapeutic markers in the study of ALT.
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