1
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Krishnamoorthy V, Foglizzo M, Dilley RL, Wu A, Datta A, Dutta P, Campbell LJ, Degtjarik O, Musgrove LJ, Calabrese AN, Zeqiraj E, Greenberg RA. The SPATA5-SPATA5L1 ATPase complex directs replisome proteostasis to ensure genome integrity. Cell 2024; 187:2250-2268.e31. [PMID: 38554706 PMCID: PMC11055677 DOI: 10.1016/j.cell.2024.03.002] [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: 02/02/2023] [Revised: 12/27/2023] [Accepted: 03/02/2024] [Indexed: 04/02/2024]
Abstract
Ubiquitin-dependent unfolding of the CMG helicase by VCP/p97 is required to terminate DNA replication. Other replisome components are not processed in the same fashion, suggesting that additional mechanisms underlie replication protein turnover. Here, we identify replisome factor interactions with a protein complex composed of AAA+ ATPases SPATA5-SPATA5L1 together with heterodimeric partners C1orf109-CINP (55LCC). An integrative structural biology approach revealed a molecular architecture of SPATA5-SPATA5L1 N-terminal domains interacting with C1orf109-CINP to form a funnel-like structure above a cylindrically shaped ATPase motor. Deficiency in the 55LCC complex elicited ubiquitin-independent proteotoxicity, replication stress, and severe chromosome instability. 55LCC showed ATPase activity that was specifically enhanced by replication fork DNA and was coupled to cysteine protease-dependent cleavage of replisome substrates in response to replication fork damage. These findings define 55LCC-mediated proteostasis as critical for replication fork progression and genome stability and provide a rationale for pathogenic variants seen in associated human neurodevelopmental disorders.
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Affiliation(s)
- Vidhya Krishnamoorthy
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6160, USA
| | - Martina Foglizzo
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Robert L Dilley
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6160, USA.
| | - Angela Wu
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6160, USA
| | - Arindam Datta
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6160, USA
| | - Parul Dutta
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6160, USA
| | - Lisa J Campbell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Oksana Degtjarik
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Laura J Musgrove
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Elton Zeqiraj
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| | - Roger A Greenberg
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6160, USA.
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2
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González-Acosta D, Lopes M. DNA replication and replication stress response in the context of nuclear architecture. Chromosoma 2024; 133:57-75. [PMID: 38055079 PMCID: PMC10904558 DOI: 10.1007/s00412-023-00813-7] [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: 08/08/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 12/07/2023]
Abstract
The DNA replication process needs to be coordinated with other DNA metabolism transactions and must eventually extend to the full genome, regardless of chromatin status, gene expression, secondary structures and DNA lesions. Completeness and accuracy of DNA replication are crucial to maintain genome integrity, limiting transformation in normal cells and offering targeting opportunities for proliferating cancer cells. DNA replication is thus tightly coordinated with chromatin dynamics and 3D genome architecture, and we are only beginning to understand the underlying molecular mechanisms. While much has recently been discovered on how DNA replication initiation is organised and modulated in different genomic regions and nuclear territories-the so-called "DNA replication program"-we know much less on how the elongation of ongoing replication forks and particularly the response to replication obstacles is affected by the local nuclear organisation. Also, it is still elusive how specific components of nuclear architecture participate in the replication stress response. Here, we review known mechanisms and factors orchestrating replication initiation, and replication fork progression upon stress, focusing on recent evidence linking genome organisation and nuclear architecture with the cellular responses to replication interference, and highlighting open questions and future challenges to explore this exciting new avenue of research.
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Affiliation(s)
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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3
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van Schie JJM, de Lint K, Molenaar TM, Moronta Gines M, Balk J, Rooimans M, Roohollahi K, Pai G, Borghuis L, Ramadhin A, Corazza F, Dorsman J, Wendt K, Wolthuis RF, de Lange J. CRISPR screens in sister chromatid cohesion defective cells reveal PAXIP1-PAGR1 as regulator of chromatin association of cohesin. Nucleic Acids Res 2023; 51:9594-9609. [PMID: 37702151 PMCID: PMC10570055 DOI: 10.1093/nar/gkad756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/22/2023] [Accepted: 09/05/2023] [Indexed: 09/14/2023] Open
Abstract
The cohesin complex regulates higher order chromosome architecture through maintaining sister chromatid cohesion and folding chromatin by DNA loop extrusion. Impaired cohesin function underlies a heterogeneous group of genetic syndromes and is associated with cancer. Here, we mapped the genetic dependencies of human cell lines defective of cohesion regulators DDX11 and ESCO2. The obtained synthetic lethality networks are strongly enriched for genes involved in DNA replication and mitosis and support the existence of parallel sister chromatid cohesion establishment pathways. Among the hits, we identify the chromatin binding, BRCT-domain containing protein PAXIP1 as a novel cohesin regulator. Depletion of PAXIP1 severely aggravates cohesion defects in ESCO2 mutant cells, leading to mitotic cell death. PAXIP1 promotes global chromatin association of cohesin, independent of DNA replication, a function that cannot be explained by indirect effects of PAXIP1 on transcription or DNA repair. Cohesin regulation by PAXIP1 requires its binding partner PAGR1 and a conserved FDF motif in PAGR1. PAXIP1 co-localizes with cohesin on multiple genomic loci, including active gene promoters and enhancers. Possibly, this newly identified role of PAXIP1-PAGR1 in regulating cohesin occupancy on chromatin is also relevant for previously described functions of PAXIP1 in transcription, immune cell maturation and DNA repair.
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Affiliation(s)
- Janne J M van Schie
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Klaas de Lint
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Thom M Molenaar
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | | | - Jesper A Balk
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Martin A Rooimans
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Khashayar Roohollahi
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Govind M Pai
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Lauri Borghuis
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Anisha R Ramadhin
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Francesco Corazza
- Erasmus Medical Centre, Department of Cell Biology, Rotterdam, The Netherlands
| | - Josephine C Dorsman
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Kerstin S Wendt
- Erasmus Medical Centre, Department of Cell Biology, Rotterdam, The Netherlands
| | - Rob M F Wolthuis
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Job de Lange
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
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4
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Ebner JN, Ritz D, von Fumetti S. Thermal acclimation results in persistent phosphoproteome changes in the freshwater planarian Crenobia alpina (Tricladida: Planariidae). J Therm Biol 2022; 110:103367. [DOI: 10.1016/j.jtherbio.2022.103367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/22/2022] [Accepted: 10/04/2022] [Indexed: 12/05/2022]
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Heijkants RC, Teunisse AFAS, de Jong D, Glinkina K, Mei H, Kielbasa SM, Szuhai K, Jochemsen AG. MDMX Regulates Transcriptional Activity of p53 and FOXO Proteins to Stimulate Proliferation of Melanoma Cells. Cancers (Basel) 2022; 14:cancers14184482. [PMID: 36139642 PMCID: PMC9496676 DOI: 10.3390/cancers14184482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/25/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary We have investigated the transcriptional changes occurring in uveal and cutaneous melanoma cell lines upon depletion of MDMX (aka:MDM4). Computational analyses of the mRNAs/genes affected upon MDMX depletion determined that many were containing a p53-bindingsite, but even more contained a FOX recognition site(s). Since connections between MDM2 and FOXO1 had already been published, we investigated whether indeed a subset of the MDMX-regulated genes are dependent on FOXO1/FOXO3 expression. Indeed, a number of such target genes, i.e., PIK3IP1, MXD4 and ZMAT3, were found to be FOXO target genes in our cell models. Some of these genes were recently identified as indirect p53-target genes, and their expression was found to be regulated by RFX7 transcription factor, which was found activated upon pharmacological activation of p53, e.g., by Nutlin-3. However, a clear involvement of RFX7 in our model could not be established, but an interplay between FOXO and RFX7 factors seems evident. Abstract The tumor suppressor protein p53 has an important role in cell-fate determination. In cancer cells, the activity of p53 is frequently repressed by high levels of MDMX and/or MDM2. MDM2 is a ubiquitin ligase whose activity results in ubiquitin- and proteasome-dependent p53 degradation, while MDMX inhibits p53-activated transcription by shielding the p53 transactivation domain. Interestingly, the oncogenic functions of MDMX appear to be more wide-spread than inhibition of p53. The present study aimed to elucidate the MDMX-controlled transcriptome. Therefore, we depleted MDMX with four distinct shRNAs from a high MDMX expressing uveal melanoma cell line and determined the effect on the transcriptome by RNAseq. Biological function analyses indicate the inhibition of the cell cycle regulatory genes and stimulation of cell death activating genes upon MDMX depletion. Although the inhibition of p53 activity clearly contributes to the transcription regulation controlled by MDMX, it appeared that the transcriptional regulation of multiple genes did not only rely on p53 expression. Analysis of gene regulatory networks indicated a role for Forkhead box (FOX) transcription factors. Depletion of FOXO proteins partly prevented the transcriptional changes upon MDMX depletion. Furthermore, depletion of FOXO proteins relatively diminished the growth inhibition upon MDMX knockdown, although the knockdown of the FOXO transcription factors also reduces cell growth. In conclusion, the p53-independent oncogenic functions of MDMX could be partially explained by its regulation of FOXO activity.
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Affiliation(s)
- Renier C. Heijkants
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Amina F. A. S. Teunisse
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Danielle de Jong
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Kseniya Glinkina
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Szymon M. Kielbasa
- Sequencing Analysis Support Core, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Karoly Szuhai
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Aart G. Jochemsen
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Correspondence:
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6
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Segeren HA, Westendorp B. Mechanisms used by cancer cells to tolerate drug-induced replication stress. Cancer Lett 2022; 544:215804. [PMID: 35750276 DOI: 10.1016/j.canlet.2022.215804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/15/2022] [Accepted: 06/19/2022] [Indexed: 11/02/2022]
Abstract
Activation of oncogenes in cancer cells forces cell proliferation, leading to DNA replication stress (RS). As a consequence, cancer cells heavily rely on the intra S-phase checkpoint for survival. This fundamental principle formed the basis for the development of inhibitors against key players of the intra S-phase checkpoint, ATR and CHK1. These drugs are often combined with chemotherapeutic drugs that interfere with DNA replication to exacerbate RS and exhaust the intra S-phase checkpoint in cancer cells. However, drug resistance impedes efficient clinical use, suggesting that some cancer cells tolerate severe RS. In this review, we describe how an increased nucleotide pool, boosted stabilization and repair of stalled forks and firing of dormant origins fortify the RS response in cancer cells. Notably, the vast majority of the genes that confer RS tolerance are regulated by the E2F and NRF2 transcription factors. These transcriptional programs are frequently activated in cancer cells, allowing simultaneous activation of multiple tolerance avenues. We propose that the E2F and NRF2 transcriptional programs can be used as biomarker to select patients for treatment with RS-inducing drugs and as novel targets to kill RS-tolerant cancer cells. Together, this review aims to provide a framework to maximally exploit RS as an Achilles' heel of cancer cells.
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Affiliation(s)
- Hendrika A Segeren
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Bart Westendorp
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
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7
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Jeppsson K, Sakata T, Nakato R, Milanova S, Shirahige K, Björkegren C. Cohesin-dependent chromosome loop extrusion is limited by transcription and stalled replication forks. SCIENCE ADVANCES 2022; 8:eabn7063. [PMID: 35687682 PMCID: PMC9187231 DOI: 10.1126/sciadv.abn7063] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 12/15/2021] [Accepted: 04/27/2022] [Indexed: 05/31/2023]
Abstract
Genome function depends on regulated chromosome folding, and loop extrusion by the protein complex cohesin is essential for this multilayered organization. The chromosomal positioning of cohesin is controlled by transcription, and the complex also localizes to stalled replication forks. However, the role of transcription and replication in chromosome looping remains unclear. Here, we show that reduction of chromosome-bound RNA polymerase weakens normal cohesin loop extrusion boundaries, allowing cohesin to form new long-range chromosome cis interactions. Stress response genes induced by transcription inhibition are also shown to act as new loop extrusion boundaries. Furthermore, cohesin loop extrusion during early S phase is jointly controlled by transcription and replication units. Together, the results reveal that replication and transcription machineries are chromosome-folding regulators that block the progression of loop-extruding cohesin, opening for new perspectives on cohesin's roles in genome function and stability.
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Affiliation(s)
- Kristian Jeppsson
- Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83 Huddinge, Sweden
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden
- Institute for Quantitative Bioscience, Tokyo University, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Toyonori Sakata
- Institute for Quantitative Bioscience, Tokyo University, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Ryuichiro Nakato
- Institute for Quantitative Bioscience, Tokyo University, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Stefina Milanova
- Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83 Huddinge, Sweden
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden
| | - Katsuhiko Shirahige
- Institute for Quantitative Bioscience, Tokyo University, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Camilla Björkegren
- Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83 Huddinge, Sweden
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden
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8
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Di Nardo M, Pallotta MM, Musio A. The multifaceted roles of cohesin in cancer. J Exp Clin Cancer Res 2022; 41:96. [PMID: 35287703 PMCID: PMC8919599 DOI: 10.1186/s13046-022-02321-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/09/2022] [Indexed: 12/13/2022] Open
Abstract
The cohesin complex controls faithful chromosome segregation by pairing sister chromatids after DNA replication until mitosis. In addition, it is crucial for hierarchal three-dimensional organization of the genome, transcription regulation and maintaining DNA integrity. The core complex subunits SMC1A, SMC3, STAG1/2, and RAD21 as well as its modulators, have been found to be recurrently mutated in human cancers. The mechanisms by which cohesin mutations trigger cancer development and disease progression are still poorly understood. Since cohesin is involved in a range of chromosome-related processes, the outcome of cohesin mutations in cancer is complex. Herein, we discuss recent discoveries regarding cohesin that provide new insight into its role in tumorigenesis.
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Affiliation(s)
- Maddalena Di Nardo
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Via Moruzzi, 1 56124, Pisa, Italy
| | - Maria M. Pallotta
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Via Moruzzi, 1 56124, Pisa, Italy
| | - Antonio Musio
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Via Moruzzi, 1 56124, Pisa, Italy
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9
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Carvalhal S, Bader I, Rooimans MA, Oostra AB, Balk JA, Feichtinger RG, Beichler C, Speicher MR, van Hagen JM, Waisfisz Q, van Haelst M, Bruijn M, Tavares A, Mayr JA, Wolthuis RMF, Oliveira RA, de Lange J. Biallelic BUB1 mutations cause microcephaly, developmental delay, and variable effects on cohesion and chromosome segregation. SCIENCE ADVANCES 2022; 8:eabk0114. [PMID: 35044816 PMCID: PMC8769543 DOI: 10.1126/sciadv.abk0114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Budding uninhibited by benzimidazoles (BUB1) contributes to multiple mitotic processes. Here, we describe the first two patients with biallelic BUB1 germline mutations, who both display microcephaly, intellectual disability, and several patient-specific features. The identified mutations cause variable degrees of reduced total protein level and kinase activity, leading to distinct mitotic defects. Both patients’ cells show prolonged mitosis duration, chromosome segregation errors, and an overall functional spindle assembly checkpoint. However, while BUB1 levels mostly affect BUBR1 kinetochore recruitment, impaired kinase activity prohibits centromeric recruitment of Aurora B, SGO1, and TOP2A, correlating with anaphase bridges, aneuploidy, and defective sister chromatid cohesion. We do not observe accelerated cohesion fatigue. We hypothesize that unresolved DNA catenanes increase cohesion strength, with concomitant increase in anaphase bridges. In conclusion, BUB1 mutations cause a neurodevelopmental disorder, with clinical and cellular phenotypes that partially resemble previously described syndromes, including autosomal recessive primary microcephaly, mosaic variegated aneuploidy, and cohesinopathies.
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Affiliation(s)
- Sara Carvalhal
- Instituto Gulbenkian de Ciência, R. Q.ta Grande 6, 2780-156 Oeiras, Portugal
- Algarve Biomedical Center Research Institute, Universidade do Algarve, 8005-139 Faro, Portugal
- Centre for Biomedical Research, Universidade do Algarve, 8005-139 Faro, Portugal
| | - Ingrid Bader
- Unit of Clinical Genetics, Paracelsus Medical University, Salzburg, Austria
| | - Martin A. Rooimans
- Cancer Center Amsterdam, Amsterdam University Medical Centers, Oncogenetics Section, De Boelelaan 1118, 1081 HV Amsterdam, Netherlands
| | - Anneke B. Oostra
- Cancer Center Amsterdam, Amsterdam University Medical Centers, Oncogenetics Section, De Boelelaan 1118, 1081 HV Amsterdam, Netherlands
| | - Jesper A. Balk
- Cancer Center Amsterdam, Amsterdam University Medical Centers, Oncogenetics Section, De Boelelaan 1118, 1081 HV Amsterdam, Netherlands
| | - René G. Feichtinger
- Department of Pediatrics, University Hospital Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Christine Beichler
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Michael R. Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Johanna M. van Hagen
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, Netherlands
| | - Quinten Waisfisz
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, Netherlands
| | - Mieke van Haelst
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, Netherlands
| | - Martijn Bruijn
- Northwest Clinics, Wilhelminalaan 12, 1815 JD Alkmaar, Netherlands
| | - Alexandra Tavares
- Instituto Gulbenkian de Ciência, R. Q.ta Grande 6, 2780-156 Oeiras, Portugal
| | - Johannes A. Mayr
- Department of Pediatrics, University Hospital Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Rob M. F. Wolthuis
- Cancer Center Amsterdam, Amsterdam University Medical Centers, Oncogenetics Section, De Boelelaan 1118, 1081 HV Amsterdam, Netherlands
| | - Raquel A. Oliveira
- Instituto Gulbenkian de Ciência, R. Q.ta Grande 6, 2780-156 Oeiras, Portugal
- Corresponding author. (R.A.O.); (J.d.L.)
| | - Job de Lange
- Cancer Center Amsterdam, Amsterdam University Medical Centers, Oncogenetics Section, De Boelelaan 1118, 1081 HV Amsterdam, Netherlands
- Corresponding author. (R.A.O.); (J.d.L.)
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10
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van Schie JJM, de Lange J. The Interplay of Cohesin and the Replisome at Processive and Stressed DNA Replication Forks. Cells 2021; 10:3455. [PMID: 34943967 PMCID: PMC8700348 DOI: 10.3390/cells10123455] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 12/12/2022] Open
Abstract
The cohesin complex facilitates faithful chromosome segregation by pairing the sister chromatids after DNA replication until mitosis. In addition, cohesin contributes to proficient and error-free DNA replication. Replisome progression and establishment of sister chromatid cohesion are intimately intertwined processes. Here, we review how the key factors in DNA replication and cohesion establishment cooperate in unperturbed conditions and during DNA replication stress. We discuss the detailed molecular mechanisms of cohesin recruitment and the entrapment of replicated sister chromatids at the replisome, the subsequent stabilization of sister chromatid cohesion via SMC3 acetylation, as well as the role and regulation of cohesin in the response to DNA replication stress.
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Affiliation(s)
- Janne J. M. van Schie
- Cancer Center Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Job de Lange
- Cancer Center Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
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11
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Bailey ML, Tieu D, Habsid A, Tong AHY, Chan K, Moffat J, Hieter P. Paralogous synthetic lethality underlies genetic dependencies of the cancer-mutated gene STAG2. Life Sci Alliance 2021; 4:e202101083. [PMID: 34462321 PMCID: PMC8408347 DOI: 10.26508/lsa.202101083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/14/2021] [Accepted: 08/16/2021] [Indexed: 12/14/2022] Open
Abstract
STAG2, a component of the mitotically essential cohesin complex, is highly mutated in several different tumour types, including glioblastoma and bladder cancer. Whereas cohesin has roles in many cancer-related pathways, such as chromosome instability, DNA repair and gene expression, the complex nature of cohesin function has made it difficult to determine how STAG2 loss might either promote tumorigenesis or be leveraged therapeutically across divergent cancer types. Here, we have performed whole-genome CRISPR-Cas9 screens for STAG2-dependent genetic interactions in three distinct cellular backgrounds. Surprisingly, STAG1, the paralog of STAG2, was the only negative genetic interaction that was shared across all three backgrounds. We also uncovered a paralogous synthetic lethal mechanism behind a genetic interaction between STAG2 and the iron regulatory gene IREB2 Finally, investigation of an unusually strong context-dependent genetic interaction in HAP1 cells revealed factors that could be important for alleviating cohesin loading stress. Together, our results reveal new facets of STAG2 and cohesin function across a variety of genetic contexts.
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Affiliation(s)
- Melanie L Bailey
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - David Tieu
- Donnelly Centre, University of Toronto, Toronto, Canada
| | - Andrea Habsid
- Donnelly Centre, University of Toronto, Toronto, Canada
| | | | | | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
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12
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Wassing IE, Graham E, Saayman X, Rampazzo L, Ralf C, Bassett A, Esashi F. The RAD51 recombinase protects mitotic chromatin in human cells. Nat Commun 2021; 12:5380. [PMID: 34508092 PMCID: PMC8433380 DOI: 10.1038/s41467-021-25643-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 08/19/2021] [Indexed: 11/09/2022] Open
Abstract
The RAD51 recombinase plays critical roles in safeguarding genome integrity, which is fundamentally important for all living cells. While interphase functions of RAD51 in maintaining genome stability are well-characterised, its role in mitosis remains contentious. In this study, we show that RAD51 protects under-replicated DNA in mitotic human cells and, in this way, promotes mitotic DNA synthesis (MiDAS) and successful chromosome segregation. In cells experiencing mild replication stress, MiDAS was detected irrespective of mitotically generated DNA damage. MiDAS broadly required de novo RAD51 recruitment to single-stranded DNA, which was supported by the phosphorylation of RAD51 by the key mitotic regulator Polo-like kinase 1. Importantly, acute inhibition of MiDAS delayed anaphase onset and induced centromere fragility, suggesting a mechanism that prevents the satisfaction of the spindle assembly checkpoint while chromosomal replication remains incomplete. This study hence identifies an unexpected function of RAD51 in promoting genomic stability in mitosis.
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Affiliation(s)
- Isabel E Wassing
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Emily Graham
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Xanita Saayman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Lucia Rampazzo
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Christine Ralf
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Fumiko Esashi
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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13
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Schuck PL, Ball LE, Stewart JA. The DNA-binding protein CST associates with the cohesin complex and promotes chromosome cohesion. J Biol Chem 2021; 297:101026. [PMID: 34339741 PMCID: PMC8390553 DOI: 10.1016/j.jbc.2021.101026] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/22/2021] [Accepted: 07/29/2021] [Indexed: 01/26/2023] Open
Abstract
Sister chromatid cohesion (SCC), the pairing of sister chromatids after DNA replication until mitosis, is established by loading of the cohesin complex on newly replicated chromatids. Cohesin must then be maintained until mitosis to prevent segregation defects and aneuploidy. However, how SCC is established and maintained until mitosis remains incompletely understood, and emerging evidence suggests that replication stress may lead to premature SCC loss. Here, we report that the ssDNA-binding protein CTC1-STN1-TEN1 (CST) aids in SCC. CST primarily functions in telomere length regulation but also has known roles in replication restart and DNA repair. After depletion of CST subunits, we observed an increase in the complete loss of SCC. In addition, we determined that CST associates with the cohesin complex. Unexpectedly, we did not find evidence of altered cohesin loading or mitotic progression in the absence of CST; however, we did find that treatment with various replication inhibitors increased the association between CST and cohesin. Because replication stress was recently shown to induce SCC loss, we hypothesized that CST may be required to maintain or remodel SCC after DNA replication fork stalling. In agreement with this idea, SCC loss was greatly increased in CST-depleted cells after exogenous replication stress. Based on our findings, we propose that CST aids in the maintenance of SCC at stalled replication forks to prevent premature cohesion loss.
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Affiliation(s)
- P Logan Schuck
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
| | - Lauren E Ball
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Jason A Stewart
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA.
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14
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Jann JC, Tothova Z. Cohesin mutations in myeloid malignancies. Blood 2021; 138:649-661. [PMID: 34157074 PMCID: PMC8394903 DOI: 10.1182/blood.2019004259] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 05/24/2021] [Indexed: 12/25/2022] Open
Abstract
Cohesin is a multisubunit protein complex that forms a ring-like structure around DNA. It is essential for sister chromatid cohesion, chromatin organization, transcriptional regulation, and DNA damage repair and plays a major role in dynamically shaping the genome architecture and maintaining DNA integrity. The core complex subunits STAG2, RAD21, SMC1, and SMC3, as well as its modulators PDS5A/B, WAPL, and NIPBL, have been found to be recurrently mutated in hematologic and solid malignancies. These mutations are found across the full spectrum of myeloid neoplasia, including pediatric Down syndrome-associated acute megakaryoblastic leukemia, myelodysplastic syndromes, chronic myelomonocytic leukemia, and de novo and secondary acute myeloid leukemias. The mechanisms by which cohesin mutations act as drivers of clonal expansion and disease progression are still poorly understood. Recent studies have described the impact of cohesin alterations on self-renewal and differentiation of hematopoietic stem and progenitor cells, which are associated with changes in chromatin and epigenetic state directing lineage commitment, as well as genomic integrity. Herein, we review the role of the cohesin complex in healthy and malignant hematopoiesis. We discuss clinical implications of cohesin mutations in myeloid malignancies and discuss opportunities for therapeutic targeting.
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Affiliation(s)
- Johann-Christoph Jann
- Department of Hematology and Oncology, University of Heidelberg, Mannheim, Germany; and
| | - Zuzana Tothova
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
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15
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Schimmel J, Muñoz-Subirana N, Kool H, van Schendel R, Tijsterman M. Small tandem DNA duplications result from CST-guided Pol α-primase action at DNA break termini. Nat Commun 2021; 12:4843. [PMID: 34376693 PMCID: PMC8355091 DOI: 10.1038/s41467-021-25154-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 07/20/2021] [Indexed: 12/11/2022] Open
Abstract
Small tandem duplications of DNA occur frequently in the human genome and are implicated in the aetiology of certain human cancers. Recent studies have suggested that DNA double-strand breaks are causal to this mutational class, but the underlying mechanism remains elusive. Here, we identify a crucial role for DNA polymerase α (Pol α)-primase in tandem duplication formation at breaks having complementary 3′ ssDNA protrusions. By including so-called primase deserts in CRISPR/Cas9-induced DNA break configurations, we reveal that fill-in synthesis preferentially starts at the 3′ tip, and find this activity to be dependent on 53BP1, and the CTC1-STN1-TEN1 (CST) and Shieldin complexes. This axis generates near-blunt ends specifically at DNA breaks with 3′ overhangs, which are subsequently repaired by non-homologous end-joining. Our study provides a mechanistic explanation for a mutational signature abundantly observed in the genomes of species and cancer cells. Error-prone repair of DNA double-strand breaks have been implied to cause cancer-associated genome alterations, but the mechanism of their formation remains unclear. Here the authors find that DNA polymerase α primase plays part in tandem duplication formation at CRISPR/Cas9-induced complementary 3′ ssDNA protrusions.
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Affiliation(s)
- Joost Schimmel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Núria Muñoz-Subirana
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hanneke Kool
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands. .,Institute of Biology Leiden, Leiden University, Leiden, The Netherlands.
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16
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Zanotti S, Vanhauwaert S, Van Neste C, Olexiouk V, Van Laere J, Verschuuren M, Van der Meulen J, Mus LM, Durinck K, Tilleman L, Deforce D, Van Nieuwerburgh F, Hogarty MD, Decaesteker B, De Vos WH, Speleman F. MYCN-induced nucleolar stress drives an early senescence-like transcriptional program in hTERT-immortalized RPE cells. Sci Rep 2021; 11:14454. [PMID: 34262099 PMCID: PMC8280219 DOI: 10.1038/s41598-021-93863-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/01/2021] [Indexed: 12/25/2022] Open
Abstract
MYCN is an oncogenic driver in neural crest-derived neuroblastoma and medulloblastoma. To better understand the early effects of MYCN activation in a neural-crest lineage context, we profiled the transcriptome of immortalized human retina pigment epithelial cells with inducible MYCN activation. Gene signatures associated with elevated MYC/MYCN activity were induced after 24 h of MYCN activation, which attenuated but sustained at later time points. Unexpectedly, MYCN activation was accompanied by reduced cell growth. Gene set enrichment analysis revealed a senescence-like signature with strong induction of p53 and p21 but in the absence of canonical hallmarks of senescence such as β-galactosidase positivity, suggesting incomplete cell fate commitment. When scrutinizing the putative drivers of this growth attenuation, differential gene expression analysis identified several regulators of nucleolar stress. This process was also reflected by phenotypic correlates such as cytoplasmic granule accrual and nucleolar coalescence. Hence, we propose that the induction of MYCN congests the translational machinery, causing nucleolar stress and driving cells into a transient pre-senescent state. Our findings shed new light on the early events induced by MYCN activation and may help unravelling which factors are required for cells to tolerate unscheduled MYCN overexpression during early malignant transformation.
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Affiliation(s)
- Sofia Zanotti
- Laboratory of Cell Biology and Histology, Dept. Veterinary Sciences, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium.,Center for Medical Genetics, Dept. Biomolecular Medicine, Ghent University, Medical Research Building (MRB), 2nd Floor, Entrance 34, Corneel Heymanslaan 10, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, 9000, Ghent, Belgium
| | - Suzanne Vanhauwaert
- Center for Medical Genetics, Dept. Biomolecular Medicine, Ghent University, Medical Research Building (MRB), 2nd Floor, Entrance 34, Corneel Heymanslaan 10, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, 9000, Ghent, Belgium
| | - Christophe Van Neste
- Center for Medical Genetics, Dept. Biomolecular Medicine, Ghent University, Medical Research Building (MRB), 2nd Floor, Entrance 34, Corneel Heymanslaan 10, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, 9000, Ghent, Belgium
| | - Volodimir Olexiouk
- Center for Medical Genetics, Dept. Biomolecular Medicine, Ghent University, Medical Research Building (MRB), 2nd Floor, Entrance 34, Corneel Heymanslaan 10, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, 9000, Ghent, Belgium
| | - Jolien Van Laere
- Center for Medical Genetics, Dept. Biomolecular Medicine, Ghent University, Medical Research Building (MRB), 2nd Floor, Entrance 34, Corneel Heymanslaan 10, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, 9000, Ghent, Belgium
| | - Marlies Verschuuren
- Laboratory of Cell Biology and Histology, Dept. Veterinary Sciences, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Joni Van der Meulen
- Center for Medical Genetics, Dept. Biomolecular Medicine, Ghent University, Medical Research Building (MRB), 2nd Floor, Entrance 34, Corneel Heymanslaan 10, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, 9000, Ghent, Belgium.,Molecular Diagnostic, Ghent University, 9000, Ghent, Belgium
| | - Liselot M Mus
- Center for Medical Genetics, Dept. Biomolecular Medicine, Ghent University, Medical Research Building (MRB), 2nd Floor, Entrance 34, Corneel Heymanslaan 10, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, 9000, Ghent, Belgium.,Bioresource Center Ghent, Health, Innovation and Research Center, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Kaat Durinck
- Center for Medical Genetics, Dept. Biomolecular Medicine, Ghent University, Medical Research Building (MRB), 2nd Floor, Entrance 34, Corneel Heymanslaan 10, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, 9000, Ghent, Belgium
| | - Laurentijn Tilleman
- Cancer Research Institute Ghent (CRIG), Ghent University, 9000, Ghent, Belgium.,Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Dieter Deforce
- Cancer Research Institute Ghent (CRIG), Ghent University, 9000, Ghent, Belgium.,Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Cancer Research Institute Ghent (CRIG), Ghent University, 9000, Ghent, Belgium.,Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Michael D Hogarty
- Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Bieke Decaesteker
- Center for Medical Genetics, Dept. Biomolecular Medicine, Ghent University, Medical Research Building (MRB), 2nd Floor, Entrance 34, Corneel Heymanslaan 10, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, 9000, Ghent, Belgium
| | - Winnok H De Vos
- Laboratory of Cell Biology and Histology, Dept. Veterinary Sciences, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Dept. Biomolecular Medicine, Ghent University, Medical Research Building (MRB), 2nd Floor, Entrance 34, Corneel Heymanslaan 10, 9000, Ghent, Belgium. .,Cancer Research Institute Ghent (CRIG), Ghent University, 9000, Ghent, Belgium.
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17
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Antony J, Chin CV, Horsfield JA. Cohesin Mutations in Cancer: Emerging Therapeutic Targets. Int J Mol Sci 2021; 22:6788. [PMID: 34202641 PMCID: PMC8269296 DOI: 10.3390/ijms22136788] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/08/2021] [Accepted: 06/18/2021] [Indexed: 12/12/2022] Open
Abstract
The cohesin complex is crucial for mediating sister chromatid cohesion and for hierarchal three-dimensional organization of the genome. Mutations in cohesin genes are present in a range of cancers. Extensive research over the last few years has shown that cohesin mutations are key events that contribute to neoplastic transformation. Cohesin is involved in a range of cellular processes; therefore, the impact of cohesin mutations in cancer is complex and can be cell context dependent. Candidate targets with therapeutic potential in cohesin mutant cells are emerging from functional studies. Here, we review emerging targets and pharmacological agents that have therapeutic potential in cohesin mutant cells.
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Affiliation(s)
- Jisha Antony
- Department of Pathology, Otago Medical School, University of Otago, Dunedin 9016, New Zealand;
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
| | - Chue Vin Chin
- Department of Pathology, Otago Medical School, University of Otago, Dunedin 9016, New Zealand;
| | - Julia A. Horsfield
- Department of Pathology, Otago Medical School, University of Otago, Dunedin 9016, New Zealand;
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
- Genetics Otago Research Centre, University of Otago, Dunedin 9016, New Zealand
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18
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ELOF1 is a transcription-coupled DNA repair factor that directs RNA polymerase II ubiquitylation. Nat Cell Biol 2021; 23:595-607. [PMID: 34108663 PMCID: PMC8890769 DOI: 10.1038/s41556-021-00688-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 04/26/2021] [Indexed: 02/05/2023]
Abstract
Cells employ transcription-coupled repair (TCR) to eliminate transcription-blocking DNA lesions. DNA damage-induced binding of the TCR-specific repair factor CSB to RNA polymerase II (RNAPII) triggers RNAPII ubiquitylation of a single lysine (K1268) by the CRL4CSA ubiquitin ligase. How CRL4CSA is specifically directed towards K1268 is unknown. Here, we identify ELOF1 as the missing link that facilitates RNAPII ubiquitylation, a key signal for the assembly of downstream repair factors. This function requires its constitutive interaction with RNAPII close to K1268, revealing ELOF1 as a specificity factor that binds and positions CRL4CSA for optimal RNAPII ubiquitylation. Drug-genetic interaction screening also revealed a CSB-independent pathway in which ELOF1 prevents R-loops in active genes and protects cells against DNA replication stress. Our study offers key insights into the molecular mechanisms of TCR and provides a genetic framework of the interplay between transcriptional stress responses and DNA replication.
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19
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Rittenhouse NL, Carico ZM, Liu YF, Stefan HC, Arruda NL, Zhou J, Dowen JM. Functional impact of cancer-associated cohesin variants on gene expression and cellular identity. Genetics 2021; 217:iyab025. [PMID: 33704438 PMCID: PMC8049558 DOI: 10.1093/genetics/iyab025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 02/08/2021] [Indexed: 01/06/2023] Open
Abstract
Cohesin is a ring-shaped protein complex that controls dynamic chromosome structure. Cohesin activity is important for a variety of biological processes, including formation of DNA loops that regulate gene expression. The precise mechanisms by which cohesin shapes local chromosome structure and gene expression are not fully understood. Recurrent mutations in cohesin complex members have been reported in various cancers, though it is not clear whether many cohesin sequence variants have phenotypes and contribute to disease. Here, we utilized CRISPR/Cas9 genome editing to introduce a variety of cohesin sequence variants into murine embryonic stem cells and investigate their molecular and cellular consequences. Some of the cohesin variants tested caused changes to transcription, including altered expression of gene encoding lineage-specifying developmental regulators. Altered gene expression was also observed at insulated neighborhoods, where cohesin-mediated DNA loops constrain potential interactions between genes and enhancers. Furthermore, some cohesin variants altered the proliferation rate and differentiation potential of murine embryonic stem cells. This study provides a functional comparison of cohesin variants found in cancer within an isogenic system, revealing the relative roles of various cohesin perturbations on gene expression and maintenance of cellular identity.
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Affiliation(s)
- Natalie L Rittenhouse
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zachary M Carico
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Cancer Epigenetics Training Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ying Frances Liu
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Holden C Stefan
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nicole L Arruda
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Junjie Zhou
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jill M Dowen
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Cancer Epigenetics Training Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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20
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Bolaños-Villegas P. The Role of Structural Maintenance of Chromosomes Complexes in Meiosis and Genome Maintenance: Translating Biomedical and Model Plant Research Into Crop Breeding Opportunities. FRONTIERS IN PLANT SCIENCE 2021; 12:659558. [PMID: 33868354 PMCID: PMC8044525 DOI: 10.3389/fpls.2021.659558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/15/2021] [Indexed: 06/06/2023]
Abstract
Cohesin is a multi-unit protein complex from the structural maintenance of chromosomes (SMC) family, required for holding sister chromatids together during mitosis and meiosis. In yeast, the cohesin complex entraps sister DNAs within tripartite rings created by pairwise interactions between the central ring units SMC1 and SMC3 and subunits such as the α-kleisin SCC1 (REC8/SYN1 in meiosis). The complex is an indispensable regulator of meiotic recombination in eukaryotes. In Arabidopsis and maize, the SMC1/SMC3 heterodimer is a key determinant of meiosis. In Arabidopsis, several kleisin proteins are also essential: SYN1/REC8 is meiosis-specific and is essential for double-strand break repair, whereas AtSCC2 is a subunit of the cohesin SCC2/SCC4 loading complex that is important for synapsis and segregation. Other important meiotic subunits are the cohesin EXTRA SPINDLE POLES (AESP1) separase, the acetylase ESTABLISHMENT OF COHESION 1/CHROMOSOME TRANSMISSION FIDELITY 7 (ECO1/CTF7), the cohesion release factor WINGS APART-LIKE PROTEIN 1 (WAPL) in Arabidopsis (AtWAPL1/AtWAPL2), and the WAPL antagonist AtSWITCH1/DYAD (AtSWI1). Other important complexes are the SMC5/SMC6 complex, which is required for homologous DNA recombination during the S-phase and for proper meiotic synapsis, and the condensin complexes, featuring SMC2/SMC4 that regulate proper clustering of rDNA arrays during interphase. Meiotic recombination is the key to enrich desirable traits in commercial plant breeding. In this review, I highlight critical advances in understanding plant chromatid cohesion in the model plant Arabidopsis and crop plants and suggest how manipulation of crossover formation during meiosis, somatic DNA repair and chromosome folding may facilitate transmission of desirable alleles, tolerance to radiation, and enhanced transcription of alleles that regulate sexual development. I hope that these findings highlight opportunities for crop breeding.
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Affiliation(s)
- Pablo Bolaños-Villegas
- Fabio Baudrit Agricultural Research Station, University of Costa Rica, Alajuela, Costa Rica
- Lankester Botanical Garden, University of Costa Rica, Cartago, Costa Rica
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21
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Su XA, Ma D, Parsons JV, Replogle JM, Amatruda JF, Whittaker CA, Stegmaier K, Amon A. RAD21 is a driver of chromosome 8 gain in Ewing sarcoma to mitigate replication stress. Genes Dev 2021; 35:556-572. [PMID: 33766983 PMCID: PMC8015718 DOI: 10.1101/gad.345454.120] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 02/25/2021] [Indexed: 01/08/2023]
Abstract
In this study, Su et al. investigate why ∼50% of Ewing sarcomas, driven by the EWS-FLI1 fusion oncogene, harbor chromosome 8 gains. Using an evolution approach, they show that trisomy 8 mitigates EWS-FLI1-induced replication stress through gain of a copy of RAD21, and deleting one copy of RAD21 in trisomy 8 cells largely neutralizes the fitness benefit of chromosome 8 gain and reduces tumorgenicity of a Ewing sarcoma cancer cell line in soft agar assays. Aneuploidy, defined as whole-chromosome gain or loss, causes cellular stress but, paradoxically, is a frequent occurrence in cancers. Here, we investigate why ∼50% of Ewing sarcomas, driven by the EWS-FLI1 fusion oncogene, harbor chromosome 8 gains. Expression of the EWS-FLI1 fusion in primary cells causes replication stress that can result in cellular senescence. Using an evolution approach, we show that trisomy 8 mitigates EWS-FLI1-induced replication stress through gain of a copy of RAD21. Low-level ectopic expression of RAD21 is sufficient to dampen replication stress and improve proliferation in EWS-FLI1-expressing cells. Conversely, deleting one copy in trisomy 8 cells largely neutralizes the fitness benefit of chromosome 8 gain and reduces tumorgenicity of a Ewing sarcoma cancer cell line in soft agar assays. We propose that RAD21 promotes tumorigenesis through single gene copy gain. Such genes may explain some recurrent aneuploidies in cancer.
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Affiliation(s)
- Xiaofeng A Su
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Duanduan Ma
- The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility, Swanson Biotechnology Center, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - James V Parsons
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - John M Replogle
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - James F Amatruda
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Charles A Whittaker
- The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility, Swanson Biotechnology Center, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Angelika Amon
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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22
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Boavida A, Santos D, Mahtab M, Pisani FM. Functional Coupling between DNA Replication and Sister Chromatid Cohesion Establishment. Int J Mol Sci 2021; 22:2810. [PMID: 33802105 PMCID: PMC8001024 DOI: 10.3390/ijms22062810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 02/26/2021] [Accepted: 03/04/2021] [Indexed: 12/28/2022] Open
Abstract
Several lines of evidence suggest the existence in the eukaryotic cells of a tight, yet largely unexplored, connection between DNA replication and sister chromatid cohesion. Tethering of newly duplicated chromatids is mediated by cohesin, an evolutionarily conserved hetero-tetrameric protein complex that has a ring-like structure and is believed to encircle DNA. Cohesin is loaded onto chromatin in telophase/G1 and converted into a cohesive state during the subsequent S phase, a process known as cohesion establishment. Many studies have revealed that down-regulation of a number of DNA replication factors gives rise to chromosomal cohesion defects, suggesting that they play critical roles in cohesion establishment. Conversely, loss of cohesin subunits (and/or regulators) has been found to alter DNA replication fork dynamics. A critical step of the cohesion establishment process consists in cohesin acetylation, a modification accomplished by dedicated acetyltransferases that operate at the replication forks. Defects in cohesion establishment give rise to chromosome mis-segregation and aneuploidy, phenotypes frequently observed in pre-cancerous and cancerous cells. Herein, we will review our present knowledge of the molecular mechanisms underlying the functional link between DNA replication and cohesion establishment, a phenomenon that is unique to the eukaryotic organisms.
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Affiliation(s)
- Ana Boavida
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (A.B.); (D.S.); (M.M.)
| | - Diana Santos
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (A.B.); (D.S.); (M.M.)
| | - Mohammad Mahtab
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (A.B.); (D.S.); (M.M.)
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Francesca M. Pisani
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (A.B.); (D.S.); (M.M.)
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23
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Tothova Z, Valton AL, Gorelov RA, Vallurupalli M, Krill-Burger JM, Holmes A, Landers CC, Haydu JE, Malolepsza E, Hartigan C, Donahue M, Popova KD, Koochaki S, Venev SV, Rivera J, Chen E, Lage K, Schenone M, D’Andrea AD, Carr SA, Morgan EA, Dekker J, Ebert BL. Cohesin mutations alter DNA damage repair and chromatin structure and create therapeutic vulnerabilities in MDS/AML. JCI Insight 2021; 6:142149. [PMID: 33351783 PMCID: PMC7934867 DOI: 10.1172/jci.insight.142149] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/16/2020] [Indexed: 12/26/2022] Open
Abstract
The cohesin complex plays an essential role in chromosome maintenance and transcriptional regulation. Recurrent somatic mutations in the cohesin complex are frequent genetic drivers in cancer, including myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). Here, using genetic dependency screens of stromal antigen 2-mutant (STAG2-mutant) AML, we identified DNA damage repair and replication as genetic dependencies in cohesin-mutant cells. We demonstrated increased levels of DNA damage and sensitivity of cohesin-mutant cells to poly(ADP-ribose) polymerase (PARP) inhibition. We developed a mouse model of MDS in which Stag2 mutations arose as clonal secondary lesions in the background of clonal hematopoiesis driven by tet methylcytosine dioxygenase 2 (Tet2) mutations and demonstrated selective depletion of cohesin-mutant cells with PARP inhibition in vivo. Finally, we demonstrated a shift from STAG2- to STAG1-containing cohesin complexes in cohesin-mutant cells, which was associated with longer DNA loop extrusion, more intermixing of chromatin compartments, and increased interaction with PARP and replication protein A complex. Our findings inform the biology and therapeutic opportunities for cohesin-mutant malignancies.
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MESH Headings
- Animals
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Line, Tumor
- Chromatin/genetics
- Chromatin/metabolism
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- DNA Damage
- DNA Repair/genetics
- Disease Models, Animal
- Female
- Humans
- K562 Cells
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Inbred NOD
- Mice, Mutant Strains
- Mice, SCID
- Mice, Transgenic
- Mutation
- Myelodysplastic Syndromes/drug therapy
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/metabolism
- Nuclear Proteins/genetics
- Phthalazines/pharmacology
- Poly(ADP-ribose) Polymerase Inhibitors/pharmacology
- U937 Cells
- Xenograft Model Antitumor Assays
- Cohesins
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Affiliation(s)
- Zuzana Tothova
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Anne-Laure Valton
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | | | - Mounica Vallurupalli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
| | | | - Amie Holmes
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - J. Erika Haydu
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
| | | | | | - Melanie Donahue
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
| | | | - Sebastian Koochaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Sergey V. Venev
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jeanne Rivera
- Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Edwin Chen
- Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Kasper Lage
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Monica Schenone
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Alan D. D’Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Steven A. Carr
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Elizabeth A. Morgan
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Cancer Program, Broad Institute, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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24
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Glykofridis IE, Knol JC, Balk JA, Westland D, Pham TV, Piersma SR, Lougheed SM, Derakhshan S, Veen P, Rooimans MA, van Mil SE, Böttger F, Poddighe PJ, van de Beek I, Drost J, Zwartkruis FJ, de Menezes RX, Meijers-Heijboer HE, Houweling AC, Jimenez CR, Wolthuis RM. Loss of FLCN-FNIP1/2 induces a non-canonical interferon response in human renal tubular epithelial cells. eLife 2021; 10:61630. [PMID: 33459596 PMCID: PMC7899648 DOI: 10.7554/elife.61630] [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: 07/31/2020] [Accepted: 01/16/2021] [Indexed: 12/14/2022] Open
Abstract
Germline mutations in the Folliculin (FLCN) tumor suppressor gene cause Birt–Hogg–Dubé (BHD) syndrome, a rare autosomal dominant disorder predisposing carriers to kidney tumors. FLCN is a conserved, essential gene linked to diverse cellular processes but the mechanism by which FLCN prevents kidney cancer remains unknown. Here, we show that disrupting FLCN in human renal tubular epithelial cells (RPTEC/TERT1) activates TFE3, upregulating expression of its E-box targets, including RRAGD and GPNMB, without modifying mTORC1 activity. Surprisingly, the absence of FLCN or its binding partners FNIP1/FNIP2 induces interferon response genes independently of interferon. Mechanistically, FLCN loss promotes STAT2 recruitment to chromatin and slows cellular proliferation. Our integrated analysis identifies STAT1/2 signaling as a novel target of FLCN in renal cells and BHD tumors. STAT1/2 activation appears to counterbalance TFE3-directed hyper-proliferation and may influence immune responses. These findings shed light on unique roles of FLCN in human renal tumorigenesis and pinpoint candidate prognostic biomarkers.
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Affiliation(s)
- Iris E Glykofridis
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Jaco C Knol
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Jesper A Balk
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Denise Westland
- University Medical Center Utrecht, Center for Molecular Medicine, Molecular Cancer Research, Universiteitsweg, Utrecht, Netherlands
| | - Thang V Pham
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Sander R Piersma
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Sinéad M Lougheed
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Sepide Derakhshan
- Princess Máxima Center for Pediatric Oncology, Oncode Institute, Heidelberglaan, Utrecht, Netherlands
| | - Puck Veen
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Martin A Rooimans
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Saskia E van Mil
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Franziska Böttger
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Pino J Poddighe
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Amsterdam, Netherlands
| | - Irma van de Beek
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Amsterdam, Netherlands
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Oncode Institute, Heidelberglaan, Utrecht, Netherlands
| | - Fried Jt Zwartkruis
- University Medical Center Utrecht, Center for Molecular Medicine, Molecular Cancer Research, Universiteitsweg, Utrecht, Netherlands
| | | | - Hanne Ej Meijers-Heijboer
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Arjan C Houweling
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Amsterdam, Netherlands
| | - Connie R Jimenez
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Rob Mf Wolthuis
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, Amsterdam, Netherlands
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25
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Idilli AI, Pazzi C, dal Pozzolo F, Roccuzzo M, Mione MC. Rad21 Haploinsufficiency Prevents ALT-Associated Phenotypes in Zebrafish Brain Tumors. Genes (Basel) 2020; 11:E1442. [PMID: 33266037 PMCID: PMC7760354 DOI: 10.3390/genes11121442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 01/17/2023] Open
Abstract
Cohesin is a protein complex consisting of four core subunits responsible for sister chromatid cohesion in mitosis and meiosis, and for 3D genome organization and gene expression through the establishment of long distance interactions regulating transcriptional activity in the interphase. Both roles are important for telomere integrity, but the role of cohesin in telomere maintenance mechanisms in highly replicating cancer cells in vivo is poorly studied. Here we used a zebrafish model of brain tumor, which uses alternative lengthening of telomeres (ALT) as primary telomere maintenance mechanism to test whether haploinsufficiency for Rad21, a member of the cohesin ring, affects ALT development. We found that a reduction in Rad21 levels prevents ALT-associated phenotypes in zebrafish brain tumors and triggers an increase in tert expression. Despite the rescue of ALT phenotypes, tumor cells in rad21+/- fish exhibit an increase in DNA damage foci, probably due to a reduction in double-strand breaks repair efficiency.
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Affiliation(s)
- Aurora Irene Idilli
- Experimental Cancer Biology, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy; (A.I.I.); (C.P.); (F.d.P.)
| | - Cecilia Pazzi
- Experimental Cancer Biology, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy; (A.I.I.); (C.P.); (F.d.P.)
| | - Francesca dal Pozzolo
- Experimental Cancer Biology, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy; (A.I.I.); (C.P.); (F.d.P.)
| | - Michela Roccuzzo
- Advanced Imaging Facility, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy;
| | - Maria Caterina Mione
- Experimental Cancer Biology, Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, 38123 Trento, Italy; (A.I.I.); (C.P.); (F.d.P.)
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26
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Zuilkoski CM, Skibbens RV. PCNA antagonizes cohesin-dependent roles in genomic stability. PLoS One 2020; 15:e0235103. [PMID: 33075068 PMCID: PMC7571713 DOI: 10.1371/journal.pone.0235103] [Citation(s) in RCA: 4] [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: 06/07/2020] [Accepted: 10/04/2020] [Indexed: 12/23/2022] Open
Abstract
PCNA sliding clamp binds factors through which histone deposition, chromatin remodeling, and DNA repair are coupled to DNA replication. PCNA also directly binds Eco1/Ctf7 acetyltransferase, which in turn activates cohesins and establishes cohesion between nascent sister chromatids. While increased recruitment thus explains the mechanism through which elevated levels of chromatin-bound PCNA rescue eco1 mutant cell growth, the mechanism through which PCNA instead worsens cohesin mutant cell growth remains unknown. Possibilities include that elevated levels of long-lived chromatin-bound PCNA reduce either cohesin deposition onto DNA or cohesin acetylation. Instead, our results reveal that PCNA increases the levels of both chromatin-bound cohesin and cohesin acetylation. Beyond sister chromatid cohesion, PCNA also plays a critical role in genomic stability such that high levels of chromatin-bound PCNA elevate genotoxic sensitivities and recombination rates. At a relatively modest increase of chromatin-bound PCNA, however, fork stability and progression appear normal in wildtype cells. Our results reveal that even a moderate increase of PCNA indeed sensitizes cohesin mutant cells to DNA damaging agents and in a process that involves the DNA damage response kinase Mec1(ATR), but not Tel1(ATM). These and other findings suggest that PCNA mis-regulation results in genome instabilities that normally are resolved by cohesin. Elevating levels of chromatin-bound PCNA may thus help target cohesinopathic cells linked that are linked to cancer.
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Affiliation(s)
- Caitlin M. Zuilkoski
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Robert V. Skibbens
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
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27
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Abstract
Mutations of the cohesin complex in human cancer were first discovered ~10 years ago. Since then, researchers worldwide have demonstrated that cohesin is among the most commonly mutated protein complexes in cancer. Inactivating mutations in genes encoding cohesin subunits are common in bladder cancers, paediatric sarcomas, leukaemias, brain tumours and other cancer types. Also in those 10 years, the prevailing view of the functions of cohesin in cell biology has undergone a revolutionary transformation. Initially, the predominant view of cohesin was as a ring that encircled and cohered replicated chromosomes until its cleavage triggered the metaphase-to-anaphase transition. As such, early studies focused on the role of tumour-derived cohesin mutations in the fidelity of chromosome segregation and aneuploidy. However, over the past 5 years the cohesin field has shifted dramatically, and research now focuses on the primary role of cohesin in generating, maintaining and regulating the intra-chromosomal DNA looping events that modulate 3D genome organization and gene expression. This Review focuses on recent discoveries in the cohesin field that provide insight into the role of cohesin inactivation in cancer pathogenesis, and opportunities for exploiting these findings for the clinical benefit of patients with cohesin-mutant cancers.
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Affiliation(s)
- Todd Waldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC, USA.
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28
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van Schie JJM, Faramarz A, Balk JA, Stewart GS, Cantelli E, Oostra AB, Rooimans MA, Parish JL, de Almeida Estéves C, Dumic K, Barisic I, Diderich KEM, van Slegtenhorst MA, Mahtab M, Pisani FM, Te Riele H, Ameziane N, Wolthuis RMF, de Lange J. Warsaw Breakage Syndrome associated DDX11 helicase resolves G-quadruplex structures to support sister chromatid cohesion. Nat Commun 2020; 11:4287. [PMID: 32855419 PMCID: PMC7452896 DOI: 10.1038/s41467-020-18066-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/30/2020] [Indexed: 02/01/2023] Open
Abstract
Warsaw Breakage Syndrome (WABS) is a rare disorder related to cohesinopathies and Fanconi anemia, caused by bi-allelic mutations in DDX11. Here, we report multiple compound heterozygous WABS cases, each displaying destabilized DDX11 protein and residual DDX11 function at the cellular level. Patient-derived cell lines exhibit sensitivity to topoisomerase and PARP inhibitors, defective sister chromatid cohesion and reduced DNA replication fork speed. Deleting DDX11 in RPE1-TERT cells inhibits proliferation and survival in a TP53-dependent manner and causes chromosome breaks and cohesion defects, independent of the expressed pseudogene DDX12p. Importantly, G-quadruplex (G4) stabilizing compounds induce chromosome breaks and cohesion defects which are strongly aggravated by inactivation of DDX11 but not FANCJ. The DNA helicase domain of DDX11 is essential for sister chromatid cohesion and resistance to G4 stabilizers. We propose that DDX11 is a DNA helicase protecting against G4 induced double-stranded breaks and concomitant loss of cohesion, possibly at DNA replication forks.
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Affiliation(s)
- Janne J M van Schie
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Atiq Faramarz
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Jesper A Balk
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Erika Cantelli
- Netherlands Cancer Institute, Division of Tumor Biology and Immunology, Amsterdam, The Netherlands
| | - Anneke B Oostra
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Martin A Rooimans
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Joanna L Parish
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | | | - Katja Dumic
- Department of Pediatric Endocrinology and Diabetes, University Hospital Centre Zagreb, University of Zagreb Medical School, Zagreb, Croatia
| | - Ingeborg Barisic
- Children's Hospital Zagreb, Center of Excellence for Reproductive and Regenerative Medicine, Medical School University of Zagreb, Zagreb, Croatia
| | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Mohammad Mahtab
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Francesca M Pisani
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Hein Te Riele
- Netherlands Cancer Institute, Division of Tumor Biology and Immunology, Amsterdam, The Netherlands
| | - Najim Ameziane
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
- Centogene, Am Strande 7, 18055, Rostock, Germany
| | - Rob M F Wolthuis
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands.
| | - Job de Lange
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands.
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29
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Benedict B, van Bueren MA, van Gemert FP, Lieftink C, Guerrero Llobet S, van Vugt MA, Beijersbergen RL, Te Riele H. The RECQL helicase prevents replication fork collapse during replication stress. Life Sci Alliance 2020; 3:3/10/e202000668. [PMID: 32820027 PMCID: PMC7441523 DOI: 10.26508/lsa.202000668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 11/24/2022] Open
Abstract
Most tumors lack the G1/S phase checkpoint and are insensitive to antigrowth signals. Loss of G1/S control can severely perturb DNA replication as revealed by slow replication fork progression and frequent replication fork stalling. Cancer cells may thus rely on specific pathways that mitigate the deleterious consequences of replication stress. To identify vulnerabilities of cells suffering from replication stress, we performed an shRNA-based genetic screen. We report that the RECQL helicase is specifically essential in replication stress conditions and protects stalled replication forks against MRE11-dependent double strand break (DSB) formation. In line with these findings, knockdown of RECQL in different cancer cells increased the level of DNA DSBs. Thus, RECQL plays a critical role in sustaining DNA synthesis under conditions of replication stress and as such may represent a target for cancer therapy.
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Affiliation(s)
- Bente Benedict
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marit Ae van Bueren
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Frank Pa van Gemert
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sergi Guerrero Llobet
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marcel Atm van Vugt
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hein Te Riele
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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30
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Wilhelm T, Said M, Naim V. DNA Replication Stress and Chromosomal Instability: Dangerous Liaisons. Genes (Basel) 2020; 11:E642. [PMID: 32532049 PMCID: PMC7348713 DOI: 10.3390/genes11060642] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/04/2020] [Accepted: 06/08/2020] [Indexed: 12/16/2022] Open
Abstract
Chromosomal instability (CIN) is associated with many human diseases, including neurodevelopmental or neurodegenerative conditions, age-related disorders and cancer, and is a key driver for disease initiation and progression. A major source of structural chromosome instability (s-CIN) leading to structural chromosome aberrations is "replication stress", a condition in which stalled or slowly progressing replication forks interfere with timely and error-free completion of the S phase. On the other hand, mitotic errors that result in chromosome mis-segregation are the cause of numerical chromosome instability (n-CIN) and aneuploidy. In this review, we will discuss recent evidence showing that these two forms of chromosomal instability can be mechanistically interlinked. We first summarize how replication stress causes structural and numerical CIN, focusing on mechanisms such as mitotic rescue of replication stress (MRRS) and centriole disengagement, which prevent or contribute to specific types of structural chromosome aberrations and segregation errors. We describe the main outcomes of segregation errors and how micronucleation and aneuploidy can be the key stimuli promoting inflammation, senescence, or chromothripsis. At the end, we discuss how CIN can reduce cellular fitness and may behave as an anticancer barrier in noncancerous cells or precancerous lesions, whereas it fuels genomic instability in the context of cancer, and how our current knowledge may be exploited for developing cancer therapies.
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Affiliation(s)
- Therese Wilhelm
- CNRS UMR9019 Genome Integrity and Cancers, Université Paris Saclay, Gustave Roussy, 94805 Villejuif, France; (T.W.); (M.S.)
- UMR144 Cell Biology and Cancer, Institut Curie, 75005 Paris, France
| | - Maha Said
- CNRS UMR9019 Genome Integrity and Cancers, Université Paris Saclay, Gustave Roussy, 94805 Villejuif, France; (T.W.); (M.S.)
| | - Valeria Naim
- CNRS UMR9019 Genome Integrity and Cancers, Université Paris Saclay, Gustave Roussy, 94805 Villejuif, France; (T.W.); (M.S.)
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31
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Eksi SE, Saldivar JC. Cohesin Is Out for Stalled Replication Fork Restart. Dev Cell 2020; 52:675-676. [PMID: 32208158 DOI: 10.1016/j.devcel.2020.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Replication stress underlies many genomic alterations in cancer cells. In this issue of Developmental Cell, Benedict et al. show that WAPL-dependent cohesin removal is needed to restart DNA synthesis at stalled forks and promote survival following replication stress, uncovering an unexpected link between stress and sister chromatid cohesion loss.
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Affiliation(s)
- Sebnem Ece Eksi
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Joshua C Saldivar
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA.
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