1
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Rossetti GG, Dommann N, Karamichali A, Dionellis VS, Asensio Aldave A, Yarahmadov T, Rodriguez-Carballo E, Keogh A, Candinas D, Stroka D, Halazonetis TD. In vivo DNA replication dynamics unveil aging-dependent replication stress. Cell 2024:S0092-8674(24)00963-2. [PMID: 39293447 DOI: 10.1016/j.cell.2024.08.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 03/16/2024] [Accepted: 08/19/2024] [Indexed: 09/20/2024]
Abstract
The genome duplication program is affected by multiple factors in vivo, including developmental cues, genotoxic stress, and aging. Here, we monitored DNA replication initiation dynamics in regenerating livers of young and old mice after partial hepatectomy to investigate the impact of aging. In young mice, the origin firing sites were well defined; the majority were located 10-50 kb upstream or downstream of expressed genes, and their position on the genome was conserved in human cells. Old mice displayed the same replication initiation sites, but origin firing was inefficient and accompanied by a replication stress response. Inhibitors of the ATR checkpoint kinase fully restored origin firing efficiency in the old mice but at the expense of an inflammatory response and without significantly enhancing the fraction of hepatocytes entering the cell cycle. These findings unveil aging-dependent replication stress and a crucial role of ATR in mitigating the stress-associated inflammation, a hallmark of aging.
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Affiliation(s)
- Giacomo G Rossetti
- Department of Molecular and Cellular Biology, University of Geneva, Geneva 1205, Switzerland
| | - Noëlle Dommann
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Angeliki Karamichali
- Department of Molecular and Cellular Biology, University of Geneva, Geneva 1205, Switzerland
| | - Vasilis S Dionellis
- Department of Molecular and Cellular Biology, University of Geneva, Geneva 1205, Switzerland
| | - Ainhoa Asensio Aldave
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Tural Yarahmadov
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Adrian Keogh
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Daniel Candinas
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Deborah Stroka
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland.
| | - Thanos D Halazonetis
- Department of Molecular and Cellular Biology, University of Geneva, Geneva 1205, Switzerland.
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2
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Ahmed SMQ, Sasikumar J, Laha S, Das SP. Multifaceted role of the DNA replication protein MCM10 in maintaining genome stability and its implication in human diseases. Cancer Metastasis Rev 2024:10.1007/s10555-024-10209-3. [PMID: 39240414 DOI: 10.1007/s10555-024-10209-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 08/29/2024] [Indexed: 09/07/2024]
Abstract
MCM10 plays a vital role in genome duplication and is crucial for DNA replication initiation, elongation, and termination. It coordinates several proteins to assemble at the fork, form a functional replisome, trigger origin unwinding, and stabilize the replication bubble. MCM10 overexpression is associated with increased aggressiveness in breast, cervical, and several other cancers. Disruption of MCM10 leads to altered replication timing associated with initiation site gains and losses accompanied by genome instability. Knockdown of MCM10 affects the proliferation and migration of cancer cells, manifested by DNA damage and replication fork arrest, and has recently been shown to be associated with clinical conditions like CNKD and RCM. Loss of MCM10 function is associated with impaired telomerase activity, leading to the accumulation of abnormal replication forks and compromised telomere length. MCM10 interacts with histones, aids in nucleosome assembly, binds BRCA2 to maintain genome integrity during DNA damage, prevents lesion skipping, and inhibits PRIMPOL-mediated repriming. It also interacts with the fork reversal enzyme SMARCAL1 and inhibits fork regression. Additionally, MCM10 undergoes several post-translational modifications and contributes to transcriptional silencing by interacting with the SIR proteins. This review explores the mechanism associated with MCM10's multifaceted role in DNA replication initiation, chromatin organization, transcriptional silencing, replication stress, fork stability, telomere length maintenance, and DNA damage response. Finally, we discuss the role of MCM10 in the early detection of cancer, its prognostic significance, and its potential use in therapeutics for cancer treatment.
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Affiliation(s)
- Sumayyah M Q Ahmed
- Cell Biology and Molecular Genetics (CBMG), Yenepoya Research Centre (YRC), Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Jayaprakash Sasikumar
- Cell Biology and Molecular Genetics (CBMG), Yenepoya Research Centre (YRC), Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Suparna Laha
- Cell Biology and Molecular Genetics (CBMG), Yenepoya Research Centre (YRC), Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Shankar Prasad Das
- Cell Biology and Molecular Genetics (CBMG), Yenepoya Research Centre (YRC), Yenepoya (Deemed to be University), Mangalore, 575018, India.
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3
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Hatoyama Y, Islam M, Bond AG, Hayashi KI, Ciulli A, Kanemaki MT. Combination of AID2 and BromoTag expands the utility of degron-based protein knockdowns. EMBO Rep 2024; 25:4062-4077. [PMID: 39179892 PMCID: PMC11387839 DOI: 10.1038/s44319-024-00224-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 08/26/2024] Open
Abstract
Acute protein knockdown is a powerful approach to dissecting protein function in dynamic cellular processes. We previously reported an improved auxin-inducible degron system, AID2, but recently noted that its ability to induce degradation of some essential replication factors, such as ORC1 and CDC6, was not enough to induce lethality. Here, we present combinational degron technologies to control two proteins or enhance target depletion. For this purpose, we initially compare PROTAC-based degrons, dTAG and BromoTag, with AID2 to reveal their key features and then demonstrate control of cohesin and condensin with AID2 and BromoTag, respectively. We develop a double-degron system with AID2 and BromoTag to enhance target depletion and accelerate depletion kinetics and demonstrate that both ORC1 and CDC6 are pivotal for MCM loading. Finally, we show that co-depletion of ORC1 and CDC6 by the double-degron system completely suppresses DNA replication, and the cells enter mitosis with single-chromatid chromosomes, indicating that DNA replication is uncoupled from cell cycle control. Our combinational degron technologies will expand the application scope for functional analyses.
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Affiliation(s)
- Yuki Hatoyama
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Mishima, Shizuoka, 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Moutushi Islam
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Mishima, Shizuoka, 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Adam G Bond
- Centre for Targeted Protein Degradation, School of Life Science, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, Scotland, UK
| | - Ken-Ichiro Hayashi
- Department of Biochemistry, Okayama University of Science, Ridai-cho 1-1, Okayama, 700-0005, Japan
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Science, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, Scotland, UK
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Mishima, Shizuoka, 411-8540, Japan.
- Graduate Institute for Advanced Studies, SOKENDAI, Yata 1111, Mishima, Shizuoka, 411-8540, Japan.
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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4
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Falbo L, Técher H, Sannino V, Robusto M, Fagà G, Pezzimenti F, Romeo F, Colombo LG, Vultaggio S, Fancelli D, Monzani S, Cecatiello V, Pasqualato S, Varasi M, Mercurio C, Costanzo V. A high-throughput screening identifies MCM chromatin loading inhibitors targeting cells with increased replication origins. iScience 2024; 27:110567. [PMID: 39184446 PMCID: PMC11342271 DOI: 10.1016/j.isci.2024.110567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/25/2024] [Accepted: 07/18/2024] [Indexed: 08/27/2024] Open
Abstract
Replication origin assembly is a pivotal step in chromosomal DNA replication. In this process, the ORC complex binds DNA and, together with the CDC6 and CDT1, promotes the loading of the MCM helicase. Chemicals targeting origin assembly might be useful to sensitize highly proliferative cancer cells. However, identifying such compounds is challenging due to the multistage nature of this process. Here, using Xenopus laevis egg extract we set up a high-throughput screening to isolate MCM chromatin loading inhibitors, which led to the identification of NSC-95397 as a powerful inhibitor of replication origin assembly that targets CDC6 protein and promotes its degradation. Using systems developed to test selective drug-induced lethality we show that NSC-95397 triggers cell death both in human cells and Xenopus embryos that have higher proliferative ability. These findings demonstrate the effectiveness of molecules disrupting DNA replication processes in targeting hyperproliferating cells, highlighting their potential as anti-cancer molecules.
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Affiliation(s)
- Lucia Falbo
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, 20133 Milan, Italy
| | - Hervé Técher
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Vincenzo Sannino
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Michela Robusto
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Giovanni Fagà
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Francesco Romeo
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, 20133 Milan, Italy
| | | | | | - Daniele Fancelli
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Silvia Monzani
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, 20141 Milan, Italy
| | - Valentina Cecatiello
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, 20141 Milan, Italy
| | - Sebastiano Pasqualato
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, 20141 Milan, Italy
| | - Mario Varasi
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Ciro Mercurio
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Vincenzo Costanzo
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, 20133 Milan, Italy
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5
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Göder A, Maric CA, Rainey MD, O’Connor A, Cazzaniga C, Shamavu D, Cadoret JC, Santocanale C. DBF4, not DRF1, is the crucial regulator of CDC7 kinase at replication forks. J Cell Biol 2024; 223:e202402144. [PMID: 38865090 PMCID: PMC11169917 DOI: 10.1083/jcb.202402144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/02/2024] [Accepted: 05/04/2024] [Indexed: 06/13/2024] Open
Abstract
CDC7 kinase is crucial for DNA replication initiation and is involved in fork processing and replication stress response. Human CDC7 requires the binding of either DBF4 or DRF1 for its activity. However, it is unclear whether the two regulatory subunits target CDC7 to a specific set of substrates, thus having different biological functions, or if they act redundantly. Using genome editing technology, we generated isogenic cell lines deficient in either DBF4 or DRF1: these cells are viable but present signs of genomic instability, indicating that both can independently support CDC7 for bulk DNA replication. Nonetheless, DBF4-deficient cells show altered replication efficiency, partial deficiency in MCM helicase phosphorylation, and alterations in the replication timing of discrete genomic regions. Notably, we find that CDC7 function at replication forks is entirely dependent on DBF4 and not on DRF1. Thus, DBF4 is the primary regulator of CDC7 activity, mediating most of its functions in unperturbed DNA replication and upon replication interference.
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Affiliation(s)
- Anja Göder
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | | | - Michael D. Rainey
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Aisling O’Connor
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Chiara Cazzaniga
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Daniel Shamavu
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | | | - Corrado Santocanale
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
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6
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Mouery BL, Baker EM, Mei L, Wolff SC, Mills CA, Fleifel D, Mulugeta N, Herring LE, Cook JG. APC/C prevents a noncanonical order of cyclin/CDK activity to maintain CDK4/6 inhibitor-induced arrest. Proc Natl Acad Sci U S A 2024; 121:e2319574121. [PMID: 39024113 PMCID: PMC11287123 DOI: 10.1073/pnas.2319574121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/21/2024] [Indexed: 07/20/2024] Open
Abstract
Regulated cell cycle progression ensures homeostasis and prevents cancer. In proliferating cells, premature S phase entry is avoided by the E3 ubiquitin ligase anaphasepromoting complex/cyclosome (APC/C), although the APC/C substrates whose degradation restrains G1-S progression are not fully known. The APC/C is also active in arrested cells that exited the cell cycle, but it is not clear whether APC/C maintains all types of arrest. Here, by expressing the APC/C inhibitor, EMI1, we show that APC/C activity is essential to prevent S phase entry in cells arrested by pharmacological cyclin-dependent kinases 4 and 6 (CDK4/6) inhibition (Palbociclib). Thus, active protein degradation is required for arrest alongside repressed cell cycle gene expression. The mechanism of rapid and robust arrest bypass from inhibiting APC/C involves CDKs acting in an atypical order to inactivate retinoblastoma-mediated E2F repression. Inactivating APC/C first causes mitotic cyclin B accumulation which then promotes cyclin A expression. We propose that cyclin A is the key substrate for maintaining arrest because APC/C-resistant cyclin A, but not cyclin B, is sufficient to induce S phase entry. Cells bypassing arrest from CDK4/6 inhibition initiate DNA replication with severely reduced origin licensing. The simultaneous accumulation of S phase licensing inhibitors, such as cyclin A and geminin, with G1 licensing activators disrupts the normal order of G1-S progression. As a result, DNA synthesis and cell proliferation are profoundly impaired. Our findings predict that cancers with elevated EMI1 expression will tend to escape CDK4/6 inhibition into a premature, underlicensed S phase and suffer enhanced genome instability.
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Affiliation(s)
- Brandon L. Mouery
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Eliyambuya M. Baker
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY10021
| | - Liu Mei
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Samuel C. Wolff
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Computational Medicine Program, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Christine A. Mills
- University of North Carolina Proteomics Core Facility, Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Dalia Fleifel
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Nebyou Mulugeta
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Laura E. Herring
- University of North Carolina Proteomics Core Facility, Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Jeanette Gowen Cook
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
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7
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Lei KC, Srinivas N, Chandra M, Kervarrec T, Coyaud E, Spassova I, Peiffer L, Houben R, Shuda M, Hoffmann D, Schrama D, Becker JC. Merkel cell polyomavirus pan-T antigen knockdown reduces cancer cell stemness and promotes neural differentiation independent of RB1. J Med Virol 2024; 96:e29789. [PMID: 38988206 DOI: 10.1002/jmv.29789] [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: 01/29/2024] [Revised: 06/10/2024] [Accepted: 07/02/2024] [Indexed: 07/12/2024]
Abstract
Merkel cell carcinoma (MCC) is a highly aggressive skin cancer associated with integration of Merkel cell polyomavirus (MCPyV). MCPyV-encoded T-antigens (TAs) are pivotal for sustaining MCC's oncogenic phenotype, i.e., repression of TAs results in reactivation of the RB pathway and subsequent cell cycle arrest. However, the MCC cell line LoKe, characterized by a homozygous loss of the RB1 gene, exhibits uninterrupted cell cycle progression after shRNA-mediated TA repression. This unique feature allows an in-depth analysis of the effects of TAs beyond inhibition of the RB pathway, revealing the decrease in expression of stem cell-related genes upon panTA-knockdown. Analysis of gene regulatory networks identified members of the E2F family (E2F1, E2F8, TFDP1) as key transcriptional regulators that maintain stem cell properties in TA-expressing MCC cells. Furthermore, minichromosome maintenance (MCM) genes, which encodes DNA-binding licensing proteins essential for stem cell maintenance, were suppressed upon panTA-knockdown. The decline in stemness occurred simultaneously with neural differentiation, marked by the increased expression of neurogenesis-related genes such as neurexins, BTG2, and MYT1L. This upregulation can be attributed to heightened activity of PBX1 and BPTF, crucial regulators of neurogenesis pathways. The observations in LoKe were confirmed in an additional MCPyV-positive MCC cell line in which RB1 was silenced before panTA-knockdown. Moreover, spatially resolved transcriptomics demonstrated reduced TA expression in situ in a part of a MCC tumor characterized by neural differentiation. In summary, TAs are critical for maintaining stemness of MCC cells and suppressing neural differentiation, irrespective of their impact on the RB-signaling pathway.
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Affiliation(s)
- Kuan Cheok Lei
- German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Translational Skin Cancer Research, German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Nalini Srinivas
- German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Translational Skin Cancer Research, German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Dermatology, University Hospital Essen, Essen, Germany
| | - Mitalee Chandra
- German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Translational Skin Cancer Research, German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Dermatology, University Hospital Essen, Essen, Germany
| | - Thibault Kervarrec
- Department of Pathology, Université de Tours, Centre Hospitalier Universitaire de Tours, Tours, France
| | - Etienne Coyaud
- Department of Biology, University Lille, INSERM, Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), Lille, France
| | - Ivelina Spassova
- German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Translational Skin Cancer Research, German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Dermatology, University Hospital Essen, Essen, Germany
| | - Lukas Peiffer
- German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Translational Skin Cancer Research, German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Roland Houben
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, Germany
| | - Masahiro Shuda
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - David Schrama
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, Germany
| | - Jürgen C Becker
- German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Translational Skin Cancer Research, German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Dermatology, University Hospital Essen, Essen, Germany
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8
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Dias MH, Friskes A, Wang S, Fernandes Neto JM, van Gemert F, Mourragui S, Papagianni C, Kuiken HJ, Mainardi S, Alvarez-Villanueva D, Lieftink C, Morris B, Dekker A, van Dijk E, Wilms LH, da Silva MS, Jansen RA, Mulero-Sánchez A, Malzer E, Vidal A, Santos C, Salazar R, Wailemann RA, Torres TE, De Conti G, Raaijmakers JA, Snaebjornsson P, Yuan S, Qin W, Kovach JS, Armelin HA, te Riele H, van Oudenaarden A, Jin H, Beijersbergen RL, Villanueva A, Medema RH, Bernards R. Paradoxical Activation of Oncogenic Signaling as a Cancer Treatment Strategy. Cancer Discov 2024; 14:1276-1301. [PMID: 38533987 PMCID: PMC11215412 DOI: 10.1158/2159-8290.cd-23-0216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 12/06/2023] [Accepted: 03/19/2024] [Indexed: 03/28/2024]
Abstract
Cancer homeostasis depends on a balance between activated oncogenic pathways driving tumorigenesis and engagement of stress response programs that counteract the inherent toxicity of such aberrant signaling. Although inhibition of oncogenic signaling pathways has been explored extensively, there is increasing evidence that overactivation of the same pathways can also disrupt cancer homeostasis and cause lethality. We show here that inhibition of protein phosphatase 2A (PP2A) hyperactivates multiple oncogenic pathways and engages stress responses in colon cancer cells. Genetic and compound screens identify combined inhibition of PP2A and WEE1 as synergistic in multiple cancer models by collapsing DNA replication and triggering premature mitosis followed by cell death. This combination also suppressed the growth of patient-derived tumors in vivo. Remarkably, acquired resistance to this drug combination suppressed the ability of colon cancer cells to form tumors in vivo. Our data suggest that paradoxical activation of oncogenic signaling can result in tumor-suppressive resistance. Significance: A therapy consisting of deliberate hyperactivation of oncogenic signaling combined with perturbation of the stress responses that result from this is very effective in animal models of colon cancer. Resistance to this therapy is associated with loss of oncogenic signaling and reduced oncogenic capacity, indicative of tumor-suppressive drug resistance.
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Affiliation(s)
- Matheus Henrique Dias
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Anoek Friskes
- Division of Cell Biology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Siying Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Joao M. Fernandes Neto
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Frank van Gemert
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Soufiane Mourragui
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, the Netherlands.
| | - Chrysa Papagianni
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Hendrik J. Kuiken
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Sara Mainardi
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Daniel Alvarez-Villanueva
- Chemoresistance and Predictive Factors Group, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet del Llobregat, Barcelona, Spain.
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, NKI Robotic and Screening Center, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Ben Morris
- Division of Molecular Carcinogenesis, NKI Robotic and Screening Center, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Anna Dekker
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Emma van Dijk
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Lieke H.S. Wilms
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Marcelo S. da Silva
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil.
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil.
| | - Robin A. Jansen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Antonio Mulero-Sánchez
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Elke Malzer
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - August Vidal
- Department of Pathology, University Hospital of Bellvitge, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain.
- Xenopat S.L., Parc Cientific de Barcelona (PCB), Barcelona, Spain.
| | - Cristina Santos
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), CIBERONC, Barcelona, Spain.
| | - Ramón Salazar
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), CIBERONC, Barcelona, Spain.
| | | | - Thompson E.P. Torres
- Center of Toxins, Immune-response and Cell Signaling, Instituto Butantan, São Paulo, Brazil.
- Department of Clinical and Experimental Oncology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil.
| | - Giulia De Conti
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Jonne A. Raaijmakers
- Division of Cell Biology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Petur Snaebjornsson
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
- University of Iceland, Faculty of Medicine, Reykjavik, Iceland.
| | - Shengxian Yuan
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Shanghai, China.
| | - Wenxin Qin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - John S. Kovach
- Lixte Biotechnology Holdings, Inc., Pasadena, California.
| | - Hugo A. Armelin
- Center of Toxins, Immune-response and Cell Signaling, Instituto Butantan, São Paulo, Brazil.
| | - Hein te Riele
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Alexander van Oudenaarden
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, the Netherlands.
| | - Haojie Jin
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Roderick L. Beijersbergen
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
- Division of Molecular Carcinogenesis, NKI Robotic and Screening Center, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Alberto Villanueva
- Chemoresistance and Predictive Factors Group, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet del Llobregat, Barcelona, Spain.
- Xenopat S.L., Parc Cientific de Barcelona (PCB), Barcelona, Spain.
| | - Rene H. Medema
- Division of Cell Biology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Rene Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
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9
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Guilz NC, Ahn YO, Fatima H, Pedroza LA, Seo S, Soni RK, Wang N, Egli D, Mace EM. Replication Stress in Activated Human NK Cells Induces Sensitivity to Apoptosis. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:40-51. [PMID: 38809096 DOI: 10.4049/jimmunol.2300843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/29/2024] [Indexed: 05/30/2024]
Abstract
NK cells are innate immune effectors that kill virally infected or malignant cells. NK cell deficiency (NKD) occurs when NK cell development or function is impaired and variants in MCM4, GINS1, MCM10, and GINS4 result in NKD. Although NK cells are strongly impacted by mutational deficiencies in helicase proteins, the mechanisms underlying this specific susceptibility are poorly understood. In this study, we induced replication stress in activated NK cells or T cells by chemical and genetic methods. We found that the CD56bright subset of NK cells accumulates more DNA damage and replication stress during activation than do CD56dim NK cells or T cells. Aphidicolin treatment increases apoptosis of CD56bright NK cells through increased pan-caspase expression and decreases perforin expression in surviving cells. These findings show that sensitivity to replication stress affects NK cell survival and function and contributes to NKD.
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Affiliation(s)
- Nicole C Guilz
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Yong-Oon Ahn
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Hijab Fatima
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Luis Alberto Pedroza
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Seungmae Seo
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Rajesh Kumar Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY
| | - Ning Wang
- Pediatrics and Obstetrics and Gynecology, Columbia Stem Cell Initiative, Naomi Berrie Diabetes Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Dieter Egli
- Pediatrics and Obstetrics and Gynecology, Columbia Stem Cell Initiative, Naomi Berrie Diabetes Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Emily M Mace
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
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10
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Ubieto-Capella P, Ximénez-Embún P, Giménez-Llorente D, Losada A, Muñoz J, Méndez J. A rewiring of DNA replication mediated by MRE11 exonuclease underlies primed-to-naive cell de-differentiation. Cell Rep 2024; 43:114024. [PMID: 38581679 DOI: 10.1016/j.celrep.2024.114024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 02/01/2024] [Accepted: 03/15/2024] [Indexed: 04/08/2024] Open
Abstract
Mouse embryonic stem cells (mESCs) in the primed pluripotency state, which resembles the post-implantation epiblast, can be de-differentiated in culture to a naive state that resembles the pre-implantation inner cell mass. We report that primed-to-naive mESC transition entails a significant slowdown of DNA replication forks and the compensatory activation of dormant origins. Using isolation of proteins on nascent DNA coupled to mass spectrometry, we identify key changes in replisome composition that are responsible for these effects. Naive mESC forks are enriched in MRE11 nuclease and other DNA repair proteins. MRE11 is recruited to newly synthesized DNA in response to transcription-replication conflicts, and its inhibition or genetic downregulation in naive mESCs is sufficient to restore the fork rate of primed cells. Transcriptomic analyses indicate that MRE11 exonuclease activity is required for the complete primed-to-naive mESC transition, demonstrating a direct link between DNA replication dynamics and the mESC de-differentiation process.
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Affiliation(s)
- Patricia Ubieto-Capella
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Pilar Ximénez-Embún
- Proteomics Unit-ProteoRed-ISCIII, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Daniel Giménez-Llorente
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Javier Muñoz
- Proteomics Unit-ProteoRed-ISCIII, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Juan Méndez
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain.
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11
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Egger T, Morano L, Blanchard MP, Basbous J, Constantinou A. Spatial organization and functions of Chk1 activation by TopBP1 biomolecular condensates. Cell Rep 2024; 43:114064. [PMID: 38578830 DOI: 10.1016/j.celrep.2024.114064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/14/2024] [Accepted: 03/21/2024] [Indexed: 04/07/2024] Open
Abstract
Assembly of TopBP1 biomolecular condensates triggers activation of the ataxia telangiectasia-mutated and Rad3-related (ATR)/Chk1 signaling pathway, which coordinates cell responses to impaired DNA replication. Here, we used optogenetics and reverse genetics to investigate the role of sequence-specific motifs in the formation and functions of TopBP1 condensates. We propose that BACH1/FANCJ is involved in the partitioning of BRCA1 within TopBP1 compartments. We show that Chk1 is activated at the interface of TopBP1 condensates and provide evidence that these structures arise at sites of DNA damage and in primary human fibroblasts. Chk1 phosphorylation depends on the integrity of a conserved arginine motif within TopBP1's ATR activation domain (AAD). Its mutation uncouples Chk1 activation from TopBP1 condensation, revealing that optogenetically induced Chk1 phosphorylation triggers cell cycle checkpoints and slows down replication forks in the absence of DNA damage. Together with previous work, these data suggest that the intrinsically disordered AAD encodes distinct molecular steps in the ATR/Chk1 pathway.
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Affiliation(s)
- Tom Egger
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France
| | - Laura Morano
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France
| | - Marie-Pierre Blanchard
- Montpellier Ressources Imageries, BioCampus, Université de Montpellier, CNRS, Montpellier, France
| | - Jihane Basbous
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France.
| | - Angelos Constantinou
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France
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12
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Rankin BD, Rankin S. The MCM2-7 Complex: Roles beyond DNA Unwinding. BIOLOGY 2024; 13:258. [PMID: 38666870 PMCID: PMC11048021 DOI: 10.3390/biology13040258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/07/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024]
Abstract
The MCM2-7 complex is a hexameric protein complex that serves as a DNA helicase. It unwinds the DNA double helix during DNA replication, thereby providing the single-stranded replication template. In recent years, it has become clear that the MCM2-7 complex has additional functions that extend well beyond its role in DNA replication. Through physical and functional interactions with different pathways, it impacts other nuclear events and activities, including folding of the genome, histone inheritance, chromosome segregation, DNA damage sensing and repair, and gene transcription. Collectively, the diverse roles of the MCM2-7 complex suggest it plays a critical role in maintaining genome integrity by integrating the regulation of DNA replication with other pathways in the nucleus.
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Affiliation(s)
- Brooke D. Rankin
- Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA;
- Cell Biology Department, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Susannah Rankin
- Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA;
- Cell Biology Department, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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13
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Tian Y, Zhou Y, Chen F, Qian S, Hu X, Zhang B, Liu Q. Research progress in MCM family: Focus on the tumor treatment resistance. Biomed Pharmacother 2024; 173:116408. [PMID: 38479176 DOI: 10.1016/j.biopha.2024.116408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/22/2024] [Accepted: 03/06/2024] [Indexed: 03/27/2024] Open
Abstract
Malignant tumors constitute a significant category of diseases posing a severe threat to human survival and health, thereby representing one of the most challenging and pressing issues in the field of biomedical research. Due to their malignant nature, which is characterized by a high potential for metastasis, rapid dissemination, and frequent recurrence, the prevailing approach in clinical oncology involves a comprehensive treatment strategy that combines surgery with radiotherapy, chemotherapy, targeted drug therapies, and other interventions. Treatment resistance remains a major obstacle in the comprehensive management of tumors, serving as a primary cause for the failure of integrated tumor therapies and a critical factor contributing to patient relapse and mortality. The Minichromosome Maintenance (MCM) protein family comprises functional proteins closely associated with the development of resistance in tumor therapy.The influence of MCMs manifests through various pathways, encompassing modulation of DNA replication, cell cycle regulation, and DNA damage repair mechanisms. Consequently, this leads to an enhanced tolerance of tumor cells to chemotherapy, targeted drugs, and radiation. Consequently, this review explores the specific roles of the MCM family in various cancer treatment strategies. Its objective is to enhance our comprehension of resistance mechanisms in tumor therapy, thereby presenting novel targets for clinical research aimed at overcoming resistance in cancer treatment. This bears substantial clinical relevance.
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Affiliation(s)
- Yuxuan Tian
- Department of Hepatobiliary and Intestinal Surgery of Hunan Cancer Hospital & the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, PR China; Department of Histology and Embryology, Basic School of Medicine Sciences, Central South University, Changsha, Hunan 410013, PR China
| | - Yanhong Zhou
- Cancer Research Institute, Basic School of Medicine Sciences, Central South University, Changsha, Hunan 410078, PR China
| | - Fuxin Chen
- Department of Histology and Embryology, Basic School of Medicine Sciences, Central South University, Changsha, Hunan 410013, PR China
| | - Siyi Qian
- Department of Histology and Embryology, Basic School of Medicine Sciences, Central South University, Changsha, Hunan 410013, PR China
| | - Xingming Hu
- The 1st Department of Thoracic Surgery of Hunan Cancer Hospital & the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, PR China
| | - Bin Zhang
- Department of Hepatobiliary and Intestinal Surgery of Hunan Cancer Hospital & the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, PR China; Department of Histology and Embryology, Basic School of Medicine Sciences, Central South University, Changsha, Hunan 410013, PR China.
| | - Qiang Liu
- Department of Hepatobiliary and Intestinal Surgery of Hunan Cancer Hospital & the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, PR China.
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14
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Yadav AK, Polasek-Sedlackova H. Quantity and quality of minichromosome maintenance protein complexes couple replication licensing to genome integrity. Commun Biol 2024; 7:167. [PMID: 38336851 PMCID: PMC10858283 DOI: 10.1038/s42003-024-05855-w] [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: 10/05/2023] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Accurate and complete replication of genetic information is a fundamental process of every cell division. The replication licensing is the first essential step that lays the foundation for error-free genome duplication. During licensing, minichromosome maintenance protein complexes, the molecular motors of DNA replication, are loaded to genomic sites called replication origins. The correct quantity and functioning of licensed origins are necessary to prevent genome instability associated with severe diseases, including cancer. Here, we delve into recent discoveries that shed light on the novel functions of licensed origins, the pathways necessary for their proper maintenance, and their implications for cancer therapies.
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Affiliation(s)
- Anoop Kumar Yadav
- Department of Cell Biology and Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Hana Polasek-Sedlackova
- Department of Cell Biology and Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
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15
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Bournaka S, Badra-Fajardo N, Arbi M, Taraviras S, Lygerou Z. The cell cycle revisited: DNA replication past S phase preserves genome integrity. Semin Cancer Biol 2024; 99:45-55. [PMID: 38346544 DOI: 10.1016/j.semcancer.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/23/2024] [Accepted: 02/05/2024] [Indexed: 02/20/2024]
Abstract
Accurate and complete DNA duplication is critical for maintaining genome integrity. Multiple mechanisms regulate when and where DNA replication takes place, to ensure that the entire genome is duplicated once and only once per cell cycle. Although the bulk of the genome is copied during the S phase of the cell cycle, increasing evidence suggests that parts of the genome are replicated in G2 or mitosis, in a last attempt to secure that daughter cells inherit an accurate copy of parental DNA. Remaining unreplicated gaps may be passed down to progeny and replicated in the next G1 or S phase. These findings challenge the long-established view that genome duplication occurs strictly during the S phase, bridging DNA replication to DNA repair and providing novel therapeutic strategies for cancer treatment.
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Affiliation(s)
- Spyridoula Bournaka
- Department of General Biology, Medical School, University of Patras, Patras 26504, Greece
| | - Nibal Badra-Fajardo
- Department of General Biology, Medical School, University of Patras, Patras 26504, Greece
| | - Marina Arbi
- Department of General Biology, Medical School, University of Patras, Patras 26504, Greece
| | - Stavros Taraviras
- Department of Physiology, Medical School, University of Patras, Patras 26504, Greece
| | - Zoi Lygerou
- Department of General Biology, Medical School, University of Patras, Patras 26504, Greece.
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16
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Leung TCN, Lu SN, Chu CN, Lee J, Liu X, Ngai SM. Temporal Quantitative Proteomic and Phosphoproteomic Profiling of SH-SY5Y and IMR-32 Neuroblastoma Cells during All- Trans-Retinoic Acid-Induced Neuronal Differentiation. Int J Mol Sci 2024; 25:1047. [PMID: 38256121 PMCID: PMC10816102 DOI: 10.3390/ijms25021047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/05/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
The human neuroblastoma cell lines SH-SY5Y and IMR-32 can be differentiated into neuron-like phenotypes through treatment with all-trans-retinoic acid (ATRA). After differentiation, these cell lines are extensively utilized as in vitro models to study various aspects of neuronal cell biology. However, temporal and quantitative profiling of the proteome and phosphoproteome of SH-SY5Y and IMR-32 cells throughout ATRA-induced differentiation has been limited. Here, we performed relative quantification of the proteomes and phosphoproteomes of SH-SY5Y and IMR-32 cells at multiple time points during ATRA-induced differentiation. Relative quantification of proteins and phosphopeptides with subsequent gene ontology analysis revealed that several biological processes, including cytoskeleton organization, cell division, chaperone function and protein folding, and one-carbon metabolism, were associated with ATRA-induced differentiation in both cell lines. Furthermore, kinase-substrate enrichment analysis predicted altered activities of several kinases during differentiation. Among these, CDK5 exhibited increased activity, while CDK2 displayed reduced activity. The data presented serve as a valuable resource for investigating temporal protein and phosphoprotein abundance changes in SH-SY5Y and IMR-32 cells during ATRA-induced differentiation.
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Affiliation(s)
- Thomas C. N. Leung
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Scott Ninghai Lu
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; (S.N.L.); (C.N.C.); (J.L.); (X.L.)
| | - Cheuk Ning Chu
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; (S.N.L.); (C.N.C.); (J.L.); (X.L.)
| | - Joy Lee
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; (S.N.L.); (C.N.C.); (J.L.); (X.L.)
| | - Xingyu Liu
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; (S.N.L.); (C.N.C.); (J.L.); (X.L.)
| | - Sai Ming Ngai
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; (S.N.L.); (C.N.C.); (J.L.); (X.L.)
- AoE Centre for Genomic Studies on Plant-Environment Interaction for Sustainable Agriculture and Food Security, The Chinese University of Hong Kong, Hong Kong, China
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17
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Akkawi R, Hidmi O, Haj-Yahia A, Monin J, Diment J, Drier Y, Stein GS, Aqeilan RI. WWOX promotes osteosarcoma development via upregulation of Myc. Cell Death Dis 2024; 15:13. [PMID: 38182577 PMCID: PMC10770339 DOI: 10.1038/s41419-023-06378-8] [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: 10/04/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 01/07/2024]
Abstract
Osteosarcoma is an aggressive bone tumor that primarily affects children and adolescents. This malignancy is highly aggressive, associated with poor clinical outcomes, and primarily metastasizes to the lungs. Due to its rarity and biological heterogeneity, limited studies on its molecular basis exist, hindering the development of effective therapies. The WW domain-containing oxidoreductase (WWOX) is frequently altered in human osteosarcoma. Combined deletion of Wwox and Trp53 using Osterix1-Cre transgenic mice has been shown to accelerate osteosarcoma development. In this study, we generated a traceable osteosarcoma mouse model harboring the deletion of Trp53 alone (single-knockout) or combined deletion of Wwox/Trp53 (double-knockout) and expressing a tdTomato reporter. By tracking Tomato expression at different time points, we detected the early presence of tdTomato-positive cells in the bone marrow mesenchymal stem cells of non-osteosarcoma-bearing mice (young BM). We found that double-knockout young BM cells, but not single-knockout young BM cells, exhibited tumorigenic traits both in vitro and in vivo. Molecular and cellular characterization of these double-knockout young BM cells revealed their resemblance to osteosarcoma tumor cells. Interestingly, one of the observed significant transcriptomic changes in double-knockout young BM cells was the upregulation of Myc and its target genes compared to single-knockout young BM cells. Intriguingly, Myc-chromatin immunoprecipitation sequencing revealed its increased enrichment on Myc targets, which were upregulated in double-knockout young BM cells. Restoration of WWOX in double-knockout young BM cells reduced Myc protein levels. As a prototype target, we demonstrated the upregulation of MCM7, a known Myc target, in double-knockout young BM relative to single-knockout young BM cells. Inhibition of MCM7 expression using simvastatin resulted in reduced proliferation and tumor cell growth of double-knockout young BM cells. Our findings reveal BM mesenchymal stem cells as a platform to study osteosarcoma and Myc and its targets as WWOX effectors and early molecular events during osteosarcomagenesis.
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Affiliation(s)
- Rania Akkawi
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Osama Hidmi
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ameen Haj-Yahia
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jonathon Monin
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Judith Diment
- Department of Pathology, Hadassah University Medical Center, Jerusalem, Israel
| | - Yotam Drier
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gary S Stein
- Department of Biochemistry, Larner College of Medicine, UVM Cancer Center, University of Vermont, Burlington, VT, USA
| | - Rami I Aqeilan
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
- Cyprus Cancer Research Institute (CCRI), Nicosia, Cyprus.
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18
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Zhao M, Wang T, Gleber-Netto FO, Chen Z, McGrail DJ, Gomez JA, Ju W, Gadhikar MA, Ma W, Shen L, Wang Q, Tang X, Pathak S, Raso MG, Burks JK, Lin SY, Wang J, Multani AS, Pickering CR, Chen J, Myers JN, Zhou G. Mutant p53 gains oncogenic functions through a chromosomal instability-induced cytosolic DNA response. Nat Commun 2024; 15:180. [PMID: 38167338 PMCID: PMC10761733 DOI: 10.1038/s41467-023-44239-2] [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: 01/04/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
Inactivating TP53 mutations leads to a loss of function of p53, but can also often result in oncogenic gain-of-function (GOF) of mutant p53 (mutp53) proteins which promotes tumor development and progression. The GOF activities of TP53 mutations are well documented, but the mechanisms involved remain poorly understood. Here, we study the mutp53 interactome and find that by targeting minichromosome maintenance complex components (MCMs), GOF mutp53 predisposes cells to replication stress and chromosomal instability (CIN), leading to a tumor cell-autonomous and cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING)-dependent cytosolic DNA response that activates downstream non-canonical nuclear factor kappa light chain enhancer of activated B cell (NC-NF-κB) signaling. Consequently, GOF mutp53-MCMs-CIN-cytosolic DNA-cGAS-STING-NC-NF-κB signaling promotes tumor cell metastasis and an immunosuppressive tumor microenvironment through antagonizing interferon signaling and regulating genes associated with pro-tumorigenic inflammation. Our findings have important implications for understanding not only the GOF activities of TP53 mutations but also the genome-guardian role of p53 and its inactivation during tumor development and progression.
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Affiliation(s)
- Mei Zhao
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Tianxiao Wang
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Head and Neck Surgery, Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Frederico O Gleber-Netto
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Zhen Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Daniel J McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, 44195, USA
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Javier A Gomez
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Wutong Ju
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mayur A Gadhikar
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Wencai Ma
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Li Shen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Qi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ximing Tang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sen Pathak
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Maria Gabriela Raso
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jared K Burks
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Asha S Multani
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Curtis R Pickering
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Surgery-Otolaryngology, Yale School of Medicine, New Haven, CT, 06250, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jeffrey N Myers
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Ge Zhou
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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19
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Engin A. Adipose Tissue Hypoxia in Obesity: Clinical Reappraisal of Hypoxia Hypothesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1460:329-356. [PMID: 39287857 DOI: 10.1007/978-3-031-63657-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
Obese subjects exhibit lower adipose tissue oxygen consumption in accordance with the lower adipose tissue blood flow. Thereby, compared to lean subjects, obese individuals have almost half lower capillary density and more than half lower vascular endothelial growth factor (VEGF). The VEGF expression together with hypoxia-inducible transcription factor-1 alpha (HIF-1α) activity also requires phosphatidylinositol 3-kinase (PI3K) and mammalian target of rapamycin (mTOR)-mediated signaling. Especially HIF-1α is an important signaling molecule for hypoxia to induce the inflammatory responses. Hypoxia contributes to several biological functions, such as angiogenesis, cell proliferation, apoptosis, inflammation, and insulin resistance (IR). Pathogenesis of obesity-related comorbidities is attributed to intermittent hypoxia (IH), which is mostly observed in visceral obesity. Proinflammatory phenotype of the adipose tissue is a crucial link between IH and the development of IR. Inhibition of adaptive unfolded protein response (UPR) in hypoxia increases β cell death. Moreover, deletion of HIF-1α worsens β cell function. Oxidative stress, as well as the release of proinflammatory cytokines/adipokines in obesity, is proportional to the severity of IH. Reactive oxygen species (ROS) generation at mitochondria is responsible for propagation of the hypoxic signal; however, mitochondrial ROS production is required for hypoxic HIF-1α protein stabilization. Alterations in oxygen availability of adipose tissue directly affect the macrophage polarization and are responsible for the dysregulated adipocytokines production in obesity. Hypoxia both inhibits adipocyte differentiation from preadipocytes and macrophage migration from the hypoxic adipose tissue. Upon reaching a hypertrophic threshold beyond the adipocyte fat loading capacity, excess extracellular matrix (ECM) components are deposited, causing fibrosis. HIF-1α initiates the whole pathological process of fibrosis and inflammation in the obese adipose tissue. In addition to stressed adipocytes, hypoxia contributes to immune cell migration and activation which further aggravates adipose tissue fibrosis. Therefore, targeting HIF-1α might be an efficient way to suppress hypoxia-induced pathological changes in the ECM. The fibrosis score of adipose tissue correlates negatively with the body mass index and metabolic parameters. Inducers of browning/beiging adipocytes and adipokines, as well as modulations of matrix remodeling enzyme inhibitors, and associated gene regulators, are potential pharmacological targets for treating obesity.
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Affiliation(s)
- Atilla Engin
- Faculty of Medicine, Department of General Surgery, Gazi University, Besevler, Ankara, Turkey.
- Mustafa Kemal Mah. 2137. Sok. 8/14, 06520, Cankaya, Ankara, Turkey.
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20
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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: 4] [Impact Index Per Article: 4.0] [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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21
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Malzl D, Peycheva M, Rahjouei A, Gnan S, Klein KN, Nazarova M, Schoeberl UE, Gilbert DM, Buonomo SCB, Di Virgilio M, Neumann T, Pavri R. RIF1 regulates early replication timing in murine B cells. Nat Commun 2023; 14:8049. [PMID: 38081811 PMCID: PMC10713614 DOI: 10.1038/s41467-023-43778-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
The mammalian DNA replication timing (RT) program is crucial for the proper functioning and integrity of the genome. The best-known mechanism for controlling RT is the suppression of late origins of replication in heterochromatin by RIF1. Here, we report that in antigen-activated, hypermutating murine B lymphocytes, RIF1 binds predominantly to early-replicating active chromatin and promotes early replication, but plays a minor role in regulating replication origin activity, gene expression and genome organization in B cells. Furthermore, we find that RIF1 functions in a complementary and non-epistatic manner with minichromosome maintenance (MCM) proteins to establish early RT signatures genome-wide and, specifically, to ensure the early replication of highly transcribed genes. These findings reveal additional layers of regulation within the B cell RT program, driven by the coordinated activity of RIF1 and MCM proteins.
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Affiliation(s)
- Daniel Malzl
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Lazarettgasse 14, Vienna, Austria
| | - Mihaela Peycheva
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Lazarettgasse 14, Vienna, Austria
| | - Ali Rahjouei
- Max-Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Stefano Gnan
- School of Biological Sciences, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Kyle N Klein
- San Diego Biomedical Research Institute, San Diego, CA, 92121, USA
| | - Mariia Nazarova
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria
| | - Ursula E Schoeberl
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria
| | - David M Gilbert
- San Diego Biomedical Research Institute, San Diego, CA, 92121, USA
| | - Sara C B Buonomo
- School of Biological Sciences, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Michela Di Virgilio
- Max-Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria.
- Quantro Therapeutics, Vienna Biocenter, 1030, Vienna, Austria.
| | - Rushad Pavri
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria.
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22
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Schuhwerk H, Brabletz T. Mutual regulation of TGFβ-induced oncogenic EMT, cell cycle progression and the DDR. Semin Cancer Biol 2023; 97:86-103. [PMID: 38029866 DOI: 10.1016/j.semcancer.2023.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/06/2023] [Accepted: 11/23/2023] [Indexed: 12/01/2023]
Abstract
TGFβ signaling and the DNA damage response (DDR) are two cellular toolboxes with a strong impact on cancer biology. While TGFβ as a pleiotropic cytokine affects essentially all hallmarks of cancer, the multifunctional DDR mostly orchestrates cell cycle progression, DNA repair, chromatin remodeling and cell death. One oncogenic effect of TGFβ is the partial activation of epithelial-to-mesenchymal transition (EMT), conferring invasiveness, cellular plasticity and resistance to various noxae. Several reports show that both individual networks as well as their interface affect chemo-/radiotherapies. However, the underlying mechanisms remain poorly resolved. EMT often correlates with TGFβ-induced slowing of proliferation, yet numerous studies demonstrate that particularly the co-activated EMT transcription factors counteract anti-proliferative signaling in a partially non-redundant manner. Collectively, evidence piled up over decades underscore a multifaceted, reciprocal inter-connection of TGFβ signaling / EMT with the DDR / cell cycle progression, which we will discuss here. Altogether, we conclude that full cell cycle arrest is barely compatible with the propagation of oncogenic EMT traits and further propose that 'EMT-linked DDR plasticity' is a crucial, yet intricate facet of malignancy, decisively affecting metastasis formation and therapy resistance.
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Affiliation(s)
- Harald Schuhwerk
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany.
| | - Thomas Brabletz
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany.
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23
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Mouery BL, Baker EM, Mills CA, Herring LE, Fleifel D, Cook JG. APC/C prevents non-canonical order of cyclin/CDK activity to maintain CDK4/6 inhibitor-induced arrest. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566394. [PMID: 37986787 PMCID: PMC10659421 DOI: 10.1101/2023.11.09.566394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Regulated cell cycle progression ensures homeostasis and prevents cancer. In proliferating cells, premature S phase entry is avoided by the E3 ubiquitin ligase APC/C (anaphase promoting complex/cyclosome), although the APC/C substrates whose degradation restrains G1-S progression are not fully known. The APC/C is also active in arrested cells that exited the cell cycle, but it is not clear if APC/C maintains all types of arrest. Here by expressing the APC/C inhibitor, EMI1, we show that APC/C activity is essential to prevent S phase entry in cells arrested by pharmacological CDK4/6 inhibition (Palbociclib). Thus, active protein degradation is required for arrest alongside repressed cell cycle gene expression. The mechanism of rapid and robust arrest bypass from inhibiting APC/C involves cyclin-dependent kinases acting in an atypical order to inactivate RB-mediated E2F repression. Inactivating APC/C first causes mitotic cyclin B accumulation which then promotes cyclin A expression. We propose that cyclin A is the key substrate for maintaining arrest because APC/C-resistant cyclin A, but not cyclin B, is sufficient to induce S phase entry. Cells bypassing arrest from CDK4/6 inhibition initiate DNA replication with severely reduced origin licensing. The simultaneous accumulation of S phase licensing inhibitors, such as cyclin A and geminin, with G1 licensing activators disrupts the normal order of G1-S progression. As a result, DNA synthesis and cell proliferation are profoundly impaired. Our findings predict that cancers with elevated EMI1 expression will tend to escape CDK4/6 inhibition into a premature, underlicensed S phase and suffer enhanced genome instability.
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Affiliation(s)
- Brandon L Mouery
- Curriculum in Genetics and Molecular Biology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
| | - Eliyambuya M Baker
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599
- Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Christine A Mills
- UNC Proteomics Core Facility, Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
- Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill NC, 27599, USA
| | - Laura E Herring
- UNC Proteomics Core Facility, Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center. The University of North Carolina at Chapel Hill. Chapel Hill NC 27599, USA
- Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill NC, 27599, USA
| | - Dalia Fleifel
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599
| | - Jeanette Gowen Cook
- Curriculum in Genetics and Molecular Biology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center. The University of North Carolina at Chapel Hill. Chapel Hill NC 27599, USA
- Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill NC, 27599, USA
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24
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Pabba MK, Ritter C, Chagin VO, Meyer J, Celikay K, Stear JH, Loerke D, Kolobynina K, Prorok P, Schmid AK, Leonhardt H, Rohr K, Cardoso MC. Replisome loading reduces chromatin motion independent of DNA synthesis. eLife 2023; 12:RP87572. [PMID: 37906089 PMCID: PMC10617993 DOI: 10.7554/elife.87572] [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] [Indexed: 11/02/2023] Open
Abstract
Chromatin has been shown to undergo diffusional motion, which is affected during gene transcription by RNA polymerase activity. However, the relationship between chromatin mobility and other genomic processes remains unclear. Hence, we set out to label the DNA directly in a sequence unbiased manner and followed labeled chromatin dynamics in interphase human cells expressing GFP-tagged proliferating cell nuclear antigen (PCNA), a cell cycle marker and core component of the DNA replication machinery. We detected decreased chromatin mobility during the S-phase compared to G1 and G2 phases in tumor as well as normal diploid cells using automated particle tracking. To gain insight into the dynamical organization of the genome during DNA replication, we determined labeled chromatin domain sizes and analyzed their motion in replicating cells. By correlating chromatin mobility proximal to the active sites of DNA synthesis, we showed that chromatin motion was locally constrained at the sites of DNA replication. Furthermore, inhibiting DNA synthesis led to increased loading of DNA polymerases. This was accompanied by accumulation of the single-stranded DNA binding protein on the chromatin and activation of DNA helicases further restricting local chromatin motion. We, therefore, propose that it is the loading of replisomes but not their catalytic activity that reduces the dynamics of replicating chromatin segments in the S-phase as well as their accessibility and probability of interactions with other genomic regions.
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Affiliation(s)
| | - Christian Ritter
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg UniversityHeidelbergGermany
| | - Vadim O Chagin
- Department of Biology, Technical University of DarmstadtDarmstadtGermany
- Institute of Cytology RASSt. PetersburgRussian Federation
| | - Janis Meyer
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg UniversityHeidelbergGermany
| | - Kerem Celikay
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg UniversityHeidelbergGermany
| | - Jeffrey H Stear
- EMBL Australia Node in Single Molecule Science, University of New South WalesSydneyAustralia
| | - Dinah Loerke
- Department of Physics & Astronomy, University of DenverDenverUnited States
| | - Ksenia Kolobynina
- Department of Biology, Technical University of DarmstadtDarmstadtGermany
| | - Paulina Prorok
- Department of Biology, Technical University of DarmstadtDarmstadtGermany
| | - Alice Kristin Schmid
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg UniversityHeidelbergGermany
| | | | - Karl Rohr
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg UniversityHeidelbergGermany
| | - M Cristina Cardoso
- Department of Biology, Technical University of DarmstadtDarmstadtGermany
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25
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Fuertes T, Álvarez-Corrales E, Gómez-Escolar C, Ubieto-Capella P, Serrano-Navarro Á, de Molina A, Méndez J, Ramiro AR, de Yébenes VG. miR-28-based combination therapy impairs aggressive B cell lymphoma growth by rewiring DNA replication. Cell Death Dis 2023; 14:687. [PMID: 37852959 PMCID: PMC10585006 DOI: 10.1038/s41419-023-06178-0] [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: 11/30/2022] [Revised: 09/07/2023] [Accepted: 09/26/2023] [Indexed: 10/20/2023]
Abstract
Diffuse large B cell lymphoma (DLBCL) is the most common aggressive B cell lymphoma and accounts for nearly 40% of cases of B cell non-Hodgkin lymphoma. DLBCL is generally treated with R-CHOP chemotherapy, but many patients do not respond or relapse after treatment. Here, we analyzed the therapeutic potential of the tumor suppressor microRNA-28 (miR-28) for DLBCL, alone and in combination with the Bruton's tyrosine kinase inhibitor ibrutinib. Combination therapy with miR-28 plus ibrutinib potentiated the anti-tumor effects of monotherapy with either agent by inducing a specific transcriptional cell-cycle arrest program that impairs DNA replication. The molecular actions of miR-28 and ibrutinib synergistically impair DNA replication by simultaneous inhibition of origin activation and fork progression. Moreover, we found that downregulation of the miR-28-plus-ibrutinib gene signature correlates with better survival of ABC-DLBCL patients. These results provide evidence for the effectiveness of a new miRNA-based ibrutinib combination therapy for DLBCL and unveil the miR-28-plus-ibrutinib gene signature as a new predictor of outcome in ABC-DLBCL patients.
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Affiliation(s)
- Teresa Fuertes
- B Cell Biology Laboratory Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Emigdio Álvarez-Corrales
- Department of Immunology, Ophthalmology and ENT, Universidad Complutense de Madrid; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Carmen Gómez-Escolar
- B Cell Biology Laboratory Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | | | - Álvaro Serrano-Navarro
- B Cell Biology Laboratory Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Antonio de Molina
- Comparative Medicine Unit. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Juan Méndez
- DNA replication Group. Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Almudena R Ramiro
- B Cell Biology Laboratory Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.
| | - Virginia G de Yébenes
- Department of Immunology, Ophthalmology and ENT, Universidad Complutense de Madrid; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain.
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26
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Fleifel D, Cook JG. G1 Dynamics at the Crossroads of Pluripotency and Cancer. Cancers (Basel) 2023; 15:4559. [PMID: 37760529 PMCID: PMC10526231 DOI: 10.3390/cancers15184559] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 08/29/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
G1 cell cycle phase dynamics are regulated by intricate networks involving cyclins, cyclin-dependent kinases (CDKs), and CDK inhibitors, which control G1 progression and ensure proper cell cycle transitions. Moreover, adequate origin licensing in G1 phase, the first committed step of DNA replication in the subsequent S phase, is essential to maintain genome integrity. In this review, we highlight the intriguing parallels and disparities in G1 dynamics between stem cells and cancer cells, focusing on their regulatory mechanisms and functional outcomes. Notably, SOX2, OCT4, KLF4, and the pluripotency reprogramming facilitator c-MYC, known for their role in establishing and maintaining stem cell pluripotency, are also aberrantly expressed in certain cancer cells. In this review, we discuss recent advances in understanding the regulatory role of these pluripotency factors in G1 dynamics in the context of stem cells and cancer cells, which may offer new insights into the interconnections between pluripotency and tumorigenesis.
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Affiliation(s)
| | - Jeanette Gowen Cook
- Department of Biochemistry & Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
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27
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Zhang W, Wang Y, Liu Y, Liu C, Wang Y, He L, Cheng X, Peng Y, Xia L, Wu X, Wu J, Zhang Y, Sun L, Chen P, Li G, Tu Q, Liang J, Shang Y. NFIB facilitates replication licensing by acting as a genome organizer. Nat Commun 2023; 14:5076. [PMID: 37604829 PMCID: PMC10442334 DOI: 10.1038/s41467-023-40846-1] [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: 04/11/2023] [Accepted: 08/12/2023] [Indexed: 08/23/2023] Open
Abstract
The chromatin-based rule governing the selection and activation of replication origins in metazoans remains to be investigated. Here we report that NFIB, a member of Nuclear Factor I (NFI) family that was initially purified in host cells to promote adenoviral DNA replication but has since mainly been investigated in transcription regulation, is physically associated with the pre-replication complex (pre-RC) in mammalian cells. Genomic analyses reveal that NFIB facilitates the assembly of the pre-RC by increasing chromatin accessibility. Nucleosome binding and single-molecule magnetic tweezers shows that NFIB binds to and opens up nucleosomes. Transmission electron microscopy indicates that NFIB promotes nucleosome eviction on parental chromatin. NFIB deficiency leads to alterations of chromosome contacts/compartments in both G1 and S phase and affects the firing of a subset of origins at early-replication domains. Significantly, cancer-associated NFIB overexpression provokes gene duplication and genomic alterations recapitulating the genetic aberrance in clinical breast cancer and empowering cancer cells to dynamically evolve growth advantage and drug resistance. Together, these results point a role for NFIB in facilitating replication licensing by acting as a genome organizer, shedding new lights on the biological function of NFIB and on the replication origin selection in eukaryotes.
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Affiliation(s)
- Wenting Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yue Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yongjie Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Cuifang Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yizhou Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lin He
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Xiao Cheng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yani Peng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Lu Xia
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Xiaodi Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Jiajing Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Yu Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Luyang Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Ping Chen
- Department of Immunology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100069, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qiang Tu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Jing Liang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
| | - Yongfeng Shang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China.
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28
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Xiang S, Luo X, Welch D, Reed DR, Alexandrow MG. Identification of Selective ATP-Competitive CMG Helicase Inhibitors for Cancer Intervention that Disrupt CMG-Replisome Function. RESEARCH SQUARE 2023:rs.3.rs-3182731. [PMID: 37609279 PMCID: PMC10441460 DOI: 10.21203/rs.3.rs-3182731/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The human CMG helicase (Cdc45-MCM-GINS) is a novel target for anti-cancer therapy due to tumor-specific weaknesses in CMG function induced by oncogenic changes and the need for CMG function during recovery from replicative stresses such as chemotherapy. Here, we developed an orthogonal biochemical screening approach and identified selective CMG inhibitors (CMGi) that inhibit ATPase and helicase activities in an ATP-competitive manner at low micromolar concentrations. Structure-activity information and in silico docking indicate that CMGi occupy ATP binding sites and channels within MCM subunits leading to the ATP clefts, which are likely used for ATP/ADP ingress or egress. CMGi inhibit cell growth and DNA replication using multiple molecular mechanisms. CMGi block helicase assembly steps that require ATP binding/hydrolysis by the MCM complex, specifically MCM ring assembly on DNA and GINS recruitment to DNA-loaded MCM hexamers. During S-phase, inhibition of MCM ATP binding/hydrolysis by CMGi causes a 'reverse allosteric' dissociation of Cdc45/GINS from the CMG that destabilizes the replisome and disrupts interactions with Ctf4, Mcm10, and DNA polymerase-α, -δ, -ε, resulting in DNA damage. These novel CMGi are selectively toxic toward tumor cells and define a new class of CMG helicase-targeted anti-cancer compounds with distinct mechanisms of action.
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Affiliation(s)
- Shengyan Xiang
- Cancer Biology and Evolution Program, Moffitt Cancer Center and Research Institute, Tampa, FL 33612
- Molecular Oncology Department, Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Xingju Luo
- Cancer Biology and Evolution Program, Moffitt Cancer Center and Research Institute, Tampa, FL 33612
- Molecular Oncology Department, Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Darcy Welch
- Cancer Biology and Evolution Program, Moffitt Cancer Center and Research Institute, Tampa, FL 33612
- Department of Individualized Cancer Management, Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Damon R. Reed
- Cancer Biology and Evolution Program, Moffitt Cancer Center and Research Institute, Tampa, FL 33612
- Department of Individualized Cancer Management, Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Mark G. Alexandrow
- Cancer Biology and Evolution Program, Moffitt Cancer Center and Research Institute, Tampa, FL 33612
- Molecular Oncology Department, Moffitt Cancer Center and Research Institute, Tampa, FL 33612
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29
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Harada Y, Mizote Y, Suzuki T, Hirayama A, Ikeda S, Nishida M, Hiratsuka T, Ueda A, Imagawa Y, Maeda K, Ohkawa Y, Murai J, Freeze HH, Miyoshi E, Higashiyama S, Udono H, Dohmae N, Tahara H, Taniguchi N. Metabolic clogging of mannose triggers dNTP loss and genomic instability in human cancer cells. eLife 2023; 12:e83870. [PMID: 37461317 DOI: 10.7554/elife.83870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 06/12/2023] [Indexed: 07/20/2023] Open
Abstract
Mannose has anticancer activity that inhibits cell proliferation and enhances the efficacy of chemotherapy. How mannose exerts its anticancer activity, however, remains poorly understood. Here, using genetically engineered human cancer cells that permit the precise control of mannose metabolic flux, we demonstrate that the large influx of mannose exceeding its metabolic capacity induced metabolic remodeling, leading to the generation of slow-cycling cells with limited deoxyribonucleoside triphosphates (dNTPs). This metabolic remodeling impaired dormant origin firing required to rescue stalled forks by cisplatin, thus exacerbating replication stress. Importantly, pharmacological inhibition of de novo dNTP biosynthesis was sufficient to retard cell cycle progression, sensitize cells to cisplatin, and inhibit dormant origin firing, suggesting dNTP loss-induced genomic instability as a central mechanism for the anticancer activity of mannose.
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Affiliation(s)
- Yoichiro Harada
- Department of Glyco-Oncology and Medical Biochemistry, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Yu Mizote
- Department of Cancer Drug Discovery and Development, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Japan
| | - Satsuki Ikeda
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
| | - Mikako Nishida
- Department of Immunology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Toru Hiratsuka
- Department of Oncogenesis and Growth Regulation, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Ayaka Ueda
- Department of Molecular Biochemistry and Clinical Investigation, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yusuke Imagawa
- Department of Oncogenesis and Growth Regulation, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Kento Maeda
- Department of Glyco-Oncology and Medical Biochemistry, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Yuki Ohkawa
- Department of Glyco-Oncology and Medical Biochemistry, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Junko Murai
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
- Division of Cell Growth and Tumor Regulation, Proteo-Science Center, Ehime University, Ehime, Japan
- Department of Biochemistry and Molecular Genetics, Graduate School of Medicine, Ehime University, Ehime, Japan
| | - Hudson H Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Eiji Miyoshi
- Department of Molecular Biochemistry and Clinical Investigation, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shigeki Higashiyama
- Department of Oncogenesis and Growth Regulation, Research Institute, Osaka International Cancer Institute, Osaka, Japan
- Division of Cell Growth and Tumor Regulation, Proteo-Science Center, Ehime University, Ehime, Japan
- Department of Biochemistry and Molecular Genetics, Graduate School of Medicine, Ehime University, Ehime, Japan
| | - Heiichiro Udono
- Department of Immunology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Hideaki Tahara
- Department of Cancer Drug Discovery and Development, Research Institute, Osaka International Cancer Institute, Osaka, Japan
- Project Division of Cancer Biomolecular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Naoyuki Taniguchi
- Department of Glyco-Oncology and Medical Biochemistry, Research Institute, Osaka International Cancer Institute, Osaka, Japan
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30
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Cacialli P, Dogan S, Linnerz T, Pasche C, Bertrand JY. Minichromosome maintenance protein 10 (mcm10) regulates hematopoietic stem cell emergence in the zebrafish embryo. Stem Cell Reports 2023; 18:1534-1546. [PMID: 37437546 PMCID: PMC10362509 DOI: 10.1016/j.stemcr.2023.05.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 07/14/2023] Open
Abstract
Hematopoietic stem cells (HSCs) guarantee the continuous supply of all blood lineages during life. In response to stress, HSCs are capable of extensive proliferative expansion, whereas in steady state, HSCs largely remain in a quiescent state to prevent their exhaustion. DNA replication is a very complex process, where many factors need to exert their functions in a perfectly concerted manner. Mini-chromosome-maintenance protein 10 (Mcm10) is an important replication factor, required for proper assembly of the eukaryotic replication fork. In this report, we use zebrafish to study the role of mcm10 during embryonic development, and we show that mcm10 specifically regulates HSC emergence from the hemogenic endothelium. We demonstrate that mcm10-deficient embryos present an accumulation of DNA damages in nascent HSCs, inducing their apoptosis. This phenotype can be rescued by knocking down p53. Taken all together, our results show that mcm10 plays an important role in the emergence of definitive hematopoiesis.
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Affiliation(s)
- Pietro Cacialli
- University of Geneva, Faculty of Medicine, Department of Pathology and Immunology, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Serkan Dogan
- University of Geneva, Faculty of Medicine, Department of Pathology and Immunology, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland; McMaster University, Faculty of Sciences, Department of Biology, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Tanja Linnerz
- University of Geneva, Faculty of Medicine, Department of Pathology and Immunology, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland; University of Auckland, Faculty of Medical and Health Sciences, Department of Molecular Medicine and Pathology, 85 Park Road, 1023 Auckland, New Zealand
| | - Corentin Pasche
- University of Geneva, Faculty of Medicine, Department of Pathology and Immunology, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Julien Y Bertrand
- University of Geneva, Faculty of Medicine, Department of Pathology and Immunology, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland; Geneva Centre for Inflammation Research, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
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31
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Hatoyama Y, Kanemaki MT. The assembly of the MCM2-7 hetero-hexamer and its significance in DNA replication. Biochem Soc Trans 2023:233028. [PMID: 37145026 DOI: 10.1042/bst20221465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/06/2023]
Abstract
The mini-chromosome maintenance proteins 2-7 (MCM2-7) hexamer is a protein complex that is key for eukaryotic DNA replication, which occurs only once per cell cycle. To achieve DNA replication, eukaryotic cells developed multiple mechanisms that control the timing of the loading of the hexamer onto chromatin and its activation as the replicative helicase. MCM2-7 is highly abundant in proliferating cells, which confers resistance to replication stress. Thus, the presence of an excess of MCM2-7 is important for maintaining genome integrity. However, the mechanism via which high MCM2-7 levels are achieved, other than the transcriptional upregulation of the MCM genes in the G1 phase, remained unknown. Recently, we and others reported that the MCM-binding protein (MCMBP) plays a role in the maintenance of high MCM2-7 levels and hypothesized that MCMBP functions as a chaperone in the assembly of the MCM2-7 hexamer. In this review, we discuss the roles of MCMBP in the control of MCM proteins and propose a model of the assembly of the MCM2-7 hexamer. Furthermore, we discuss a potential mechanism of the licensing checkpoint, which arrests the cells in the G1 phase when the levels of chromatin-bound MCM2-7 are reduced, and the possibility of targeting MCMBP as a chemotherapy for cancer.
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Affiliation(s)
- Yuki Hatoyama
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Yata 1111, Mishima, Shizuoka 411-8540, Japan
- Department of Biological Science, The University of Tokyo, Tokyo 113-0033, Japan
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32
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Ter Brugge P, Moser SC, Bièche I, Kristel P, Ibadioune S, Eeckhoutte A, de Bruijn R, van der Burg E, Lutz C, Annunziato S, de Ruiter J, Masliah Planchon J, Vacher S, Courtois L, El-Botty R, Dahmani A, Montaudon E, Morisset L, Sourd L, Huguet L, Derrien H, Nemati F, Chateau-Joubert S, Larcher T, Salomon A, Decaudin D, Reyal F, Coussy F, Popova T, Wesseling J, Stern MH, Jonkers J, Marangoni E. Homologous recombination deficiency derived from whole-genome sequencing predicts platinum response in triple-negative breast cancers. Nat Commun 2023; 14:1958. [PMID: 37029129 PMCID: PMC10082194 DOI: 10.1038/s41467-023-37537-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 03/22/2023] [Indexed: 04/09/2023] Open
Abstract
The high frequency of homologous recombination deficiency (HRD) is the main rationale of testing platinum-based chemotherapy in triple-negative breast cancer (TNBC), however, the existing methods to identify HRD are controversial and there is a medical need for predictive biomarkers. We assess the in vivo response to platinum agents in 55 patient-derived xenografts (PDX) of TNBC to identify determinants of response. The HRD status, determined from whole genome sequencing, is highly predictive of platinum response. BRCA1 promoter methylation is not associated with response, in part due to residual BRCA1 gene expression and homologous recombination proficiency in different tumours showing mono-allelic methylation. Finally, in 2 cisplatin sensitive tumours we identify mutations in XRCC3 and ORC1 genes that are functionally validated in vitro. In conclusion, our results demonstrate that the genomic HRD is predictive of platinum response in a large cohort of TNBC PDX and identify alterations in XRCC3 and ORC1 genes driving cisplatin response.
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Affiliation(s)
- Petra Ter Brugge
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Sarah C Moser
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ivan Bièche
- Genetics Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Petra Kristel
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Sabrina Ibadioune
- Genetics Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Alexandre Eeckhoutte
- INSERM U830, Institut Curie, PSL University, 75005, Paris, France
- Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Roebi de Bruijn
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Eline van der Burg
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Catrin Lutz
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Stefano Annunziato
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Julian de Ruiter
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Sophie Vacher
- Genetics Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Laura Courtois
- Genetics Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Rania El-Botty
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Ahmed Dahmani
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Elodie Montaudon
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Ludivine Morisset
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Laura Sourd
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Léa Huguet
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Heloise Derrien
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Fariba Nemati
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | | | | | - Anne Salomon
- Department of Pathology, Institut Curie, PSL University, 75005, Paris, France
| | - Didier Decaudin
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Fabien Reyal
- Department of Surgery, Institut Curie, PSL University, 75005, Paris, France
| | - Florence Coussy
- Department of Medical Oncology, Institut Curie, PSL University, 75005, Paris, France
| | - Tatiana Popova
- INSERM U830, Institut Curie, PSL University, 75005, Paris, France
- Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Jelle Wesseling
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Marc-Henri Stern
- Genetics Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
- INSERM U830, Institut Curie, PSL University, 75005, Paris, France
- Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands.
| | - Elisabetta Marangoni
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France.
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33
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Debaugnies M, Rodríguez-Acebes S, Blondeau J, Parent MA, Zocco M, Song Y, de Maertelaer V, Moers V, Latil M, Dubois C, Coulonval K, Impens F, Van Haver D, Dufour S, Uemura A, Sotiropoulou PA, Méndez J, Blanpain C. RHOJ controls EMT-associated resistance to chemotherapy. Nature 2023; 616:168-175. [PMID: 36949199 PMCID: PMC10076223 DOI: 10.1038/s41586-023-05838-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 02/14/2023] [Indexed: 03/24/2023]
Abstract
The resistance of cancer cells to therapy is responsible for the death of most patients with cancer1. Epithelial-to-mesenchymal transition (EMT) has been associated with resistance to therapy in different cancer cells2,3. However, the mechanisms by which EMT mediates resistance to therapy remain poorly understood. Here, using a mouse model of skin squamous cell carcinoma undergoing spontaneous EMT during tumorigenesis, we found that EMT tumour cells are highly resistant to a wide range of anti-cancer therapies both in vivo and in vitro. Using gain and loss of function studies in vitro and in vivo, we found that RHOJ-a small GTPase that is preferentially expressed in EMT cancer cells-controls resistance to therapy. Using genome-wide transcriptomic and proteomic profiling, we found that RHOJ regulates EMT-associated resistance to chemotherapy by enhancing the response to replicative stress and activating the DNA-damage response, enabling tumour cells to rapidly repair DNA lesions induced by chemotherapy. RHOJ interacts with proteins that regulate nuclear actin, and inhibition of actin polymerization sensitizes EMT tumour cells to chemotherapy-induced cell death in a RHOJ-dependent manner. Together, our study uncovers the role and the mechanisms through which RHOJ acts as a key regulator of EMT-associated resistance to chemotherapy.
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Affiliation(s)
- Maud Debaugnies
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
- CHU Saint-Pierre, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Sara Rodríguez-Acebes
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Jeremy Blondeau
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Marie-Astrid Parent
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Manuel Zocco
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Yura Song
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Viviane de Maertelaer
- Institute of Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles (ULB), Brussels, Belgium
- ULB-Cancer Research Center (U-crc), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Virginie Moers
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Mathilde Latil
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Christine Dubois
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Katia Coulonval
- Institute of Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles (ULB), Brussels, Belgium
- ULB-Cancer Research Center (U-crc), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Francis Impens
- VIB Center for Medical Biotechnology, VIB Proteomics Core, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Delphi Van Haver
- VIB Center for Medical Biotechnology, VIB Proteomics Core, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Sara Dufour
- VIB Center for Medical Biotechnology, VIB Proteomics Core, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Akiyoshi Uemura
- Department of Retinal Vascular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | | | - Juan Méndez
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Cédric Blanpain
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium.
- WELBIO, Université Libre de Bruxelles (ULB), Brussels, Belgium.
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34
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Han Z, Andrš M, Madhavan BK, Kaymak S, Sulaj A, Kender Z, Kopf S, Kihm L, Pepperkok R, Janscak P, Nawroth P, Kumar V. The importance of nuclear RAGE-Mcm2 axis in diabetes or cancer-associated replication stress. Nucleic Acids Res 2023; 51:2298-2318. [PMID: 36807739 PMCID: PMC10018352 DOI: 10.1093/nar/gkad085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 01/18/2023] [Accepted: 01/26/2023] [Indexed: 02/23/2023] Open
Abstract
An elevated frequency of DNA replication defects is associated with diabetes and cancer. However, data linking these nuclear perturbations to the onset or progression of organ complications remained unexplored. Here, we report that RAGE (Receptor for Advanced Glycated Endproducts), previously believed to be an extracellular receptor, upon metabolic stress localizes to the damaged forks. There it interacts and stabilizes the minichromosome-maintenance (Mcm2-7) complex. Accordingly, RAGE deficiency leads to slowed fork progression, premature fork collapse, hypersensitivity to replication stress agents and reduction of viability, which was reversed by the reconstitution of RAGE. This was marked by the 53BP1/OPT-domain expression and the presence of micronuclei, premature loss-of-ciliated zones, increased incidences of tubular-karyomegaly, and finally, interstitial fibrosis. More importantly, the RAGE-Mcm2 axis was selectively compromised in cells expressing micronuclei in human biopsies and mouse models of diabetic nephropathy and cancer. Thus, the functional RAGE-Mcm2/7 axis is critical in handling replication stress in vitro and human disease.
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Affiliation(s)
- Zhe Han
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
| | - Martin Andrš
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, CZ-14300 Prague, Czech Republic
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Bindhu K Madhavan
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
| | - Serap Kaymak
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
| | - Alba Sulaj
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
- German Center of Diabetes Research (DZD), Neuherberg, Germany
| | - Zoltan Kender
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
- German Center of Diabetes Research (DZD), Neuherberg, Germany
| | - Stefan Kopf
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
- German Center of Diabetes Research (DZD), Neuherberg, Germany
| | - Lars Kihm
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
| | - Rainer Pepperkok
- European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Heidelberg, Germany
| | - Pavel Janscak
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, CZ-14300 Prague, Czech Republic
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Peter Nawroth
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
- Institute for Immunology, University Hospital of Heidelberg, INF 305, Heidelberg, Germany
- German Center of Diabetes Research (DZD), Neuherberg, Germany
| | - Varun Kumar
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
- Institute for Immunology, University Hospital of Heidelberg, INF 305, Heidelberg, Germany
- European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Heidelberg, Germany
- German Center of Diabetes Research (DZD), Neuherberg, Germany
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35
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Hu Y, Stillman B. Origins of DNA replication in eukaryotes. Mol Cell 2023; 83:352-372. [PMID: 36640769 PMCID: PMC9898300 DOI: 10.1016/j.molcel.2022.12.024] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023]
Abstract
Errors occurring during DNA replication can result in inaccurate replication, incomplete replication, or re-replication, resulting in genome instability that can lead to diseases such as cancer or disorders such as autism. A great deal of progress has been made toward understanding the entire process of DNA replication in eukaryotes, including the mechanism of initiation and its control. This review focuses on the current understanding of how the origin recognition complex (ORC) contributes to determining the location of replication initiation in the multiple chromosomes within eukaryotic cells, as well as methods for mapping the location and temporal patterning of DNA replication. Origin specification and configuration vary substantially between eukaryotic species and in some cases co-evolved with gene-silencing mechanisms. We discuss the possibility that centromeres and origins of DNA replication were originally derived from a common element and later separated during evolution.
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Affiliation(s)
- Yixin Hu
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; Program in Molecular and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Bruce Stillman
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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36
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Willemsen M, Staels F, Gerbaux M, Neumann J, Schrijvers R, Meyts I, Humblet-Baron S, Liston A. DNA replication-associated inborn errors of immunity. J Allergy Clin Immunol 2023; 151:345-360. [PMID: 36395985 DOI: 10.1016/j.jaci.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022]
Abstract
Inborn errors of immunity are a heterogeneous group of monogenic immunologic disorders caused by mutations in genes with critical roles in the development, maintenance, or function of the immune system. The genetic basis is frequently a mutation in a gene with restricted expression and/or function in immune cells, leading to an immune disorder. Several classes of inborn errors of immunity, however, result from mutation in genes that are ubiquitously expressed. Despite the genes participating in cellular processes conserved between cell types, immune cells are disproportionally affected, leading to inborn errors of immunity. Mutations in DNA replication, DNA repair, or DNA damage response factors can result in monogenic human disease, some of which are classified as inborn errors of immunity. Genetic defects in the DNA repair machinery are a well-known cause of T-B-NK+ severe combined immunodeficiency. An emerging class of inborn errors of immunity is those caused by mutations in DNA replication factors. Considerable heterogeneity exists within the DNA replication-associated inborn errors of immunity, with diverse immunologic defects and clinical manifestations observed. These differences are suggestive for differential sensitivity of certain leukocyte subsets to deficiencies in specific DNA replication factors. Here, we provide an overview of DNA replication-associated inborn errors of immunity and discuss the emerging mechanistic insights that can explain the observed immunologic heterogeneity.
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Affiliation(s)
- Mathijs Willemsen
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.
| | - Frederik Staels
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
| | - Margaux Gerbaux
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; Pediatric Department, Academic Children Hospital Queen Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Julika Neumann
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Rik Schrijvers
- Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium; Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Isabelle Meyts
- Department of Microbiology, Immunology and Transplantation, Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium; Department of Pediatrics, Division of Primary Immunodeficiencies, University Hospitals Leuven, Leuven, Belgium; ERN-RITA Core Center Member, Leuven, Belgium
| | - Stephanie Humblet-Baron
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium.
| | - Adrian Liston
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium; Immunology Program, The Babraham Institute, Babraham Research Campus, Cambridge.
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The CMG helicase and cancer: a tumor "engine" and weakness with missing mutations. Oncogene 2023; 42:473-490. [PMID: 36522488 PMCID: PMC9948756 DOI: 10.1038/s41388-022-02572-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022]
Abstract
The replicative Cdc45-MCM-GINS (CMG) helicase is a large protein complex that functions in the DNA melting and unwinding steps as a component of replisomes during DNA replication in mammalian cells. Although the CMG performs this important role in cell growth, the CMG is not a simple bystander in cell cycle events. Components of the CMG, specifically the MCM precursors, are also involved in maintaining genomic stability by regulating DNA replication fork speeds, facilitating recovery from replicative stresses, and preventing consequential DNA damage. Given these important functions, MCM/CMG complexes are highly regulated by growth factors such as TGF-ß1 and by signaling factors such as Myc, Cyclin E, and the retinoblastoma protein. Mismanagement of MCM/CMG complexes when these signaling mediators are deregulated, and in the absence of the tumor suppressor protein p53, leads to increased genomic instability and is a contributor to tumorigenic transformation and tumor heterogeneity. The goal of this review is to provide insight into the mechanisms and dynamics by which the CMG is regulated during its assembly and activation in mammalian genomes, and how errors in CMG regulation due to oncogenic changes promote tumorigenesis. Finally, and most importantly, we highlight the emerging understanding of the CMG helicase as an exploitable vulnerability and novel target for therapeutic intervention in cancer.
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38
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Song H, Shen R, Mahasin H, Guo Y, Wang D. DNA replication: Mechanisms and therapeutic interventions for diseases. MedComm (Beijing) 2023; 4:e210. [PMID: 36776764 PMCID: PMC9899494 DOI: 10.1002/mco2.210] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 02/09/2023] Open
Abstract
Accurate and integral cellular DNA replication is modulated by multiple replication-associated proteins, which is fundamental to preserve genome stability. Furthermore, replication proteins cooperate with multiple DNA damage factors to deal with replication stress through mechanisms beyond their role in replication. Cancer cells with chronic replication stress exhibit aberrant DNA replication and DNA damage response, providing an exploitable therapeutic target in tumors. Numerous evidence has indicated that posttranslational modifications (PTMs) of replication proteins present distinct functions in DNA replication and respond to replication stress. In addition, abundant replication proteins are involved in tumorigenesis and development, which act as diagnostic and prognostic biomarkers in some tumors, implying these proteins act as therapeutic targets in clinical. Replication-target cancer therapy emerges as the times require. In this context, we outline the current investigation of the DNA replication mechanism, and simultaneously enumerate the aberrant expression of replication proteins as hallmark for various diseases, revealing their therapeutic potential for target therapy. Meanwhile, we also discuss current observations that the novel PTM of replication proteins in response to replication stress, which seems to be a promising strategy to eliminate diseases.
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Affiliation(s)
- Hao‐Yun Song
- School of Basic Medical SciencesLanzhou UniversityLanzhouGansuChina
| | - Rong Shen
- School of Basic Medical SciencesLanzhou UniversityLanzhouGansuChina
| | - Hamid Mahasin
- School of Basic Medical SciencesLanzhou UniversityLanzhouGansuChina
| | - Ya‐Nan Guo
- School of Basic Medical SciencesLanzhou UniversityLanzhouGansuChina
| | - De‐Gui Wang
- School of Basic Medical SciencesLanzhou UniversityLanzhouGansuChina
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39
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Jin S, Park JH, Yun HJ, Oh YN, Oh S, Choi YH, Kim BW, Kwon HJ. Cedrol, a Sesquiterpene Isolated from Juniperus chinensis, Inhibits Human Colorectal Tumor Growth associated through Downregulation of Minichromosome Maintenance Proteins. J Cancer Prev 2022; 27:221-228. [PMID: 36713942 PMCID: PMC9836914 DOI: 10.15430/jcp.2022.27.4.221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/18/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023] Open
Abstract
Cedrol, a sesquiterpene alcohol, isolated from Juniperus chinensis has been reported to inhibit minichromosome maintenance (MCM) proteins as cancer biomarkers in human lung cancer in vitro. In the present study, we investigated the anti-cancer activity of cedrol in vitro and in vivo using human colorectal cancer HT29 cells and a human colorectal tumor xenograft model. Cedrol inhibited MCM protein expression and cell growth in HT29 cells, which are associated with G1 arrest and the induction of apoptosis. We demonstrated that cedrol effectively reduced HT29 tumor growth without apparent weight loss in a human tumor xenograft model. Compared with vehicle- and adriamycin-treated tumor tissues, cedrol induced changes in the tumor tissue structure, resulting in a reduced cell density within the tumor parenchyma and reduced vascularization. Moreover, the expression of MCM7, an important subunit of MCM helicase, was significantly suppressed by cedrol in tumor tissue. Collectively, these results suggest that cedrol may act as a potential anti-cancer agent for colorectal cancer by inhibiting MCM protein expression and tumor growth.
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Affiliation(s)
- Soojung Jin
- Core-Facility Center for Tissue Regeneration, Dong-eui University, Busan, Korea
| | - Jung-ha Park
- Core-Facility Center for Tissue Regeneration, Dong-eui University, Busan, Korea,Biopharmaceutical Engineering Major, Division of Applied Bioengineering, College of Engineering, Dong-eui University, Busan, Korea,Department of Biopharmaceutics, Dong-eui University Graduate School, Busan, Korea
| | - Hee Jung Yun
- Biopharmaceutical Engineering Major, Division of Applied Bioengineering, College of Engineering, Dong-eui University, Busan, Korea,Department of Biopharmaceutics, Dong-eui University Graduate School, Busan, Korea
| | - You Na Oh
- Core-Facility Center for Tissue Regeneration, Dong-eui University, Busan, Korea
| | - Seunghye Oh
- Department of Biopharmaceutics, Dong-eui University Graduate School, Busan, Korea
| | - Yung Hyun Choi
- Core-Facility Center for Tissue Regeneration, Dong-eui University, Busan, Korea,Department of Biochemistry, College of Korean Medicine, Busan, Korea
| | - Byung Woo Kim
- Biopharmaceutical Engineering Major, Division of Applied Bioengineering, College of Engineering, Dong-eui University, Busan, Korea,Department of Biopharmaceutics, Dong-eui University Graduate School, Busan, Korea,Blue-Bio Industry Regional Innovation Center, Dong-eui University, Busan, Korea,Byung Woo Kim, E-mail: , https://orcid.org/0000-0001-7940-1074
| | - Hyun Ju Kwon
- Core-Facility Center for Tissue Regeneration, Dong-eui University, Busan, Korea,Biopharmaceutical Engineering Major, Division of Applied Bioengineering, College of Engineering, Dong-eui University, Busan, Korea,Department of Biopharmaceutics, Dong-eui University Graduate School, Busan, Korea,Blue-Bio Industry Regional Innovation Center, Dong-eui University, Busan, Korea,Correspondence to Hyun Ju Kwon, E-mail: , https://orcid.org/0000-0002-1375-0906
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40
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Schuhwerk H, Kleemann J, Gupta P, van Roey R, Armstark I, Kreileder M, Feldker N, Ramesh V, Hajjaj Y, Fuchs K, Mahapatro M, Hribersek M, Volante M, Groenewoud A, Engel FB, Ceppi P, Eckstein M, Hartmann A, Müller F, Kroll T, Stemmler MP, Brabletz S, Brabletz T. The EMT transcription factor ZEB1 governs a fitness-promoting but vulnerable DNA replication stress response. Cell Rep 2022; 41:111819. [PMID: 36516781 DOI: 10.1016/j.celrep.2022.111819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 10/14/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
The DNA damage response (DDR) and epithelial-to-mesenchymal transition (EMT) are two crucial cellular programs in cancer biology. While the DDR orchestrates cell-cycle progression, DNA repair, and cell death, EMT promotes invasiveness, cellular plasticity, and intratumor heterogeneity. Therapeutic targeting of EMT transcription factors, such as ZEB1, remains challenging, but tumor-promoting DDR alterations elicit specific vulnerabilities. Using multi-omics, inhibitors, and high-content microscopy, we discover a chemoresistant ZEB1-high-expressing sub-population (ZEB1hi) with co-rewired cell-cycle progression and proficient DDR across tumor entities. ZEB1 stimulates accelerated S-phase entry via CDK6, inflicting endogenous DNA replication stress. However, DDR buildups involving constitutive MRE11-dependent fork resection allow homeostatic cycling and enrichment of ZEB1hi cells during transforming growth factor β (TGF-β)-induced EMT and chemotherapy. Thus, ZEB1 promotes G1/S transition to launch a progressive DDR benefitting stress tolerance, which concurrently manifests a targetable vulnerability in chemoresistant ZEB1hi cells. Our study thus highlights the translationally relevant intercept of the DDR and EMT.
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Affiliation(s)
- Harald Schuhwerk
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany.
| | - Julia Kleemann
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Pooja Gupta
- Core Unit for Bioinformatics, Data Integration and Analysis, Center for Medical Information and Communication Technology, University Hospital Erlangen, Erlangen Germany
| | - Ruthger van Roey
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Isabell Armstark
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Martina Kreileder
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Nora Feldker
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Vignesh Ramesh
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Yussuf Hajjaj
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Kathrin Fuchs
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Mousumi Mahapatro
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Mojca Hribersek
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Marco Volante
- Department of Oncology, University of Turin, Orbassano, Turin, Italy
| | - Arwin Groenewoud
- Experimental Renal and Cardiovascular Research, Department of Nephropathology, Institute of Pathology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Felix B Engel
- Experimental Renal and Cardiovascular Research, Department of Nephropathology, Institute of Pathology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Paolo Ceppi
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Markus Eckstein
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen- Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen- Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Fabian Müller
- Department of Internal Medicine 5, Haematology and Oncology, University Hospital Erlangen, Erlangen Germany
| | - Torsten Kroll
- Leibniz Institute on Aging - Fritz-Lipmann Institute (FLI), Jena, Germany
| | - Marc P Stemmler
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Simone Brabletz
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Thomas Brabletz
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany.
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41
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Böhly N, Schmidt AK, Zhang X, Slusarenko BO, Hennecke M, Kschischo M, Bastians H. Increased replication origin firing links replication stress to whole chromosomal instability in human cancer. Cell Rep 2022; 41:111836. [PMID: 36516748 DOI: 10.1016/j.celrep.2022.111836] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 09/12/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
Chromosomal instability (CIN) is a hallmark of cancer and comprises structural CIN (S-CIN) and numerical or whole chromosomal CIN (W-CIN). Recent work indicated that replication stress (RS), known to contribute to S-CIN, also affects mitotic chromosome segregation, possibly explaining the common co-existence of S-CIN and W-CIN in human cancer. Here, we show that RS-induced increased origin firing is sufficient to trigger W-CIN in human cancer cells. We discovered that overexpression of origin firing genes, including GINS1 and CDC45, correlates with W-CIN in human cancer specimens and causes W-CIN in otherwise chromosomally stable human cells. Furthermore, modulation of the ATR-CDK1-RIF1 axis increases the number of firing origins and leads to W-CIN. Importantly, chromosome missegregation upon additional origin firing is mediated by increased mitotic microtubule growth rates, a mitotic defect prevalent in chromosomally unstable cancer cells. Thus, our study identifies increased replication origin firing as a cancer-relevant trigger for chromosomal instability.
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Affiliation(s)
- Nicolas Böhly
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany
| | - Ann-Kathrin Schmidt
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany
| | - Xiaoxiao Zhang
- University of Applied Sciences Koblenz, Department of Mathematics and Technology, 53424 Remagen, Germany; Technical University of Munich, Department of Informatics, 81675 Munich, Germany
| | - Benjamin O Slusarenko
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany
| | - Magdalena Hennecke
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany
| | - Maik Kschischo
- University of Applied Sciences Koblenz, Department of Mathematics and Technology, 53424 Remagen, Germany
| | - Holger Bastians
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany.
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42
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Guan M, Ji W, Xu Y, Yan L, Chen D, Li S, Zhang X. Molecular fingerprints of polar narcotic chemicals based on heterozygous essential gene knockout library in Saccharomyces cerevisiae. CHEMOSPHERE 2022; 308:136343. [PMID: 36087727 DOI: 10.1016/j.chemosphere.2022.136343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 08/02/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Cytotoxicity of non-polar narcotic chemicals can be predicted by quantitative structure activity relationship (QSAR) models, but the polar narcotic chemicals' actual cytotoxicity exceeds the predicted values by their chemical structures. This discrepancy indicates that the molecular mechanism by which polar narcotic chemicals exert their toxicity is unclear. Taking advantage of Saccharomyces cerevisiae (yeast) functional genome-wide heterozygous essential gene knockout mutants, we here have identified the specific molecular fingerprints of two main chemical structure groups (phenols and anilines) of polar narcotic chemicals (dichlorophen (DCP), 4-chlorophenol (4-CP), 2, 4, 6-trichlorophenol (TCP), 3, 4-dichloroaniline (DCA) and N-methylaniline (NMA)) and one non-polar narcotic chemical 2, 2, 2-trichloroethanol (TCE). Especially, we identify 33, 57, 54, 46, 59 and 53 responsive strains through exposure to TCE, DCP, 4-CP, TCP, DCA and NMA with three test concentrations, respectively, revealing that these polar narcotic chemicals have more responsive strains than the non-polar narcotic chemical. Remarkably, we find that the molecular fingerprints of polar narcotic chemicals in different chemical structure groups are obviously varied, particularly phenols and anilines have their own specific molecular fingerprints. Interestingly, our results demonstrate that the molecular toxicity mechanisms of anilines are associated with DNA replication, but phenols are related with pathway of RNA degradation. Additionally, we find that the two knockout strains (SME1 and DIS3) and the three knockout strains (TSC11, RSP5 and HSF1) can specifically respond to exposure to phenols and anilines, respectively. Thus, they may be served as potential biomarkers to distinguish phenols from anilines. Collectively, our works demonstrate that the functional genomic platform of yeast essential gene mutants can not only act as an effective tool to identify key specific molecular fingerprints for polar narcotic chemicals, but also help to understand the molecular mechanisms of polar narcotic chemicals.
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Affiliation(s)
- Miao Guan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, Jiangsu, 210023, China.
| | - Wenya Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, Jiangsu, 210023, China
| | - Yue Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, Jiangsu, 210023, China
| | - Lu Yan
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, China
| | - Dong Chen
- Jiangsu Provincial Academy of Environmental Science, 176 North Jiangdong Rd., Nanjing, Jiangsu, 210036, China
| | - Shengjie Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, Jiangsu, 210023, China; School of Food Science, Nanjing Xiaozhuang University, Jiangsu, Nanjing, 211171, China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, China.
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43
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Jodkowska K, Pancaldi V, Rigau M, Almeida R, Fernández-Justel J, Graña-Castro O, Rodríguez-Acebes S, Rubio-Camarillo M, Carrillo-de Santa Pau E, Pisano D, Al-Shahrour F, Valencia A, Gómez M, Méndez J. 3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells. Nucleic Acids Res 2022; 50:12149-12165. [PMID: 36453993 PMCID: PMC9757045 DOI: 10.1093/nar/gkac1111] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 10/31/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
In mammalian cells, chromosomal replication starts at thousands of origins at which replisomes are assembled. Replicative stress triggers additional initiation events from 'dormant' origins whose genomic distribution and regulation are not well understood. In this study, we have analyzed origin activity in mouse embryonic stem cells in the absence or presence of mild replicative stress induced by aphidicolin, a DNA polymerase inhibitor, or by deregulation of origin licensing factor CDC6. In both cases, we observe that the majority of stress-responsive origins are also active in a small fraction of the cell population in a normal S phase, and stress increases their frequency of activation. In a search for the molecular determinants of origin efficiency, we compared the genetic and epigenetic features of origins displaying different levels of activation, and integrated their genomic positions in three-dimensional chromatin interaction networks derived from high-depth Hi-C and promoter-capture Hi-C data. We report that origin efficiency is directly proportional to the proximity to transcriptional start sites and to the number of contacts established between origin-containing chromatin fragments, supporting the organization of origins in higher-level DNA replication factories.
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Affiliation(s)
| | | | | | | | - José M Fernández-Justel
- Functional Organization of the Mammalian Genome Group, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Madrid, Spain
| | - Osvaldo Graña-Castro
- Bioinformatics Unit, Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain,Institute of Applied Molecular Medicine (IMMA-Nemesio Díez), San Pablo-CEU University, Boadilla del Monte, Madrid, Spain
| | - Sara Rodríguez-Acebes
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Miriam Rubio-Camarillo
- Bioinformatics Unit, Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - David Pisano
- Bioinformatics Unit, Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Fátima Al-Shahrour
- Bioinformatics Unit, Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Alfonso Valencia
- Computational Biology Life Sciences Group, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - María Gómez
- Correspondence may also be addressed to María Gómez. Tel: +34 911964724; Fax: +34 911964420;
| | - Juan Méndez
- To whom correspondence should be addressed. Tel: +34 917328000; Fax: +34 917328033;
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44
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Richards L, Lord CL, Benton ML, Capra JA, Nordman JT. Nucleoporins facilitate ORC loading onto chromatin. Cell Rep 2022; 41:111590. [PMID: 36351393 PMCID: PMC10040217 DOI: 10.1016/j.celrep.2022.111590] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/10/2022] [Accepted: 10/11/2022] [Indexed: 11/11/2022] Open
Abstract
The origin recognition complex (ORC) binds throughout the genome to initiate DNA replication. In metazoans, it is still unclear how ORC is targeted to specific loci to facilitate helicase loading and replication initiation. Here, we perform immunoprecipitations coupled with mass spectrometry for ORC2 in Drosophila embryos. Surprisingly, we find that ORC2 associates with multiple subunits of the Nup107-160 subcomplex of the nuclear pore. Bioinformatic analysis reveals that, relative to all modENCODE factors, nucleoporins are among the most enriched factors at ORC2 binding sites. Critically, depletion of the nucleoporin Elys, a member of the Nup107-160 complex, decreases ORC2 loading onto chromatin. Depleting Elys also sensitizes cells to replication fork stalling, which could reflect a defect in establishing dormant replication origins. Our work reveals a connection between ORC, replication initiation, and nucleoporins, suggesting a function for nucleoporins in metazoan replication initiation.
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Affiliation(s)
- Logan Richards
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Christopher L Lord
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | | | - John A Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA 94143, USA
| | - Jared T Nordman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA.
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45
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MCM2 in human cancer: functions, mechanisms, and clinical significance. Mol Med 2022; 28:128. [PMID: 36303105 PMCID: PMC9615236 DOI: 10.1186/s10020-022-00555-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/10/2022] [Indexed: 11/18/2022] Open
Abstract
Background Aberrant DNA replication is the main source of genomic instability that leads to tumorigenesis and progression. MCM2, a core subunit of eukaryotic helicase, plays a vital role in DNA replication. The dysfunction of MCM2 results in the occurrence and progression of multiple cancers through impairing DNA replication and cell proliferation. Conclusions MCM2 is a vital regulator in DNA replication. The overexpression of MCM2 was detected in multiple types of cancers, and the dysfunction of MCM2 was correlated with the progression and poor prognoses of malignant tumors. According to the altered expression of MCM2 and its correlation with clinicopathological features of cancer patients, MCM2 was thought to be a sensitive biomarker for cancer diagnosis, prognosis, and chemotherapy response. The anti-tumor effect induced by MCM2 inhibition implies the potential of MCM2 to be a novel therapeutic target for cancer treatment. Since DNA replication stress, which may stimulate anti-tumor immunity, frequently occurs in MCM2 deficient cells, it also proposes the possibility that MCM2 targeting improves the effect of tumor immunotherapy.
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46
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Shi W, Hu R, Zhao R, Zhu J, Shen H, Li H, Wang L, Yang Z, Jiang Q, Qiao Y, Jiang G, Cheng J, Wan X. Transcriptome analysis of hepatopancreas and gills of Palaemon gravieri under salinity stress. Gene 2022; 851:147013. [DOI: 10.1016/j.gene.2022.147013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 09/01/2022] [Accepted: 10/25/2022] [Indexed: 11/04/2022]
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47
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Safeguarding DNA Replication: A Golden Touch of MiDAS and Other Mechanisms. Int J Mol Sci 2022; 23:ijms231911331. [PMID: 36232633 PMCID: PMC9570362 DOI: 10.3390/ijms231911331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/21/2022] Open
Abstract
DNA replication is a tightly regulated fundamental process allowing the correct duplication and transfer of the genetic information from the parental cell to the progeny. It involves the coordinated assembly of several proteins and protein complexes resulting in replication fork licensing, firing and progression. However, the DNA replication pathway is strewn with hurdles that affect replication fork progression during S phase. As a result, cells have adapted several mechanisms ensuring replication completion before entry into mitosis and segregating chromosomes with minimal, if any, abnormalities. In this review, we describe the possible obstacles that a replication fork might encounter and how the cell manages to protect DNA replication from S to the next G1.
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Peycheva M, Neumann T, Malzl D, Nazarova M, Schoeberl UE, Pavri R. DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations. Science 2022; 377:eabj5502. [DOI: 10.1126/science.abj5502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Chromosomal translocations result from the joining of DNA double-strand breaks (DSBs) and frequently cause cancer. However, the steps linking DSB formation to DSB ligation remain undeciphered. We report that DNA replication timing (RT) directly regulates lymphomagenic
Myc
translocations during antibody maturation in B cells downstream of DSBs and independently of DSB frequency. Depletion of minichromosome maintenance complexes alters replication origin activity, decreases translocations, and deregulates global RT. Ablating a single origin at
Myc
causes an early-to-late RT switch, loss of translocations, and reduced proximity with the immunoglobulin heavy chain (
Igh
) gene, its major translocation partner. These phenotypes were reversed by restoring early RT. Disruption of early RT also reduced tumorigenic translocations in human leukemic cells. Thus, RT constitutes a general mechanism in translocation biogenesis linking DSB formation to DSB ligation.
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Affiliation(s)
- Mihaela Peycheva
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna Biocenter, 1030 Vienna, Austria
| | - Daniel Malzl
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
| | - Mariia Nazarova
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
| | - Ursula E. Schoeberl
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
| | - Rushad Pavri
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
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Matsukawa T, Yin M, Baslan T, Chung YJ, Cao D, Bertoli R, Zhu YJ, Walker RL, Freeland A, Knudsen E, Lowe SW, Meltzer PS, Aplan PD. Mcm2 hypomorph leads to acute leukemia or hematopoietic stem cell failure, dependent on genetic context. FASEB J 2022; 36:e22430. [PMID: 35920299 PMCID: PMC9377154 DOI: 10.1096/fj.202200061rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 11/11/2022]
Abstract
Minichromosome maintenance proteins (Mcm2-7) form a hexameric complex that unwinds DNA ahead of a replicative fork. The deficiency of Mcm proteins leads to replicative stress and consequent genomic instability. Mice with a germline insertion of a Cre cassette into the 3'UTR of the Mcm2 gene (designated Mcm2Cre ) have decreased Mcm2 expression and invariably develop precursor T-cell lymphoblastic leukemia/lymphoma (pre-T LBL), due to 100-1000 kb deletions involving important tumor suppressor genes. To determine whether mice that were protected from pre-T LBL would develop non-T-cell malignancies, we used two approaches. Mice engrafted with Mcm2Cre/Cre Lin- Sca-1+ Kit+ hematopoietic stem/progenitor cells did not develop hematologic malignancy; however, these mice died of hematopoietic stem cell failure by 6 months of age. Placing the Mcm2Cre allele onto an athymic nu/nu background completely prevented pre-T LBL and extended survival of these mice three-fold (median 296.5 vs. 80.5 days). Ultimately, most Mcm2Cre/Cre ;nu/nu mice developed B-cell precursor acute lymphoblastic leukemia (BCP-ALL). We identified recurrent deletions of 100-1000 kb that involved genes known or suspected to be involved in BCP-ALL, including Pax5, Nf1, Ikzf3, and Bcor. Moreover, whole-exome sequencing identified recurrent mutations of genes known to be involved in BCP-ALL progression, such as Jak1/Jak3, Ptpn11, and Kras. These findings demonstrate that an Mcm2Cre/Cre hypomorph can induce hematopoietic dysfunction via hematopoietic stem cell failure as well as a "deletor" phenotype affecting known or suspected tumor suppressor genes.
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Affiliation(s)
- Toshihiro Matsukawa
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- These authors contributed equally to this work
| | - Mianmian Yin
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- These authors contributed equally to this work
| | - Timour Baslan
- Cancer Biology and Genetics Program, Sloan-Kettering Institute, NY, USA
| | - Yang Jo Chung
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dengchao Cao
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ryan Bertoli
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yuelin J. Zhu
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Robert L. Walker
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy Freeland
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Erik Knudsen
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Scott W. Lowe
- Cancer Biology and Genetics Program, Sloan-Kettering Institute, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Paul S. Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter D. Aplan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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50
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NCOA4 links iron bioavailability to DNA metabolism. Cell Rep 2022; 40:111207. [PMID: 35977492 DOI: 10.1016/j.celrep.2022.111207] [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: 04/25/2021] [Revised: 05/20/2022] [Accepted: 07/22/2022] [Indexed: 12/22/2022] Open
Abstract
Iron is essential for deoxyribonucleotides production and for enzymes containing an Fe-S cluster involved in DNA replication and repair. How iron bioavailability and DNA metabolism are coordinated remains poorly understood. NCOA4 protein mediates autophagic degradation of ferritin to maintain iron homeostasis and inhibits DNA replication origin activation via hindrance of the MCM2-7 DNA helicase. Here, we show that iron deficiency inhibits DNA replication, parallel to nuclear NCOA4 stabilization. In iron-depleted cells, NCOA4 knockdown leads to unscheduled DNA synthesis, with replication stress, genome instability, and cell death. In mice, NCOA4 genetic inactivation causes defective intestinal regeneration upon dextran sulfate sodium-mediated injury, with DNA damage, defective cell proliferation, and cell death; in intestinal organoids, this is fostered by iron depletion. In summary, we describe a NCOA4-dependent mechanism that coordinates iron bioavailability and DNA replication. This function prevents replication stress, maintains genome integrity, and sustains high rates of cell proliferation during tissue regeneration.
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