1
|
Jahjah T, Singh JK, Gottifredi V, Quinet A. Tolerating DNA damage by repriming: Gap filling in the spotlight. DNA Repair (Amst) 2024; 142:103758. [PMID: 39236419 DOI: 10.1016/j.dnarep.2024.103758] [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: 05/17/2024] [Revised: 08/14/2024] [Accepted: 08/25/2024] [Indexed: 09/07/2024]
Abstract
Timely and accurate DNA replication is critical for safeguarding genome integrity and ensuring cell viability. Yet, this process is challenged by DNA damage blocking the progression of the replication machinery. To counteract replication fork stalling, evolutionary conserved DNA damage tolerance (DDT) mechanisms promote DNA damage bypass and fork movement. One of these mechanisms involves "skipping" DNA damage through repriming downstream of the lesion, leaving single-stranded DNA (ssDNA) gaps behind the advancing forks (also known as post-replicative gaps). In vertebrates, repriming in damaged leading templates is proposed to be mainly promoted by the primase and polymerase PRIMPOL. In this review, we discuss recent advances towards our understanding of the physiological and pathological conditions leading to repriming activation in human models, revealing a regulatory network of PRIMPOL activity. Upon repriming by PRIMPOL, post-replicative gaps formed can be filled-in by the DDT mechanisms translesion synthesis and template switching. We discuss novel findings on how these mechanisms are regulated and coordinated in time to promote gap filling. Finally, we discuss how defective gap filling and aberrant gap expansion by nucleases underlie the cytotoxicity associated with post-replicative gap accumulation. Our increasing knowledge of this repriming mechanism - from gap formation to gap filling - is revealing that targeting the last step of this pathway is a promising approach to exploit post-replicative gaps in anti-cancer therapeutic strategies.
Collapse
Affiliation(s)
- Tiya Jahjah
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, Fontenay-aux-Roses F-92265, France; Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, Fontenay-aux-Roses F-92265, France
| | - Jenny K Singh
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, Fontenay-aux-Roses F-92265, France; Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, Fontenay-aux-Roses F-92265, France
| | - Vanesa Gottifredi
- Fundación Instituto Leloir, IIBBA, CONICET, Buenos Aires 1405, Argentina
| | - Annabel Quinet
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, Fontenay-aux-Roses F-92265, France; Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, Fontenay-aux-Roses F-92265, France.
| |
Collapse
|
2
|
D'Souza J, Hickson ID. Replication fork barriers to study site-specific DNA replication perturbation. DNA Repair (Amst) 2024; 141:103735. [PMID: 39079395 DOI: 10.1016/j.dnarep.2024.103735] [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: 05/21/2024] [Revised: 07/02/2024] [Accepted: 07/19/2024] [Indexed: 08/18/2024]
Abstract
DNA replication ensures the complete and accurate duplication of the genome. The traditional approach to analysing perturbation of DNA replication is to use chemical inhibitors, such as hydroxyurea or aphidicolin, that slow or stall replication fork progression throughout the genome. An alternative approach is to perturb replication at a single site in the genome that permits a more forensic investigation of the cellular response to the stalling or disruption of a replication fork. This has been achieved in several organisms using different systems that share the common feature of utilizing the high affinity binding of a protein to a defined DNA sequence that is integrated into a specific locus in the host genome. Protein-mediated replication fork blocking systems of this sort have proven very valuable in defining how cells cope with encountering a barrier to fork progression. In this review, we compare protein-based replication fork barrier systems from different organisms that have been developed to generate site-specific replication fork perturbation.
Collapse
Affiliation(s)
- Jenevieve D'Souza
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Ian D Hickson
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark.
| |
Collapse
|
3
|
Chudy P, Kochan J, Wawro M, Nguyen P, Gorczyca M, Varanko A, Retka A, Ghadei SS, Napieralska E, Grochot-Przęczek A, Szade K, Berendes LS, Park J, Sokołowski G, Yu Q, Józkowicz A, Nowak WN, Krzeptowski W. Heme oxygenase-1 protects cells from replication stress. Redox Biol 2024; 75:103247. [PMID: 39047636 PMCID: PMC11321372 DOI: 10.1016/j.redox.2024.103247] [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: 05/17/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024] Open
Abstract
Heme oxygenase-1 (HO-1, HMOX1) degrades heme protecting cells from heme-induced oxidative damage. Beyond its well-established cellular functions, heme has emerged as a stabilizer of G-quadruplexes. These secondary DNA structures interfere with DNA replication. We recently revealed that nuclear HO-1 colocalizes with DNA G-quadruplexes and promotes their removal. Here, we investigate whether HO-1 safeguards cells against replication stress. Experiments were conducted in control and HMOX1-deficient HEK293T cell lines. Immunostaining unveiled that DNA G-quadruplexes accumulated in the absence of HO-1, the effect that was further enhanced in response to δ-aminolevulinic acid (ALA), a substrate in heme synthesis. This was associated with replication stress, as evidenced by an elevated proportion of stalled forks analyzed by fiber assay. We observed the same effects in hematopoietic stem cells isolated from Hmox1 knockout mice and in a lymphoblastoid cell line from an HMOX1-deficient patient. Interestingly, in the absence of HO-1, the speed of fork progression was higher, and the response to DNA conformational hindrance less stringent, indicating dysfunction of the PARP1-p53-p21 axis. PARP1 activity was not decreased in the absence of HO-1. Instead, we observed that HO-1 deficiency impairs the nuclear import and accumulation of p53, an effect dependent on the removal of excess heme. We also demonstrated that administering ALA is a more specific method for increasing intracellular free heme compared to treatment with hemin, which in turn induces strong lipid peroxidation. Our results indicate that protection against replication stress is a universal feature of HO-1, presumably contributing to its widely recognized cytoprotective activity.
Collapse
Affiliation(s)
- Patryk Chudy
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Jakub Kochan
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Mateusz Wawro
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Phu Nguyen
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Monika Gorczyca
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Aliaksandra Varanko
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Aleksandra Retka
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Swati Sweta Ghadei
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Emilija Napieralska
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Anna Grochot-Przęczek
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Krzysztof Szade
- Laboratory of Stem Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Lea-Sophie Berendes
- Department of General Pediatrics, University Hospital Münster, Münster, Germany
| | - Julien Park
- Department of General Pediatrics, University Hospital Münster, Münster, Germany
| | - Grzegorz Sokołowski
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Qiuliyang Yu
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, China
| | - Alicja Józkowicz
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Witold N Nowak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland; August Chełkowski Institute of Physics, Faculty of Science and Technology, University of Silesia, Chorzów, Poland.
| | - Wojciech Krzeptowski
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
| |
Collapse
|
4
|
Kawale AS, Zou L. Regulation, functional impact, and therapeutic targeting of APOBEC3A in cancer. DNA Repair (Amst) 2024; 141:103734. [PMID: 39047499 PMCID: PMC11330346 DOI: 10.1016/j.dnarep.2024.103734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
Enzymes of the apolipoprotein B mRNA editing catalytic polypeptide like (APOBEC) family are cytosine deaminases that convert cytosine to uracil in DNA and RNA. Among these proteins, APOBEC3 sub-family members, APOBEC3A (A3A) and APOBEC3B (A3B), are prominent sources of mutagenesis in cancer cells. The aberrant expression of A3A and A3B in cancer cells leads to accumulation of mutations with specific single-base substitution (SBS) signatures, characterized by C→T and C→G changes, in a number of tumor types. In addition to fueling mutagenesis, A3A and A3B, particularly A3A, induce DNA replication stress, DNA damage, and chromosomal instability through their catalytic activities, triggering a range of cellular responses. Thus, A3A/B have emerged as key drivers of genome evolution during cancer development, contributing to tumorigenesis, tumor heterogeneity, and therapeutic resistance. Yet, the expression of A3A/B in cancer cells presents a cancer vulnerability that can be exploited therapeutically. In this review, we discuss the recent studies that shed light on the mechanisms regulating A3A expression and the impact of A3A in cancer. We also review recent advances in the development of A3A inhibitors and provide perspectives on the future directions of A3A research.
Collapse
Affiliation(s)
- Ajinkya S Kawale
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Lee Zou
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA.
| |
Collapse
|
5
|
Ramirez-Otero MA, Costanzo V. "Bridging the DNA divide": Understanding the interplay between replication- gaps and homologous recombination proteins RAD51 and BRCA1/2. DNA Repair (Amst) 2024; 141:103738. [PMID: 39084178 DOI: 10.1016/j.dnarep.2024.103738] [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: 03/31/2024] [Revised: 06/24/2024] [Accepted: 07/25/2024] [Indexed: 08/02/2024]
Abstract
A key but often neglected component of genomic instability is the emergence of single-stranded DNA (ssDNA) gaps during DNA replication in the absence of functional homologous recombination (HR) proteins, such as RAD51 and BRCA1/2. Research in prokaryotes has shed light on the dual role of RAD51's bacterial ortholog, RecA, in HR and the protection of replication forks, emphasizing its essential role in preventing the formation of ssDNA gaps, which is vital for cellular viability. This phenomenon was corroborated in eukaryotic cells deficient in HR, where the formation of ssDNA gaps within newly synthesized DNA and their subsequent processing by the MRE11 nuclease were observed. Without functional HR proteins, cells employ alternative ssDNA gap-filling mechanisms to ensure survival, though this compensatory response can compromise genomic stability. A notable example is the involvement of the translesion synthesis (TLS) polymerase POLζ, along with the repair protein POLθ, in the suppression of replicative ssDNA gaps. Persistent ssDNA gaps may result in replication fork collapse, chromosomal anomalies, and cell death, which contribute to cancer progression and resistance to therapy. Elucidating the processes that avert ssDNA gaps and safeguard replication forks is critical for enhancing cancer treatment approaches by exploiting the vulnerabilities of cancer cells in these pathways.
Collapse
Affiliation(s)
| | - Vincenzo Costanzo
- IFOM ETS - The AIRC Institute of Molecular Oncology, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy.
| |
Collapse
|
6
|
Li C, Fan S, Li P, Bai Y, Wang Y, Cui Y, Li M, Wang R, Shao Y, Wang Y, Zheng S, Wang R, Gao L, Li M, Zheng Y, Wang F, Gao S, Feng S, Wang J, Qu X, Li X. A sophisticated mechanism governs Pol ζ activity in response to replication stress. Nat Commun 2024; 15:7562. [PMID: 39215012 PMCID: PMC11364643 DOI: 10.1038/s41467-024-52112-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024] Open
Abstract
DNA polymerase ζ (Pol ζ) plays an essential role in replicating damaged DNA templates but contributes to mutagenesis due to its low fidelity. Therefore, ensuring tight control of Pol ζ's activity is critical for continuous and accurate DNA replication, yet the specific mechanisms remain unclear. This study reveals a regulation mechanism of Pol ζ activity in human cells. Under normal conditions, an autoinhibition mechanism keeps the catalytic subunit, REV3L, inactive. Upon encountering replication stress, however, ATR-mediated phosphorylation of REV3L's S279 cluster activates REV3L and triggers its degradation via a caspase-mediated pathway. This regulation confines the activity of Pol ζ, balancing its essential role against its mutations causing potential during replication stress. Overall, our findings elucidate a control scheme that fine tunes the low-fidelity polymerase activity of Pol ζ under challenging replication scenarios.
Collapse
Affiliation(s)
- Chun Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Shuchen Fan
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Pan Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yuzhen Bai
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Ye Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yueyun Cui
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Mengdi Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Ruru Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yuan Shao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yingying Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Shuo Zheng
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Rong Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Lijun Gao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Miaomiao Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yuanyuan Zheng
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Fengting Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Sihang Gao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Shiguo Feng
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Jianing Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Xinqi Qu
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Xialu Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, 100048, China.
| |
Collapse
|
7
|
Westhorpe R, Roske JJ, Yeeles JTP. Mechanisms controlling replication fork stalling and collapse at topoisomerase 1 cleavage complexes. Mol Cell 2024:S1097-2765(24)00658-0. [PMID: 39236719 DOI: 10.1016/j.molcel.2024.08.004] [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: 03/08/2024] [Revised: 06/14/2024] [Accepted: 08/02/2024] [Indexed: 09/07/2024]
Abstract
Topoisomerase 1 cleavage complexes (Top1-ccs) comprise a DNA-protein crosslink and a single-stranded DNA break that can significantly impact the DNA replication machinery (replisome). Consequently, inhibitors that trap Top1-ccs are used extensively in research and clinical settings to generate DNA replication stress, yet how the replisome responds upon collision with a Top1-cc remains obscure. By reconstituting collisions between budding yeast replisomes, assembled from purified proteins, and site-specific Top1-ccs, we have uncovered mechanisms underlying replication fork stalling and collapse. We find that stalled replication forks are surprisingly stable and that their stability is influenced by the template strand that Top1 is crosslinked to, the fork protection complex proteins Tof1-Csm3 (human TIMELESS-TIPIN), and the convergence of replication forks. Moreover, nascent-strand mapping and cryoelectron microscopy (cryo-EM) of stalled forks establishes replisome remodeling as a key factor in the initial response to Top1-ccs. These findings have important implications for the use of Top1 inhibitors in research and in the clinic.
Collapse
Affiliation(s)
- Rose Westhorpe
- Protein and Nucleic Acid Chemistry Division, Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Johann J Roske
- Protein and Nucleic Acid Chemistry Division, Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Joseph T P Yeeles
- Protein and Nucleic Acid Chemistry Division, Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
| |
Collapse
|
8
|
de Jaime-Soguero A, Hattemer J, Bufe A, Haas A, van den Berg J, van Batenburg V, Das B, di Marco B, Androulaki S, Böhly N, Landry JJM, Schoell B, Rosa VS, Villacorta L, Baskan Y, Trapp M, Benes V, Chabes A, Shahbazi M, Jauch A, Engel U, Patrizi A, Sotillo R, van Oudenaarden A, Bageritz J, Alfonso J, Bastians H, Acebrón SP. Developmental signals control chromosome segregation fidelity during pluripotency and neurogenesis by modulating replicative stress. Nat Commun 2024; 15:7404. [PMID: 39191776 DOI: 10.1038/s41467-024-51821-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 08/09/2024] [Indexed: 08/29/2024] Open
Abstract
Human development relies on the correct replication, maintenance and segregation of our genetic blueprints. How these processes are monitored across embryonic lineages, and why genomic mosaicism varies during development remain unknown. Using pluripotent stem cells, we identify that several patterning signals-including WNT, BMP, and FGF-converge into the modulation of DNA replication stress and damage during S-phase, which in turn controls chromosome segregation fidelity in mitosis. We show that the WNT and BMP signals protect from excessive origin firing, DNA damage and chromosome missegregation derived from stalled forks in pluripotency. Cell signalling control of chromosome segregation declines during lineage specification into the three germ layers, but re-emerges in neural progenitors. In particular, we find that the neurogenic factor FGF2 induces DNA replication stress-mediated chromosome missegregation during the onset of neurogenesis, which could provide a rationale for the elevated chromosomal mosaicism of the developing brain. Our results highlight roles for morphogens and cellular identity in genome maintenance that contribute to somatic mosaicism during mammalian development.
Collapse
Affiliation(s)
| | - Janina Hattemer
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Anja Bufe
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Alexander Haas
- Department of Molecular Oncology, Section for Cellular Oncology, University Medical Center Göttingen (UMG), Göttingen, Germany
| | - Jeroen van den Berg
- Oncode Institute, Utrecht, The Netherlands
- Hubrecht Institute, Utrecht, The Netherlands
- KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Vincent van Batenburg
- Oncode Institute, Utrecht, The Netherlands
- Hubrecht Institute, Utrecht, The Netherlands
- KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Biswajit Das
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Barbara di Marco
- Department of Clinical Neurobiology, University Hospital Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefania Androulaki
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Nicolas Böhly
- Department of Molecular Oncology, Section for Cellular Oncology, University Medical Center Göttingen (UMG), Göttingen, Germany
| | - Jonathan J M Landry
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Brigitte Schoell
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | | | - Laura Villacorta
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Yagmur Baskan
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Marleen Trapp
- Schaller Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | | | - Anna Jauch
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Ulrike Engel
- Nikon Imaging Center at the University of Heidelberg, Bioquant, Heidelberg, Germany
| | - Annarita Patrizi
- Schaller Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexander van Oudenaarden
- Oncode Institute, Utrecht, The Netherlands
- Hubrecht Institute, Utrecht, The Netherlands
- KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Josephine Bageritz
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Julieta Alfonso
- Department of Clinical Neurobiology, University Hospital Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Holger Bastians
- Department of Molecular Oncology, Section for Cellular Oncology, University Medical Center Göttingen (UMG), Göttingen, Germany
| | - Sergio P Acebrón
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany.
| |
Collapse
|
9
|
Dixit S, Nagraj T, Bhattacharya D, Saxena S, Sahoo S, Chittela RK, Somyajit K, Nagaraju G. RTEL1 helicase counteracts RAD51-mediated homologous recombination and fork reversal to safeguard replicating genomes. Cell Rep 2024; 43:114594. [PMID: 39116203 DOI: 10.1016/j.celrep.2024.114594] [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: 10/05/2023] [Revised: 05/23/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
Homologous recombination (HR) plays an essential role in the repair of DNA double-strand breaks (DSBs), replication stress responses, and genome maintenance. However, unregulated HR during replication can impair genome duplication and compromise genome stability. The mechanisms underlying HR regulation during DNA replication are obscure. Here, we find that RTEL1 helicase, RAD51, and RAD51 paralogs are enriched at stalled replication sites. The absence of RTEL1 leads to an increase in the RAD51-mediated HR and fork reversal during replication and affects genome-wide replication, which can be rescued by co-depleting RAD51 and RAD51 paralogs. Interestingly, co-depletion of fork remodelers such as SMARCAL1/ZRANB3/HLTF/FBH1 and expression of HR-defective RAD51 mutants also rescues replication defects in RTEL1-deficient cells. The anti-recombinase function of RTEL1 during replication depends on its interaction with PCNA and helicase activity. Together, our data identify the role of RTEL1 helicase in restricting RAD51-mediated fork reversal and HR activity to facilitate error-free genome duplication.
Collapse
Affiliation(s)
- Suruchi Dixit
- Department of Biochemistry Indian Institute of Science, Bangalore 560012, India
| | - Tarun Nagraj
- Department of Biochemistry Indian Institute of Science, Bangalore 560012, India
| | | | - Sneha Saxena
- Department of Biochemistry Indian Institute of Science, Bangalore 560012, India
| | - Satyaranjan Sahoo
- Department of Biochemistry Indian Institute of Science, Bangalore 560012, India
| | - Rajani Kant Chittela
- Applied Genomics Section, Bioscience Group, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Kumar Somyajit
- Department of Biochemistry Indian Institute of Science, Bangalore 560012, India; Functional Genomics & Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark.
| | - Ganesh Nagaraju
- Department of Biochemistry Indian Institute of Science, Bangalore 560012, India.
| |
Collapse
|
10
|
Lin JX, Ge M, Liu CY, Holewinski R, Andresson T, Yu ZX, Gebregiorgis T, Spolski R, Li P, Leonard WJ. Tyrosine phosphorylation of both STAT5A and STAT5B is necessary for maximal IL-2 signaling and T cell proliferation. Nat Commun 2024; 15:7372. [PMID: 39191751 PMCID: PMC11349758 DOI: 10.1038/s41467-024-50925-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 07/25/2024] [Indexed: 08/29/2024] Open
Abstract
Cytokine-mediated STAT5 protein activation is vital for lymphocyte development and function. In vitro tyrosine phosphorylation of a C-terminal tyrosine is critical for activation of STAT5A and STAT5B; however, the importance of STAT5 tyrosine phosphorylation in vivo has not been assessed. Here we generate Stat5a and Stat5b tyrosine-to-phenylalanine mutant knockin mice and find they have greatly reduced CD8+ T-cell numbers and profoundly diminished IL-2-induced proliferation of these cells, and this correlates with reduced induction of Myc, pRB, a range of cyclins and CDKs, and a partial G1→S phase-transition block. These mutant CD8+ T cells also exhibit decreased IL-2-mediated activation of pERK and pAKT, which we attribute in part to diminished expression of IL-2Rβ and IL-2Rγ. Our findings thus demonstrate that tyrosine phosphorylation of both STAT5A and STAT5B is essential for maximal IL-2 signaling. Moreover, our transcriptomic and proteomic analyses elucidate the molecular basis of the IL-2-induced proliferation of CD8+ T cells.
Collapse
Affiliation(s)
- Jian-Xin Lin
- Laboratory of Molecular Immunology and Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892-1674, USA.
| | - Meili Ge
- Laboratory of Molecular Immunology and Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892-1674, USA
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, PR China
| | - Cheng-Yu Liu
- Transgenic Mouse Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892-8018, USA
| | - Ronald Holewinski
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA
| | - Thorkell Andresson
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA
| | - Zu-Xi Yu
- Pathology Core, National Heart Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tesfay Gebregiorgis
- Laboratory of Molecular Immunology and Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892-1674, USA
| | - Rosanne Spolski
- Laboratory of Molecular Immunology and Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892-1674, USA
| | - Peng Li
- Laboratory of Molecular Immunology and Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892-1674, USA
- Amgen, Inc., 2301 Research Blvd., Rockville, MD, 20850, USA
| | - Warren J Leonard
- Laboratory of Molecular Immunology and Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892-1674, USA.
| |
Collapse
|
11
|
Zhai Z, Cui Z, Zhang Y, Song P, Wu J, Tan Z, Lin S, Ma X, Guan F, Kang H. Integrated pan-cancer analysis and experimental verification of the roles of meiotic nuclear divisions 1 in breast cancer. Biochem Biophys Res Commun 2024; 739:150600. [PMID: 39191147 DOI: 10.1016/j.bbrc.2024.150600] [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: 07/11/2024] [Revised: 08/08/2024] [Accepted: 08/22/2024] [Indexed: 08/29/2024]
Abstract
INTRODUCTION The aberrant up-regulation of meiotic nuclear division 1 (MND1) in somatic cells is considered as one of the driving factors of oncogenesis, whereas its expression and role in breast invasive cancer (BRCA) remain unclear. Hence, this study embarked on a comprehensive evaluation of MND1 across various cancers and identified its roles in BRCA. METHODS Based on publicly available databases, including but not limited to UCSC Xena, TCGA, GTEx, GEO, STRING, GeneMANIA, and CancerSEA, we evaluated the expression patterns, genomic features, and biological functions of MND1 from a pan-cancer viewpoint and delved into the implications of MND1 in the prognosis and treatment of BRCA. Further molecular biology experiments were undertaken to identify the role of MND1 in proliferation, migration, and apoptosis in BRCA cells. RESULTS Elevated levels of MND1 were notably observed in a wide array of tumor types, especially in BRCA, COAD, HNSC, LIHC, LUAD, LUSC, STAD, and UCEC. Elevated MND1 expression was markedly associated with shortened OS in several tumors, including BRCA (HR = 1.52 [95%CI, 1.10-2.09], P = 0.011). The up-regulation of MND1 in BRCA was validated in external cohorts and clinical samples. Survival analyses demonstrated that elevated MND1 expression was associated with decreased survival for patients with BRCA. Co-expressed genes of MND1 were identified, and subsequent pathway analyses based on significantly associated genes indicated that MND1 plays key roles in DNA replication, cell cycle regulation, and DNA damage repair. The observed abnormal elevation and activation of MND1 led to increased proliferation and migration, along with decreased apoptosis in BRCA cells. CONCLUSIONS MND1 emerges as a promising biomarker for diagnostic and therapeutic targeting in various cancers, including BRCA. The abnormal up-regulation and activation of MND1 are linked to carcinogenesis and poor prognosis among BRCA patients, which may be attributed to its involvement in HR-dependent ALT, warranting further scrutiny.
Collapse
Affiliation(s)
- Zhen Zhai
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China; Comprehensive Breast Care Center, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China
| | - Zhiwei Cui
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Xi' an, China
| | - Yu Zhang
- Department of Infectious Diseases, Honghui-hospital, Xi'an Jiaotong University, Shanghua Road, Xi'an, China
| | - Ping Song
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No. 157, West Fifth Road, Xi'an, China
| | - Jinpeng Wu
- College of Life Sciences, Northwest University, No. 229, Taibai North Road, Xi'an, China
| | - Zengqi Tan
- Institute of Hematology, Provincial Key Laboratory of Biotechnology, School of Medicine, Northwest University, No. 229, Taibai North Road, Xi'an, China
| | - Shuai Lin
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China; Comprehensive Breast Care Center, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China
| | - Xiaobin Ma
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China; Comprehensive Breast Care Center, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China
| | - Feng Guan
- College of Life Sciences, Northwest University, No. 229, Taibai North Road, Xi'an, China.
| | - Huafeng Kang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China; Comprehensive Breast Care Center, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China.
| |
Collapse
|
12
|
Do BT, Hsu PP, Vermeulen SY, Wang Z, Hirz T, Abbott KL, Aziz N, Replogle JM, Bjelosevic S, Paolino J, Nelson SA, Block S, Darnell AM, Ferreira R, Zhang H, Milosevic J, Schmidt DR, Chidley C, Harris IS, Weissman JS, Pikman Y, Stegmaier K, Cheloufi S, Su XA, Sykes DB, Vander Heiden MG. Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress. Dev Cell 2024; 59:2203-2221.e15. [PMID: 38823395 DOI: 10.1016/j.devcel.2024.05.010] [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: 01/30/2024] [Revised: 04/14/2024] [Accepted: 05/09/2024] [Indexed: 06/03/2024]
Abstract
Control of cellular identity requires coordination of developmental programs with environmental factors such as nutrient availability, suggesting that perturbing metabolism can alter cell state. Here, we find that nucleotide depletion and DNA replication stress drive differentiation in human and murine normal and transformed hematopoietic systems, including patient-derived acute myeloid leukemia (AML) xenografts. These cell state transitions begin during S phase and are independent of ATR/ATM checkpoint signaling, double-stranded DNA break formation, and changes in cell cycle length. In systems where differentiation is blocked by oncogenic transcription factor expression, replication stress activates primed regulatory loci and induces lineage-appropriate maturation genes despite the persistence of progenitor programs. Altering the baseline cell state by manipulating transcription factor expression causes replication stress to induce genes specific for alternative lineages. The ability of replication stress to selectively activate primed maturation programs across different contexts suggests a general mechanism by which changes in metabolism can promote lineage-appropriate cell state transitions.
Collapse
Affiliation(s)
- Brian T Do
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Harvard-MIT Health Sciences and Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peggy P Hsu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA; Massachusetts General Hospital Cancer Center, Boston, MA 02113, USA; Rogel Cancer Center and Division of Hematology and Oncology, Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Sidney Y Vermeulen
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zhishan Wang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Taghreed Hirz
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Keene L Abbott
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Najihah Aziz
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Joseph M Replogle
- Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stefan Bjelosevic
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan Paolino
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Samantha A Nelson
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Samuel Block
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alicia M Darnell
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Raphael Ferreira
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Hanyu Zhang
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Jelena Milosevic
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Daniel R Schmidt
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Christopher Chidley
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Isaac S Harris
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jonathan S Weissman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kimberly Stegmaier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sihem Cheloufi
- Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA; Stem Cell Center, University of California, Riverside, Riverside, CA 92521, USA; Center for RNA Biology and Medicine, Riverside, CA 92521, USA
| | - Xiaofeng A Su
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| |
Collapse
|
13
|
Biniaris-Georgallis SI, Aschman T, Stergioula K, Schreiber F, Jafari V, Taranko A, Karmalkar T, Kasapi A, Lenac Rovis T, Jelencic V, Bejarano DA, Fabry L, Papacharalampous M, Mattiola I, Molgora M, Hou J, Hublitz KW, Heinrich F, Guerra GM, Durek P, Patone G, Lindberg EL, Maatz H, Hölsken O, Krönke G, Mortha A, Voll RE, Clarke AJ, Hauser AE, Colonna M, Thurley K, Schlitzer A, Schneider C, Stamatiades EG, Mashreghi MF, Jonjic S, Hübner N, Diefenbach A, Kanda M, Triantafyllopoulou A. Amplification of autoimmune organ damage by NKp46-activated ILC1s. Nature 2024:10.1038/s41586-024-07907-x. [PMID: 39137897 DOI: 10.1038/s41586-024-07907-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 08/05/2024] [Indexed: 08/15/2024]
Abstract
In systemic lupus erythematosus, loss of immune tolerance, autoantibody production and immune complex deposition are required but not sufficient for organ damage1. How inflammatory signals are initiated and amplified in the setting of autoimmunity remains elusive. Here we set out to dissect layers and hierarchies of autoimmune kidney inflammation to identify tissue-specific cellular hubs that amplify autoinflammatory responses. Using high-resolution single-cell profiling of kidney immune and parenchymal cells, in combination with antibody blockade and genetic deficiency, we show that tissue-resident NKp46+ innate lymphoid cells (ILCs) are crucial signal amplifiers of disease-associated macrophage expansion and epithelial cell injury in lupus nephritis, downstream of autoantibody production. NKp46 signalling in a distinct subset of group 1 ILCs (ILC1s) instructed an unconventional immune-regulatory transcriptional program, which included the expression of the myeloid cell growth factor CSF2. CSF2 production by NKp46+ ILCs promoted the population expansion of monocyte-derived macrophages. Blockade of the NKp46 receptor (using the antibody clone mNCR1.15; ref. 2) or genetic deficiency of NKp46 abrogated epithelial cell injury. The same cellular and molecular patterns were operative in human lupus nephritis. Our data provide support for the idea that NKp46+ ILC1s promote parenchymal cell injury by granting monocyte-derived macrophages access to epithelial cell niches. NKp46 activation in ILC1s therefore constitutes a previously unrecognized, crucial tissue rheostat that amplifies organ damage in autoimmune hosts, with broad implications for inflammatory pathologies and therapies.
Collapse
Affiliation(s)
- Stylianos-Iason Biniaris-Georgallis
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin Campus Mitte, Berlin, Germany
- German Rheumatology Research Center (DRFZ), A Leibniz Institute, Berlin, Germany
- Institute of Microbiology, Infectious Diseases and Immunology (I-MIDI), Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Free University of Berlin, Berlin, Germany
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin Campus Mitte, Berlin, Germany
| | - Tom Aschman
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin Campus Mitte, Berlin, Germany
- German Rheumatology Research Center (DRFZ), A Leibniz Institute, Berlin, Germany
- Institute of Microbiology, Infectious Diseases and Immunology (I-MIDI), Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Berlin, Germany
- Department of Rheumatology and Clinical Immunology, Medical Center -University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Neuropathology, Charité-Universitätsmedizin Berlin Campus Mitte, Berlin, Germany
| | - Katerina Stergioula
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin Campus Mitte, Berlin, Germany
- German Rheumatology Research Center (DRFZ), A Leibniz Institute, Berlin, Germany
- Institute of Microbiology, Infectious Diseases and Immunology (I-MIDI), Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Free University of Berlin, Berlin, Germany
| | - Frauke Schreiber
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin Campus Mitte, Berlin, Germany
- German Rheumatology Research Center (DRFZ), A Leibniz Institute, Berlin, Germany
- Institute of Microbiology, Infectious Diseases and Immunology (I-MIDI), Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Berlin, Germany
| | - Vajiheh Jafari
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin Campus Mitte, Berlin, Germany
- German Rheumatology Research Center (DRFZ), A Leibniz Institute, Berlin, Germany
- Institute of Microbiology, Infectious Diseases and Immunology (I-MIDI), Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Free University of Berlin, Berlin, Germany
| | - Anna Taranko
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin Campus Mitte, Berlin, Germany
- German Rheumatology Research Center (DRFZ), A Leibniz Institute, Berlin, Germany
- Institute of Microbiology, Infectious Diseases and Immunology (I-MIDI), Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Free University of Berlin, Berlin, Germany
| | - Tejal Karmalkar
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin Campus Mitte, Berlin, Germany
- German Rheumatology Research Center (DRFZ), A Leibniz Institute, Berlin, Germany
- Institute of Microbiology, Infectious Diseases and Immunology (I-MIDI), Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Free University of Berlin, Berlin, Germany
| | - Ana Kasapi
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin Campus Mitte, Berlin, Germany
- German Rheumatology Research Center (DRFZ), A Leibniz Institute, Berlin, Germany
- Institute of Microbiology, Infectious Diseases and Immunology (I-MIDI), Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Berlin, Germany
| | - Tihana Lenac Rovis
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Vedrana Jelencic
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - David A Bejarano
- Quantitative Systems Biology, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Lea Fabry
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin Campus Mitte, Berlin, Germany
- German Rheumatology Research Center (DRFZ), A Leibniz Institute, Berlin, Germany
- Institute of Microbiology, Infectious Diseases and Immunology (I-MIDI), Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Berlin, Germany
| | - Michail Papacharalampous
- Department of Rheumatology and Clinical Immunology, Medical Center -University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Irene Mattiola
- German Rheumatology Research Center (DRFZ), A Leibniz Institute, Berlin, Germany
- Institute of Microbiology, Infectious Diseases and Immunology (I-MIDI), Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Berlin, Germany
| | - Martina Molgora
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jinchao Hou
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Anesthesiology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Karolin W Hublitz
- Institute of Microbiology, Infectious Diseases and Immunology (I-MIDI), Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Berlin, Germany
| | - Frederik Heinrich
- German Rheumatology Research Center (DRFZ), A Leibniz Institute, Berlin, Germany
| | | | - Pawel Durek
- German Rheumatology Research Center (DRFZ), A Leibniz Institute, Berlin, Germany
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Eric L Lindberg
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Henrike Maatz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- DZHK, German Centre for Cardiovascular Research, Partner Site Berlin, Berlin, Germany
| | - Oliver Hölsken
- German Rheumatology Research Center (DRFZ), A Leibniz Institute, Berlin, Germany
- Institute of Microbiology, Infectious Diseases and Immunology (I-MIDI), Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Berlin, Germany
- Department of Anesthesiology and Intensive Care Medicine, Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Berlin, Germany
- Berlin Institute of Health at Charité Universitätsmedizin, Berlin, BIH Academy, Junior Clinician Scientist Program, Berlin, Germany
| | - Gerhard Krönke
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin Campus Mitte, Berlin, Germany
- German Rheumatology Research Center (DRFZ), A Leibniz Institute, Berlin, Germany
| | - Arthur Mortha
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Reinhard E Voll
- Department of Rheumatology and Clinical Immunology, Medical Center -University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Anja E Hauser
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin Campus Mitte, Berlin, Germany
- German Rheumatology Research Center (DRFZ), A Leibniz Institute, Berlin, Germany
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Kevin Thurley
- German Rheumatology Research Center (DRFZ), A Leibniz Institute, Berlin, Germany
- Biomathematics Division, Institute of Experimental Oncology, University Hospital Bonn, Bonn, Germany
| | - Andreas Schlitzer
- Quantitative Systems Biology, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | | | - Efstathios G Stamatiades
- Institute of Microbiology, Infectious Diseases and Immunology (I-MIDI), Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Berlin, Germany
| | - Mir-Farzin Mashreghi
- German Rheumatology Research Center (DRFZ), A Leibniz Institute, Berlin, Germany
- German Center for Child and Adolescent Health (DZKJ), Partner Site Berlin, Berlin, Germany
| | - Stipan Jonjic
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Norbert Hübner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- DZHK, German Centre for Cardiovascular Research, Partner Site Berlin, Berlin, Germany
- Charité-Universitätsmedizin, Berlin, Germany
| | - Andreas Diefenbach
- German Rheumatology Research Center (DRFZ), A Leibniz Institute, Berlin, Germany.
- Institute of Microbiology, Infectious Diseases and Immunology (I-MIDI), Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Berlin, Germany.
| | - Masatoshi Kanda
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
- Department of Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan.
| | - Antigoni Triantafyllopoulou
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin Campus Mitte, Berlin, Germany.
- German Rheumatology Research Center (DRFZ), A Leibniz Institute, Berlin, Germany.
- Institute of Microbiology, Infectious Diseases and Immunology (I-MIDI), Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Berlin, Germany.
| |
Collapse
|
14
|
Schelker RC, Fioravanti J, Mastrogiovanni F, Baldwin JG, Rana N, Li P, Chen P, Vadász T, Spolski R, Heuser-Loy C, Slavkovic-Lukic D, Noronha P, Damiano G, Raccosta L, Maggioni D, Pullugula S, Lin JX, Oh J, Grandinetti P, Lecce M, Hesse L, Kocks E, Martín-Santos A, Gebhard C, Telford WG, Ji Y, Restifo NP, Russo V, Rehli M, Herr W, Leonard WJ, Gattinoni L. LIM-domain-only 4 (LMO4) enhances CD8 + T-cell stemness and tumor rejection by boosting IL-21-STAT3 signaling. Signal Transduct Target Ther 2024; 9:199. [PMID: 39117617 PMCID: PMC11310520 DOI: 10.1038/s41392-024-01915-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 06/13/2024] [Accepted: 07/04/2024] [Indexed: 08/10/2024] Open
Abstract
High frequencies of stem-like memory T cells in infusion products correlate with superior patient outcomes across multiple T cell therapy trials. Herein, we analyzed a published CRISPR activation screening to identify transcriptional regulators that could be harnessed to augment stem-like behavior in CD8+ T cells. Using IFN-γ production as a proxy for CD8+ T cell terminal differentiation, LMO4 emerged among the top hits inhibiting the development of effectors cells. Consistently, we found that Lmo4 was downregulated upon CD8+ T cell activation but maintained under culture conditions facilitating the formation of stem-like T cells. By employing a synthetic biology approach to ectopically express LMO4 in antitumor CD8+ T cells, we enabled selective expansion and enhanced persistence of transduced cells, while limiting their terminal differentiation and senescence. LMO4 overexpression promoted transcriptional programs regulating stemness, increasing the numbers of stem-like CD8+ memory T cells and enhancing their polyfunctionality and recall capacity. When tested in syngeneic and xenograft tumor models, LMO4 overexpression boosted CD8+ T cell antitumor immunity, resulting in enhanced tumor regression. Rather than directly modulating gene transcription, LMO4 bound to JAK1 and potentiated STAT3 signaling in response to IL-21, inducing the expression of target genes (Tcf7, Socs3, Junb, and Zfp36) crucial for memory responses. CRISPR/Cas9-deletion of Stat3 nullified the enhanced memory signature conferred by LMO4, thereby abrogating the therapeutic benefit of LMO4 overexpression. These results establish LMO4 overexpression as an effective strategy to boost CD8+ T cell stemness, providing a new synthetic biology tool to bolster the efficacy of T cell-based immunotherapies.
Collapse
Affiliation(s)
- Roland C Schelker
- Division of Functional Immune Cell Modulation, Leibniz Institute for Immunotherapy, Regensburg, Germany.
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.
| | - Jessica Fioravanti
- Division of Functional Immune Cell Modulation, Leibniz Institute for Immunotherapy, Regensburg, Germany
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Fabio Mastrogiovanni
- Division of Functional Immune Cell Modulation, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Jeremy G Baldwin
- Division of Functional Immune Cell Modulation, Leibniz Institute for Immunotherapy, Regensburg, Germany
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nisha Rana
- Division of Functional Immune Cell Modulation, Leibniz Institute for Immunotherapy, Regensburg, Germany
- Next Generation Sequencing Core, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Peng Li
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ping Chen
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Timea Vadász
- Division of Functional Immune Cell Modulation, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Rosanne Spolski
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christoph Heuser-Loy
- Division of Functional Immune Cell Modulation, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Dragana Slavkovic-Lukic
- Division of Functional Immune Cell Modulation, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Pedro Noronha
- Division of Functional Immune Cell Modulation, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Giuseppe Damiano
- Immuno-Biotherapy of Melanoma and Solid Tumors Unit, Division of Experimental Oncology, IRCCS Scientific Institute San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Laura Raccosta
- Immuno-Biotherapy of Melanoma and Solid Tumors Unit, Division of Experimental Oncology, IRCCS Scientific Institute San Raffaele, Milan, Italy
| | - Daniela Maggioni
- Immuno-Biotherapy of Melanoma and Solid Tumors Unit, Division of Experimental Oncology, IRCCS Scientific Institute San Raffaele, Milan, Italy
| | - Sree Pullugula
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jian-Xin Lin
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jangsuk Oh
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Patrick Grandinetti
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mario Lecce
- Division of Functional Immune Cell Modulation, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Leo Hesse
- Division of Functional Immune Cell Modulation, Leibniz Institute for Immunotherapy, Regensburg, Germany
- University of Regensburg, Regensburg, Germany
| | - Emilia Kocks
- Division of Functional Immune Cell Modulation, Leibniz Institute for Immunotherapy, Regensburg, Germany
- University of Regensburg, Regensburg, Germany
| | - Azucena Martín-Santos
- Division of Functional Immune Cell Modulation, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Claudia Gebhard
- Next Generation Sequencing Core, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - William G Telford
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yun Ji
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nicholas P Restifo
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vincenzo Russo
- Immuno-Biotherapy of Melanoma and Solid Tumors Unit, Division of Experimental Oncology, IRCCS Scientific Institute San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Michael Rehli
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
- Next Generation Sequencing Core, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Wolfgang Herr
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
- National Center for Tumor Diseases, WERA Site, Würzburg-Erlangen-Regensburg-Augsburg, Germany
- Center for Immunomedicine in Transplantation and Oncology, University Hospital Regensburg, Regensburg, Germany
| | - Warren J Leonard
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Luca Gattinoni
- Division of Functional Immune Cell Modulation, Leibniz Institute for Immunotherapy, Regensburg, Germany.
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
- University of Regensburg, Regensburg, Germany.
- Center for Immunomedicine in Transplantation and Oncology, University Hospital Regensburg, Regensburg, Germany.
| |
Collapse
|
15
|
Otarbayev D, Myung K. Exploring factors influencing choice of DNA double-strand break repair pathways. DNA Repair (Amst) 2024; 140:103696. [PMID: 38820807 DOI: 10.1016/j.dnarep.2024.103696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/20/2024] [Accepted: 05/20/2024] [Indexed: 06/02/2024]
Abstract
DNA double-strand breaks (DSBs) represent one of the most severe threats to genomic integrity, demanding intricate repair mechanisms within eukaryotic cells. A diverse array of factors orchestrates the complex choreography of DSB signaling and repair, encompassing repair pathways, such as non-homologous end-joining, homologous recombination, and polymerase-θ-mediated end-joining. This review looks into the intricate decision-making processes guiding eukaryotic cells towards a particular repair pathway, particularly emphasizing the processing of two-ended DSBs. Furthermore, we elucidate the transformative role of Cas9, a site-specific endonuclease, in revolutionizing our comprehension of DNA DSB repair dynamics. Additionally, we explore the burgeoning potential of Cas9's remarkable ability to induce sequence-specific DSBs, offering a promising avenue for precise targeting of tumor cells. Through this comprehensive exploration, we unravel the intricate molecular mechanisms of cellular responses to DSBs, shedding light on both fundamental repair processes and cutting-edge therapeutic strategies.
Collapse
Affiliation(s)
- Daniyar Otarbayev
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, South Korea; Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, South Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, South Korea; Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, South Korea.
| |
Collapse
|
16
|
Jirapongwattana N, Bunting SF, Ronning DR, Ghosal G, Karpf AR. RHNO1: at the crossroads of DNA replication stress, DNA repair, and cancer. Oncogene 2024; 43:2613-2620. [PMID: 39107463 DOI: 10.1038/s41388-024-03117-x] [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: 06/03/2024] [Revised: 07/24/2024] [Accepted: 07/26/2024] [Indexed: 08/28/2024]
Abstract
The DNA replication stress (DRS) response is a crucial homeostatic mechanism for maintaining genome integrity in the face of intrinsic and extrinsic barriers to DNA replication. Importantly, DRS is often significantly increased in tumor cells, making tumors dependent on the cellular DRS response for growth and survival. Rad9-Hus1-Rad1 Interacting Nuclear Orphan 1 (RHNO1), a protein involved in the DRS response, has recently emerged as a potential therapeutic target in cancer. RHNO1 interacts with the 9-1-1 checkpoint clamp and TopBP1 to activate the ATR/Chk1 signaling pathway, the crucial mediator of the DRS response. Moreover, RHNO1 was also recently identified as a key facilitator of theta-mediated end joining (TMEJ), a DNA repair mechanism implicated in cancer progression and chemoresistance. In this literature review, we provide an overview of our current understanding of RHNO1, including its structure, function in the DRS response, and role in DNA repair, and discuss its potential as a cancer therapeutic target. Therapeutic targeting of RHNO1 holds promise for tumors with elevated DRS as well as tumors with DNA repair deficiencies, including homologous recombination DNA repair deficient (HRD) tumors. Further investigation into RHNO1 function in cancer, and development of approaches to target RHNO1, are expected to yield novel strategies for cancer treatment.
Collapse
Affiliation(s)
- Niphat Jirapongwattana
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - Samuel F Bunting
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854-8021, USA
| | - Donald R Ronning
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - Gargi Ghosal
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - Adam R Karpf
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA.
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA.
| |
Collapse
|
17
|
Nie P, Zhang C, Wu F, Chen S, Wang L. The Compromised Fanconi Anemia Pathway in Prelamin A-Expressing Cells Contributes to Replication Stress-Induced Genomic Instability. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307751. [PMID: 38894550 PMCID: PMC11321653 DOI: 10.1002/advs.202307751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 04/30/2024] [Indexed: 06/21/2024]
Abstract
Genomic instability is not only a hallmark of senescent cells but also a key factor driving cellular senescence, and replication stress is the main source of genomic instability. Defective prelamin A processing caused by lamin A/C (LMNA) or zinc metallopeptidase STE24 (ZMPSTE24) gene mutations results in premature aging. Although previous studies have shown that dysregulated lamin A interferes with DNA replication and causes replication stress, the relationship between lamin A dysfunction and replication stress remains largely unknown. Here, an increase in baseline replication stress and genomic instability is found in prelamin A-expressing cells. Moreover, prelamin A confers hypersensitivity of cells to exogenous replication stress, resulting in decreased cell survival and exacerbated genomic instability. These effects occur because prelamin A promotes MRE11-mediated resection of stalled replication forks. Fanconi anemia (FA) proteins, which play important roles in replication fork maintenance, are downregulated by prelamin A in a retinoblastoma (RB)/E2F-dependent manner. Additionally, prelamin A inhibits the activation of the FA pathway upon replication stress. More importantly, FA pathway downregulation is an upstream event of p53-p21 axis activation during the induction of prelamin A expression. Overall, these findings highlight the critical role of FA pathway dysfunction in driving replication stress-induced genomic instability and cellular senescence in prelamin A-expressing cells.
Collapse
Affiliation(s)
- Pengqing Nie
- Department of GastroenterologyHubei Clinical Center and Key Laboratory of Intestinal and Colorectal DiseaseMinistry of Education Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryTaikang Center for Life and Medical SciencesZhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan UniversityWuhan430071China
- Department of Infectious DiseasesInstitute of PediatricsShenzhen Children's HospitalShenzhenGuangdong518038China
| | - Cheng Zhang
- Department of GastroenterologyHubei Clinical Center and Key Laboratory of Intestinal and Colorectal DiseaseMinistry of Education Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryTaikang Center for Life and Medical SciencesZhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan UniversityWuhan430071China
| | - Fengyi Wu
- Department of GastroenterologyHubei Clinical Center and Key Laboratory of Intestinal and Colorectal DiseaseMinistry of Education Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryTaikang Center for Life and Medical SciencesZhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan UniversityWuhan430071China
| | - Shi Chen
- Department of GastroenterologyHubei Clinical Center and Key Laboratory of Intestinal and Colorectal DiseaseMinistry of Education Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryTaikang Center for Life and Medical SciencesZhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan UniversityWuhan430071China
- Department of Burn and Plastic SurgeryShenzhen Institute of Translational Medicine, Medical Innovation Technology Transformation Center of Shenzhen Second People's HospitalShenzhen Key Laboratory of Microbiology in Genomic Modification & Editing and ApplicationGuangdong Provincial Key Laboratory of Systems Biology and Synthetic Biology for Urogenital TumorsShenzhen University Medical School, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen UniversityShenzhen518035China
| | - Lianrong Wang
- Department of GastroenterologyHubei Clinical Center and Key Laboratory of Intestinal and Colorectal DiseaseMinistry of Education Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryTaikang Center for Life and Medical SciencesZhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan UniversityWuhan430071China
- Department of Infectious DiseasesInstitute of PediatricsShenzhen Children's HospitalShenzhenGuangdong518038China
| |
Collapse
|
18
|
Petroulia S, Hockemeyer K, Tiwari S, Berico P, Shamloo S, Banijamali SE, Vega-Saenz de Miera E, Gong Y, Thandapani P, Wang E, Schulz M, Tsirigos A, Osman I, Aifantis I, Imig J. CRISPR-inhibition screen for lncRNAs linked to melanoma growth and metastasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.24.604899. [PMID: 39211068 PMCID: PMC11361079 DOI: 10.1101/2024.07.24.604899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Melanoma being one of the most common and deadliest skin cancers, has been rising since the past decade. Patients at advanced stages of the disease have very poor prognoses, as opposed to at the earlier stages. Nowadays the standard-of-care of advanced melanoma is resection followed by immune checkpoint inhibition based immunotherapy. However, a substantial proportion of patients either do not respond or develop resistances. This underscores a need for novel approaches and therapeutic targets as well as a better understanding of the mechanisms of melanoma pathogenesis. Long non-coding RNAs (lncRNAs) comprise a poorly characterized class of functional players and promising targets in promoting malignancy. Certain lncRNAs have been identified to play integral roles in melanoma progression and drug resistances, however systematic screens to uncover novel functional lncRNAs are scarce. Here, we profile differentially expressed lncRNAs in patient derived short-term metastatic cultures and BRAF-MEK-inhibition resistant cells. We conduct a focused growth-related CRISPR-inhibition screen of overexpressed lncRNAs, validate and functionally characterize lncRNA hits with respect to cellular growth, invasive capacities and apoptosis in vitro as well as the transcriptomic impact of our lead candidate the novel lncRNA XLOC_030781. In sum, we extend the current knowledge of ncRNAs and their potential relevance on melanoma. Significance Previously considered as transcriptional noise, lncRNAs have emerged as novel players in regulating many cellular aspects in health and disease including melanoma. However, the number and as well as the extent of functional significance of most lncRNAs remains elusive. We provide a comprehensive strategy to identify functionally relevant lncRNAs in melanoma by combining expression profiling with CRISPR-inhibition growths screens lowering the experimental effort. We also provide a larger resource of differentially expressed lncRNAs with potential implications in melanoma growth and invasion. Our results broaden the characterized of lncRNAs as potential targets for future therapeutic applications.
Collapse
|
19
|
Kushinsky S, Puccetti MV, Adams CM, Shkundina I, James N, Mahon BM, Michener P, Eischen CM. DNA fork remodeling proteins, Zranb3 and Smarcal1, are uniquely essential for aging hematopoiesis. Aging Cell 2024:e14281. [PMID: 39044358 DOI: 10.1111/acel.14281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/25/2024] [Accepted: 07/01/2024] [Indexed: 07/25/2024] Open
Abstract
Over a lifetime, hematopoietic stem and progenitor cells (HSPCs) are forced to repeatedly proliferate to maintain hematopoiesis, increasing their susceptibility to DNA damaging replication stress. However, the proteins that mitigate this stress, protect HSPC replication, and prevent aging-driven dysregulation are unknown. We report two evolutionarily conserved, ubiquitously expressed chromatin remodeling enzymes with similar DNA replication fork reversal biochemical functions, Zranb3 and Smarcal1, have surprisingly specialized roles in distinct HSPC populations. While both proteins actively mitigate replication stress and prevent DNA damage and breaks during lifelong hematopoiesis, the loss of either resulted in distinct biochemical and biological consequences. Notably, defective long-term HSC function, revealed with bone marrow transplantation, caused hematopoiesis abnormalities in young mice lacking Zranb3. Aging significantly worsened these hematopoiesis defects in Zranb3-deficient mice, including accelerating the onset of myeloid-biased hematopoietic dysregulation to early in life. Such Zranb3-deficient HSPC abnormalities with age were driven by accumulated DNA damage and replication stress. Conversely, Smarcal1 loss primarily negatively affected progenitor cell functions that were exacerbated with aging, resulting in a lymphoid bias. Simultaneous loss of both Zranb3 and Smarcal1 compounded HSPC defects. Additionally, HSPC DNA replication fork dynamics had unanticipated HSPC type and age plasticity that depended on the stress and Zranb3 and/or Smarcal1. Our data reveal both Zranb3 and Smarcal1 have essential HSPC cell intrinsic functions in lifelong hematopoiesis that protect HSPCs from replication stress and DNA damage in unexpected, unique ways.
Collapse
Affiliation(s)
- Saul Kushinsky
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Matthew V Puccetti
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Clare M Adams
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Irina Shkundina
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Nikkole James
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Brittany M Mahon
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Peter Michener
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Christine M Eischen
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| |
Collapse
|
20
|
Sobh A, Encinas E, Patel A, Surapaneni G, Bonilla E, Kaestner C, Poullard J, Clerio M, Vasan K, Freeman T, Lv D, Dupéré-Richer D, Riva A, Barwick BG, Zhou D, Boise LH, Mitsiades CS, Kim B, Bennett RL, Chandel NS, Licht JD. NSD2 drives t(4;14) myeloma cell dependence on adenylate kinase 2 by diverting one-carbon metabolism to the epigenome. Blood 2024; 144:283-295. [PMID: 38598835 DOI: 10.1182/blood.2023022859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/15/2024] [Accepted: 03/29/2024] [Indexed: 04/12/2024] Open
Abstract
ABSTRACT Chromosomal translocation (4;14), an adverse prognostic factor in multiple myeloma (MM), drives overexpression of the histone methyltransferase nuclear receptor binding SET domain protein 2 (NSD2). A genome-wide CRISPR screen in MM cells identified adenylate kinase 2 (AK2), an enzyme critical for high-energy phosphate transfer from the mitochondria, as an NSD2-driven vulnerability. AK2 suppression in t(4;14) MM cells decreased nicotinamide adenine dinucleotide phosphate (NADP[H]) critical for conversion of ribonucleotides to deoxyribonucleosides, leading to replication stress, DNA damage, and apoptosis. Driving a large genome-wide increase in chromatin methylation, NSD2 overexpression depletes S-adenosylmethionine, compromising the synthesis of creatine from its precursor, guanidinoacetate. Creatine supplementation restored NADP(H) levels, reduced DNA damage, and rescued AK2-deficient t(4;14) MM cells. As the creatine phosphate shuttle constitutes an alternative means for mitochondrial high-energy phosphate transport, these results indicate that NSD2-driven creatine depletion underlies the hypersensitivity of t(4;14) MM cells to AK2 loss. Furthermore, AK2 depletion in t(4;14) cells impaired protein folding in the endoplasmic reticulum, consistent with impaired use of mitochondrial adenosine triphosphate (ATP). Accordingly, AK2 suppression increased the sensitivity of MM cells to proteasome inhibition. These findings delineate a novel mechanism in which aberrant transfer of carbon to the epigenome creates a metabolic vulnerability, with direct therapeutic implications for t(4;14) MM.
Collapse
Affiliation(s)
- Amin Sobh
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Elena Encinas
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Alisha Patel
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Greeshma Surapaneni
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Emilie Bonilla
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Charlotte Kaestner
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Janai Poullard
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Monica Clerio
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Karthik Vasan
- Department of Medicine, Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Tzipporah Freeman
- Center for ViroScience and Cure, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Dongwen Lv
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center San Antonio, San Antonio, TX
| | - Daphné Dupéré-Richer
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Alberto Riva
- Interdisciplinary Center for Biotechnology Research, The University of Florida, Gainesville, FL
| | - Benjamin G Barwick
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - Daohong Zhou
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center San Antonio, San Antonio, TX
| | - Lawrence H Boise
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Baek Kim
- Center for ViroScience and Cure, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Richard L Bennett
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Navdeep S Chandel
- Department of Medicine, Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Jonathan D Licht
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| |
Collapse
|
21
|
Chauhan AS, Jhujh SS, Stewart GS. E3 ligases: a ubiquitous link between DNA repair, DNA replication and human disease. Biochem J 2024; 481:923-944. [PMID: 38985307 PMCID: PMC11346458 DOI: 10.1042/bcj20240124] [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: 03/20/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 07/11/2024]
Abstract
Maintenance of genome stability is of paramount importance for the survival of an organism. However, genomic integrity is constantly being challenged by various endogenous and exogenous processes that damage DNA. Therefore, cells are heavily reliant on DNA repair pathways that have evolved to deal with every type of genotoxic insult that threatens to compromise genome stability. Notably, inherited mutations in genes encoding proteins involved in these protective pathways trigger the onset of disease that is driven by chromosome instability e.g. neurodevelopmental abnormalities, neurodegeneration, premature ageing, immunodeficiency and cancer development. The ability of cells to regulate the recruitment of specific DNA repair proteins to sites of DNA damage is extremely complex but is primarily mediated by protein post-translational modifications (PTMs). Ubiquitylation is one such PTM, which controls genome stability by regulating protein localisation, protein turnover, protein-protein interactions and intra-cellular signalling. Over the past two decades, numerous ubiquitin (Ub) E3 ligases have been identified to play a crucial role not only in the initiation of DNA replication and DNA damage repair but also in the efficient termination of these processes. In this review, we discuss our current understanding of how different Ub E3 ligases (RNF168, TRAIP, HUWE1, TRIP12, FANCL, BRCA1, RFWD3) function to regulate DNA repair and replication and the pathological consequences arising from inheriting deleterious mutations that compromise the Ub-dependent DNA damage response.
Collapse
Affiliation(s)
- Anoop S. Chauhan
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
| | - Satpal S. Jhujh
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
| | - Grant S. Stewart
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
| |
Collapse
|
22
|
Huang CY, Chung YH, Wu SY, Wang HY, Lin CY, Yang TJ, Fang JM, Hu CM, Chang ZF. Glutathione determines chronic myeloid leukemia vulnerability to an inhibitor of CMPK and TMPK. Commun Biol 2024; 7:843. [PMID: 38987326 PMCID: PMC11237035 DOI: 10.1038/s42003-024-06547-1] [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: 01/22/2024] [Accepted: 07/04/2024] [Indexed: 07/12/2024] Open
Abstract
Bcr-Abl transformation leads to chronic myeloid leukemia (CML). The acquirement of T315I mutation causes tyrosine kinase inhibitors (TKI) resistance. This study develops a compound, JMF4073, inhibiting thymidylate (TMP) and cytidylate (CMP) kinases, aiming for a new therapy against TKI-resistant CML. In vitro and in vivo treatment of JMF4073 eliminates WT-Bcr-Abl-32D CML cells. However, T315I-Bcr-Abl-32D cells are less vulnerable to JMF4073. Evidence is presented that ATF4-mediated upregulation of GSH causes T315I-Bcr-Abl-32D cells to be less sensitive to JMF4073. Reducing GSH biosynthesis generates replication stress in T315I-Bcr-Abl-32D cells that require dTTP/dCTP synthesis for survival, thus enabling JMF4073 susceptibility. It further shows that the levels of ATF4 and GSH in several human CML blast-crisis cell lines are inversely correlated with JMF4073 sensitivity, and the combinatory treatment of JMF4073 with GSH reducing agent leads to synthetic lethality in these CML blast-crisis lines. Altogether, the investigation indicates an alternative option in CML therapy.
Collapse
MESH Headings
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Glutathione/metabolism
- Humans
- Animals
- Mice
- Protein Kinase Inhibitors/pharmacology
- Drug Resistance, Neoplasm/drug effects
- Cell Line, Tumor
- Fusion Proteins, bcr-abl/metabolism
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/antagonists & inhibitors
Collapse
Affiliation(s)
- Chang-Yu Huang
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yin-Hsuan Chung
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Sheng-Yang Wu
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsin-Yen Wang
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chih-Yu Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Tsung-Jung Yang
- Institute of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Jim-Min Fang
- Institute of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Chun-Mei Hu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Zee-Fen Chang
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.
- Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.
| |
Collapse
|
23
|
Jo U, Arakawa Y, Zimmermann A, Taniyama D, Mizunuma M, Jenkins LM, Maity T, Kumar S, Zenke FT, Takebe N, Pommier Y. The Novel ATR Inhibitor M1774 Induces Replication Protein Overexpression and Broad Synergy with DNA-targeted Anticancer Drugs. Mol Cancer Ther 2024; 23:911-923. [PMID: 38466804 DOI: 10.1158/1535-7163.mct-23-0402] [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: 06/25/2023] [Revised: 12/09/2023] [Accepted: 02/29/2024] [Indexed: 03/13/2024]
Abstract
Ataxia telangiectasia and Rad3-related (ATR) checkpoint kinase inhibitors are in clinical trials. Here we explored the molecular pharmacology and therapeutic combination strategies of the oral ATR inhibitor M1774 (Tuvusertib) with DNA-damaging agents (DDA). As single agent, M1774 suppressed cancer cell viability at nanomolar concentrations, showing greater activity than ceralasertib and berzosertib, but less potency than gartisertib and elimusertib in the small cell lung cancer H146, H82, and DMS114 cell lines. M1774 also efficiently blocked the activation of the ATR-CHK1 checkpoint pathway caused by replication stress induced by TOP1 inhibitors. Combination with non-toxic dose of M1774 enhanced TOP1 inhibitor-induced cancer cell death by enabling unscheduled replication upon replicative damage, thereby increasing genome instability. Tandem mass tag-based quantitative proteomics uncovered that M1774, in the presence of DDA, forces the expression of proteins activating replication (CDC45) and G2-M progression (PLK1 and CCNB1). In particular, the fork protection complex proteins (TIMELESS and TIPIN) were enriched. Low dose of M1774 was found highly synergistic with a broad spectrum of clinical DDAs including TOP1 inhibitors (SN-38/irinotecan, topotecan, exatecan, and exatecan), the TOP2 inhibitor etoposide, cisplatin, the RNA polymerase II inhibitor lurbinectedin, and the PARP inhibitor talazoparib in various models including cancer cell lines, patient-derived organoids, and mouse xenograft models. Furthermore, we demonstrate that M1774 reverses chemoresistance to anticancer DDAs in cancer cells lacking SLFN11 expression, suggesting that SLFN11 can be utilized for patient selection in upcoming clinical trials.
Collapse
Affiliation(s)
- Ukhyun Jo
- Developmental Therapeutics Branch and Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
- Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Yasuhiro Arakawa
- Developmental Therapeutics Branch and Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | | | - Daiki Taniyama
- Developmental Therapeutics Branch and Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Makito Mizunuma
- Developmental Therapeutics Branch and Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Tapan Maity
- Laboratory of Cell Biology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Suresh Kumar
- Developmental Therapeutics Branch and Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | | | - Naoko Takebe
- Developmental Therapeutics Branch and Division of Cancer Treatment and Diagnosis, NCI, NIH, Bethesda, Maryland
| | - Yves Pommier
- Developmental Therapeutics Branch and Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| |
Collapse
|
24
|
Znachorova T, Dudko N, Ming H, Jiang Z, Fulka H. The timing of pronuclear transfer critically affects the developmental competence and quality of embryos. Mol Hum Reprod 2024; 30:gaae024. [PMID: 38991843 PMCID: PMC11262804 DOI: 10.1093/molehr/gaae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 06/14/2024] [Indexed: 07/13/2024] Open
Abstract
Pronuclear transfer has been successfully used in human-assisted reproduction to suppress the adverse effects of a defective oocyte cytoplasm or to bypass an idiopathic developmental arrest. However, the effects of the initial parental genome remodelling in a defective cytoplasm on the subsequent development after pronucleus transfer have not been systematically studied. By performing pronuclear transfer in pre-replication and post-replication mouse embryos, we show that the timing of the procedure plays a critical role. Although apparently morphologically normal blastocysts were obtained in both pre- and post-replication pronuclear transfer groups, post-replication pronuclear transfer led to a decrease in developmental competence and profound changes in embryonic gene expression. By inhibiting the replication in the abnormal cytoplasm before pronuclear transfer into a healthy cytoplasm, the developmental potential of embryos could be largely restored. This shows that the conditions under which the first embryonic replication occurs strongly influence developmental potential. Although pronuclear transfer is the method of choice for mitigating the impact of a faulty oocyte cytoplasm on early development, our results show that the timing of this intervention should be restricted to the pre-replication phase.
Collapse
Affiliation(s)
- Tereza Znachorova
- Department of Cell Nucleus Plasticity, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Nataliia Dudko
- Department of Cell Nucleus Plasticity, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hao Ming
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Zongliang Jiang
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Helena Fulka
- Department of Cell Nucleus Plasticity, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Biology of Reproduction, Institute of Animal Science, Prague, Czech Republic
| |
Collapse
|
25
|
Bessho T. Up-Regulation of Non-Homologous End-Joining by MUC1. Genes (Basel) 2024; 15:808. [PMID: 38927743 PMCID: PMC11203369 DOI: 10.3390/genes15060808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/10/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024] Open
Abstract
Ionizing radiation (IR) and chemotherapy with DNA-damaging drugs such as cisplatin are vital cancer treatment options. These treatments induce double-strand breaks (DSBs) as cytotoxic DNA damage; thus, the DSB repair activity in each cancer cell significantly influences the efficacy of the treatments. Pancreatic cancers are known to be resistant to these treatments, and the overexpression of MUC1, a member of the glycoprotein mucins, is associated with IR- and chemo-resistance. Therefore, we investigated the impact of MUC1 on DSB repair. This report examined the effect of the overexpression of MUC1 on homologous recombination (HR) and non-homologous end-joining (NHEJ) using cell-based DSB repair assays. In addition, the therapeutic potential of NHEJ inhibitors including HDAC inhibitors was also studied using pancreatic cancer cell lines. The MUC1-overexpression enhances NHEJ, while partially suppressing HR. Also, MUC1-overexpressed cancer cell lines are preferentially killed by a DNA-PK inhibitor and HDAC1/2 inhibitors. Altogether, MUC1 induces metabolic changes that create an imbalance between NHEJ and HR activities, and this imbalance can be a target for selective killing by HDAC inhibitors. This is a novel mechanism of MUC1-mediated IR-resistance and will form the basis for targeting MUC1-overexpressed pancreatic cancer.
Collapse
Affiliation(s)
- Tadayoshi Bessho
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198, USA
| |
Collapse
|
26
|
Fajri N, Petryk N. Monitoring and quantifying replication fork dynamics with high-throughput methods. Commun Biol 2024; 7:729. [PMID: 38877080 PMCID: PMC11178896 DOI: 10.1038/s42003-024-06412-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 06/04/2024] [Indexed: 06/16/2024] Open
Abstract
Before each cell division, eukaryotic cells must replicate their chromosomes to ensure the accurate transmission of genetic information. Chromosome replication involves more than just DNA duplication; it also includes chromatin assembly, inheritance of epigenetic marks, and faithful resumption of all genomic functions after replication. Recent progress in quantitative technologies has revolutionized our understanding of the complexity and dynamics of DNA replication forks at both molecular and genomic scales. Here, we highlight the pivotal role of these novel methods in uncovering the principles and mechanisms of chromosome replication. These technologies have illuminated the regulation of genome replication programs, quantified the impact of DNA replication on genomic mutations and evolutionary processes, and elucidated the mechanisms of replication-coupled chromatin assembly and epigenome maintenance.
Collapse
Affiliation(s)
- Nora Fajri
- UMR9019 - CNRS, Intégrité du Génome et Cancers, Université Paris-Saclay, Gustave Roussy, Villejuif, France, 114 rue Edouard Vaillant, 94805, Villejuif, France
| | - Nataliya Petryk
- UMR9019 - CNRS, Intégrité du Génome et Cancers, Université Paris-Saclay, Gustave Roussy, Villejuif, France, 114 rue Edouard Vaillant, 94805, Villejuif, France.
| |
Collapse
|
27
|
Saxena S, Nabel CS, Seay TW, Patel PS, Kawale AS, Crosby CR, Tigro H, Oh E, Vander Heiden MG, Hata AN, Suo Z, Zou L. Unprocessed genomic uracil as a source of DNA replication stress in cancer cells. Mol Cell 2024; 84:2036-2052.e7. [PMID: 38688279 PMCID: PMC11162326 DOI: 10.1016/j.molcel.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 03/26/2024] [Accepted: 04/05/2024] [Indexed: 05/02/2024]
Abstract
Alterations of bases in DNA constitute a major source of genomic instability. It is believed that base alterations trigger base excision repair (BER), generating DNA repair intermediates interfering with DNA replication. Here, we show that genomic uracil, a common type of base alteration, induces DNA replication stress (RS) without being processed by BER. In the absence of uracil DNA glycosylase (UNG), genomic uracil accumulates to high levels, DNA replication forks slow down, and PrimPol-mediated repriming is enhanced, generating single-stranded gaps in nascent DNA. ATR inhibition in UNG-deficient cells blocks the repair of uracil-induced gaps, increasing replication fork collapse and cell death. Notably, a subset of cancer cells upregulates UNG2 to suppress genomic uracil and limit RS, and these cancer cells are hypersensitive to co-treatment with ATR inhibitors and drugs increasing genomic uracil. These results reveal unprocessed genomic uracil as an unexpected source of RS and a targetable vulnerability of cancer cells.
Collapse
Affiliation(s)
- Sneha Saxena
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Christopher S Nabel
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Turner W Seay
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL, USA
| | - Parasvi S Patel
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Ajinkya S Kawale
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Caroline R Crosby
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Helene Tigro
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL, USA
| | - Eugene Oh
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Aaron N Hata
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA, USA; Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Zucai Suo
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL, USA
| | - Lee Zou
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA.
| |
Collapse
|
28
|
Teresa BGD, Ayala-Zambrano C, González-Suárez M, Molina B, Torres L, Rodríguez A, Frías S. Reversion from basal histone H4 hypoacetylation at the replication fork increases DNA damage in FANCA deficient cells. PLoS One 2024; 19:e0298032. [PMID: 38820384 PMCID: PMC11142588 DOI: 10.1371/journal.pone.0298032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 01/16/2024] [Indexed: 06/02/2024] Open
Abstract
The FA/BRCA pathway safeguards DNA replication by repairing interstrand crosslinks (ICL) and maintaining replication fork stability. Chromatin structure, which is in part regulated by histones posttranslational modifications (PTMs), has a role in maintaining genomic integrity through stabilization of the DNA replication fork and promotion of DNA repair. An appropriate balance of PTMs, especially acetylation of histones H4 in nascent chromatin, is required to preserve a stable DNA replication fork. To evaluate the acetylation status of histone H4 at the replication fork of FANCA deficient cells, we compared histone acetylation status at the DNA replication fork of isogenic FANCA deficient and FANCA proficient cell lines by using accelerated native immunoprecipitation of nascent DNA (aniPOND) and in situ protein interactions in the replication fork (SIRF) assays. We found basal hypoacetylation of multiple residues of histone H4 in FA replication forks, together with increased levels of Histone Deacetylase 1 (HDAC1). Interestingly, high-dose short-term treatment with mitomycin C (MMC) had no effect over H4 acetylation abundance at the replication fork. However, chemical inhibition of histone deacetylases (HDAC) with Suberoylanilide hydroxamic acid (SAHA) induced acetylation of the FANCA deficient DNA replication forks to levels comparable to their isogenic control counterparts. This forced permanence of acetylation impacted FA cells homeostasis by inducing DNA damage and promoting G2 cell cycle arrest. Altogether, this caused reduced RAD51 foci formation and increased markers of replication stress, including phospho-RPA-S33. Hypoacetylation of the FANCA deficient replication fork, is part of the cellular phenotype, the perturbation of this feature by agents that prevent deacetylation, such as SAHA, have a deleterious effect over the delicate equilibrium they have reached to perdure despite a defective FA/BRCA pathway.
Collapse
Affiliation(s)
- Benilde García-de Teresa
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Mexico City, Ciudad de México, Mexico
- Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Ciudad de México, Mexico
| | - Cecilia Ayala-Zambrano
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Mexico City, Ciudad de México, Mexico
- Doctorado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Ciudad de México, Mexico
| | - Mirna González-Suárez
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Mexico City, Ciudad de México, Mexico
| | - Bertha Molina
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Mexico City, Ciudad de México, Mexico
| | - Leda Torres
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Mexico City, Ciudad de México, Mexico
| | - Alfredo Rodríguez
- Laboratorio de Falla Medular y Carcinogénesis, Unidad de Genética de la Nutrición, Instituto Nacional de Pediatría, Mexico City, Ciudad de México, Mexico
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Ciudad de México, Mexico
| | - Sara Frías
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Mexico City, Ciudad de México, Mexico
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Ciudad de México, Mexico
| |
Collapse
|
29
|
Batenburg NL, Sowa DJ, Walker JR, Andres SN, Zhu XD. CSB and SMARCAL1 compete for RPA32 at stalled forks and differentially control the fate of stalled forks in BRCA2-deficient cells. Nucleic Acids Res 2024; 52:5067-5087. [PMID: 38416570 PMCID: PMC11109976 DOI: 10.1093/nar/gkae154] [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: 10/03/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/01/2024] Open
Abstract
CSB (Cockayne syndrome group B) and SMARCAL1 (SWI/SNF-related, matrix-associated, actin-dependent, regulator of chromatin, subfamily A-like 1) are DNA translocases that belong to the SNF2 helicase family. They both are enriched at stalled replication forks. While SMARCAL1 is recruited by RPA32 to stalled forks, little is known about whether RPA32 also regulates CSB's association with stalled forks. Here, we report that CSB directly interacts with RPA, at least in part via a RPA32C-interacting motif within the N-terminal region of CSB. Modeling of the CSB-RPA32C interaction suggests that CSB binds the RPA32C surface previously shown to be important for binding of UNG2 and SMARCAL1. We show that this interaction is necessary for promoting fork slowing and fork degradation in BRCA2-deficient cells but dispensable for mediating restart of stalled forks. CSB competes with SMARCAL1 for RPA32 at stalled forks and acts non-redundantly with SMARCAL1 to restrain fork progression in response to mild replication stress. In contrast to CSB stimulated restart of stalled forks, SMARCAL1 inhibits restart of stalled forks in BRCA2-deficient cells, likely by suppressing BIR-mediated repair of collapsed forks. Loss of CSB leads to re-sensitization of SMARCAL1-depleted BRCA2-deficient cells to chemodrugs, underscoring a role of CSB in targeted cancer therapy.
Collapse
Affiliation(s)
- Nicole L Batenburg
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Dana J Sowa
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - John R Walker
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Sara N Andres
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Xu-Dong Zhu
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| |
Collapse
|
30
|
Herr LM, Schaffer ED, Fuchs KF, Datta A, Brosh RM. Replication stress as a driver of cellular senescence and aging. Commun Biol 2024; 7:616. [PMID: 38777831 PMCID: PMC11111458 DOI: 10.1038/s42003-024-06263-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: 12/13/2023] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Replication stress refers to slowing or stalling of replication fork progression during DNA synthesis that disrupts faithful copying of the genome. While long considered a nexus for DNA damage, the role of replication stress in aging is under-appreciated. The consequential role of replication stress in promotion of organismal aging phenotypes is evidenced by an extensive list of hereditary accelerated aging disorders marked by molecular defects in factors that promote replication fork progression and operate uniquely in the replication stress response. Additionally, recent studies have revealed cellular pathways and phenotypes elicited by replication stress that align with designated hallmarks of aging. Here we review recent advances demonstrating the role of replication stress as an ultimate driver of cellular senescence and aging. We discuss clinical implications of the intriguing links between cellular senescence and aging including application of senotherapeutic approaches in the context of replication stress.
Collapse
Affiliation(s)
- Lauren M Herr
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Ethan D Schaffer
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Kathleen F Fuchs
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Arindam Datta
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Robert M Brosh
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
| |
Collapse
|
31
|
Uhrig ME, Sharma N, Maxwell P, Selemenakis P, Mazin AV, Wiese C. Disparate requirements for RAD54L in replication fork reversal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.26.550704. [PMID: 37546955 PMCID: PMC10402051 DOI: 10.1101/2023.07.26.550704] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
RAD54L is a DNA motor protein with multiple roles in homologous recombination DNA repair (HR). In vitro , RAD54L was shown to also catalyze the reversal and restoration of model replication forks. In cells, however, little is known about how RAD54L may regulate the dynamics of DNA replication. Here, we show that RAD54L restrains the progression of replication forks and functions as a fork remodeler in human cells. Analogous to HLTF, SMARCAL1, and FBH1, and consistent with a role in fork reversal, RAD54L decelerates fork progression in response to replication stress and suppresses the formation of replication-associated ssDNA gaps. Interestingly, loss of RAD54L prevents nascent strand DNA degradation in both BRCA1/2- and 53BP1-deficient cells, suggesting that RAD54L functions in both pathways of RAD51-mediated replication fork reversal. In the HLTF/SMARCAL1 pathway, RAD54L is critical, but its ability to catalyze branch migration is dispensable, indicative of its function downstream of HLTF/SMARCAL1. Conversely, in the FBH1 pathway, branch migration activity of RAD54L is essential, and FBH1 engagement is dependent on its concerted action with RAD54L. Collectively, our results reveal disparate requirements for RAD54L in two distinct RAD51-mediated fork reversal pathways, positing its potential as a future therapeutic target.
Collapse
|
32
|
Shah P, Hill R, Dion C, Clark SJ, Abakir A, Willems J, Arends MJ, Garaycoechea JI, Leitch HG, Reik W, Crossan GP. Primordial germ cell DNA demethylation and development require DNA translesion synthesis. Nat Commun 2024; 15:3734. [PMID: 38702312 PMCID: PMC11068800 DOI: 10.1038/s41467-024-47219-2] [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: 06/21/2023] [Accepted: 03/25/2024] [Indexed: 05/06/2024] Open
Abstract
Mutations in DNA damage response (DDR) factors are associated with human infertility, which affects up to 15% of the population. The DDR is required during germ cell development and meiosis. One pathway implicated in human fertility is DNA translesion synthesis (TLS), which allows replication impediments to be bypassed. We find that TLS is essential for pre-meiotic germ cell development in the embryo. Loss of the central TLS component, REV1, significantly inhibits the induction of human PGC-like cells (hPGCLCs). This is recapitulated in mice, where deficiencies in TLS initiation (Rev1-/- or PcnaK164R/K164R) or extension (Rev7 -/-) result in a > 150-fold reduction in the number of primordial germ cells (PGCs) and complete sterility. In contrast, the absence of TLS does not impact the growth, function, or homeostasis of somatic tissues. Surprisingly, we find a complete failure in both activation of the germ cell transcriptional program and in DNA demethylation, a critical step in germline epigenetic reprogramming. Our findings show that for normal fertility, DNA repair is required not only for meiotic recombination but for progression through the earliest stages of germ cell development in mammals.
Collapse
Affiliation(s)
- Pranay Shah
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
| | - Ross Hill
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Camille Dion
- MRC Laboratory of Medical Sciences, London, W12 0HS, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0HS, UK
| | - Stephen J Clark
- Altos Labs, Cambridge, UK
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Abdulkadir Abakir
- Altos Labs, Cambridge, UK
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Jeroen Willems
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, The Netherlands
| | | | - Juan I Garaycoechea
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, The Netherlands
| | - Harry G Leitch
- MRC Laboratory of Medical Sciences, London, W12 0HS, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0HS, UK
| | - Wolf Reik
- Altos Labs, Cambridge, UK
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Gerry P Crossan
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
| |
Collapse
|
33
|
Gong Y, Wang Z, Zong W, Shi R, Sun W, Wang S, Peng B, Takeda S, Wang ZQ, Xu X. PARP1 UFMylation ensures the stability of stalled replication forks. Proc Natl Acad Sci U S A 2024; 121:e2322520121. [PMID: 38657044 PMCID: PMC11066985 DOI: 10.1073/pnas.2322520121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/19/2024] [Indexed: 04/26/2024] Open
Abstract
The S-phase checkpoint involving CHK1 is essential for fork stability in response to fork stalling. PARP1 acts as a sensor of replication stress and is required for CHK1 activation. However, it is unclear how the activity of PARP1 is regulated. Here, we found that UFMylation is required for the efficient activation of CHK1 by UFMylating PARP1 at K548 during replication stress. Inactivation of UFL1, the E3 enzyme essential for UFMylation, delayed CHK1 activation and inhibits nascent DNA degradation during replication blockage as seen in PARP1-deficient cells. An in vitro study indicated that PARP1 is UFMylated at K548, which enhances its catalytic activity. Correspondingly, a PARP1 UFMylation-deficient mutant (K548R) and pathogenic mutant (F553L) compromised CHK1 activation, the restart of stalled replication forks following replication blockage, and chromosome stability. Defective PARP1 UFMylation also resulted in excessive nascent DNA degradation at stalled replication forks. Finally, we observed that PARP1 UFMylation-deficient knock-in mice exhibited increased sensitivity to replication stress caused by anticancer treatments. Thus, we demonstrate that PARP1 UFMylation promotes CHK1 activation and replication fork stability during replication stress, thus safeguarding genome integrity.
Collapse
Affiliation(s)
- Yamin Gong
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong518060, China
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena07745, Germany
| | - Zhifeng Wang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong518060, China
| | - Wen Zong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
| | - Ruifeng Shi
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong518060, China
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena07745, Germany
| | - Wenli Sun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
| | - Sijia Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
| | - Bin Peng
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong518060, China
| | - Shunichi Takeda
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong518060, China
| | - Zhao-Qi Wang
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena07745, Germany
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao266237, China
- Faculty of Biology and Pharmacy, Friedrich-Schiller University of Jena, Jena07743, Germany
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong518060, China
| |
Collapse
|
34
|
Sang PB, Jaiswal RK, Lyu X, Chai W. Human CST complex restricts excessive PrimPol repriming upon UV induced replication stress by suppressing p21. Nucleic Acids Res 2024; 52:3778-3793. [PMID: 38348929 DOI: 10.1093/nar/gkae078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 04/25/2024] Open
Abstract
DNA replication stress, caused by various endogenous and exogenous agents, halt or stall DNA replication progression. Cells have developed diverse mechanisms to tolerate and overcome replication stress, enabling them to continue replication. One effective strategy to overcome stalled replication involves skipping the DNA lesion using a specialized polymerase known as PrimPol, which reinitiates DNA synthesis downstream of the damage. However, the mechanism regulating PrimPol repriming is largely unclear. In this study, we observe that knockdown of STN1 or CTC1, components of the CTC1/STN1/TEN1 complex, leads to enhanced replication progression following UV exposure. We find that such increased replication is dependent on PrimPol, and PrimPol recruitment to stalled forks increases upon CST depletion. Moreover, we find that p21 is upregulated in STN1-depleted cells in a p53-independent manner, and p21 depletion restores normal replication rates caused by STN1 deficiency. We identify that p21 interacts with PrimPol, and STN1 depletion stimulates p21-PrimPol interaction and facilitates PrimPol recruitment to stalled forks. Our findings reveal a previously undescribed interplay between CST, PrimPol and p21 in promoting repriming in response to stalled replication, and shed light on the regulation of PrimPol repriming at stalled forks.
Collapse
Affiliation(s)
- Pau Biak Sang
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Rishi K Jaiswal
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
| | - Xinxing Lyu
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Weihang Chai
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
| |
Collapse
|
35
|
Nguyen DT, Mahajan U, Angappulige DH, Doshi A, Mahajan NP, Mahajan K. Amino Terminal Acetylation of HOXB13 Regulates the DNA Damage Response in Prostate Cancer. Cancers (Basel) 2024; 16:1622. [PMID: 38730575 PMCID: PMC11083449 DOI: 10.3390/cancers16091622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 05/13/2024] Open
Abstract
Advanced localized prostate cancers (PC) recur despite chemotherapy, radiotherapy and/or androgen deprivation therapy. We recently reported HOXB13 lysine (K)13 acetylation as a gain-of-function modification that regulates interaction with the SWI/SNF chromatin remodeling complex and is critical for anti-androgen resistance. However, whether acetylated HOXB13 promotes PC cell survival following treatment with genotoxic agents is not known. Herein, we show that K13-acetylated HOXB13 is induced rapidly in PC cells in response to DNA damage induced by irradiation (IR). It colocalizes with the histone variant γH2AX at sites of double strand breaks (DSBs). Treatment of PCs with the Androgen Receptor (AR) antagonist Enzalutamide (ENZ) did not suppress DNA-damage-induced HOXB13 acetylation. In contrast, HOXB13 depletion or loss of acetylation overcame resistance of PC cells to ENZ and synergized with IR. HOXB13K13A mutants show diminished replication fork progression, impaired G2/M arrest with significant cell death following DNA damage. Mechanistically, we found that amino terminus regulates HOXB13 nuclear puncta formation that is essential for proper DNA damage response. Therefore, targeting HOXB13 acetylation with CBP/p300 inhibitors in combination with DNA damaging therapy may be an effective strategy to overcome anti-androgen resistance of PCs.
Collapse
Affiliation(s)
- Duy T. Nguyen
- Division of Urologic Surgery, Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224, USA
| | - Urvashi Mahajan
- Division of Urologic Surgery, Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- A.T. Still University of Health Sciences, Kirksville, MO 63501, USA
| | - Duminduni Hewa Angappulige
- Division of Urologic Surgery, Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Aashna Doshi
- Division of Urologic Surgery, Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Nupam P. Mahajan
- Division of Urologic Surgery, Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Kiran Mahajan
- Division of Urologic Surgery, Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| |
Collapse
|
36
|
Arvanitaki ES, Goulielmaki E, Gkirtzimanaki K, Niotis G, Tsakani E, Nenedaki E, Rouska I, Kefalogianni M, Xydias D, Kalafatakis I, Psilodimitrakopoulos S, Karagogeos D, Schumacher B, Stratakis E, Garinis GA. Microglia-derived extracellular vesicles trigger age-related neurodegeneration upon DNA damage. Proc Natl Acad Sci U S A 2024; 121:e2317402121. [PMID: 38635632 PMCID: PMC11047102 DOI: 10.1073/pnas.2317402121] [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: 10/09/2023] [Accepted: 03/22/2024] [Indexed: 04/20/2024] Open
Abstract
DNA damage and neurodegenerative disorders are intimately linked but the underlying mechanism remains elusive. Here, we show that persistent DNA lesions in tissue-resident macrophages carrying an XPF-ERCC1 DNA repair defect trigger neuroinflammation and neuronal cell death in mice. We find that microglia accumulate dsDNAs and chromatin fragments in the cytosol, which are sensed thereby stimulating a viral-like immune response in Er1Cx/- and naturally aged murine brain. Cytosolic DNAs are packaged into extracellular vesicles (EVs) that are released from microglia and discharge their dsDNA cargo into IFN-responsive neurons triggering cell death. To remove cytosolic dsDNAs and prevent inflammation, we developed targeting EVs to deliver recombinant DNase I to Er1Cx/- brain microglia in vivo. We show that EV-mediated elimination of cytosolic dsDNAs is sufficient to prevent neuroinflammation, reduce neuronal apoptosis, and delay the onset of neurodegenerative symptoms in Er1Cx/- mice. Together, our findings unveil a causal mechanism leading to neuroinflammation and provide a rationalized therapeutic strategy against age-related neurodegeneration.
Collapse
Affiliation(s)
- Ermioni S. Arvanitaki
- Department of Biology, University of Crete, HeraklionGR71409, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, HeraklionGR70013, Crete, Greece
| | - Evi Goulielmaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, HeraklionGR70013, Crete, Greece
| | - Katerina Gkirtzimanaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, HeraklionGR70013, Crete, Greece
| | - George Niotis
- Department of Biology, University of Crete, HeraklionGR71409, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, HeraklionGR70013, Crete, Greece
| | - Edisona Tsakani
- Department of Biology, University of Crete, HeraklionGR71409, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, HeraklionGR70013, Crete, Greece
| | - Electra Nenedaki
- Department of Biology, University of Crete, HeraklionGR71409, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, HeraklionGR70013, Crete, Greece
| | - Iliana Rouska
- Department of Biology, University of Crete, HeraklionGR71409, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, HeraklionGR70013, Crete, Greece
| | - Mary Kefalogianni
- Department of Physics, University of Crete, HeraklionGR71003, Crete, Greece
- Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas, HeraklionGR71110, Crete, Greece
| | - Dionysios Xydias
- Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas, HeraklionGR71110, Crete, Greece
- Materials Science and Technology Department, University of Crete, HeraklionGR70013, Crete, Greece
| | - Ilias Kalafatakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, HeraklionGR70013, Crete, Greece
- Medical School, Division of Basic Sciences, University of Crete, HeraklionGR71003, Crete, Greece
| | - Sotiris Psilodimitrakopoulos
- Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas, HeraklionGR71110, Crete, Greece
| | - Domna Karagogeos
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, HeraklionGR70013, Crete, Greece
- Medical School, Division of Basic Sciences, University of Crete, HeraklionGR71003, Crete, Greece
| | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University and University Hospital of Cologne, Cologne50931, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne50931, Germany
| | - Emmanuel Stratakis
- Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas, HeraklionGR71110, Crete, Greece
| | - George A. Garinis
- Department of Biology, University of Crete, HeraklionGR71409, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, HeraklionGR70013, Crete, Greece
| |
Collapse
|
37
|
Boddu PC, Gupta AK, Roy R, De La Peña Avalos B, Olazabal-Herrero A, Neuenkirchen N, Zimmer JT, Chandhok NS, King D, Nannya Y, Ogawa S, Lin H, Simon MD, Dray E, Kupfer GM, Verma A, Neugebauer KM, Pillai MM. Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape. Mol Cell 2024; 84:1475-1495.e18. [PMID: 38521065 PMCID: PMC11061666 DOI: 10.1016/j.molcel.2024.02.032] [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: 03/28/2023] [Revised: 11/26/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024]
Abstract
Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human diseases remains unexplored. Using isogenic cell lines, patient samples, and a mutant mouse model, we investigated how cancer-associated mutations in SF3B1 alter transcription. We found that these mutations reduce the elongation rate of RNA polymerase II (RNAPII) along gene bodies and its density at promoters. The elongation defect results from disrupted pre-spliceosome assembly due to impaired protein-protein interactions of mutant SF3B1. The decreased promoter-proximal RNAPII density reduces both chromatin accessibility and H3K4me3 marks at promoters. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC/H3K4me pathway, which, when modulated, reverse both transcription and chromatin changes. Our findings reveal how splicing factor mutant states behave functionally as epigenetic disorders through impaired transcription-related changes to the chromatin landscape. We also present a rationale for targeting the Sin3/HDAC complex as a therapeutic strategy.
Collapse
Affiliation(s)
- Prajwal C Boddu
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Abhishek K Gupta
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Rahul Roy
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Bárbara De La Peña Avalos
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center (UTHSC) at San Antonio, San Antonio, TX, USA
| | - Anne Olazabal-Herrero
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Nils Neuenkirchen
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Joshua T Zimmer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Namrata S Chandhok
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Darren King
- Section of Hematology and Medical Oncology, Department of Internal Medicine and Rogel Cancer Center, University of Michigan Health, Ann Arbor, MI, USA
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Haifan Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Eloise Dray
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center (UTHSC) at San Antonio, San Antonio, TX, USA
| | - Gary M Kupfer
- Department of Oncology and Pediatrics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Amit Verma
- Division of Hemato-Oncology, Department of Medicine and Department of Developmental and Molecular Biology, Albert Einstein-Montefiore Cancer Center, New York, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University, New Haven, CT, USA
| | - Manoj M Pillai
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
| |
Collapse
|
38
|
Guo Y, Li S, Shi Z, Chen B, Wan Z, Yu P, Zheng B, Gong W, Chai R, Tu S, Yuan H. EEPD1 is identified as a predictor of prognosis and immune microenvironment through pan-cancer analysis and related to progression of colorectal cancer. Heliyon 2024; 10:e29285. [PMID: 38633650 PMCID: PMC11021989 DOI: 10.1016/j.heliyon.2024.e29285] [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: 08/16/2023] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024] Open
Abstract
Background EEPD1 is vital in homologous recombination, while its role in cancer remains unclear. Methods We performed multiple pan-cancer analyses of EEPD1 with bioinformatics methods, such as gene expression, gene alterations, Prognosis and enrichment analysis, tumor microenvironment, immune cell infiltration, TMB, MSI, immunotherapy, co-expression of genes, and drug resistance. Finally, RT-qPCR, EdU, and transwell assays helped investigate the impact of EEPD1 on CRC cells. Results EEPD1 was dysregulated and correlated with bad prognosis in several cancers. GSVA and GSEA revealed that EEPD1 was primarily associated with the "WNT_BETA_CATENIN_SIGNALING," "ribonucleoprotein complex biogenesis," "Ribosome," and "rRNA processing." The infiltration of CD8+ T cells, MAIT cells, iTreg cells, NK cells, Tc cells, Tex cells, Tfh cells, and Th1 cells were negatively correlated with EEPD1 expression. Additionally, EEPD1 is significantly associated with TMB and MSI in COAD, while enhanced CRC cell proliferation and migration. Conclusions EEPD1 was dysregulated in human cancers and correlated with various cancer patient prognoses. The dysregulated EEPD1 expression can affect tumor-infiltrating immune cells and immunotherapy response. Therefore, EEPD1 could act as an oncogene associated with immune cell infiltration in CRC.
Collapse
Affiliation(s)
- Yang Guo
- General Surgery, Cancer Center, Department of Colorectal Surgery, Zhejiang Provincial People's Hospital(Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, 310014, PR China
| | - Shujin Li
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, PR China
| | - Zhan Shi
- General Surgery, Cancer Center, Department of Colorectal Surgery, Zhejiang Provincial People's Hospital(Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, 310014, PR China
| | - Bingchen Chen
- General Surgery, Cancer Center, Department of Colorectal Surgery, Zhejiang Provincial People's Hospital(Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, 310014, PR China
| | - Ziang Wan
- General Surgery, Cancer Center, Department of Colorectal Surgery, Zhejiang Provincial People's Hospital(Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, 310014, PR China
| | - Peng Yu
- General Surgery, Cancer Center, Department of Colorectal Surgery, Zhejiang Provincial People's Hospital(Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, 310014, PR China
| | - Boan Zheng
- General Surgery, Cancer Center, Department of Colorectal Surgery, Zhejiang Provincial People's Hospital(Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, 310014, PR China
| | - Wenjing Gong
- General Surgery, Cancer Center, Department of Colorectal Surgery, Zhejiang Provincial People's Hospital(Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, 310014, PR China
| | - Rui Chai
- General Surgery, Cancer Center, Department of Colorectal Surgery, Zhejiang Provincial People's Hospital(Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, 310014, PR China
| | - Shiliang Tu
- General Surgery, Cancer Center, Department of Colorectal Surgery, Zhejiang Provincial People's Hospital(Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, 310014, PR China
| | - Hang Yuan
- General Surgery, Cancer Center, Department of Colorectal Surgery, Zhejiang Provincial People's Hospital(Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, 310014, PR China
| |
Collapse
|
39
|
Jurkovic CM, Boisvert FM. Evolution of techniques and tools for replication fork proteome and protein interaction studies. Biochem Cell Biol 2024; 102:135-144. [PMID: 38113480 DOI: 10.1139/bcb-2023-0215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023] Open
Abstract
Understanding the complex network of protein-protein interactions (PPI) that govern cellular functions is essential for unraveling the molecular basis of biological processes and diseases. Mass spectrometry (MS) has emerged as a powerful tool for studying protein dynamics, enabling comprehensive analysis of protein function, structure, post-translational modifications, interactions, and localization. This article provides an overview of MS techniques and their applications in proteomics studies, with a focus on the replication fork proteome. The replication fork is a multi-protein assembly involved in DNA replication, and its proper functioning is crucial for maintaining genomic integrity. By combining quantitative MS labeling techniques with various data acquisition methods, researchers have made significant strides in elucidating the complex processes and molecular mechanisms at the replication fork. Overall, MS has revolutionized our understanding of protein dynamics, offering valuable insights into cellular processes and potential targets for therapeutic interventions.
Collapse
Affiliation(s)
- Carla-Marie Jurkovic
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - François-Michel Boisvert
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| |
Collapse
|
40
|
Giudice E, Huang TT, Nair JR, Zurcher G, McCoy A, Nousome D, Radke MR, Swisher EM, Lipkowitz S, Ibanez K, Donohue D, Malys T, Lee MJ, Redd B, Levy E, Rastogi S, Sato N, Trepel JB, Lee JM. The CHK1 inhibitor prexasertib in BRCA wild-type platinum-resistant recurrent high-grade serous ovarian carcinoma: a phase 2 trial. Nat Commun 2024; 15:2805. [PMID: 38555285 PMCID: PMC10981752 DOI: 10.1038/s41467-024-47215-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 03/25/2024] [Indexed: 04/02/2024] Open
Abstract
The multi-cohort phase 2 trial NCT02203513 was designed to evaluate the clinical activity of the CHK1 inhibitor (CHK1i) prexasertib in patients with breast or ovarian cancer. Here we report the activity of CHK1i in platinum-resistant high-grade serous ovarian carcinoma (HGSOC) with measurable and biopsiable disease (cohort 5), or without biopsiable disease (cohort 6). The primary endpoint was objective response rate (ORR). Secondary outcomes were safety and progression-free survival (PFS). 49 heavily pretreated patients were enrolled (24 in cohort 5, 25 in cohort 6). Among the 39 RECISTv1.1-evaluable patients, ORR was 33.3% in cohort 5 and 28.6% in cohort 6. Primary endpoint was not evaluable due to early stop of the trial. The median PFS was 4 months in cohort 5 and 6 months in cohort 6. Toxicity was manageable. Translational research was an exploratory endpoint. Potential biomarkers were investigated using pre-treatment fresh biopsies and serial blood samples. Transcriptomic analysis revealed high levels of DNA replication-related genes (POLA1, POLE, GINS3) associated with lack of clinical benefit [defined post-hoc as PFS < 6 months]. Subsequent preclinical experiments demonstrated significant cytotoxicity of POLA1 silencing in combination with CHK1i in platinum-resistant HGSOC cell line models. Therefore, POLA1 expression may be predictive for CHK1i resistance, and the concurrent POLA1 inhibition may improve the efficacy of CHK1i monotherapy in this hard-to-treat population, deserving further investigation.
Collapse
Affiliation(s)
- Elena Giudice
- Women's Malignancies Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
- Institute of Obstetrics and Gynecology, Università Cattolica del Sacro Cuore, Largo Agostino Gemelli 8, 00168, Rome, Italy
| | - Tzu-Ting Huang
- Women's Malignancies Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Jayakumar R Nair
- Women's Malignancies Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Grant Zurcher
- Women's Malignancies Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Ann McCoy
- Women's Malignancies Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Darryl Nousome
- Center for Cancer Research Collaborative Bioinformatics Resource, CCR, NCI, NIH, Bethesda, MD, 20892, USA
| | - Marc R Radke
- Department of Ob/Gyn, University of Washington, Seattle, WA, 98195, USA
| | | | - Stanley Lipkowitz
- Women's Malignancies Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Kristen Ibanez
- Women's Malignancies Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Duncan Donohue
- Statistical Consulting and Scientific Programming Group, Computer and Statistical Services, Data Management Services, Inc. (a BRMI company), NCI, Frederick, MD, 21702, USA
| | - Tyler Malys
- Statistical Consulting and Scientific Programming Group, Computer and Statistical Services, Data Management Services, Inc. (a BRMI company), NCI, Frederick, MD, 21702, USA
| | - Min-Jung Lee
- Developmental Therapeutics Branch, CCR, NCI, NIH, Bethesda, MD, 20892, USA
| | - Bernadette Redd
- Clinical Image Processing Service, Department of Radiology and Imaging Sciences, CCR, NCI, NIH, Bethesda, MD, 20892, USA
| | - Elliot Levy
- Interventional Radiology, CCR, NCI, NIH, Bethesda, MD, 20892, USA
| | - Shraddha Rastogi
- Developmental Therapeutics Branch, CCR, NCI, NIH, Bethesda, MD, 20892, USA
| | - Nahoko Sato
- Developmental Therapeutics Branch, CCR, NCI, NIH, Bethesda, MD, 20892, USA
| | - Jane B Trepel
- Developmental Therapeutics Branch, CCR, NCI, NIH, Bethesda, MD, 20892, USA
| | - Jung-Min Lee
- Women's Malignancies Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, 20892, USA.
| |
Collapse
|
41
|
Yang K, Jeltema D, Yan N. Innate immune sensing of macromolecule homeostasis. Adv Immunol 2024; 161:17-51. [PMID: 38763701 DOI: 10.1016/bs.ai.2024.03.004] [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: 05/21/2024]
Abstract
The innate immune system uses a distinct set of germline-encoded pattern recognition receptors to recognize molecular patterns initially thought to be unique to microbial invaders, named pathogen-associated molecular patterns. The concept was later further developed to include similar molecular patterns originating from host cells during tissue damage, known as damage-associated molecular patterns. However, recent advances in the mechanism of monogenic inflammatory diseases have highlighted a much more expansive repertoire of cellular functions that are monitored by innate immunity. Here, we summarize several examples in which an innate immune response is triggered when homeostasis of macromolecule in the cell is disrupted in non-infectious or sterile settings. These ever-growing sensing mechanisms expand the repertoire of innate immune recognition, positioning it not only as a key player in host defense but also as a gatekeeper of cellular homeostasis. Therapeutics inspired by these advances to restore cellular homeostasis and correct the immune system could have far-reaching implications.
Collapse
Affiliation(s)
- Kun Yang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Devon Jeltema
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Nan Yan
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States.
| |
Collapse
|
42
|
Żabka A, Gocek N, Polit JT, Maszewski J. Oxidative replication stress induced by long-term exposure to hydroxyurea in root meristem cells of Vicia faba. PLANT CELL REPORTS 2024; 43:87. [PMID: 38460026 DOI: 10.1007/s00299-024-03187-x] [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: 01/03/2024] [Accepted: 02/28/2024] [Indexed: 03/11/2024]
Abstract
KEY MESSAGE Low concentrations of hydroxyurea, an inhibitor of DNA replication, induced oxidative and replicative stress in root apical meristem (RAM) cells of Vicia faba. Plant cells are constantly exposed to low-level endogenous stress factors that can affect DNA replication and lead to DNA damage. Long-term treatments of Vicia faba root apical meristems (RAMs) with HU leads to the appearance of atypical cells with intranuclear asynchrony. This rare form of abnormality was manifested by a gradual condensation of chromatin, from interphase to mitosis (so-called IM cells). Moreover, HU-treated root cells revealed abnormal chromosome structure, persisting DNA replication, and elevated levels of intracellular hydrogen peroxide (H2O2) and superoxide anion (O2∙-). Immunocytochemical studies have shown an increased number of fluorescent foci of H3 histones acetylated at lysine 56 (H3K56Ac; canonically connected with the DNA replication process). We show that continuous 3-day exposure to low concentrations (0.75 mM) of hydroxyurea (HU; an inhibitor of DNA replication) induces cellular response to reactive oxygen species and to DNA replication stress conditions.
Collapse
Affiliation(s)
- Aneta Żabka
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, 90-236, Lodz, Poland.
| | - Natalia Gocek
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, 90-236, Lodz, Poland
| | - Justyna Teresa Polit
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, 90-236, Lodz, Poland
| | - Janusz Maszewski
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, 90-236, Lodz, Poland
| |
Collapse
|
43
|
Zhao X, Singhal A, Park S, Kong J, Bachelder R, Ideker T. Cancer Mutations Converge on a Collection of Protein Assemblies to Predict Resistance to Replication Stress. Cancer Discov 2024; 14:508-523. [PMID: 38236062 PMCID: PMC10905674 DOI: 10.1158/2159-8290.cd-23-0641] [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: 06/12/2023] [Revised: 10/25/2023] [Accepted: 12/21/2023] [Indexed: 01/19/2024]
Abstract
Rapid proliferation is a hallmark of cancer associated with sensitivity to therapeutics that cause DNA replication stress (RS). Many tumors exhibit drug resistance, however, via molecular pathways that are incompletely understood. Here, we develop an ensemble of predictive models that elucidate how cancer mutations impact the response to common RS-inducing (RSi) agents. The models implement recent advances in deep learning to facilitate multidrug prediction and mechanistic interpretation. Initial studies in tumor cells identify 41 molecular assemblies that integrate alterations in hundreds of genes for accurate drug response prediction. These cover roles in transcription, repair, cell-cycle checkpoints, and growth signaling, of which 30 are shown by loss-of-function genetic screens to regulate drug sensitivity or replication restart. The model translates to cisplatin-treated cervical cancer patients, highlighting an RTK-JAK-STAT assembly governing resistance. This study defines a compendium of mechanisms by which mutations affect therapeutic responses, with implications for precision medicine. SIGNIFICANCE Zhao and colleagues use recent advances in machine learning to study the effects of tumor mutations on the response to common therapeutics that cause RS. The resulting predictive models integrate numerous genetic alterations distributed across a constellation of molecular assemblies, facilitating a quantitative and interpretable assessment of drug response. This article is featured in Selected Articles from This Issue, p. 384.
Collapse
Affiliation(s)
- Xiaoyu Zhao
- Division of Human Genomics and Precision Medicine, Department of Medicine, University of California, San Diego, La Jolla, California
| | - Akshat Singhal
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California
| | - Sungjoon Park
- Division of Human Genomics and Precision Medicine, Department of Medicine, University of California, San Diego, La Jolla, California
| | - JungHo Kong
- Division of Human Genomics and Precision Medicine, Department of Medicine, University of California, San Diego, La Jolla, California
- Moores Cancer Center, School of Medicine, University of California, San Diego, La Jolla, California
| | - Robin Bachelder
- Division of Human Genomics and Precision Medicine, Department of Medicine, University of California, San Diego, La Jolla, California
| | - Trey Ideker
- Division of Human Genomics and Precision Medicine, Department of Medicine, University of California, San Diego, La Jolla, California
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California
- Moores Cancer Center, School of Medicine, University of California, San Diego, La Jolla, California
- Department of Bioengineering, University of California, San Diego, La Jolla, California
| |
Collapse
|
44
|
Liu L, Hu X, Feng J, Lei A, Huang S, Liu X, Liu H, Luo L, Yao W. Suppression of DNMT1 combined with ATM or ATR inhibitor as a therapeutic combination of acute myeloid leukemia. Anticancer Drugs 2024; 35:251-262. [PMID: 38164802 PMCID: PMC10833198 DOI: 10.1097/cad.0000000000001564] [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: 11/03/2023] [Accepted: 11/03/2023] [Indexed: 01/03/2024]
Abstract
The potential treatment option of targeting DNA methyltransferase 1 (DNMT1) has been explored, but further investigation is required to assess the efficacy of combination therapy in acute myeloid leukemia (AML). In this study, bioinformatics and online databases were utilized to select the combined therapeutic targets. The potential kinases associated with DNMT1-related genes in AML were analyzed using the Cancer Genome Atlas (TCGA) database and X2K Appyter (Expression2Kinases) database. In-vitro evaluations were conducted to assess the synergistic effects between DNMT1 and ATR/ATM in five AML cell lines (MOLM-16, NB-4, HEL 92.1.7, HEL, EOL-1). In our study, ATR and ATM are primarily the kinases associated with DNMT1-related genes in AML. We observed a significant upregulation of DNMT1, ATR, and ATM expression in AML tissues and cell lines. The five AML cell lines demonstrated sensitivity to monotherapy with GSK-368, AZD-1390, or AZD-6738 (EC50 value ranges from 5.461 to 7.349 nM, 5.821 to 10.120 nM, and 7.618 to 10.100 nM, respectively). A considerable synergistic effect was observed in AML cell lines when combining GSK-368 and AZD-1390, GSK-368 and AZD-6738, or AZD-1390 and AZD-6738, resulting in induced cell apoptosis and inhibited cell growth. DNMT1, ATM, and ATR possess potential as therapeutic targets for AML. Both individual targeting and combination targeting of these molecules have been confirmed as promising therapeutic approaches for AML.
Collapse
Affiliation(s)
- Lei Liu
- Department of Hematology and Oncology, The First People’s Hospital of Guiyang, Guiyang city, Guizhou Province, China
| | - Xiaoyan Hu
- Department of Hematology and Oncology, The First People’s Hospital of Guiyang, Guiyang city, Guizhou Province, China
| | - Jing Feng
- Department of Hematology and Oncology, The First People’s Hospital of Guiyang, Guiyang city, Guizhou Province, China
| | - Anhui Lei
- Department of Hematology and Oncology, The First People’s Hospital of Guiyang, Guiyang city, Guizhou Province, China
| | - Shiying Huang
- Department of Hematology and Oncology, The First People’s Hospital of Guiyang, Guiyang city, Guizhou Province, China
| | - Xian Liu
- Department of Hematology and Oncology, The First People’s Hospital of Guiyang, Guiyang city, Guizhou Province, China
| | - Hui Liu
- Department of Hematology and Oncology, The First People’s Hospital of Guiyang, Guiyang city, Guizhou Province, China
| | - Lan Luo
- Department of Hematology and Oncology, The First People’s Hospital of Guiyang, Guiyang city, Guizhou Province, China
| | - Wenyan Yao
- Department of Hematology and Oncology, The First People’s Hospital of Guiyang, Guiyang city, Guizhou Province, China
| |
Collapse
|
45
|
Bhatia S, Khanna KK, Duijf PHG. Targeting chromosomal instability and aneuploidy in cancer. Trends Pharmacol Sci 2024; 45:210-224. [PMID: 38355324 DOI: 10.1016/j.tips.2024.01.009] [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: 12/21/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/16/2024]
Abstract
Cancer development and therapy resistance are driven by chromosomal instability (CIN), which causes chromosome gains and losses (i.e., aneuploidy) and structural chromosomal alterations. Technical limitations and knowledge gaps have delayed therapeutic targeting of CIN and aneuploidy in cancers. However, our toolbox for creating and studying aneuploidy in cell models has greatly expanded recently. Moreover, accumulating evidence suggests that seven conventional antimitotic chemotherapeutic drugs achieve clinical response by inducing CIN instead of mitotic arrest, although additional anticancer activities may also contribute in vivo. In this review, we discuss these recent developments. We also highlight new discoveries, which together show that 25 chromosome arm aneuploidies (CAAs) may be targetable by 36 drugs across 14 types of cancer. Collectively, these advances offer many new opportunities to improve cancer treatment.
Collapse
Affiliation(s)
- Sugandha Bhatia
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health and Centre for Biomedical Technologies at the Translational Research Institute, Woolloongabba, QLD 4102, Australia.
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia; Mater Research Institute, The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Pascal H G Duijf
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health and Centre for Biomedical Technologies at the Translational Research Institute, Woolloongabba, QLD 4102, Australia; Centre for Cancer Biology, Clinical and Health Sciences, University of South Australia and SA Pathology, Adelaide, SA 5001, Australia; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
| |
Collapse
|
46
|
Wu W, Wu W, Zhou Y, Yang Q, Zhuang S, Zhong C, Li W, Li A, Zhao W, Yin X, Zu X, Chak-Lui Wong C, Yin D, Hu K, Cai M. The dePARylase NUDT16 promotes radiation resistance of cancer cells by blocking SETD3 for degradation via reversing its ADP-ribosylation. J Biol Chem 2024; 300:105671. [PMID: 38272222 PMCID: PMC10926213 DOI: 10.1016/j.jbc.2024.105671] [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: 06/20/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/27/2024] Open
Abstract
Poly(ADP-ribosyl)ation (PARylation) is a critical posttranslational modification that plays a vital role in maintaining genomic stability via a variety of molecular mechanisms, including activation of replication stress and the DNA damage response. The nudix hydrolase NUDT16 was recently identified as a phosphodiesterase that is responsible for removing ADP-ribose units and that plays an important role in DNA repair. However, the roles of NUDT16 in coordinating replication stress and cell cycle progression remain elusive. Here, we report that SETD3, which is a member of the SET-domain containing protein (SETD) family, is a novel substrate for NUDT16, that its protein levels fluctuate during cell cycle progression, and that its stability is strictly regulated by NUDT16-mediated dePARylation. Moreover, our data indicated that the E3 ligase CHFR is responsible for the recognition and degradation of endogenous SETD3 in a PARP1-mediated PARylation-dependent manner. Mechanistically, we revealed that SETD3 associates with BRCA2 and promotes its recruitment to stalled replication fork and DNA damage sites upon replication stress or DNA double-strand breaks, respectively. Importantly, depletion of SETD3 in NUDT16-deficient cells did not further exacerbate DNA breaks or enhance the sensitivity of cancer cells to IR exposure, suggesting that the NUDT16-SETD3 pathway may play critical roles in the induction of tolerance to radiotherapy. Collectively, these data showed that NUDT16 functions as a key upstream regulator of SETD3 protein stability by reversing the ADP-ribosylation of SETD3, and NUDT16 participates in the resolution of replication stress and facilitates HR repair.
Collapse
Affiliation(s)
- Weijun Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Wenjing Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Breast Oncology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yingshi Zhou
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Ultrasound, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Qiao Yang
- Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Shuting Zhuang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Caixia Zhong
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Wenjia Li
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Aixin Li
- Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Wanzhen Zhao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Xiaomin Yin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Xuyu Zu
- Cancer Research Institute, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Carmen Chak-Lui Wong
- Li Ka Shing Faculty of Medicine, Department of Pathology, The University of Hong Kong, Hong Kong, Guangdong, China
| | - Dong Yin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Kaishun Hu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Manbo Cai
- Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China.
| |
Collapse
|
47
|
Banerjee S, Mondal S, Islam J, Sarkar R, Saha B, Sen A. Rhizospheric nano-remediation salvages arsenic genotoxicity: Zinc-oxide nanoparticles articulate better oxidative stress management, reduce arsenic uptake, and increase yield in Pisum sativum (L.). THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169493. [PMID: 38151134 DOI: 10.1016/j.scitotenv.2023.169493] [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: 10/12/2023] [Revised: 12/13/2023] [Accepted: 12/17/2023] [Indexed: 12/29/2023]
Abstract
Pea (Pisum sativum L.), a legume, has a high nutritional content, but arsenic (As) in the agro-ecosystem poses a significant bottleneck to its yield, especially in South East Asia, by severely hampering ontogeny. The present study proposes a rhizospheric nano-remediation strategy to evade As-genotoxicity and improve crop yield using biogenic zinc-oxide nanoparticles (ZnONPs). Similar to any other source of environmental stress, As-toxicity caused rapid oxidative bursts with deterioration in morpho-physiological attributes (germination rate, shoot length, and root length decreased by 62 %, 16 %, and 14.9 % respectively in the negative control, over normal control). Reactive oxygen species (ROS) accumulation (12.8 and 9-fold increase in leaves and roots) overburdened antioxidative defense, and loss of cellular homeostasis resulted in membrane damage (82.75 % increase) and electrolyte-leakage (2.6-fold increase) in negative control. The study also reveals a significant increase in nuclear area, nuclear fragmentation, and micronuclei formation in root tip cells under As-stress, indicating severe genomic instability and increased programmed cell death (3.3-fold increase in early apoptotic cells) due to leaky plasma membrane and unrepaired DNA damage. Application of ZnONPs significantly reduced As-toxicity in peas due to its adsorption in the rhizosphere, causing diminished As-uptake and better antioxidant response. Improved phytochelatin synthesis enhanced vacuolar sequestration of arsenic, which reduced As-interference. Comparatively better flowering time (7.74-19.36 % reduction in flowering delay) with greater transcript abundance of GIGANTIA (GI), CONSTANS (CO), and FLOWERING LOCUS T (FT) genes; better photosynthetic activity (1.3-1.9-fold increased chlorophyll autofluorescence); increased pollen viability; lesser genotoxicity (decreased tail DNA in comet assay) was noticed. A maximum increase of 37.5 % in pod number and seed zinc content (1.67-fold) was observed while seed arsenic content decreased under ZnONPs treatment. However, the highest dose of ZnONPs (400 mg L-1) induced NP-toxicity in pea plants under our experimental conditions, while optimum stress-alleviation was observed up to 300 mg L-1.
Collapse
Affiliation(s)
- Swarnendra Banerjee
- Molecular Genetics Laboratory, Department of Botany, University of North Bengal, Siliguri 734013, India
| | - Sourik Mondal
- Molecular Genetics Laboratory, Department of Botany, University of North Bengal, Siliguri 734013, India
| | - Jarzis Islam
- Molecular Genetics Laboratory, Department of Botany, University of North Bengal, Siliguri 734013, India
| | - Rajarshi Sarkar
- Molecular Genetics Laboratory, Department of Botany, University of North Bengal, Siliguri 734013, India
| | - Bedabrata Saha
- Plant Pathology and Weed Research Department, Newe Ya'ar Research Centre, Agricultural Research Organization (ARO), Ramat Yishay 3009500, Israel
| | - Arnab Sen
- Molecular Genetics Laboratory, Department of Botany, University of North Bengal, Siliguri 734013, India.
| |
Collapse
|
48
|
Olson CL, Wuttke DS. Guardians of the Genome: How the Single-Stranded DNA-Binding Proteins RPA and CST Facilitate Telomere Replication. Biomolecules 2024; 14:263. [PMID: 38540683 PMCID: PMC10968030 DOI: 10.3390/biom14030263] [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: 12/21/2023] [Revised: 02/02/2024] [Accepted: 02/20/2024] [Indexed: 04/26/2024] Open
Abstract
Telomeres act as the protective caps of eukaryotic linear chromosomes; thus, proper telomere maintenance is crucial for genome stability. Successful telomere replication is a cornerstone of telomere length regulation, but this process can be fraught due to the many intrinsic challenges telomeres pose to the replication machinery. In addition to the famous "end replication" problem due to the discontinuous nature of lagging strand synthesis, telomeres require various telomere-specific steps for maintaining the proper 3' overhang length. Bulk telomere replication also encounters its own difficulties as telomeres are prone to various forms of replication roadblocks. These roadblocks can result in an increase in replication stress that can cause replication forks to slow, stall, or become reversed. Ultimately, this leads to excess single-stranded DNA (ssDNA) that needs to be managed and protected for replication to continue and to prevent DNA damage and genome instability. RPA and CST are single-stranded DNA-binding protein complexes that play key roles in performing this task and help stabilize stalled forks for continued replication. The interplay between RPA and CST, their functions at telomeres during replication, and their specialized features for helping overcome replication stress at telomeres are the focus of this review.
Collapse
Affiliation(s)
- Conner L. Olson
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Deborah S. Wuttke
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| |
Collapse
|
49
|
Peripolli S, Meneguello L, Perrod C, Singh T, Patel H, Rahman ST, Kiso K, Thorpe P, Calvanese V, Bertoli C, de Bruin RAM. Oncogenic c-Myc induces replication stress by increasing cohesins chromatin occupancy in a CTCF-dependent manner. Nat Commun 2024; 15:1579. [PMID: 38383676 PMCID: PMC10881979 DOI: 10.1038/s41467-024-45955-z] [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: 11/04/2020] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
Oncogene-induced replication stress is a crucial driver of genomic instability and one of the key events contributing to the onset and evolution of cancer. Despite its critical role in cancer, the mechanisms that generate oncogene-induced replication stress remain not fully understood. Here, we report that an oncogenic c-Myc-dependent increase in cohesins on DNA contributes to the induction of replication stress. Accumulation of cohesins on chromatin is not sufficient to cause replication stress, but also requires cohesins to accumulate at specific sites in a CTCF-dependent manner. We propose that the increased accumulation of cohesins at CTCF site interferes with the progression of replication forks, contributing to oncogene-induced replication stress. This is different from, and independent of, previously suggested mechanisms of oncogene-induced replication stress. This, together with the reported protective role of cohesins in preventing replication stress-induced DNA damage, supports a double-edge involvement of cohesins in causing and tolerating oncogene-induced replication stress.
Collapse
Affiliation(s)
- Silvia Peripolli
- Laboratory Molecular Cell Biology, University College London, Gower Street, London, UK
| | - Leticia Meneguello
- Laboratory Molecular Cell Biology, University College London, Gower Street, London, UK
- UCL Cancer Institute, University College London, Gower Street, London, UK
| | - Chiara Perrod
- Laboratory Molecular Cell Biology, University College London, Gower Street, London, UK
| | - Tanya Singh
- Laboratory Molecular Cell Biology, University College London, Gower Street, London, UK
| | | | - Sazia T Rahman
- Laboratory Molecular Cell Biology, University College London, Gower Street, London, UK
| | - Koshiro Kiso
- Laboratory Molecular Cell Biology, University College London, Gower Street, London, UK
| | - Peter Thorpe
- Queen Mary University, Mile End Road, London, UK
| | - Vincenzo Calvanese
- Laboratory Molecular Cell Biology, University College London, Gower Street, London, UK
| | - Cosetta Bertoli
- Laboratory Molecular Cell Biology, University College London, Gower Street, London, UK.
| | - Robertus A M de Bruin
- Laboratory Molecular Cell Biology, University College London, Gower Street, London, UK.
- UCL Cancer Institute, University College London, Gower Street, London, UK.
| |
Collapse
|
50
|
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.
Collapse
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.
| |
Collapse
|