1
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Isik E, Shukla K, Pospisilova M, König C, Andrs M, Rao S, Rosano V, Dobrovolna J, Krejci L, Janscak P. MutSβ-MutLβ-FANCJ axis mediates the restart of DNA replication after fork stalling at cotranscriptional G4/R-loops. SCIENCE ADVANCES 2024; 10:eadk2685. [PMID: 38324687 PMCID: PMC10849593 DOI: 10.1126/sciadv.adk2685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024]
Abstract
Transcription-replication conflicts (TRCs) induce formation of cotranscriptional RNA:DNA hybrids (R-loops) stabilized by G-quadruplexes (G4s) on the displaced DNA strand, which can cause fork stalling. Although it is known that these stalled forks can resume DNA synthesis in a process initiated by MUS81 endonuclease, how TRC-associated G4/R-loops are removed to allow fork passage remains unclear. Here, we identify the mismatch repair protein MutSβ, an MLH1-PMS1 heterodimer termed MutLβ, and the G4-resolving helicase FANCJ as factors that are required for MUS81-initiated restart of DNA replication at TRC sites in human cells. This DNA repair process depends on the G4-binding activity of MutSβ, the helicase activity of FANCJ, and the binding of FANCJ to MLH1. Furthermore, we show that MutSβ, MutLβ, and MLH1-FANCJ interaction mediate FANCJ recruitment to G4s. These data suggest that MutSβ, MutLβ, and FANCJ act in conjunction to eliminate G4/R-loops at TRC sites, allowing replication restart.
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Affiliation(s)
- Esin Isik
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Kaustubh Shukla
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 143 00 Prague, Czech Republic
| | - Michaela Pospisilova
- Department of Biology and National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A7, Brno 62500, Czech Republic
- International Clinical Research Center, St Anne's University Hospital, Pekarska 53, Brno 656 91, Czech Republic
| | - Christiane König
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Andrs
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Satyajeet Rao
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Vinicio Rosano
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jana Dobrovolna
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 143 00 Prague, Czech Republic
| | - Lumir Krejci
- Department of Biology and National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A7, Brno 62500, Czech Republic
- International Clinical Research Center, St Anne's University Hospital, Pekarska 53, Brno 656 91, Czech Republic
| | - Pavel Janscak
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 143 00 Prague, Czech Republic
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2
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Boavida A, Napolitano LM, Santos D, Cortone G, Jegadesan NK, Onesti S, Branzei D, Pisani FM. FANCJ DNA helicase is recruited to the replisome by AND-1 to ensure genome stability. EMBO Rep 2024; 25:876-901. [PMID: 38177925 PMCID: PMC10897178 DOI: 10.1038/s44319-023-00044-y] [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: 10/09/2023] [Revised: 12/05/2023] [Accepted: 12/15/2023] [Indexed: 01/06/2024] Open
Abstract
FANCJ, a DNA helicase linked to Fanconi anemia and frequently mutated in cancers, counteracts replication stress by dismantling unconventional DNA secondary structures (such as G-quadruplexes) that occur at the DNA replication fork in certain sequence contexts. However, how FANCJ is recruited to the replisome is unknown. Here, we report that FANCJ directly binds to AND-1 (the vertebrate ortholog of budding yeast Ctf4), a homo-trimeric protein adaptor that connects the CDC45/MCM2-7/GINS replicative DNA helicase with DNA polymerase α and several other factors at DNA replication forks. The interaction between FANCJ and AND-1 requires the integrity of an evolutionarily conserved Ctf4-interacting protein (CIP) box located between the FANCJ helicase motifs IV and V. Disruption of the CIP box significantly reduces FANCJ association with the replisome, causing enhanced DNA damage, decreased replication fork recovery and fork asymmetry in cells unchallenged or treated with Pyridostatin, a G-quadruplex-binder, or Mitomycin C, a DNA inter-strand cross-linking agent. Cancer-relevant FANCJ CIP box variants display reduced AND-1-binding and enhanced DNA damage, a finding that suggests their potential role in cancer predisposition.
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Affiliation(s)
- Ana Boavida
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples, Italy
- Università degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy
| | | | - Diana Santos
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples, Italy
- Università degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Giuseppe Cortone
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples, Italy
| | | | - Silvia Onesti
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste, Trieste, Italy
| | - Dana Branzei
- IFOM ETS-The AIRC Institute of Molecular Oncology, Milan, Italy
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy
| | - Francesca M Pisani
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples, Italy.
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3
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Horan TS, Ascenção CFR, Mellor C, Wang M, Smolka MB, Cohen PE. The DNA helicase FANCJ (BRIP1) functions in double strand break repair processing, but not crossover formation during prophase I of meiosis in male mice. PLoS Genet 2024; 20:e1011175. [PMID: 38377115 PMCID: PMC10906868 DOI: 10.1371/journal.pgen.1011175] [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: 11/16/2023] [Revised: 03/01/2024] [Accepted: 02/07/2024] [Indexed: 02/22/2024] Open
Abstract
Meiotic recombination between homologous chromosomes is initiated by the formation of hundreds of programmed double-strand breaks (DSBs). Approximately 10% of these DSBs result in crossovers (COs), sites of physical DNA exchange between homologs that are critical to correct chromosome segregation. Virtually all COs are formed by coordinated efforts of the MSH4/MSH5 and MLH1/MLH3 heterodimers, the latter representing the defining marks of CO sites. The regulation of CO number and position is poorly understood, but undoubtedly requires the coordinated action of multiple repair pathways. In a previous report, we found gene-trap disruption of the DNA helicase, FANCJ (BRIP1/BACH1), elicited elevated numbers of MLH1 foci and chiasmata. In somatic cells, FANCJ interacts with numerous DNA repair proteins including MLH1, and we hypothesized that FANCJ functions with MLH1 to regulate the major CO pathway. To further elucidate the meiotic function of FANCJ, we produced three new Fancj mutant mouse lines via CRISPR/Cas9 gene editing: a full-gene deletion, truncation of the N-terminal Helicase domain, and a C-terminal dual-tagged allele. We also generated an antibody against the C-terminus of the mouse FANCJ protein. Surprisingly, none of our Fancj mutants show any change in either MLH1 focus counts during pachynema or total CO number at diakinesis of prophase I. We find evidence that FANCJ and MLH1 do not interact in meiosis; further, FANCJ does not co-localize with MSH4, MLH1, or MLH3 in meiosis. Instead, FANCJ co-localizes with BRCA1 and TOPBP1, forming discrete foci along the chromosome cores beginning in early meiotic prophase I and densely localized to unsynapsed chromosome axes in late zygonema and to the XY chromosomes in early pachynema. Fancj mutants also exhibit a subtle persistence of DSBs in pachynema. Collectively, these data indicate a role for FANCJ in early DSB repair, but they rule out a role for FANCJ in MLH1-mediated CO events.
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Affiliation(s)
- Tegan S. Horan
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, United States of America
- Cornell Reproductive Sciences Center, Cornell University, Ithaca, New York, United States of America
| | - Carolline F. R. Ascenção
- Cornell Reproductive Sciences Center, Cornell University, Ithaca, New York, United States of America
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Christopher Mellor
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States of America
| | - Meng Wang
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States of America
| | - Marcus B. Smolka
- Cornell Reproductive Sciences Center, Cornell University, Ithaca, New York, United States of America
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Paula E. Cohen
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, United States of America
- Cornell Reproductive Sciences Center, Cornell University, Ithaca, New York, United States of America
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4
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Kulikowicz T, Sommers JA, Fuchs KF, Wu Y, Brosh RM. Purification and biochemical characterization of the G4 resolvase and DNA helicase FANCJ. Methods Enzymol 2024; 695:1-27. [PMID: 38521581 DOI: 10.1016/bs.mie.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
G-quadruplex (G4) DNA or RNA poses a unique nucleic acid structure in genomic transactions. Because of the unique topology presented by G4, cells have exquisite mechanisms and pathways to metabolize G4 that arise in guanine-rich regions of the genome such as telomeres, promoter regions, ribosomal DNA, and other chromosomal elements. G4 resolvases are often represented by a class of molecular motors known as helicases that disrupt the Hoogsteen hydrogen bonds in G4 by harnessing the chemical energy of nucleoside triphosphate hydrolysis. Of special interest to researchers in the field, including us, is the human FANCJ DNA helicase that efficiently resolves G4 DNA structures. Notably, FANCJ mutations are linked to Fanconi Anemia and are prominent in breast and ovarian cancer. Since our discovery that FANCJ efficiently resolves G4 DNA structures 15 years ago, we and other labs have characterized mechanistic aspects of FANCJ-catalyzed G4 resolution and its biological importance in genomic integrity and cellular DNA replication. In addition to its G4 resolvase function, FANCJ is also a classic DNA helicase that acts on conventional duplex DNA structures, which are relevant to the enzyme's role in interstrand cross link repair, double-strand break repair via homologous recombination, and response to replication stress. Here, we describe detailed procedures for the purification of recombinant FANCJ protein and characterization of its G4 resolvase and duplex DNA helicase activity.
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Affiliation(s)
- Tomasz Kulikowicz
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, United States
| | - Joshua A Sommers
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, United States
| | - Kathleen F Fuchs
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, United States
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Robert M Brosh
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, United States.
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5
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Horan TS, Ascenção CFR, Mellor CA, Wang M, Smolka MB, Cohen PE. The DNA helicase FANCJ (BRIP1) functions in Double Strand Break repair processing, but not crossover formation during Prophase I of meiosis in male mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.06.561296. [PMID: 37873301 PMCID: PMC10592954 DOI: 10.1101/2023.10.06.561296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
During meiotic prophase I, recombination between homologous parental chromosomes is initiated by the formation of hundreds of programmed double-strand breaks (DSBs), each of which must be repaired with absolute fidelity to ensure genome stability of the germline. One outcome of these DSB events is the formation of Crossovers (COs), the sites of physical DNA exchange between homologs that are critical to ensure the correct segregation of parental chromosomes. However, COs account for only a small (~10%) proportion of all DSB repair events; the remaining 90% are repaired as non-crossovers (NCOs), most by synthesis dependent strand annealing. Virtually all COs are formed by coordinated efforts of the MSH4/MSH5 and MLH1/MLH3 heterodimers. The number and positioning of COs is exquisitely controlled via mechanisms that remain poorly understood, but which undoubtedly require the coordinated action of multiple repair pathways downstream of the initiating DSB. In a previous report we found evidence suggesting that the DNA helicase and Fanconi Anemia repair protein, FANCJ (BRIP1/BACH1), functions to regulate meiotic recombination in mouse. A gene-trap disruption of Fancj showed an elevated number of MLH1 foci and COs. FANCJ is known to interact with numerous DNA repair proteins in somatic cell repair contexts, including MLH1, BLM, BRCA1, and TOPBP1, and we hypothesized that FANCJ regulates CO formation through a direct interaction with MLH1 to suppress the major CO pathway. To further elucidate the function of FANCJ in meiosis, we produced three new Fancj mutant mouse lines via CRISPR/Cas9 gene editing: a full-gene deletion, a mutant line lacking the MLH1 interaction site and the N-terminal region of the Helicase domain, and a C-terminal 6xHIS-HA dual-tagged allele of Fancj. We also generated an antibody against the C-terminus of the mouse FANCJ protein. Surprisingly, while Fanconi-like phenotypes are observed within the somatic cell lineages of the full deletion Fancj line, none of the Fancj mutants show any change in either MLH1 focus counts during pachynema or total CO number at diakinesis of prophase I of meiosis. We find evidence that FANCJ and MLH1 do not interact in meiosis; further, FANCJ does not co-localize with MSH4, MLH1, or MLH3 during late prophase I. Instead, FANCJ forms discrete foci along the chromosome cores beginning in early meiotic prophase I, occasionally co-localizing with MSH4, and then becomes densely localized on unsynapsed chromosome axes in late zygonema and to the XY chromosomes in early pachynema. Strikingly, this localization strongly overlaps with BRCA1 and TOPBP1. Fancj mutants also exhibit a subtle persistence of DSBs in pachynema. Collectively, these data suggest a role for FANCJ in early DSB repair events, and possibly in the formation of NCOs, but they rule out a role for FANCJ in MLH1-mediated CO events. Thus, the role of FANCJ in meiotic cells involves different pathways and different interactors to those described in somatic cell lineages.
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Affiliation(s)
- Tegan S Horan
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853
- Cornell Reproductive Sciences Center, Cornell University, Ithaca, NY 14853
| | - Carolline F R Ascenção
- Cornell Reproductive Sciences Center, Cornell University, Ithaca, NY 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | | | - Meng Wang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853
| | - Marcus B Smolka
- Cornell Reproductive Sciences Center, Cornell University, Ithaca, NY 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Paula E Cohen
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
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6
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Jiang K, Ding Y, Dong C, Shan F, Guo K, Zhang J, Zhang F. BCLAF1, a functional partner of BACH1, participates in DNA damage response. DNA Repair (Amst) 2022; 118:103371. [DOI: 10.1016/j.dnarep.2022.103371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 07/02/2022] [Accepted: 07/08/2022] [Indexed: 11/26/2022]
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7
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Brosh RM, Wu Y. An emerging picture of FANCJ's role in G4 resolution to facilitate DNA replication. NAR Cancer 2021; 3:zcab034. [PMID: 34873585 DOI: 10.1093/narcan/zcab034] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/28/2021] [Accepted: 08/13/2021] [Indexed: 02/06/2023] Open
Abstract
A well-accepted hallmark of cancer is genomic instability, which drives tumorigenesis. Therefore, understanding the molecular and cellular defects that destabilize chromosomal integrity is paramount to cancer diagnosis, treatment and cure. DNA repair and the replication stress response are overarching paradigms for maintenance of genomic stability, but the devil is in the details. ATP-dependent helicases serve to unwind DNA so it is replicated, transcribed, recombined and repaired efficiently through coordination with other nucleic acid binding and metabolizing proteins. Alternatively folded DNA structures deviating from the conventional anti-parallel double helix pose serious challenges to normal genomic transactions. Accumulating evidence suggests that G-quadruplex (G4) DNA is problematic for replication. Although there are multiple human DNA helicases that can resolve G4 in vitro, it is debated which helicases are truly important to resolve such structures in vivo. Recent advances have begun to elucidate the principal helicase actors, particularly in cellular DNA replication. FANCJ, a DNA helicase implicated in cancer and the chromosomal instability disorder Fanconi Anemia, takes center stage in G4 resolution to allow smooth DNA replication. We will discuss FANCJ's role with its protein partner RPA to remove G4 obstacles during DNA synthesis, highlighting very recent advances and implications for cancer therapy.
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Affiliation(s)
- Robert M Brosh
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
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8
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Cong K, Peng M, Kousholt AN, Lee WTC, Lee S, Nayak S, Krais J, VanderVere-Carozza PS, Pawelczak KS, Calvo J, Panzarino NJ, Turchi JJ, Johnson N, Jonkers J, Rothenberg E, Cantor SB. Replication gaps are a key determinant of PARP inhibitor synthetic lethality with BRCA deficiency. Mol Cell 2021; 81:3128-3144.e7. [PMID: 34216544 PMCID: PMC9089372 DOI: 10.1016/j.molcel.2021.06.011] [Citation(s) in RCA: 148] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/19/2021] [Accepted: 06/09/2021] [Indexed: 01/04/2023]
Abstract
Mutations in BRCA1 or BRCA2 (BRCA) is synthetic lethal with poly(ADP-ribose) polymerase inhibitors (PARPi). Lethality is thought to derive from DNA double-stranded breaks (DSBs) necessitating BRCA function in homologous recombination (HR) and/or fork protection (FP). Here, we report instead that toxicity derives from replication gaps. BRCA1- or FANCJ-deficient cells, with common repair defects but distinct PARPi responses, reveal gaps as a distinguishing factor. We further uncouple HR, FP, and fork speed from PARPi response. Instead, gaps characterize BRCA-deficient cells, are diminished upon resistance, restored upon resensitization, and, when exposed, augment PARPi toxicity. Unchallenged BRCA1-deficient cells have elevated poly(ADP-ribose) and chromatin-associated PARP1, but aberrantly low XRCC1 consistent with defects in backup Okazaki fragment processing (OFP). 53BP1 loss resuscitates OFP by restoring XRCC1-LIG3 that suppresses the sensitivity of BRCA1-deficient cells to drugs targeting OFP or generating gaps. We highlight gaps as a determinant of PARPi toxicity changing the paradigm for synthetic lethal interactions.
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Affiliation(s)
- Ke Cong
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Min Peng
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Arne Nedergaard Kousholt
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Wei Ting C Lee
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Silviana Lee
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Sumeet Nayak
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - John Krais
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | | | | | - Jennifer Calvo
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nicholas J Panzarino
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - John J Turchi
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA; NERx Biosciences, 212 W. 10th St., Suite A480, Indianapolis, IN 46202, USA
| | - Neil Johnson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Sharon B Cantor
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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9
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Muhseena N K, Mathukkada S, Das SP, Laha S. The repair gene BACH1 - a potential oncogene. Oncol Rev 2021; 15:519. [PMID: 34322202 PMCID: PMC8273628 DOI: 10.4081/oncol.2021.519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 03/02/2021] [Indexed: 12/12/2022] Open
Abstract
BACH1 encodes for a protein that belongs to RecQ DEAH helicase family and interacts with the BRCT repeats of BRCA1. The N-terminus of BACH1 functions in DNA metabolism as DNA-dependent ATPase and helicase. The C-terminus consists of BRCT domain, which interacts with BRCA1 and this interaction is one of the major regulator of BACH1 function. BACH1 plays important roles both in phosphorylated as well as dephosphorylated state and functions in coordination with multiple signaling molecules. The active helicase property of BACH1 is maintained by its dephosphorylated state. Imbalance between these two states enhances the development and progression of the diseased condition. Currently BACH1 is known as a tumor suppressor gene based on the presence of its clinically relevant mutations in different cancers. Through this review we have justified it to be named as an oncogene. In this review, we have explained the mechanism of how BACH1 in collaboration with BRCA1 or independently regulates various pathways like cell cycle progression, DNA replication during both normal and stressed situation, recombination and repair of damaged DNA, chromatin remodeling and epigenetic modifications. Mutation and overexpression of BACH1 are significantly found in different cancer types. This review enlists the molecular players which interact with BACH1 to regulate DNA metabolic functions, thereby revealing its potential for cancer therapeutics. We have identified the most mutated functional domain of BACH1, the hot spot for tumorigenesis, justifying it as a target molecule in different cancer types for therapeutics. BACH1 has high potentials of transforming a normal cell into a tumor cell if compromised under certain circumstances. Thus, through this review, we justify BACH1 as an oncogene along with the existing role of being a tumor suppressant.
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Affiliation(s)
- Katheeja Muhseena N
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Sooraj Mathukkada
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Shankar Prasad Das
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Suparna Laha
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
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10
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Harrell K, Day M, Smolikove S. Recruitment of MRE-11 to complex DNA damage is modulated by meiosis-specific chromosome organization. Mutat Res 2021; 822:111743. [PMID: 33975127 DOI: 10.1016/j.mrfmmm.2021.111743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/11/2021] [Accepted: 04/15/2021] [Indexed: 12/15/2022]
Abstract
DNA double-strand breaks (DSBs) are one of the most dangerous assaults on the genome, and yet their natural and programmed production are inherent to life. When DSBs arise close together they are particularly deleterious, and their repair may require an altered form of the DNA damage response. Our understanding of how clustered DSBs are repaired in the germline is unknown. Using laser microirradiation, we examine early events in the repair of clustered DSBs in germ cells within Caenorhabditis elegans. We use precise temporal resolution to show how the recruitment of MRE-11 to complex damage is regulated, and that clustered DNA damage can recruit proteins from various repair pathways. Abrogation of non-homologous end joining or COM-1 attenuates the recruitment of MRE-11 through distinct mechanisms. The synaptonemal complex plays both positive and negative regulatory roles in these mutant contexts. These findings indicate that MRE-11 is regulated by modifying its accessibility to chromosomes.
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Affiliation(s)
- Kailey Harrell
- Department of Biology, University of Iowa, Iowa City, IA, 52241, USA
| | - Madison Day
- Department of Biology, University of Iowa, Iowa City, IA, 52241, USA
| | - Sarit Smolikove
- Department of Biology, University of Iowa, Iowa City, IA, 52241, USA.
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11
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Calvo JA, Fritchman B, Hernandez D, Persky NS, Johannessen CM, Piccioni F, Kelch BA, Cantor SB. Comprehensive Mutational Analysis of the BRCA1-Associated DNA Helicase and Tumor-Suppressor FANCJ/BACH1/BRIP1. Mol Cancer Res 2021; 19:1015-1025. [PMID: 33619228 DOI: 10.1158/1541-7786.mcr-20-0828] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/27/2021] [Accepted: 02/18/2021] [Indexed: 12/15/2022]
Abstract
FANCJ (BRIP1/BACH1) is a hereditary breast and ovarian cancer (HBOC) gene encoding a DNA helicase. Similar to HBOC genes, BRCA1 and BRCA2, FANCJ is critical for processing DNA inter-strand crosslinks (ICL) induced by chemotherapeutics, such as cisplatin. Consequently, cells deficient in FANCJ or its catalytic activity are sensitive to ICL-inducing agents. Unfortunately, the majority of FANCJ clinical mutations remain uncharacterized, limiting therapeutic opportunities to effectively use cisplatin to treat tumors with mutated FANCJ. Here, we sought to perform a comprehensive screen to identify FANCJ loss-of-function (LOF) mutations. We developed a FANCJ lentivirus mutation library representing approximately 450 patient-derived FANCJ nonsense and missense mutations to introduce FANCJ mutants into FANCJ knockout (K/O) HeLa cells. We performed a high-throughput screen to identify FANCJ LOF mutants that, as compared with wild-type FANCJ, fail to robustly restore resistance to ICL-inducing agents, cisplatin or mitomycin C (MMC). On the basis of the failure to confer resistance to either cisplatin or MMC, we identified 26 missense and 25 nonsense LOF mutations. Nonsense mutations elucidated a relationship between location of truncation and ICL sensitivity, as the majority of nonsense mutations before amino acid 860 confer ICL sensitivity. Further validation of a subset of LOF mutations confirmed the ability of the screen to identify FANCJ mutations unable to confer ICL resistance. Finally, mapping the location of LOF mutations to a new homology model provides additional functional information. IMPLICATIONS: We identify 51 FANCJ LOF mutations, providing important classification of FANCJ mutations that will afford additional therapeutic strategies for affected patients.
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Affiliation(s)
- Jennifer A Calvo
- Department of Molecular Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Briana Fritchman
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Nicole S Persky
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | - Brian A Kelch
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Sharon B Cantor
- Department of Molecular Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts.
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12
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Lejault P, Mitteaux J, Sperti FR, Monchaud D. How to untie G-quadruplex knots and why? Cell Chem Biol 2021; 28:436-455. [PMID: 33596431 DOI: 10.1016/j.chembiol.2021.01.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/08/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022]
Abstract
For over two decades, the prime objective of the chemical biology community studying G-quadruplexes (G4s) has been to use chemicals to interact with and stabilize G4s in cells to obtain mechanistic interpretations. This strategy has been undoubtedly successful, as demonstrated by recent advances. However, these insights have also led to a fundamental rethinking of G4-targeting strategies: due to the prevalence of G4s in the human genome, transcriptome, and ncRNAome (collectively referred to as the G4ome), and their involvement in human diseases, should we continue developing G4-stabilizing ligands or should we invest in designing molecular tools to unfold G4s? Here, we first focus on how, when, and where G4s fold in cells; then, we describe the enzymatic systems that have evolved to counteract G4 folding and how they have been used as tools to manipulate G4s in cells; finally, we present strategies currently being implemented to devise new molecular G4 unwinding agents.
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Affiliation(s)
- Pauline Lejault
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Jérémie Mitteaux
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France.
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13
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Awate S, Sommers JA, Datta A, Nayak S, Bellani MA, Yang O, Dunn CA, Nicolae CM, Moldovan GL, Seidman MM, Cantor SB, Brosh RM. FANCJ compensates for RAP80 deficiency and suppresses genomic instability induced by interstrand cross-links. Nucleic Acids Res 2020; 48:9161-9180. [PMID: 32797166 DOI: 10.1093/nar/gkaa660] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 07/24/2020] [Accepted: 07/28/2020] [Indexed: 12/16/2022] Open
Abstract
FANCJ, a DNA helicase and interacting partner of the tumor suppressor BRCA1, is crucial for the repair of DNA interstrand crosslinks (ICL), a highly toxic lesion that leads to chromosomal instability and perturbs normal transcription. In diploid cells, FANCJ is believed to operate in homologous recombination (HR) repair of DNA double-strand breaks (DSB); however, its precise role and molecular mechanism is poorly understood. Moreover, compensatory mechanisms of ICL resistance when FANCJ is deficient have not been explored. In this work, we conducted a siRNA screen to identify genes of the DNA damage response/DNA repair regime that when acutely depleted sensitize FANCJ CRISPR knockout cells to a low concentration of the DNA cross-linking agent mitomycin C (MMC). One of the top hits from the screen was RAP80, a protein that recruits repair machinery to broken DNA ends and regulates DNA end-processing. Concomitant loss of FANCJ and RAP80 not only accentuates DNA damage levels in human cells but also adversely affects the cell cycle checkpoint, resulting in profound chromosomal instability. Genetic complementation experiments demonstrated that both FANCJ's catalytic activity and interaction with BRCA1 are important for ICL resistance when RAP80 is deficient. The elevated RPA and RAD51 foci in cells co-deficient of FANCJ and RAP80 exposed to MMC are attributed to single-stranded DNA created by Mre11 and CtIP nucleases. Altogether, our cell-based findings together with biochemical studies suggest a critical function of FANCJ to suppress incompletely processed and toxic joint DNA molecules during repair of ICL-induced DNA damage.
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Affiliation(s)
- Sanket Awate
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Joshua A Sommers
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Arindam Datta
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Sumeet Nayak
- Department of Cancer Biology, University of Massachusetts Medical School - UMASS Memorial Cancer Center, Worcester, MA, USA
| | - Marina A Bellani
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Olivia Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Christopher A Dunn
- Flow Cytometry Unit, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, USA
| | - Michael M Seidman
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Sharon B Cantor
- Department of Cancer Biology, University of Massachusetts Medical School - UMASS Memorial Cancer Center, Worcester, MA, USA
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, Baltimore, MD, USA
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14
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Dhar S, Datta A, Brosh RM. DNA helicases and their roles in cancer. DNA Repair (Amst) 2020; 96:102994. [PMID: 33137625 DOI: 10.1016/j.dnarep.2020.102994] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 12/15/2022]
Abstract
DNA helicases, known for their fundamentally important roles in genomic stability, are high profile players in cancer. Not only are there monogenic helicase disorders with a strong disposition to cancer, it is well appreciated that helicase variants are associated with specific cancers (e.g., breast cancer). Flipping the coin, DNA helicases are frequently overexpressed in cancerous tissues and reduction in helicase gene expression results in reduced proliferation and growth capacity, as well as DNA damage induction and apoptosis of cancer cells. The seminal roles of helicases in the DNA damage and replication stress responses, as well as DNA repair pathways, validate their vital importance in cancer biology and suggest their potential values as targets in anti-cancer therapy. In recent years, many laboratories have characterized the specialized roles of helicase to resolve transcription-replication conflicts, maintain telomeres, mediate cell cycle checkpoints, remodel stalled replication forks, and regulate transcription. In vivo models, particularly mice, have been used to interrogate helicase function and serve as a bridge for preclinical studies that may lead to novel therapeutic approaches. In this review, we will summarize our current knowledge of DNA helicases and their roles in cancer, emphasizing the latest developments.
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Affiliation(s)
- Srijita Dhar
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Arindam Datta
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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15
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Nath S, Nagaraju G. FANCJ helicase promotes DNA end resection by facilitating CtIP recruitment to DNA double-strand breaks. PLoS Genet 2020; 16:e1008701. [PMID: 32251466 PMCID: PMC7162537 DOI: 10.1371/journal.pgen.1008701] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 04/16/2020] [Accepted: 02/28/2020] [Indexed: 12/13/2022] Open
Abstract
FANCJ helicase mutations are known to cause hereditary breast and ovarian cancers as well as bone marrow failure syndrome Fanconi anemia. FANCJ plays an important role in the repair of DNA inter-strand crosslinks and DNA double-strand breaks (DSBs) by homologous recombination (HR). Nonetheless, the molecular mechanism by which FANCJ controls HR mediated DSB repair is obscure. Here, we show that FANCJ promotes DNA end resection by recruiting CtIP to the sites of DSBs. This recruitment of CtIP is dependent on FANCJ K1249 acetylation. Notably, FANCJ acetylation is dependent on FANCJ S990 phosphorylation by CDK. The CDK mediated phosphorylation of FANCJ independently facilitates its interaction with BRCA1 at damaged DNA sites and promotes DNA end resection by CtIP recruitment. Strikingly, mutational studies reveal that ATP binding competent but hydrolysis deficient FANCJ partially supports end resection, indicating that in addition to the scaffolding role of FANCJ in CtIP recruitment, its helicase activity is important for promoting end resection. Together, these data unravel a novel function of FANCJ helicase in DNA end resection and provide mechanistic insights into its role in repairing DSBs by HR and in genome maintenance. Homologous recombination has been considered as an error-free pathway in repairing DSBs and maintaining genome stability. Cyclin-dependent kinases (CDKs) and various factors including MRE11, CtIP, EXO1, and BLM helicase participate in DNA end resection to promote HR mediated DSB repair. Despite the identification of FANCJ helicase role in HR and tumor suppression, the molecular mechanism by which FANCJ helicase participates in HR is obscure. Here, we show that FANCJ helicase controls DNA end resection by recruiting CtIP to the sites of DSBs. The loading of CtIP is dependent on FANCJ acetylation which is mediated by CDK dependent phosphorylation of FANCJ. Moreover, in addition to FANCJ mediated CtIP recruitment, its helicase activity is also essential for DNA end resection. Our data identify FANCJ as a novel player in the DNA end resection and provide insights into its role in HR mediated DSB repair.
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Affiliation(s)
- Sarmi Nath
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Ganesh Nagaraju
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
- * E-mail:
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16
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Warren NJH, Eastman A. Comparison of the different mechanisms of cytotoxicity induced by checkpoint kinase I inhibitors when used as single agents or in combination with DNA damage. Oncogene 2020; 39:1389-1401. [PMID: 31659257 PMCID: PMC7023985 DOI: 10.1038/s41388-019-1079-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 12/31/2022]
Abstract
Inhibition of the DNA damage response is an emerging strategy to treat cancer. Understanding how DNA damage response inhibitors cause cytotoxicity in cancer cells is crucial to their further clinical development. This review focuses on three different mechanisms of cell killing by checkpoint kinase I inhibitors (CHK1i). DNA damage induced by chemotherapy drugs, such as topoisomerase I inhibitors, results in S and G2 phase arrest. Addition of CHK1i promotes cell cycle progression before repair is completed resulting in mitotic catastrophe. Ribonucleotide reductase inhibitors such as gemcitabine also arrest cells in S phase by preventing dNTP synthesis. Addition of CHK1i re-activates the DNA helicase to unwind DNA, but in the absence of dNTPs, this leads to excessive single-strand DNA that exceeds the protective capacity of the single-strand-binding protein RPA. Unprotected DNA is subjected to nuclease cleavage, resulting in replication catastrophe. CHK1i alone also kills a subset of cell lines through MRE11 and MUS81-mediated DNA cleavage in S phase cells. The choice of mechanism depends on the activation state of CDK2. Low level activation of CDK2 mediates helicase activation, cell cycle progression, and both replication and mitotic catastrophe. In contrast, high CDK2 activity is required for sensitivity to CHK1i as monotherapy. This high CDK2 activity threshold usually occurs late in the cell cycle to prepare for mitosis, but in CHK1i-sensitive cells, high activity can be attained in early S phase, resulting in DNA cleavage and cell death. This sensitivity to CHK1i has previously been associated with endogenous replication stress, but the dependence on high CDK2 activity, as well as MRE11, contradicts this hypothesis. The major unresolved question is why some cell lines fail to restrain their high CDK2 activity and hence succumb to CHK1i in S phase. Resolving this question will facilitate stratification of patients for treatment with CHK1i as monotherapy.
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Affiliation(s)
- Nicholas J H Warren
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756, USA
| | - Alan Eastman
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756, USA.
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756, USA.
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17
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Chang EYC, Tsai S, Aristizabal MJ, Wells JP, Coulombe Y, Busatto FF, Chan YA, Kumar A, Dan Zhu Y, Wang AYH, Fournier LA, Hieter P, Kobor MS, Masson JY, Stirling PC. MRE11-RAD50-NBS1 promotes Fanconi Anemia R-loop suppression at transcription-replication conflicts. Nat Commun 2019; 10:4265. [PMID: 31537797 PMCID: PMC6753070 DOI: 10.1038/s41467-019-12271-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 08/30/2019] [Indexed: 12/25/2022] Open
Abstract
Ectopic R-loop accumulation causes DNA replication stress and genome instability. To avoid these outcomes, cells possess a range of anti-R-loop mechanisms, including RNaseH that degrades the RNA moiety in R-loops. To comprehensively identify anti-R-loop mechanisms, we performed a genome-wide trigenic interaction screen in yeast lacking RNH1 and RNH201. We identified >100 genes critical for fitness in the absence of RNaseH, which were enriched for DNA replication fork maintenance factors including the MRE11-RAD50-NBS1 (MRN) complex. While MRN has been shown to promote R-loops at DNA double-strand breaks, we show that it suppresses R-loops and associated DNA damage at transcription-replication conflicts. This occurs through a non-nucleolytic function of MRE11 that is important for R-loop suppression by the Fanconi Anemia pathway. This work establishes a novel role for MRE11-RAD50-NBS1 in directing tolerance mechanisms at transcription-replication conflicts.
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Affiliation(s)
| | - Shuhe Tsai
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
| | - Maria J Aristizabal
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Vancouver, V5Z 4H4, Canada
| | - James P Wells
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
| | - Yan Coulombe
- Centre Hospitalier Universitaire de Québec-Universite Laval, Oncology Axis, Quebec City, G1R 2J6, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, G1V 0A6, Canada
| | - Franciele F Busatto
- Centre Hospitalier Universitaire de Québec-Universite Laval, Oncology Axis, Quebec City, G1R 2J6, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, G1V 0A6, Canada
| | - Yujia A Chan
- The Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA
| | - Arun Kumar
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
| | - Yi Dan Zhu
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
| | | | | | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Vancouver, V5Z 4H4, Canada
| | - Jean-Yves Masson
- Centre Hospitalier Universitaire de Québec-Universite Laval, Oncology Axis, Quebec City, G1R 2J6, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, G1V 0A6, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, Canada.
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18
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Nieminuszczy J, Broderick R, Bellani MA, Smethurst E, Schwab RA, Cherdyntseva V, Evmorfopoulou T, Lin YL, Minczuk M, Pasero P, Gagos S, Seidman MM, Niedzwiedz W. EXD2 Protects Stressed Replication Forks and Is Required for Cell Viability in the Absence of BRCA1/2. Mol Cell 2019; 75:605-619.e6. [PMID: 31255466 PMCID: PMC6695479 DOI: 10.1016/j.molcel.2019.05.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 04/15/2019] [Accepted: 05/17/2019] [Indexed: 12/15/2022]
Abstract
Accurate DNA replication is essential to preserve genomic integrity and prevent chromosomal instability-associated diseases including cancer. Key to this process is the cells' ability to stabilize and restart stalled replication forks. Here, we show that the EXD2 nuclease is essential to this process. EXD2 recruitment to stressed forks suppresses their degradation by restraining excessive fork regression. Accordingly, EXD2 deficiency leads to fork collapse, hypersensitivity to replication inhibitors, and genomic instability. Impeding fork regression by inactivation of SMARCAL1 or removal of RECQ1's inhibition in EXD2-/- cells restores efficient fork restart and genome stability. Moreover, purified EXD2 efficiently processes substrates mimicking regressed forks. Thus, this work identifies a mechanism underpinned by EXD2's nuclease activity, by which cells balance fork regression with fork restoration to maintain genome stability. Interestingly, from a clinical perspective, we discover that EXD2's depletion is synthetic lethal with mutations in BRCA1/2, implying a non-redundant role in replication fork protection.
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Affiliation(s)
| | | | - Marina A Bellani
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD, USA
| | | | | | - Veronica Cherdyntseva
- Laboratory of Genetics, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Theodora Evmorfopoulou
- Laboratory of Genetics, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Yea-Lih Lin
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Sarantis Gagos
- Laboratory of Genetics, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Michael M Seidman
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD, USA
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19
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Bharti SK, Sommers JA, Awate S, Bellani MA, Khan I, Bradley L, King GA, Seol Y, Vidhyasagar V, Wu Y, Abe T, Kobayashi K, Shin-Ya K, Kitao H, Wold MS, Branzei D, Neuman KC, Brosh RM. A minimal threshold of FANCJ helicase activity is required for its response to replication stress or double-strand break repair. Nucleic Acids Res 2019; 46:6238-6256. [PMID: 29788478 PMCID: PMC6159516 DOI: 10.1093/nar/gky403] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 05/01/2018] [Indexed: 01/24/2023] Open
Abstract
Fanconi Anemia (FA) is characterized by bone marrow failure, congenital abnormalities, and cancer. Of over 20 FA-linked genes, FANCJ uniquely encodes a DNA helicase and mutations are also associated with breast and ovarian cancer. fancj−/− cells are sensitive to DNA interstrand cross-linking (ICL) and replication fork stalling drugs. We delineated the molecular defects of two FA patient-derived FANCJ helicase domain mutations. FANCJ-R707C was compromised in dimerization and helicase processivity, whereas DNA unwinding by FANCJ-H396D was barely detectable. DNA binding and ATP hydrolysis was defective for both FANCJ-R707C and FANCJ-H396D, the latter showing greater reduction. Expression of FANCJ-R707C or FANCJ-H396D in fancj−/− cells failed to rescue cisplatin or mitomycin sensitivity. Live-cell imaging demonstrated a significantly compromised recruitment of FANCJ-R707C to laser-induced DNA damage. However, FANCJ-R707C expressed in fancj-/- cells conferred resistance to the DNA polymerase inhibitor aphidicolin, G-quadruplex ligand telomestatin, or DNA strand-breaker bleomycin, whereas FANCJ-H396D failed. Thus, a minimal threshold of FANCJ catalytic activity is required to overcome replication stress induced by aphidicolin or telomestatin, or to repair bleomycin-induced DNA breakage. These findings have implications for therapeutic strategies relying on DNA cross-link sensitivity or heightened replication stress characteristic of cancer cells.
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Affiliation(s)
- Sanjay Kumar Bharti
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Joshua A Sommers
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Sanket Awate
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Marina A Bellani
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Irfan Khan
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Lynda Bradley
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Graeme A King
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Venkatasubramanian Vidhyasagar
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Yuliang Wu
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Takuye Abe
- IFOM, the FIRC Institute for Molecular Oncology Foundation, Milan, Italy
| | - Koji Kobayashi
- IFOM, the FIRC Institute for Molecular Oncology Foundation, Milan, Italy
| | - Kazuo Shin-Ya
- Department of Life Science and Biotechnology Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST) 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Hiroyuki Kitao
- Department of Molecular Cancer Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Marc S Wold
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Dana Branzei
- IFOM, the FIRC Institute for Molecular Oncology Foundation, Milan, Italy
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, 251 Bayview Blvd, Baltimore, MD 21224, USA
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20
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Awate S, Dhar S, Sommers JA, Brosh RM. Cellular Assays to Study the Functional Importance of Human DNA Repair Helicases. Methods Mol Biol 2019; 1999:185-207. [PMID: 31127577 PMCID: PMC9123881 DOI: 10.1007/978-1-4939-9500-4_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
DNA helicases represent a specialized class of enzymes that play crucial roles in the DNA damage response. Using the energy of nucleoside triphosphate binding and hydrolysis, helicases behave as molecular motors capable of efficiently disrupting the many noncovalent hydrogen bonds that stabilize DNA molecules with secondary structure. In addition to their importance in DNA damage sensing and signaling, DNA helicases facilitate specific steps in DNA repair mechanisms that require polynucleotide tract unwinding or resolution. Because they play fundamental roles in the DNA damage response and DNA repair, defects in helicases disrupt cellular homeostasis. Thus, helicase deficiency or inhibition may result in reduced cell proliferation and survival, apoptosis, DNA damage induction, defective localization of repair proteins to sites of genomic DNA damage, chromosomal instability, and defective DNA repair pathways such as homologous recombination of double-strand breaks. In this chapter, we will describe step-by-step protocols to assay the functional importance of human DNA repair helicases in genome stability and cellular homeostasis.
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Affiliation(s)
- Sanket Awate
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, Baltimore, MD, USA
| | - Srijita Dhar
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, Baltimore, MD, USA
| | - Joshua A Sommers
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, Baltimore, MD, USA
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, Baltimore, MD, USA.
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21
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Abstract
Timely recruitment of DNA damage response proteins to sites of genomic structural lesions is very important for signaling mechanisms to activate appropriate cell cycle checkpoints but also repair the altered DNA sequence to suppress mutagenesis. The eukaryotic cell is characterized by a complex cadre of players and pathways to ensure genomic stability in the face of replication stress or outright genomic insult by endogenous metabolites or environmental agents. Among the key performers are molecular motor DNA unwinding enzymes known as helicases that sense genomic perturbations and separate structured DNA strands so that replacement of a damaged base or sugar-phosphate backbone lesion can occur efficiently. Mutations in the BLM gene encoding the DNA helicase BLM leads to a rare chromosomal instability disorder known as Bloom's syndrome. In a recent paper by the Sengupta lab, BLM's role in the correction of double-strand breaks (DSB), a particularly dangerous form of DNA damage, was investigated. Adding to the complexity, BLM appears to be a key ringmaster of DSB repair as it acts both positively and negatively to regulate correction pathways of high or low fidelity. The FANCJ DNA helicase, mutated in another chromosomal instability disorder known as Fanconi Anemia, is an important player that likely coordinates with BLM in the balancing act. Further studies to dissect the roles of DNA helicases like FANCJ and BLM in DSB repair are warranted.
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Affiliation(s)
- Srijita Dhar
- a Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health , NIH Biomedical Research Center , Baltimore , MD , USA
| | - Robert M Brosh
- a Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health , NIH Biomedical Research Center , Baltimore , MD , USA
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22
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Peng M, Cong K, Panzarino NJ, Nayak S, Calvo J, Deng B, Zhu LJ, Morocz M, Hegedus L, Haracska L, Cantor SB. Opposing Roles of FANCJ and HLTF Protect Forks and Restrain Replication during Stress. Cell Rep 2018; 24:3251-3261. [PMID: 30232006 PMCID: PMC6218949 DOI: 10.1016/j.celrep.2018.08.065] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 06/23/2018] [Accepted: 08/22/2018] [Indexed: 02/07/2023] Open
Abstract
The DNA helicase FANCJ is mutated in hereditary breast and ovarian cancer and Fanconi anemia (FA). Nevertheless, how loss of FANCJ translates to disease pathogenesis remains unclear. We addressed this question by analyzing proteins associated with replication forks in cells with or without FANCJ. We demonstrate that FANCJ-knockout (FANCJ-KO) cells have alterations in the replisome that are consistent with enhanced replication stress, including an aberrant accumulation of the fork remodeling factor helicase-like transcription factor (HLTF). Correspondingly, HLTF contributes to fork degradation in FANCJ-KO cells. Unexpectedly, the unrestrained DNA synthesis that characterizes HLTF-deficient cells is FANCJ dependent and correlates with S1 nuclease sensitivity and fork degradation. These results suggest that FANCJ and HLTF promote replication fork integrity, in part by counteracting each other to keep fork remodeling and elongation in check. Indicating one protein compensates for loss of the other, loss of both HLTF and FANCJ causes a more severe replication stress response.
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Affiliation(s)
- Min Peng
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ke Cong
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nicholas J Panzarino
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Sumeet Nayak
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jennifer Calvo
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Bin Deng
- Department of Biology/VGN Proteomics Facility, University of Vermont, Burlington, VT 05405, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Monika Morocz
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged 6726, Temesvari krt. 62, Hungary
| | - Lili Hegedus
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged 6726, Temesvari krt. 62, Hungary
| | - Lajos Haracska
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged 6726, Temesvari krt. 62, Hungary
| | - Sharon B Cantor
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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23
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Nath S, Somyajit K, Mishra A, Scully R, Nagaraju G. FANCJ helicase controls the balance between short- and long-tract gene conversions between sister chromatids. Nucleic Acids Res 2017; 45:8886-8900. [PMID: 28911102 PMCID: PMC5587752 DOI: 10.1093/nar/gkx586] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/28/2017] [Indexed: 01/01/2023] Open
Abstract
The FANCJ DNA helicase is linked to hereditary breast and ovarian cancers as well as bone marrow failure disorder Fanconi anemia (FA). Although FANCJ has been implicated in the repair of DNA double-strand breaks (DSBs) by homologous recombination (HR), the molecular mechanism underlying the tumor suppressor functions of FANCJ remains obscure. Here, we demonstrate that FANCJ deficient human and hamster cells exhibit reduction in the overall gene conversions in response to a site-specific chromosomal DSB induced by I-SceI endonuclease. Strikingly, the gene conversion events were biased in favour of long-tract gene conversions in FANCJ depleted cells. The fine regulation of short- (STGC) and long-tract gene conversions (LTGC) by FANCJ was dependent on its interaction with BRCA1 tumor suppressor. Notably, helicase activity of FANCJ was essential for controlling the overall HR and in terminating the extended repair synthesis during sister chromatid recombination (SCR). Moreover, cells expressing FANCJ pathological mutants exhibited defective SCR with an increased frequency of LTGC. These data unravel the novel function of FANCJ helicase in regulating SCR and SCR associated gene amplification/duplications and imply that these functions of FANCJ are crucial for the genome maintenance and tumor suppression.
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Affiliation(s)
- Sarmi Nath
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Kumar Somyajit
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Anup Mishra
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Ralph Scully
- Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Avenue, Boston, MA, USA
| | - Ganesh Nagaraju
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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24
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Dutta A, Eckelmann B, Adhikari S, Ahmed KM, Sengupta S, Pandey A, Hegde PM, Tsai MS, Tainer JA, Weinfeld M, Hegde ML, Mitra S. Microhomology-mediated end joining is activated in irradiated human cells due to phosphorylation-dependent formation of the XRCC1 repair complex. Nucleic Acids Res 2017; 45:2585-2599. [PMID: 27994036 PMCID: PMC5389627 DOI: 10.1093/nar/gkw1262] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 12/15/2016] [Indexed: 02/06/2023] Open
Abstract
Microhomology-mediated end joining (MMEJ), an error-prone pathway for DNA double-strand break (DSB) repair, is implicated in genomic rearrangement and oncogenic transformation; however, its contribution to repair of radiation-induced DSBs has not been characterized. We used recircularization of a linearized plasmid with 3΄-P-blocked termini, mimicking those at X-ray-induced strand breaks, to recapitulate DSB repair via MMEJ or nonhomologous end-joining (NHEJ). Sequence analysis of the circularized plasmids allowed measurement of relative activity of MMEJ versus NHEJ. While we predictably observed NHEJ to be the predominant pathway for DSB repair in our assay, MMEJ was significantly enhanced in preirradiated cells, independent of their radiation-induced arrest in the G2/M phase. MMEJ activation was dependent on XRCC1 phosphorylation by casein kinase 2 (CK2), enhancing XRCC1's interaction with the end resection enzymes MRE11 and CtIP. Both endonuclease and exonuclease activities of MRE11 were required for MMEJ, as has been observed for homology-directed DSB repair (HDR). Furthermore, the XRCC1 co-immunoprecipitate complex (IP) displayed MMEJ activity in vitro, which was significantly elevated after irradiation. Our studies thus suggest that radiation-mediated enhancement of MMEJ in cells surviving radiation therapy may contribute to their radioresistance and could be therapeutically targeted.
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Affiliation(s)
- Arijit Dutta
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Bradley Eckelmann
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA.,Texas A&M Health Science Center, College of Medicine, Bryan, TX 77807, USA
| | | | - Kazi Mokim Ahmed
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Shiladitya Sengupta
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA.,Weill Cornell Medical College, New York, NY 10065, USA
| | - Arvind Pandey
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Pavana M Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Miaw-Sheue Tsai
- Department of Cell and Molecular Biology, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
| | - John A Tainer
- Department of Cell and Molecular Biology, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael Weinfeld
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada
| | - Muralidhar L Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA.,Weill Cornell Medical College, New York, NY 10065, USA.,Houston Methodist Neurological Institute, Houston, TX 77030, USA
| | - Sankar Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA.,Texas A&M Health Science Center, College of Medicine, Bryan, TX 77807, USA.,Weill Cornell Medical College, New York, NY 10065, USA
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25
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Gadgil R, Barthelemy J, Lewis T, Leffak M. Replication stalling and DNA microsatellite instability. Biophys Chem 2016; 225:38-48. [PMID: 27914716 DOI: 10.1016/j.bpc.2016.11.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/05/2016] [Accepted: 11/05/2016] [Indexed: 01/08/2023]
Abstract
Microsatellites are short, tandemly repeated DNA motifs of 1-6 nucleotides, also termed simple sequence repeats (SRSs) or short tandem repeats (STRs). Collectively, these repeats comprise approximately 3% of the human genome Subramanian et al. (2003), Lander and Lander (2001) [1,2], and represent a large reservoir of loci highly prone to mutations Sun et al. (2012), Ellegren (2004) [3,4] that contribute to human evolution and disease. Microsatellites are known to stall and reverse replication forks in model systems Pelletier et al. (2003), Samadashwily et al. (1997), Kerrest et al. (2009) [5-7], and are hotspots of chromosomal double strand breaks (DSBs). We briefly review the relationship of these repeated sequences to replication stalling and genome instability, and present recent data on the impact of replication stress on DNA fragility at microsatellites in vivo.
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Affiliation(s)
- R Gadgil
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - J Barthelemy
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - T Lewis
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - M Leffak
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA.
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26
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Wu W, Togashi Y, Johmura Y, Miyoshi Y, Nobuoka S, Nakanishi M, Ohta T. HP1 regulates the localization of FANCJ at sites of DNA double-strand breaks. Cancer Sci 2016; 107:1406-1415. [PMID: 27399284 PMCID: PMC5084677 DOI: 10.1111/cas.13008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 07/03/2016] [Accepted: 07/06/2016] [Indexed: 12/19/2022] Open
Abstract
The breast and ovarian cancer predisposition protein BRCA1 forms three mutually exclusive complexes with Fanconi anemia group J protein (FANCJ, also called BACH1 or BRIP1), CtIP, and Abraxas/RAP80 through its BRCA1 C terminus (BRCT) domains, while its RING domain binds to BRCA1‐associated RING domain 1 (BARD1). We recently found that the interaction between heterochromatin protein 1 (HP1) and BARD1 is required for the accumulation of BRCA1 and CtIP at sites of DNA double‐strand breaks. Here, we investigated the importance of HP1 and BARD1–HP1 interaction in the localization of FANCJ together with the other BRCA1–BRCT binding proteins to clarify the separate role of the HP1‐mediated pathway from the RNF8/RNF168‐induced ubiquitin‐mediated pathway for BRCA1 function. FANCJ interacts with HP1γ in a BARD1‐dependent manner, and this interaction was enhanced by ionizing radiation or irinotecan hydrochloride treatment. Simultaneous depletion of all three HP1 isoforms with shRNAs disrupts the accumulation of FANCJ and CtIP, but not RAP80, at double‐strand break sites. Replacement of endogenous BARD1 with a mutant BARD1 that is incapable of binding to HP1 also disrupts the accumulation of FANCJ and CtIP, but not RAP80. In contrast, RNF168 depletion disrupts the accumulation of only RAP80, but not FANCJ or CtIP. Consequently, the accumulation of conjugated ubiquitin was only inhibited by RNF168 depletion, whereas the accumulation of RAD51 and sister chromatid exchange were only inhibited by HP1 depletion or disruption of the BARD1–HP1 interaction. Taken together, the results suggest that the BRCA1–FANCJ and BRCA1–CtIP complexes are not downstream of the RNF8/RNF168/ubiquitin pathway, but are instead regulated by the HP1 pathway that precedes homologous recombination DNA repair.
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Affiliation(s)
- Wenwen Wu
- Department of Translational Oncology, St. Marianna University Graduate School of Medicine, Kawasaki, Japan
| | - Yukiko Togashi
- Department of Translational Oncology, St. Marianna University Graduate School of Medicine, Kawasaki, Japan
| | - Yoshikazu Johmura
- Department of Cell Biology, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Yasuo Miyoshi
- Division of Breast and Endocrine Surgery, Department of Surgery, Hyogo College of Medicine, Hyogo, Japan
| | - Sachihiko Nobuoka
- Laboratory Medicine, St. Marianna University Graduate School of Medicine, Kawasaki, Japan
| | - Makoto Nakanishi
- Department of Cell Biology, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan.,Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tomohiko Ohta
- Department of Translational Oncology, St. Marianna University Graduate School of Medicine, Kawasaki, Japan.
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27
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Oussalah A, Avogbe PH, Guyot E, Chery C, Guéant-Rodriguez RM, Ganne-Carrié N, Cobat A, Moradpour D, Nalpas B, Negro F, Poynard T, Pol S, Bochud PY, Abel L, Jeulin H, Schvoerer E, Chabi N, Amouzou E, Sanni A, Barraud H, Rouyer P, Josse T, Goffinet L, Jouve JL, Minello A, Bonithon-Kopp C, Thiefin G, Di Martino V, Doffoël M, Richou C, Raab JJ, Hillon P, Bronowicki JP, Guéant JL. BRIP1 coding variants are associated with a high risk of hepatocellular carcinoma occurrence in patients with HCV- or HBV-related liver disease. Oncotarget 2016; 8:62842-62857. [PMID: 28968953 PMCID: PMC5609885 DOI: 10.18632/oncotarget.11327] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/19/2016] [Indexed: 12/21/2022] Open
Abstract
The molecular mechanisms of hepatocellular carcinoma (HCC) carcinogenesis are still not fully understood. DNA repair defects may influence HCC risk. The aim of the study was to look for potential genetic variants of DNA repair genes associated with HCC risk among patients with alcohol- or viral-induced liver disease. We performed four case-control studies on 2,006 European- (Derivation#1 and #2 studies) and African-ancestry (Validation#1 and #2 studies) patients originating from several cohorts in order to assess the association between genetic variants on DNA repair genes and HCC risk using a custom array encompassing 94 genes. In the Derivation#1 study, the BRIP1 locus reached array-wide significance (Chi-squared SV-Perm, P=5.00×10-4) among the 253 haplotype blocks tested for their association with HCC risk, in patients with viral cirrhosis but not among those with alcoholic cirrhosis. The BRIP1 haplotype block included three exonic variants (rs4986763, rs4986764, rs4986765). The BRIP1 'AAA' haplotype was significantly associated with an increased HCC risk [odds ratio (OR), 2.01 (1.19-3.39); false discovery rate (FDR)-P=1.31×10-2]. In the Derivation#2 study, results were confirmed for the BRIP1 'GGG' haplotype [OR, 0.53 (0.36-0.79); FDR-P=3.90×10-3]. In both Validation#1 and #2 studies, BRIP1 'AAA' haplotype was significantly associated with an increased risk of HCC [OR, 1.71 (1.09-2.68); FDR-P=7.30×10-2; and OR, 6.45 (4.17-9.99); FDR-P=2.33×10-19, respectively]. Association between the BRIP1 locus and HCC risk suggests that impaired DNA mismatch repair might play a role in liver carcinogenesis, among patients with HCV- or HBV-related liver disease.
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Affiliation(s)
- Abderrahim Oussalah
- INSERM, U954, NGERE - Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, Vandoeuvre-lès-Nancy, France.,Department of Molecular Medicine and Personalized Therapeutics, Department of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy, Vandoeuvre-lès-Nancy, France
| | - Patrice Hodonou Avogbe
- INSERM, U954, NGERE - Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, Vandoeuvre-lès-Nancy, France
| | - Erwan Guyot
- Biochemistry Unit, Jean Verdier Hospital, APHP, Bondy, France and University Paris 13-UFR SMBH/INSERM, Bobigny, France
| | - Céline Chery
- INSERM, U954, NGERE - Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, Vandoeuvre-lès-Nancy, France.,Department of Molecular Medicine and Personalized Therapeutics, Department of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy, Vandoeuvre-lès-Nancy, France
| | - Rosa-Maria Guéant-Rodriguez
- INSERM, U954, NGERE - Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, Vandoeuvre-lès-Nancy, France.,Department of Molecular Medicine and Personalized Therapeutics, Department of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy, Vandoeuvre-lès-Nancy, France
| | - Nathalie Ganne-Carrié
- Liver Unit and Liver biobank CRB des Hôpitaux Universitaires Paris-Seine-Saint-Denis BB-0033-00027, Jean Verdier Hospital, APHP, Bondy, France.,INSERM, U1162, Génomique fonctionnelle des Tumeurs solides, Paris, France
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Darius Moradpour
- Division of Gastroenterology and Hepatology, University Hospital and University of Lausanne, Switzerland
| | - Bertrand Nalpas
- Département d'Hépatologie, Hôpital Cochin (AP-HP), Université Paris Descartes, Paris, France
| | - Francesco Negro
- Division of Clinical Pathology and Division of Gastroenterology and Hepatology, University Hospitals, Geneva, Switzerland
| | - Thierry Poynard
- Université Pierre et Marie Curie, Service d'Hépato-gastroentérologie, Hôpital Pitié-Salpêtrière (AP-HP), Paris, France
| | - Stanislas Pol
- Département d'Hépatologie, Hôpital Cochin (AP-HP), Université Paris Descartes, Paris, France.,INSERM UMS20, Institut Pasteur, Paris, France
| | - Pierre-Yves Bochud
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Switzerland
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, NY, USA
| | - Hélène Jeulin
- Virology Laboratory, Centre Hospitalier Universitaire de Nancy, Vandoeuvre-lès-Nancy, France
| | - Evelyne Schvoerer
- Virology Laboratory, Centre Hospitalier Universitaire de Nancy, Vandoeuvre-lès-Nancy, France
| | - Nicodème Chabi
- Laboratory of Biochemistry and Molecular Biology, University of Cotonou, Cotonou, Benin
| | - Emile Amouzou
- Laboratory of Biochemistry and Nutrition, Lomé, University of Kara, Togo
| | - Ambaliou Sanni
- Laboratory of Biochemistry and Molecular Biology, University of Cotonou, Cotonou, Benin
| | - Hélène Barraud
- Department of Hepato-Gastroenterology, University Hospital of Nancy, Vandoeuvre-lès-Nancy, France
| | - Pierre Rouyer
- INSERM, U954, NGERE - Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, Vandoeuvre-lès-Nancy, France
| | - Thomas Josse
- Department of Molecular Medicine and Personalized Therapeutics, Department of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy, Vandoeuvre-lès-Nancy, France
| | - Laetitia Goffinet
- INSERM, U954, NGERE - Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, Vandoeuvre-lès-Nancy, France
| | - Jean-Louis Jouve
- INSERM, U866 and INSERM, CIE 01, University Hospital of Dijon, University of Burgundy, Dijon, France
| | - Anne Minello
- INSERM, U866 and INSERM, CIE 01, University Hospital of Dijon, University of Burgundy, Dijon, France
| | - Claire Bonithon-Kopp
- INSERM, U866 and INSERM, CIE 01, University Hospital of Dijon, University of Burgundy, Dijon, France
| | - Gérard Thiefin
- Department of Hepato-Gastroenterology, Reims University Hospital, Reims, France
| | - Vincent Di Martino
- Department of Hepatology, University Hospital of Besançon, Besançon, France
| | - Michel Doffoël
- Department of Hepato-Gastroenterology, University Hospital of Strasbourg, Strasbourg, France
| | - Carine Richou
- Department of Hepatology, University Hospital of Besançon, Besançon, France
| | | | - Patrick Hillon
- INSERM, U866 and INSERM, CIE 01, University Hospital of Dijon, University of Burgundy, Dijon, France
| | - Jean-Pierre Bronowicki
- INSERM, U954, NGERE - Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, Vandoeuvre-lès-Nancy, France.,Department of Hepato-Gastroenterology, University Hospital of Nancy, Vandoeuvre-lès-Nancy, France
| | - Jean-Louis Guéant
- INSERM, U954, NGERE - Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, Vandoeuvre-lès-Nancy, France.,Department of Molecular Medicine and Personalized Therapeutics, Department of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy, Vandoeuvre-lès-Nancy, France
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28
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Lopez-Martinez D, Liang CC, Cohn MA. Cellular response to DNA interstrand crosslinks: the Fanconi anemia pathway. Cell Mol Life Sci 2016; 73:3097-114. [PMID: 27094386 PMCID: PMC4951507 DOI: 10.1007/s00018-016-2218-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 04/04/2016] [Accepted: 04/05/2016] [Indexed: 12/22/2022]
Abstract
Interstrand crosslinks (ICLs) are a highly toxic form of DNA damage. ICLs can interfere with vital biological processes requiring separation of the two DNA strands, such as replication and transcription. If ICLs are left unrepaired, it can lead to mutations, chromosome breakage and mitotic catastrophe. The Fanconi anemia (FA) pathway can repair this type of DNA lesion, ensuring genomic stability. In this review, we will provide an overview of the cellular response to ICLs. First, we will discuss the origin of ICLs, comparing various endogenous and exogenous sources. Second, we will describe FA proteins as well as FA-related proteins involved in ICL repair, and the post-translational modifications that regulate these proteins. Finally, we will review the process of how ICLs are repaired by both replication-dependent and replication-independent mechanisms.
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Affiliation(s)
- David Lopez-Martinez
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Chih-Chao Liang
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Martin A Cohn
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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29
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Barthelemy J, Hanenberg H, Leffak M. FANCJ is essential to maintain microsatellite structure genome-wide during replication stress. Nucleic Acids Res 2016; 44:6803-16. [PMID: 27179029 PMCID: PMC5001596 DOI: 10.1093/nar/gkw433] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 05/06/2016] [Indexed: 12/15/2022] Open
Abstract
Microsatellite DNAs that form non-B structures are implicated in replication fork stalling, DNA double strand breaks (DSBs) and human disease. Fanconi anemia (FA) is an inherited disorder in which mutations in at least nineteen genes are responsible for the phenotypes of genome instability and cancer predisposition. FA pathway proteins are active in the resolution of non-B DNA structures including interstrand crosslinks, G quadruplexes and DNA triplexes. In FANCJ helicase depleted cells, we show that hydroxyurea or aphidicolin treatment leads to loss of microsatellite polymerase chain reaction signals and to chromosome recombination at an ectopic hairpin forming CTG/CAG repeat in the HeLa genome. Moreover, diverse endogenous microsatellite signals were also lost upon replication stress after FANCJ depletion, and in FANCJ null patient cells. The phenotype of microsatellite signal instability is specific for FANCJ apart from the intact FA pathway, and is consistent with DSBs at microsatellites genome-wide in FANCJ depleted cells following replication stress.
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Affiliation(s)
- Joanna Barthelemy
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - Helmut Hanenberg
- Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany Department of Otorhinolaryngology & Head/Neck Surgery, Heinrich Heine University, 40225 Duesseldorf, Germany
| | - Michael Leffak
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
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30
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Mutational analysis of FANCJ helicase. Methods 2016; 108:118-29. [PMID: 27107905 DOI: 10.1016/j.ymeth.2016.04.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 04/15/2016] [Accepted: 04/19/2016] [Indexed: 11/21/2022] Open
Abstract
FANCJ is a superfamily 2 DNA helicase, which also belongs to the iron-sulfur domain containing helicases that include XPD, ChlR1 (DDX11), and RTEL1. Mutations in FANCJ are genetically linked to Fanconi anemia (FA), breast cancer, and ovarian cancer. FANCJ plays a critical role in genome stability and participates in DNA interstrand crosslink and double-strand break repair. Enormous sequence alterations in exons and introns of FANCJ have been identified in patients, including 15 mutations in the coding region which are linked to breast cancer, 12 to FA, and two to ovarian cancer. We and other groups have characterized several FANCJ missense mutations, including M299I, A349P, R251C, and Q255H. As an increasing number of clinically relevant FANCJ mutations are identified, understanding the mechanism whereby FANCJ mutation leads to diseases is critical. Mutational analysis of FANCJ will help us elucidate the pathogenesis and potentially lead to therapeutic strategies by targeting FANCJ.
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Cantor SB, Nayak S. FANCJ at the FORK. Mutat Res 2016; 788:7-11. [PMID: 26926912 DOI: 10.1016/j.mrfmmm.2016.02.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 01/28/2016] [Accepted: 02/10/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Sharon B Cantor
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, UMASS Memorial Cancer Center, Worcester, Massachusetts 01605, USA.
| | - Sumeet Nayak
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, UMASS Memorial Cancer Center, Worcester, Massachusetts 01605, USA
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Iyama T, Wilson DM. Elements That Regulate the DNA Damage Response of Proteins Defective in Cockayne Syndrome. J Mol Biol 2015; 428:62-78. [PMID: 26616585 DOI: 10.1016/j.jmb.2015.11.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 11/18/2015] [Accepted: 11/18/2015] [Indexed: 10/22/2022]
Abstract
Cockayne syndrome (CS) is a premature aging disorder characterized by developmental defects, multisystem progressive degeneration and sensitivity to ultraviolet light. CS is divided into two primary complementation groups, A and B, with the CSA and CSB proteins presumably functioning in DNA repair and transcription. Using laser microirradiation and confocal microscopy, we characterized the nature and regulation of the CS protein response to oxidative DNA damage, double-strand breaks (DSBs), angelicin monoadducts and trioxsalen interstrand crosslinks (ICLs). Our data indicate that CSB recruitment is influenced by the type of DNA damage and is most rapid and robust as follows: ICLs>DSBs>monoadducts>oxidative lesions. Transcription inhibition reduced accumulation of CSB at sites of monoadducts and ICLs, but it did not affect recruitment to (although slightly affected retention at) oxidative damage. Inhibition of histone deacetylation altered the dynamics of CSB assembly, suggesting a role for chromatin status in the response to DNA damage, whereas the proteasome inhibitor MG132 had no effect. The C-terminus of CSB and, in particular, its ubiquitin-binding domain were critical to recruitment, while the N-terminus and a functional ATPase domain played a minor role at best in facilitating protein accumulation. Although the absence of CSA had no effect on CSB recruitment, CSA itself localized at sites of ICLs, DSBs and monoadducts but not at oxidative lesions. Our results reveal molecular components of the CS protein response and point to a major involvement of complex lesions in the pathology of CS.
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Affiliation(s)
- Teruaki Iyama
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Suite 100, Baltimore, MD 21224, USA
| | - David M Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Suite 100, Baltimore, MD 21224, USA.
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Clark DW, Tripathi K, Dorsman JC, Palle K. FANCJ protein is important for the stability of FANCD2/FANCI proteins and protects them from proteasome and caspase-3 dependent degradation. Oncotarget 2015; 6:28816-32. [PMID: 26336824 PMCID: PMC4745694 DOI: 10.18632/oncotarget.5006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 08/11/2015] [Indexed: 01/31/2023] Open
Abstract
Fanconi anemia (FA) is a rare genome instability syndrome with progressive bone marrow failure and cancer susceptibility. FANCJ is one of 17 genes mutated in FA-patients, comprises a DNA helicase that is vital for properly maintaining genomic stability and is known to function in the FA-BRCA DNA repair pathway. While exact role(s) of FANCJ in this repair process is yet to be determined, it is known to interact with primary effector FANCD2. However, FANCJ is not required for FANCD2 activation but is important for its ability to fully respond to DNA damage. In this report, we determined that transient depletion of FANCJ adversely affects stability of FANCD2 and its co-regulator FANCI in multiple cell lines. Loss of FANCJ does not significantly alter cell cycle progression or FANCD2 transcription. However, in the absence of FANCJ, the majority of FANCD2 is degraded by both the proteasome and Caspase-3 dependent mechanism. FANCJ is capable of complexing with and stabilizing FANCD2 even in the absence of a functional helicase domain. Furthermore, our data demonstrate that FANCJ is important for FANCD2 stability and proper activation of DNA damage responses to replication blocks induced by hydroxyurea.
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Affiliation(s)
- David W. Clark
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Kaushlendra Tripathi
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Josephine C. Dorsman
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Komaraiah Palle
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
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Abstract
Figuring out what is wrong in Fanconi anemia (FA) patient cells is critical to understanding the contributions of the FA pathway to DNA repair and tumor suppression. Although FA patients exhibit a wide range of disease manifestation as well as severity (asymptomatic to congenital abnormalities, bone marrow failure, and cancer), cells from FA patients share underlying defects in their ability to process DNA lesions that interfere with DNA replication. In particular, FA cells are very sensitive to agents that induce DNA interstrand crosslinks (ICLs). The cause of this pronounced ICL sensitivity is not fully understood, but has been linked to the aberrant activation of DNA damage repair proteins, checkpoints and pathways. Thus, regulation of these responses through coordination of repair processing at stalled replication forks is an essential function of the FA pathway. Here, we briefly summarize some of the aberrant DNA damage responses contributing to defects in FA cells, and detail the newly-identified relationship between FA and the mismatch repair protein, MSH2. Understanding the contribution of MSH2 and/or other proteins to the replication problem in FA cells will be key to assessing therapeutic options to improve the health of FA patients. Moreover, loss of these factors, if linked to improved replication, could be a key event in the progression of FA cells to cancer cells. Likewise, loss of these factors could synergize to enhance tumorigenesis or confer chemoresistance in tumors defective in FA-BRCA pathway proteins and provide a basis for biomarkers for disease progression and response.
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Affiliation(s)
- Sharon B Cantor
- a Department of Cancer Biology ; University of Massachusetts Medical School; UMASS Memorial Cancer Center ; Worcester , MA USA
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Xu Y, Wu X, Her C. hMSH5 Facilitates the Repair of Camptothecin-induced Double-strand Breaks through an Interaction with FANCJ. J Biol Chem 2015; 290:18545-58. [PMID: 26055704 DOI: 10.1074/jbc.m115.642884] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Indexed: 12/18/2022] Open
Abstract
Replication stress from stalled or collapsed replication forks is a major challenge to genomic integrity. The anticancer agent camptothecin (CPT) is a DNA topoisomerase I inhibitor that causes fork collapse and double-strand breaks amid DNA replication. Here we report that hMSH5 promotes cell survival in response to CPT-induced DNA damage. Cells deficient in hMSH5 show elevated CPT-induced γ-H2AX and RPA2 foci with concomitant reduction of Rad51 foci, indicative of impaired homologous recombination. In addition, CPT-treated hMSH5-deficient cells exhibit aberrant activation of Chk1 and Chk2 kinases and therefore abnormal cell cycle progression. Furthermore, the hMSH5-FANCJ chromatin recruitment underlies the effects of hMSH5 on homologous recombination and Chk1 activation. Intriguingly, FANCJ depletion desensitizes hMSH5-deficient cells to CPT-elicited cell killing. Collectively, our data point to the existence of a functional interplay between hMSH5 and FANCJ in double-strand break repair induced by replication stress.
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Affiliation(s)
- Yang Xu
- From the School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, Washington 99164-7520
| | - Xiling Wu
- From the School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, Washington 99164-7520
| | - Chengtao Her
- From the School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, Washington 99164-7520
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36
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Sommers JA, Suhasini AN, Brosh RM. Protein degradation pathways regulate the functions of helicases in the DNA damage response and maintenance of genomic stability. Biomolecules 2015; 5:590-616. [PMID: 25906194 PMCID: PMC4496686 DOI: 10.3390/biom5020590] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 04/09/2015] [Accepted: 04/13/2015] [Indexed: 12/18/2022] Open
Abstract
Degradation of helicases or helicase-like proteins, often mediated by ubiquitin-proteasomal pathways, plays important regulatory roles in cellular mechanisms that respond to DNA damage or replication stress. The Bloom’s syndrome helicase (BLM) provides an example of how helicase degradation pathways, regulated by post-translational modifications and protein interactions with components of the Fanconi Anemia (FA) interstrand cross-link (ICL) repair pathway, influence cell cycle checkpoints, DNA repair, and replication restart. The FANCM DNA translocase can be targeted by checkpoint kinases that exert dramatic effects on FANCM stability and chromosomal integrity. Other work provides evidence that degradation of the F-box DNA helicase (FBH1) helps to balance translesion synthesis (TLS) and homologous recombination (HR) repair at blocked replication forks. Degradation of the helicase-like transcription factor (HLTF), a DNA translocase and ubiquitylating enzyme, influences the choice of post replication repair (PRR) pathway. Stability of the Werner syndrome helicase-nuclease (WRN) involved in the replication stress response is regulated by its acetylation. Turning to transcription, stability of the Cockayne Syndrome Group B DNA translocase (CSB) implicated in transcription-coupled repair (TCR) is regulated by a CSA ubiquitin ligase complex enabling recovery of RNA synthesis. Collectively, these studies demonstrate that helicases can be targeted for degradation to maintain genome homeostasis.
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Affiliation(s)
- Joshua A Sommers
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Blvd, Baltimore, MD 21224, USA.
| | - Avvaru N Suhasini
- Department of Medicine, Division of Hematology & Medical Oncology, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Blvd, Baltimore, MD 21224, USA.
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Aarts M, Bajrami I, Herrera-Abreu MT, Elliott R, Brough R, Ashworth A, Lord CJ, Turner NC. Functional Genetic Screen Identifies Increased Sensitivity to WEE1 Inhibition in Cells with Defects in Fanconi Anemia and HR Pathways. Mol Cancer Ther 2015; 14:865-76. [PMID: 25673822 PMCID: PMC6485454 DOI: 10.1158/1535-7163.mct-14-0845] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 02/04/2015] [Indexed: 01/11/2023]
Abstract
WEE1 kinase regulates CDK1 and CDK2 activity to facilitate DNA replication during S-phase and to prevent unscheduled entry into mitosis. WEE1 inhibitors synergize with DNA-damaging agents that arrest cells in S-phase by triggering direct mitotic entry without completing DNA synthesis, resulting in catastrophic chromosome fragmentation and apoptosis. Here, we investigated how WEE1 inhibition could be best exploited for cancer therapy by performing a functional genetic screen to identify novel determinants of sensitivity to WEE1 inhibition. Inhibition of kinases that regulate CDK activity, CHK1 and MYT1, synergized with WEE1 inhibition through both increased replication stress and forced mitotic entry of S-phase cells. Loss of multiple components of the Fanconi anemia (FA) and homologous recombination (HR) pathways, in particular DNA helicases, sensitized to WEE1 inhibition. Silencing of FA/HR genes resulted in excessive replication stress and nucleotide depletion following WEE1 inhibition, which ultimately led to increased unscheduled mitotic entry. Our results suggest that cancers with defects in FA and HR pathways may be targeted by WEE1 inhibition, providing a basis for a novel synthetic lethal strategy for cancers harboring FA/HR defects.
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Affiliation(s)
- Marieke Aarts
- CRUK Gene Function Laboratory, Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Ilirjana Bajrami
- CRUK Gene Function Laboratory, Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Maria T Herrera-Abreu
- CRUK Gene Function Laboratory, Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Richard Elliott
- CRUK Gene Function Laboratory, Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Rachel Brough
- CRUK Gene Function Laboratory, Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Alan Ashworth
- CRUK Gene Function Laboratory, Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Christopher J Lord
- CRUK Gene Function Laboratory, Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Nicholas C Turner
- CRUK Gene Function Laboratory, Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom. Breast Unit, Royal Marsden Hospital, London, United Kingdom.
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Aberrant recombination and repair during immunoglobulin class switching in BRCA1-deficient human B cells. Proc Natl Acad Sci U S A 2015; 112:2157-62. [PMID: 25646469 DOI: 10.1073/pnas.1418947112] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Breast cancer type 1 susceptibility protein (BRCA1) has a multitude of functions that contribute to genome integrity and tumor suppression. Its participation in the repair of DNA double-strand breaks (DSBs) during homologous recombination (HR) is well recognized, whereas its involvement in the second major DSB repair pathway, nonhomologous end-joining (NHEJ), remains controversial. Here we have studied the role of BRCA1 in the repair of DSBs in switch (S) regions during immunoglobulin class switch recombination, a physiological, deletion/recombination process that relies on the classical NHEJ machinery. A shift to the use of microhomology-based, alternative end-joining (A-EJ) and increased frequencies of intra-S region deletions as well as insertions of inverted S sequences were observed at the recombination junctions amplified from BRCA1-deficient human B cells. Furthermore, increased use of long microhomologies was found at recombination junctions derived from E3 ubiquitin-protein ligase RNF168-deficient, Fanconi anemia group J protein (FACJ, BRIP1)-deficient, or DNA endonuclease RBBP8 (CtIP)-compromised cells, whereas an increased frequency of S-region inversions was observed in breast cancer type 2 susceptibility protein (BRCA2)-deficient cells. Thus, BRCA1, together with its interaction partners, seems to play an important role in repairing DSBs generated during class switch recombination by promoting the classical NHEJ pathway. This may not only provide a general mechanism underlying BRCA1's function in maintaining genome stability and tumor suppression but may also point to a previously unrecognized role of BRCA1 in B-cell lymphomagenesis.
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39
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Brosh RM, Cantor SB. Molecular and cellular functions of the FANCJ DNA helicase defective in cancer and in Fanconi anemia. Front Genet 2014; 5:372. [PMID: 25374583 PMCID: PMC4204437 DOI: 10.3389/fgene.2014.00372] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 10/05/2014] [Indexed: 01/11/2023] Open
Abstract
The FANCJ DNA helicase is mutated in hereditary breast and ovarian cancer as well as the progressive bone marrow failure disorder Fanconi anemia (FA). FANCJ is linked to cancer suppression and DNA double strand break repair through its direct interaction with the hereditary breast cancer associated gene product, BRCA1. FANCJ also operates in the FA pathway of interstrand cross-link repair and contributes to homologous recombination. FANCJ collaborates with a number of DNA metabolizing proteins implicated in DNA damage detection and repair, and plays an important role in cell cycle checkpoint control. In addition to its role in the classical FA pathway, FANCJ is believed to have other functions that are centered on alleviating replication stress. FANCJ resolves G-quadruplex (G4) DNA structures that are known to affect cellular replication and transcription, and potentially play a role in the preservation and functionality of chromosomal structures such as telomeres. Recent studies suggest that FANCJ helps to maintain chromatin structure and preserve epigenetic stability by facilitating smooth progression of the replication fork when it encounters DNA damage or an alternate DNA structure such as a G4. Ongoing studies suggest a prominent but still not well-understood role of FANCJ in transcriptional regulation, chromosomal structure and function, and DNA damage repair to maintain genomic stability. This review will synthesize our current understanding of the molecular and cellular functions of FANCJ that are critical for chromosomal integrity.
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Affiliation(s)
- Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health Baltimore, MD, USA
| | - Sharon B Cantor
- Department of Cancer Biology, University of Massachusetts Medical School - UMASS Memorial Cancer Center Worcester, MA, USA
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40
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Peng M, Xie J, Ucher A, Stavnezer J, Cantor SB. Crosstalk between BRCA-Fanconi anemia and mismatch repair pathways prevents MSH2-dependent aberrant DNA damage responses. EMBO J 2014; 33:1698-712. [PMID: 24966277 PMCID: PMC4194102 DOI: 10.15252/embj.201387530] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Several proteins in the BRCA-Fanconi anemia (FA) pathway, such as FANCJ, BRCA1, and FANCD2, interact with mismatch repair (MMR) pathway factors, but the significance of this link remains unknown. Unlike the BRCA-FA pathway, the MMR pathway is not essential for cells to survive toxic DNA interstrand crosslinks (ICLs), although MMR proteins bind ICLs and other DNA structures that form at stalled replication forks. We hypothesized that MMR proteins corrupt ICL repair in cells that lack crosstalk between BRCA-FA and MMR pathways. Here, we show that ICL sensitivity of cells lacking the interaction between FANCJ and the MMR protein MLH1 is suppressed by depletion of the upstream mismatch recognition factor MSH2. MSH2 depletion suppresses an aberrant DNA damage response, restores cell cycle progression, and promotes ICL resistance through a Rad18-dependent mechanism. MSH2 depletion also suppresses ICL sensitivity in cells deficient for BRCA1 or FANCD2, but not FANCA. Rescue by Msh2 loss was confirmed in Fancd2-null primary mouse cells. Thus, we propose that regulation of MSH2-dependent DNA damage response underlies the importance of interactions between BRCA-FA and MMR pathways.
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Affiliation(s)
- Min Peng
- Department of Cancer Biology, University of Massachusetts Medical School, Women's Cancers Program, UMASS Memorial Cancer Center, Worcester, MA, USA
| | - Jenny Xie
- Department of Cancer Biology, University of Massachusetts Medical School, Women's Cancers Program, UMASS Memorial Cancer Center, Worcester, MA, USA
| | - Anna Ucher
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Women's Cancers Program, UMASS Memorial Cancer Center, Worcester, MA, USA
| | - Janet Stavnezer
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Women's Cancers Program, UMASS Memorial Cancer Center, Worcester, MA, USA
| | - Sharon B Cantor
- Department of Cancer Biology, University of Massachusetts Medical School, Women's Cancers Program, UMASS Memorial Cancer Center, Worcester, MA, USA
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McCrane MP, Hutchinson MA, Ad O, Rokita SE. Oxidative quenching of quinone methide adducts reveals transient products of reversible alkylation in duplex DNA. Chem Res Toxicol 2014; 27:1282-93. [PMID: 24896651 DOI: 10.1021/tx500152d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
ortho-Quinone methides (ortho-QM) and para-quinone methides are generated by xenobiotic metabolism of numerous compounds including environmental toxins and therapeutic agents. These intermediates are highly electrophilic and have the potential to alkylate DNA. Assessing their genotoxicity can be difficult when all or some of their resulting adducts form reversibly. Stable adducts are most easily detected but are not necessarily the most prevalent products formed initially as DNA repair commences. Selective oxidation of ortho-QM-DNA adducts by bis[(trifluoroacetoxy)iodo]benzene (BTI) rapidly quenches their reversibility to prevent QM regeneration and allows for observation of the kinetic products. The resulting derivatives persist through standard enzymatic digestion, chromatography, and mass spectral analysis. The structural standards required for this approach have been synthesized and confirmed by two-dimensional NMR spectroscopy. The adducts of dA N(6), dG N1, dG N(2), and guanine N7 are converted to the expected para-quinol derivatives within 5 min after addition of BTI under aqueous conditions (pH 7). Concurrently, the adduct of dA N1 forms a spiro derivative comparable to that characterized previously after oxidation of the corresponding dC N3 adduct. By application of this oxidative quenching strategy, the dC N3 and dA N1 adducts have been identified as the dominant products formed by both single- and double-stranded DNA under initial conditions. As expected, however, these labile adducts dissipate within 24 h if not quenched with BTI. Still, the products favored by kinetics are responsible for inducing the first response to ortho-QM exposure in cells, and hence, they are also key to establishing the relationship between biological activity and molecular structure.
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Affiliation(s)
- Michael P McCrane
- Department of Chemistry and Biochemistry, University of Maryland , College Park, Maryland 20742 United States
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42
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Guo M, Vidhyasagar V, Ding H, Wu Y. Insight into the roles of helicase motif Ia by characterizing Fanconi anemia group J protein (FANCJ) patient mutations. J Biol Chem 2014; 289:10551-10565. [PMID: 24573678 DOI: 10.1074/jbc.m113.538892] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Helicases are molecular motors that couple the energy of ATP hydrolysis to the unwinding and remodeling of structured DNA or RNA, which is coordinated by conserved helicase motifs. FANCJ is a DNA helicase that is genetically linked to Fanconi anemia, breast cancer, and ovarian cancer. Here, we characterized two Fanconi anemia patient mutations, R251C and Q255H, that are localized in helicase motif Ia. Our genetic complementation analysis revealed that both the R251C and Q255H alleles failed to rescue cisplatin sensitivity of a FANCJ null cell line as detected by cell survival or γ-H2AX foci formation. Furthermore, our biochemical assays demonstrated that both purified recombinant proteins abolished DNA helicase activity and failed to disrupt the DNA-protein complex. Intriguingly, R251C impaired DNA binding ability to single-strand DNA and double-strand DNA, whereas Q255H retained higher binding activity to these DNA substrates compared with wild-type FANCJ protein. Consequently, R251C abolished its DNA-dependent ATP hydrolysis activity, whereas Q255H retained normal ATPase activity. Physically, R251C had reduced ATP binding ability, whereas Q255H had normal ATP binding ability and could translocate on single-strand DNA. Although both proteins were recruited to damage sites in our laser-activated confocal assays, they lost their DNA repair function, which explains why they exerted a domain negative effect when expressed in a wild-type background. Taken together, our work not only reveals the structural function of helicase motif Ia but also provides the molecular pathology of FANCJ in related diseases.
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Affiliation(s)
- Manhong Guo
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Venkatasubramanian Vidhyasagar
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Hao Ding
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Yuliang Wu
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, Saskatoon, Saskatchewan, S7N 5E5, Canada.
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Guillemette S, Branagan A, Peng M, Dhruva A, Schärer OD, Cantor SB. FANCJ localization by mismatch repair is vital to maintain genomic integrity after UV irradiation. Cancer Res 2013; 74:932-44. [PMID: 24351291 DOI: 10.1158/0008-5472.can-13-2474] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Nucleotide excision repair (NER) is critical for the repair of DNA lesions induced by UV radiation, but its contribution in replicating cells is less clear. Here, we show that dual incision by NER endonucleases, including XPF and XPG, promotes the S-phase accumulation of the BRCA1 and Fanconi anemia-associated DNA helicase FANCJ to sites of UV-induced damage. FANCJ promotes replication protein A phosphorylation and the arrest of DNA synthesis following UV irradiation. Interaction defective mutants of FANCJ reveal that BRCA1 binding is not required for FANCJ localization, whereas interaction with the mismatch repair (MMR) protein MLH1 is essential. Correspondingly, we find that FANCJ, its direct interaction with MLH1, and the MMR protein MSH2 function in a common pathway in response to UV irradiation. FANCJ-deficient cells are not sensitive to killing by UV irradiation, yet we find that DNA mutations are significantly enhanced. Thus, we considered that FANCJ deficiency could be associated with skin cancer. Along these lines, in melanoma we found several somatic mutations in FANCJ, some of which were previously identified in hereditary breast cancer and Fanconi anemia. Given that, mutations in XPF can also lead to Fanconi anemia, we propose collaborations between Fanconi anemia, NER, and MMR are necessary to initiate checkpoint activation in replicating human cells to limit genomic instability.
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Affiliation(s)
- Shawna Guillemette
- Authors' Affiliations: Department of Cancer Biology, University of Massachusetts Medical School, Women's Cancers Program, UMASS Memorial Cancer Center, Worcester, Massachusetts; and Department of Pharmacological Sciences & Department of Chemistry, Stony Brook University, Stony Brook, New York
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44
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Abstract
Helicases have major roles in genome maintenance by unwinding structured nucleic acids. Their prominence is marked by various cancers and genetic disorders that are linked to helicase defects. Although considerable effort has been made to understand the functions of DNA helicases that are important for genomic stability and cellular homeostasis, the complexity of the DNA damage response leaves us with unanswered questions regarding how helicase-dependent DNA repair pathways are regulated and coordinated with cell cycle checkpoints. Further studies may open the door to targeting helicases in order to improve cancer treatments based on DNA-damaging chemotherapy or radiation.
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Affiliation(s)
- Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Boulevard, Baltimore, Maryland 21224, USA.
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