1
|
Lieu DJ, Crowder MK, Kryza JR, Tamilselvam B, Kaminski PJ, Kim IJ, Li Y, Jeong E, Enkhbaatar M, Chen H, Son SB, Mok H, Bradley KA, Phillips H, Blanke SR. Autophagy suppression in DNA damaged cells occurs through a newly identified p53-proteasome-LC3 axis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595139. [PMID: 38826216 PMCID: PMC11142043 DOI: 10.1101/2024.05.21.595139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Macroautophagy is thought to have a critical role in shaping and refining cellular proteostasis in eukaryotic cells recovering from DNA damage. Here, we report a mechanism by which autophagy is suppressed in cells exposed to bacterial toxin-, chemical-, or radiation-mediated sources of genotoxicity. Autophagy suppression is directly linked to cellular responses to DNA damage, and specifically the stabilization of the tumor suppressor p53, which is both required and sufficient for regulating the ubiquitination and proteasome-dependent reduction in cellular pools of microtubule-associated protein 1 light chain 3 (LC3A/B), a key precursor of autophagosome biogenesis and maturation, in both epithelial cells and an ex vivo organoid model. Our data indicate that suppression of autophagy, through a newly identified p53-proteasome-LC3 axis, is a conserved cellular response to multiple sources of genotoxicity. Such a mechanism could potentially be important for realigning proteostasis in cells undergoing DNA damage repair.
Collapse
|
2
|
Liu J, Li W, Jin X, Lin F, Han J, Zhang Y. Optimal tagging strategies for illuminating expression profiles of genes with different abundance in zebrafish. Commun Biol 2023; 6:1300. [PMID: 38129658 PMCID: PMC10739737 DOI: 10.1038/s42003-023-05686-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
CRISPR-mediated knock-in (KI) technology opens a new era of fluorescent-protein labeling in zebrafish, a preferred model organism for in vivo imaging. We described here an optimized zebrafish gene-tagging strategy, which enables easy and high-efficiency KI, ensures high odds of obtaining seamless KI germlines and is suitable for wide applications. Plasmid donors for 3'-labeling were optimized by shortening the microhomologous arms and by reducing the number and reversing the sequence of the consensus Cas9/sgRNA binding sites. To allow for scar-less KI across the genome, linearized dsDNA donors with 5'-chemical modifications were generated and successfully incorporated into our method. To refine the germline screen workflow and expedite the screen process, we combined fluorescence enrichment and caudal-fin junction-PCR. Furthermore, to trace proteins expressed at a low abundance, we developed a fluorescent signal amplifier using the transcriptional activation strategy. Together, our strategies enable efficient gene-tagging and sensitive expression detection for almost every gene in zebrafish.
Collapse
Affiliation(s)
- Jiannan Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China
| | - Wenyuan Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China
| | - Xuepu Jin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China
| | - Fanjia Lin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China
| | - Jiahuai Han
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China.
- Laboratory Animal Center, Xiamen University, 361102, Xiamen, Fujian, China.
- Research Unit of Cellular Stress of CAMS, Cancer Research Center of Xiamen University, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, 361102, Xiamen, Fujian, China.
| | - Yingying Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China.
| |
Collapse
|
3
|
Frey B, Borgmann K, Jost T, Greve B, Oertel M, Micke O, Eckert F. DNA as the main target in radiotherapy-a historical overview from first isolation to anti-tumour immune response. Strahlenther Onkol 2023; 199:1080-1090. [PMID: 37620671 DOI: 10.1007/s00066-023-02122-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/10/2023] [Indexed: 08/26/2023]
Abstract
DNA damage is one of the foremost mechanisms of irradiation at the biological level. After the first isolation of DNA by Friedrich Miescher in the 19th century, the structure of DNA was described by Watson and Crick. Several Nobel Prizes have been awarded for DNA-related discoveries. This review aims to describe the historical perspective of DNA in radiation biology. Over the decades, DNA damage has been identified and quantified after irradiation. Depending on the type of sensing, different proteins are involved in sensing DNA damage and repairing the damage, if possible. For double-strand breaks, the main repair mechanisms are non-homologous end joining and homologous recombination. Additional mechanisms are the Fanconi anaemia pathway and base excision repair. Different methods have been developed for the detection of DNA double-strand breaks. Several drugs have been developed that interfere with different DNA repair mechanisms, e.g., PARP inhibitors. These drugs have been established in the standard treatment of different tumour entities and are being applied in several clinical trials in combination with radiotherapy. Over the past decades, it has become apparent that DNA damage mechanisms are also directly linked to the immune response in tumours. For example, cytosolic DNA fragments activate the innate immune system via the cGAS STING pathway.
Collapse
Affiliation(s)
- Benjamin Frey
- Translational Radiation Biology, Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Kerstin Borgmann
- Laboratory of Radiobiology and Radiation Oncology, Department of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tina Jost
- Translational Radiation Biology, Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Burkhard Greve
- Department of Radiation Oncology, University Hospital Muenster, Muenster, Germany
| | - Michael Oertel
- Department of Radiation Oncology, University Hospital Muenster, Muenster, Germany
| | - Oliver Micke
- Department of Radiotherapy and Radiation Oncology, Franziskus Hospital Bielefeld, Kiskerst. 26, 33615, Bielefeld, Germany.
| | - Franziska Eckert
- Department of Radiation Oncology, AKH, Comprehensive Cancer Center Vienna, Medical University Vienna, Vienna, Austria
| |
Collapse
|
4
|
Morris E, Abreu A, Scordilis SP. Effect of Tamoxifen on Proteome Expression during In Vitro Myogenesis in Murine Skeletal Muscle C 2C 12 Cells. J Proteome Res 2023; 22:3040-3053. [PMID: 37552804 PMCID: PMC10476267 DOI: 10.1021/acs.jproteome.3c00340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Indexed: 08/10/2023]
Abstract
Tamoxifen (TMX), a selective estrogen receptor modulator, is commonly used in the treatment of hormone-responsive cancers. However, the effects of TMX in anabolic tissues harboring estrogen receptors, such as skeletal muscle, are poorly understood. We report a tandem mass-tag approach to TMX-treated myogenesis in C2C12 cells, a well-characterized model of in vitro murine skeletal muscle differentiation. A longitudinal analysis of >10,000 proteins identified in untreated C2C12 myogenesis revealed a novel subset of 1,062 myogenically regulated proteins. These proteins clustered into five distinct longitudinal expression trends which significantly overlap those obtained in similar analyses performed in human myocytes. We document a specific functional enrichment for adiponectin-signaling unique to TMX-treated myogenesis, as well as a subset of 198 proteins that are differentially expressed in TMX-treated cells relative to controls at one or more stages of myogenesis, the majority of which were involved in steroid and lipid metabolism. Further analysis highlights metallothionein-1 as a novel target of TMX treatment at each stage of C2C12 myogenesis. Finally, we present a powerful, self-validating pipeline for analyzing the total proteomic response to in vitro treatment across every stage of muscle cell development which can be easily adapted to study the effects of other drugs on myogenesis.
Collapse
Affiliation(s)
- Emily
A. Morris
- Department
of Microbiology and Immunology, Geisel School
of Medicine at Dartmouth, Borwell Building 644E, Lebanon, New Hampshire 03756, United States
| | - Ahlenne Abreu
- Department
of Cancer Biology, Perelman School of Medicine,
University of Pennsylvania Medical School, 421 Curie Blvd. Room 612 BRB II/III, Philadelphia, Pennsylvania 19104, United States
| | - Stylianos P. Scordilis
- Department
of Biological Sciences, Smith College, Ford Hall 202 B, Northampton, Massachusetts 01063, United States
| |
Collapse
|
5
|
Batool T, Irshad S, Riaz M, Mahmood Baig S, Nuernberg P, Hussain MS. Recurrence mutation in RBBP8 gene causing non-syndromic autosomal recessive primary microcephaly; geometric simulation approach for insight into predicted computational models. J Hum Genet 2023; 68:469-475. [PMID: 36864288 DOI: 10.1038/s10038-023-01132-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/18/2023] [Accepted: 02/06/2023] [Indexed: 03/04/2023]
Abstract
Primary microcephaly is a rare, congenital, and genetically heterogeneous disorder in which occipitofrontal head circumference is reduced by a minimum of three standard deviations (SDs) from average because of the defect in fetal brain development. OBJECTIVE Mapping of RBBP8 gene mutation that produce autosomal recessive primary microcephaly. Insilco RBBP8 protein models prediction and analysis. METHODS Consanguineous Pakistani family affected with non-syndromic primary microcephaly was mapped a biallelic sequence variant (c.1807_1808delAT) in the RBBP8 gene via whole-exome sequencing. The deleted variant in the RBBP8 gene in affected siblings (V:4, V:6) of primary microcephaly was confirmed by sanger sequencing. RESULTS Identified variant c.1807_1808delAT that truncated the protein translation p. Ile603Lysfs*7 and impaired the functioning of RBBP8 protein. This sequence variant was only reported previously in Atypical Seckel syndrome and Jawad syndrome, while we mapped it in the non-syndromic primary microcephaly family. We predicted 3D protein models by using Insilco tools like I TASSER, Swiss model, and phyre2 of wild RBBP8 protein of 897 amino acids and 608 amino acids of the mutant protein. These models were validated through the online SAVES server and Ramachandran plot and refined by using the Galaxy WEB server. A predicted and refined wild protein 3D model was deposited with accession number PM0083523 in Protein Model Database. A normal mode-based geometric simulation approach was used through the NMSim program, to find out the structural diversity of wild and mutant proteins which were evaluated by RMSD and RMSF. Higher RMSD and RMSF in mutant protein reduced the stability of the protein. CONCLUSION The high possibility of this variant results in nonsense-mediated decay of mRNA, leading to the loss of protein functioning which causes primary microcephaly.
Collapse
Affiliation(s)
- Tahira Batool
- School of Biochemistry and Biotechnology (SBB), University of the Punjab, Lahore-54590, Pakistan
| | - Saba Irshad
- School of Biochemistry and Biotechnology (SBB), University of the Punjab, Lahore-54590, Pakistan.
| | - Muhammad Riaz
- Department of Allied Health Sciences, University of Sargodha, Sargodha, 40100, Pakistan
| | | | - Peter Nuernberg
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931, Cologne, Germany
| | - Muhammad Sajid Hussain
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931, Cologne, Germany
| |
Collapse
|
6
|
Koo SY, Park EJ, Noh HJ, Jo SM, Ko BK, Shin HJ, Lee CW. Ubiquitination Links DNA Damage and Repair Signaling to Cancer Metabolism. Int J Mol Sci 2023; 24:ijms24098441. [PMID: 37176148 PMCID: PMC10179089 DOI: 10.3390/ijms24098441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
Changes in the DNA damage response (DDR) and cellular metabolism are two important factors that allow cancer cells to proliferate. DDR is a set of events in which DNA damage is recognized, DNA repair factors are recruited to the site of damage, the lesion is repaired, and cellular responses associated with the damage are processed. In cancer, DDR is commonly dysregulated, and the enzymes associated with DDR are prone to changes in ubiquitination. Additionally, cellular metabolism, especially glycolysis, is upregulated in cancer cells, and enzymes in this metabolic pathway are modulated by ubiquitination. The ubiquitin-proteasome system (UPS), particularly E3 ligases, act as a bridge between cellular metabolism and DDR since they regulate the enzymes associated with the two processes. Hence, the E3 ligases with high substrate specificity are considered potential therapeutic targets for treating cancer. A number of small molecule inhibitors designed to target different components of the UPS have been developed, and several have been tested in clinical trials for human use. In this review, we discuss the role of ubiquitination on overall cellular metabolism and DDR and confirm the link between them through the E3 ligases NEDD4, APC/CCDH1, FBXW7, and Pellino1. In addition, we present an overview of the clinically important small molecule inhibitors and implications for their practical use.
Collapse
Affiliation(s)
- Seo-Young Koo
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Eun-Ji Park
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Hyun-Ji Noh
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Su-Mi Jo
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Bo-Kyoung Ko
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Hyun-Jin Shin
- Team of Radiation Convergence Research, Korea Institute of Radiological & Medical Sciences, Seoul 01812, Republic of Korea
| | - Chang-Woo Lee
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
- SKKU Institute for Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
| |
Collapse
|
7
|
ATM suppresses c-Myc overexpression in the mammary epithelium in response to estrogen. Cell Rep 2023; 42:111909. [PMID: 36640339 PMCID: PMC10023214 DOI: 10.1016/j.celrep.2022.111909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/27/2022] [Accepted: 12/12/2022] [Indexed: 12/31/2022] Open
Abstract
ATM gene mutation carriers are predisposed to estrogen-receptor-positive breast cancer (BC). ATM prevents BC oncogenesis by activating p53 in every cell; however, much remains unknown about tissue-specific oncogenesis after ATM loss. Here, we report that ATM controls the early transcriptional response to estrogens. This response depends on topoisomerase II (TOP2), which generates TOP2-DNA double-strand break (DSB) complexes and rejoins the breaks. When TOP2-mediated ligation fails, ATM facilitates DSB repair. After estrogen exposure, TOP2-dependent DSBs arise at the c-MYC enhancer in human BC cells, and their defective repair changes the activation profile of enhancers and induces the overexpression of many genes, including the c-MYC oncogene. CRISPR/Cas9 cleavage at the enhancer also causes c-MYC overexpression, indicating that this DSB causes c-MYC overexpression. Estrogen treatment induced c-Myc protein overexpression in mammary epithelial cells of ATM-deficient mice. In conclusion, ATM suppresses the c-Myc-driven proliferative effects of estrogens, possibly explaining such tissue-specific oncogenesis.
Collapse
|
8
|
Mann A, Ramirez-Otero MA, De Antoni A, Hanthi YW, Sannino V, Baldi G, Falbo L, Schrempf A, Bernardo S, Loizou J, Costanzo V. POLθ prevents MRE11-NBS1-CtIP-dependent fork breakage in the absence of BRCA2/RAD51 by filling lagging-strand gaps. Mol Cell 2022; 82:4218-4231.e8. [PMID: 36400008 DOI: 10.1016/j.molcel.2022.09.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/16/2022] [Accepted: 09/09/2022] [Indexed: 11/18/2022]
Abstract
POLθ promotes repair of DNA double-strand breaks (DSBs) resulting from collapsed forks in homologous recombination (HR) defective tumors. Inactivation of POLθ results in synthetic lethality with the loss of HR genes BRCA1/2, which induces under-replicated DNA accumulation. However, it is unclear whether POLθ-dependent DNA replication prevents HR-deficiency-associated lethality. Here, we isolated Xenopus laevis POLθ and showed that it processes stalled Okazaki fragments, directly visualized by electron microscopy, thereby suppressing ssDNA gaps accumulating on lagging strands in the absence of RAD51 and preventing fork reversal. Inhibition of POLθ DNA polymerase activity leaves fork gaps unprotected, enabling their cleavage by the MRE11-NBS1-CtIP endonuclease, which produces broken forks with asymmetric single-ended DSBs, hampering BRCA2-defective cell survival. These results reveal a POLθ-dependent genome protection function preventing stalled forks rupture and highlight possible resistance mechanisms to POLθ inhibitors.
Collapse
Affiliation(s)
- Anjali Mann
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Miguel Angel Ramirez-Otero
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Anna De Antoni
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Yodhara Wijesekara Hanthi
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Vincenzo Sannino
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Giorgio Baldi
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Lucia Falbo
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Anna Schrempf
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Centre, Medical University of Vienna, Vienna, Austria
| | - Sara Bernardo
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Centre, Medical University of Vienna, Vienna, Austria
| | - Joanna Loizou
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Centre, Medical University of Vienna, Vienna, Austria
| | - Vincenzo Costanzo
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy.
| |
Collapse
|
9
|
Sun Y, Soans E, Mishina M, Petricci E, Pommier Y, Nitiss KC, Nitiss JL. Requirements for MRN endonuclease processing of topoisomerase II-mediated DNA damage in mammalian cells. Front Mol Biosci 2022; 9:1007064. [PMID: 36213114 PMCID: PMC9537633 DOI: 10.3389/fmolb.2022.1007064] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/29/2022] [Indexed: 12/03/2022] Open
Abstract
During a normal topoisomerase II (TOP2) reaction, the enzyme forms a covalent enzyme DNA intermediate consisting of a 5′ phosphotyrosyl linkage between the enzyme and DNA. While the enzyme typically rejoins the transient breakage after strand passage, a variety of conditions including drugs targeting TOP2 can inhibit DNA resealing, leading to enzyme-mediated DNA damage. A critical aspect of the repair of TOP2-mediated damage is the removal of the TOP2 protein covalently bound to DNA. While proteolysis plays a role in repairing this damage, nucleolytic enzymes must remove the phosphotyrosyl-linked peptide bound to DNA. The MRN complex has been shown to participate in the removal of TOP2 protein from DNA following cellular treatment with TOP2 poisons. In this report we used an optimized ICE (In vivo Complex of Enzyme) assay to measure covalent TOP2/DNA complexes. In agreement with previous independent reports, we find that the absence or inhibition of the MRE11 endonuclease results in elevated levels of both TOP2α and TOP2β covalent complexes. We also examined levels of TOP2 covalent complexes in cells treated with the proteasome inhibitor MG132. Although MRE11 inhibition plus MG132 was not synergistic in etoposide-treated cells, ectopic overexpression of MRE11 resulted in removal of TOP2 even in the presence of MG132. We also found that VCP/p97 inhibition led to elevated TOP2 covalent complexes and prevented the removal of TOP2 covalent complexes by MRE11 overexpression. Our results demonstrate the existence of multiple pathways for proteolytic processing of TOP2 prior to nucleolytic processing, and that MRE11 can process TOP2 covalent complexes even when the proteasome is inhibited. The interactions between VCP/p97 and proteolytic processing of TOP2 covalent complexes merit additional investigation.
Collapse
Affiliation(s)
- Yilun Sun
- Pharmaceutical Sciences Department, University of Illinois College of Pharmacy, Rockford, IL, United States
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Yilun Sun, ; John L. Nitiss,
| | - Eroica Soans
- St. Jude Children’s Research Hospital Memphis, Memphis, TN, United States
| | - Margarita Mishina
- St. Jude Children’s Research Hospital Memphis, Memphis, TN, United States
| | | | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Karin C. Nitiss
- Pharmaceutical Sciences Department, University of Illinois College of Pharmacy, Rockford, IL, United States
| | - John L. Nitiss
- Pharmaceutical Sciences Department, University of Illinois College of Pharmacy, Rockford, IL, United States
- *Correspondence: Yilun Sun, ; John L. Nitiss,
| |
Collapse
|
10
|
Oh W, Wu TT, Jeong SY, You HJ, Lee JH. CtIP Regulates Mitotic Spindle Assembly by Modulating the TPX2-Aurora A Signaling Axis. Cells 2022; 11:cells11182814. [PMID: 36139389 PMCID: PMC9497199 DOI: 10.3390/cells11182814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
CtBP-interacting protein (CtIP) plays a critical role in controlling the homologous recombination-mediated DNA double-stranded break (DSB) repair pathway through DNA end resection, and recent studies suggest that it also plays a role in mitosis. However, the mechanism by which CtIP contributes to mitosis regulation remains elusive. Here, we show that depletion of CtIP leads to a delay in anaphase progression resulting in misaligned chromosomes, an aberrant number of centrosomes, and defects in chromosome segregation. Additionally, we demonstrate that CtIP binds and colocalizes with Targeting protein for Xklp2 (TPX2) during mitosis to regulate the recruitment of TPX2 to the spindle poles. Furthermore, depletion of CtIP resulted in both a lower concentration of Aurora A, its downstream target, and very low microtubule intensity at the spindle poles, suggesting an important role for the CtIP-TPX2-Auroa A complex in microtubule dynamics at the centrosomal spindles. Our findings reveal a novel function of CtIP in regulating spindle dynamics through interactions with TPX2 and indicate that CtIP is involved in the proper execution of the mitotic program, where deregulation may lead to chromosomal instability.
Collapse
Affiliation(s)
- Wonkyung Oh
- Laboratory of Genomic Instability and Cancer Therapeutics, Cancer Mutation Research Center, School of Medicine, Chosun University, 375 Seosuk-dong, Gwangju 61452, Korea
| | - Ting Ting Wu
- Laboratory of Genomic Instability and Cancer Therapeutics, Cancer Mutation Research Center, School of Medicine, Chosun University, 375 Seosuk-dong, Gwangju 61452, Korea
| | - Seo-Yeon Jeong
- Laboratory of Genomic Instability and Cancer Therapeutics, Cancer Mutation Research Center, School of Medicine, Chosun University, 375 Seosuk-dong, Gwangju 61452, Korea
| | - Ho Jin You
- Laboratory of Genomic Instability and Cancer Therapeutics, Cancer Mutation Research Center, School of Medicine, Chosun University, 375 Seosuk-dong, Gwangju 61452, Korea
- Department of Pharmacology, School of Medicine, Chosun University, 375 Seosuk-dong, Gwangju 61452, Korea
| | - Jung-Hee Lee
- Laboratory of Genomic Instability and Cancer Therapeutics, Cancer Mutation Research Center, School of Medicine, Chosun University, 375 Seosuk-dong, Gwangju 61452, Korea
- Department of Cellular and Molecular Medicine, School of Medicine, Chosun University, 375 Seosuk-dong, Gwangju 61452, Korea
| |
Collapse
|
11
|
Nickoloff JA. Targeting Replication Stress Response Pathways to Enhance Genotoxic Chemo- and Radiotherapy. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27154736. [PMID: 35897913 PMCID: PMC9330692 DOI: 10.3390/molecules27154736] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 12/12/2022]
Abstract
Proliferating cells regularly experience replication stress caused by spontaneous DNA damage that results from endogenous reactive oxygen species (ROS), DNA sequences that can assume secondary and tertiary structures, and collisions between opposing transcription and replication machineries. Cancer cells face additional replication stress, including oncogenic stress that results from the dysregulation of fork progression and origin firing, and from DNA damage induced by radiotherapy and most cancer chemotherapeutic agents. Cells respond to such stress by activating a complex network of sensor, signaling and effector pathways that protect genome integrity. These responses include slowing or stopping active replication forks, protecting stalled replication forks from collapse, preventing late origin replication firing, stimulating DNA repair pathways that promote the repair and restart of stalled or collapsed replication forks, and activating dormant origins to rescue adjacent stressed forks. Currently, most cancer patients are treated with genotoxic chemotherapeutics and/or ionizing radiation, and cancer cells can gain resistance to the resulting replication stress by activating pro-survival replication stress pathways. Thus, there has been substantial effort to develop small molecule inhibitors of key replication stress proteins to enhance tumor cell killing by these agents. Replication stress targets include ATR, the master kinase that regulates both normal replication and replication stress responses; the downstream signaling kinase Chk1; nucleases that process stressed replication forks (MUS81, EEPD1, Metnase); the homologous recombination catalyst RAD51; and other factors including ATM, DNA-PKcs, and PARP1. This review provides an overview of replication stress response pathways and discusses recent pre-clinical studies and clinical trials aimed at improving cancer therapy by targeting replication stress response factors.
Collapse
Affiliation(s)
- Jac A Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA
| |
Collapse
|
12
|
Lin YT, Takeuchi T, Youk B, Umen J, Sears BB, Benning C. Chlamydomonas CHT7 is involved in repressing DNA replication and mitotic genes during synchronous growth. G3 GENES|GENOMES|GENETICS 2022; 12:6523978. [PMID: 35137070 PMCID: PMC8895990 DOI: 10.1093/g3journal/jkac023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022]
Abstract
In the green alga Chlamydomonas reinhardtii, regulation of the cell cycle in response to external cues is critical for survival in a changing environment. The loss of the nuclear COMPROMISED HYDROLYSIS OF TRIACYLGLYCEROLS 7 (CHT7) protein affects the expression of many genes especially in response to nitrogen availability. Cells lacking CHT7 exhibit abnormal cell morphology following nitrogen deprivation and fail to resume normal cell division after N resupply. To investigate the function of CHT7 in the regulation of cell cycle-related pathways, cells were synchronized, and RNA-seq analysis was performed during various stages of the cell cycle. In the cht7 mutant following nitrogen deprivation, the cells were not dividing, but a subset of cell cycle genes involved in DNA replication and mitosis were found to be derepressed, suggesting that the CHT7 protein plays a role in cell cycle regulation that is opposite to that of the mitotic cyclin-dependent kinases. Furthermore, genes for cell wall synthesis and remodeling were found to be abnormally induced in nondividing cht7 cells; this misregulation may deplete cellular resources and thus contribute to cell death following nitrogen deprivation. Lastly, 43 minimally characterized kinases were found to be highly misregulated in cht7. Further analysis suggested that some of these CHT7-regulated kinases may be related to the MAP3K and Aurora-like kinases, while others are unique. Together, these results suggest a role of CHT7 in transcriptional regulation of the cell cycle and reveal several pathways and genes whose expression appears to be subject to a CHT7-mediated regulatory network.
Collapse
Affiliation(s)
- Yang-Tsung Lin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Tomomi Takeuchi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Brian Youk
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - James Umen
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Barbara B Sears
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
13
|
Zhang C, Zhou B, Gu F, Liu H, Wu H, Yao F, Zheng H, Fu H, Chong W, Cai S, Huang M, Ma X, Guo Z, Li T, Deng W, Zheng M, Ji Q, Zhao Y, Ma Y, Wang QE, Tang TS, Guo C. Micropeptide PACMP inhibition elicits synthetic lethal effects by decreasing CtIP and poly(ADP-ribosyl)ation. Mol Cell 2022; 82:1297-1312.e8. [DOI: 10.1016/j.molcel.2022.01.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 11/19/2021] [Accepted: 01/24/2022] [Indexed: 12/19/2022]
|
14
|
Hausmann M, Hildenbrand G, Pilarczyk G. Networks and Islands of Genome Nano-architecture and Their Potential Relevance for Radiation Biology : (A Hypothesis and Experimental Verification Hints). Results Probl Cell Differ 2022; 70:3-34. [PMID: 36348103 DOI: 10.1007/978-3-031-06573-6_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The cell nucleus is a complex biological system in which simultaneous reactions and functions take place to keep the cell as an individualized, specialized system running well. The cell nucleus contains chromatin packed in various degrees of density and separated in volumes of chromosome territories and subchromosomal domains. Between the chromatin, however, there is enough "free" space for floating RNA, proteins, enzymes, ATPs, ions, water molecules, etc. which are trafficking by super- and supra-diffusion to the interaction points where they are required. It seems that this trafficking works somehow automatically and drives the system perfectly. After exposure to ionizing radiation causing DNA damage from single base damage up to chromatin double-strand breaks, the whole system "cell nucleus" responds, and repair processes are starting to recover the fully functional and intact system. In molecular biology, many individual epigenetic pathways of DNA damage response or repair of single and double-strand breaks are described. How these responses are embedded into the response of the system as a whole is often out of the focus of consideration. In this article, we want to follow the hypothesis of chromatin architecture's impact on epigenetic pathways and vice versa. Based on the assumption that chromatin acts like an "aperiodic solid state within a limited volume," functionally determined networks and local topologies ("islands") can be defined that drive the appropriate repair process at a given damage site. Experimental results of investigations of the chromatin nano-architecture and DNA repair clusters obtained by means of single-molecule localization microscopy offer hints and perspectives that may contribute to verifying the hypothesis.
Collapse
Affiliation(s)
- Michael Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, Heidelberg, Germany.
| | - Georg Hildenbrand
- Kirchhoff-Institute for Physics, Heidelberg University, Heidelberg, Germany
| | - Götz Pilarczyk
- Kirchhoff-Institute for Physics, Heidelberg University, Heidelberg, Germany
| |
Collapse
|
15
|
Iliaki S, Beyaert R, Afonina IS. Polo-like kinase 1 (PLK1) signaling in cancer and beyond. Biochem Pharmacol 2021; 193:114747. [PMID: 34454931 DOI: 10.1016/j.bcp.2021.114747] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023]
Abstract
PLK1 is an evolutionary conserved Ser/Thr kinase that is best known for its role in cell cycle regulation and is expressed predominantly during the G2/S and M phase of the cell cycle. PLK1-mediated phosphorylation of specific substrates controls cell entry into mitosis, centrosome maturation, spindle assembly, sister chromatid cohesion and cytokinesis. In addition, a growing body of evidence describes additional roles of PLK1 beyond the cell cycle, more specifically in the DNA damage response, autophagy, apoptosis and cytokine signaling. PLK1 has an indisputable role in cancer as it controls several key transcription factors and promotes cell proliferation, transformation and epithelial-to-mesenchymal transition. Furthermore, deregulation of PLK1 results in chromosome instability and aneuploidy. PLK1 is overexpressed in many cancers, which is associated with poor prognosis, making PLK1 an attractive target for cancer treatment. Additionally, PLK1 is involved in immune and neurological disorders including Graft versus Host Disease, Huntington's disease and Alzheimer's disease. Unfortunately, newly developed small compound PLK1 inhibitors have only had limited success so far, due to low therapeutic response rates and toxicity. In this review we will highlight the current knowledge about the established roles of PLK1 in mitosis regulation and beyond. In addition, we will discuss its tumor promoting but also tumor suppressing capacities, as well as the available PLK1 inhibitors, elaborating on their efficacy and limitations.
Collapse
Affiliation(s)
- Styliani Iliaki
- Center for Inflammation Research, Unit of Molecular Signal Transduction in Inflammation, VIB, B-9052 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
| | - Rudi Beyaert
- Center for Inflammation Research, Unit of Molecular Signal Transduction in Inflammation, VIB, B-9052 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium.
| | - Inna S Afonina
- Center for Inflammation Research, Unit of Molecular Signal Transduction in Inflammation, VIB, B-9052 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
| |
Collapse
|
16
|
Sanchez A, Lee D, Kim DI, Miller KM. Making Connections: Integrative Signaling Mechanisms Coordinate DNA Break Repair in Chromatin. Front Genet 2021; 12:747734. [PMID: 34659365 PMCID: PMC8514019 DOI: 10.3389/fgene.2021.747734] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/31/2021] [Indexed: 01/25/2023] Open
Abstract
DNA double-strand breaks (DSBs) are hazardous to genome integrity and can promote mutations and disease if not handled correctly. Cells respond to these dangers by engaging DNA damage response (DDR) pathways that are able to identify DNA breaks within chromatin leading ultimately to their repair. The recognition and repair of DSBs by the DDR is largely dependent on the ability of DNA damage sensing factors to bind to and interact with nucleic acids, nucleosomes and their modified forms to target these activities to the break site. These contacts orientate and localize factors to lesions within chromatin, allowing signaling and faithful repair of the break to occur. Coordinating these events requires the integration of several signaling and binding events. Studies are revealing an enormously complex array of interactions that contribute to DNA lesion recognition and repair including binding events on DNA, as well as RNA, RNA:DNA hybrids, nucleosomes, histone and non-histone protein post-translational modifications and protein-protein interactions. Here we examine several DDR pathways that highlight and provide prime examples of these emerging concepts. A combination of approaches including genetic, cellular, and structural biology have begun to reveal new insights into the molecular interactions that govern the DDR within chromatin. While many questions remain, a clearer picture has started to emerge for how DNA-templated processes including transcription, replication and DSB repair are coordinated. Multivalent interactions with several biomolecules serve as key signals to recruit and orientate proteins at DNA lesions, which is essential to integrate signaling events and coordinate the DDR within the milieu of the nucleus where competing genome functions take place. Genome architecture, chromatin structure and phase separation have emerged as additional vital regulatory mechanisms that also influence genome integrity pathways including DSB repair. Collectively, recent advancements in the field have not only provided a deeper understanding of these fundamental processes that maintain genome integrity and cellular homeostasis but have also started to identify new strategies to target deficiencies in these pathways that are prevalent in human diseases including cancer.
Collapse
Affiliation(s)
- Anthony Sanchez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Doohyung Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Dae In Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States.,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
| |
Collapse
|
17
|
Tessier TM, Dodge MJ, MacNeil KM, Evans AM, Prusinkiewicz MA, Mymryk JS. Almost famous: Human adenoviruses (and what they have taught us about cancer). Tumour Virus Res 2021; 12:200225. [PMID: 34500123 PMCID: PMC8449131 DOI: 10.1016/j.tvr.2021.200225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/25/2021] [Accepted: 09/03/2021] [Indexed: 12/11/2022] Open
Abstract
Papillomaviruses, polyomaviruses and adenoviruses are collectively categorized as the small DNA tumour viruses. Notably, human adenoviruses were the first human viruses demonstrated to be able to cause cancer, albeit in non-human animal models. Despite their long history, no human adenovirus is a known causative agent of human cancers, unlike a subset of their more famous cousins, including human papillomaviruses and human Merkel cell polyomavirus. Nevertheless, seminal research using human adenoviruses has been highly informative in understanding the basics of cell cycle control, gene expression, apoptosis and cell differentiation. This review highlights the contributions of human adenovirus research in advancing our knowledge of the molecular basis of cancer.
Collapse
Affiliation(s)
- Tanner M Tessier
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Mackenzie J Dodge
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Katelyn M MacNeil
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Andris M Evans
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Martin A Prusinkiewicz
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Joe S Mymryk
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada; Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON, Canada; Department of Oncology, The University of Western Ontario, London, ON, Canada; London Regional Cancer Program, Lawson Health Research Institute, London, ON, Canada.
| |
Collapse
|
18
|
Nickoloff JA, Sharma N, Allen CP, Taylor L, Allen SJ, Jaiswal AS, Hromas R. Roles of homologous recombination in response to ionizing radiation-induced DNA damage. Int J Radiat Biol 2021; 99:903-914. [PMID: 34283012 PMCID: PMC9629169 DOI: 10.1080/09553002.2021.1956001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/04/2021] [Accepted: 07/05/2021] [Indexed: 02/06/2023]
Abstract
PURPOSE Ionizing radiation induces a vast array of DNA lesions including base damage, and single- and double-strand breaks (SSB, DSB). DSBs are among the most cytotoxic lesions, and mis-repair causes small- and large-scale genome alterations that can contribute to carcinogenesis. Indeed, ionizing radiation is a 'complete' carcinogen. DSBs arise immediately after irradiation, termed 'frank DSBs,' as well as several hours later in a replication-dependent manner, termed 'secondary' or 'replication-dependent DSBs. DSBs resulting from replication fork collapse are single-ended and thus pose a distinct problem from two-ended, frank DSBs. DSBs are repaired by error-prone nonhomologous end-joining (NHEJ), or generally error-free homologous recombination (HR), each with sub-pathways. Clarifying how these pathways operate in normal and tumor cells is critical to increasing tumor control and minimizing side effects during radiotherapy. CONCLUSIONS The choice between NHEJ and HR is regulated during the cell cycle and by other factors. DSB repair pathways are major contributors to cell survival after ionizing radiation, including tumor-resistance to radiotherapy. Several nucleases are important for HR-mediated repair of replication-dependent DSBs and thus replication fork restart. These include three structure-specific nucleases, the 3' MUS81 nuclease, and two 5' nucleases, EEPD1 and Metnase, as well as three end-resection nucleases, MRE11, EXO1, and DNA2. The three structure-specific nucleases evolved at very different times, suggesting incremental acceleration of replication fork restart to limit toxic HR intermediates and genome instability as genomes increased in size during evolution, including the gain of large numbers of HR-prone repetitive elements. Ionizing radiation also induces delayed effects, observed days to weeks after exposure, including delayed cell death and delayed HR. In this review we highlight the roles of HR in cellular responses to ionizing radiation, and discuss the importance of HR as an exploitable target for cancer radiotherapy.
Collapse
Affiliation(s)
- Jac A. Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Neelam Sharma
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Christopher P. Allen
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
- Department of Microbiology, Immunology and Pathology, Flow Cytometry and Cell Sorting Facility, Colorado State University, Fort Collins, CO, USA
| | - Lynn Taylor
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Sage J. Allen
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Aruna S. Jaiswal
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
| | - Robert Hromas
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
| |
Collapse
|
19
|
Fijen C, Rothenberg E. The evolving complexity of DNA damage foci: RNA, condensates and chromatin in DNA double-strand break repair. DNA Repair (Amst) 2021; 105:103170. [PMID: 34256335 DOI: 10.1016/j.dnarep.2021.103170] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 06/08/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023]
Abstract
Formation of biomolecular condensates is increasingly recognized as a mechanism employed by cells to deal with stress and to optimize enzymatic reactions. Recent studies have characterized several DNA repair foci as phase-separated condensates, behaving like liquid droplets. Concomitantly, the apparent importance of long non-coding RNAs and RNA-binding proteins for the repair of double-strand breaks has raised many questions about their exact contribution to the repair process. Here we discuss how RNA molecules can participate in condensate formation and how RNA-binding proteins can act as molecular scaffolds. We furthermore summarize our current knowledge about how properties of condensates can influence the choice of repair pathway (homologous recombination or non-homologous end joining) and identify the open questions in this field of emerging importance.
Collapse
Affiliation(s)
- Carel Fijen
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, USA.
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, USA.
| |
Collapse
|
20
|
Morton CR, Rzechorzek NJ, Maman JD, Kuramochi M, Sekiguchi H, Rambo R, Sasaki YC, Davies OR, Pellegrini L. Structural basis for the coiled-coil architecture of human CtIP. Open Biol 2021; 11:210060. [PMID: 34129781 PMCID: PMC8205527 DOI: 10.1098/rsob.210060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The DNA repair factor CtIP has a critical function in double-strand break (DSB) repair by homologous recombination, promoting the assembly of the repair apparatus at DNA ends and participating in DNA-end resection. However, the molecular mechanisms of CtIP function in DSB repair remain unclear. Here, we present an atomic model for the three-dimensional architecture of human CtIP, derived from a multi-disciplinary approach that includes X-ray crystallography, small-angle X-ray scattering (SAXS) and diffracted X-ray tracking (DXT). Our data show that CtIP adopts an extended dimer-of-dimers structure, in agreement with a role in bridging distant sites on chromosomal DNA during the recombinational repair. The zinc-binding motif in the CtIP N-terminus alters dynamically the coiled-coil structure, with functional implications for the long-range interactions of CtIP with DNA. Our results provide a structural basis for the three-dimensional arrangement of chains in the CtIP tetramer, a key aspect of CtIP function in DNA DSB repair.
Collapse
Affiliation(s)
- C R Morton
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - N J Rzechorzek
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - J D Maman
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - M Kuramochi
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.,AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Kashiwa, Japan
| | - H Sekiguchi
- Centre for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - R Rambo
- Diamond Light Source, Didcot, Oxfordshire OX11 0DE, UK
| | - Y C Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.,AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Kashiwa, Japan.,Centre for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - O R Davies
- Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - L Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| |
Collapse
|
21
|
Mendez-Dorantes C, Tsai LJ, Jahanshir E, Lopezcolorado FW, Stark JM. BLM has Contrary Effects on Repeat-Mediated Deletions, based on the Distance of DNA DSBs to a Repeat and Repeat Divergence. Cell Rep 2021; 30:1342-1357.e4. [PMID: 32023454 PMCID: PMC7085117 DOI: 10.1016/j.celrep.2020.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/08/2019] [Accepted: 12/31/2019] [Indexed: 12/30/2022] Open
Abstract
Repeat-mediated deletions (RMDs) often involve repetitive elements (e.g., short interspersed elements) with sequence divergence that is separated by several kilobase pairs (kbps). We have examined RMDs induced by DNA double-strand breaks (DSBs) under varying conditions of repeat sequence divergence (identical versus 1% and 3% divergent) and DSB/repeat distance (16 bp–28.4 kbp). We find that the BLM helicase promotes RMDs with long DSB/repeat distances (e.g., 28.4 kbp), which is consistent with a role in extensive DSB end resection, because the resection nucleases EXO1 and DNA2 affect RMDs similarly to BLM. In contrast, BLM suppresses RMDs with sequence divergence and intermediate (e.g., 3.3 kbp) DSB/repeat distances, which supports a role in heteroduplex rejection. The role of BLM in heteroduplex rejection is not epistatic with MSH2 and is independent of the annealing factor RAD52. Accordingly, the role of BLM on RMDs is substantially affected by DSB/repeat distance and repeat sequence divergence. Mendez-Dorantes et al. identify the BLM helicase as a key regulator of repeat-mediated deletions (RMDs). BLM, EXO1, and DNA2 mediate RMDs with remarkably long DNA break/repeat distances. BLM suppresses RMDs with sequence divergence that is optimal with a long non-homologous tail and is independent of MSH2 and RAD52.
Collapse
Affiliation(s)
- Carlos Mendez-Dorantes
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - L Jillianne Tsai
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Eva Jahanshir
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | | | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA.
| |
Collapse
|
22
|
Rivero S, Rodríguez-Real G, Marín I, Huertas P. MRGBP, a member of the NuA4 complex, inhibits DNA double-strand break repair. FEBS Open Bio 2021; 11:622-632. [PMID: 33354938 PMCID: PMC7931222 DOI: 10.1002/2211-5463.13071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/20/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022] Open
Abstract
The repair of DNA breaks takes place in the context of chromatin and thus involves the activity of chromatin remodelers. The nucleosome acetyltransferase of H4 (NuA4) remodeler complex enables DNA break repair by relaxing flanking chromatin. Here, we show that MRG domain binding protein (MRGBP), a member of this complex, acts as a general inhibitor of DNA double‐strand break repair. Upon its downregulation, repair is generally increased. This is particularly evident for the stimulation of early events of homologous recombination. Thus, MRGBP has an opposing role to the main catalytic subunits of the NuA4 complex. Our data suggest that MRGBP acts by limiting the activity of this complex in DNA repair, specifically by narrowing the extent of DNA‐end resection.
Collapse
Affiliation(s)
- Sabrina Rivero
- Department of Normal and Pathological Histology and Cytology, University of Seville School of Medicine, Spain.,Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Spain
| | - Guillermo Rodríguez-Real
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Spain.,Department of Genetics, University of Seville, Spain
| | - Inés Marín
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Spain
| | - Pablo Huertas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Spain.,Department of Genetics, University of Seville, Spain
| |
Collapse
|
23
|
Prados-Carvajal R, Rodriguez-Real G, Gutierrez-Pozo G, Huertas P. CtIP -mediated alternative mRNA splicing finetunes the DNA damage response. RNA (NEW YORK, N.Y.) 2020; 27:rna.078519.120. [PMID: 33298529 PMCID: PMC7901839 DOI: 10.1261/rna.078519.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
In order to survive to the exposure of DNA damaging agents, cells activate a complex response that coordinates the cellular metabolism, cell cycle progression and DNA repair. Among many other events, recent evidence has described global changes in mRNA splicing in cells treated with genotoxic agents. Here, we explore further this DNA damage-dependent alternative splicing. Indeed, we show that both the splicing factor SF3B2 and the repair protein CtIP contribute to the global pattern of splicing both in cells treated or not to DNA damaging agents. Additionally, we focus on a specific DNA damage- and CtIP-dependent alternative splicing event of the helicase PIF1 and explore its relevance for the survival of cells upon exposure to ionizing radiation. Indeed, we described how the nuclear, active form of PIF1 is substituted by a splicing variant, named vPIF1, in a fashion that requires both the presence of DNA damage and CtIP. Interestingly, timely expression of vPIF1 is required for optimal survival to exposure to DNA damaging agents, but early expression of this isoform delays early events of the DNA damage response. On the contrary, expression of the full length PIF1 facilitates those early events, but increases the sensitivity to DNA damaging agents if the expression is maintained long-term.
Collapse
|
24
|
Carballar R, Martínez-Láinez JM, Samper B, Bru S, Bállega E, Mirallas O, Ricco N, Clotet J, Jiménez J. CDK-mediated Yku80 Phosphorylation Regulates the Balance Between Non-homologous End Joining (NHEJ) and Homologous Directed Recombination (HDR). J Mol Biol 2020; 432:166715. [PMID: 33217428 DOI: 10.1016/j.jmb.2020.11.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 11/04/2020] [Accepted: 11/11/2020] [Indexed: 11/28/2022]
Abstract
There are two major pathways for repairing DNA double-strand breaks (DSBs): homologous directed recombination (HDR) and non-homologous end-joining (NHEJ). While NHEJ functions throughout the cell cycle, HDR is only possible during S/G2 phases, suggesting that there are cell cycle-specific mechanisms regulating the balance between the two repair systems. The regulation exerted by CDKs on HDR has been extensively demonstrated, and here we present evidence that the CDK Pho85, in association with the G1 cyclin Pcl1, phosphorylates Yku80 on Ser 623 to regulate NHEJ activity. Cells bearing a non-phosphorylatable version of Yku80 show increased NHEJ and reduced HDR activity. Accordingly, yku80S623A cells present diminished viability upon treatment with the DSB-producer bleomycin, specifically in the G2 phase of the cell cycle. Interestingly, the mutation of the equivalent residue in human Ku80 increases sensitivity to bleomycin in several cancer cell lines, suggesting that this mechanism is conserved in humans. Altogether, our results reveal a new mechanism whereby G1-CDKs mediate the choice between HDR and NHEJ repair pathways, putting the error prone NHEJ on a leash and enabling error free HDR in G2 when homologous sequences are available.
Collapse
Affiliation(s)
- Reyes Carballar
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Joan M Martínez-Láinez
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Bàrbara Samper
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Samuel Bru
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Elisabet Bállega
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Oriol Mirallas
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Natalia Ricco
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Josep Clotet
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain.
| | - Javier Jiménez
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain.
| |
Collapse
|
25
|
de Vries G, Rosas-Plaza X, Meersma GJ, Leeuwenburgh VC, Kok K, Suurmeijer AJH, van Vugt MATM, Gietema JA, de Jong S. Establishment and characterisation of testicular cancer patient-derived xenograft models for preclinical evaluation of novel therapeutic strategies. Sci Rep 2020; 10:18938. [PMID: 33144587 PMCID: PMC7641131 DOI: 10.1038/s41598-020-75518-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/03/2020] [Indexed: 12/11/2022] Open
Abstract
Testicular cancer (TC) is the most common solid tumour in young men. While cisplatin-based chemotherapy is highly effective in TC patients, chemoresistance still accounts for 10% of disease-related deaths. Pre-clinical models that faithfully reflect patient tumours are needed to assist in target discovery and drug development. Tumour pieces from eight TC patients were subcutaneously implanted in NOD scid gamma (NSG) mice. Three patient-derived xenograft (PDX) models of TC, including one chemoresistant model, were established containing yolk sac tumour and teratoma components. PDX models and corresponding patient tumours were characterised by H&E, Ki-67 and cyclophilin A immunohistochemistry, showing retention of histological subtypes over several passages. Whole-exome sequencing, copy number variation analysis and RNA-sequencing was performed on these TP53 wild type PDX tumours to assess the effects of passaging, showing high concordance of molecular features between passages. Cisplatin sensitivity of PDX models corresponded with patients' response to cisplatin-based chemotherapy. MDM2 and mTORC1/2 targeted drugs showed efficacy in the cisplatin sensitive PDX models. In conclusion, we describe three PDX models faithfully reflecting chemosensitivity of TC patients. These models can be used for mechanistic studies and pre-clinical validation of novel therapeutic strategies in testicular cancer.
Collapse
Affiliation(s)
- Gerda de Vries
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Ximena Rosas-Plaza
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Gert Jan Meersma
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Vincent C Leeuwenburgh
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Klaas Kok
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Albert J H Suurmeijer
- Department of Pathology, Cancer Research Center Groningen, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Jourik A Gietema
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Steven de Jong
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.
| |
Collapse
|
26
|
Abstract
Prostate cancer (PCa) is a clinically heterogeneous disease and has poor patient outcome when tumours progress to castration-resistant and metastatic states. Understanding the mechanistic basis for transition to late stage aggressive disease is vital for both assigning patient risk status in the localised setting and also identifying novel treatment strategies to prevent progression. Subregions of intratumoral hypoxia are found in all solid tumours and are associated with many biologic drivers of tumour progression. Crucially, more recent findings show the co-presence of hypoxia and genomic instability can confer a uniquely adverse prognosis in localised PCa patients. In-depth informatic and functional studies suggests a role for hypoxia in co-operating with oncogenic drivers (e.g. loss of PTEN) and suppressing DNA repair capacity to alter clonal evolution due to an aggressive mutator phenotype. More specifically, hypoxic suppression of homologous recombination represents a “contextual lethal“ vulnerability in hypoxic prostate tumours which could extend the application of existing DNA repair targeting agents such as poly-ADP ribose polymerase inhibitors. Further investigation is now required to assess this relationship on the background of existing genomic alterations relevant to PCa, and also characterise the role of hypoxia in driving early metastatic spread. On this basis, PCa patients with hypoxic tumours can be better stratified into risk categories and treated with appropriate therapies to prevent progression.
Collapse
Affiliation(s)
- Jack Ashton
- Translational Oncogenomics, CRUK Manchester Institute and CRUK Manchester Centre, Manchester, United Kingdom
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Robert Bristow
- Translational Oncogenomics, CRUK Manchester Institute and CRUK Manchester Centre, Manchester, United Kingdom
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Christie NHS Foundation Trust, Manchester, UK
| |
Collapse
|
27
|
Mozaffari NL, Pagliarulo F, Sartori AA. Human CtIP: A 'double agent' in DNA repair and tumorigenesis. Semin Cell Dev Biol 2020; 113:47-56. [PMID: 32950401 DOI: 10.1016/j.semcdb.2020.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/20/2020] [Accepted: 09/02/2020] [Indexed: 12/14/2022]
Abstract
Human CtIP was originally identified as an interactor of the retinoblastoma protein and BRCA1, two bona fide tumour suppressors frequently mutated in cancer. CtIP is renowned for its role in the resection of DNA double-strand breaks (DSBs) during homologous recombination, a largely error-free DNA repair pathway crucial in maintaining genome integrity. However, CtIP-dependent DNA end resection is equally accountable for alternative end-joining, a mutagenic DSB repair mechanism implicated in oncogenic chromosomal translocations. In addition, CtIP contributes to transcriptional regulation of G1/S transition, DNA damage checkpoint signalling, and replication fork protection pathways. In this review, we present a perspective on the current state of knowledge regarding the tumour-suppressive and oncogenic properties of CtIP and provide an overview of their relevance for cancer development, progression, and therapy.
Collapse
Affiliation(s)
- Nour L Mozaffari
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Fabio Pagliarulo
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
| |
Collapse
|
28
|
XRN2 Links RNA:DNA Hybrid Resolution to Double Strand Break Repair Pathway Choice. Cancers (Basel) 2020; 12:cancers12071821. [PMID: 32645903 PMCID: PMC7408924 DOI: 10.3390/cancers12071821] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/02/2020] [Accepted: 07/02/2020] [Indexed: 12/17/2022] Open
Abstract
It was recently shown that the 5’ to 3’ exoribonuclease XRN2 is involved in the DNA damage response. Importantly, loss of XRN2 abrogates DNA double stranded break repair via the non-homologous end-joining pathway. However, the mechanistic details of how XRN2 functions in the non-homologous end-joining repair process are unknown. In this study, we elucidated that XRN2-mediated RNA:DNA hybrid resolution is required to allow Ku70 binding to DNA ends. These data suggest that XRN2 is required for the initiation of non-homologous end-joining repair. Interestingly, we uncovered a role for XRN2 in the homologous recombination repair pathway. Loss of XRN2 lead to a decrease in the repair of double strand breaks by homologous recombination. Strikingly, when we removed RNA:DNA hybrids by RNaseH1 over-expression, homologous recombination was not restored. We found RNA:DNA hybrid formation at and downstream of the DSB site, suggesting that unregulated transcription inhibits homologous recombination repair. In summary, our results indicate a relation between RNA:DNA hybrid resolution and double strand break repair pathway choice.
Collapse
|
29
|
Checa-Rodríguez C, Cepeda-García C, Ramón J, López-Saavedra A, Balestra FR, Domínguez-Sánchez MS, Gómez-Cabello D, Huertas P. Methylation of the central transcriptional regulator KLF4 by PRMT5 is required for DNA end resection and recombination. DNA Repair (Amst) 2020; 94:102902. [PMID: 32623319 DOI: 10.1016/j.dnarep.2020.102902] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 06/04/2020] [Accepted: 06/08/2020] [Indexed: 01/12/2023]
Abstract
Cell fitness and survival upon exposure to DNA damage depends on the repair of DNA lesions. Interestingly, cellular identity does affect and finetunes such response, although the molecular basis of such differences between tissues and cell types is not well understood. Thus, a possibility is that DNA repair itself is controlled by the mechanisms that govern cell identity. Here we show that the KLF4, involved in cellular homeostasis, proliferation, cell reprogramming and cancer development, directly regulates resection and homologous recombination proficiency. Indeed, resection efficiency follows KLF4 protein levels, i.e. decreases upon KLF4 downregulation and increases when is overexpressed. Moreover, KLF4 role in resection requires its methylation by the methyl-transferase PRMT5. Thus, PRMT5 depletion not only mimics KLF4 downregulation, but also showed an epistatic genetic relationship. Our data support a model in which the methylation of KLF4 by PRMT5 is a priming event required to license DNA resection and homologous recombination.
Collapse
Affiliation(s)
- Cintia Checa-Rodríguez
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain; Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Cristina Cepeda-García
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Javier Ramón
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain; Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Ana López-Saavedra
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain; Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Fernando R Balestra
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain; Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - María S Domínguez-Sánchez
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Daniel Gómez-Cabello
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Pablo Huertas
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain; Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain.
| |
Collapse
|
30
|
Cleary JM, Aguirre AJ, Shapiro GI, D'Andrea AD. Biomarker-Guided Development of DNA Repair Inhibitors. Mol Cell 2020; 78:1070-1085. [PMID: 32459988 PMCID: PMC7316088 DOI: 10.1016/j.molcel.2020.04.035] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/02/2020] [Accepted: 04/28/2020] [Indexed: 02/06/2023]
Abstract
Anti-cancer drugs targeting the DNA damage response (DDR) exploit genetic or functional defects in this pathway through synthetic lethal mechanisms. For example, defects in homologous recombination (HR) repair arise in cancer cells through inherited or acquired mutations in BRCA1, BRCA2, or other genes in the Fanconi anemia/BRCA pathway, and these tumors have been shown to be particularly sensitive to inhibitors of the base excision repair (BER) protein poly (ADP-ribose) polymerase (PARP). Recent work has identified additional genomic and functional assays of DNA repair that provide new predictive and pharmacodynamic biomarkers for these targeted therapies. Here, we examine the development of selective agents targeting DNA repair, including PARP inhibitors; inhibitors of the DNA damage kinases ataxia-telangiectasia and Rad3 related (ATR), CHK1, WEE1, and ataxia-telangiectasia mutated (ATM); and inhibitors of classical non-homologous end joining (cNHEJ) and alternative end joining (Alt EJ). We also review the biomarkers that guide the use of these agents and current clinical trials with these therapies.
Collapse
Affiliation(s)
- James M Cleary
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Andrew J Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Geoffrey I Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alan D D'Andrea
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| |
Collapse
|
31
|
Mejías-Navarro F, Rodríguez-Real G, Ramón J, Camarillo R, Huertas P. ALC1/eIF4A1-mediated regulation of CtIP mRNA stability controls DNA end resection. PLoS Genet 2020; 16:e1008787. [PMID: 32392243 PMCID: PMC7241833 DOI: 10.1371/journal.pgen.1008787] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 05/21/2020] [Accepted: 04/22/2020] [Indexed: 11/18/2022] Open
Abstract
During repair of DNA double-strand breaks, resection of DNA ends influences how these lesions will be repaired. If resection is activated, the break will be channeled through homologous recombination; if not, it will be simply ligated using the non-homologous end-joining machinery. Regulation of resection relies greatly on modulating CtIP, which can be done by modifying: i) its interaction partners, ii) its post-translational modifications, or iii) its cellular levels, by regulating transcription, splicing and/or protein stability/degradation. Here, we have analyzed the role of ALC1, a chromatin remodeler previously described as an integral part of the DNA damage response, in resection. Strikingly, we found that ALC1 affects resection independently of chromatin remodeling activity or its ability to bind damaged chromatin. In fact, it cooperates with the RNA-helicase eIF4A1 to help stabilize the most abundant splicing form of CtIP mRNA. This function relies on the presence of a specific RNA sequence in the 5' UTR of CtIP. Therefore, we describe an additional layer of regulation of CtIP-at the level of mRNA stability through ALC1 and eIF4A1.
Collapse
Affiliation(s)
- Fernando Mejías-Navarro
- Department of Genetics, University of Seville, Sevilla, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - Guillermo Rodríguez-Real
- Department of Genetics, University of Seville, Sevilla, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - Javier Ramón
- Department of Genetics, University of Seville, Sevilla, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - Rosa Camarillo
- Department of Genetics, University of Seville, Sevilla, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - Pablo Huertas
- Department of Genetics, University of Seville, Sevilla, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
- * E-mail:
| |
Collapse
|
32
|
Palmer N, Kaldis P. Less-well known functions of cyclin/CDK complexes. Semin Cell Dev Biol 2020; 107:54-62. [PMID: 32386818 DOI: 10.1016/j.semcdb.2020.04.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 12/31/2022]
Abstract
Cyclin-dependent kinases (CDKs) are activated by cyclins, which play important roles in dictating the actions of CDK/cyclin complexes. Cyclin binding influences the substrate specificity of these complexes in addition to their susceptibility to inhibition or degradation. CDK/cyclin complexes are best known to promote cell cycle progression in the mitotic cell cycle but are also crucial for important cellular processes not strictly associated with cellular division. This chapter primarily explores the understudied topic of CDK/cyclin complex functionality during the DNA damage response. We detail how CDK/cyclin complexes perform dual roles both as targets of DNA damage checkpoint signaling as well as effectors of DNA repair. Additionally, we discuss the potential CDK-independent roles of cyclins in these processes and the impact of such roles in human diseases such as cancer. Our goal is to place the spotlight on these important functions of cyclins either acting as independent entities or within CDK/cyclin complexes which have attracted less attention in the past. We consider that this will be important for a more complete understanding of the intricate functions of cell cycle proteins in the DNA damage response.
Collapse
Affiliation(s)
- Nathan Palmer
- Institute of Molecular and Cell Biology (IMCB), A⁎STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore; National University of Singapore (NUS), Department of Biochemistry, Singapore, 117597, Republic of Singapore
| | - Philipp Kaldis
- Institute of Molecular and Cell Biology (IMCB), A⁎STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore; National University of Singapore (NUS), Department of Biochemistry, Singapore, 117597, Republic of Singapore; Department of Clinical Sciences, Lund University, Clinical Research Centre (CRC), Box 50332, SE-202 13, Malmö, Sweden.
| |
Collapse
|
33
|
Mi Y, Dong H, Sun X, Ren F, Tang Y, Zheng P. The association of Helicobacter pylori CagA EPIYA motifs and vacA genotypes with homologous recombination repair markers during the gastric precancerous cascade. Int J Biol Markers 2020; 35:49-55. [PMID: 32286927 DOI: 10.1177/1724600820914935] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Helicobacter pylori-induced DNA damage and impaired homologous recombination repair are vital molecular mechanisms for gastric cancer, which mainly count on its virulence factors cytotoxic-associated gene A (CagA) and vacuolating cytotoxin A (VacA). However, the relationship between H. pylori CagA EPIYA motifs and vacA genotypes with DNA damage and homologous recombination repair markers is still not clear. METHODS H. pylori positive and negative gastric biopsies were taken from 165 subjects with different gastric precancerous pathologic stages, and DNA damage marker γH2AX and key homologous recombination repair proteins (CtIP and Rad51) were investigated for their association with H. pylori CagA EPIYA motifs and vacAs-, m-, i-, and d-region genotypes and histology (Sydney classification). RESULTS Out of 165 patients, 78 were identified as H. pylori-positive. CagA EPIYA motifs were identified as AB, ABC, and ABD in 2 (3.3%), 21 (35%), and 37 (61.7%) patients, respectively, while vacA alleles were identified as: s1, s2, m1, m2, i1, i2, d1, and d2 in 50 (89.3%), 6 (10.7%), 24 (42.9%), 32 (57.1%), 45 (80.4%), 11 (19.6%), 40 (71.4%), and 16 (28.6%) patients, respectively. vacAs1m1i1d1, s1m2i1d1, and s1m2i2d2 were the most prevailing genotypes. γH2AX was highly localized in H. pylori-positive tissues with corresponding CagA EPIYA motifs and vacA genotypes, while Rad51 and CtIP signals were weak. CONCLUSION H. pylori were positively correlated with the DNA damage marker in precancerous lesions, but were negatively correlated with the key homologous recombination repair proteins, which may be due to the specific CagA EPIYA motifs and vacA genotypes.
Collapse
Affiliation(s)
- Yang Mi
- Key Laboratory of Helicobacter pylori & Microbiota and GI cancer in Henan Province, Marshall Medical Research Center of Zhengzhou University, the 5th Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Haibin Dong
- Key Laboratory of Helicobacter pylori & Microbiota and GI cancer in Henan Province, Marshall Medical Research Center of Zhengzhou University, the 5th Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China.,Tshinghua Changgung Hospital, Tsinghua University, Beijing, P.R. China
| | - Xiangdong Sun
- Key Laboratory of Helicobacter pylori & Microbiota and GI cancer in Henan Province, Marshall Medical Research Center of Zhengzhou University, the 5th Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Feifei Ren
- Key Laboratory of Helicobacter pylori & Microbiota and GI cancer in Henan Province, Marshall Medical Research Center of Zhengzhou University, the 5th Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Youcai Tang
- Department of Pediatrics, the 5th Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Pengyuan Zheng
- Key Laboratory of Helicobacter pylori & Microbiota and GI cancer in Henan Province, Marshall Medical Research Center of Zhengzhou University, the 5th Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| |
Collapse
|
34
|
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: 15] [Impact Index Per Article: 3.8] [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.
Collapse
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:
| |
Collapse
|
35
|
The dichotomous effects of caffeine on homologous recombination in mammalian cells. DNA Repair (Amst) 2020; 88:102805. [PMID: 32062581 DOI: 10.1016/j.dnarep.2020.102805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 01/15/2020] [Accepted: 01/19/2020] [Indexed: 11/23/2022]
Abstract
This study was initiated to examine the effects of caffeine on the DNA damage response (DDR) and homologous recombination (HR) in mammalian cells. A 5 mM caffeine treatment caused the cell cycle to stall at G2/M and cells eventually underwent apoptosis. Caffeine exposure also induced a strong DDR along with subsequent activation of wildtype p53 protein. An unexpected observation was the caffeine-induced depletion of Rad51 (and Brca2) proteins. Consequently, caffeine-treated cells were expected to be inefficient in HR. However, a dichotomy in the HR response of cells to caffeine treatment was revealed. Caffeine treatment rendered cells significantly better at performing the nascent DNA synthesis that accompanies the early strand invasion steps of HR. Additionally, caffeine treatment increased chromatin accessibility and elevated the efficiency of illegitimate recombination. Conversely, the increase in nascent DNA synthesis did not translate into a higher number of gene targeting events. Thus, prolonged caffeine exposure stalls the cell cycle, induces a p53-mediated apoptotic response and a down-regulation of critical HR proteins, and for reasons discussed, stimulates early steps of HR, but not the formation of complete recombination products.
Collapse
|
36
|
Deshpande RA, Myler LR, Soniat MM, Makharashvili N, Lee L, Lees-Miller SP, Finkelstein IJ, Paull TT. DNA-dependent protein kinase promotes DNA end processing by MRN and CtIP. SCIENCE ADVANCES 2020; 6:eaay0922. [PMID: 31934630 PMCID: PMC6949041 DOI: 10.1126/sciadv.aay0922] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
The repair of DNA double-strand breaks occurs through nonhomologous end joining or homologous recombination in vertebrate cells-a choice that is thought to be decided by a competition between DNA-dependent protein kinase (DNA-PK) and the Mre11/Rad50/Nbs1 (MRN) complex but is not well understood. Using ensemble biochemistry and single-molecule approaches, here, we show that the MRN complex is dependent on DNA-PK and phosphorylated CtIP to perform efficient processing and resection of DNA ends in physiological conditions, thus eliminating the competition model. Endonucleolytic removal of DNA-PK-bound DNA ends is also observed at double-strand break sites in human cells. The involvement of DNA-PK in MRN-mediated end processing promotes an efficient and sequential transition from nonhomologous end joining to homologous recombination by facilitating DNA-PK removal.
Collapse
Affiliation(s)
- Rajashree A. Deshpande
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Logan R. Myler
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY 10065, USA
| | - Michael M. Soniat
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Nodar Makharashvili
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Linda Lee
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta T2N 1N4, Canada
| | - Susan P. Lees-Miller
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta T2N 1N4, Canada
| | - Ilya J. Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Tanya T. Paull
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
37
|
Jimeno S, Camarillo R, Mejías-Navarro F, Fernández-Ávila MJ, Soria-Bretones I, Prados-Carvajal R, Huertas P. The Helicase PIF1 Facilitates Resection over Sequences Prone to Forming G4 Structures. Cell Rep 2019; 24:3262-3273.e4. [PMID: 30232007 DOI: 10.1016/j.celrep.2018.08.047] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 07/16/2018] [Accepted: 08/16/2018] [Indexed: 10/28/2022] Open
Abstract
DNA breaks are complex lesions that can be repaired either by non-homologous end joining (NHEJ) or by homologous recombination (HR). The decision between these two routes of DNA repair is a key point of the DNA damage response (DDR) that is controlled by DNA resection. The core machinery catalyzing the resection process is well established. However, little is known about the additional requirements of DNA resection over DNA structures with high complexity. Here, we found evidence that the human helicase PIF1 has a role in DNA resection, specifically for defined DNA regions, such as those prone to form G-quadruplexes. Indeed, PIF1 is recruited to the site of DNA damage and physically interacts with proteins involved in DNA resection, and its depletion causes DNA damage sensitivity and a reduction of HR efficiency. Moreover, G4 stabilization by itself hampers DNA resection, a phenomenon suppressed by PIF1 overexpression.
Collapse
Affiliation(s)
- Sonia Jimeno
- Departamento de Genética, Universidad de Sevilla, Sevilla 41080, Spain; Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain.
| | - Rosa Camarillo
- Departamento de Genética, Universidad de Sevilla, Sevilla 41080, Spain; Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain
| | - Fernando Mejías-Navarro
- Departamento de Genética, Universidad de Sevilla, Sevilla 41080, Spain; Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain
| | - Maria Jesús Fernández-Ávila
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain
| | - Isabel Soria-Bretones
- Departamento de Genética, Universidad de Sevilla, Sevilla 41080, Spain; Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain
| | - Rosario Prados-Carvajal
- Departamento de Genética, Universidad de Sevilla, Sevilla 41080, Spain; Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain
| | - Pablo Huertas
- Departamento de Genética, Universidad de Sevilla, Sevilla 41080, Spain; Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain.
| |
Collapse
|
38
|
Abstract
The repair of DNA double-strand breaks occurs through a series of defined steps that are evolutionarily conserved and well-understood in most experimental organisms. However, it is becoming increasingly clear that repair does not occur in isolation from other DNA transactions. Transcription of DNA produces topological changes, RNA species, and RNA-dependent protein complexes that can dramatically influence the efficiency and outcomes of DNA double-strand break repair. The transcription-associated history of several double-strand break repair factors is reviewed here, with an emphasis on their roles in regulating R-loops and the emerging role of R-loops in coordination of repair events. Evidence for nucleolytic processing of R-loops is also discussed, as well as the molecular tools commonly used to measure RNA-DNA hybrids in cells.
Collapse
Affiliation(s)
- Tanya T Paull
- The Department of Molecular Biosciences and the Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX, USA
| |
Collapse
|
39
|
Korsholm LM, Gál Z, Lin L, Quevedo O, Ahmad DA, Dulina E, Luo Y, Bartek J, Larsen DH. Double-strand breaks in ribosomal RNA genes activate a distinct signaling and chromatin response to facilitate nucleolar restructuring and repair. Nucleic Acids Res 2019; 47:8019-8035. [PMID: 31184714 PMCID: PMC6735822 DOI: 10.1093/nar/gkz518] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 12/21/2022] Open
Abstract
The nucleolus is a nuclear sub-domain containing the most highly transcribed genes in the genome. Hundreds of human ribosomal RNA (rRNA) genes, located in the nucleolus, rely on constant maintenance. DNA double-strand breaks (DSBs) in rRNA genes activate the ATM kinase, repress rRNA transcription and induce nucleolar cap formation. Yet how ribosomal-DNA (rDNA) lesions are detected and processed remains elusive. Here, we use CRISPR/Cas9-mediated induction of DSBs and report a chromatin response unique to rDNA depending on ATM-phosphorylation of the nucleolar protein TCOF1 and recruitment of the MRE11-RAD50-NBS1 (MRN) complex via the NBS1-subunit. NBS1- and MRE11-depleted cells fail to suppress rRNA transcription and to translocate rDNA into nucleolar caps. Furthermore, the DNA damage response (DDR) kinase ATR operates downstream of the ATM-TCOF1-MRN interplay and is required to fully suppress rRNA transcription and complete DSB-induced nucleolar restructuring. Unexpectedly, we find that DSBs in rDNA neither activate checkpoint kinases CHK1/CHK2 nor halt cell-cycle progression, yet the nucleolar-DDR protects against genomic aberrations and cell death. Our data highlight the concept of a specialized nucleolar DNA damage response (n-DDR) with a distinct protein composition, spatial organization and checkpoint communication. The n-DDR maintains integrity of ribosomal RNA genes, with implications for cell physiology and disease.
Collapse
Affiliation(s)
- Lea M Korsholm
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Zita Gál
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Lin Lin
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
- China National GeneBank, BGI-Shenzhen, 518083 Shenzhen, China
| | - Oliver Quevedo
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Diana A Ahmad
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Ekaterina Dulina
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
- China National GeneBank, BGI-Shenzhen, 518083 Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, 266555 Qingdao, China
| | - Jiri Bartek
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Genome Biology, Karolinska Institutet, SE-171 65 Solna, Sweden
| | - Dorthe H Larsen
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| |
Collapse
|
40
|
Fleischmann M, Martin D, Peña-Llopis S, Oppermann J, von der Grün J, Diefenhardt M, Chatzikonstantinou G, Fokas E, Rödel C, Strebhardt K, Becker S, Rödel F, Tselis N. Association of Polo-Like Kinase 3 and PhosphoT273 Caspase 8 Levels With Disease-Related Outcomes Among Cervical Squamous Cell Carcinoma Patients Treated With Chemoradiation and Brachytherapy. Front Oncol 2019; 9:742. [PMID: 31475104 PMCID: PMC6702309 DOI: 10.3389/fonc.2019.00742] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/23/2019] [Indexed: 12/22/2022] Open
Abstract
Introduction: Definitive chemoradiation (CRT) followed by high-dose-rate (HDR) brachytherapy (BT) represents state-of-the-art treatment for locally-advanced cervical cancer. Despite use of this treatment paradigm, disease-related outcomes have stagnated in recent years, indicating the need for biomarker development and improved patient stratification. Here, we report the association of Polo-like kinase (PLK) 3 expression and Caspase 8 T273 phosphorylation levels with survival among patients with cervical squamous cell carcinoma (CSCC) treated with CRT plus BT. Methods: We identified 74 patients with FIGO Stage Ib to IVb cervix squamous cell carcinoma. Baseline immunohistochemical scoring of PLK3 and pT273 Caspase 8 levels was performed on pre-treatment samples. Correlation was then assessed between marker expression and clinical endpoints, including cumulative incidences of local and distant failure, cancer-specific survival (CSS) and overall survival (OS). Data were then validated using The Cancer Genome Atlas (TCGA) dataset. Results: PLK3 expression levels were associated with pT273 Caspase 8 levels (p = 0.009), as well as N stage (p = 0.046), M stage (p = 0.026), and FIGO stage (p = 0.001). By the same token, pT273 Caspase 8 levels were associated with T stage (p = 0.031). Increased PLK3 levels corresponded to a lower risk of distant relapse (p = 0.009), improved CSS (p = 0.001), and OS (p = 0.003). Phospho T273 Caspase 8 similarly corresponded to decreased risk of distant failure (p = 0.021), and increased CSS (p < 0.001) and OS (p < 0.001) and remained a significant predictor for OS on multivariate analysis. TCGA data confirmed the association of low PLK3 expression with resistance to radiotherapy and BT (p < 0.05), as well as increased propensity for metastasis (p = 0.019). Finally, a combined PLK3 and pT273 Caspase 8 score predicted for decreased distant relapse (p = 0.005), and both improved CSS (p < 0.001) and OS (p < 0.001); this combined score independently predicted distant failure (p = 0.041) and CSS (p = 0.003) on multivariate analyses. Conclusion: Increased pre-treatment tumor levels of PLK3 and pT273 Caspase 8 correspond to improved disease-related outcomes among cervical cancer patients treated with CRT plus BT, representing a potential biomarker in this context.
Collapse
Affiliation(s)
- Max Fleischmann
- Department of Radiotherapy and Oncology, Goethe-University, Frankfurt, Germany
| | - Daniel Martin
- Department of Radiotherapy and Oncology, Goethe-University, Frankfurt, Germany
| | - Samuel Peña-Llopis
- Division of Solid Tumor Translational Oncology, West German Cancer Center, Essen University Hospital, Essen, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK) Partner Site, Essen/Düsseldorf, Germany
| | - Julius Oppermann
- Department of Radiotherapy and Oncology, Goethe-University, Frankfurt, Germany
| | - Jens von der Grün
- Department of Radiotherapy and Oncology, Goethe-University, Frankfurt, Germany
| | - Markus Diefenhardt
- Department of Radiotherapy and Oncology, Goethe-University, Frankfurt, Germany
| | | | - Emmanouil Fokas
- Department of Radiotherapy and Oncology, Goethe-University, Frankfurt, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Frankfurt Cancer Institute (FCI), University of Frankfurt, Frankfurt, Germany.,German Cancer Consortium (DKTK) Partner Site, Frankfurt/Mainz, Germany
| | - Claus Rödel
- Department of Radiotherapy and Oncology, Goethe-University, Frankfurt, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Frankfurt Cancer Institute (FCI), University of Frankfurt, Frankfurt, Germany.,German Cancer Consortium (DKTK) Partner Site, Frankfurt/Mainz, Germany
| | - Klaus Strebhardt
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK) Partner Site, Frankfurt/Mainz, Germany.,Department of Gynecology, Goethe-University, Frankfurt, Germany
| | - Sven Becker
- Department of Gynecology, Goethe-University, Frankfurt, Germany
| | - Franz Rödel
- Department of Radiotherapy and Oncology, Goethe-University, Frankfurt, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Frankfurt Cancer Institute (FCI), University of Frankfurt, Frankfurt, Germany.,German Cancer Consortium (DKTK) Partner Site, Frankfurt/Mainz, Germany
| | - Nikolaos Tselis
- Department of Radiotherapy and Oncology, Goethe-University, Frankfurt, Germany
| |
Collapse
|
41
|
Jimeno S, Prados-Carvajal R, Huertas P. The role of RNA and RNA-related proteins in the regulation of DNA double strand break repair pathway choice. DNA Repair (Amst) 2019; 81:102662. [PMID: 31303544 DOI: 10.1016/j.dnarep.2019.102662] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA end resection is a critical step in the repair of DNA double strand breaks. It controls the way the lesion is going to be repaired, thus its regulation has a great importance in maintaining genomic stability. In this review, we focus in recent discoveries in the field that point to a modulation of resection by RNA molecules and RNA-related proteins. Moreover, we aim to reconcile contradictory reports on the positive or negative effect of DNA:RNA hybrids in the resection process.
Collapse
Affiliation(s)
- Sonia Jimeno
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain; Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Rosario Prados-Carvajal
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain; Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Pablo Huertas
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain; Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain.
| |
Collapse
|
42
|
Liu YM, Fang XY, Fang F, Wu ZY. Investigation of hairpin DNA and chelerythrine interaction by a single bio-nanopore sensing interface. Analyst 2019; 144:4081-4085. [PMID: 31169284 DOI: 10.1039/c9an00113a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Chelerythrine (CHE) is one of the potential drugs for cancer treatments. The interaction between hairpin DNA and CHE has been investigated by spectral and mass spectrometry methods. In this paper, the stability of hairpin DNA with different loop bases and its interaction with CHE were explored with a single α-hemolysin (α-HL) nanopore sensing interface. The results showed that the characteristic current pulses not only relate to the loop composition changes of the hairpin DNA, but also provide interaction information between CHE and the hairpin DNA molecules. The dwell time of current pulses for hairpin DNA was significantly increased (hundreds of ms) due to the addition of CHE, and two characteristic current distributions were recognized for the hairpin with T3 and C3 loops. The two characteristic current groups could be ascribed to the hairpin DNA and the ones with CHE. This study indicates that it is possible to study the interaction between single CHE and single hairpin DNA molecules by the single-nanopore sensing interface as an alternative method to conventional spectrometric methods for therapeutic mechanism and drug screening purposes.
Collapse
Affiliation(s)
- Yuan-Min Liu
- Research Center for Analytical Sciences, Chemistry Department, College of Sciences, Northeastern University, Shenyang 110819, China.
| | | | | | | |
Collapse
|
43
|
Scully R, Panday A, Elango R, Willis NA. DNA double-strand break repair-pathway choice in somatic mammalian cells. Nat Rev Mol Cell Biol 2019; 20:698-714. [PMID: 31263220 DOI: 10.1038/s41580-019-0152-0] [Citation(s) in RCA: 753] [Impact Index Per Article: 150.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2019] [Indexed: 11/09/2022]
Abstract
The major pathways of DNA double-strand break (DSB) repair are crucial for maintaining genomic stability. However, if deployed in an inappropriate cellular context, these same repair functions can mediate chromosome rearrangements that underlie various human diseases, ranging from developmental disorders to cancer. The two major mechanisms of DSB repair in mammalian cells are non-homologous end joining (NHEJ) and homologous recombination. In this Review, we consider DSB repair-pathway choice in somatic mammalian cells as a series of 'decision trees', and explore how defective pathway choice can lead to genomic instability. Stalled, collapsed or broken DNA replication forks present a distinctive challenge to the DSB repair system. Emerging evidence suggests that the 'rules' governing repair-pathway choice at stalled replication forks differ from those at replication-independent DSBs.
Collapse
Affiliation(s)
- Ralph Scully
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.
| | - Arvind Panday
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Rajula Elango
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Nicholas A Willis
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
44
|
Ginsenoside Rg1 impairs homologous recombination repair by targeting CtBP-interacting protein and sensitizes hepatoblastoma cells to DNA damage. Anticancer Drugs 2019; 29:756-766. [PMID: 29952772 DOI: 10.1097/cad.0000000000000646] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The ginsenoside Rg1, the primary pharmacologically active ingredient of the traditional Chinese herb ginseng, is widely used in the clinical treatment of diseases of the immune and nervous systems. Recent studies have shown that it also has an antitumor effect. In this study, we explored the effects of Rg1 on hepatoblastoma (HB) and its underlying mechanisms. We demonstrated that Rg1 significantly inhibited HB cell growth both in vivo and in vitro. Mechanistic studies revealed that Rg1 impaired homologous recombination and triggered double-strand breaks in HB cells by directly targeting CtBP-interacting protein (CtIP), a key double-strand break repair factor, which is highly expressed in HB tissues. Moreover, we also demonstrated that Rg1 sensitized HB cells to DNA-damaging agents both in vitro and in vivo. In conclusion, our data not only demonstrate the potential clinical application of Rg1 as a novel chemotherapeutic candidate but also offer a mechanism-based therapeutic option by which DNA-damaging agents can be used in combination with Rg1 to target HB.
Collapse
|
45
|
Sheppard EC, Rogers S, Harmer NJ, Chahwan R. A universal fluorescence-based toolkit for real-time quantification of DNA and RNA nuclease activity. Sci Rep 2019; 9:8853. [PMID: 31222049 PMCID: PMC6586798 DOI: 10.1038/s41598-019-45356-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/31/2019] [Indexed: 12/12/2022] Open
Abstract
DNA and RNA nucleases play a critical role in a growing number of cellular processes ranging from DNA repair to immune surveillance. Nevertheless, many nucleases have unknown or poorly characterized activities. Elucidating nuclease substrate specificities and co-factors can support a more definitive understanding of cellular mechanisms in physiology and disease. Using fluorescence-based methods, we present a quick, safe, cost-effective, and real-time versatile nuclease assay, which uniquely studies nuclease enzyme kinetics. In conjunction with a substrate library we can now analyse nuclease catalytic rates, directionality, and substrate preferences. The assay is sensitive enough to detect kinetics of repair enzymes when confronted with DNA mismatches or DNA methylation sites. We have also extended our analysis to study the kinetics of human single-strand DNA nuclease TREX2, DNA polymerases, RNA, and RNA:DNA nucleases. These nucleases are involved in DNA repair, immune regulation, and have been associated with various diseases, including cancer and immune disorders.
Collapse
Affiliation(s)
- Emily C Sheppard
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Sally Rogers
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Nicholas J Harmer
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Richard Chahwan
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK. .,Institute of Experimental Immunology, University of Zurich, 8057, Zurich, Switzerland.
| |
Collapse
|
46
|
Godau J, Ferretti LP, Trenner A, Dubois E, von Aesch C, Marmignon A, Simon L, Kapusta A, Guérois R, Bétermier M, Sartori AA. Identification of a miniature Sae2/Ctp1/CtIP ortholog from Paramecium tetraurelia required for sexual reproduction and DNA double-strand break repair. DNA Repair (Amst) 2019; 77:96-108. [DOI: 10.1016/j.dnarep.2019.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 01/28/2019] [Accepted: 03/21/2019] [Indexed: 12/24/2022]
|
47
|
|
48
|
Lewis TW, Barthelemy JR, Virts EL, Kennedy FM, Gadgil RY, Wiek C, Linka RM, Zhang F, Andreassen PR, Hanenberg H, Leffak M. Deficiency of the Fanconi anemia E2 ubiqitin conjugase UBE2T only partially abrogates Alu-mediated recombination in a new model of homology dependent recombination. Nucleic Acids Res 2019; 47:3503-3520. [PMID: 30715513 PMCID: PMC6468168 DOI: 10.1093/nar/gkz026] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 01/04/2019] [Accepted: 01/30/2019] [Indexed: 12/11/2022] Open
Abstract
The primary function of the UBE2T ubiquitin conjugase is in the monoubiquitination of the FANCI-FANCD2 heterodimer, a central step in the Fanconi anemia (FA) pathway. Genetic inactivation of UBE2T is responsible for the phenotypes of FANCT patients; however, a FANCT patient carrying a maternal duplication and a paternal deletion in the UBE2T loci displayed normal peripheral blood counts and UBE2T protein levels in B-lymphoblast cell lines. To test whether reversion by recombination between UBE2T AluYa5 elements could have occurred in the patient's hematopoietic stem cells despite the defects in homologous recombination (HR) in FA cells, we constructed HeLa cell lines containing the UBE2T AluYa5 elements and neighboring intervening sequences flanked by fluorescent reporter genes. Introduction of a DNA double strand break in the model UBE2T locus in vivo promoted single strand annealing (SSA) between proximal Alu elements and deletion of the intervening color marker gene, recapitulating the reversion of the UBE2T duplication in the FA patient. To test whether UBE2T null cells retain HR activity, the UBE2T genes were knocked out in HeLa cells and U2OS cells. CRISPR/Cas9-mediated genetic knockout of UBE2T only partially reduced HR, demonstrating that UBE2T-independent pathways can compensate for the recombination defect in UBE2T/FANCT null cells.
Collapse
Affiliation(s)
- Todd W Lewis
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH, USA
| | - Joanna R Barthelemy
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH, USA
| | - Elizabeth L Virts
- Department of Pediatrics and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Felicia M Kennedy
- Department of Pediatrics and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Rujuta Y Gadgil
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH, USA
| | - Constanze Wiek
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich Heine University, 40225 Duüsseldorf, Germany
| | - Rene M Linka
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich Heine University, 40225 Duüsseldorf, Germany
| | - Feng Zhang
- Division of Experimental Hematology & Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Paul R Andreassen
- Division of Experimental Hematology & Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Helmut Hanenberg
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich Heine University, 40225 Duüsseldorf, Germany
- Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany
| | - Michael Leffak
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH, USA
| |
Collapse
|
49
|
Liu M, Rehman S, Tang X, Gu K, Fan Q, Chen D, Ma W. Methodologies for Improving HDR Efficiency. Front Genet 2019; 9:691. [PMID: 30687381 PMCID: PMC6338032 DOI: 10.3389/fgene.2018.00691] [Citation(s) in RCA: 170] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/11/2018] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) is a precise genome manipulating technology that can be programmed to induce double-strand break (DSB) in the genome wherever needed. After nuclease cleavage, DSBs can be repaired by non-homologous end joining (NHEJ) or homology-directed repair (HDR) pathway. For producing targeted gene knock-in or other specific mutations, DSBs should be repaired by the HDR pathway. While NHEJ can cause various length insertions/deletion mutations (indels), which can lead the targeted gene to lose its function by shifting the open reading frame (ORF). Furthermore, HDR has low efficiency compared with the NHEJ pathway. In order to modify the gene precisely, numerous methods arose by inhibiting NHEJ or enhancing HDR, such as chemical modulation, synchronized expression, and overlapping homology arm. Here we focus on the efficiency and other considerations of these methodologies.
Collapse
Affiliation(s)
- Mingjie Liu
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Saad Rehman
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Xidian Tang
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Kui Gu
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Qinlei Fan
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Dekun Chen
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Wentao Ma
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| |
Collapse
|
50
|
Jimeno S, Mejías-Navarro F, Prados-Carvajal R, Huertas P. Controlling the balance between chromosome break repair pathways. DNA Repair (Amst) 2019; 115:95-134. [DOI: 10.1016/bs.apcsb.2018.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|