51
|
Fried W, Tyagi M, Minakhin L, Chandramouly G, Tredinnick T, Ramanjulu M, Auerbacher W, Calbert M, Rusanov T, Hoang T, Borisonnik N, Betsch R, Krais JJ, Wang Y, Vekariya UM, Gordon J, Morton G, Kent T, Skorski T, Johnson N, Childers W, Chen XS, Pomerantz RT. Discovery of a small-molecule inhibitor that traps Polθ on DNA and synergizes with PARP inhibitors. Nat Commun 2024; 15:2862. [PMID: 38580648 PMCID: PMC10997755 DOI: 10.1038/s41467-024-46593-1] [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: 08/14/2023] [Accepted: 03/04/2024] [Indexed: 04/07/2024] Open
Abstract
The DNA damage response (DDR) protein DNA Polymerase θ (Polθ) is synthetic lethal with homologous recombination (HR) factors and is therefore a promising drug target in BRCA1/2 mutant cancers. We discover an allosteric Polθ inhibitor (Polθi) class with 4-6 nM IC50 that selectively kills HR-deficient cells and acts synergistically with PARP inhibitors (PARPi) in multiple genetic backgrounds. X-ray crystallography and biochemistry reveal that Polθi selectively inhibits Polθ polymerase (Polθ-pol) in the closed conformation on B-form DNA/DNA via an induced fit mechanism. In contrast, Polθi fails to inhibit Polθ-pol catalytic activity on A-form DNA/RNA in which the enzyme binds in the open configuration. Remarkably, Polθi binding to the Polθ-pol:DNA/DNA closed complex traps the polymerase on DNA for more than forty minutes which elucidates the inhibitory mechanism of action. These data reveal a unique small-molecule DNA polymerase:DNA trapping mechanism that induces synthetic lethality in HR-deficient cells and potentiates the activity of PARPi.
Collapse
Affiliation(s)
- William Fried
- Molecular and Computational Biology, Department of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Mrityunjay Tyagi
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Leonid Minakhin
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Gurushankar Chandramouly
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Taylor Tredinnick
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Mercy Ramanjulu
- Recombination Therapeutics, Pennsylvania Biotechnology Center, Doylestown, PA, 18902, USA
| | - William Auerbacher
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Marissa Calbert
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
- Fels Cancer Institute for Personalized Medicine, Philadelphia, PA, USA
| | - Timur Rusanov
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | | | | | - Robert Betsch
- Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - John J Krais
- Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Yifan Wang
- Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Umeshkumar M Vekariya
- Fels Cancer Institute for Personalized Medicine, Philadelphia, PA, USA
- Department of Cancer and Cellular Biology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - John Gordon
- Fels Cancer Institute for Personalized Medicine, Philadelphia, PA, USA
| | - George Morton
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA, USA
| | - Tatiana Kent
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Tomasz Skorski
- Fels Cancer Institute for Personalized Medicine, Philadelphia, PA, USA
- Department of Cancer and Cellular Biology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Neil Johnson
- Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Wayne Childers
- Recombination Therapeutics, Pennsylvania Biotechnology Center, Doylestown, PA, 18902, USA
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology, Department of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, USA
- Recombination Therapeutics, Pennsylvania Biotechnology Center, Doylestown, PA, 18902, USA
| | - Richard T Pomerantz
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
- Recombination Therapeutics, Pennsylvania Biotechnology Center, Doylestown, PA, 18902, USA.
| |
Collapse
|
52
|
Peng Y, Zheng W, Chen Y, Lei X, Yang Z, Yang Y, Liang W, Sun K, Li G, Yu J. POLQ inhibition attenuates the stemness and ferroptosis resistance in gastric cancer cells via downregulation of dihydroorotate dehydrogenase. Cell Death Dis 2024; 15:248. [PMID: 38575587 PMCID: PMC10995193 DOI: 10.1038/s41419-024-06618-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024]
Abstract
Gastric cancer (GC) contains subpopulations of cancer stem cells (CSCs), which are described as the main contributors in tumor initiation and metastasis. It is necessary to clarify the molecular mechanism underlying CSCs phenotype and develop novel biomarkers and therapeutic targets for gastric cancer. Here, we show that POLQ positively regulates stem cell-like characteristics of gastric cancer cells, knockdown of POLQ suppressed the stemness of GC cells in vitro and in vivo. Further mechanistic studies revealed that POLQ knockdown could downregulate the expression of dihydroorotate dehydrogenase (DHODH). DHODH overexpression rescued the reduced stemness resulted by POLQ knockdown. Furthermore, we found that POLQ expression correlated with resistance to ferroptosis, and POLQ inhibition renders gastric cancer cells more vulnerable to ferroptosis. Further investigation revealed that POLQ regulated DHODH expression via the transcription factors E2F4, thereby regulating ferroptosis resistance and stemness of gastric cancer cells. Given the importance of POLQ in stemness and ferroptosis resistance of GC, we further evaluated the therapeutic potential of POLQ inhibitor novobiocin, the results show that novobiocin attenuates the stemness of GC cells and increased ferroptosis sensitivity. Moreover, the combination of POLQ inhibitor and ferroptosis inducer synergistically suppressed MGC-803 xenograft tumor growth and diminished metastasis. Our results identify a POLQ-mediated stemness and ferroptosis defense mechanism and provide a new therapeutic strategy for gastric cancer.
Collapse
Affiliation(s)
- Yanmei Peng
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Wenbo Zheng
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Yuehong Chen
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Xuetao Lei
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Zhijing Yang
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Yuxuan Yang
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Weiqi Liang
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Kai Sun
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China.
| | - Guoxin Li
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China.
- Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 102218, China.
| | - Jiang Yu
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China.
| |
Collapse
|
53
|
Wang Y, Wang C, Liu J, Sun D, Meng F, Zhang M, Aliper A, Ren F, Zhavoronkov A, Ding X. Discovery of 3-hydroxymethyl-azetidine derivatives as potent polymerase theta inhibitors. Bioorg Med Chem 2024; 103:117662. [PMID: 38493730 DOI: 10.1016/j.bmc.2024.117662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/25/2024] [Accepted: 02/27/2024] [Indexed: 03/19/2024]
Abstract
Inhibition of the low fidelity DNA polymerase Theta (Polθ) is emerging as an attractive, synthetic-lethal antitumor strategy in BRCA-deficient tumors. Here we report the AI-enabled development of 3-hydroxymethyl-azetidine derivatives as a novel class of Polθ inhibitors featuring central scaffolding rings. Structure-based drug design first identified A7 as a lead compound, which was further optimized to the more potent derivative B3 and the metabolically stable deuterated compound C1. C1 exhibited significant antiproliferative properties in DNA repair-compromised cells and demonstrated favorable pharmacokinetics, showcasing that 3-hydroxymethyl-azetidine is an effective bio-isostere of pyrrolidin-3-ol and emphasizing the potential of AI in medicinal chemistry for precise molecular modifications.
Collapse
Affiliation(s)
- Yazhou Wang
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
| | - Chao Wang
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
| | - Jinxin Liu
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
| | - Deheng Sun
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
| | - Fanye Meng
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
| | - Man Zhang
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
| | - Alex Aliper
- Insilico Medicine AI Limited, Masdar City, Abu Dhabi 145748, United Arab Emirates
| | - Feng Ren
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China
| | - Alex Zhavoronkov
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China; Insilico Medicine AI Limited, Masdar City, Abu Dhabi 145748, United Arab Emirates
| | - Xiao Ding
- Insilico Medicine Shanghai Ltd, Suite 901, Tower C, Changtai Plaza, 2889 Jinke Road, Pudong New District, Shanghai 201203, China.
| |
Collapse
|
54
|
Konstantinopoulos PA, Cheng SC, Lee EK, da Costa AABA, Gulhan D, Wahner Hendrickson AE, Kochupurakkal B, Kolin DL, Kohn EC, Liu JF, Penson RT, Stover EH, Curtis J, Sawyer H, Polak M, Chowdhury D, D'Andrea AD, Färkkilä A, Shapiro GI, Matulonis UA. Randomized Phase II Study of Gemcitabine With or Without ATR Inhibitor Berzosertib in Platinum-Resistant Ovarian Cancer: Final Overall Survival and Biomarker Analyses. JCO Precis Oncol 2024; 8:e2300635. [PMID: 38635934 DOI: 10.1200/po.23.00635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/28/2023] [Accepted: 02/29/2024] [Indexed: 04/20/2024] Open
Abstract
PURPOSE The multicenter, open-label, randomized phase 2 NCI-9944 study (NCT02595892) demonstrated that addition of ATR inhibitor (ATRi) berzosertib to gemcitabine increased progression-free survival (PFS) compared to gemcitabine alone (hazard ratio [HR]=0.57, one-sided log-rank P = .044, which met the one-sided significance level of 0.1 used for sample size calculation). METHODS We report here the final overall survival (OS) analysis and biomarker correlations (ATM expression by immunohistochemistry, mutational signature 3 and a genomic biomarker of replication stress) along with post-hoc exploratory analyses to adjust for crossover from gemcitabine to gemcitabine/berzosertib. RESULTS At the data cutoff of January 27, 2023 (>30 months of additional follow-up from the primary analysis), median OS was 59.4 weeks with gemcitabine/berzosertib versus 43.0 weeks with gemcitabine alone (HR 0.79, 90% CI 0.52 to 1.2, one-sided log-rank P = .18). An OS benefit with addition of berzosertib to gemcitabine was suggested in patients stratified into the platinum-free interval ≤3 months (N = 26) subgroup (HR, 0.48, 90% CI 0.22 to 1.01, one-sided log-rank P =.04) and in patients with ATM-negative/low (N = 24) tumors (HR, 0.50, 90% CI 0.23 to 1.08, one-sided log-rank P = .06). CONCLUSION The results of this follow-up analysis continue to support the promise of combined gemcitabine/ATRi therapy in platinum resistant ovarian cancer, an active area of investigation with several ongoing clinical trials.
Collapse
Affiliation(s)
| | - Su-Chun Cheng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Elizabeth K Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Alexandre André B A da Costa
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA
| | - Doga Gulhan
- Department of Biomedical Informatics and Ludwig Center at Harvard, Harvard Medical School, Boston, MA
| | | | - Bose Kochupurakkal
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA
| | - David L Kolin
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Elise C Kohn
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD
| | - Joyce F Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Richard T Penson
- Department of Medical Oncology, Massachusetts General Hospital, Boston, MA
| | - Elizabeth H Stover
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Jennifer Curtis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Hannah Sawyer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Madeline Polak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA
| | - Anniina Färkkilä
- Research Program in Systems Oncology, FIMM and HiLife, University of Helsinki, Helsinki, Finland
| | - Geoffrey I Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Ursula A Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| |
Collapse
|
55
|
Ditonno F, Bianchi A, Malandra S, Porcaro AB, Fantinel E, Negrelli R, Ferro M, Milella M, Brunelli M, Autorino R, Cerruto MA, Veccia A, Antonelli A. PARP Inhibitors in Metastatic Prostate Cancer: A Comprehensive Systematic Review and Meta-analysis of Existing Evidence. Clin Genitourin Cancer 2024; 22:402-412.e17. [PMID: 38281877 DOI: 10.1016/j.clgc.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/05/2023] [Accepted: 12/16/2023] [Indexed: 01/30/2024]
Abstract
Poly (ADP-ribose) polymerase inhibitors (PARPi) represent an option in selected cases of metastatic castration-resistant prostate cancer (mCRPC). The aim of the present systematic review and meta-analysis is to evaluate the efficacy and safety of approved (Olaparib, Rucaparib) and investigational (Talazoparib, Niraparib, Veliparib) PARPi in mCRPC patients. Three databases were queried for studies analyzing oncological outcomes and adverse events of mCRPC patients receiving PARPi. Primary outcome was a PSA decline ≥ 50% from baseline. Secondary outcomes were objective response rate, progression-free survival (PFS), radiological PFS, overall survival (OS), conversion of circulating tumor cell count, and time to PSA progression. The number and rate of any grade adverse events (AEs), grade ≥ 3 AEs, and most common grade ≥ 3 AEs were registered. A subanalysis of outcomes per mutation type, prospective trials, and studies adopting combination therapies was performed. Overall, 31 studies were included in this systematic review, 28 of which are available for meta-analysis. The most frequently investigated drug was Olaparib. The most frequent mutation was BRCA2. A PSA decline rate of 43% (95% CI 0.32-0.54) was observed in the overall population. Mean OS was 15.9 (95% CI 12.9-19.0) months. In BRCA2 patients, PSA decline rate was 66% (95% CI 0.57-0.7) and OS 23.4 months (95% CI 22.8-24.1). Half of the patients suffered from grade 3 and 4 AEs (0.50 [95% CI 0.39-0.60]). Most common AEs were hematological, the most frequent being anemia (21.5%). PARP inhibitors represent a viable option for mCRPC patients. Current evidence suggests an increased effectiveness in homologous recombination repair (HRR) gene mutation carriers, especially BRCA2.
Collapse
Affiliation(s)
- Francesco Ditonno
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata (AOUI) Verona, Verona, Italy; Department of Urology, Rush University, Chicago, IL, USA
| | - Alberto Bianchi
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata (AOUI) Verona, Verona, Italy
| | - Sarah Malandra
- Department of Surgery, Dentistry, Pediatrics and Ginecology, University of Verona, Azienda Ospedaliera Universitaria Integrata (AOUI) Verona, Verona, Italy
| | - Antonio Benito Porcaro
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata (AOUI) Verona, Verona, Italy
| | - Emanuela Fantinel
- Section of Oncology, Department of Medicine, University of Verona, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Riccardo Negrelli
- Department of Radiology, University of Verona, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Matteo Ferro
- Department of Urology, European Institute of Oncology (IEO) IRCCS, Milan, Italy
| | - Michele Milella
- Section of Oncology, Department of Medicine, University of Verona, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Matteo Brunelli
- Department of Diagnostic and Public Health, Section of Pathology, University of Verona, Italy
| | | | - Maria Angela Cerruto
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata (AOUI) Verona, Verona, Italy
| | - Alessandro Veccia
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata (AOUI) Verona, Verona, Italy.
| | - Alessandro Antonelli
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata (AOUI) Verona, Verona, Italy
| |
Collapse
|
56
|
Stroik S, Luthman AJ, Ramsden DA. Templated insertions-DNA repair gets acrobatic. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024; 65 Suppl 1:82-89. [PMID: 37438951 PMCID: PMC10962320 DOI: 10.1002/em.22564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/28/2023] [Accepted: 07/07/2023] [Indexed: 07/14/2023]
Abstract
Deletions associated with the repair of DNA double-strand breaks is a source of genetic alternation and a recognized source of disease-causing mutagenesis. Theta-mediated end joining is a DNA repair mechanism, which guarantees deletions by its employment of microhomology (MH) alignment to facilitate end joining. A lesser-characterized templated insertion ability of this pathway, on the other hand, is associated with both deletion and insertion. This mechanism is characterized by at least one round of polymerase θ-mediated synthesis, which does not result in successful repair, followed by a subsequent round of polymerase engagement and synthesis that does lead to repair. Here we focus on the mechanisms by which polymerase θ introduces these insertions-direct, inverse, and a new class which we have termed strand switching. We observe this new class of templated insertions at multiple loci and across multiple species, often at a comparable frequency to those previously characterized. Templated insertion mutations are often enriched in cancer genomes and repeat expansion disorders. This repair mechanism thus contributes to disease-associated mutagenesis, and may plausibly even promote disease. Characterization of the types of polymerase θ-dependent insertions can provide new insight into these diseases and clinical promise for treatment.
Collapse
Affiliation(s)
- Susanna Stroik
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adam J. Luthman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill NC, USA
| | - Dale A. Ramsden
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
57
|
Kralemann LEM, van Tol N, Hooykaas PJJ, Tijsterman M. Molecular analysis of the role of polymerase theta in gene targeting in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:255-262. [PMID: 38402589 DOI: 10.1111/tpj.16689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/05/2024] [Accepted: 02/07/2024] [Indexed: 02/27/2024]
Abstract
Precise genetic modification can be achieved via a sequence homology-mediated process known as gene targeting (GT). Whilst established for genome engineering purposes, the application of GT in plants still suffers from a low efficiency for which an explanation is currently lacking. Recently reported reduced rates of GT in A. thaliana deficient in polymerase theta (Polθ), a core component of theta-mediated end joining (TMEJ) of DNA breaks, have led to the suggestion of a direct involvement of this enzyme in the homology-directed process. Here, by monitoring homology-driven gene conversion in plants with CRISPR reagent and donor sequences pre-integrated at random sites in the genome (in planta GT), we demonstrate that Polθ action is not required for GT, but instead suppresses the process, likely by promoting the repair of the DNA break by end-joining. This finding indicates that lack of donor integration explains the previously established reduced GT rates seen upon transformation of Polθ-deficient plants. Our study additionally provides insight into ectopic gene targeting (EGT), recombination events between donor and target that do not map to the target locus. EGT, which occurs at similar frequencies as "true" GT during transformation, was rare in our in planta GT experiments arguing that EGT predominantly results from target locus recombination with nonintegrated T-DNA molecules. By describing mechanistic features of GT our study provides directions for the improvement of precise genetic modification of plants.
Collapse
Affiliation(s)
- Lejon E M Kralemann
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Niels van Tol
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Paul J J Hooykaas
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Marcel Tijsterman
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2300 RC, Leiden, The Netherlands
| |
Collapse
|
58
|
Kannan S, Gillespie SW, Picking WL, Picking WD, Lorson CL, Singh K. Inhibitors against DNA Polymerase I Family of Enzymes: Novel Targets and Opportunities. BIOLOGY 2024; 13:204. [PMID: 38666816 PMCID: PMC11048162 DOI: 10.3390/biology13040204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/18/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024]
Abstract
DNA polymerases replicate cellular genomes and/or participate in the maintenance of genome integrity. DNA polymerases sharing high sequence homology with E. coli DNA polymerase I (pol I) have been grouped in Family A. Pol I participates in Okazaki fragment maturation and in bacterial genome repair. Since its discovery in 1956, pol I has been extensively studied, primarily to gain deeper insights into the mechanism of DNA replication. As research on DNA polymerases advances, many novel functions of this group of polymerases are being uncovered. For example, human DNA polymerase θ (a Family A DNA pol) has been shown to synthesize DNA using RNA as a template, a function typically attributed to retroviral reverse transcriptase. Increased interest in drug discovery against pol θ has emerged due to its roles in cancer. Likewise, Pol I family enzymes also appear attractive as drug-development targets against microbial infections. Development of antimalarial compounds targeting apicoplast apPOL, an ortholog of Pol I, further extends the targeting of this family of enzymes. Here, we summarize reported drug-development efforts against Family A polymerases and future perspective regarding these enzymes as antibiotic targets. Recently developed techniques, such as artificial intelligence, can be used to facilitate the development of new drugs.
Collapse
Affiliation(s)
- Saathvik Kannan
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; (S.K.); (S.W.G.); (W.L.P.); (W.D.P.); (C.L.L.)
| | - Samuel W. Gillespie
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; (S.K.); (S.W.G.); (W.L.P.); (W.D.P.); (C.L.L.)
| | - Wendy L. Picking
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; (S.K.); (S.W.G.); (W.L.P.); (W.D.P.); (C.L.L.)
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - William D. Picking
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; (S.K.); (S.W.G.); (W.L.P.); (W.D.P.); (C.L.L.)
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Christian L. Lorson
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; (S.K.); (S.W.G.); (W.L.P.); (W.D.P.); (C.L.L.)
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Kamal Singh
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; (S.K.); (S.W.G.); (W.L.P.); (W.D.P.); (C.L.L.)
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| |
Collapse
|
59
|
Graham E, Esashi F. DNA strand breaks at centromeres: Friend or foe? Semin Cell Dev Biol 2024; 156:141-151. [PMID: 37872040 DOI: 10.1016/j.semcdb.2023.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/22/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023]
Abstract
Centromeres are large structural regions in the genomic DNA, which are essential for accurately transmitting a complete set of chromosomes to daughter cells during cell division. In humans, centromeres consist of highly repetitive α-satellite DNA sequences and unique epigenetic components, forming large proteinaceous structures required for chromosome segregation. Despite their biological importance, there is a growing body of evidence for centromere breakage across the cell cycle, including periods of quiescence. In this review, we provide an up-to-date examination of the distinct centromere environments at different stages of the cell cycle, highlighting their plausible contribution to centromere breakage. Additionally, we explore the implications of these breaks on centromere function, both in terms of negative consequences and potential positive effects.
Collapse
Affiliation(s)
- Emily Graham
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Fumiko Esashi
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
| |
Collapse
|
60
|
Ma L, Chen W, Yang M, Ha S, Xiong S, Zhu J, Xiang H, Luo G. Discovery and Proof of Concept of Potent Dual Polθ/PARP Inhibitors for Efficient Treatment of Homologous Recombination-Deficient Tumors. J Med Chem 2024; 67:3606-3625. [PMID: 38375763 DOI: 10.1021/acs.jmedchem.3c02096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
DNA polymerase theta (Polθ) has recently emerged as a new attractive synthetic lethal target involved in DNA damage repair. Inactivating Polθ alone or in combination with PARP inhibitors has demonstrated substantial therapeutic potential against tumors with homologous recombination (HR) defects such as alternation of BRCA genes. Herein, we report the design and proof of concept of a highly potent dual Polθ/PARP inhibitor 25d, which exhibited low nanomolar inhibitory activities against both Polθ and PARP1. Compared to combination treatment, 25d demonstrated superior antitumor efficacy in both MDA-MB-436 cells and xenografts by inducing more DNA damage and apoptosis. Importantly, 25d retained sensitivity in PARP inhibitor-resistant MDA-MB-436 cells with 53BP1 defect. Altogether, these findings illustrate the potential advantages of 25d, a first-in-class dual Polθ/PARP inhibitor, over monotherapy in treating HR-deficient tumors, including those with acquired PARP inhibitor resistance.
Collapse
Affiliation(s)
- Luyu Ma
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, College of Pharmacy, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Wei Chen
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, College of Pharmacy, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Ming Yang
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, College of Pharmacy, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Si Ha
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, College of Pharmacy, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Shuangshuang Xiong
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, College of Pharmacy, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Jiacheng Zhu
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, College of Pharmacy, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Hua Xiang
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, College of Pharmacy, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Guoshun Luo
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, College of Pharmacy, China Pharmaceutical University, Nanjing 211198, P. R. China
| |
Collapse
|
61
|
Anbil S, Reiss KA. Targeting BRCA and PALB2 in Pancreatic Cancer. Curr Treat Options Oncol 2024; 25:346-363. [PMID: 38311708 DOI: 10.1007/s11864-023-01174-0] [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] [Accepted: 12/22/2023] [Indexed: 02/06/2024]
Abstract
OPINION STATEMENT An important subgroup of pancreatic ductal adenocarcinomas (PDACs) harbor pathogenic variants in BRCA1, BRCA2, or PALB2. These tumors are exquisitely sensitive to platinum-based chemotherapy and patients may experience deep and durable responses to this treatment. PARP inhibitors offer potential respite from the cumulative toxicities of chemotherapy as they significantly extend progression-free survival compared to a chemotherapy holiday. Given the lack of proven survival benefit, the decision to use a maintenance PARP inhibitor rather than continue chemotherapy should be individualized. Interestingly, in both published clinical trials of maintenance PARP inhibitors, there is a striking range of interpatient benefit: Even in the platinum-sensitive setting, roughly 25% of tumors appear to be PARP inhibitor refractory (progressive disease within 2 months of starting treatment), 50% sustain moderate benefit (up to 2 years), and 25% are hyper-responsive (more than 2 years of benefit). This finding highlights the need to refine our understanding of which patients will respond to maintenance PARP inhibitors, both by being able to identify biallelic loss and by deepening our knowledge of resistance mechanisms and who develops them. Recent data supports that reversion mutations are common in PARP inhibitor refractory patients, but we have little understanding of the mechanisms that drive delayed resistance and long-term responses. Identifying which patients are more prone to certain mechanisms of resistance and tackling them with specific treatment strategies are areas of active investigation. Additionally, given that PARP inhibitors have limited overall efficacy for most patients, upfront combination strategies are an important future strategy.
Collapse
Affiliation(s)
- Sriram Anbil
- Abramson Cancer Center, 10th Floor Perelman Center South, The University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19121, USA
| | - Kim A Reiss
- Abramson Cancer Center, 10th Floor Perelman Center South, The University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19121, USA.
| |
Collapse
|
62
|
Liu QW, Yang ZW, Tang QH, Wang WE, Chu DS, Ji JF, Fan QY, Jiang H, Yang QX, Zhang H, Liu XY, Xu XS, Wang XF, Liu JB, Fu D, Tao K, Yu H. The power and the promise of synthetic lethality for clinical application in cancer treatment. Biomed Pharmacother 2024; 172:116288. [PMID: 38377739 DOI: 10.1016/j.biopha.2024.116288] [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: 01/04/2024] [Revised: 02/08/2024] [Accepted: 02/17/2024] [Indexed: 02/22/2024] Open
Abstract
Synthetic lethality is a phenomenon wherein the simultaneous deficiency of two or more genes results in cell death, while the deficiency of any individual gene does not lead to cell death. In recent years, synthetic lethality has emerged as a significant topic in the field of targeted cancer therapy, with certain drugs based on this concept exhibiting promising outcomes in clinical trials. Nevertheless, the presence of tumor heterogeneity and the intricate DNA repair mechanisms pose challenges to the effective implementation of synthetic lethality. This review aims to explore the concepts, development, and ethical quandaries surrounding synthetic lethality. Additionally, it will provide an in-depth analysis of the clinical application and underlying mechanism of synthetic lethality.
Collapse
Affiliation(s)
- Qian-Wen Liu
- Department of Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province 225300, China; General Surgery, Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Zhi-Wen Yang
- Department of Pharmacy, Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai, Shanghai 200050, China
| | - Qing-Hai Tang
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region and College of Life Sciences, Hengyang Normal University, Hengyang, Hunan Province 421008, China
| | - Wen-Er Wang
- General Surgery, the Fourth Hospital Of Changsha, Changsha Hospital Of Hunan Normal University, Changsha, Hunan Province 410006, China
| | - Da-Sheng Chu
- Second Cadre Rest Medical and Health Center of Changning District, Shanghai Garrison, Shanghai226631, China
| | - Jin-Feng Ji
- Department of Integrated Traditional Chinese and Western Internal Medicine, Affiliated Tumor Hospital of Nantong University, Nantong Tumor Hospital, Nantong, Jiangsu Province 226631, China
| | - Qi-Yu Fan
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu Province 226631, China
| | - Hong Jiang
- Department of Thoracic Surgery, the 905th Hospital of Chinese People's Liberation Army Navy, Shanghai 200050, China
| | - Qin-Xin Yang
- Department of Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province 225300, China
| | - Hui Zhang
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu Province 226631, China
| | - Xin-Yun Liu
- Department of Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province 225300, China
| | - Xiao-Sheng Xu
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China.
| | - Xiao-Feng Wang
- Department of Orthopedics, Xiamen Hospital, Zhongshan Hospital, Fudan University, Xiamen, Fujian Province 361015, China.
| | - Ji-Bin Liu
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu Province 226631, China.
| | - Da Fu
- General Surgery, Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China.
| | - Kun Tao
- Department of Pathology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China.
| | - Hong Yu
- Department of Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province 225300, China; Department of Pathology, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, Jiangsu Province 225300, China.
| |
Collapse
|
63
|
Rajendra E, Grande D, Mason B, Di Marcantonio D, Armstrong L, Hewitt G, Elinati E, Galbiati A, Boulton SJ, Heald RA, Smith GCM, Robinson HMR. Quantitative, titratable and high-throughput reporter assays to measure DNA double strand break repair activity in cells. Nucleic Acids Res 2024; 52:1736-1752. [PMID: 38109306 PMCID: PMC10899754 DOI: 10.1093/nar/gkad1196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023] Open
Abstract
Repair of DNA damage is essential for the maintenance of genome stability and cell viability. DNA double strand breaks (DSBs) constitute a toxic class of DNA lesion and multiple cellular pathways exist to mediate their repair. Robust and titratable assays of cellular DSB repair (DSBR) are important to functionally interrogate the integrity and efficiency of these mechanisms in disease models as well as in response to genetic or pharmacological perturbations. Several variants of DSBR reporters are available, however these are often limited by throughput or restricted to specific cellular models. Here, we describe the generation and validation of a suite of extrachromosomal reporter assays that can efficiently measure the major DSBR pathways of homologous recombination (HR), classical nonhomologous end joining (cNHEJ), microhomology-mediated end joining (MMEJ) and single strand annealing (SSA). We demonstrate that these assays can be adapted to a high-throughput screening format and that they are sensitive to pharmacological modulation, thus providing mechanistic and quantitative insights into compound potency, selectivity, and on-target specificity. We propose that these reporter assays can serve as tools to dissect the interplay of DSBR pathway networks in cells and will have broad implications for studies of DSBR mechanisms in basic research and drug discovery.
Collapse
Affiliation(s)
- Eeson Rajendra
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | - Diego Grande
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | - Bethany Mason
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | | | - Lucy Armstrong
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | | | - Elias Elinati
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | | | - Simon J Boulton
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
- The Francis Crick Institute, London NW1 1AT, UK
| | - Robert A Heald
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | - Graeme C M Smith
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | | |
Collapse
|
64
|
Tsukada K, Jones SE, Bannister J, Durin MA, Vendrell I, Fawkes M, Fischer R, Kessler BM, Chapman JR, Blackford AN. BLM and BRCA1-BARD1 coordinate complementary mechanisms of joint DNA molecule resolution. Mol Cell 2024; 84:640-658.e10. [PMID: 38266639 DOI: 10.1016/j.molcel.2023.12.040] [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: 03/18/2023] [Revised: 10/10/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
The Bloom syndrome helicase BLM interacts with topoisomerase IIIα (TOP3A), RMI1, and RMI2 to form the BTR complex, which dissolves double Holliday junctions and DNA replication intermediates to promote sister chromatid disjunction before cell division. In its absence, structure-specific nucleases like the SMX complex (comprising SLX1-SLX4, MUS81-EME1, and XPF-ERCC1) can cleave joint DNA molecules instead, but cells deficient in both BTR and SMX are not viable. Here, we identify a negative genetic interaction between BLM loss and deficiency in the BRCA1-BARD1 tumor suppressor complex. We show that this is due to a previously overlooked role for BARD1 in recruiting SLX4 to resolve DNA intermediates left unprocessed by BLM in the preceding interphase. Consequently, cells with defective BLM and BRCA1-BARD1 accumulate catastrophic levels of chromosome breakage and micronucleation, leading to cell death. Thus, we reveal mechanistic insights into SLX4 recruitment to DNA lesions, with potential clinical implications for treating BRCA1-deficient tumors.
Collapse
Affiliation(s)
- Kaima Tsukada
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Samuel E Jones
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Julius Bannister
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Mary-Anne Durin
- MRC Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Iolanda Vendrell
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Matthew Fawkes
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Roman Fischer
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - J Ross Chapman
- MRC Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Andrew N Blackford
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.
| |
Collapse
|
65
|
van de Kooij B, Schreuder A, Pavani R, Garzero V, Uruci S, Wendel TJ, van Hoeck A, San Martin Alonso M, Everts M, Koerse D, Callen E, Boom J, Mei H, Cuppen E, Luijsterburg MS, van Vugt MATM, Nussenzweig A, van Attikum H, Noordermeer SM. EXO1 protects BRCA1-deficient cells against toxic DNA lesions. Mol Cell 2024; 84:659-674.e7. [PMID: 38266640 DOI: 10.1016/j.molcel.2023.12.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 10/14/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
Inactivating mutations in the BRCA1 and BRCA2 genes impair DNA double-strand break (DSB) repair by homologous recombination (HR), leading to chromosomal instability and cancer. Importantly, BRCA1/2 deficiency also causes therapeutically targetable vulnerabilities. Here, we identify the dependency on the end resection factor EXO1 as a key vulnerability of BRCA1-deficient cells. EXO1 deficiency generates poly(ADP-ribose)-decorated DNA lesions during S phase that associate with unresolved DSBs and genomic instability in BRCA1-deficient but not in wild-type or BRCA2-deficient cells. Our data indicate that BRCA1/EXO1 double-deficient cells accumulate DSBs due to impaired repair by single-strand annealing (SSA) on top of their HR defect. In contrast, BRCA2-deficient cells retain SSA activity in the absence of EXO1 and hence tolerate EXO1 loss. Consistent with a dependency on EXO1-mediated SSA, we find that BRCA1-mutated tumors show elevated EXO1 expression and increased SSA-associated genomic scars compared with BRCA1-proficient tumors. Overall, our findings uncover EXO1 as a promising therapeutic target for BRCA1-deficient tumors.
Collapse
Affiliation(s)
- Bert van de Kooij
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Department of Medical Oncology, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Anne Schreuder
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Oncode Institute, Utrecht 3521 AL, the Netherlands
| | - Raphael Pavani
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Veronica Garzero
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Oncode Institute, Utrecht 3521 AL, the Netherlands
| | - Sidrit Uruci
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands
| | - Tiemen J Wendel
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Oncode Institute, Utrecht 3521 AL, the Netherlands
| | - Arne van Hoeck
- Oncode Institute, Utrecht 3521 AL, the Netherlands; Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht 3584 CG, the Netherlands
| | - Marta San Martin Alonso
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Oncode Institute, Utrecht 3521 AL, the Netherlands
| | - Marieke Everts
- Department of Medical Oncology, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Dana Koerse
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jasper Boom
- Sequencing Analysis Support Core, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands
| | - Edwin Cuppen
- Oncode Institute, Utrecht 3521 AL, the Netherlands; Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht 3584 CG, the Netherlands; Hartwig Medical Foundation, Amsterdam 1098 XH, the Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands.
| | - Sylvie M Noordermeer
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Oncode Institute, Utrecht 3521 AL, the Netherlands.
| |
Collapse
|
66
|
Kanev PB, Atemin A, Stoynov S, Aleksandrov R. PARP1 roles in DNA repair and DNA replication: The basi(c)s of PARP inhibitor efficacy and resistance. Semin Oncol 2024; 51:2-18. [PMID: 37714792 DOI: 10.1053/j.seminoncol.2023.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/10/2023] [Indexed: 09/17/2023]
Abstract
Genome integrity is under constant insult from endogenous and exogenous sources. In order to cope, eukaryotic cells have evolved an elaborate network of DNA repair that can deal with diverse lesion types and exhibits considerable functional redundancy. PARP1 is a major sensor of DNA breaks with established and putative roles in a number of pathways within the DNA repair network, including repair of single- and double-strand breaks as well as protection of the DNA replication fork. Importantly, PARP1 is the major target of small-molecule PARP inhibitors (PARPi), which are employed in the treatment of homologous recombination (HR)-deficient tumors, as the latter are particularly susceptible to the accumulation of DNA damage due to an inability to efficiently repair highly toxic double-strand DNA breaks. The clinical success of PARPi has fostered extensive research into PARP biology, which has shed light on the involvement of PARP1 in various genomic transactions. A major goal within the field has been to understand the relationship between catalytic inhibition and PARP1 trapping. The specific consequences of inhibition and trapping on genomic stability as a basis for the cytotoxicity of PARP inhibitors remain a matter of debate. Finally, PARP inhibition is increasingly recognized for its capacity to elicit/modulate anti-tumor immunity. The clinical potential of PARP inhibition is, however, hindered by the development of resistance. Hence, extensive efforts are invested in identifying factors that promote resistance or sensitize cells to PARPi. The current review provides a summary of advances in our understanding of PARP1 biology, the mechanistic nature, and molecular consequences of PARP inhibition, as well as the mechanisms that give rise to PARPi resistance.
Collapse
Affiliation(s)
- Petar-Bogomil Kanev
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Aleksandar Atemin
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Stoyno Stoynov
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| | - Radoslav Aleksandrov
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| |
Collapse
|
67
|
Nakamura K, Hayashi H, Kawano R, Ishikawa M, Aimono E, Mizuno T, Kuroda H, Kojima Y, Niikura N, Kawanishi A, Takeshita K, Suzuki S, Ueno S, Okuwaki K, Sasaki J, Yamaguchi M, Masuda K, Chiyoda T, Yamagami W, Okada C, Nohara S, Tanishima S, Nishihara H. BRCA1/2 reversion mutations in a pan-cancer cohort. Cancer Sci 2024; 115:635-647. [PMID: 38041241 PMCID: PMC10859608 DOI: 10.1111/cas.16033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/09/2023] [Accepted: 11/17/2023] [Indexed: 12/03/2023] Open
Abstract
Tumor sensitivity to platinum (Pt)-based chemotherapy and poly(adenosine diphosphate ribose) polymerase (PARP) inhibitors is increased by homologous recombination deficiency-causing mutations; in particular, reversion mutations cause drug resistance by restoring protein function. Treatment response is predicted by breast cancer susceptibility gene 1/2 (BRCA1/2) mutations; however, BRCA1/2 reversion mutations have not been comprehensively studied in pan-cancer cohorts. We aimed to characterize BRCA1/2 reversion mutations in a large pan-cancer cohort of Japanese patients by retrospectively analyzing sequencing data for BRCA1/2 pathogenic/likely pathogenic mutations in 3738 patients with 32 cancer types. We identified somatic mutations in tumors or circulating cell-free DNA that could restore the ORF of adverse alleles, including reversion mutations. We identified 12 (0.32%) patients with somatic BRCA1 (n = 3) and BRCA2 (n = 9) reversion mutations in breast (n = 4), ovarian/fallopian tube/peritoneal (n = 4), pancreatic (n = 2), prostate (n = 1), and gallbladder (n = 1) cancers. We identified 21 reversion events-BRCA1 (n = 3), BRCA2 (n = 18)-including eight pure deletions, one single-nucleotide variant, six multinucleotide variants, and six deletion-insertions. Seven (33.3%) reversion deletions showed a microhomology length greater than 1 bp, suggesting microhomology-mediated end-join repair. Disease course data were obtained for all patients with reversion events: four patients acquired mutations after PARP-inhibitor treatment failure, two showed somatic reversion mutations after disease progression, following Pt-based treatment, five showed mutations after both treatments, one patient with pancreatic cancer and BRCA1 reversion mutations had no history of either treatment. Although reversion mutations commonly occur in BRCA-associated cancers, our findings suggest that reversion mutations due to Pt-chemotherapy might be correlated with BRCA1/2-mediated tumorigenesis even in non-BRCA-associated histologies.
Collapse
Affiliation(s)
- Kohei Nakamura
- Genomics Unit, Keio Cancer CenterKeio University School of MedicineTokyoJapan
- Department of Obstetrics and GynecologyKumagaya General HospitalKumagayaJapan
| | - Hideyuki Hayashi
- Genomics Unit, Keio Cancer CenterKeio University School of MedicineTokyoJapan
| | - Ryutaro Kawano
- Genomics Unit, Keio Cancer CenterKeio University School of MedicineTokyoJapan
| | - Marin Ishikawa
- Genomics Unit, Keio Cancer CenterKeio University School of MedicineTokyoJapan
| | - Eriko Aimono
- Genomics Unit, Keio Cancer CenterKeio University School of MedicineTokyoJapan
- Department of Cancer Pathology, Faculty of MedicineHokkaido UniversitySapporoJapan
| | - Takaaki Mizuno
- Genomics Unit, Keio Cancer CenterKeio University School of MedicineTokyoJapan
| | - Hajime Kuroda
- Department of Diagnostic Pathology, Adachi Medical CenterTokyo Women's Medical UniversityTokyoJapan
| | - Yasuyuki Kojima
- Showa University Institute for Clinical Genetics and GenomicsTokyoJapan
| | - Naoki Niikura
- Department of Breast OncologyTokai University School of MedicineIseharaJapan
| | - Aya Kawanishi
- Division of Gastroenterology and Hepatology, Department of Internal MedicineTokai University School of MedicineIseharaJapan
| | - Kei Takeshita
- Department of Clinical GeneticsTokai University HospitalIseharaJapan
| | | | - Shinichi Ueno
- Cancer CenterKagoshima University HospitalKagoshimaJapan
| | - Kosuke Okuwaki
- Department of GastroenterologyKitasato University School of MedicineSagamiharaJapan
| | - Jiichiro Sasaki
- Division of Clinical Oncology, Department of Comprehensive Medicine, Research and Development Center for New Medical FrontiersKitasato University School of MedicineSagamiharaJapan
| | | | - Kenta Masuda
- Department of Obstetrics and GynecologyKeio University School of MedicineTokyoJapan
| | - Tatsuyuki Chiyoda
- Department of Obstetrics and GynecologyKeio University School of MedicineTokyoJapan
| | - Wataru Yamagami
- Department of Obstetrics and GynecologyKeio University School of MedicineTokyoJapan
| | - Chihiro Okada
- Department of Biomedical Informatics, Communication Engineering Center, Electronic Systems Business GroupMitsubishi Electric Software Co., Ltd.AmagasakiJapan
| | - Sachio Nohara
- Department of Biomedical Informatics, Communication Engineering Center, Electronic Systems Business GroupMitsubishi Electric Software Co., Ltd.AmagasakiJapan
| | - Shigeki Tanishima
- Department of Biomedical Informatics, Communication Engineering Center, Electronic Systems Business GroupMitsubishi Electric Software Co., Ltd.AmagasakiJapan
| | - Hiroshi Nishihara
- Genomics Unit, Keio Cancer CenterKeio University School of MedicineTokyoJapan
| |
Collapse
|
68
|
He Y, Chen Y, Li Z, Wu C. The m 6A demethylase FTO targets POLQ to promote ccRCC cell proliferation and genome stability maintenance. J Cancer Res Clin Oncol 2024; 150:30. [PMID: 38270643 PMCID: PMC10810938 DOI: 10.1007/s00432-023-05541-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024]
Abstract
BACKGROUND AND AIM As the first identified m6A demethylase, FTO has been implicated in the progression of various cancers. However, the specific mechanism of FTO in clear cell renal cell carcinoma (ccRCC) remains incompletely understood. In this study, we aimed to explore the potential molecular mechanisms influencing the progression of ccRCC. METHODS We initially assessed the expression of FTO in tumor and adjacent tissues using TCGA database, RT-qPCR, and Western blot. We then conducted CCK-8, cell cycle analysis, and colony formation assay to investigate the impact of FTO on ccRCC cell proliferation. MeRIP-seq and RNA-seq were employed to identify potential downstream targets of FTO in ccRCC, and these findings were further validated through dual-luciferase reporter assays and MeRIP-qPCR. Then, DNA damage and cell death were assessed separately through gammaH2AX immunofluorescence detection and the LIVE/DEAD Fixable Dead Cell Stain assay, respectively. Subsequently, we identified downstream pathways influenced by FTO's regulation of POLQ through TCGA database analysis and GSEA enrichment analysis. Validation was carried out through Western blot. RESULTS FTO is highly expressed in ccRCC tissues and cell lines. Furthermore, ROC curve demonstrates that FTO contributes to the diagnosis of ccRCC. FTO modulates m6A modification, consequently influencing the expression of POLQ, thus facilitating cell proliferation and maintaining genome stability in ccRCC. CONCLUSION FTO could potentially serve as a diagnostic marker for ccRCC. FTO promotes the progression of ccRCC by regulating m6A modification, making the inhibition of FTO a potential novel therapeutic strategy in ccRCC.
Collapse
Affiliation(s)
- Yichen He
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, China
- Institute of Cell Therapy, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, China
- Department of Urology, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, China
| | - Yimeng Chen
- Department of Urology, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, China
| | - Zhengsheng Li
- Department of Urology, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, China
| | - Changping Wu
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, China.
- Institute of Cell Therapy, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, China.
- Department of Oncology, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, China.
| |
Collapse
|
69
|
Wang J, Chen Y, Li S, Liu W, Zhou XA, Luo Y, Xu Z, Xiong Y, Cheng K, Ruan M, Yu W, Li X, Wang W, Wang J. PP2A inhibition causes synthetic lethality in BRCA2-mutated prostate cancer models via spindle assembly checkpoint reactivation. J Clin Invest 2024; 134:e172137. [PMID: 37934606 PMCID: PMC10760972 DOI: 10.1172/jci172137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/31/2023] [Indexed: 11/09/2023] Open
Abstract
Mutations in the BRCA2 tumor suppressor gene have been associated with an increased risk of developing prostate cancer. One of the paradoxes concerning BRCA2 is the fact that its inactivation affects genetic stability and is deleterious for cellular and organismal survival, while BRCA2-mutated cancer cells adapt to this detriment and malignantly proliferate. Therapeutic strategies for tumors arising from BRCA2 mutations may be discovered by understanding these adaptive mechanisms. In this study, we conducted forward genetic synthetic viability screenings in Caenorhabditis elegans brc-2 (Cebrc-2) mutants and found that Ceubxn-2 inactivation rescued the viability of Cebrc-2 mutants. Moreover, loss of NSFL1C, the mammalian ortholog of CeUBXN-2, suppressed the spindle assembly checkpoint (SAC) activation and promoted the survival of BRCA2-deficient cells. Mechanistically, NSFL1C recruited USP9X to inhibit the polyubiquitination of AURKB and reduce the removal of AURKB from the centromeres by VCP, which is essential for SAC activation. SAC inactivation is common in BRCA2-deficient prostate cancer patients, but PP2A inhibitors could reactivate the SAC and achieve BRCA2-deficient prostate tumor synthetic lethality. Our research reveals the survival adaptation mechanism of BRCA2-deficient prostate tumor cells and provides different angles for exploring synthetic lethal inhibitors in addition to targeting DNA damage repair pathways.
Collapse
Affiliation(s)
- Jian Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Yuke Chen
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Shiwei Li
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Wanchang Liu
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Xiao Albert Zhou
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Yefei Luo
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Zhanzhan Xu
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Yundong Xiong
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Kaiqi Cheng
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Mingjian Ruan
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Wei Yu
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Xiaoman Li
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Weibin Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Jiadong Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| |
Collapse
|
70
|
Nagelli S, Westermarck J. CIP2A coordinates phosphosignaling, mitosis, and the DNA damage response. Trends Cancer 2024; 10:52-64. [PMID: 37793965 DOI: 10.1016/j.trecan.2023.09.001] [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: 07/14/2023] [Revised: 08/18/2023] [Accepted: 09/04/2023] [Indexed: 10/06/2023]
Abstract
Human cancers share requirements for phosphorylation-dependent signaling, mitotic hyperactivity, and survival after DNA damage. The oncoprotein CIP2A (cancerous inhibitor of PP2A) can coordinate all these cancer cell characteristics. In addition to controlling cancer cell phosphoproteomes via inhibition of protein phosphatase PP2A, CIP2A directly interacts with the DNA damage protein TopBP1 (topoisomerase II-binding protein 1). Consequently, CIP2A allows DNA-damaged cells to enter mitosis and is essential for mitotic cells that are defective in homologous recombination (HR)-mediated DNA repair (e.g., BRCA mutants). The CIP2A-TopBP1 complex is also important for clustering fragmented chromosomes at mitosis. Clinically, CIP2A is a disease driver for basal-like triple-negative breast cancer (BL-TNBC) and a promising cancer therapy target across many cancer types.
Collapse
Affiliation(s)
- Srikar Nagelli
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; Institute of Biomedicine and FICANWest Cancer Center, University of Turku, Turku, Finland
| | - Jukka Westermarck
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; Institute of Biomedicine and FICANWest Cancer Center, University of Turku, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku, Finland.
| |
Collapse
|
71
|
Yueh WT, Glass DJ, Johnson N. Brca1 Mouse Models: Functional Insights and Therapeutic Opportunities. J Mol Biol 2024; 436:168372. [PMID: 37979908 PMCID: PMC10882579 DOI: 10.1016/j.jmb.2023.168372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 11/20/2023]
Abstract
Brca1 mouse models were first reported in the mid-1990's shortly after cloning the human gene. Since then, many mouse models with a range of mutations have been generated, some mimic patient mutations, others are designed to probe specific protein domains and functions. In this review, we discuss early and recent studies using engineered Brca1 mouse alleles, and their implications for understanding Brca1 protein function in the context of DNA repair, tumorigenesis, and anti-cancer therapeutics.
Collapse
Affiliation(s)
- Wei-Ting Yueh
- Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - David J Glass
- Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Neil Johnson
- Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
| |
Collapse
|
72
|
Nassour J, Przetocka S, Karlseder J. Telomeres as hotspots for innate immunity and inflammation. DNA Repair (Amst) 2024; 133:103591. [PMID: 37951043 PMCID: PMC10842095 DOI: 10.1016/j.dnarep.2023.103591] [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: 07/24/2023] [Revised: 10/05/2023] [Accepted: 10/24/2023] [Indexed: 11/13/2023]
Abstract
Aging is marked by the gradual accumulation of deleterious changes that disrupt organ function, creating an altered physiological state that is permissive for the onset of prevalent human diseases. While the exact mechanisms governing aging remain a subject of ongoing research, there are several cellular and molecular hallmarks that contribute to this biological process. This review focuses on two factors, namely telomere dysfunction and inflammation, which have emerged as crucial contributors to the aging process. We aim to discuss the mechanistic connections between these two distinct hallmarks and provide compelling evidence highlighting the loss of telomere protection as a driver of pro-inflammatory states associated with aging. By reevaluating the interplay between telomeres, innate immunity, and inflammation, we present novel perspectives on the etiology of aging and its associated diseases.
Collapse
Affiliation(s)
- Joe Nassour
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, 12801 E. 17th Ave, Aurora, CO 80045, USA; The Salk Institute for Biological Studies, 10010 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Sara Przetocka
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Jan Karlseder
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Rd, La Jolla, CA 92037, USA.
| |
Collapse
|
73
|
Sallmyr A, Bhandari SK, Naila T, Tomkinson AE. Mammalian DNA ligases; roles in maintaining genome integrity. J Mol Biol 2024; 436:168276. [PMID: 37714297 PMCID: PMC10843057 DOI: 10.1016/j.jmb.2023.168276] [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: 06/18/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
The joining of breaks in the DNA phosphodiester backbone is essential for genome integrity. Breaks are generated during normal processes such as DNA replication, cytosine demethylation during differentiation, gene rearrangement in the immune system and germ cell development. In addition, they are generated either directly by a DNA damaging agent or indirectly due to damage excision during repair. Breaks are joined by a DNA ligase that catalyzes phosphodiester bond formation at DNA nicks with 3' hydroxyl and 5' phosphate termini. Three human genes encode ATP-dependent DNA ligases. These enzymes have a conserved catalytic core consisting of three subdomains that encircle nicked duplex DNA during ligation. The DNA ligases are targeted to different nuclear DNA transactions by specific protein-protein interactions. Both DNA ligase IIIα and DNA ligase IV form stable complexes with DNA repair proteins, XRCC1 and XRCC4, respectively. There is functional redundancy between DNA ligase I and DNA ligase IIIα in DNA replication, excision repair and single-strand break repair. Although DNA ligase IV is a core component of the major double-strand break repair pathway, non-homologous end joining, the other enzymes participate in minor, alternative double-strand break repair pathways. In contrast to the nucleus, only DNA ligase IIIα is present in mitochondria and is essential for maintaining the mitochondrial genome. Human immunodeficiency syndromes caused by mutations in either LIG1 or LIG4 have been described. Preclinical studies with DNA ligase inhibitors have identified potentially targetable abnormalities in cancer cells and evidence that DNA ligases are potential targets for cancer therapy.
Collapse
Affiliation(s)
- Annahita Sallmyr
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States
| | - Seema Khattri Bhandari
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States
| | - Tasmin Naila
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States
| | - Alan E Tomkinson
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States.
| |
Collapse
|
74
|
Bugbee T, Gathoni M, Payne C, Blubaugh M, Matlock K, Wixson T, Lu A, Stancic S, Chung PA, Palinski R, Wallace N. Inhibition of p300 increases cytotoxicity of cisplatin in pancreatic cancer cells. Gene 2023; 888:147762. [PMID: 37666373 PMCID: PMC10563798 DOI: 10.1016/j.gene.2023.147762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/29/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Pancreatic cancer is a notoriously deadly disease with a five-year survival rate around 10 percent. Since early detection of these tumors is difficult, pancreatic cancers are often diagnosed at advanced stages. At this point, genotoxic chemotherapeutics can be used to manage tumor growth. However, side effects of these drugs are severe, limiting the amount of treatment that can be given and resulting in sub-optimal dosing. Thus, there is an urgent need to identify chemo-sensitizing agents that can lower the effective dose of genotoxic agents and as a result reduce the side effects. Here, we use transformed and non-transformed pancreatic cell lines to evaluate DNA repair inhibitors as chemo-sensitizing agents. We used a novel next generation sequencing approach to demonstrate that pancreatic cancer cells have a reduced ability to faithfully repair DNA damage. We then determine the extent that two DNA repair inhibitors (CCS1477, a small molecule inhibitor of p300, and ART558, a small molecule inhibitor of polymerase theta) can exploit this repair deficiency to make pancreatic cancer cells more sensitive to cisplatin, a commonly used genotoxic chemotherapeutic. Immunofluorescence microscopy and cell viability assays show that CCS1477 delayed repair and significantly sensitized pancreatic cancer cells to cisplatin. The increased toxicity was not seen in a non-transformed pancreatic cell line. We also found that while ART558 sensitizes pancreatic cancer cells to cisplatin, it also sensitized non-transformed pancreatic cancer cells.
Collapse
Affiliation(s)
- Taylor Bugbee
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Mary Gathoni
- Department of Biology, Pittsburg State University, Pittsburg, KS 66762, USA
| | - Carlie Payne
- Department of Biology, Pittsburg State University, Pittsburg, KS 66762, USA
| | - Morgan Blubaugh
- Department of Biology, Pittsburg State University, Pittsburg, KS 66762, USA
| | - Kaydn Matlock
- Department of Biology, Pittsburg State University, Pittsburg, KS 66762, USA
| | - Taylor Wixson
- Department of Biology, Pittsburg State University, Pittsburg, KS 66762, USA
| | - Andrea Lu
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA
| | - Steven Stancic
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA
| | - Peter A Chung
- Department of Biology, Pittsburg State University, Pittsburg, KS 66762, USA
| | - Rachel Palinski
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA; Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Nicholas Wallace
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA.
| |
Collapse
|
75
|
Zhou J, Nie R, He Z, Cai X, Chen J, Lin W, Yin Y, Xiang Z, Zhu T, Xie J, Zhang Y, Wang X, Lin P, Xie D, D'Andrea AD, Cai M. STAG2 Regulates Homologous Recombination Repair and Sensitivity to ATM Inhibition. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302494. [PMID: 37985839 PMCID: PMC10754142 DOI: 10.1002/advs.202302494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 10/15/2023] [Indexed: 11/22/2023]
Abstract
Stromal antigen 2 (STAG2), a subunit of the cohesin complex, is recurrently mutated in various tumors. However, the role of STAG2 in DNA repair and its therapeutic implications are largely unknown. Here it is reported that knockout of STAG2 results in increased double-stranded breaks (DSBs) and chromosomal aberrations by reducing homologous recombination (HR) repair, and confers hypersensitivity to inhibitors of ataxia telangiectasia mutated (ATMi), Poly ADP Ribose Polymerase (PARPi), or the combination of both. Of note, the impaired HR by STAG2-deficiency is mainly attributed to the restored expression of KMT5A, which in turn methylates H4K20 (H4K20me0) to H4K20me1 and thereby decreases the recruitment of BRCA1-BARD1 to chromatin. Importantly, STAG2 expression correlates with poor prognosis of cancer patients. STAG2 is identified as an important regulator of HR and a potential therapeutic strategy for STAG2-mutant tumors is elucidated.
Collapse
Affiliation(s)
- Jie Zhou
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
- Guangxi International Travel Healthcare Centre (Port Clinic of Nanning Customs District)NanningGuangxi530021China
| | - Run‐Cong Nie
- Department of Gastric SurgeryState Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Zhang‐Ping He
- Department of PathologyState Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Xiao‐Xia Cai
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Jie‐Wei Chen
- Department of PathologyState Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Wen‐ping Lin
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Yi‐Xin Yin
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Zhi‐Cheng Xiang
- Department of PathologyState Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Tian‐Chen Zhu
- Department of PathologyState Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Juan‐Juan Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - You‐Cheng Zhang
- Department of PathologyState Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Xin Wang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Peng Lin
- Department of Thoracic SurgeryState Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Dan Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
- Department of PathologyState Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Alan D D'Andrea
- Department of Radiation OncologyDana‐Farber Cancer InstituteBostonMA02215USA
- Center for DNA Damage and RepairDana‐Farber Cancer InstituteBostonMA02215USA
| | - Mu‐Yan Cai
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
- Department of PathologyState Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060China
| |
Collapse
|
76
|
Mai N, Abuhadra N, Jhaveri K. Molecularly Targeted Therapies for Triple Negative Breast Cancer: History, Advances, and Future Directions. Clin Breast Cancer 2023; 23:784-799. [PMID: 37336650 DOI: 10.1016/j.clbc.2023.05.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/16/2023] [Accepted: 05/21/2023] [Indexed: 06/21/2023]
Abstract
Triple negative breast cancer (TNBC) remains the subtype with poorest prognosis. Despite the subtype's heterogeneity, there is still a paucity in effective targeted therapeutics that offer both good efficacy and tolerability, and chemotherapy remains the backbone of modern TNBC therapy. In the past few years, immunotherapy as well as novel therapeutic modalities like antibody-drug conjugates (ADCs) have shown clinical benefit and have been FDA approved in various clinical stages of unselected TNBC. However, there has not been similar advancement in molecularly targeted therapies, especially when compared to advancements seen in hormone receptor (HR)-positive or HER2-positive breast cancer. PARP inhibitors have been approved for BRCA-mutated TNBC, but responses are short-lived, and resistance remains a barrier for current treatment. PI3K pathway inhibitors approved in HR+ breast cancer has not worked for TNBC and continue to have significant dose-limiting adverse effects. EGFR inhibition has been thoroughly explored in TNBC, but all trials so far have shown minimal efficacy. Nevertheless, despite these setbacks, current research in targeted therapy for TNBC holds great promise in overcoming the barriers of the past and developing novel therapeutic approaches for the future. In this review, we describe molecular targets both identified and validated in the treatment of TNBC, discuss the historical efforts towards development of targeted agents and current areas of improvement, and address promising advances that have the potential to improve outcomes in this heterogenous and aggressive breast cancer subtype. Immunotherapy, ADCs, and AR targeting will be discussed in separate reviews of this edition.
Collapse
Affiliation(s)
- Nicholas Mai
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nour Abuhadra
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Komal Jhaveri
- Memorial Sloan Kettering Cancer Center, New York, NY.
| |
Collapse
|
77
|
Classen S, Petersen C, Borgmann K. Crosstalk between immune checkpoint and DNA damage response inhibitors for radiosensitization of tumors. Strahlenther Onkol 2023; 199:1152-1163. [PMID: 37420037 PMCID: PMC10674014 DOI: 10.1007/s00066-023-02103-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/16/2023] [Indexed: 07/09/2023]
Abstract
PURPOSE This review article is intended to provide a perspective overview of potential strategies to overcome radiation resistance of tumors through the combined use of immune checkpoint and DNA repair inhibitors. METHODS A literature search was conducted in PubMed using the terms ("DNA repair* and DNA damage response* and intracellular immune response* and immune checkpoint inhibition* and radio*") until January 31, 2023. Articles were manually selected based on their relevance to the topics analyzed. RESULTS Modern radiotherapy offers a wide range of options for tumor treatment. Radiation-resistant subpopulations of the tumor pose a particular challenge for complete cure. This is due to the enhanced activation of molecular defense mechanisms that prevent cell death because of DNA damage. Novel approaches to enhance tumor cure are provided by immune checkpoint inhibitors, but their effectiveness, especially in tumors without increased mutational burden, also remains limited. Combining inhibitors of both immune checkpoints and DNA damage response with radiation may be an attractive option to augment existing therapies and is the subject of the data summarized here. CONCLUSION The combination of tested inhibitors of DNA damage and immune responses in preclinical models opens additional attractive options for the radiosensitization of tumors and represents a promising application for future therapeutic approaches.
Collapse
Affiliation(s)
- Sandra Classen
- Laboratory of Radiobiology and Radiation Oncology, Department of Radiotherapy and Radiation Oncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Cordula Petersen
- Department of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Kerstin Borgmann
- Laboratory of Radiobiology and Radiation Oncology, Department of Radiotherapy and Radiation Oncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
| |
Collapse
|
78
|
Ronson GE, Starowicz K, Anthony EJ, Piberger AL, Clarke LC, Garvin AJ, Beggs AD, Whalley CM, Edmonds MJ, Beesley JFJ, Morris JR. Mechanisms of synthetic lethality between BRCA1/2 and 53BP1 deficiencies and DNA polymerase theta targeting. Nat Commun 2023; 14:7834. [PMID: 38030626 PMCID: PMC10687250 DOI: 10.1038/s41467-023-43677-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 11/16/2023] [Indexed: 12/01/2023] Open
Abstract
A synthetic lethal relationship exists between disruption of polymerase theta (Polθ), and loss of either 53BP1 or homologous recombination (HR) proteins, including BRCA1; however, the mechanistic basis of these observations are unclear. Here we reveal two distinct mechanisms of Polθ synthetic lethality, identifying dual influences of 1) whether Polθ is lost or inhibited, and 2) the underlying susceptible genotype. Firstly, we find that the sensitivity of BRCA1/2- and 53BP1-deficient cells to Polθ loss, and 53BP1-deficient cells to Polθ inhibition (ART558) requires RAD52, and appropriate reduction of RAD52 can ameliorate these phenotypes. We show that in the absence of Polθ, RAD52 accumulations suppress ssDNA gap-filling in G2/M and encourage MRE11 nuclease accumulation. In contrast, the survival of BRCA1-deficient cells treated with Polθ inhibitor are not restored by RAD52 suppression, and ssDNA gap-filling is prevented by the chemically inhibited polymerase itself. These data define an additional role for Polθ, reveal the mechanism underlying synthetic lethality between 53BP1, BRCA1/2 and Polθ loss, and indicate genotype-dependent Polθ inhibitor mechanisms.
Collapse
Affiliation(s)
- George E Ronson
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Katarzyna Starowicz
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Adthera Bio, Lyndon House, 62 Hagley Road, Birmingham, B16 8PE, UK
| | - Elizabeth J Anthony
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ann Liza Piberger
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Lucy C Clarke
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- West Midlands Regional Genetics Laboratory, Birmingham Women's Hospital, Mindelsohn Way, Birmingham, B15 2TG, UK
| | - Alexander J Garvin
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- University of Leeds, Leeds, UK
| | - Andrew D Beggs
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Genomics Birmingham, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Celina M Whalley
- Genomics Birmingham, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Matthew J Edmonds
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Certara Insight, Danebrook Court, Oxford Office Village, Kidlington, Oxfordshire, OX5 1LQ, UK
| | - James F J Beesley
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Joanna R Morris
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| |
Collapse
|
79
|
Nickoloff JA, Jaiswal AS, Sharma N, Williamson EA, Tran MT, Arris D, Yang M, Hromas R. Cellular Responses to Widespread DNA Replication Stress. Int J Mol Sci 2023; 24:16903. [PMID: 38069223 PMCID: PMC10707325 DOI: 10.3390/ijms242316903] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Replicative DNA polymerases are blocked by nearly all types of DNA damage. The resulting DNA replication stress threatens genome stability. DNA replication stress is also caused by depletion of nucleotide pools, DNA polymerase inhibitors, and DNA sequences or structures that are difficult to replicate. Replication stress triggers complex cellular responses that include cell cycle arrest, replication fork collapse to one-ended DNA double-strand breaks, induction of DNA repair, and programmed cell death after excessive damage. Replication stress caused by specific structures (e.g., G-rich sequences that form G-quadruplexes) is localized but occurs during the S phase of every cell division. This review focuses on cellular responses to widespread stress such as that caused by random DNA damage, DNA polymerase inhibition/nucleotide pool depletion, and R-loops. Another form of global replication stress is seen in cancer cells and is termed oncogenic stress, reflecting dysregulated replication origin firing and/or replication fork progression. Replication stress responses are often dysregulated in cancer cells, and this too contributes to ongoing genome instability that can drive cancer progression. Nucleases play critical roles in replication stress responses, including MUS81, EEPD1, Metnase, CtIP, MRE11, EXO1, DNA2-BLM, SLX1-SLX4, XPF-ERCC1-SLX4, Artemis, XPG, FEN1, and TATDN2. Several of these nucleases cleave branched DNA structures at stressed replication forks to promote repair and restart of these forks. We recently defined roles for EEPD1 in restarting stressed replication forks after oxidative DNA damage, and for TATDN2 in mitigating replication stress caused by R-loop accumulation in BRCA1-defective cells. We also discuss how insights into biological responses to genome-wide replication stress can inform novel cancer treatment strategies that exploit synthetic lethal relationships among replication stress response factors.
Collapse
Affiliation(s)
- Jac A. Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, CO 80523, USA
| | - Aruna S. Jaiswal
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Neelam Sharma
- Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, CO 80523, USA
| | - Elizabeth A. Williamson
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Manh T. Tran
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Dominic Arris
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Ming Yang
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Robert Hromas
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| |
Collapse
|
80
|
Krais JJ, Glass DJ, Chudoba I, Wang Y, Feng W, Simpson D, Patel P, Liu Z, Neumann-Domer R, Betsch RG, Bernhardy AJ, Bradbury AM, Conger J, Yueh WT, Nacson J, Pomerantz RT, Gupta GP, Testa JR, Johnson N. Genetic separation of Brca1 functions reveal mutation-dependent Polθ vulnerabilities. Nat Commun 2023; 14:7714. [PMID: 38001070 PMCID: PMC10673838 DOI: 10.1038/s41467-023-43446-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Homologous recombination (HR)-deficiency induces a dependency on DNA polymerase theta (Polθ/Polq)-mediated end joining, and Polθ inhibitors (Polθi) are in development for cancer therapy. BRCA1 and BRCA2 deficient cells are thought to be synthetic lethal with Polθ, but whether distinct HR gene mutations give rise to equivalent Polθ-dependence, and the events that drive lethality, are unclear. In this study, we utilized mouse models with separate Brca1 functional defects to mechanistically define Brca1-Polθ synthetic lethality. Surprisingly, homozygous Brca1 mutant, Polq-/- cells were viable, but grew slowly and had chromosomal instability. Brca1 mutant cells proficient in DNA end resection were significantly more dependent on Polθ for viability; here, treatment with Polθi elevated RPA foci, which persisted through mitosis. In an isogenic system, BRCA1 null cells were defective, but PALB2 and BRCA2 mutant cells exhibited active resection, and consequently stronger sensitivity to Polθi. Thus, DNA end resection is a critical determinant of Polθi sensitivity in HR-deficient cells, and should be considered when selecting patients for clinical studies.
Collapse
Affiliation(s)
- John J Krais
- Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - David J Glass
- Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
- Temple University, Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Ilse Chudoba
- MetaSystems Probes, GmbH, Industriestr, 68804, Altlussheim, Germany
| | - Yifan Wang
- Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Wanjuan Feng
- Department of Radiation Oncology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Dennis Simpson
- Department of Radiation Oncology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Pooja Patel
- Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Zemin Liu
- Cytogenetics Laboratory, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Ryan Neumann-Domer
- Cytogenetics Laboratory, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Robert G Betsch
- Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Andrea J Bernhardy
- Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Alice M Bradbury
- Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Jason Conger
- Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Wei-Ting Yueh
- Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Joseph Nacson
- Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Richard T Pomerantz
- Thomas Jefferson University, Sidney Kimmel Cancer Center, Department of Biochemistry and Molecular Biology, Philadelphia, PA, 19107, USA
| | - Gaorav P Gupta
- Cancer Control and Prevention Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Joseph R Testa
- Cytogenetics Laboratory, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
- Cancer Control and Prevention Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Neil Johnson
- Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
| |
Collapse
|
81
|
Zhang X, Joseph S, Wu D, Bowser JL, Vaziri C. The DNA Damage Response (DDR) landscape of endometrial cancer defines discrete disease subtypes and reveals therapeutic opportunities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567919. [PMID: 38045328 PMCID: PMC10690150 DOI: 10.1101/2023.11.20.567919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Genome maintenance is an enabling characteristic that allows neoplastic cells to tolerate the inherent stresses of tumorigenesis and evade therapy-induced genotoxicity. Neoplastic cells also deploy mis-expressed germ cell proteins termed Cancer Testes Antigens (CTAs) to promote genome maintenance and survival. Here, we present the first comprehensive characterization of the DNA Damage Response (DDR) and CTA transcriptional landscapes of endometrial cancer in relation to conventional histological and molecular subtypes. We show endometrial serous carcinoma (ESC), an aggressive endometrial cancer subtype, is defined by gene expression signatures comprising members of the Replication Fork Protection Complex (RFPC) and Fanconi Anemia (FA) pathway and CTAs with mitotic functions. DDR and CTA- based profiling also defines a subset of highly aggressive endometrioid endometrial carcinomas (EEC) with poor clinical outcomes that share similar profiles to ESC yet have distinct characteristics based on conventional histological and genomic features. Using an unbiased CRISPR-based genetic screen and a candidate gene approach, we confirm that DDR and CTA genes that constitute the ESC and related EEC gene signatures are required for proliferation and therapy-resistance of cultured endometrial cancer cells. Our study validates the use of DDR and CTA-based tumor classifiers and reveals new vulnerabilities of aggressive endometrial cancer where none currently exist.
Collapse
|
82
|
Zhou X, Sekino Y, Li HT, Fu G, Yang Z, Zhao S, Gujar H, Zu X, Weisenberger DJ, Gill IS, Tulpule V, D’souza A, Quinn DI, Han B, Liang G. SETD2 Deficiency Confers Sensitivity to Dual Inhibition of DNA Methylation and PARP in Kidney Cancer. Cancer Res 2023; 83:3813-3826. [PMID: 37695044 PMCID: PMC10843145 DOI: 10.1158/0008-5472.can-23-0401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/18/2023] [Accepted: 09/06/2023] [Indexed: 09/12/2023]
Abstract
SETD2 deficiency alters the epigenetic landscape by causing depletion of H3K36me3 and plays an important role in diverse forms of cancer, most notably in aggressive and metastatic clear-cell renal cell carcinomas (ccRCC). Development of an effective treatment scheme targeting SETD2-compromised cancer is urgently needed. Considering that SETD2 is involved in DNA methylation and DNA repair, a combination treatment approach using DNA hypomethylating agents (HMA) and PARP inhibitors (PARPi) could have strong antitumor activity in SETD2-deficient kidney cancer. We tested the effects of the DNA HMA 5-aza-2'-dexoxydytidine (DAC), the PARPi talazoparib (BMN-673), and both in combination in human ccRCC models with or without SETD2 deficiency. The combination treatment of DAC and BMN-673 synergistically increased cytotoxicity in vitro in SETD2-deficient ccRCC cell lines but not in SETD2-proficient cell lines. DAC and BMN-673 led to apoptotic induction, increased DNA damage, insufficient DNA damage repair, and increased genomic instability. Furthermore, the combination treatment elevated immune responses, upregulated STING, and enhanced viral mimicry by activating transposable elements. Finally, the combination effectively suppressed the growth of SETD2-deficient ccRCC in in vivo mouse models. Together, these findings indicate that combining HMA and PARPi is a promising potential therapeutic strategy for treating SETD2-compromised ccRCC. SIGNIFICANCE SETD2 deficiency creates a vulnerable epigenetic status that is targetable using a DNA hypomethylating agent and PARP inhibitor combination to suppress renal cell carcinoma, identifying a precision medicine-based approach for SETD2-compromised cancers.
Collapse
Affiliation(s)
- Xinyi Zhou
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Urology, Xiangya Hospital, Central South University, Hunan, Changsha 410008, China
| | - Yohei Sekino
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Urology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hong-Tao Li
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Guanghou Fu
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Zhi Yang
- Department of Surgery, Keck School of Medicine of USC, Los Angeles, California; Department of Surgery and Biomedical Engineering, Keck School of Medicine USC, Los Angeles, CA, USA
| | - Shuqing Zhao
- Department of Surgery, Keck School of Medicine of USC, Los Angeles, California; Department of Surgery and Biomedical Engineering, Keck School of Medicine USC, Los Angeles, CA, USA
| | - Hemant Gujar
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xiongbing Zu
- Department of Urology, Xiangya Hospital, Central South University, Hunan, Changsha 410008, China
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Inderbir S. Gill
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Varsha Tulpule
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Anishka D’souza
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David I Quinn
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Bo Han
- Department of Surgery, Keck School of Medicine of USC, Los Angeles, California; Department of Surgery and Biomedical Engineering, Keck School of Medicine USC, Los Angeles, CA, USA
| | - Gangning Liang
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
83
|
Rautajoki KJ, Jaatinen S, Hartewig A, Tiihonen AM, Annala M, Salonen I, Valkonen M, Simola V, Vuorinen EM, Kivinen A, Rauhala MJ, Nurminen R, Maass KK, Lahtela SL, Jukkola A, Yli-Harja O, Helén P, Pajtler KW, Ruusuvuori P, Haapasalo J, Zhang W, Haapasalo H, Nykter M. Genomic characterization of IDH-mutant astrocytoma progression to grade 4 in the treatment setting. Acta Neuropathol Commun 2023; 11:176. [PMID: 37932833 PMCID: PMC10629206 DOI: 10.1186/s40478-023-01669-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023] Open
Abstract
As the progression of low-grade diffuse astrocytomas into grade 4 tumors significantly impacts patient prognosis, a better understanding of this process is of paramount importance for improved patient care. In this project, we analyzed matched IDH-mutant astrocytomas before and after progression to grade 4 from six patients (discovery cohort) with genome-wide sequencing, 21 additional patients with targeted sequencing, and 33 patients from Glioma Longitudinal AnalySiS cohort for validation. The Cancer Genome Atlas data from 595 diffuse gliomas provided supportive information. All patients in our discovery cohort received radiation, all but one underwent chemotherapy, and no patient received temozolomide (TMZ) before progression to grade 4 disease. One case in the discovery cohort exhibited a hypermutation signature associated with the inactivation of the MSH2 and DNMT3A genes. In other patients, the number of chromosomal rearrangements and deletions increased in grade 4 tumors. The cell cycle checkpoint gene CDKN2A, or less frequently RB1, was most commonly inactivated after receiving both chemo- and radiotherapy when compared to other treatment groups. Concomitant activating PDGFRA/MET alterations were detected in tumors that acquired a homozygous CDKN2A deletion. NRG3 gene was significantly downregulated and recurrently altered in progressed tumors. Its decreased expression was associated with poorer overall survival in both univariate and multivariate analysis. We also detected progression-related alterations in RAD51B and other DNA repair pathway genes associated with the promotion of error-prone DNA repair, potentially facilitating tumor progression. In our retrospective analysis of patient treatment and survival timelines (n = 75), the combination of postoperative radiation and chemotherapy (mainly TMZ) outperformed radiation, especially in the grade 3 tumor cohort, in which it was typically given after primary surgery. Our results provide further insight into the contribution of treatment and genetic alterations in cell cycle, growth factor signaling, and DNA repair-related genes to tumor evolution and progression.
Collapse
Affiliation(s)
- Kirsi J Rautajoki
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland.
- Tampere Institute for Advanced Study, Tampere University, Tampere, Finland.
| | - Serafiina Jaatinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Anja Hartewig
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Aliisa M Tiihonen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Matti Annala
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Iida Salonen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Masi Valkonen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Vili Simola
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Elisa M Vuorinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Anni Kivinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Minna J Rauhala
- Department of Neurosurgery, Tampere University Hospital and Tampere University, Tampere, Finland
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Riikka Nurminen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Kendra K Maass
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro Oncology, German Cancer Research Center, German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Sirpa-Liisa Lahtela
- Department of Oncology, Tampere University Hospital and Tays Cancer Centre, Tampere, Finland
| | - Arja Jukkola
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
- Department of Oncology, Tampere University Hospital and Tays Cancer Centre, Tampere, Finland
| | - Olli Yli-Harja
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
- Institute for Systems Biology, Seattle, WA, USA
| | - Pauli Helén
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro Oncology, German Cancer Research Center, German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Pekka Ruusuvuori
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Joonas Haapasalo
- Department of Neurosurgery, Tampere University Hospital and Tampere University, Tampere, Finland
- Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland
| | - Wei Zhang
- Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA
| | - Hannu Haapasalo
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
- Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| |
Collapse
|
84
|
Jacobson DH, Pan S, Fisher J, Secrier M. Multi-scale characterisation of homologous recombination deficiency in breast cancer. Genome Med 2023; 15:90. [PMID: 37919776 PMCID: PMC10621207 DOI: 10.1186/s13073-023-01239-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 09/26/2023] [Indexed: 11/04/2023] Open
Abstract
BACKGROUND Homologous recombination is a robust, broadly error-free mechanism of double-strand break repair, and deficiencies lead to PARP inhibitor sensitivity. Patients displaying homologous recombination deficiency can be identified using 'mutational signatures'. However, these patterns are difficult to reliably infer from exome sequencing. Additionally, as mutational signatures are a historical record of mutagenic processes, this limits their utility in describing the current status of a tumour. METHODS We apply two methods for characterising homologous recombination deficiency in breast cancer to explore the features and heterogeneity associated with this phenotype. We develop a likelihood-based method which leverages small insertions and deletions for high-confidence classification of homologous recombination deficiency for exome-sequenced breast cancers. We then use multinomial elastic net regression modelling to develop a transcriptional signature of heterogeneous homologous recombination deficiency. This signature is then applied to single-cell RNA-sequenced breast cancer cohorts enabling analysis of homologous recombination deficiency heterogeneity and differential patterns of tumour microenvironment interactivity. RESULTS We demonstrate that the inclusion of indel events, even at low levels, improves homologous recombination deficiency classification. Whilst BRCA-positive homologous recombination deficient samples display strong similarities to those harbouring BRCA1/2 defects, they appear to deviate in microenvironmental features such as hypoxic signalling. We then present a 228-gene transcriptional signature which simultaneously characterises homologous recombination deficiency and BRCA1/2-defect status, and is associated with PARP inhibitor response. Finally, we show that this signature is applicable to single-cell transcriptomics data and predict that these cells present a distinct milieu of interactions with their microenvironment compared to their homologous recombination proficient counterparts, typified by a decreased cancer cell response to TNFα signalling. CONCLUSIONS We apply multi-scale approaches to characterise homologous recombination deficiency in breast cancer through the development of mutational and transcriptional signatures. We demonstrate how indels can improve homologous recombination deficiency classification in exome-sequenced breast cancers. Additionally, we demonstrate the heterogeneity of homologous recombination deficiency, especially in relation to BRCA1/2-defect status, and show that indications of this feature can be captured at a single-cell level, enabling further investigations into interactions between DNA repair deficient cells and their tumour microenvironment.
Collapse
Affiliation(s)
- Daniel H Jacobson
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
- UCL Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK
| | - Shi Pan
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Jasmin Fisher
- UCL Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK
| | - Maria Secrier
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK.
| |
Collapse
|
85
|
Maeda J, Shellenberger KD, Kurihara W, Haga T, Kato TA. Sulfoquinovosyl acylpropanediol (SQAP): Inhibition of poly(ADP-ribose) metabolism and enhanced cytotoxicity in homologous recombination repair-deficient Chinese hamster-derived cells. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2023; 892:503703. [PMID: 37973295 DOI: 10.1016/j.mrgentox.2023.503703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 11/19/2023]
Abstract
Sulfoquinovosyl acylpropanediol (SQAP; a synthetic derivative of the sulfoglycolipid natural product sulfoquinovosyl acylglycerol, SQAG), has anti-tumor and radiosensitizing activities in tumor xenograft mouse models. Here, we have studied the PARP inhibitory activity of SQAP and synthetic lethality in BRCA2-deficient cells. In initial screening studies with DNA repair-deficient Chinese hamster ovary cells, homologous recombination repair-deficient cell lines showed increased sensitivity to SQAP, compared to wild-type cells or other DNA repair-deficient mutants. Chinese hamster lung V79 cells and the derivative cell lines V-C8 (BRCA2-deficient) and V-C8 + BRCA2 gene corrections were used to test the role of BRCA2 in SQAP cytotoxicity. The findings were confirmed in studies of the human colon cancer cell lines DLD-1 and its BRCA2-knockout derivative. SQAP inhibited the enzymes poly(ADP-ribose) polymerase (PARP) and poly(ADP-ribose) glycohydrolase (PARG). SQAP pretreatment decreased H2O2induced poly(ADP-ribose) formation in V79 cells. SQAP caused DNA double-strand breaks and chromosome aberrations in V79 BRCA2-mutated cells but did not affect cells in the G2 phase. We have demonstrated that SQAP induces synthetic lethality in BRCA2-deficient Chinese hamster-derived cells via its effects on poly(ADP-ribose) metabolism, motivating further examination of its therapeutic potential, especially against tumors that are deficient in homologous recombination repair due to mutations in BRCA2 or other genes.
Collapse
Affiliation(s)
- Junko Maeda
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Kaitlyn D Shellenberger
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Wataru Kurihara
- M.T.3 (Malignant Tumor Treatment Technologies) Inc, Tokyo, Japan
| | - Tomohiro Haga
- M.T.3 (Malignant Tumor Treatment Technologies) Inc, Tokyo, Japan; M.T.3USA, Denver, CO, USA
| | - Takamitsu A Kato
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA.
| |
Collapse
|
86
|
Park SH, Kim N, Kang N, Ryu E, Lee EA, Ra JS, Gartner A, Kang S, Myung K, Lee KY. Short-range end resection requires ATAD5-mediated PCNA unloading for faithful homologous recombination. Nucleic Acids Res 2023; 51:10519-10535. [PMID: 37739427 PMCID: PMC10602867 DOI: 10.1093/nar/gkad776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/01/2023] [Accepted: 09/12/2023] [Indexed: 09/24/2023] Open
Abstract
Homologous recombination (HR) requires bidirectional end resection initiated by a nick formed close to a DNA double-strand break (DSB), dysregulation favoring error-prone DNA end-joining pathways. Here we investigate the role of the ATAD5, a PCNA unloading protein, in short-range end resection, long-range resection not being affected by ATAD5 deficiency. Rapid PCNA loading onto DNA at DSB sites depends on the RFC PCNA loader complex and MRE11-RAD50-NBS1 nuclease complexes bound to CtIP. Based on our cytological analyses and on an in vitro system for short-range end resection, we propose that PCNA unloading by ATAD5 is required for the completion of short-range resection. Hampering PCNA unloading also leads to failure to remove the KU70/80 complex from the termini of DSBs hindering DNA repair synthesis and the completion of HR. In line with this model, ATAD5-depleted cells are defective for HR, show increased sensitivity to camptothecin, a drug forming protein-DNA adducts, and an augmented dependency on end-joining pathways. Our study highlights the importance of PCNA regulation at DSB for proper end resection and HR.
Collapse
Affiliation(s)
- Su Hyung Park
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Namwoo Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
- Department of Biological Sciences, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Nalae Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
| | - Eunjin Ryu
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
- Department of Biological Sciences, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Eun A Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
| | - Jae Sun Ra
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
| | - Anton Gartner
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
- Department of Biological Sciences, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Kyoo-young Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
- Department of Biochemistry, College of Medicine, Hallym University, Chuncheon 24252, Korea
| |
Collapse
|
87
|
Fang W, Wang J, Ma X, Shao N, Ye K, Zhang D, Shi C, Luo L. A Progressively Disassembled DNA Repair Inhibitors Nanosystem for the Treatment of BRCA Wild-Type Triple-Negative Breast Cancer. Int J Nanomedicine 2023; 18:6001-6019. [PMID: 37901361 PMCID: PMC10612513 DOI: 10.2147/ijn.s426639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/05/2023] [Indexed: 10/31/2023] Open
Abstract
Background Olaparib, a poly (adenosine diphosphate-ribose) polymerase (PARP) inhibitor has demonstrated promising efficacy in patients with triple-negative breast cancer (TNBC) carrying breast cancer gene (BRCA) mutations. However, its impact on BRCA wild-type (BRCAwt) TNBC is limited. Hence, it is crucial to sensitize BRCAwt TNBC cells to olaparib for effective clinical practice. Novobiocin, a DNA polymerase theta (POLθ) inhibitor, exhibits sensitivity towards BRCA-mutated cancer cells that have acquired resistance to PARP inhibitors. Although both of these DNA repair inhibitors demonstrate therapeutic efficacy in BRCA-mutated cancers, their nanomedicine formulations' antitumor effects on wild-type cancer remain unclear. Furthermore, ensuring effective drug accumulation and release at the cancer site is essential for the clinical application of olaparib. Materials and Methods Herein, we designed a progressively disassembled nanosystem of DNA repair inhibitors as a novel strategy to enhance the effectiveness of olaparib in BRCAwt TNBC. The nanosystem enabled synergistic delivery of two DNA repair inhibitors olaparib and novobiocin, within an ultrathin silica framework interconnected by disulfide bonds. Results The designed nanosystem demonstrated remarkable capabilities, including long-term molecular storage and specific drug release triggered by the tumor microenvironment. Furthermore, the nanosystem exhibited potent inhibitory effects on cell viability, enhanced accumulation of DNA damage, and promotion of apoptosis in BRCAwt TNBC cells. Additionally, the nanosystem effectively accumulated within BRCAwt TNBC, leading to significant growth inhibition and displaying vascular regulatory abilities as assessed by magnetic resonance imaging (MRI). Conclusion Our results provided the inaugural evidence showcasing the potential of a progressively disassembled nanosystem of DNA repair inhibitors, as a promising strategy for the treatment of BRCA wild-type triple-negative breast cancer.
Collapse
Affiliation(s)
- Weimin Fang
- Medical Imaging Center, the First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, People’s Republic of China
- The Guangzhou Key Laboratory of Molecular and Functional Imaging for Clinical Translation, Jinan University, Guangzhou, Guangdong, People’s Republic of China
| | - Jinghao Wang
- Department of Pharmacy, the First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, People’s Republic of China
| | - Xiaocong Ma
- Medical Imaging Center, the First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, People’s Republic of China
- The Guangzhou Key Laboratory of Molecular and Functional Imaging for Clinical Translation, Jinan University, Guangzhou, Guangdong, People’s Republic of China
| | - Ni Shao
- Medical Imaging Center, the First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, People’s Republic of China
- The Guangzhou Key Laboratory of Molecular and Functional Imaging for Clinical Translation, Jinan University, Guangzhou, Guangdong, People’s Republic of China
| | - Kunlin Ye
- Medical Imaging Center, the First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, People’s Republic of China
- The Guangzhou Key Laboratory of Molecular and Functional Imaging for Clinical Translation, Jinan University, Guangzhou, Guangdong, People’s Republic of China
| | - Dong Zhang
- Medical Imaging Center, the First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, People’s Republic of China
- The Guangzhou Key Laboratory of Molecular and Functional Imaging for Clinical Translation, Jinan University, Guangzhou, Guangdong, People’s Republic of China
| | - Changzheng Shi
- Medical Imaging Center, the First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, People’s Republic of China
- The Guangzhou Key Laboratory of Molecular and Functional Imaging for Clinical Translation, Jinan University, Guangzhou, Guangdong, People’s Republic of China
| | - Liangping Luo
- Medical Imaging Center, the First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, People’s Republic of China
- The Guangzhou Key Laboratory of Molecular and Functional Imaging for Clinical Translation, Jinan University, Guangzhou, Guangdong, People’s Republic of China
| |
Collapse
|
88
|
Paniagua I, Jacobs JJL. Freedom to err: The expanding cellular functions of translesion DNA polymerases. Mol Cell 2023; 83:3608-3621. [PMID: 37625405 DOI: 10.1016/j.molcel.2023.07.008] [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: 02/24/2023] [Revised: 06/02/2023] [Accepted: 07/07/2023] [Indexed: 08/27/2023]
Abstract
Translesion synthesis (TLS) DNA polymerases were originally described as error-prone enzymes involved in the bypass of DNA lesions. However, extensive research over the past few decades has revealed that these enzymes play pivotal roles not only in lesion bypass, but also in a myriad of other cellular processes. Such processes include DNA replication, DNA repair, epigenetics, immune signaling, and even viral infection. This review discusses the wide range of functions exhibited by TLS polymerases, including their underlying biochemical mechanisms and associated mutagenicity. Given their multitasking ability to alleviate replication stress, TLS polymerases represent a cellular dependency and a critical vulnerability of cancer cells. Hence, this review also highlights current and emerging strategies for targeting TLS polymerases in cancer therapy.
Collapse
Affiliation(s)
- Inés Paniagua
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Jacqueline J L Jacobs
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands.
| |
Collapse
|
89
|
Syed A, Filandr F, Patterson-Fortin J, Bacolla A, Ravindranathan R, Zhou J, McDonald D, Albuhluli M, Verway-Cohen A, Newman J, Tsai MS, Jones D, Schriemer D, D’Andrea A, Tainer J. Novobiocin blocks nucleic acid binding to Polθ and inhibits stimulation of its ATPase activity. Nucleic Acids Res 2023; 51:9920-9937. [PMID: 37665033 PMCID: PMC10570058 DOI: 10.1093/nar/gkad727] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 08/10/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023] Open
Abstract
Polymerase theta (Polθ) acts in DNA replication and repair, and its inhibition is synthetic lethal in BRCA1 and BRCA2-deficient tumor cells. Novobiocin (NVB) is a first-in-class inhibitor of the Polθ ATPase activity, and it is currently being tested in clinical trials as an anti-cancer drug. Here, we investigated the molecular mechanism of NVB-mediated Polθ inhibition. Using hydrogen deuterium exchange-mass spectrometry (HX-MS), biophysical, biochemical, computational and cellular assays, we found NVB is a non-competitive inhibitor of ATP hydrolysis. NVB sugar group deletion resulted in decreased potency and reduced HX-MS interactions, supporting a specific NVB binding orientation. Collective results revealed that NVB binds to an allosteric site to block DNA binding, both in vitro and in cells. Comparisons of The Cancer Genome Atlas (TCGA) tumors and matched controls implied that POLQ upregulation in tumors stems from its role in replication stress responses to increased cell proliferation: this can now be tested in fifteen tumor types by NVB blocking ssDNA-stimulation of ATPase activity, required for Polθ function at replication forks and DNA damage sites. Structural and functional insights provided in this study suggest a path for developing NVB derivatives with improved potency for Polθ inhibition by targeting ssDNA binding with entropically constrained small molecules.
Collapse
Affiliation(s)
- Aleem Syed
- Division of Radiation and Genome Instability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Frantisek Filandr
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jeffrey Patterson-Fortin
- Division of Radiation and Genome Instability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ramya Ravindranathan
- Division of Radiation and Genome Instability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Jia Zhou
- Division of Radiation and Genome Instability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Drew T McDonald
- Biological and System Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mohammed E Albuhluli
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Amy Verway-Cohen
- Biological and System Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Joseph A Newman
- Center for Medicines Discovery, University of Oxford, OX1 3QU, UK
| | - Miaw-Sheue Tsai
- Biological and System Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Darin E Jones
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Alan D D’Andrea
- Division of Radiation and Genome Instability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| |
Collapse
|
90
|
Mladenov E, Mladenova V, Stuschke M, Iliakis G. New Facets of DNA Double Strand Break Repair: Radiation Dose as Key Determinant of HR versus c-NHEJ Engagement. Int J Mol Sci 2023; 24:14956. [PMID: 37834403 PMCID: PMC10573367 DOI: 10.3390/ijms241914956] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/01/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023] Open
Abstract
Radiation therapy is an essential component of present-day cancer management, utilizing ionizing radiation (IR) of different modalities to mitigate cancer progression. IR functions by generating ionizations in cells that induce a plethora of DNA lesions. The most detrimental among them are the DNA double strand breaks (DSBs). In the course of evolution, cells of higher eukaryotes have evolved four major DSB repair pathways: classical non-homologous end joining (c-NHEJ), homologous recombination (HR), alternative end-joining (alt-EJ), and single strand annealing (SSA). These mechanistically distinct repair pathways have different cell cycle- and homology-dependencies but, surprisingly, they operate with widely different fidelity and kinetics and therefore contribute unequally to cell survival and genome maintenance. It is therefore reasonable to anticipate tight regulation and coordination in the engagement of these DSB repair pathway to achieve the maximum possible genomic stability. Here, we provide a state-of-the-art review of the accumulated knowledge on the molecular mechanisms underpinning these repair pathways, with emphasis on c-NHEJ and HR. We discuss factors and processes that have recently come to the fore. We outline mechanisms steering DSB repair pathway choice throughout the cell cycle, and highlight the critical role of DNA end resection in this process. Most importantly, however, we point out the strong preference for HR at low DSB loads, and thus low IR doses, for cells irradiated in the G2-phase of the cell cycle. We further explore the molecular underpinnings of transitions from high fidelity to low fidelity error-prone repair pathways and analyze the coordination and consequences of this transition on cell viability and genomic stability. Finally, we elaborate on how these advances may help in the development of improved cancer treatment protocols in radiation therapy.
Collapse
Affiliation(s)
- Emil Mladenov
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany; (V.M.); (M.S.)
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany
| | - Veronika Mladenova
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany; (V.M.); (M.S.)
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany
| | - Martin Stuschke
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany; (V.M.); (M.S.)
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - George Iliakis
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany; (V.M.); (M.S.)
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany
| |
Collapse
|
91
|
Soung YH, Chung J. Combination Treatment Strategies to Overcome PARP Inhibitor Resistance. Biomolecules 2023; 13:1480. [PMID: 37892162 PMCID: PMC10604269 DOI: 10.3390/biom13101480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Poly(ADP-ribose) polymerase (PARP) enzymes have been shown to be essential for DNA repair pathways, including homologous recombination repair (HRR). Cancers with HRR defects (e.g., BRCA1 and BRCA2 mutations) are targets for PARP inhibitors (PARPis) based on the exploitation of "synthetic lethality". As a result, PARPis offer a promising treatment option for advanced ovarian and breast cancers with deficiencies in HRR. However, acquired resistance to PARPis has been reported for most tumors, and not all patients with BRCA1/2 mutations respond to PARPis. Therefore, the formulation of effective treatment strategies to overcome resistance to PARPis is urgently necessary. This review summarizes the molecular mechanism of therapeutic action and resistance to PARPis, in addition to emerging combination treatment options involving PARPis.
Collapse
Affiliation(s)
| | - Jun Chung
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA;
| |
Collapse
|
92
|
Akash S, Bayıl I, Hossain MS, Islam MR, Hosen ME, Mekonnen AB, Nafidi HA, Bin Jardan YA, Bourhia M, Bin Emran T. Novel computational and drug design strategies for inhibition of human papillomavirus-associated cervical cancer and DNA polymerase theta receptor by Apigenin derivatives. Sci Rep 2023; 13:16565. [PMID: 37783745 PMCID: PMC10545697 DOI: 10.1038/s41598-023-43175-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 09/20/2023] [Indexed: 10/04/2023] Open
Abstract
The present study deals with the advanced in-silico analyses of several Apigenin derivatives to explore human papillomavirus-associated cervical cancer and DNA polymerase theta inhibitor properties by molecular docking, molecular dynamics, QSAR, drug-likeness, PCA, a dynamic cross-correlation matrix and quantum calculation properties. The initial literature study revealed the potent antimicrobial and anticancer properties of Apigenin, prompting the selection of its potential derivatives to investigate their abilities as inhibitors of human papillomavirus-associated cervical cancer and DNA polymerase theta. In silico molecular docking was employed to streamline the findings, revealing promising energy-binding interactions between all Apigenin derivatives and the targeted proteins. Notably, Apigenin 4'-O-Rhamnoside and Apigenin-4'-Alpha-L-Rhamnoside demonstrated higher potency against the HPV45 oncoprotein E7 (PDB ID 2EWL), while Apigenin and Apigenin 5-O-Beta-D-Glucopyranoside exhibited significant binding energy against the L1 protein in humans. Similarly, a binding affinity range of - 7.5 kcal/mol to - 8.8 kcal/mol was achieved against DNA polymerase theta, indicating the potential of Apigenin derivatives to inhibit this enzyme (PDB ID 8E23). This finding was further validated through molecular dynamic simulation for 100 ns, analyzing parameters such as RMSD, RMSF, SASA, H-bond, and RoG profiles. The results demonstrated the stability of the selected compounds during the simulation. After passing the stability testing, the compounds underwent screening for ADMET, pharmacokinetics, and drug-likeness properties, fulfilling all the necessary criteria. QSAR, PCA, dynamic cross-correlation matrix, and quantum calculations were conducted, yielding satisfactory outcomes. Since this study utilized in silico computational approaches and obtained outstanding results, further validation is crucial. Therefore, additional wet-lab experiments should be conducted under in vivo and in vitro conditions to confirm the findings.
Collapse
Affiliation(s)
- Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Birulia, Ashulia, Dhaka, 1216, Bangladesh.
| | - Imren Bayıl
- Department of Bioinformatics and Computational Biology, Gaziantep University, Gaziantep, Turkey
| | - Md Saddam Hossain
- Department of Biomedical Engineering, Faculty of Engineering & Technology, Islamic University, Kushtia, Bangladesh
| | - Md Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Birulia, Ashulia, Dhaka, 1216, Bangladesh
| | - Md Eram Hosen
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | | | - Hiba-Allah Nafidi
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, 2325, Quebec City, QC, G1V 0A6, Canada
| | - Yousef A Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, 70000, Laayoune, Morocco
| | - Talha Bin Emran
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, United States.
| |
Collapse
|
93
|
Bhamidipati D, Haro-Silerio JI, Yap TA, Ngoi N. PARP inhibitors: enhancing efficacy through rational combinations. Br J Cancer 2023; 129:904-916. [PMID: 37430137 PMCID: PMC10491787 DOI: 10.1038/s41416-023-02326-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 05/18/2023] [Accepted: 06/12/2023] [Indexed: 07/12/2023] Open
Abstract
Poly (ADP-ribose) polymerase inhibitors (PARPi) have significantly changed the treatment landscape for tumours harbouring defects in genes involved in homologous repair (HR) such as BRCA1 and BRCA2. Despite initial responsiveness to PARPi, tumours eventually develop resistance through a variety of mechanisms. Rational combination strategies involving PARPi have been explored and are in various stages of clinical development. PARPi combinations have the potential to enhance efficacy through synergistic activity, and also potentially sensitise innately PARPi-resistant tumours to PARPi. Initial combinations involving PARPi with chemotherapy were hindered by significant overlapping haematologic toxicity, but newer combinations with fewer toxicities and more targeted approaches are undergoing evaluation. In this review, we discuss the mechanisms of PARPi resistance and review the rationale and clinical evidence for various PARPi combinations including combinations with chemotherapy, immunotherapy, and targeted therapies. We also highlight emerging PARPi combinations with promising preclinical evidence.
Collapse
Affiliation(s)
- Deepak Bhamidipati
- Department of Cancer Medicine Fellowship Program, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Timothy A Yap
- Department of Investigational Cancer Therapeutics (Phase I Program), The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- The Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Natalie Ngoi
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, Singapore
| |
Collapse
|
94
|
Liu W, Polaczek P, Roubal I, Meng Y, Choe WC, Caron MC, Sedgeman C, Xi Y, Liu C, Wu Q, Zheng L, Masson JY, Shen B, Campbell J. FANCD2 and RAD51 recombinase directly inhibit DNA2 nuclease at stalled replication forks and FANCD2 acts as a novel RAD51 mediator in strand exchange to promote genome stability. Nucleic Acids Res 2023; 51:9144-9165. [PMID: 37526271 PMCID: PMC10516637 DOI: 10.1093/nar/gkad624] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 06/17/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023] Open
Abstract
FANCD2 protein, a key coordinator and effector of the interstrand crosslink repair pathway, is also required to prevent excessive nascent strand degradation at hydroxyurea-induced stalled forks. The RAD51 recombinase has also been implicated in regulation of resection at stalled replication forks. The mechanistic contributions of these proteins to fork protection are not well understood. Here, we used purified FANCD2 and RAD51 to study how each protein regulates DNA resection at stalled forks. We characterized three mechanisms of FANCD2-mediated fork protection: (1) The N-terminal domain of FANCD2 inhibits the essential DNA2 nuclease activity by directly binding to DNA2 accounting for over-resection in FANCD2 defective cells. (2) Independent of dimerization with FANCI, FANCD2 itself stabilizes RAD51 filaments to inhibit multiple nucleases, including DNA2, MRE11 and EXO1. (3) Unexpectedly, we uncovered a new FANCD2 function: by stabilizing RAD51 filaments, FANCD2 acts to stimulate the strand exchange activity of RAD51. Our work biochemically explains non-canonical mechanisms by which FANCD2 and RAD51 protect stalled forks. We propose a model in which the strand exchange activity of FANCD2 provides a simple molecular explanation for genetic interactions between FANCD2 and BRCA2 in the FA/BRCA fork protection pathway.
Collapse
Affiliation(s)
- Wenpeng Liu
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
- Colleges of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Piotr Polaczek
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ivan Roubal
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yuan Meng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
- Colleges of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Won-chae Choe
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Marie-Christine Caron
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada
| | - Carl A Sedgeman
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yu Xi
- Colleges of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Changwei Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
- Colleges of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Qiong Wu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
| | - Judith L Campbell
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| |
Collapse
|
95
|
Ayala-Zambrano C, Yuste M, Frias S, Garcia-de-Teresa B, Mendoza L, Azpeitia E, Rodríguez A, Torres L. A Boolean network model of the double-strand break repair pathway choice. J Theor Biol 2023; 573:111608. [PMID: 37595867 DOI: 10.1016/j.jtbi.2023.111608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/29/2023] [Accepted: 08/09/2023] [Indexed: 08/20/2023]
Abstract
Double strand break (DSB) repair is critical to maintaining the integrity of the genome. DSB repair deficiency underlies multiple pathologies, including cancer, chromosome instability syndromes, and, potentially, neurodevelopmental defects. DSB repair is mainly handled by two pathways: highly accurate homologous recombination (HR), which requires a sister chromatid for template-based repair, limited to S/G2 phases of the cell cycle, and canonical non-homologous end joining (c-NHEJ), available throughout the cell cycle in which minimum homology is sufficient for highly efficient yet error-prone repair. Some circumstances, such as cancer, require alternative highly mutagenic DSB repair pathways like microhomology-mediated end-joining (MMEJ) and single-strand annealing (SSA), which are triggered to attend to DNA damage. These non-canonical repair alternatives are emerging as prominent drivers of resistance in drug-based tumor therapies. Multiple DSB repair options require tight inter-pathway regulation to prevent unscheduled activities. In addition to this complexity, epigenetic modifications of the histones surrounding the DSB region are emerging as critical regulators of the DSB repair pathway choice. Modeling approaches to understanding DSBs repair pathway choice are advantageous to perform simulations and generate predictions on previously uncharacterized aspects of DSBs response. In this work, we present a Boolean network model of the DSB repair pathway choice that incorporates the knowledge, into a dynamic system, of the inter-pathways regulation involved in DSB repair, i.e., HR, c-NHEJ, SSA, and MMEJ. Our model recapitulates the well-characterized HR activity observed in wild-type cells in response to DSBs. It also recovers clinically relevant behaviors of BRCA1/FANCS mutants, and their corresponding drug resistance mechanisms ascribed to DNA repair gain-of-function pathogenic variants. Since epigenetic modifiers are dynamic and possible druggable targets, we incorporated them into our model to better characterize their involvement in DSB repair. Our model predicted that loss of the TIP60 complex and its corresponding histone acetylation activity leads to activation of SSA in response to DSBs. Our experimental validation showed that TIP60 effectively prevents activation of RAD52, a key SSA executor, and confirms the suitable use of Boolean network modeling for understanding DNA DSB repair.
Collapse
Affiliation(s)
- Cecilia Ayala-Zambrano
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Mariana Yuste
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México, Morelia, Mexico
| | - Sara Frias
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico; Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Apartado Postal 70228, Ciudad de México 04510, Mexico
| | | | - Luis Mendoza
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Apartado Postal 70228, Ciudad de México 04510, Mexico
| | - Eugenio Azpeitia
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México, Morelia, Mexico
| | - Alfredo Rodríguez
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Apartado Postal 70228, Ciudad de México 04510, Mexico; Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico.
| | - Leda Torres
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico.
| |
Collapse
|
96
|
Li Q, Qian W, Zhang Y, Hu L, Chen S, Xia Y. A new wave of innovations within the DNA damage response. Signal Transduct Target Ther 2023; 8:338. [PMID: 37679326 PMCID: PMC10485079 DOI: 10.1038/s41392-023-01548-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/01/2023] [Accepted: 06/27/2023] [Indexed: 09/09/2023] Open
Abstract
Genome instability has been identified as one of the enabling hallmarks in cancer. DNA damage response (DDR) network is responsible for maintenance of genome integrity in cells. As cancer cells frequently carry DDR gene deficiencies or suffer from replicative stress, targeting DDR processes could induce excessive DNA damages (or unrepaired DNA) that eventually lead to cell death. Poly (ADP-ribose) polymerase (PARP) inhibitors have brought impressive benefit to patients with breast cancer gene (BRCA) mutation or homologous recombination deficiency (HRD), which proves the concept of synthetic lethality in cancer treatment. Moreover, the other two scenarios of DDR inhibitor application, replication stress and combination with chemo- or radio- therapy, are under active clinical exploration. In this review, we revisited the progress of DDR targeting therapy beyond the launched first-generation PARP inhibitors. Next generation PARP1 selective inhibitors, which could maintain the efficacy while mitigating side effects, may diversify the application scenarios of PARP inhibitor in clinic. Albeit with unavoidable on-mechanism toxicities, several small molecules targeting DNA damage checkpoints (gatekeepers) have shown great promise in preliminary clinical results, which may warrant further evaluations. In addition, inhibitors for other DNA repair pathways (caretakers) are also under active preclinical or clinical development. With these progresses and efforts, we envision that a new wave of innovations within DDR has come of age.
Collapse
Affiliation(s)
- Qi Li
- Domestic Discovery Service Unit, WuXi AppTec, 200131, Shanghai, China
| | - Wenyuan Qian
- Domestic Discovery Service Unit, WuXi AppTec, 200131, Shanghai, China
| | - Yang Zhang
- Domestic Discovery Service Unit, WuXi AppTec, 200131, Shanghai, China
| | - Lihong Hu
- Domestic Discovery Service Unit, WuXi AppTec, 200131, Shanghai, China
| | - Shuhui Chen
- Domestic Discovery Service Unit, WuXi AppTec, 200131, Shanghai, China
| | - Yuanfeng Xia
- Domestic Discovery Service Unit, WuXi AppTec, 200131, Shanghai, China.
| |
Collapse
|
97
|
Konstantinopoulos PA, Matulonis UA. Clinical and translational advances in ovarian cancer therapy. NATURE CANCER 2023; 4:1239-1257. [PMID: 37653142 DOI: 10.1038/s43018-023-00617-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/17/2023] [Indexed: 09/02/2023]
Abstract
Ovarian cancer is an aggressive disease that is frequently detected at advanced stages and is initially very responsive to platinum-based chemotherapy. However, the majority of patients relapse following initial surgery and chemotherapy, highlighting the urgent need to develop new therapeutic strategies. In this Review, we outline the main therapeutic principles behind the management of newly diagnosed and recurrent epithelial ovarian cancer and discuss the current landscape of targeted and immune-based approaches.
Collapse
|
98
|
Beneyton A, Nonfoux L, Gagné JP, Rodrigue A, Kothari C, Atalay N, Hendzel M, Poirier G, Masson JY. The dynamic process of covalent and non-covalent PARylation in the maintenance of genome integrity: a focus on PARP inhibitors. NAR Cancer 2023; 5:zcad043. [PMID: 37609662 PMCID: PMC10440794 DOI: 10.1093/narcan/zcad043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/24/2023] Open
Abstract
Poly(ADP-ribosylation) (PARylation) by poly(ADP-ribose) polymerases (PARPs) is a highly regulated process that consists of the covalent addition of polymers of ADP-ribose (PAR) through post-translational modifications of substrate proteins or non-covalent interactions with PAR via PAR binding domains and motifs, thereby reprogramming their functions. This modification is particularly known for its central role in the maintenance of genomic stability. However, how genomic integrity is controlled by an intricate interplay of covalent PARylation and non-covalent PAR binding remains largely unknown. Of importance, PARylation has caught recent attention for providing a mechanistic basis of synthetic lethality involving PARP inhibitors (PARPi), most notably in homologous recombination (HR)-deficient breast and ovarian tumors. The molecular mechanisms responsible for the anti-cancer effect of PARPi are thought to implicate both catalytic inhibition and trapping of PARP enzymes on DNA. However, the relative contribution of each on tumor-specific cytotoxicity is still unclear. It is paramount to understand these PAR-dependent mechanisms, given that resistance to PARPi is a challenge in the clinic. Deciphering the complex interplay between covalent PARylation and non-covalent PAR binding and defining how PARP trapping and non-trapping events contribute to PARPi anti-tumour activity is essential for developing improved therapeutic strategies. With this perspective, we review the current understanding of PARylation biology in the context of the DNA damage response (DDR) and the mechanisms underlying PARPi activity and resistance.
Collapse
Affiliation(s)
- Adèle Beneyton
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
| | - Louis Nonfoux
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Jean-Philippe Gagné
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Amélie Rodrigue
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
| | - Charu Kothari
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Nurgul Atalay
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Michael J Hendzel
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue, Edmonton, AlbertaT6G 1Z2, Canada
| | - Guy G Poirier
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Jean-Yves Masson
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
| |
Collapse
|
99
|
Chakraborty S, Schirmeisen K, Lambert SA. The multifaceted functions of homologous recombination in dealing with replication-associated DNA damages. DNA Repair (Amst) 2023; 129:103548. [PMID: 37541027 DOI: 10.1016/j.dnarep.2023.103548] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023]
Abstract
The perturbation of DNA replication, a phenomena termed "replication stress", is a driving force of genome instability and a hallmark of cancer cells. Among the DNA repair mechanisms that contribute to tolerating replication stress, the homologous recombination pathway is central to the alteration of replication fork progression. In many organisms, defects in the homologous recombination machinery result in increased cell sensitivity to replication-blocking agents and a higher risk of cancer in humans. Moreover, the status of homologous recombination in cancer cells often correlates with the efficacy of anti-cancer treatment. In this review, we discuss our current understanding of the different functions of homologous recombination in fixing replication-associated DNA damage and contributing to complete genome duplication. We also examine which functions are pivotal in preventing cancer and genome instability.
Collapse
Affiliation(s)
- Shrena Chakraborty
- Institut Curie, Université PSL, CNRS UMR3348, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, 91400 Orsay, France; Equipe Labelisée Ligue Nationale Contre le Cancer, France
| | - Kamila Schirmeisen
- Institut Curie, Université PSL, CNRS UMR3348, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, 91400 Orsay, France; Equipe Labelisée Ligue Nationale Contre le Cancer, France
| | - Sarah Ae Lambert
- Institut Curie, Université PSL, CNRS UMR3348, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, 91400 Orsay, France; Equipe Labelisée Ligue Nationale Contre le Cancer, France.
| |
Collapse
|
100
|
Riesenberg S, Kanis P, Macak D, Wollny D, Düsterhöft D, Kowalewski J, Helmbrecht N, Maricic T, Pääbo S. Efficient high-precision homology-directed repair-dependent genome editing by HDRobust. Nat Methods 2023; 20:1388-1399. [PMID: 37474806 PMCID: PMC10482697 DOI: 10.1038/s41592-023-01949-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 06/12/2023] [Indexed: 07/22/2023]
Abstract
Homology-directed repair (HDR), a method for repair of DNA double-stranded breaks can be leveraged for the precise introduction of mutations supplied by synthetic DNA donors, but remains limited by low efficiency and off-target effects. In this study, we report HDRobust, a high-precision method that, via the combined transient inhibition of nonhomologous end joining and microhomology-mediated end joining, resulted in the induction of point mutations by HDR in up to 93% (median 60%, s.e.m. 3) of chromosomes in populations of cells. We found that, using this method, insertions, deletions and rearrangements at the target site, as well as unintended changes at other genomic sites, were largely abolished. We validated this approach for 58 different target sites and showed that it allows efficient correction of pathogenic mutations in cells derived from patients suffering from anemia, sickle cell disease and thrombophilia.
Collapse
Affiliation(s)
- Stephan Riesenberg
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Philipp Kanis
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Dominik Macak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Damian Wollny
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Dorothee Düsterhöft
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Johannes Kowalewski
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nelly Helmbrecht
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tomislav Maricic
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Human Evolutionary Genomics Unit, Okinawa Institute of Science and Technology, Onna-son, Japan
| |
Collapse
|