scholarly journals WRN Helicase is a Synthetic Lethal Target in Microsatellite Unstable Cancers

2018 ◽  
Author(s):  
Edmond Chan ◽  
Tsukasa Shibue ◽  
James McFarland ◽  
Benjamin Gaeta ◽  
Justine McPartlan ◽  
...  
Keyword(s):  
Dna Repair ◽  
Cell Lines ◽  
Large Scale ◽  
Synthetic Lethality ◽  
Cancer Therapeutics ◽  
Dna Helicase ◽  
Dna Breaks ◽  
Synthetic Lethal ◽  
Dna Mismatch ◽  
Double Strand Dna Breaks

Synthetic lethality, an interaction whereby the co-occurrence of two or more genetic events lead to cell death but one event alone does not, can be exploited to develop novel cancer therapeutics. DNA repair processes represent attractive synthetic lethal targets since many cancers exhibit an impaired DNA repair pathway, which can lead these cells to become dependent on specific repair proteins. The success of poly (ADP-ribose) polymerase 1 (PARP-1) inhibitors in homologous recombination-deficient cancers highlights the potential of this approach in clinical oncology. Hypothesizing that other DNA repair defects would give rise to alternative synthetic lethal relationships, we asked if there are specific dependencies in cancers with microsatellite instability (MSI), which results from impaired DNA mismatch repair (MMR). Here we analyzed data from large-scale CRISPR/Cas9 knockout and RNA interference (RNAi) silencing screens and found that the RecQ DNA helicase was selectively essential in MSI cell lines, yet dispensable in microsatellite stable (MSS) cell lines. WRN depletion induced double-strand DNA breaks and promoted apoptosis and cell cycle arrest selectively in MSI models. MSI cancer models specifically required the helicase activity, but not the exonuclease activity of WRN. These findings expose WRN as a synthetic lethal vulnerability and promising drug target in MSI cancers.

scholarly journals Histone H2A Phosphorylation Controls Crb2 Recruitment at DNA Breaks, Maintains Checkpoint Arrest, and Influences DNA Repair in Fission Yeast

2004 ◽  
Vol 24 (14) ◽  
pp. 6215-6230 ◽  
Author(s):  
Toru M. Nakamura ◽  
Li-Lin Du ◽  
Christophe Redon ◽  
Paul Russell
Keyword(s):  
Dna Repair ◽  
Fission Yeast ◽  
Large Scale ◽  
Dna Helicase ◽  
Histone H2a ◽  
Dna Breaks ◽  
Histone H2ax ◽  
Wide Range ◽  
Carboxy Terminal ◽  
Damaged Dna

ABSTRACT Mammalian ATR and ATM checkpoint kinases modulate chromatin structures near DNA breaks by phosphorylating a serine residue in the carboxy-terminal tail SQE motif of histone H2AX. Histone H2A is similarly regulated in Saccharomyces cerevisiae. The phosphorylated forms of H2AX and H2A, known as γ-H2AX and γ-H2A, are thought to be important for DNA repair, although their evolutionarily conserved roles are unknown. Here, we investigate γ-H2A in the fission yeast Schizosaccharomyces pombe. We show that formation of γ-H2A redundantly requires the ATR/ATM-related kinases Rad3 and Tel1. Mutation of the SQE motif to AQE (H2A-AQE) in the two histone H2A genes caused sensitivity to a wide range of genotoxic agents, increased spontaneous DNA damage, and impaired checkpoint maintenance. The H2A-AQE mutations displayed a striking synergistic interaction with rad22Δ (Rad52 homolog) in ionizing radiation (IR) survival. These phenotypes correlated with defective phosphorylation of the checkpoint proteins Crb2 and Chk1 and a failure to recruit large amounts of Crb2 to damaged DNA. Surprisingly, the H2A-AQE mutations substantially suppressed the IR hypersensitivity of crb2Δ cells by a mechanism that required the RecQ-like DNA helicase Rqh1. We propose that γ-H2A modulates checkpoint and DNA repair through large-scale recruitment of Crb2 to damaged DNA. This function correlates with evidence that γ-H2AX regulates recruitment of several BRCA1 carboxyl terminus domain-containing proteins (NBS1, 53BP1, MDC1/NFBD1, and BRCA1) in mammals.

scholarly journals Novel 2-Benzoyl-6-(2,3-Dimethoxybenzylidene)-Cyclohexenol Confers Selectivity toward Human MLH1 Defective Cancer Cells through Synthetic Lethality

2019 ◽  
Vol 24 (5) ◽  
pp. 548-562
Author(s):  
Dedrick Soon Seng Song ◽  
Sze Wei Leong ◽  
Kwok Wen Ng ◽  
Faridah Abas ◽  
Khozirah Shaari ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Cancer Patients ◽  
Cell Lines ◽  
Cancer Cell ◽  
Synthetic Lethality ◽  
Treatment Options ◽  
Cancer Cell Lines ◽  
Selective Toxicity ◽  
Synthetic Lethal ◽  
Dna Mismatch

DNA mismatch repair (MMR) deficiency has been associated with a higher risk of developing colorectal, endometrial, and ovarian cancer, and confers resistance in conventional chemotherapy. In addition to the lack of treatment options that work efficaciously on these MMR-deficient cancer patients, there is a great need to discover new drug leads for this purpose. In this study, we screened through a library of commercial and semisynthetic natural compounds to identify potential synthetic lethal drugs that may selectively target MLH1 mutants using MLH1 isogenic colorectal cancer cell lines and various cancer cell lines with known MLH1 status. We identified a novel diarylpentanoid analogue, 2-benzoyl-6-(2,3-dimethoxybenzylidene)-cyclohexenol, coded as AS13, that demonstrated selective toxicity toward MLH1-deficient cancer cells. Subsequent analysis suggested AS13 induced elevated levels of oxidative stress, resulting in DNA damage where only the proficient MLH1 cells were able to be repaired and hence escaping cellular death. While AS13 is modest in potency and selectivity, this discovery has the potential to lead to further drug development that may offer better treatment options for cancer patients with MLH1 deficiency.

scholarly journals RecQ helicases in DNA repair and cancer targets

2020 ◽  
Vol 64 (5) ◽  
pp. 819-830
Author(s):  
Joseph A. Newman ◽  
Opher Gileadi
Keyword(s):  
Dna Repair ◽  
Small Molecules ◽  
Atp Hydrolysis ◽  
Cancer Therapeutics ◽  
Genome Integrity ◽  
Mechanistic Study ◽  
Synthetic Lethal ◽  
Recq Helicases ◽  
Repair Pathways ◽  
Higher Eukaryotes

Abstract Helicases are enzymes that use the energy derived from ATP hydrolysis to catalyze the unwinding of DNA or RNA. The RecQ family of helicases is conserved through evolution from prokaryotes to higher eukaryotes and plays important roles in various DNA repair pathways, contributing to the maintenance of genome integrity. Despite their roles as general tumor suppressors, there is now considerable interest in exploiting RecQ helicases as synthetic lethal targets for the development of new cancer therapeutics. In this review, we summarize the latest developments in the structural and mechanistic study of RecQ helicases and discuss their roles in various DNA repair pathways. Finally, we consider the potential to exploit RecQ helicases as therapeutic targets and review the recent progress towards the development of small molecules targeting RecQ helicases as cancer therapeutics.

Escherichia coli and colorectal cancer: Unfolding the enigmatic relationship

2021 ◽  
Vol 22 ◽  
Author(s):  
Rogayeh Nouri ◽  
Alka Hasani ◽  
Kourosh Masnadi Shirazi ◽  
Mohammad Reza Aliand ◽  
Bita Sepehri ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Escherichia Coli ◽  
Mammalian Cells ◽  
Chromosomal Rearrangements ◽  
Current Evidence ◽  
Dna Breaks ◽  
Colon Cells ◽  
E Coli ◽  
Dna Mismatch ◽  
Double Strand Dna Breaks

: Colorectal cancer (CRC) is one of the deadliest cancers in the world. Specific strains of intestinal Escherichia coli (E. coli) may influence the initiation and development of CRC by exploiting virulence factors and inflammatory pathways. Mucosa-associated E. coli strains are more prevalent in CRC biopsies in comparison to healthy controls. Moreover, these strains can survive and replicate within macrophages and induce a pro-inflammatory response. Chronic exposure to inflammatory mediators can lead to increased cell proliferation and cancer. Production of colobactin toxin by the majority of mucosa-associated E. coli isolated from CRC patients is another notable finding. Colibactin-producing E. coli strains, in particular, induce double-strand DNA breaks, stop the cell cycle, involve in chromosomal rearrangements of mammalian cells and are implicated in carcinogenic effects in animal models. Moreover, some enteropathogenic E. coli (EPEC) strains are able to survive and replicate in colon cells as chronic intracellular pathogens and may promote susceptibility to CRC by downregulation of DNA Mismatch Repair (MMR) proteins. In this review, we discuss current evidence and focus on the mechanisms by which E. coli can influence the development of CRC.

scholarly journals The Schizosaccharomyces pombe rad60 Gene Is Essential for Repairing Double-Strand DNA Breaks Spontaneously Occurring during Replication and Induced by DNA-Damaging Agents

2002 ◽  
Vol 22 (10) ◽  
pp. 3537-3548 ◽  
Author(s):  
Takashi Morishita ◽  
Yasuhiro Tsutsui ◽  
Hiroshi Iwasaki ◽  
Hideo Shinagawa
Keyword(s):  
Schizosaccharomyces Pombe ◽  
Strand Break ◽  
Temperature Sensitive ◽  
Restrictive Temperature ◽  
Multicopy Plasmid ◽  
Dna Breaks ◽  
Γ Irradiation ◽  
Synthetic Lethal ◽  
Double Strand Dna Breaks ◽  
Dna Double Strand Break

ABSTRACT To identify novel genes involved in DNA double-strand break (DSB) repair, we previously isolated Schizosaccharomyces pombe mutants which are hypersensitive to methyl methanesulfonate (MMS) and synthetic lethals with rad2. This study characterizes one of these mutants, rad60-1. The gene that complements the MMS sensitivity of this mutant was cloned and designated rad60. rad60 encodes a protein with 406 amino acids which has the conserved ubiquitin-2 motif found in ubiquitin family proteins. rad60-1 is hypersensitive to UV and γ rays, epistatic to rhp51, and defective in the repair of DSBs caused by γ-irradiation. The rad60-1 mutant is also temperature sensitive for growth. At the restrictive temperature (37°C), rad60-1 cells grow for several divisions and then arrest with 2C DNA content; the arrested cells accumulate DSBs and have a diffuse and often aberrantly shaped nuclear chromosomal domain. The rad60-1 mutant is a synthetic lethal with rad18-X, and expression of wild-type rad60 from a multicopy plasmid partially suppresses the MMS sensitivity of rad18-X cells. rad18 encodes a conserved protein of the structural maintenance of chromosomes (SMC) family (A. R. Lehmann, M. Walicka, D. J. Griffiths, J. M. Murray, F. Z. Watts, S. McCready, and A. M. Carr, Mol. Cell. Biol. 15:7067-7080, 1995). These results suggest that S. pombe Rad60 is required to repair DSBs, which accumulate during replication, by recombination between sister chromatids. Rad60 may perform this function in concert with the SMC protein Rad18.

scholarly journals Inhibition of PARP Sensitizes Chondrosarcoma Cell Lines to Chemo- and Radiotherapy Irrespective of the IDH1 or IDH2 Mutation Status

Cancers ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 1918 ◽  
Author(s):  
Sanne Venneker ◽  
Alwine B. Kruisselbrink ◽  
Inge H. Briaire-de Bruijn ◽  
Yvonne de Jong ◽  
Andre J. van Wijnen ◽  
...  
Keyword(s):  
Dna Repair ◽  
Cell Lines ◽  
Dna Methyltransferase ◽  
Synthetic Lethality ◽  
Parp Inhibitor ◽  
Parp Inhibition ◽  
Idh Mutation ◽  
Mutation Status ◽  
Chondrosarcoma Cell ◽  
Idh Mutations

Chondrosarcomas are chemo- and radiotherapy resistant and frequently harbor mutations in isocitrate dehydrogenase (IDH1 or IDH2), causing increased levels of D-2-hydroxyglutarate (D-2-HG). DNA repair defects and synthetic lethality with poly(ADP-ribose) polymerase (PARP) inhibition occur in IDH mutant glioma and leukemia models. Here we evaluated DNA repair and PARP inhibition, alone or combined with chemo- or radiotherapy, in chondrosarcoma cell lines with or without endogenous IDH mutations. Chondrosarcoma cell lines treated with the PARP inhibitor talazoparib were examined for dose–response relationships, as well as underlying cell death mechanisms and DNA repair functionality. Talazoparib was combined with chemo- or radiotherapy to evaluate potential synergy. Cell lines treated long term with an inhibitor normalizing D-2-HG levels were investigated for synthetic lethality with talazoparib. We report that talazoparib sensitivity was variable and irrespective of IDH mutation status. All cell lines expressed Ataxia Telangiectasia Mutated (ATM), but a subset was impaired in poly(ADP-ribosyl)ation (PARylation) capacity, homologous recombination, and O-6-methylguanine-DNA methyltransferase (MGMT) expression. Talazoparib synergized with temozolomide or radiation, independent of IDH1 mutant inhibition. This study suggests that talazoparib combined with temozolomide or radiation are promising therapeutic strategies for chondrosarcoma, irrespective of IDH mutation status. A subset of chondrosarcomas may be deficient in nonclassical DNA repair pathways, suggesting that PARP inhibitor sensitivity is multifactorial in chondrosarcoma.

scholarly journals Predicting synthetic lethal interactions in human cancers using graph regularized self-representative matrix factorization

2019 ◽  
Vol 20 (S19) ◽  
Author(s):  
Jiang Huang ◽  
Min Wu ◽  
Fan Lu ◽  
Le Ou-Yang ◽  
Zexuan Zhu
Keyword(s):  
Matrix Factorization ◽  
Drug Targets ◽  
Synthetic Lethality ◽  
Cancer Therapeutics ◽  
The Self ◽  
Interaction Data ◽  
Synthetic Lethal Interaction ◽  
Synthetic Lethal ◽  
Interaction Prediction ◽  
Synthetic Lethal Interactions

Abstract Background Synthetic lethality has attracted a lot of attentions in cancer therapeutics due to its utility in identifying new anticancer drug targets. Identifying synthetic lethal (SL) interactions is the key step towards the exploration of synthetic lethality in cancer treatment. However, biological experiments are faced with many challenges when identifying synthetic lethal interactions. Thus, it is necessary to develop computational methods which could serve as useful complements to biological experiments. Results In this paper, we propose a novel graph regularized self-representative matrix factorization (GRSMF) algorithm for synthetic lethal interaction prediction. GRSMF first learns the self-representations from the known SL interactions and further integrates the functional similarities among genes derived from Gene Ontology (GO). It can then effectively predict potential SL interactions by leveraging the information provided by known SL interactions and functional annotations of genes. Extensive experiments on the synthetic lethal interaction data downloaded from SynLethDB database demonstrate the superiority of our GRSMF in predicting potential synthetic lethal interactions, compared with other competing methods. Moreover, case studies of novel interactions are conducted in this paper for further evaluating the effectiveness of GRSMF in synthetic lethal interaction prediction. Conclusions In this paper, we demonstrate that by adaptively exploiting the self-representation of original SL interaction data, and utilizing functional similarities among genes to enhance the learning of self-representation matrix, our GRSMF could predict potential SL interactions more accurately than other state-of-the-art SL interaction prediction methods.

Nucleophosmin expression in ovarian cancer.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. e15582-e15582
Author(s):  
Dineo Khabele ◽  
Andrew J Wilson ◽  
Annie Y Liu ◽  
Joseph Roland ◽  
Sarah Fletcher ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Overall Survival ◽  
Dna Repair ◽  
Progression Free Survival ◽  
High Grade ◽  
Dna Breaks ◽  
Free Survival ◽  
Ovarian Cancers ◽  
Double Strand Dna Breaks ◽  
The Relationship

e15582 Background: The nucleolar protein, nucleophosmin (NPM1) is implicated multiple cellular processes, including proliferation, duplication of centrosomes, ARF-HDM2-p53 signaling. NPM1 is associated with sites of double strand DNA breaks, with persistence of its expression indicative of impaired DNA repair. Data from the TCGA data have emphasized that genomic instability through impaired DNA repair processes is a characteristic feature of many ovarian cancers. Our aim was to determine the expression of NPM1 in ovarian cancers and to determine the relationship between NPM1 expression and clinical outcomes including overall survival (OS), progression-free survival (PFS) and chemotherapy response. Methods: Tissue microarrays were created from 209 patients treated for ovarian cancer at a single institution from 1994-2004. Expression levels of NPM1 were examined by immunohistochemical staining. Slides were scored using the an automated image capture and analysis system. Positive nuclear staining was used to stratify tumors into high (>50%) and low (<50%) groups, and the results were related to overall survival (OS) and progression-free survival (PFS) via Kaplan-Meier analysis. The relationship between ki67, a proliferation marker and pH2AX, a mark of double strand DNA breaks was measured with Spearman rank correlation coefficient analyses. Results: The majority of tumors, 140/209 (69%) were of serous histology, advanced stage 146/209 (70%) and high grade 158/209 (76%). There was >50% NPM1 expression in 83/209 (40%) and <50% in 126/209 (60%) of the cases. Expression of NPM1 was higher in high grade tumors, and its expression alone was a significant predictor of PFS (p=0.022) but not OS (p=0.053). When adjusting for other predictors, NPM1 expression was predictive of PFS (p=0.047), but not OS (p=0.054). No relationship between NPM1 expression and response to platinum chemotherapy was observed. However, NPM1 expression correlated with Ki67 (r=0.43, p<0.0001) and pH2AX (r=0.22, p=0.0014). Conclusions: NPM1 expression is a mark of poor prognosis in ovarian cancer. Whether these observations reflect increased proliferation and/or genomic instability in ovarian cancer cells will be the focus of future investigation.

scholarly journals DDX5 resolves R-loops at DNA double-strand breaks to promote DNA repair and avoid chromosomal deletions

NAR Cancer ◽  
2020 ◽  
Vol 2 (3) ◽  
Author(s):  
Zhenbao Yu ◽  
Sofiane Y Mersaoui ◽  
Laure Guitton-Sert ◽  
Yan Coulombe ◽  
Jingwen Song ◽  
...  
Keyword(s):  
Dna Repair ◽  
Protein A ◽  
Helicase Domain ◽  
Dependent Manner ◽  
Dna Double Strand Breaks ◽  
Dna Breaks ◽  
Rna Transcripts ◽  
Chromosomal Deletions ◽  
Double Strand Dna Breaks ◽  
Dna Strand

Abstract R-loops are three-stranded structures consisting of a DNA/RNA hybrid and a displaced DNA strand. The regulatory factors required to process this fundamental genetic structure near double-strand DNA breaks (DSBs) are not well understood. We previously reported that cellular depletion of the ATP-dependent DEAD box RNA helicase DDX5 increases R-loops genome-wide causing genomic instability. In this study, we define a pivotal role for DDX5 in clearing R-loops at or near DSBs enabling proper DNA repair to avoid aberrations such as chromosomal deletions. Remarkably, using the non-homologous end joining reporter gene (EJ5-GFP), we show that DDX5-deficient U2OS cells exhibited asymmetric end deletions on the side of the DSBs where there is overlap with a transcribed gene. Cross-linking and immunoprecipitation showed that DDX5 bound RNA transcripts near DSBs and required its helicase domain and the presence of DDX5 near DSBs was also shown by chromatin immunoprecipitation. DDX5 was excluded from DSBs in a transcription- and ATM activation-dependent manner. Using DNA/RNA immunoprecipitation, we show DDX5-deficient cells had increased R-loops near DSBs. Finally, DDX5 deficiency led to delayed exonuclease 1 and replication protein A recruitment to laser irradiation-induced DNA damage sites, resulting in homologous recombination repair defects. Our findings define a role for DDX5 in facilitating the clearance of RNA transcripts overlapping DSBs to ensure proper DNA repair.

scholarly journals Increased efficacy of histone methyltransferase G9a inhibitors against MYCN-amplified Neuroblastoma

2019 ◽  
Author(s):  
Jacob Bellamy ◽  
Marianna Szemes ◽  
Zsombor Melegh ◽  
Anthony Dallosso ◽  
Madhu Kollareddy ◽  
...  
Keyword(s):  
Cell Lines ◽  
Small Molecule ◽  
Small Molecule Inhibitors ◽  
Cancer Therapeutics ◽  
Histone Methyltransferase ◽  
Tumour Suppressor Genes ◽  
Synthetic Lethal ◽  
Ezh2 Expression ◽  
Primary Determinant ◽  
Targeted Inhibition

AbstractTargeted inhibition of proteins modulating epigenetic changes is an increasingly important priority in cancer therapeutics, and many small molecule inhibitors are currently being developed. In the case of neuroblastoma (NB), a paediatric solid tumour with a paucity of intragenic mutations, epigenetic deregulation may be especially important. In this study we validate the histone methyltransferase G9a/EHMT2 as being associated with indicators of poor prognosis in NB. Immunological analysis of G9a protein shows it to be more highly expressed in NB cell-lines with MYCN amplification, which is a primary determinant of dismal outcome in NB patients. Furthermore, G9a protein in primary tumours is expressed at higher levels in poorly differentiated/undifferentiated NB, and correlates with high EZH2 expression, a known co-operative oncoprotein in NB. Our functional analyses demonstrate that siRNA-mediated G9a depletion inhibits cell growth in all NB cell lines, but, strikingly, only triggers apoptosis in NB cells with MYCN amplification, suggesting a synthetic lethal relationship between G9a and MYCN. This pattern of sensitivity is also evident when using small molecule inhibitors of G9a, UNC0638 and UNC0642. The increased efficacy of G9a inhibition in the presence of MYCN-overexpression is also demonstrated in the SHEP-21N isogenic model with tet-regulatable MYCN. Finally, using RNA sequencing, we identify several potential tumour suppressor genes that are reactivated by G9a inhibition in NB, including the CLU, FLCN, AMHR2 and AKR1C1-3. Together, our study underlines the under-appreciated role of G9a in NB, especially in MYCN-amplified tumours.

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