Ena-DATASET-EMC-29-01-2018-10:48:52:289-175 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001003929 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Homologous recombination (HR) serves multiple roles in DNA repair that are essential for maintaining genomic stability. The central HR protein, RAD51, is frequently overexpressed in human malignancies, thereby elevating HR proficiency and promoting resistance to DNA-damaging therapies. Here we find that non-canonical NF-κB factors control the expression of RAD51 andother HR-promoting proteins. Transcriptional silencing of p100/p52 reduces RAD51 protein levels in multiple human cancer subtypes. RNA-seq after p100/p52 silencing identifies RAD51 as the most differentially expressed gene among 40 genes with known relevance to HR. While p100/p52 depletion inhibits HR function in human tumor cells, it does not influence the function of other double-strand DNA repair pathways including single-strand annealing, microhomology mediated annealing, or non-homologous end joining.
2022-06-07 | GSE148511 | GEO
Project description:Homologous recombination (HR) mediates the error-free repair of DNA double-strand breaks to maintain genomic stability. Here we characterize C17orf53/MCM8IP, an OB-fold containing protein that binds ssDNA, as a DNA repair factor involved in HR. MCM8IP-deficient cells exhibit HR defects, especially in long-tract gene conversion, occurring downstream of RAD51 loading, consistent with a role for MCM8IP in HR-dependent DNA synthesis. Moreover, loss of MCM8IP confers cellular sensitivity to crosslinking agents and PARP inhibition. Importantly, we report that MCM8IP directly associates with MCM8-9, a helicase complex mutated in primary ovarian insufficiency, and RPA1. We additionally show that the interactions of MCM8IP with MCM8-9 and RPA facilitate HR and promote replication fork progression and cellular viability in response to treatment with crosslinking agents. Mechanistically, MCM8IP stimulates the helicase activity of MCM8-9. Collectively, our work identifies MCM8IP as a key regulator of DNA damage-associated DNA synthesis during DNA recombination and replication.
2020-06-15 | PXD019156 | Pride
Project description:Expression of RAD51, a crucial player in homologous recombination (HR) and DNA double-strand break (DSB) repair, is dysregulated in human tumors, and can contribute to genomic instability and tumor progression. To further understand RAD51 regulation we functionally characterized a long non-coding (lnc) RNA, AK125393, dubbed TODRA (Transcribed in the Opposite Direction of RAD51), transcribed 69bp upstream to RAD51, in the opposite direction. TODRA overexpression in HeLa cells induced expression of TPIP, a member of the TPTE family which includes PTEN. Similar to PTEN, we found that TPIP co-activates E2F1 induction of RAD51.
2015-02-19 | GSE66062 | GEO
Project description:The inhibitor of DNA-binding 3 (ID3) is a transcriptional regulator that limits interaction of basic helix-loop-helix transcription factors with their target DNA sequences. We previously reported that ID3 loss is associated with mutational signatures linked to DNA repair defects. Here we demonstrate that ID3 exhibits a dual role to promote DNA double-strand break (DSB) repair, particularly homologous recombination (HR). ID3 interacts with the MRN complex and RECQL helicase to activate DSB repair and it facilitates RAD51 loading and downstream steps of HR. In addition, ID3 promotes the expression of HR genes in response to ionizing radiation by regulating both chromatin accessibility and activity of the transcription factor E2F1. Consistently, analyses of TCGA cancer patient data demonstrate that low ID3 expression is associated with impaired HR. The loss of ID3 leads to sensitivity of tumor cells to PARP inhibition, offering new therapeutic opportunities in ID3-deficient tumors.
2022-02-17 | PXD028946 | Pride
Project description:DNA double-strand breaks (DSBs) are a prominent source of genetic instability/variability frequently associating genome rearrangements with the capture of ectopic chromosomal sequences (ECSs) at junctions. Homologous recombination (HR) is considered in textbooks as an error-free DSB repair mechanism that protects against genome instability. Contradicting this dogma, we show that silencing the central HR players RAD51 or BRCA2 suppresses the sequence homology-independent capture of ECS at the junctions of distant DSBs, especially in 53BP1-depleted cells. We confirmed the requirement of RAD51 for ECS capture at a genome-wide level through high-throughput genome translocation sequencing.
2022-01-17 | GSE126546 | GEO
Project description:Sister chromatid exchanges (SCEs) are a product of joint DNA molecules resolution, and are considered to require homologous recombination (HR). Canonical HR factors BRCA1, BRCA2 and RAD51 were indeed essential for SCE induction in response to irradiation-induced DNA breaks. By contrast, replication-blocking agents, including PARP inhibitors, induced SCEs independently of BRCA1, BRCA2 or RAD51. HR-independent SCEs were associated with incomplete DNA replication, as evidenced by post-replicative single-stranded DNA (ssDNA) accumulation and enrichment of PARP inhibitor-induced SCEs at common fragile sites (CFSs). Importantly, PARP-induced DNA lesions were transmitted into mitosis, pointing towards SCEs originating from mitotic processing of underreplicated DNA. We found polymerase theta to be associated to mitotic DNA lesions, to be required for SCE formation and to prevent chromosome fragmentation upon PARP inhibition in HR-defective cells. Combined, our data show that replication-blocking agents lead to underreplicated DNA in mitosis, which is processed into SCEs independently of canonical HR factors.
2023-03-11 | PXD028670 | Pride
Project description:RAD51 protein is an evolutionarily conserved recombinase that plays a central role in homologous recombination (HR) and DNA double strand break (DSB) repair. RAD51 inactivation by small molecules has been proposed as a strategy to impair the BRCA2/RAD51 binding and, ultimately, the HR pathway, with the aim to make cancer cells more sensitive to PARP inhibitors (PARPi). This strategy, which mimics a synthetic lethality (SL) approach, has been successfully assayed in vitro by using myr-BRC4, a peptide derived from the fourth BRC repeat of BRCA2, being the strongest reported natural RAD51 binder. The present study applies a method to obtain a proteomic fingerprint for RAD51 inhibition by the myr-BRC4 peptide (designed for a more efficient cell entry) using a mass spectroscopy (MS) proteomic approach. We performed a comparative proteomic profiling of the myr-BRC4 treated vs. untreated BxPC-3 pancreatic cancer cells and evaluated the differential expression of proteins. Among the identified proteomic hits, we focused our attention on proteins shared by both the RAD51 and the BRCA2 interactomes, and on those whose reduction showed high statistical significance. Three downregulated proteins were identified (FANCI, FANCD2, and RPA3) and protein downregulation was confirmed through immunoblotting analysis, validating the MS approach. Our results suggest that, being a direct consequence of RAD51 inhibition, the detection of FANCD2, FANCI, and RPA3 downregulation could be used as an indicator for monitoring HR impairment.
2023-08-15 | PXD042696 | Pride
Project description:Expression of RAD51, a crucial player in homologous recombination (HR) and DNA double-strand break (DSB) repair, is dysregulated in human tumors, and can contribute to genomic instability and tumor progression. To further understand RAD51 regulation we functionally characterized a long non-coding (lnc) RNA, AK125393, dubbed TODRA (Transcribed in the Opposite Direction of RAD51), transcribed 69bp upstream to RAD51, in the opposite direction. TODRA overexpression in HeLa cells induced expression of TPIP, a member of the TPTE family which includes PTEN. Similar to PTEN, we found that TPIP co-activates E2F1 induction of RAD51. HeLa cells were transfected with either an empty vector or an AK1253893 minigene. RNA was extracted from duplicates of each experiment and hybridized to affymetrix microarray.
2015-02-19 | E-GEOD-66062 | biostudies-arrayexpress
Project description:Early relapse after platinum chemotherapy in epithelial ovarian cancer (EOC) portends poor survival. A-priori identification of platinum-resistance is therefore crucial to improve on standard first-line carboplatin-paclitaxel treatment. The DNA repair pathway Homologous Recombination (HR) repairs platinum-induced damage, and the HR recombinase RAD51 is overexpressed in cancer. We therefore designed a REMARK-compliant study of pre-treatment RAD51 expression in EOC, using fluorescent quantitative immunohistochemistry (qIHC) to overcome challenges in quantitation of protein-expression in-situ. In a discovery cohort (n=284), RAD51-High tumours had shorter progression-free and overall survival compared to RAD51-Low cases in univariate and multivariate analyses. The association of RAD51 with relapse/survival was validated in a carboplatin-monotherapy SCOTROC4 clinical trial cohort (n=264), and was predominantly noted in HR-proficient cancers (Myriad HRDscore<42). Interestingly, overexpression of RAD51 modified expression of immune-regulatory pathways in-vitro, while high-RAD51 tumours showed exclusion of cytotoxic-T-cells in-situ. Our findings highlight RAD51 expression as a determinant of platinum resistance, and suggest possible roles for therapy to overcome immune exclusion in high-RAD51 EOC. The qIHC approach is generalizable to other proteins with a continuum instead of discrete/bimodal expression.
2021-02-11 | GSE166539 | GEO
Project description:ARF is a tumour suppressor activated by oncogenic stress, which stabilizes p53. Although p53 is a key component of the response to DNA damage, a similar function for ARF has not been ascribed. In this work we show that homologous recombination (HR) -deficient primary mouse and human cells accumulate DNA damage, which triggers checkpoint signalling and ARF activation. We also show that in the absence of ARF p53 is induce in response to DNA damage, but surprisingly fails to trigger senescence. The hypothesis tested in this study was that ARF deficiency alters the spectrum of genes activated by p53 in response to HR deficiency. Using mRNA microarray analysis and expression profiling, we identified genes upregulated in wild type primary MEFs treated with RAD51 shRNA, whose expression was not induced in similarly treated Arf -/- primary MEFs. Clustering analysis of p53 transcriptional targets with increased expression in RAD51-depleted cells revealed three groups: genes requiring functional ARF for their expression, genes transcribed in an ARF-independent manner and genes that are upregulated in both ARF-proficient and ARF-deficient cells. Among the genes in the last group we found Cdkn1a(p21), encoding the p21 inhibitor of cyclindependent kinases and well-characterized effector of the p53 role in promoting senescence. The subset of p53 targets requiring ARF for their transcription was specifically upregulated in response to RAD51 inhibition in wild type, but not Arf -/- MEFs. Among these genes, two encoded the dual specificity phosphatase (DUSP) family members DUSP4 and DUSP7, which act as ERK phosphatases and negative regulators of the MAPK kinase pathway in mammalian cells. Four samples were analysed (WT or ARF negative cells transfected with GFP or RAD51 shRNAs) in duplicate. Samples treated with GFP shRNA are the reference samples and the ones treated with RAD51 shRNA are the experimental ones (RAD51 depletion leads to HR deficiency). The WT cell line is our control cell line to study the effect of HR deficiency on the transcription of p53 target genes
2014-12-04 | E-GEOD-51354 | biostudies-arrayexpress