204 research outputs found
Involvement of Exo1b in DNA damage-induced apoptosis
Apoptosis is essential for the maintenance of inherited genomic integrity. During DNA damage-induced apoptosis, mechanisms of cell survival, such as DNA repair are inactivated to allow cell death to proceed. Here, we describe a role for the mammalian DNA repair enzyme Exonuclease 1 (Exo1) in DNA damage-induced apoptosis. Depletion of Exo1 in human fibroblasts, or mouse embryonic fibroblasts led to a delay in DNA damage-induced apoptosis. Furthermore, we show that Exo1 acts upstream of caspase-3, DNA fragmentation and cytochrome c release. In addition, induction of apoptosis with DNA-damaging agents led to cleavage of both isoforms of Exo1. The cleavage of Exo1 was mapped to Asp514, and shown to be mediated by caspase-3. Expression of a caspase-3 cleavage site mutant form of Exo1, Asp514Ala, prevented formation of the previously observed fragment without any affect on the onset of apoptosis. We conclude that Exo1 has a role in the timely induction of apoptosis and that it is subsequently cleaved and degraded during apoptosis, potentially inhibiting DNA damage repair
ATM mediated phosphorylation of CHD4 contributes to genome maintenance
Background: In order to maintain cellular viability and genetic integrity cells must respond quickly following the\ud
induction of cytotoxic double strand DNA breaks (DSB). This response requires a number of processes including\ud
stabilisation of the DSB, signalling of the break and repair. It is becoming increasingly apparent that one key step\ud
in this process is chromatin remodelling.\ud
Results: Here we describe the chromodomain helicase DNA-binding protein (CHD4) as a target of ATM kinase. We\ud
show that ionising radiation (IR)-induced phosphorylation of CHD4 affects its intranuclear organization resulting in\ud
increased chromatin binding/retention. We also show assembly of phosphorylated CHD4 foci at sites of DNA\ud
damage, which might be required to fulfil its function in the regulation of DNA repair. Consistent with this, cells\ud
overexpressing a phospho-mutant version of CHD4 that cannot be phosphorylated by ATM fail to show enhanced\ud
chromatin retention after DSBs and display high rates of spontaneous damage.\ud
Conclusion: These results provide insight into how CHD4 phosphorylation might be required to remodel\ud
chromatin around DNA breaks allowing efficient DNA repair to occur
Complex-based analysis of dysregulated cellular processes in cancer
Background: Differential expression analysis of (individual) genes is often
used to study their roles in diseases. However, diseases such as cancer are a
result of the combined effect of multiple genes. Gene products such as proteins
seldom act in isolation, but instead constitute stable multi-protein complexes
performing dedicated functions. Therefore, complexes aggregate the effect of
individual genes (proteins) and can be used to gain a better understanding of
cancer mechanisms. Here, we observe that complexes show considerable changes in
their expression, in turn directed by the concerted action of transcription
factors (TFs), across cancer conditions. We seek to gain novel insights into
cancer mechanisms through a systematic analysis of complexes and their
transcriptional regulation.
Results: We integrated large-scale protein-interaction (PPI) and
gene-expression datasets to identify complexes that exhibit significant changes
in their expression across different conditions in cancer. We devised a
log-linear model to relate these changes to the differential regulation of
complexes by TFs. The application of our model on two case studies involving
pancreatic and familial breast tumour conditions revealed: (i) complexes in
core cellular processes, especially those responsible for maintaining genome
stability and cell proliferation (e.g. DNA damage repair and cell cycle) show
considerable changes in expression; (ii) these changes include decrease and
countering increase for different sets of complexes indicative of compensatory
mechanisms coming into play in tumours; and (iii) TFs work in cooperative and
counteractive ways to regulate these mechanisms. Such aberrant complexes and
their regulating TFs play vital roles in the initiation and progression of
cancer.Comment: 22 pages, BMC Systems Biolog
hSSB1 interacts directly with the MRN complex stimulating its recruitment to DNA double-strand breaks and its endo-nuclease activity
hSSB1 is a recently discovered single-stranded DNA binding protein that is essential for efficient repair of DNA double-strand breaks (DSBs) by the homologous recombination pathway. hSSB1 is required for the efficient recruitment of the MRN complex to sites of DSBs and for the efficient initiation of ATM dependent signalling. Here we explore the interplay between hSSB1 and MRN. We demonstrate that hSSB1 binds directly to NBS1, a component of the MRN complex, in a DNA damage independent manner. Consistent with the direct interaction, we observe that hSSB1 greatly stimulates the endo-nuclease activity of the MRN complex, a process that requires the C-terminal tail of hSSB1. Interestingly, analysis of two point mutations in NBS1, associated with Nijmegen breakage syndrome, revealed weaker binding to hSSB1, suggesting a possible disease mechanism.Publisher PDFPeer reviewe
Optimizing poly (ADP-ribose) polymerase inhibition through combined epigenetic and immunotherapy
Triple‐negative breast cancer (TNBC) is an aggressive breast cancer subtype with poor survival outcomes. Currently, there are no targeted therapies available for TNBCs despite remarkable progress in targeted and immune‐directed therapies for other solid organ malignancies. Poly (ADP‐ribose) polymerase inhibitors (PARPi) are effective anticancer drugs that produce good initial clinical responses, especially in homologous recombination DNA repair‐deficient cancers. However, resistance is the rule rather than the exception, and recurrent tumors tend to have an aggressive phenotype associated with poor survival. Many efforts have been made to overcome PARPi resistance, mostly by targeting genes and effector proteins participating in homologous recombination that are overexpressed during PARPi therapy. Due to many known and unknown compensatory pathways, genes, and effector proteins, overlap and shared resistance are common. Overexpression of programmed cell death‐ligand 1 (PD‐L1) and cancer stem cell (CSC) sparing are novel PARPi resistance hypotheses. Although adding programmed cell death‐1 (PD‐1)/PD‐L1 inhibitors to PARPi might improve immunogenic cell death and be crucial for durable responses, they are less likely to target the CSC population that drives recurrent tumor growth. Lysine‐specific histone demethylase‐1A and histone deacetylase inhibitors have shown promising activity against CSCs. Combining epigenetic drugs such as lysine‐specific histone demethylase‐1A inhibitors or histone deacetylase inhibitors with PARPi/anti‐PD‐1/PD‐L1 is a novel, potentially synergistic strategy for priming tumors and overcoming resistance. Furthermore, such an approach could pave the way for the identification of new upstream epigenetic and genetic signatures.This work was supported by the National Health and Medical
Research Council (Grant ID APP1068065) and the UC Deepwater
Scholarship (TP)
Understanding the functional impact of copy number alterations in breast cancer using a network modeling approach
Copy number alterations (CNAs) are thought to account for 85% of the
variation in gene expression observed among breast tumours. The expression of
cis-associated genes is impacted by CNAs occurring at proximal loci of these
genes, whereas the expression of trans-associated genes is impacted by CNAs
occurring at distal loci. While a majority of these CNA-driven genes
responsible for breast tumourigenesis are cis-associated, trans-associated
genes are thought to further abet the development of cancer and influence
disease outcomes in patients. Here we present a network-based approach that
integrates copy-number and expression profiles to identify putative cis- and
trans-associated genes in breast cancer pathogenesis. We validate these cis-
and trans-associated genes by employing them to subtype a large cohort of
breast tumours obtained from the METABRIC consortium, and demonstrate that
these genes accurately reconstruct the ten subtypes of breast cancer. We
observe that individual breast cancer subtypes are driven by distinct sets of
cis- and trans-associated genes. Among the cis-associated genes, we recover
several known drivers of breast cancer (e.g. CCND1, ERRB2, MDM2 and ZNF703) and
some novel putative drivers (e.g. BRF2 and SF3B3). siRNA-mediated knockdown of
BRF2 across a panel of breast cancer cell lines showed significant reduction
specifically in cell proliferation in HER2+ lines, thereby indicating that BRF2
could be a context-dependent oncogene and potentially targetable in these
lines. Among the trans-associated genes, we identify modules of immune-response
(CD2, CD19, CD38 and CD79B), mitotic/cell-cycle kinases (e.g. AURKB, MELK, PLK1
and TTK), and DNA-damage response genes (e.g. RFC4 and FEN1).Comment: 23 pages, 2 tables, 7 figure
Beta-amyloid increases the expression level of ATBF1 responsible for death in cultured cortical neurons
Background: Recently, several lines of evidence have shown the aberrant expression of cell-cycle-related proteins and tumor suppressor proteins in vulnerable neurons of the Alzheimer's disease (AD) brain and transgenic mouse models of AD; these proteins are associated with various paradigms of neuronal death. It has been reported that ATBF1 induces cell cycle arrest associated with neuronal differentiation in the developing rat brain, and that gene is one of the candidate tumor suppressor genes for prostate and breast cancers in whose cells overexpressed ATBF1 induces cell cycle arrest. However, the involvement of ATBF1 in AD pathogenesis is as yet unknown. Results: We found that ATBF1 was up-regulated in the brains of 17-month-old Tg2576 mice compared with those of age-matched wild-type mice. Moreover, our in vitro studies showed that Aβ1-42 and DNA-damaging drugs, namely, etoposide and homocysteine, increased the expression ATBF1 level in primary rat cortical neurons, whereas the knockdown of ATBF1 in these neurons protected against neuronal death induced by Aβ1-42, etoposide, and homocysteine, indicating that ATBF1 mediates neuronal death in response to these substances. In addition, we found that ATBF1-mediated neuronal death is dependent on ataxia-telangiectasia mutated (ATM) because the blockage of ATM activity by treatment with ATM inhibitors, caffeine and KU55933, abolished ATBF1 function in neuronal death. Furthermore, Aβ1-42 phosphorylates ATM, and ATBF1 interacts with phosphorylated ATM. Conclusions: To the best of our knowledge, this is the first report that Aβ1-42 and DNA-damaging drugs increased the ATBF1 expression level in primary rat cortical neurons; this increase, in turn, may activate ATM signaling responsible for neuronal death through the binding of ATBF1 to phosphorylated ATM. ATBF1 may therefore be a suitable target for therapeutic intervention of AD
Personalised pathway analysis reveals association between DNA repair pathway dysregulation and chromosomal instability in sporadic breast cancer
The Homologous Recombination (HR) pathway is crucial for the repair of DNA double-strand breaks (DSBs) generated during DNA replication. Defects in HR repair have been linked to the initiation and development of a wide variety of human malignancies, and exploited in chemical, radiological and targeted therapies. In this study, we performed a personalised pathway analysis independently for four large sporadic breast cancer cohorts to investigate the status of HR pathway dysregulation in individual sporadic breast tumours, its association with HR repair deficiency and its impact on tumour characteristics. Specifically, we first manually curated a list of HR genes according to our recent review on this pathway (Liu et al., 2014), and then applied a personalised pathway analysis method named Pathifier (Drier et al., 2013) on the expression levels of the curated genes to obtain an HR score quantifying HR pathway dysregulation in individual tumours. Based on the score, we observed a great diversity in HR dysregulation between and within gene expression-based breast cancer subtypes, and by using two published HR-defect signatures, we found HR pathway dysregulation reflects HR repair deficiency. Furthermore, we identified a novel association between HR pathway dysregulation and chromosomal instability (CIN) in sporadic breast cancer. Although GIN has long been considered as a hallmark of most solid tumours, with recent extensive studies highlighting its importance in tumour evolution and drug resistance, the molecular basis of CIN in sporadic cancers remains poorly understood. Our results imply that HR pathway dysregulation might contribute to CIN in sporadic breast cancer. (C) 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved
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