BRCA-FA pathway as a target for anti-tumor drugs

DNA Damage Response (DDR) proteins in canine cancer as potential research targets in comparative oncology

The DNA damage response (DDR) is a complex signal transduction network that is activated when endogenous or exogenous genotoxins damage or interfere with the replication of genomic DNA. Under such conditions, the DDR promotes DNA repair and ensures accurate replication and division of the genome. High levels of genomic instability are frequently observed in cancers and can stem from germline loss‐of‐function mutations in certain DDR genes, such as BRCA1, BRCA2, and p53, that form the basis of human cancer predisposition syndromes. In addition, mutation and/or aberrant expression of multiple DDR genes are frequently observed in sporadic human cancers. As a result, the DDR is considered to represent a viable target for cancer therapy in humans and a variety of strategies are under investigation. Cancer is also a significant cause of mortality in dogs, a species that offers certain advantages for experimental oncology. Domestic dogs present numerous inbred lines, many of which display predisposition to specific forms of cancer and the study of which may provide insight into the biological basis of this susceptibility. In addition, clinical trials are possible in dogs and may lead to therapeutic insights that could ultimately be extended to humans. Here we review what is known specifically about the DDR in dogs and discuss how this knowledge could be extended and exploited to advance experimental oncology in this species.

Identification of a genetic signature enriching for response to ibrutinib in relapsed/refractory follicular lymphoma in the DAWN phase 2 trial

Background

The single‐arm DAWN trial (NCT01779791) of ibrutinib monotherapy in patients with relapsed/refractory follicular lymphoma (FL) showed an overall response rate (ORR) of 20.9% and a median response duration of 19.4 months. This biomarker analysis of the DAWN dataset sought to determine genetic classifiers for prediction of response to ibrutinib treatment.

Methods

Whole exome sequencing was performed on baseline tumor samples. Potential germline variants were excluded; a custom set of 1216 cancer‐related genes was examined. Responder‐ versus nonresponder‐associated variants were identified using Fisher's exact test. Classifiers with increasing numbers of genes were created using a greedy algorithm that repeatedly selected genes, adding the most nonresponders to the existing “predicted nonresponders” set and were evaluated with 10‐fold cross‐validation.

Results

Exome data were generated from 88 patient samples and 13,554 somatic mutation variants were inferred. Response data were available for 83 patients (17 responders, 66 nonresponders). Each sample showed 100 to >500 mutated genes, with greater variance across nonresponders. The overall variant pattern was consistent with previous FL studies; 75 genes had mutations in >10% of patients, including genes previously reported as associated with FL. Univariate analysis yielded responder‐associated genes FANCA, HISTH1B, ANXA6, BTG1, and PARP10, highlighting the importance of functions outside of B‐cell receptor signaling, including epigenetic processes, DNA damage repair, cell cycle/proliferation, and cell motility/invasiveness. While nonresponder‐associated genes included well‐known TP53 and CARD11, genetic classifiers developed using nonresponder‐associated genes included ATP6AP1, EP400, ARID1A, SOCS1, and TBL1XR1, suggesting resistance to ibrutinib may be related to broad biological functions connected to epigenetic modification, telomere maintenance, and cancer‐associated signaling pathways (mTOR, JAK/STAT, NF‐κB).

Conclusion

The results from univariate and genetic classifier analyses provide insights into genes associated with response or resistance to ibrutinib in FL and identify a classifier developed using nonresponder‐associated genes, which warrants further investigation.

Trial registration: NCT01779791.

Hypermethylation of tumor suppressor genes is a risk factor for poor prognosis in ovarian cancer: A meta-analysis

OBJECTIVE

DNA methylation is the earliest and most studied epigenetic modification in cancer. The literature reported that the abnormal methylation level of multiple genes was associated with poor prognosis in ovarian cancer. However, due to a small sample size, the results reported in the literature vary widely. In this study, the correlation between aberrant methylation level of genes and poor prognosis of ovarian cancer was reviewed in order to clarify the role of DNA methylation in the prognosis of ovarian cancer.

METHODS

A systematic research of PubMed, EMbase, Cochrane Library, China Biology Medicine disc (CBMdisc), China National Knowledge Infrastructure (CNKI), Wanfang databases, and EMBASE was performed, and calculated the hazard ratio (HR) of overall survival (OS) and progression-free survival (PFS) and its 95% confidence interval.

RESULTS

HR of the OS obtained of target genes was 2.32 (95% CI: 1.54-3.48, P = .000); HR of the PFS obtained of target genes was 1.318 (95% CI: 0.848-2.050, P = .220). HR of OS achieved by tumor suppressor genes was 3.09 (95% CI 1.80 - 5.30, P = .000).

CONCLUSION

Hypermethylation of tumor suppressor genes indicate poor prognosis of ovarian cancer.

CD10-/ALDH- cells are the sole cisplatin-resistant component of a novel ovarian cancer stem cell hierarchy

It is long established that tumour-initiating cancer stem cells (CSCs) possess chemoresistant properties. However, little is known of the mechanisms involved, particularly with respect to the organisation of CSCs as stem-progenitor-differentiated cell hierarchies. Here we aimed to elucidate the relationship between CSC hierarchies and chemoresistance in an ovarian cancer model. Using a single cell-based approach to CSC discovery and validation, we report a novel, four-component CSC hierarchy based around the markers cluster of differentiation 10 (CD10) and aldehyde dehydrogenase (ALDH). In a change to our understanding of CSC biology, resistance to chemotherapy drug cisplatin was found to be the sole property of CD10⁻/ALDH⁻ CSCs, while all four CSC types were sensitive to chemotherapy drug paclitaxel. Cisplatin treatment quickly altered the hierarchy, resulting in a three-component hierarchy dominated by the cisplatin-resistant CD10⁻/ALDH⁻ CSC. This organisation was found to be hard-wired in a long-term cisplatin-adapted model, where again CD10⁻/ALDH⁻ CSCs were the sole cisplatin-resistant component, and all CSC types remained paclitaxel-sensitive. Molecular analysis indicated that cisplatin resistance is associated with inherent- and adaptive-specific drug efflux and DNA-damage repair mechanisms. Clinically, low CD10 expression was consistent with a specific set of ovarian cancer patient samples. Collectively, these data advance our understanding of the relationship between CSC hierarchies and chemoresistance, which was shown to be CSC- and drug-type specific, and facilitated by specific and synergistic inherent and adaptive mechanisms. Furthermore, our data indicate that primary stage targeting of CD10⁻/ALDH⁻ CSCs in specific ovarian cancer patients in future may facilitate targeting of recurrent disease, before it ever develops.

Curcumin reverses cisplatin resistance in cisplatin-resistant lung caner cells by inhibiting FA/BRCA pathway

Cisplatin (DDP) is the most widely used chemotherapy agent for treatment of malignancies including lung cancer. However, the effectiveness of DDP is often weakened by acquired resistance of tumor cells. DDP kills cancer cells primarily by creating intrastrand and interstrand DNA cross-links, which block DNA replication. The Fanconi anemia (FA)/BRCA pathway is a DNA cross-link damage repair pathway, which regulates cellular resistance to DNA cross-link agents, such as DDP. Some study has shown that natural compound curcumin sensitize human ovarian and breast cancer cells to DDP. However, whether curcumin may reverse resistance to DDP in DDP-resistant lung cancer cells has not been understood. In this study, we showed that curcumin enhanced the proliferation inhibitory effect of DDP and promote DDP-induced apoptosis in A549/DDP cells (DDP-resistant lung adenocarcinoma cells). Moreover, we observed that FA/BRCA pathway DNA damage repair processes, such as DDP-induced FANCD2 monoubiquitination and nuclear foci formation were downregulated in the presence of curcumin, suggesting that curcumin enhanced sensitivity to DDP in A549/DDP cells through the inhibition of FA/BRCA pathway. Furthermore, the calculation of q value and apoptosis analyses revealed that curcumin in combination with DDP could exert a synergistic cytotoxic effect in A549/DDP cells, further demonstrating that curcumin can reverse cisplatin resistance of A549/DDP cells. In conclusion, by suppressing the FA/BRCA pathway DNA repair, curcumin potentiates DDP-induced proliferation inhibitory effect and apoptosis in A549/DDP cell, indicating that curcumin may serve as a chemosensitizer to cross-link-inducing anticancer drugs DDP.

Combined experimental and computational analysis of DNA damage signaling reveals context-dependent roles for Erk in apoptosis and G1/S arrest after genotoxic stress

Following DNA damage, cells display complex multi-pathway signaling dynamics that connect cell-cycle arrest and DNA repair in G1, S, or G2/M phase with phenotypic fate decisions made between survival, cell-cycle re-entry and proliferation, permanent cell-cycle arrest, or cell death. How these phenotypic fate decisions are determined remains poorly understood, but must derive from integrating genotoxic stress signals together with inputs from the local microenvironment. To investigate this in a systematic manner, we undertook a quantitative time-resolved cell signaling and phenotypic response study in U2OS cells receiving doxorubicin-induced DNA damage in the presence or absence of TNFα co-treatment; we measured key nodes in a broad set of DNA damage signal transduction pathways along with apoptotic death and cell-cycle regulatory responses. Two relational modeling approaches were then used to identify network-level relationships between signals and cell phenotypic events: a partial least squares regression approach and a complementary new technique which we term 'time-interval stepwise regression.' Taken together, the results from these analysis methods revealed complex, cytokine-modulated inter-relationships among multiple signaling pathways following DNA damage, and identified an unexpected context-dependent role for Erk in both G1/S arrest and apoptotic cell death following treatment with this commonly used clinical chemotherapeutic drug.

Fanconi anaemia: from a monogenic disease to sporadic cancer

The dissection of the molecular pathways participating in genetic instability disorders has rendered invaluable information about the mechanisms of cancer pathogenesis and progression, and is offering a unique opportunity to establish targeted anticancer therapies. Fanconi anaemia (FA) is a paradigm of cancer-prone inherited monogenic disorders. Moreover, accumulated evidence indicates that genetic and epigenetic alterations in FA genes can also play an important role in sporadic cancer in the general population. Here, we summarise current progress in the understanding of the molecular biology of FA and review the principal mechanisms accounting for a disrupted FA pathway in sporadic cancer. Additionally, we discuss the impact of these findings in the development of new anticancer therapies, particularly with DNA interstrand crosslinkers and with new inhibitors of the FA and/or alternative DNA repair pathways.

Transcriptional regulation of the base excision repair pathway by BRCA1

Inactivation of the breast cancer susceptibility gene BRCA1 plays a significant role in the development of a subset of breast cancers, although the major tumor suppressor function of this gene remains unclear. Previously, we showed that BRCA1 induces antioxidant-response gene expression and protects cells against oxidative stress. We now report that BRCA1 stimulates the base excision repair pathway, a major mechanism for the repair of oxidized DNA, by stimulating the activity of key base excision repair (BER) enzymes, including 8-oxoguanine DNA glycosylase (OGG1), the DNA glycosylase NTH1, and the apurinic endonuclease redox factor 1/apurinic endonuclease 1 (REF1/APE1), in human breast carcinoma cells. The increase in BER enzyme activity appears to be due, primarily, to an increase in enzyme expression. The ability of BRCA1 to stimulate the expression of the three BER enzymes and to enhance NTH1 promoter activity was dependent upon the octamer-binding transcription factor OCT1. Finally, we found that OGG1, NTH1, and REF1/APE1 each contribute to the BRCA1 protection against oxidative stress due to hydrogen peroxide and that hydrogen peroxide stimulates the expression of BRCA1 and the three BER enzymes. These findings identify a novel mechanism through which BRCA1 may regulate the repair of oxidative DNA damage.

Susceptibility pathways in Fanconi's anemia and breast cancer

The study of rare genetic diseases can lead to insights into the cause and treatment of common diseases. An example is the rare chromosomal instability disorder, Fanconi Anemia (FA). Studies of this disease have elucidated general mechanisms of bone marrow failure, cancer pathogenesis, and resistance to chemotherapy. The principal features of FA are aplastic anemia in childhood, susceptibility to cancer or leukemia, and hypersensitivity of FA cells to DNA cross-linking agents. There are thirteen FA genes, and one of these genes is identical to the well known breast cancer susceptibility gene, BRCA2. The corresponding FA proteins cooperate in the recognition and repair of damaged DNA. Inactivation of FA genes occurs not only in FA patients but also in a variety of cancers in the general population. These findings have broad implications for predicting the sensitivity and resistance of tumors to conventional anti-cancer agents, to inhibitors of poly-ADP ribose polymerase 1, an enzyme involved in DNA repair, and to other inhibitors of DNA repair.

Article Commentary: Targeting DNA Damage and Repair by Curcumin

Curcumin is a compound with anti-tumor effects in a tolerable dose. A recent paper by Rowe et al described that curcumin induced DNA damage in triple negative breast cancer cells and regulated BRCA1 protein expression and modification. 1 Related research and potential use of curcumin will be discussed in this article.

Targeting DNA damage and repair by curcumin

Curcumin is a compound with anti-tumor effects in a tolerable dose. A recent paper by Rowe et al described that curcumin induced DNA damage in triple negative breast cancer cells and regulated BRCA1 protein expression and modification.1 Related research and potential use of curcumin will be discussed in this article.

Human synthetic lethal inference as potential anti-cancer target gene detection

Background

Two genes are called synthetic lethal (SL) if mutation of either alone is not lethal, but mutation of both leads to death or a significant decrease in organism's fitness. The detection of SL gene pairs constitutes a promising alternative for anti-cancer therapy. As cancer cells exhibit a large number of mutations, the identification of these mutated genes' SL partners may provide specific anti-cancer drug candidates, with minor perturbations to the healthy cells. Since existent SL data is mainly restricted to yeast screenings, the road towards human SL candidates is limited to inference methods.

Results

In the present work, we use phylogenetic analysis and database manipulation (BioGRID for interactions, Ensembl and NCBI for homology, Gene Ontology for GO attributes) in order to reconstruct the phylogenetically-inferred SL gene network for human. In addition, available data on cancer mutated genes (COSMIC and Cancer Gene Census databases) as well as on existent approved drugs (DrugBank database) supports our selection of cancer-therapy candidates.

Conclusions

Our work provides a complementary alternative to the current methods for drug discovering and gene target identification in anti-cancer research. Novel SL screening analysis and the use of highly curated databases would contribute to improve the results of this methodology.

OMICS-rooted studies of milk proteins, oligosaccharides and lipids

Milk has co-evolved with mammals and mankind to nourish their offspring and is a biological fluid of unique complexity and richness. It contains all necessary nutrients for the growth and development of the newborn. Structure and function of biomolecules in milk such as the macronutrients (glyco-) proteins, lipids, and oligosaccharides are central topics in nutritional research. Omics disciplines such as proteomics, glycomics, glycoproteomics, and lipidomics enable comprehensive analysis of these biomolecule components in food science and industry. Mass spectrometry has largely expanded our knowledge on these milk bioactives as it enables identification, quantification and characterization of milk proteins, carbohydrates, and lipids. In this article, we describe the biological importance of milk macronutrients and review the application of proteomics, glycomics, glycoproteomics, and lipidomics to the analysis of milk. Proteomics is a central platform among the Omics tools that have more recently been adapted and applied to nutrition and health research in order to deliver biomarkers for health and comfort as well as to discover beneficial food bioactives.

Hitting the bull's eye: novel directed cancer therapy through helicase-targeted synthetic lethality

Designing strategies for anti-cancer therapy have posed a significant challenge. One approach has been to inhibit specific DNA repair proteins and their respective pathways to enhance chemotherapy and radiation therapy used to treat cancer patients. Synthetic lethality represents an approach that exploits pre-existing DNA repair deficiencies in certain tumors to develop inhibitors of DNA repair pathways that compensate for the tumor-associated repair deficiency. Since helicases play critical roles in the DNA damage response and DNA repair, particularly in actively dividing and replicating cells, it is proposed that the identification and characterization of synthetic lethal relationships of DNA helicases will be of value in developing improved anti-cancer treatment strategies. In this review, we discuss this hypothesis and current evidence for synthetic lethal interactions of eukaryotic DNA helicases in model systems.