Bryan T Hennessy

Royal College of Surgeons in Ireland, Dublin, Leinster, Ireland

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Publications (130)895.02 Total impact

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    ABSTRACT: Peroxiredoxin-1 (PRDX1) is a multifunctional protein, acting as a hydrogen peroxide (H2O2) scavenger, molecular chaperone and immune modulator. Although differential PRDX1 expression has been described in many tumors, the potential role of PRDX1 in breast cancer remains highly ambiguous. Using a comprehensive antibody-based proteomics approach, we interrogated PRDX1 protein as a putative biomarker in estrogen receptor (ER)-positive breast cancer.
    Breast cancer research: BCR 07/2014; 16(4):R79. · 5.87 Impact Factor
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    ABSTRACT: Locally advanced rectal cancer (LARC: T3/4 and/or node-positive) is treated with preoperative/neoadjuvant chemoradiotherapy (CRT), but responses are not uniform. The phosphatidylinositol 3-kinase (PI3K), MAP kinase (MAPK), and related pathways are implicated in rectal cancer tumorigenesis. Here, we investigated the association between genetic mutations in these pathways and LARC clinical outcomes. We genotyped 234 potentially clinically relevant nonsynonymous mutations in 33 PI3K and MAPK pathway-related genes, including PIK3CA, PIK3R1, AKT, STK11, KRAS, BRAF, MEK, CTNNB1, EGFR, MET, and NRAS, using the Sequenom platform. DNA samples were extracted from pretreatment LARC biopsy samples taken from 201 patients who were then treated with long-course neoadjuvant CRT followed by surgical resection. Sixty-two mutations were detected in 15 genes, with the highest frequencies occurring in KRAS (47 %), PIK3CA (14 %), STK11 (6.5 %), and CTNNB1 (6 %). Mutations were detected in BRAF, NRAS, AKT1, PIK3R1, EGFR, GNAS, MEK1, PDGFRA, ALK, and TNK2, but at frequencies of <5 %. As expected, a pathologic complete response (pCR) was associated with improved 5-year recurrence-free survival (RFS; hazard ratio, 0.074; 95 % CI 0.01-0.54; p = 0.001). Mutations in PI3K pathway-related genes (odds ratio, 5.146; 95 % CI 1.17-22.58; p = 0.030), but not MAPK pathway-related genes (p = 0.911), were associated with absence of pCR after neoadjuvant CRT. In contrast, in patients who did not achieve pCR, mutations in PI3K pathway-related genes were not associated with recurrence-free survival (p = 0.987). However, in these patients, codon 12 (G12D/G12 V/G12S) and 13 mutations in KRAS were associated with poor recurrence-free survival (hazard ratio, 1.579; 95 % confidence ratio, 1.00-2.48; p = 0.048). Mutations in kinase signaling pathways modulate treatment responsiveness and clinical outcomes in LARC and may constitute rational targets for novel therapies.
    Annals of Surgical Oncology 04/2014; · 4.12 Impact Factor
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    ABSTRACT: The cytotoxicity of PARP inhibitors olaparib, veliparib, and CEP-8983 were investigated in two P-glycoprotein (P-gp) overexpressing drug-resistant cell models (IGROVCDDP and KB-8-5-11). IGROVCDDP and KB-8-5-11 were both resistant to olaparib and resistance was reversible with the P-gp inhibitors elacridar, zosuquidar, and valspodar. In contrast, the P-gp overexpressing models were not resistant to veliparib or CEP-8983. Olaparib and veliparib did not induce protein expression of P-gp in IGROVCDDP or KB-8-5-11 at doses that successfully inhibit PARP. Olaparib therefore appears to be a P-gp substrate. Veliparib and CEP-8983 do not appear to be substrates. Veliparib and CEP-8983 may therefore be more useful in combined chemotherapy regimens with P-gp substrates and may be active in platinum and taxane-resistant ovarian cancer. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci
    Journal of Pharmaceutical Sciences 04/2014; · 3.13 Impact Factor
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    ABSTRACT: Reverse-phase protein array (RPPA) analysis is a powerful, rel- atively new platform that allows for high-throughput, quantitative analysis of protein networks. One of the challenges that currently limit the potential of this technology is the lack of methods that al- low for accurate data modeling and identification of related networks and samples. Such models may improve the accuracy of biological sample classification based on patterns of protein network activation and provide insight into the distinct biological relationships underly- ing different types of cancer. Motivated by RPPA data, we propose a Bayesian sparse graphical modeling approach that uses selection priors on the conditional relationships in the presence of class infor- mation. The novelty of our Bayesian model lies in the ability to draw information from the network data as well as from the associated categorical outcome in a unified hierarchical model for classification. In addition, our method allows for intuitive integration of a priori network information directly in the model and allows for posterior inference on the network topologies both within and between classes. Applying our methodology to an RPPA data set generated from pan- els of human breast cancer and ovarian cancer cell lines, we demon- strate that the model is able to distinguish the different cancer cell types more accurately than several existing models and to identify differential regulation of components of a critical signaling network (the PI3K-AKT pathway) between these two types of cancer. This approach represents a powerful new tool that can be used to improve our understanding of protein networks in cancer.
    03/2014;
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    ABSTRACT: Ovarian cancer is now recognized as a number of distinct diseases primarily defined by histological subtype. Both clear cell ovarian carcinomas (CCC) and ovarian endometrioid carcinomas (EC) may arise from endometriosis and frequently harbor mutations in the ARID1A tumor suppressor gene. We studied the influence of histological subtype on protein expression with reverse phase protein array (RPPA) and assessed proteomic changes associated with ARID1A mutation/BAF250a expression in EC and CCC. Immunohistochemistry (IHC) for BAF250a expression was performed on 127 chemotherapy-naive ovarian carcinomas (33 CCC, 29 EC, and 65 high-grade serous ovarian carcinomas (HGSC)). Whole tumor lysates were prepared from frozen banked tumor samples and profiled by RPPA using 116 antibodies. ARID1A mutations were identified by exome sequencing, and PIK3CA mutations were characterized by MALDI-TOF mass spectrometry. SAM (Significance Analysis of Microarrays) was performed to determine differential protein expression by histological subtype and ARID1A mutation status. Multivariate logistic regression was used to assess the impact of ARID1A mutation status/BAF250a expression on AKT phosphorylation (pAKT). PIK3CA mutation type and PTEN expression were included in the model. BAF250a knockdown was performed in 3 clear cell lines using siRNA to ARID1A. Marked differences in protein expression were observed that are driven by histotype. Compared to HGSC, SAM identified over 50 proteins that are differentially expressed in CCC and EC. These included PI3K/AKT pathway proteins, those regulating the cell cycle, apoptosis, transcription, and other signaling pathways including steroid hormone signaling. Multivariate models showed that tumors with loss of BAF250a expression showed significantly higher levels of AKT-Thr308 and AKT-Ser 473 phosphorylation (p < 0.05). In 31 CCC cases, pAKT was similarly significantly increased in tumors with BAF250a loss on IHC. Knockdown of BAF250a by siRNA in three CCC cell lines wild type for ARID1A showed no increase in either pAKT-Thr308 or pAKT-S473 suggesting that pAKT in tumor tissues is indirectly regulated by BAF250a expression. Proteomic assessment of CCC and EC demonstrates remarkable differences in protein expression that are dependent on histotype, thereby further characterizing these cancers. AKT phosphorylation is associated with ARID1A/BAF250a deficient tumors, however in ovarian cancers the mechanism remains to be elucidated.
    BMC Cancer 02/2014; 14(1):120. · 3.33 Impact Factor
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    ABSTRACT: Homologous recombination (HR) repair deficiency predisposes to cancer development, but also sensitizes cancer cells to DNA damage-inducing therapeutics. Here we identify an HR defect (HRD) gene signature that can be used to functionally assess HR repair status without interrogating individual genetic alterations in cells. By using this HRD gene signature as a functional network analysis tool, we discover that simultaneous loss of two major tumour suppressors BRCA1 and PTEN extensively rewire the HR repair-deficient phenotype, which is found in cells with defects in either BRCA1 or PTEN alone. Moreover, the HRD gene signature serves as an effective drug discovery platform to identify agents targeting HR repair as potential chemo/radio sensitizers. More importantly, this HRD gene signature is able to predict clinical outcomes across multiple cancer lineages. Our findings, therefore, provide a molecular profile of HR repair to assess its status at a functional network level, which can provide both biological insights and have clinical implications in cancer.
    Nature Communications 02/2014; 5:3361. · 10.02 Impact Factor
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    ABSTRACT: The prognosis of epithelial ovarian cancer is poor in part due to the high frequency of chemoresistance. Recent evidence points to the Toll-like receptor-4 (TLR4), and particularly its adaptor protein MyD88, as one potential mediator of this resistance. This study aims to provide further evidence that MyD88 positive cancer cells are clinically significant, stem-like and reproducibly detectable for the purposes of prognostic stratification. Expression of TLR4 and MyD88 was assessed immunohistochemically in 198 paraffin-embedded ovarian tissues and in an embryonal carcinoma model of cancer stemness. In parallel, expression of TLR4 and MyD88 mRNA and regulatory microRNAs (miR-21 and miR-146a) was assessed, as well as in a series of chemosensitive and resistant cancer cells lines. Functional analysis of the pathway was assessed in chemoresistant SKOV-3 ovarian cancer cells. TLR4 and MyD88 expression can be reproducibly assessed via immunohistochemistry using a semi-quantitative scoring system. TLR4 expression was present in all ovarian epithelium (normal and neoplastic), whereas MyD88 was restricted to neoplastic cells, independent of tumour grade and associated with reduced progression-free and overall survival, in an immunohistological specific subset of serous carcinomas, p<0.05. MiR-21 and miR-146a expression was significantly increased in MyD88 negative cancers (p<0.05), indicating their participation in regulation. Significant alterations in MyD88 mRNA expression were observed between chemosensitive and chemoresistant cells and tissue. Knockdown of TLR4 in SKOV-3 ovarian cells recovered chemosensitivity. Knockdown of MyD88 alone did not. MyD88 expression was down-regulated in differentiated embryonal carcinoma (NTera2) cells, supporting the MyD88+ cancer stem cell hypothesis. Our findings demonstrate that expression of MyD88 is associated with significantly reduced patient survival and altered microRNA levels and suggest an intact/functioning TLR4/MyD88 pathway is required for acquisition of the chemoresistant phenotype. Ex vivo manipulation of ovarian cancer stem cell (CSC) differentiation can decrease MyD88 expression, providing a potentially valuable CSC model for ovarian cancer.
    PLoS ONE 01/2014; 9(6):e100816. · 3.73 Impact Factor
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    ABSTRACT: To date, there is no uniform consensus whether tumour regression grade (TRG) is predictive of outcome in rectal cancer. Furthermore, the lack of standardization of TRG grading is a major source of variability in published studies. The aim of this study was to evaluate the prognostic impact of TRG in a cohort of patients with locally advanced rectal cancer treated with neoadjuvant chemoradiation therapy (CRT). In addition to Mandard TRG, we utilized four TRG systems modified from the Mandard TRG system and applied them to the cohort to assess which TRG system is most informative. 153 patients with a T3/T4 and/or a node positive rectal cancer underwent neoadjuvant 5-fluorouracil-based CRT followed by surgical resection. Thirty-six (23.5%) patients achieving complete pathologic response (ypCR) had a 5-year disease-free survival (DFS) of 100% vs. 74% for 117 (76.5%) patients without ypCR (P=0.003). The Royal College of Pathologists (RCPath) TRG best condenses the Mandard 5-point TRG by stratifying patients into three groups with distinct 5-year DFS rates of 100%, 86% and 67%, respectively (P=0.001). In multivariate analysis, pathological nodal status and circumferential resection margin (CRM) status, but not TRG, remained significant predictors of DFS (P=0.002, 0.035, 0.310, respectively). Our findings support the notion that ypCR status, nodal status after neoadjuvant CRT and CRM status but not TRG are predictors of long-term survival in patients with locally advanced rectal cancer. This article is protected by copyright. All rights reserved.
    Colorectal Disease 10/2013; · 2.08 Impact Factor
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    ABSTRACT: Background: An online database was needed for the Cochrane review “Taxanes for the treatment of platinum pre-treated epithelial ovarian cancer” for several reasons. Firstly, a large amount of clinical parameters were to be extracted from 68 identified studies and the data was to be subdivided into 16 different subgroups. Secondly, there were 6 authors performing data extraction for this Cochrane review, working at 4 different institutions. Therefore data could not be entered and stored centrally at one institution. Objectives: Development of a cloud computing database accessible online for all authors performing data extraction. Methods: The database utilises cloud computing, such that the information is stored online and can be accessed from anywhere and is populated through a web-based user interface. Results: Using an online database-as-a-service and cloud computing to query and compare data allows the elimination of transaction concurrency conflicts. That is, the 2 authors can simultaneously review the same study without breaking the database. In the data extraction phase the cloud computing model allows authors to all work remotely. Each study in our review must have the data extracted by 2 review authors. The database will crosscheck information entered by two authors and flag discrepancies that need to be resolved by discussion. In the analysis phase the database allows each relevant paper containing data for each subgroup to be easily identified amongst the identified studies. Data to be presented will include a demonstration of functionality of the database and excerpts of results highlighting the usefulness of the database in complex subgroup categorisation. Conclusions: The cloud computing database was invaluable for performing this Cochrane review as the subgroups overlapped in many publications. Many complex Cochrane reviews could benefit from this approach to data extraction which facilitates collaboration across multiple institutions.
    21st Cochrane Colloqium, Quebec City, Quebec, Canada; 09/2013
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    ABSTRACT: Platelet hyperreactivity is associated with an increased risk of thrombosis. Cancer patients are at an increased risk of thrombosis, a risk that increases with disease progression. While cancer patients show evidence of platelet activation in vivo, few studies have extensively assessed whether these patients display platelet hyperreactivity. We hypothesized that patients with metastatic cancer would display platelet hyperreactivity, reflecting their associated high risk of thrombosis. In a cohort of patients with metastatic cancer (n = 13), we assessed platelet function using well-established assays of platelet reactivity (agonist-induced platelet aggregation, spontaneous platelet aggregation, and agonist-induced P-selectin expression). In comparison with healthy controls (n = 10), patients with metastatic cancer displayed global platelet hyperreactivity. Agonist-induced platelet aggregation responses to ADP (adenosine diphosphate), epinephrine, collagen, arachidonic acid, and PAR-1 (protease-activated receptor-1) activating peptide, as well as spontaneous platelet aggregation, were significantly increased in patients with metastatic cancer. Furthermore, agonist-induced platelet P-selectin expression was also significantly increased within the patient cohort. We demonstrate that patients with metastatic cancer are characterized by global platelet hyperreactivity, a factor that may contribute to their increased risk of thrombosis. We assessed platelet function in a cohort of patients with metastatic cancer (n = 13) using well-established assays of platelet reactivity. Agonist-induced platelet aggregation and activation in response to platelet agonists, as well as spontaneous platelet aggregation, was significantly increased in cancer patients compared with healthy controls. We demonstrate that patients with metastatic cancer are characterized by global platelet hyperreactivity, a factor that may contribute to their increased risk of thrombosis.
    Cancer medicine. 08/2013; 2(4):564-70.
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    ABSTRACT: Worldwide there are more than 204,000 new cases of ovarian cancer each year, accounting for around 4% of all cancers diagnosed in women. Suitable laboratory cell models are needed to study potential therapeutic strategies. An Affymetrix 500K SNP chip was performed on DNA from 41 ovarian cell lines. Chromosomal copy number analysis revealed that 7 of the ovarian cancer cell lines had very few chromosomal abnormalities, and many of these are the most commonly studied ovarian cell models in the literature (A2780, DOV13, EFO27, HOC-1, HOC-7, IGROV-1 and PA1). The chromosomal profiles of these 7 cell lines are close to the normal 2 copies of each per cell. In contrast, when ovarian tumours are profiled many chromosome aberrations are observed with 3-4 copies of each chromosome present. Many copy number variations (CNVs) have been identified in phenotypically normal individuals and are regarded as benign. The PN cell lines all have tiny regions of increased or decreased chromosomal copy number. These regions will be identified and then searched for using the Database of Genomic Variants and Database of The International Standards for Cytogenetic Arrays Consortium. The CNVs will be categorised as a benign or cancerous if they are reported at least 3 times independently in normal or cancerous samples respectively. The discovery of pseudo-normal (PN) chromosomes is not unique to ovarian cancer. Cell lines and low-grade tumours from other cancer types have also been found to have a PN profile. The PN cells may be Type I ovarian cancer, cells of low grade cancer or from ovarian tumours of low malignant potential. Alternatively, these cells may not be cancer cells at all. It is important to understand if the cell lines with PN chromosomes are representative of clinical ovarian cancer so that suitable cell models are used in the laboratory.
    9th European Cytogenetics Conference, Dublin, Ireland; 06/2013
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    ABSTRACT: Weighted gene coexpression network analysis (WGCNA) is a powerful "guilt-by-association" based method to extract coexpressed groups of genes from large heterogeneous mRNA expression datasets. We have utilised WGCNA to identify 11 corregulated gene clusters across 2342 breast cancer samples from 13 microarray-based gene expression studies. A number of these transcriptional modules were found to be correlated to clinicopathological variables (e.g. tumour grade), survival endpoints for breast cancer as a whole (disease free survival (DFS), distant disease free survival (DDFS) and overall survival (OS)) and also its molecular subtypes (luminal A, luminal B, HER2+ and basal-like). Examples of findings arising from this work include the identification of a cluster of proliferation-related genes, that when upregulated correlated to increased tumour grade and were associated with poor survival in general. The prognostic potential of novel genes e.g. ubiquitin-conjugating enzyme E2S (UBE2S) within this group were confirmed in an independent dataset. In addition, gene clusters were also associated with survival for breast cancer molecular subtypes including a cluster of genes that was found to correlate with prognosis exclusively for basal-like breast cancer. The upregulation of several single genes within this coexpression cluster e.g. the potassium channel, subfamily K, member 5 (KCNK5) were associated with poor outcome for the basal-like molecular subtype. We have developed an online database to allow user friendly access to the coexpression patterns and the survival analysis outputs uncovered in this study (Availability: http://glados.ucd.ie/Coexpression/).
    Carcinogenesis 06/2013; · 5.64 Impact Factor
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    ABSTRACT: For a panel of cancer related proteins, the aim was to shed light on which molecular level the expression of each protein was mainly regulated in breast tumors, and to investigate whether differences in regulation were reflected in different molecular subtypes. DNA, mRNA and protein lysates from 251 breast tumor specimens were analyzed using appropriate microarray technologies. Data from all three levels were available for 52 proteins selected for their known involvement in cancer, primarily through the PI3K/Akt pathway. For every protein, in cis Spearman rank correlations between the three molecular levels were calculated across all samples and within each intrinsic gene expression subtype, enabling 63 comparisons altogether due to multiple gene probes matching to single proteins. Subtype-specific relationships between the three molecular levels were studied by calculating the variance of subtype-specific correlation and differences between overall and average subtype-specific correlation. The findings were validated in an external dataset comprising 703 breast tumor specimens. The proteins were sorted into four groups based on the calculated rank correlation values between the three molecular levels. Group A consisted of eight proteins with significant correlation between DNA copy number levels and mRNA expression, and between mRNA expression and protein expression (Bonferroni adjusted p < 0.05). Group B consisted of 14 proteins with significant correlation between mRNA expression and protein expression. Group C consisted of 15 proteins with significant correlation between copy number levels and mRNA expression. For the remaining 25 proteins (group D), no significant correlations was observed. Stratification of tumors according to intrinsic subtype enabled identification of positive correlations between copy number levels, mRNA and protein expression that were undetectable when considering the entire sample set. Protein pairings that either demonstrated high variance in correlation values between subtypes, or between subtypes and the total dataset were studied in particular. The protein expression of cleaved caspase 7 was most highly expressed, and correlated highest to CASP7 gene expression within the basal-like subtype, accompanied by the lowest amounts of hsa-miR-29c. Luminal A-like subtype demonstrated highest amounts of hsa-miR-29c (a miRNA with a putative target sequence in CASP7 mRNA), low expression of cleaved caspase 7 and low correlation to CASP7 gene expression. Such pattern might be an indication of hsa-miR-29c miRNA functioning as a repressor of translation of CASP7 within the luminal-A subtype. Across the entire cohort no correlation was found between CCNB1 copy number and gene expression. However, within most gene intrinsic subtypes, mRNA and protein expression of cyclin B1 was found positively correlated to copy number data, suggesting that copy number can affect the overall expression of this protein. Aberrations of cyclin B1 copy number also identified patients with reduced overall survival within each subtype. Based on correlation between the three molecular levels, genes and their products could be sorted into four groups for which the expression was likely to be regulated at different molecular levels. Further stratification suggested subtype-specific regulation that was not evident across the entire sample set.
    Molecular oncology 03/2013; · 6.70 Impact Factor
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    ABSTRACT: Mutations in BRCA1/2 increase the risk of developing breast and ovarian cancer. Germline BRCA1/2 mutations occur in 8.6-13.7% of unselected epithelial ovarian cancers, somatic mutations are also frequent. BRCA1/2 mutated or dysfunctional cells may be sensitive to PARP inhibition by synthetic lethality. The aim of this study is to comprehensively characterise the BRCA1/2 status of a large panel of ovarian cancer cell lines available to the research community to assist in biomarker studies of novel drugs and in particular of PARP inhibitors. The BRCA1/2 genes were sequenced in 41 ovarian cell lines, mRNA expression of BRCA1/2 and gene methylation status of BRCA1 was also examined. The cytotoxicity of PARP inhibitors olaparib and veliparib was examined in 20 cell lines. The cell line SNU-251 has a deleterious BRCA1 mutation at 5564G > A, and is the only deleterious BRCA1/2 mutant in the panel. Two cell lines (UPN-251 and PEO1) had deleterious mutations as well as additional reversion mutations that restored the protein functionality. Heterozygous mutations in BRCA1/2 were relatively common, found in 14.6% of cell lines. BRCA1 was methylated in two cell lines (OVCAR8, A1847) and there was a corresponding decrease in gene expression. The BRCA1 methylated cell lines were more sensitive to PARP inhibition than wild-type cells. The SNU-251 deleterious mutant was more sensitive to PARP inhibition, but only in a long-term exposure to correct for its slow growth rate. Cell lines derived from metastatic disease are significantly more resistant to veliparib (2.0 fold p = 0.03) compared to those derived from primary tumours. Resistance to olaparib and veliparib was correlated Pearsons-R 0.5393, p = 0.0311. The incidence of BRCA1/2 deleterious mutations 1/41 cell lines derived from 33 different patients (3.0%) is much lower than the population incidence. The reversion mutations and high frequency of heterozygous mutations suggest that there is a selective pressure against BRCA1/2 in cell culture similar to the selective pressure seen in the clinic after treatment with chemotherapy. PARP inhibitors may be useful in patients with BRCA1 deleterious mutations or gene methylation.
    Molecular oncology 01/2013; · 6.70 Impact Factor
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    ABSTRACT: Breast cancer remains a significant scientific, clinical and societal challenge. This gap analysis has reviewed and critically assessed enduring issues and new challenges emerging from recent research, and proposes strategies for translating solutions into practice. More than 100 internationally recognised specialist breast cancer scientists, clinicians and healthcare professionals collaborated to address nine thematic areas: genetics, epigenetics and epidemiology; molecular pathology and cell biology; hormonal influences and endocrine therapy; imaging, detection and screening; current/novel therapies and biomarkers; drug resistance; metastasis, angiogenesis, circulating tumour cells, cancer 'stem' cells; risk and prevention; living with and managing breast cancer and its treatment. The groups developed summary papers through an iterative process which, following further appraisal from experts and patients, were melded into this summary account. The 10 major gaps identified were: (1) understanding the functions and contextual interactions of genetic and epigenetic changes in normal breast development and during malignant transformation; (2) how to implement sustainable lifestyle changes (diet, exercise and weight) and chemopreventive strategies; (3) the need for tailored screening approaches including clinically actionable tests; (4) enhancing knowledge of molecular drivers behind breast cancer subtypes, progression and metastasis; (5) understanding the molecular mechanisms of tumour heterogeneity, dormancy, de novo or acquired resistance and how to target key nodes in these dynamic processes; (6) developing validated markers for chemosensitivity and radiosensitivity; (7) understanding the optimal duration, sequencing and rational combinations of treatment for improved personalised therapy; (8) validating multimodality imaging biomarkers for minimally invasive diagnosis and monitoring of responses in primary and metastatic disease; (9) developing interventions and support to improve the survivorship experience; (10) a continuing need for clinical material for translational research derived from normal breast, blood, primary, relapsed, metastatic and drug-resistant cancers with expert bioinformatics support to maximise its utility. The proposed infrastructural enablers include enhanced resources to support clinically relevant in vitro and in vivo tumour models; improved access to appropriate, fully annotated clinical samples; extended biomarker discovery, validation and standardisation; and facilitated cross-discipline working. With resources to conduct further high-quality targeted research focusing on the gaps identified, increased knowledge translating into improved clinical care should be achievable within five years.
    Breast cancer research: BCR 01/2013; 15(5):R92. · 5.87 Impact Factor
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    ABSTRACT: The 2012 IMPAKT task force investigated the medical usefulness of current methods for the classification of breast cancer into the 'intrinsic' molecular subtypes (luminal A, luminal B, basal-like and HER2). A panel of breast cancer and/or gene expression profiling experts evaluated the analytical validity, clinical validity and clinical utility of two approaches for molecular subtyping of breast cancer: the prediction analysis of microarray (PAM)50 assay and an immuno-histochemical (IHC) surrogate panel including oestrogen receptor (ER), HER2 and Ki67. The panel found the currently available evidence on the analytical validity and clinical utility of Ki67 based on a 14% cut-off and PAM50 to be inadequate. The majority of the working group members found the available evidence on the analytical validity, clinical validity and clinical utility of ER/HER2 to be convincing. The panel concluded that breast cancer classification into molecular subtypes based on the IHC assessment of ER, HER2 and Ki67 with a 14% cut-off and on the PAM50 test does not provide sufficiently robust information to modify systemic treatment decisions, and recommended the use IHC for ER and HER2 for the identification of clinically relevant subtypes of breast cancers. Methods for breast cancer classification into molecular subtypes should, however, be incorporated into clinical trial design.
    Annals of Oncology 12/2012; 23(12):2997-3006. · 7.38 Impact Factor
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    ABSTRACT: INTRODUCTION: Translation initiation is activated in cancer through increase in eukaryotic initiation factor 4E (eIF4E), eIF4G, phosphorylated eIF4E-binding protein (p4E-BP1) and ribosomal protein S6 (pS6), and decreased programmed cell death protein 4 (pdcd4), a translational inhibitor. Further, translation elongation is deregulated though alterations in eukaryotic elongation factor 2 (eEF2) and eEF2 kinase (eEF2K). We sought to determine the association of these translational aberrations with clinical-pathologic factors and survival outcomes in hormone receptor-positive breast cancer. METHODS: Primary tumors were collected from 190 patients with Stage I-III hormone receptor-positive breast cancer. Expression of eIF4E, eIF4G, 4E-BP1, p4E-BP1 T37/46, p4E-BP1 S65, p4E-BP1 T70, S6, pS6 S235/236, pS6 S240/244, pdcd4, eEF2 and eEF2K was assessed by reverse phase protein arrays. Univariable and multivariable analyses for recurrence-free survival (RFS) and overall survival (OS) were performed. RESULTS: High eEF2, S6, pS6 S240/244, p4E-BP1 T70, and low pdcd4 were significantly associated with node-positivity. Median follow-up for living patients was 96 months. High p4E-BP1 T36/47, p4E-BP1 S65, p4E-BP1 T70 and 4E-BP1 were associated with worse RFS. High p4E-BP1 T70 and pS6 S235/236, and low pdcd4, were associated with worse OS. In multivariable analysis, in addition to positive nodes, p4E-BP1 S65 remained a significant predictor of RFS (HR=1.62, 95%CI=1.13-2.31; P=0.008). In addition to age, pS6 S235/236 (HR=1.73, 95%CI=1.03-2.90, P=0.039), eEF2K (HR=2.19, 95%CI=1.35-3.56, P=0.002) and pdcd4 (HR=0.42, 95%CI=0.25-0.70, P=0.001) were associated with OS. CONCLUSIONS: Increased pS6, p4E-BP1, eEF2K and decreased pdcd4 are associated with poor prognosis in hormone receptor-positive breast cancer, suggesting their role as prognostic markers and therapeutic targets.
    Breast cancer research: BCR 10/2012; 14(5):R138. · 5.87 Impact Factor
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    ABSTRACT: Introduction: Germline mutations in DNA repair genes BRCA1/2 increase the risk of developing breast and ovarian cancer. Germline BRCA1/2 mutations occur in 8.6-13.7% of unselected epithelial ovarian cancers, somatic mutations are also frequent. BRCA1/2 mutated or dysfunctional cells may be sensitive to cisplatin by reduced DNA repair capacity as well PARP inhibition by synthetic lethality, the inhibition of two major DNA repair pathways. Methods: The cytotoxicity of cisplatin, olaparib and veliparib was examined in a panel of 17 ovarian cancer cell lines by acid phosphatase assay. 15 cell lines were BRCA1/2 wild-type, one was BRCA1 methylated (OVCAR-8) and one had a deleterious BRCA1 mutation (SNU-251). ANOVAs were performed to determine which cell lines were relatively resistant or sensitive to each chemotherapy agent. Affymetrix whole genome arrays were performed on RNA from the 17 cell lines and bioinformatics performed to study drug resistance relationships between platinum and parp inhibitors. Results: Cross resistance was observed between parp inhibitors olaparib and veliparib, correlation R = 0.5393, p = 0.03. Two cell lines were relatively sensitive to both olaparib and veliparib (A2780 and ES-2). However, the most highly resistant cell lines were different for olaparib (OVCAR432, HEY, IGROV-1) compared to veliparib (SKOV3, UPN-251, OVCAR420). This suggests a common mechanism of sensitivity but a divergent mechanism of resistance. Cross resistance was not observed in the overall cell line panel between cisplatin and the parp inhibitors (cisplatin vs olaparib R = 0.0577, p = 0.831 and cisplatin vs veliparib R = -0.326 p = 0.201). However, two cell lines were relatively resistant to both cisplatin and olaparib (OVCAR432 and HEY) suggesting that cross resistance can occur between these agents. OVCAR433 was relatively resistant to cisplatin, but relatively sensitive to veliparib. This suggests that veliparib could be used to treat a subset of cisplatin resistant ovarian cancers. Analysis of Affymetrix whole genome arrays will be presented identifying biomarkers of sensitivity and resistance to each chemotherapy agent as well as markers of cross resistance between the agents. Conclusions: This study will identify biomarkers of sensitivity and resistance to platinums and parp inhibitors in ovarian cancer to complement BRCA1 mutation and methylation analyses. These biomarkers may be of use in the clinical management of ovarian cancer.
    11th International Symposium on Platinum Coordination Compounds in Cancer Chemotherapy, Verona, Italy; 10/2012
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    ABSTRACT: BACKGROUND: Defects in BRCA1, BRCA2, and other members of the homologous recombination pathway have potential therapeutic relevance when used to support agents that introduce or exploit double-stranded DNA breaks. This study examines the association between homologous recombination defects and genomic patterns of loss of heterozygosity (LOH). METHODS: Ovarian tumours from two independent data sets were characterised for defects in BRCA1, BRCA2, and RAD51C, and LOH profiles were generated. Publically available data were downloaded for a third independent data set. The same analyses were performed on 57 cancer cell lines. RESULTS: Loss of heterozygosity regions of intermediate size were observed more frequently in tumours with defective BRCA1 or BRCA2 (P=10�-11). The homologous recombination deficiency (HRD) score was defined as the number of these regions observed in a tumour sample. The association between HRD score and BRCA deficiency was validated in two independent ovarian cancer data sets (P=10-�5 and 10�-29), and identified breast and pancreatic cell lines with BRCA defects. CONCLUSION: The HRD score appears capable of detecting homologous recombination defects regardless of aetiology or mechanism. This score could facilitate the use of PARP inhibitors and platinum in breast, ovarian, and other cancers.
    British Journal of Cancer 10/2012; · 5.08 Impact Factor
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    ABSTRACT: Endometrial cancer is the most common gynecological malignancy, with more than 280,000 cases occurring annually worldwide. Although previous studies have identified important common somatic mutations in endometrial cancer, they have primarily focused on a small set of known cancer genes and have thus provided a limited view of the molecular basis underlying this disease. Here we have developed an integrated systems-biology approach to identifying novel cancer genes contributing to endometrial tumorigenesis. We first performed whole-exome sequencing on 13 endometrial cancers and matched normal samples, systematically identifying somatic alterations with high precision and sensitivity. We then combined bioinformatics prioritization with high-throughput screening (including both shRNA-mediated knockdown and expression of wild-type and mutant constructs) in a highly sensitive cell viability assay. Our results revealed 12 potential driver cancer genes including 10 tumor-suppressor candidates (ARID1A, INHBA, KMO, TTLL5, GRM8, IGFBP3, AKTIP, PHKA2, TRPS1, and WNT11) and two oncogene candidates (ERBB3 and RPS6KC1). The results in the "sensor" cell line were recapitulated by siRNA-mediated knockdown in endometrial cancer cell lines. Focusing on ARID1A, we integrated mutation profiles with functional proteomics in 222 endometrial cancer samples, demonstrating that ARID1A mutations frequently co-occur with mutations in the phosphatidylinositol 3-kinase (PI3K) pathway and are associated with PI3K pathway activation. siRNA knockdown in endometrial cancer cell lines increased AKT phosphorylation supporting ARID1A as a novel regulator of PI3K pathway activity. Our study presents the first unbiased view of somatic coding mutations in endometrial cancer and provides functional evidence for diverse driver genes and mutations in this disease.
    Genome Research 10/2012; · 14.40 Impact Factor

Publication Stats

6k Citations
895.02 Total Impact Points

Institutions

  • 2012–2014
    • Royal College of Surgeons in Ireland
      • Centre for Systems Medicine
      Dublin, Leinster, Ireland
    • Our Lady Of Lourdes Hospital, Drogheda
      Damhliag, Leinster, Ireland
    • Memorial Sloan-Kettering Cancer Center
      New York City, New York, United States
    • Our Lady of Lourdes Hospital
      Camden, New Jersey, United States
  • 2013
    • Trinity College Dublin
      Dublin, Leinster, Ireland
  • 2010–2012
    • Beaumont Hospital
      Dublin, Leinster, Ireland
    • Imperial College London
      • Department of Surgery and Cancer
      Londinium, England, United Kingdom
  • 2007–2011
    • University of Miami Miller School of Medicine
      • • Sylvester Comprehensive Cancer Center
      • • Braman Family Breast Cancer Institute
      Miami, FL, United States
  • 2004–2010
    • University of Texas MD Anderson Cancer Center
      • • Department of Systems Biology
      • • Department of Molecular Therapeutics
      • • Department of Medical Oncology
      • • Department of Leukemia
      Houston, TX, United States
  • 2001–2004
    • St. James's Hospital
      Dublin, Leinster, Ireland
  • 2003
    • Cork University Hospital
      Corcaigh, Munster, Ireland