Biochemistry and Pharmacology - Research Publications

Permanent URI for this collection

Search Results

Now showing 1 - 10 of 14
  • Item
    No Preview Available
    A Role for Common Genomic Variants in the Assessment of Familial Breast Cancer
    Sawyer, S ; Mitchell, G ; McKinley, J ; Chenevix-Trench, G ; Beesley, J ; Chen, XQ ; Bowtell, D ; Trainer, AH ; Harris, M ; Lindeman, GJ ; James, PA (AMER SOC CLINICAL ONCOLOGY, 2012-12-10)
    PURPOSE: Genome-wide association studies have identified common genomic variants associated with increased susceptibility to breast cancer. In the general population, the risk associated with these known variants seems insufficient to inform clinical management. Their contribution to the development of familial breast cancer is less clear. PATIENTS AND METHODS: We studied 1,143 women with breast cancer who had completed BRCA1 and BRCA2 mutation screening as a result of a high risk for hereditary breast cancer. Genotyping of 22 breast cancer-associated genomic variants was performed. A polygenic risk score (PRS), calculated as the sum of the log odds ratios for each allele, was compared with the same metric in 892 controls from the Australian Ovarian Cancer Study. The clinical features associated with the high and low ends of the polygenic risk distribution were compared. RESULTS: Women affected by familial breast cancer had a highly significant excess of risk alleles compared with controls (P = 1.0 × 10(-16)). Polygenic risk (measured by the PRS) was greater in women who tested negative for a BRCA1 or BRCA2 mutation compared with mutation carriers (P = 2.3 × 10(-6)). Non-BRCA1/2 women in the top quartile of the polygenic risk distribution were more likely to have had early-onset breast cancer (< 30 years of age, odds ratio [OR]= 3.37, P = .03) and had a higher rate of second breast cancer (OR 1.96, P = .02) compared with women with low polygenic risk. CONCLUSION: Genetic testing for common risk variants in women undergoing assessment for familial breast cancer may identify a distinct group of high-risk women in whom the role of risk-reducing interventions should be explored.
  • Item
    No Preview Available
    A Dynamic Inflammatory Cytokine Network in the Human Ovarian Cancer Microenvironment
    Kulbe, H ; Chakravarty, P ; Leinster, DA ; Charles, KA ; Kwong, J ; Thompson, RG ; Coward, JI ; Schioppa, T ; Robinson, SC ; Gallagher, WM ; Galletta, L ; Salako, MA ; Smyth, JF ; Hagemann, T ; Brennan, DJ ; Bowtell, DD ; Balkwill, FR (AMER ASSOC CANCER RESEARCH, 2012-01-01)
    Constitutive production of inflammatory cytokines is a characteristic of many human malignant cell lines; however, the in vitro and in vivo interdependence of these cytokines, and their significance to the human cancer microenvironment, are both poorly understood. Here, we describe for the first time how three key cytokine/chemokine mediators of cancer-related inflammation, TNF, CXCL12, and interleukin 6, are involved in an autocrine cytokine network, the "TNF network," in human ovarian cancer. We show that this network has paracrine actions on angiogenesis, infiltration of myeloid cells, and NOTCH signaling in both murine xenografts and human ovarian tumor biopsies. Neutralizing antibodies or siRNA to individual members of this TNF network reduced angiogenesis, myeloid cell infiltration, and experimental peritoneal ovarian tumor growth. The dependency of network genes on TNF was shown by their downregulation in tumor cells from patients with advanced ovarian cancer following the infusion of anti-TNF antibodies. Together, the findings define a network of inflammatory cytokine interactions that are crucial to tumor growth and validate this network as a key therapeutic target in ovarian cancer.
  • Item
    No Preview Available
    Cyclin E1 Deregulation Occurs Early in Secretory Cell Transformation to Promote Formation of Fallopian Tube-Derived High-Grade Serous Ovarian Cancers
    Karst, AM ; Jones, PM ; Vena, N ; Ligon, AH ; Liu, JF ; Hirsch, MS ; Etemadmoghadam, D ; Bowtell, DDL ; Drapkin, R (AMER ASSOC CANCER RESEARCH, 2014-02-15)
    The fallopian tube is now generally considered the dominant site of origin for high-grade serous ovarian carcinoma. However, the molecular pathogenesis of fallopian tube-derived serous carcinomas is poorly understood and there are few experimental studies examining the transformation of human fallopian tube cells. Prompted by recent genomic analyses that identified cyclin E1 (CCNE1) gene amplification as a candidate oncogenic driver in high-grade serous ovarian carcinoma, we evaluated the functional role of cyclin E1 in serous carcinogenesis. Cyclin E1 was expressed in early- and late-stage human tumor samples. In primary human fallopian tube secretory epithelial cells, cyclin E1 expression imparted malignant characteristics to untransformed cells if p53 was compromised, promoting an accumulation of DNA damage and altered transcription of DNA damage response genes related to DNA replication stress. Together, our findings corroborate the hypothesis that cyclin E1 dysregulation acts to drive malignant transformation in fallopian tube secretory cells that are the site of origin of high-grade serous ovarian carcinomas.
  • Item
    No Preview Available
    Enhanced GAB2 Expression Is Associated with Improved Survival in High-Grade Serous Ovarian Cancer and Sensitivity to PI3K Inhibition
    Davis, SJ ; Sheppard, KE ; Anglesio, MS ; George, J ; Traficante, N ; Fereday, S ; Intermaggio, MP ; Menon, U ; Gentry-Maharaj, A ; Lubinski, J ; Gronwald, J ; Pearce, CL ; Pike, MC ; Wu, A ; Kommoss, S ; Pfisterer, J ; du Bois, A ; Hilpert, F ; Ramus, SJ ; Bowtell, DDL ; Huntsman, DG ; Pearson, RB ; Simpson, KJ ; Campbell, IG ; Gorringe, KL (AMER ASSOC CANCER RESEARCH, 2015-06-01)
    Identification of genomic alterations defining ovarian carcinoma subtypes may aid the stratification of patients to receive targeted therapies. We characterized high-grade serous ovarian carcinoma (HGSC) for the association of amplified and overexpressed genes with clinical outcome using gene expression data from 499 HGSC patients in the Ovarian Tumor Tissue Analysis cohort for 11 copy number amplified genes: ATP13A4, BMP8B, CACNA1C, CCNE1, DYRK1B, GAB2, PAK4, RAD21, TPX2, ZFP36, and URI. The Australian Ovarian Cancer Study and The Cancer Genome Atlas datasets were also used to assess the correlation between gene expression, patient survival, and tumor classification. In a multivariate analysis, high GAB2 expression was associated with improved overall and progression-free survival (P = 0.03 and 0.02), whereas high BMP8B and ATP13A4 were associated with improved progression-free survival (P = 0.004 and P = 0.02). GAB2 overexpression and copy number gain were enriched in the AOCS C4 subgroup. High GAB2 expression correlated with enhanced sensitivity in vitro to the dual PI3K/mTOR inhibitor PF-04691502 and could be used as a genomic marker for identifying patients who will respond to treatments inhibiting PI3K signaling.
  • Item
    Thumbnail Image
    Mutational landscape of mucinous ovarian carcinoma and its neoplastic precursors
    Ryland, GL ; Hunter, SM ; Doyle, MA ; Caramia, F ; Li, J ; Rowley, SM ; Christie, M ; Allan, PE ; Stephens, AN ; Bowtell, DDL ; Campbell, IG ; Gorringe, KL (BMC, 2015-08-07)
    BACKGROUND: Mucinous ovarian tumors are an unusual group of rare neoplasms with an apparently clear progression from benign to borderline to carcinoma, yet with a controversial cell of origin in the ovarian surface epithelium. They are thought to be molecularly distinct from other ovarian tumors but there have been no exome-level sequencing studies performed to date. METHODS: To understand the genetic etiology of mucinous ovarian tumors and assess the presence of novel therapeutic targets or pathways, we undertook exome sequencing of 24 tumors encompassing benign (5), borderline (8) and carcinoma (11) histologies and also assessed a validation cohort of 58 tumors for specific gene regions including exons 4-9 of TP53. RESULTS: The predominant mutational signature was of C>T transitions in a NpCpG context, indicative of deamination of methyl-cytosines. As well as mutations in known drivers (KRAS, BRAF and CDKN2A), we identified a high percentage of carcinomas with TP53 mutations (52 %), and recurrent mutations in RNF43, ELF3, GNAS, ERBB3 and KLF5. CONCLUSIONS: The diversity of mutational targets suggests multiple routes to tumorigenesis in this heterogeneous group of tumors that is generally distinct from other ovarian subtypes.
  • Item
    Thumbnail Image
    Molecular profiling of low grade serous ovarian tumours identifies novel candidate driver genes
    Hunter, SM ; Anglesio, MS ; Ryland, GL ; Sharma, R ; Chiew, YE ; Rowley, SM ; Doyle, MA ; Li, J ; Gilks, CB ; Moss, P ; Allan, PE ; Stephens, AN ; Huntsman, DG ; deFazio, A ; Bowtell, DD ; Australian Ovarian Cancer Study, G ; Gorringe, KL ; Campbell, IG (Impact Journals, 2015-11-10)
    Low grade serous ovarian tumours are a rare and under-characterised histological subtype of epithelial ovarian tumours, with little known of the molecular drivers and facilitators of tumorigenesis beyond classic oncogenic RAS/RAF mutations. With a move towards targeted therapies due to the chemoresistant nature of this subtype, it is pertinent to more fully characterise the genetic events driving this tumour type, some of which may influence response to therapy and/or development of drug resistance. We performed genome-wide high-resolution genomic copy number analysis (Affymetrix SNP6.0) and mutation hotspot screening (KRAS, BRAF, NRAS, HRAS, ERBB2 and TP53) to compare a large cohort of ovarian serous borderline tumours (SBTs, n = 57) with low grade serous carcinomas (LGSCs, n = 19). Whole exome sequencing was performed for 13 SBTs, nine LGSCs and one mixed low/high grade carcinoma. Copy number aberrations were detected in 61% (35/57) of SBTs, compared to 100% (19/19) of LGSCs. Oncogenic RAS/RAF/ERBB2 mutations were detected in 82.5% (47/57) of SBTs compared to 63% (12/19) of LGSCs, with NRAS mutations detected only in LGSC. Some copy number aberrations appeared to be enriched in LGSC, most significantly loss of 9p and homozygous deletions of the CDKN2A/2B locus. Exome sequencing identified BRAF, KRAS, NRAS, USP9X and EIF1AX as the most frequently mutated genes. We have identified markers of progression from borderline to LGSC and novel drivers of LGSC. USP9X and EIF1AX have both been linked to regulation of mTOR, suggesting that mTOR inhibitors may be a key companion treatment for targeted therapy trials of MEK and RAF inhibitors.
  • Item
    No Preview Available
    Germline Mutation in BRCA1 or BRCA2 and Ten-Year Survival for Women Diagnosed with Epithelial Ovarian Cancer
    Candido-dos-Reis, FJ ; Song, H ; Goode, EL ; Cunningham, JM ; Fridley, BL ; Larson, MC ; Alsop, K ; Dicks, E ; Harrington, P ; Ramus, SJ ; de Fazio, A ; Mitchell, G ; Fereday, S ; Bolton, KL ; Gourley, C ; Michie, C ; Karlan, B ; Lester, J ; Walsh, C ; Cass, I ; Olsson, H ; Gore, M ; Benitez, JJ ; Garcia, MJ ; Andrulis, I ; Mulligan, AM ; Glendon, G ; Blanco, I ; Lazaro, C ; Whittemore, AS ; McGuire, V ; Sieh, W ; Montagna, M ; Alducci, E ; Sadetzki, S ; Chetrit, A ; Kwong, A ; Kjaer, SK ; Jensen, A ; Hogdall, E ; Neuhausen, S ; Nussbaum, R ; Daly, M ; Greene, MH ; Mai, PL ; Loud, JT ; Moysich, K ; Toland, AE ; Lambrechts, D ; Ellis, S ; Frost, D ; Brenton, JD ; Tischkowitz, M ; Easton, DF ; Antoniou, A ; Chenevix-Trench, G ; Gayther, SA ; Bowtell, D ; Pharoah, PDP (AMER ASSOC CANCER RESEARCH, 2015-02-01)
    PURPOSE: To analyze the effect of germline mutations in BRCA1 and BRCA2 on mortality in patients with ovarian cancer up to 10 years after diagnosis. EXPERIMENTAL DESIGN: We used unpublished survival time data for 2,242 patients from two case-control studies and extended survival time data for 4,314 patients from previously reported studies. All participants had been screened for deleterious germline mutations in BRCA1 and BRCA2. Survival time was analyzed for the combined data using Cox proportional hazard models with BRCA1 and BRCA2 as time-varying covariates. Competing risks were analyzed using Fine and Gray model. RESULTS: The combined 10-year overall survival rate was 30% [95% confidence interval (CI), 28%-31%] for non-carriers, 25% (95% CI, 22%-28%) for BRCA1 carriers, and 35% (95% CI, 30%-41%) for BRCA2 carriers. The HR for BRCA1 was 0.53 at time zero and increased over time becoming greater than one at 4.8 years. For BRCA2, the HR was 0.42 at time zero and increased over time (predicted to become greater than 1 at 10.5 years). The results were similar when restricted to 3,202 patients with high-grade serous tumors and to ovarian cancer-specific mortality. CONCLUSIONS: BRCA1/2 mutations are associated with better short-term survival, but this advantage decreases over time and in BRCA1 carriers is eventually reversed. This may have important implications for therapy of both primary and relapsed disease and for analysis of long-term survival in clinical trials of new agents, particularly those that are effective in BRCA1/2 mutation carriers.
  • Item
    No Preview Available
    Pericytes Promote Malignant Ovarian Cancer Progression in Mice and Predict Poor Prognosis in Serous Ovarian Cancer Patients
    Sinha, D ; Chong, L ; George, J ; Schlueter, H ; Moenchgesang, S ; Mills, S ; Li, J ; Parish, C ; Bowtell, D ; Kaur, P (AMER ASSOC CANCER RESEARCH, 2016-04-01)
    PURPOSE: The aim of this study was to investigate the role of pericytes in regulating malignant ovarian cancer progression. EXPERIMENTAL DESIGN: The pericyte mRNA signature was used to interrogate ovarian cancer patient datasets to determine its prognostic value for recurrence and mortality. Xenograft models of ovarian cancer were used to determine if co-injection with pericytes affected tumor growth rate and metastasis, whereas co-culture models were utilized to investigate the direct effect of pericytes on ovarian cancer cells. Pericyte markers were used to stain patient tissue samples to ascertain their use in prognosis. RESULTS: Interrogation of two serous ovarian cancer patient datasets [the Australian Ovarian Cancer Study, n= 215; and the NCI TCGA (The Cancer Genome Atlas), n= 408] showed that a high pericyte score is highly predictive for poor patient prognosis. Co-injection of ovarian cancer (OVCAR-5 & -8) cells with pericytes in a xenograft model resulted in accelerated ovarian tumor growth, and aggressive metastases, without altering tumor vasculature. Pericyte co-culture in vitro promoted ovarian cancer cell proliferation and invasion. High αSMA protein levels in patient tissue microarrays were correlated with more aggressive disease and earlier recurrence. CONCLUSIONS: High pericyte score provides the best means to date of identifying patients with ovarian cancer at high risk of rapid relapse and mortality (mean progression-free survival time < 9 months). The stroma contains rare yet extremely potent locally resident mesenchymal stem cells-a subset of "cancer-associated fibroblasts" that promote aggressive tumor growth and metastatic dissemination, underlying the prognostic capacity of a high pericyte score to strongly predict earlier relapse and mortality.
  • Item
    Thumbnail Image
    Precision Medicine: Dawn of Supercomputing in ‘omics Research
    Reumann, M ; Holt, KE ; Inouye, M ; Stinear, T ; Goudey, B ; Abraham, G ; WANG, Q ; Shi, F ; Kowalczyk, A ; Pearce, A ; Isaac, A ; Pope, BJ ; Butzkueven, H ; Wagner, J ; Moore, S ; Downton, M ; Church, PC ; Turner, SJ ; Field, J ; Southey, M ; Bowtell, D ; Schmidt, D ; Makalic, E ; Zobel, J ; Hopper, J ; Petrovski, S ; O'Brien, T (eResearch Australasia, 2011)
  • Item
    Thumbnail Image
    Pre-Invasive Ovarian Mucinous Tumors Are Characterized by CDKN2A and RAS Pathway Aberrations
    Hunter, SM ; Gorringe, KL ; Christie, M ; Rowley, SM ; Bowtell, DD ; Campbell, IG (AMER ASSOC CANCER RESEARCH, 2012-10-01)
    INTRODUCTION: Mucinous tumors are the second most common form of epithelial ovarian tumor, yet the cell of origin for this histologic subtype remains undetermined. Although these tumors are thought to arise through a stepwise progression from benign cystadenoma to borderline tumor to invasive carcinoma, few studies have attempted to comprehensively characterize the genetic changes specific to this subtype or its precursors. METHODS: To explore the spectrum of genomic alterations common to mucinous tumors we carried out high-resolution genome-wide copy number analysis, mutation screening by Sanger sequencing and immunohistochemistry on a series of primary ovarian mucinous cystadenomas (n = 20) and borderline tumors (n = 22). RESULTS: Integration of copy number data, targeted mutation screening of RAS/RAF pathway members and immunohistochemistry reveals that p16 loss and RAS/RAF pathway alterations are highly recurrent events that occur early during mucinous tumor development. The frequency of concurrence of these events was observed in 40% of benign cystadenomas and 68% of borderline tumors. CONCLUSIONS: This study is the largest and highest resolution analysis of mucinous benign and borderline tumors carried out to date and provides strong support for these lesions being precursors of primary ovarian mucinous adenocarcinoma. The high level of uniformity in the molecular events underlying the pathogenesis of mucinous ovarian tumors provides an opportunity for treatments targeting specific mutations and pathways.