A comprehensive clinically informed map of dependencies in cancer cells and framework for target prioritization

Genetic screens in cancer cell lines inform gene function and drug discovery. More comprehensive screen datasets with multi-omics data are needed to enhance opportunities to functionally map genetic vulnerabilities. Here, we construct a second-generation map of cancer dependencies by annotating 930 cancer cell lines with multi-omic data and analyze relationships between molecular markers and cancer dependencies derived from CRISPR-Cas9 screens. We identify dependency-associated gene expression markers beyond driver genes, and observe many gene addiction relationships driven by gain of function rather than synthetic lethal effects. By combining clinically informed dependency-marker associations with protein-protein interaction networks, we identify 370 anti-cancer priority targets for 27 cancer types, many of which have network-based evidence of a functional link with a marker in a cancer type. Mapping these targets to sequenced tumor cohorts identifies tractable targets in different cancer types. This target prioritization map enhances understanding of gene dependencies and identifies candidate anti-cancer targets for drug development.

MicroRNAs as biomarkers for prostate cancer prognosis: a systematic review and a systematic reanalysis of public data

Background

Reliable prognostic biomarkers to distinguish indolent from aggressive prostate cancer (PCa) are lacking. Many studies investigated microRNAs (miRs) as PCa prognostic biomarkers, often reporting inconsistent findings. We present a systematic review of these; also systematic reanalysis of public miR-profile datasets to identify tissue-derived miRs prognostic of biochemical recurrence (BCR) in patients undergoing radical prostatectomy.

Methods

Independent PubMed searches were performed for relevant articles from January 2007 to December 2019. For the review, 128 studies were included. Pooled-hazard-ratios (HRs) for miRs in multiple studies were calculated using a random-effects model (REM). For the reanalysis, five studies were included and Cox proportional-hazard models, testing miR association with BCR, performed for miRs profiled in all.

Results

Systematic review identified 120 miRs as prognostic. Five (let-7b-5p, miR-145-5p, miR152-3p, miR-195-5p, miR-224-5p) were consistently associated with progression in multiple cohorts/studies. In the reanalysis, ten (let-7a-5p, miR-148a-3p, miR-203a-3p, miR-26b-5p, miR30a-3p, miR-30c-5p, miR-30e-3p, miR-374a-5p, miR-425-3p, miR-582-5p) were significantly prognostic of BCR. Of these, miR-148a-3p (HR = 0.80/95% CI = 0.68-0.94) and miR-582-5p (HR = 0.73/95% CI = 0.61-0.87) were also reported in prior publication(s) in the review.

Conclusions

Fifteen miRs were consistently associated with disease progression in multiple publications or datasets. Further research into their biological roles is warranted to support investigations into their performance as prognostic PCa biomarkers.

Abstract A10: Phenotypic and genomic characterization of intratumoral heterogeneity in high-grade serous ovarian cancer

High-grade serous ovarian cancer (HGSOC) is the most common subtype of ovarian cancer, accounting for more than 70% of all epithelial ovarian cancers. It is characterized by high degrees of genomic instability and heterogeneity, with the majority of patients eventually acquiring resistance to platinum chemotherapy. The diversity in platinum-resistance mechanisms and limited effective predictive biomarkers mean delivering the best treatment options for patient tumor remains challenging. The purpose of this study is to understand the extent of intratumoral heterogeneity (ITH) in advanced-stage HGSOC and how this changes over time at relapse, to describe the molecular mechanisms behind peritoneal dissemination, and to delineate the link between ITH at the molecular and phenotypic levels. Patients undergoing radical upfront debulking for advanced HGS ovarian cancer underwent tumor mapping of their tumor dissemination patterns (n=50). Biopsies were collected from disseminated tumors (range 4-15, median=9), snap frozen, and placed in short-term cultures. Tumor cultures were treated with cisplatin, apoptosis/viability assayed and IC50 for cisplatin determined. DNA was extracted from frozen tumors (5 tumors per patient plus germline) and Illumina Human OmniExpress genotyping performed. Allele-specific copy number (CN) was quantified using ASCAT. Genomic heterogeneity was quantified as the estimated number of CN aberration events distinct between each pair of deposits. Clonal diversity within a patient’s deposits was calculated using the difference between within-patient and between-patient heterogeneity. When relapsed, patients had paired biopsies collected for genomic and phenotypic analysis. Broad heterogeneity was observed in response to platinum treatment in vitro across cases at the phenotypic level (n=50), with higher variances in apoptosis induction observed in patients with platinum-resistant disease. Genomic analysis of copy number data revealed widespread variations in patterns of evolution for different patients’ tumors, including the relationship between primary deposits and relapsed disease. Variations in CCNE1 CN were observed across multiple tumors in the same patients, and overall higher CCNE1 CN associated with poorer patient outcome (p=0.041). Extensive heterogeneity is observed at the phenotypic and genomic levels in HGSOC patients, which correlates with the subsequent development of platinum-resistant disease. CCNE1 copy number variations across multiple intra-abdominal samples within patients indicate that single-site biopsies do not truly represent overall disseminated HGSOC biology and may have implications for overinterpretation of studies relating to outcome and platinum resistance.

Citation Format: Paula Cunnea, Ed Curry, Katherine Nixon, Ratri Wulandari, Kerstin Thol, Chun Hei Kwok, Jennifer Ploski, Iain McNeish, Elizabeth Christie, David Bowtell, Christina Fotopoulou. Phenotypic and genomic characterization of intratumoral heterogeneity in high-grade serous ovarian cancer [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr A10.

A mathematical-descriptor of tumor-mesoscopic-structure from computed-tomography images annotates prognostic- and molecular-phenotypes of epithelial ovarian cancer

The five-year survival rate of epithelial ovarian cancer (EOC) is approximately 35-40% despite maximal treatment efforts, highlighting a need for stratification biomarkers for personalized treatment. Here we extract 657 quantitative mathematical descriptors from the preoperative CT images of 364 EOC patients at their initial presentation. Using machine learning, we derive a non-invasive summary-statistic of the primary ovarian tumor based on 4 descriptors, which we name "Radiomic Prognostic Vector" (RPV). RPV reliably identifies the 5% of patients with median overall survival less than 2 years, significantly improves established prognostic methods, and is validated in two independent, multi-center cohorts. Furthermore, genetic, transcriptomic and proteomic analysis from two independent datasets elucidate that stromal phenotype and DNA damage response pathways are activated in RPV-stratified tumors. RPV and its associated analysis platform could be exploited to guide personalized therapy of EOC and is potentially transferrable to other cancer types.

108 Fecal metabolite monitoring as a tool to assess sexual maturation in polar bears

Polar bears (Ursus maritimus) in managed care generally are paired for breeding starting around the age of 5 or 6 years; however, DNA analyses of the wild population indicate that males as young as 2 or 3 may sire offspring and females as young as 4 can produce cubs. There are no reports describing longitudinal reproductive hormone parameters in juvenile polar bears. The objective of the current study was to determine if seasonal shifts in testosterone and progesterone (P4) metabolites are detectable in feces of polar bears 2-3 years old as part of a greater effort to characterise reproductive metabolites in a large cohort of juveniles throughout sexual maturation. Subjects were 2-year-old male (n=3) and female (n=3) polar bears residing at 5 zoological institutions in the USA. Individuals were monitored for 1 (1.1) or 2 (2.2) years. Fecal samples were collected noninvasively 3-4 times/week and hormone metabolites were extracted as previously described. Testosterone was evaluated as an indicator of gonadal activity in both sexes, whereas P4 was measured in samples collected from females only. Metabolites were quantified in duplicate using established enzyme immunoassay techniques. Student’s and paired t-tests were used to compare mean metabolite concentrations between seasons [breeding (BS; January-June) and nonbreeding (NBS; July-December)] by sex and within individual, respectively. All values are reported as mean concentration (ng metabolite/g dried feces±standard error of the means) and P-values less than 0.05 indicated statistical significance. Mean testosterone concentration of the 2-year-old males was 153.1±112.5. Overall, testosterone concentrations were higher in samples collected from 2-year-old males during BS versus NBS; however, when examined within individual, this held true for only 1 of 3 males. Mean testosterone of the 3-year-old male was 170.2±19.6 and values were significantly higher in BS (282.1±27.2) versus NBS (74.6±7.3). The overall mean testosterone and P4 concentrations of the 2-year-old females were 56.0±21.7 and 57.4±7.5, respectively. Two of the 3 females exhibited significantly higher testosterone concentrations during BS compared to NBS and all 3 exhibited higher P4 in the breeding versus the NBS. The 3-year-old female had significantly higher testosterone in BS (63.7±4.1) versus NBS (40.5±2.4) and showed evidence of regular ovarian cycles during BS. Despite no detectable differences in mean P4 between seasons (56.3±7.9 and 55.1±3.7), this female exhibited a distinct increase in P4 from October to November compared to the rest of NBS (85.7±8 v. 43.5±2.8), suggestive of pseudopregnancy. These results indicate that fecal reproductive hormone metabolite monitoring can be used to detect changes in metabolite excretion patterns associated with sexual maturation in polar bears and that males and females as young as 2 years old may exhibit seasonal variations in reproductive hormones. These data suggest bears in zoological institutions may be achieving sexual maturation earlier than believed previously and should be considered when managing bears in human care.

Clinical value of bioelectrical properties of cancerous tissue in advanced epithelial ovarian cancer patients

Currently, there are no valid pre-operatively established biomarkers or algorithms that can accurately predict surgical and clinical outcome for patients with advanced epithelial ovarian cancer (EOC). In this study, we suggest that profiling of tumour parameters such as bioelectrical-potential and metabolites, detectable by electronic sensors, could facilitate the future development of devices to better monitor disease and predict surgical and treatment outcomes. Biopotential was recorded, using a potentiometric measurement system, in ex vivo paired non-cancerous and cancerous omental tissues from advanced stage EOC (n = 36), and lysates collected for metabolite measurement by microdialysis. Consistently different biopotential values were detected in cancerous tissue versus non-cancerous tissue across all cases (p < 0.001). High tumour biopotential levels correlated with advanced tumour stage (p = 0.048) and tumour load, and negatively correlated with stroma. Within our EOC cohort and specifically the high-grade serous subtype, low biopotential levels associated with poorer progression-free survival (p = 0.0179, p = 0.0143 respectively). Changes in biopotential levels significantly correlated with common apoptosis related pathways. Lactate and glucose levels measured in paired tissues showed significantly higher lactate/glucose ratio in tissues with low biopotential (p < 0.01, n = 12). Our study proposes the feasibility of biopotential and metabolite monitoring as a biomarker modality profiling EOC to predict surgical and clinical outcomes.

Meter-Scale Terahertz-Driven Acceleration of a Relativistic Beam

Terahertz (THz) radiation promises breakthrough advances in compact advanced accelerators due to the gigavolts-per-meter fields achievable, but the challenge of maintaining overlap and synchronism between beams and short laser-generated THz pulses has so far limited interactions to the few-millimeter scale. We implement a novel scheme for simultaneous group and phase velocity matching of nearly single-cycle THz radiation with a relativistic electron beam for meter-scale inverse free-electron laser interaction in a magnetic undulator, resulting in energy modulations of up to 150 keV using modest THz pulse energies (≤1  μJ). Using this scheme, we demonstrate for the first time the use of a laser-based THz source for bunch-length compression and time-stamping of a relativistic electron beam.

A putative biomarker signature for clinically effective AKT inhibition: correlation of in vitro, in vivo and clinical data identifies the importance of modulation of the mTORC1 pathway

Our identification of dysregulation of the AKT pathway in ovarian cancer as a platinum resistance specific event led to a comprehensive analysis of in vitro, in vivo and clinical behaviour of the AKT inhibitor GSK2141795. Proteomic biomarker signatures correlating with effects of GSK2141795 were developed using in vitro and in vivo models, well characterised for related molecular, phenotypic and imaging endpoints. Signatures were validated in temporally paired biopsies from patients treated with GSK2141795 in a clinical study. GSK2141795 caused growth-arrest as single agent in vitro, enhanced cisplatin-induced apoptosis in vitro and reduced tumour volume in combination with platinum in vivo. GSK2141795 treatment in vitro and in vivo resulted in ~50-90% decrease in phospho-PRAS40 and 20-80% decrease in fluoro-deoxyglucose (FDG) uptake. Proteomic analysis of GSK2141795 in vitro and in vivo identified a signature of pathway inhibition including changes in AKT and p38 phosphorylation and total Bim, IGF1R, AR and YB1 levels. In patient biopsies, prior to treatment with GSK2141795 in a phase 1 clinical trial, this signature was predictive of post-treatment changes in the response marker CA125. Development of this signature represents an opportunity to demonstrate the clinical importance of AKT inhibition for re-sensitisation of platinum resistant ovarian cancer to platinum.

118 A RAPID, MINIMALLY INVASIVE METHOD OF COLLECTING SEMEN FROM POLAR BEARS

Due to reproductive challenges faced by both captive and wild polar bears (Ursus maritimus), there is growing interest in developing assisted reproductive technologies (ART) to overcome infertility and preserve valuable genetics in this species. A polar bear sperm bank is essential in supporting ART endeavors; however, the traditional method of semen collection from wildlife, electro-ejaculation, has been relatively unsuccessful in polar bears. The goal of this study was to evaluate an alternative method of semen collection previously developed for use in cats. Medetomidine, an α2-adrenergic agonist commonly used to anesthetize captive polar bears, has side effects that facilitate semen collection: it stimulates epididymal receptors, causing semen to enter the urethra while concurrently stimulating receptors in the neck of the bladder, preventing urine contamination. The objective of this study was to assess the feasibility of collecting semen via urethral catheterization from male polar bears anesthetized with medetomidine. From 2012–2015, semen collection attempts (n = 9) were performed opportunistically on captive male polar bears (n = 8) in the USA. All males were considered sexually mature, with a mean age of 17.2 years (±2.8). Although all were housed with females, only 2 had sired offspring. Procedures were performed during breeding (n = 7) and nonbreeding seasons (n = 2). Individuals were anesthetized with medetomidine (0.025–0.060 mg kg–1) in conjunction with tiletamine/zolazepam or ketamine, and anesthesia was maintained using isoflurane. A sterile, lubricated, polypropylene urinary catheter (8 Fr) was inserted ~40 cm at the first 8 procedures and then 80 cm during the final procedure after a necropsy revealed the polar bear urethra is 100 cm in length. Catheters were left in place for 1 min and then retracted slowly while using a syringe to maintain negative pressure. Bears were catheterized 1–3 times during an immobilization. Any fluid recovered in the catheter was then flushed into a sterile tube and sperm motility was assessed microscopically. All values are presented as mean ± standard error of the mean. Semen containing motile spermatozoa was obtained at 8 of 9 (88.9%) procedures. Total semen volume was 509 ± 292 µL, with the highest volume (2500 µL) obtained using the longer (80 cm) catheter. Total sperm count was 2.6 ± 1.6 × 108. Sperm concentration and motility were 6.3 ± 3.7 × 108 mL–1 and 64.3 ± 9.0%, respectively. Although the percentage of motile sperm and sperm concentration appeared higher during the breeding season, seasonal differences could not be established statistically due to small sample sizes. This study demonstrates that urethral catheterization is an effective method of obtaining semen from polar bears anesthetized with medetomidine, and that longer catheters may be preferable for maximizing sample volume. Although polar bears are seasonal breeders, semen was recovered at both collections during the nonbreeding season, suggesting that spermatogenesis occurs year-round. This minimally invasive procedure is rapid and requires little equipment, rendering it practical for fieldwork.

117 DEVELOPMENT OF A NONINVASIVE, FECAL PROTEIN PREGNANCY TEST FOR POLAR BEARS

Differentiating between pregnancy and nonpregnancy noninvasively is difficult in species that experience pseudopregnancy, including polar bears (Ursus maritimus). These bears usually breed in the spring, undergo delayed implantation until late summer or early fall, and give birth in late fall. In other species, the placental protein transthyretin (TTR) has been shown to be essential for early fetal growth, responsible for transporting thyroid hormone from the mother to the fetus during early pregnancy. Preliminary data obtained via 2D-DIGE indicated that fecal TTR is elevated during polar bear pregnancy, but further research is needed to validate its use as an accurate biomarker of pregnancy. The aim of this study was to develop a bench-side assay to characterize TTR in longitudinal fecal samples from pregnant and nonpregnant polar bears. Specific objectives were to 1) develop an effective method for total fecal protein extraction; 2) identify antibodies that cross-react with polar bear fecal TTR; 3) validate an EIA for measuring fecal TTR; and, for proof of concept, 4) compare fecal TTR concentrations among pregnant, pseudopregnant, and nonpregnant polar bears. Fecal samples (n = 205) were collected from females that produced cubs (pregnant; n = 2), did not breed but exhibited a prolonged increase in progesterone (P4; pseudopregnant; n = 2), or did not breed and did not exhibit an increase in P4 (nonpregnant; n = 2). Total protein of each sample was extracted using a modified ammonium sulfate method. Protein concentrations were quantified using the Bradford assay. Western blot was used to determine commercial antibody compatibility with polar bear fecal TTR. A sandwich EIA was optimized using a standard curve ranging from 12.5 to 400 pg of human TTR/well. A parallelism was performed using two-fold serial dilutions of pooled fecal protein. Fecal TTR concentrations were measured in duplicate and are reported as femtograms of TTR per micrograms of total protein. Mean TTR concentrations in samples collected from July–December were compared among groups. Values are reported as mean ± standard error of the mean. Total fecal protein yield was 459.38 ± 284.38 µg g–1 of feces. Successful binding of 2 polyclonal antibodies to the 15-kDa subunit of the TTR protein was verified via western blot and indicated that fecal proteins can retain antibody-binding capacity. The parallelism exhibited strong correlation with the standard curve (R2 = 0.989). Data suggest that fecal TTR is higher during late summer or early fall in pregnant bears (588.40 ± 116.52) when compared to the pseudopregnant state (111.23 ± 15.98) and the nonpregnant state (250.83 ± 34.34). This is the first EIA developed to measure fecal TTR in any species. Although preliminary, these data suggest that the fecal TTR EIA may be useful in diagnosing pregnancy in polar bears.

Abstract A2-13: Targeting genomic instability to identify molecular drivers of poor prognosis in cancer

Background: Cancer is a disease of the genome whereby mutational events that confer a survival advantage to cells are selectively retained. Consequently, genome instability and evasion of cell death are fundamental hallmarks of cancer. Certain cancers, including epithelial ovarian cancers (EOC), pancreatic ductal adenocarcinomas (PDAC) and a subset of sarcomas with complex karyotypes are characterized as being very genomically unstable suggesting that such tumors are driven by defects in DNA damage recognition and repair. Additionally, these tumors are also characterized by a high frequency of p53 mutation, extensive intra-tumoral heterogeneity and resistance, acquired or intrinsic, to DNA damaging chemotherapeutic agents: these tumor types consequently carry a poor prognosis. This highlights the need for detailed molecular characterization to identify new therapeutic targets and stratification biomarkers.

Aims: The aim of the study is to use a bioinformatic approach to identify commonly amplified genes, that function in DNA damage response and apoptotic processes, across the three tumor types, and which confer a poorer prognosis in these patients.

Methods: For target identification, datasets for EOC and PDAC (obtained from TCGA) and sarcoma (obtained from GEO, NCBI) were analyzed for common copy number aberrations (CNA) in 734 genes relating to DNA damage response and apoptosis, and confer a poor prognosis in progression-free survival (PFS) data in EOC patients. Genes with prognostic significance (p &lt;0.05) using the log rank test were picked from the top 100 most frequently amplified loci. Next, the targets were functionally validated by siRNA-mediated knockdown, overexpression and/or pharmacological inhibition using apoptosis, proliferation and migration assays.

Results: Four genes, SGK3, c19orf40, MRPS12 and ZBTB32 were highlighted as being commonly amplified across all three tumor types, of which only SGK3 and c19orf40 were statistically significant in circular binary segmentation CNA calling when examining PFS data in EOC patients. SGK3, a member of the serum/glucocorticoid regulated kinase (SGK) family appeared interesting as it has similar functions and substrates to the AKT kinase family, which we have previously shown to have key roles in tumor cell survival in response to therapy. Intra-patient paired platinum sensitive (PEA1) and resistant (PEA2) and SKOV3 ovarian cancer cell lines, and Aspc1 and Panc-1 pancreatic cancer cell lines were used for validation studies. siRNA-mediated knockdown of SGK3 did not alter induction of caspase 3/7 activity in response to chemotherapy, relative to control treatments in all cell lines. To account for any compensatory effects by the other SGK members in the presence of SGK3 knockdown, all three SGK members (SGK1-3) were knocked down by siRNA and this also did not increase induction of caspase 3/7 activity. Wound healing migration assays however, revealed that over-expression of SGK3 increases cell motility suggesting SGK3's role in prognosis is via migration/tumor spread rather than response to therapy. The remaining targets identified in the bioinfomatic analysis are currently undergoing validation and preliminary results will be summarized.

Conclusion: To conclude, bioinformatic analysis highlighted four genes related to DNA damage response/apoptosis that were commonly amplified across tumors characterized by genomic instability and resistance to chemotherapy. One of these genes, SGK3, appears to have a role in poor prognosis via migration.

Citation Format: Karen A. Menezes, Paula Cunnea, Phillip Lawton, Ed Curry, Hani Gabra, Harpreet Wasan, Surinder K. Sharma, Euan A. Stronach. Targeting genomic instability to identify molecular drivers of poor prognosis in cancer.. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-13.

LARP1 post-transcriptionally regulates mTOR and contributes to cancer progression

RNA-binding proteins (RBPs) bind to and post-transcriptionally regulate the stability of mRNAs. La-related protein 1 (LARP1) is a conserved RBP that interacts with poly-A-binding protein and is known to regulate 5'-terminal oligopyrimidine tract (TOP) mRNA translation. Here, we show that LARP1 is complexed to 3000 mRNAs enriched for cancer pathways. A prominent member of the LARP1 interactome is mTOR whose mRNA transcript is stabilized by LARP1. At a functional level, we show that LARP1 promotes cell migration, invasion, anchorage-independent growth and in vivo tumorigenesis. Furthermore, we show that LARP1 expression is elevated in epithelial cancers such as cervical and non-small cell lung cancers, where its expression correlates with disease progression and adverse prognosis, respectively. We therefore conclude that, through the post-transcriptional regulation of genes such as mTOR within cancer pathways, LARP1 contributes to cancer progression.

Abstract AS20: DNA-PKcs is amplified in high grade serous ovarian cancer (HGSC), correlates with poor outcome and drives resistance to platinum therapy via the AKT signaling pathway

High grade serous ovarian cancer is typified by p53 mutation, high degrees of genomic instability and the development of chemo-resistance. Genomic translocations result from incorrectly repaired DNA double strand breaks (DSBs). DNA-PKcs is a central catalytic component of the error prone non-homologous end joining (NHEJ) DSB repair mechanism. We report here that DNA-PKcs is frequently amplified in copy number in HGSC and that amplification correlates with higher DNA-PKcs gene expression and poorer patient outcome (PFS/OS) using both in-house and publicly available datasets (TCGA). Targeting DNA-PKcs, pharmacologically or by RNAi, enhances apoptosis in response to platinum treatment in platinum resistant cell lines and primary models. Furthermore we report that inhibition of DNA-PK restores response to cisplatin in chemoresistant ovarian cancer cells in vivo. SKOV-3 tumor xenografts were implanted subcutaneously into Balb/c Nu/Nu mice and treated with DNA-PKcs inhibitor NU7441 for 2 weeks alone or in combination with cisplatin. DNA-PK inhibition or cisplatin treatment alone were ineffective however in combination they decreased tumor growth at 14 days by 90%, relative to platinum only treatment. On investigating the mechanism of DNA-PKcs mediated chemoresistance we revealed that, in response to DNA damage, DNA-PKcs phosphorylates AKT on serine residue 473 in the nucleus of platinum resistant ovarian tumor cells, but not sensitive cells from the same patient. Phosphorylation at AKT threonine 308 is unaffected and DNA-PK inhibition does not interfere with insulin-mediated phosphorylation of AKT S473. DNA-PK mediated AKT activation in chemoresistant cells results in inhibitory phosphorylation of the pro-apoptotic protein BAD and stabilisation of the anti-apoptotic Bcl-2 protein resulting in the observed attenuation of apoptotic response to platinum treatment. DNA-PK inhibition is an attractive therapeutic strategy for resensitising resistant tumors to platinum based therapy, directly linking the DNA damage caused by platinum to the pro-survival AKT pathway, without interfering with normal physiological roles of AKT.

Citation Format: Curry E, Cheraghchi-Bashi-Astaneh A, Chen M, Cunnea P, De Sousa C, Maginn E, Dai Y, Liu E, Wasan H, Mills G, Bowtell D, Gabra H & Stronach EA. DNA-PKcs is amplified in high grade serous ovarian cancer (HGSC), correlates with poor outcome and drives resistance to platinum therapy via the AKT signaling pathway [abstract]. In: Proceedings of the 10th Biennial Ovarian Cancer Research Symposium; Sep 8-9, 2014; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(16 Suppl):Abstract nr AS20.

Epigenome-wide association study reveals decreased average methylation levels years before breast cancer diagnosis

BACKGROUND

Interest in the potential of DNA methylation in peripheral blood as a biomarker of cancer risk is increasing. We aimed to assess whether epigenome-wide DNA methylation measured in peripheral blood samples obtained before onset of the disease is associated with increased risk of breast cancer. We report on three independent prospective nested case-control studies from the European Prospective Investigation into Cancer and Nutrition (EPIC-Italy; n = 162 matched case-control pairs), the Norwegian Women and Cancer study (NOWAC; n = 168 matched pairs), and the Breakthrough Generations Study (BGS; n = 548 matched pairs). We used the Illumina 450k array to measure methylation in the EPIC and NOWAC cohorts. Whole-genome bisulphite sequencing (WGBS) was performed on the BGS cohort using pooled DNA samples, combined to reach 50× coverage across ~16 million CpG sites in the genome including 450k array CpG sites. Mean β values over all probes were calculated as a measurement for epigenome-wide methylation.

RESULTS

In EPIC, we found that high epigenome-wide methylation was associated with lower risk of breast cancer (odds ratio (OR) per 1 SD = 0.61, 95 % confidence interval (CI) 0.47-0.80; -0.2 % average difference in epigenome-wide methylation for cases and controls). Specifically, this was observed in gene bodies (OR = 0.51, 95 % CI 0.38-0.69) but not in gene promoters (OR = 0.92, 95 % CI 0.64-1.32). The association was not replicated in NOWAC (OR = 1.03 95 % CI 0.81-1.30). The reasons for heterogeneity across studies are unclear. However, data from the BGS cohort was consistent with epigenome-wide hypomethylation in breast cancer cases across the overlapping 450k probe sites (difference in average epigenome-wide methylation in case and control DNA pools = -0.2 %).

CONCLUSIONS

We conclude that epigenome-wide hypomethylation of DNA from pre-diagnostic blood samples may be predictive of breast cancer risk and may thus be useful as a clinical biomarker.

Whole-genome characterization of chemoresistant ovarian cancer

Patients with high-grade serous ovarian cancer (HGSC) have experienced little improvement in overall survival, and standard treatment has not advanced beyond platinum-based combination chemotherapy, during the past 30 years. To understand the drivers of clinical phenotypes better, here we use whole-genome sequencing of tumour and germline DNA samples from 92 patients with primary refractory, resistant, sensitive and matched acquired resistant disease. We show that gene breakage commonly inactivates the tumour suppressors RB1, NF1, RAD51B and PTEN in HGSC, and contributes to acquired chemotherapy resistance. CCNE1 amplification was common in primary resistant and refractory disease. We observed several molecular events associated with acquired resistance, including multiple independent reversions of germline BRCA1 or BRCA2 mutations in individual patients, loss of BRCA1 promoter methylation, an alteration in molecular subtype, and recurrent promoter fusion associated with overexpression of the drug efflux pump MDR1.

Whole-genome characterization of chemoresistant ovarian cancer

Patients with high-grade serous ovarian cancer (HGSC) have experienced little improvement in overall survival, and standard treatment has not advanced beyond platinum-based combination chemotherapy, during the past 30 years. To understand the drivers of clinical phenotypes better, here we use whole-genome sequencing of tumour and germline DNA samples from 92 patients with primary refractory, resistant, sensitive and matched acquired resistant disease. We show that gene breakage commonly inactivates the tumour suppressors RB1, NF1, RAD51B and PTEN in HGSC, and contributes to acquired chemotherapy resistance. CCNE1 amplification was common in primary resistant and refractory disease. We observed several molecular events associated with acquired resistance, including multiple independent reversions of germline BRCA1 or BRCA2 mutations in individual patients, loss of BRCA1 promoter methylation, an alteration in molecular subtype, and recurrent promoter fusion associated with overexpression of the drug efflux pump MDR1.

Chromatin H3K27me3/H3K4me3 histone marks define gene sets in high-grade serous ovarian cancer that distinguish malignant, tumour-sustaining and chemo-resistant ovarian tumour cells

In embryonic stem (ES) cells, bivalent chromatin domains containing H3K4me3 and H3K27me3 marks silence developmental genes, while keeping them poised for activation following differentiation. We have identified gene sets associated with H3K27me3 and H3K4me3 marks at transcription start sites in a high-grade ovarian serous tumour and examined their association with epigenetic silencing and malignant progression. This revealed novel silenced bivalent marked genes, not described previously for ES cells, which are significantly enriched for the PI3K (P<10(-7)) and TGF-β signalling pathways (P<10(-5)). We matched histone marked gene sets to gene expression sets of eight normal fallopian tubes and 499 high-grade serous malignant ovarian samples. This revealed a significant decrease in gene expression for the H3K27me3 and bivalent gene sets in malignant tissue. We then correlated H3K27me3 and bivalent gene sets to gene expression data of ovarian tumour 'stem cell-like' sustaining cells versus non-sustaining cells. This showed a significantly lower expression for the H3K27me3 and bivalent gene sets in the tumour-sustaining cells. Similarly, comparison of matched chemo-sensitive and chemo-resistant ovarian cell lines showed a significantly lower expression of H3K27me3/bivalent marked genes in the chemo-resistant compared with the chemo-sensitive cell line. Our analysis supports the hypothesis that bivalent marks are associated with epigenetic silencing in ovarian cancer. However it also suggests that additional tumour specific bivalent marks, to those known in ES cells, are present in tumours and may potentially influence the subsequent development of drug resistance and tumour progression.

Non-invasive detection of candidate pregnancy protein biomarkers in the feces of captive polar bears (Ursus maritimus)

Currently, there is no method of accurately and non-invasively diagnosing pregnancy in polar bears. Specific proteins may exhibit altered profiles in the feces of pregnant bears, but predicting appropriate candidate proteins to investigate is speculative at best. The objective of this study was to identify potential pregnancy biomarker proteins based on their increased abundance in the feces of pregnant polar bears compared to pseudopregnant females (controls) using two-dimensional in-gel electrophoresis (2D-DIGE) and mass spectrometry (MS). Three 2D-DIGE gels were performed to evaluate fecal protein profiles from controls (n=3) and pregnant polar bears (n=3). There were 2224.67±52.39 (mean±SEM) spots resolved per gel. Of these, only five proteins were elevated in the pregnant group (P<0.05), and seven additional spots tended to be higher (0.05<P<0.10). All 12 were submitted for MS analysis and the identities of 11 were ascertained with a >99.9% confidence interval. The 11 spots represented seven distinct proteins, five of which were significantly more abundant in the pregnant group: IgGFc-binding protein, filamin-C, carboxypeptidase B, transthyretin, and immunoglobulin heavy chain variable region. To our knowledge, this was the first study that employed 2D-DIGE to identify differentially expressed proteins in fecal samples to characterize a physiological condition other than those related to gastrointestinal disorders. These promising results provided a strong foundation for ensuing efforts to develop a non-invasive pregnancy assay for use in both captive and wild polar bears.

260 EFFECTIVENESS OF A COMMERCIALLY AVAILABLE POST-THAW BOVINE SEMEN SEXING KIT IN BOTH MULTIPLE-AND SINGLE-OVULATING COWS

Currently, there is no inexpensive method for commercially separating X- and Y-bearing bovine sperm cells. Because dairy heifer calves are significantly more valuable than bull calves, a reliable method of swaying the bovine sex ratio in favor of females is desirable in the dairy industry. The objective of these experiments was to determine the efficacy of a commercially available post-thaw semen sexing kit, HeiferPlus™ (Emlab Genetics, Arcola, IL, USA), which claims to sway the bovine sex ratio in favor of female calves. Three trials included the insemination of hyperstimulated cows with control or HeiferPlus (HP)-treated semen, nonsurgical embryo collection on Day 7, and a novel combined PCR/Southern blot assay to determine sex. Overall, 271 embryos were collected and a sex was assigned to 265 of them. Chi-square analysis showed that the control group produced a significantly higher proportion (P < 0.005) of female embryos than the HP group (65.0% and 43.0%, respectively). There was no difference in the proportion of transferable versus degenerate embryos, and ANOVA showed no difference in the number of ovulations, embryos, and unfertilized oocytes collected in the control versus the HP groups. Another trial involved the artificial insemination of cows synchronized via OvSynch� (ABS Global, Deforest, WI, USA) followed by fetal sexing via ultrasonography between Days 55 and 58. Of the 152 cows inseminated, 51.3% were pregnant at Day 35. Of the cows inseminated with HP-treated semen, 54.5% became pregnant and 48.0% of the controls were pregnant. HP-treated cows resulted in 54.8% male (23/42) and 45.2% female (19/42) fetuses. Control cows had 52.8% male (19/36) and 47.2% female (17/36) fetuses at 58 days of gestation. Calving records confirmed the ultrasound sexing data and showed that three controls and one HP calf died after 58 days of gestation, and one control and one HP calf died within 2 weeks following birth. Chi-square analysis showed no significant difference in the sex ratio. Semen from six bulls was used in this trial, and pregnancy rates among bulls did not differ (P > 0.05). Computer-assisted semen analysis showed no significant difference in motility or progressive forward motility of control versus HP-treated sperm in any of the bulls. Results of these studies indicated that the HeiferPlus semen sexing kit did not sway the sex ratio in favor of females in either multiple- or single-ovulating cows. In the hyperstimulated cows, the control group actually produced a significantly higher proportion of female embryos than the HP group. No differences in embryo production or embryo grade were observed. Further research is needed to investigate the effects of semen incubation or manipulation on the sex ratio of cattle.

Switching from methadone to a different opioid: What is the equianalgesic dose ratio?

8617

Background: Methadone (ME) is a highly effective opioid agonist used for difficult pain syndromes. However, the rotation from ME to another opioid may be difficult because of the absence of a uniformly accepted conversion ratio. Methods: We retrospectively reviewed consecutive medical records of Pts undergoing an opioid rotation from ME to an alternative opioid. For inclusion, Pts were required to have received ME for at least 3 days prior to the switch and reach a stable dose of the alternative opioid(s) during 7 days following. Stable dose was defined as a 30% or less change in opioid dose from one day to the next. For purposes of analysis, on the day before the switch, doses, were divided into ME doses and the oral morphine equivalent daily dose (MEDD), based on medication and route of all other opioids taken on that day, using standard equinalgesic tables. All doses after the switch were converted to the MEDD. For Pts receiving ME and a second opioid prior to the switch, the MEDD of the second opioid was subtracted from the MEDD calculated for the day when stable dose was reached. The remainder was used to calculate the equianalgesic raio with the previous ME dose. Results: Records on 39 Pts met inclusion criteria. Excluded from analysis were 5 Pts who were restarted on ME in < 8 days, 2 whose opioid dose markedly decreased of post switch, and 3 due to concerns about reliability of multiple routes used for fentanyl. Data from 29 Pts, 10 female, mean age 48 ±14.4 were evaluable. The ratio for: oral ME to MEDD was 1:4.7 (CL 3.0–6.5)(n=16), IV ME to MEDD was 1:13.5 (CL6.6–20.5)(n=13), p=0.06. ME dose is significantly correlated to stable MEDD after switching opioids for both ME IV and oral (Spearman=0.86,p=0.0001 and Spearman=0.72, p=0.0024, respectively. Mean day of achieving stable dose was on day 2.5 ±0.2 for IV ME and day 2.6±0.3 for oral ME. Conclusions: These dose ratios are new findings that will assist in switching Pts more safely to alternative opioids, when side effects or pain problems occur.An important difference in analgesic potency appears to exist between IV and oral ME. Further research with prospective studies is required.

No significant financial relationships to disclose.

The use of palliative sedation for intractable symptoms in a palliative care unit (PCU) in a comprehensive cancer center

8577

Background: There is wide variation in the frequency of reported use of palliative sedation (PS) to control intractable and refractory symptoms. Institutions have established policies for midazolam infusion in cases of PS. The indications and outcomes of this procedure have not been well characterized Methods: Our midazolam policy for PS requires 1:1 nursing for the first 24 hours and documentation of discussions regarding sedation. We reviewed our PCU database for all admissions for the first 11 months of 2005. We used pharmacy records for all patients who received medications used for sedation (chlorpromazine, lorazepam, midazolam). We reviewed all charts of pts who received any of these drugs to establish if the indication had been PS. Results: 148/484 admissions died in the PCU [31%]. 65/484 admissions (13%), and 47/ 148 patients who died (32%) received PS. Median age of patients (pts) was 58, 42 pts were male [65%], and the most frequent primaries observed were lung 24 [37%], hematologic 12 [18%], head and neck 7 [11%], and gastrointestinal 7 [11%]. Results are indicated in the table. * 2 patients had more than one indication for sedation The main causes for PS in our patients were delirium 57 [88%], dyspnea 6 [9%], and bleeding 4 [6%]. 18/65 patients who received PS [35%] were discharged alive, versus 318/419 [76%] who did not receive PS [p< 0.001]. Midazolam was used in 11/65 episodes [17%]. 4/6 pts with PS for dyspnea received midazolam [66%], versus 8/57 with PS for delirium or bleeding [14%], p=0.01]. 18/54 pts who received PS using other drug were discharged alive [33%], versus 0/11 pts who received midazolam [p=0.02]. Conclusions: Palliative sedation was required in 32% of pts who died in the hospital. Reporting midazolam utilization rates for monitoring overall PS outcomes, results in significant under reporting. Midazolam was used more frequently in cases of progressive dyspnea and poor prognosis. Less restrictive policies in the use of midazolam may result in more use for PS. Data accrual continues.

[Table: see text]

No significant financial relationships to disclose.

Identification of lesion components that influence visual function in age related macular degeneration

AIMS

To explore the relation between lesion composition as assessed by fundus photography and fluorescein angiography with clinical measures of vision in eyes of patients with age related macular degeneration (AMD).

METHODS

A standardised visual function assessment along with colour stereo pair fundus photography was carried out in both eyes of 58 subjects with a confirmed clinical diagnosis of AMD. The size, location, and composition of the macular lesion (blood, exudate, subretinal fluid, pigment, membrane, atrophy, and fibrosis) were measured on the colour photographs using computer assisted image analysis. Of the 58 subjects, 44 also had concurrent fluorescein angiography. Classic and occult choroidal neovascularisation (CNV), blood, blocked fluorescence, fibrosis, geographic atrophy, and the total area of abnormal fluorescence were measured. Multiple linear regression was used to examine the relation between clinical measures of vision and the location and extent of lesion components identified by both colour and fluorescein image capture.

RESULTS

The composition of the macular lesion strongly influenced visual function, with atrophy (p=0.001) and fibrosis (p=0.002) accounting for most of the variation. When the location of the lesion with respect to the fovea was examined, fibrosis within the fovea significantly influenced all clinical measures of vision (p=0.008). The regression model selected the total area of abnormal fluorescence and a composite parameter (a semiquantitative measure of the following characteristics: atrophy, exudates, blood, and fibrosis ) from colour photography (r(2) =0.52) as the variables that explained most of the variation in clinical measures of vision.

CONCLUSIONS

The composition and extent of the macular lesion strongly influences visual function in eyes with AMD. Both colour photography and angiography yielded information, which together explained considerably more of the variation in the clinical measures of vision than either on its own.

Composite dialysis access grafts

Hemodialysis access devices constructed of expanded polytetrafluoroethylene (ePTFE) require a maturation period of seven to 14 days before cannulation. Percutaneously placed dual-lumen catheters can be used for temporary access during this interval but are associated with significant short and long term complications. Access devices constructed of Plasma-TFE (pl-TFE) (Atrium, Hollis) conduits have been reported to tolerate cannulation immediately after placement, but long term patency is inferior to that of conventional ePTFE. To combine the immediate access advantages of pl-TFE and the long term patency of ePTFE, composite grafts were constructed, which consisted of 10 to 12 centimeters of pl-TFE and the remainder of ePTFE. The pl-TFE segment was made available for immediate access and the ePTFE segment after an appropriate maturation period. Thirty percent of composite grafts were cannulated on the day of placement and 83.8 percent were cannulated within 72 hours. No complications of early access of the pl-TFE segment occurred. These grafts were compared with a cohort of conventional ePTFE grafts for the occurrence of thrombosis, infection and pseudoaneurysm. No significant differences were noted. Event-free patency of the two groups was equal (327.7 versus 346.3 days, p = 0.282). Patency after an initial thrombotic episode was slightly better in the composite group. We conclude that composite dialysis access grafts can be cannulated immediately after placement and demonstrate long term performance at least equal to that of conventional ePTFE grafts. Use of the composite graft concept should be considered when immediate dialysis is needed and to avoid the use of temporary access catheters.

The determination of hemodialysis blood recirculation using blood urea nitrogen measurements

The determination of blood recirculation using blood urea nitrogen (BUN) measurements in hemodialysis patients is a standard technique. The accuracy and reproducibility of these calculations have never been determined. Two pairs of recirculation studies (study A and study B) were performed in 13 patients during a single dialysis treatment. Blood samples were analyzed for BUN and recirculation was calculated. The first recirculation study (study A) was performed within 1 hour of the initiation of dialysis, with a duplicate test of recirculation performed within 15 minutes. In study B, the dialyzer blood lines were reversed in an attempt to enhance blood recirculation. After 15 minutes, duplicate tests of recirculation were again performed. Calculated recirculations before the line reversal (study A) ranged from -3.3% to 11.9% in the first test and -2.9% to 12.2% in the second test. In study A, there was no correlation (P > 0.05, r = 0.09) between the first and second calculated recirculations. In study B, an increase in recirculation was observed. Calculated recirculations ranged from 16.3% to 53.5% for the first test and 5.4% to 58.1% for the second test. A significant relationship was observed in the calculated recirculation in study B (P < 0.05, r = 0.81). The results from the present study show that the use of BUN measurements may not provide a consistent indicator of access recirculation in a patient with a low recirculation. This lack of consistency should be considered when determining further clinical treatment.

Non-invasive determination of recirculation in the patient on dialysis

Recirculation of blood flow occurs when the fistula flow rate is inadequate to support the desired dialyzer blood flow. The percentage recirculation is normally calculated using the blood urea nitrogen of blood samples from the two dialyzer blood lines and a peripheral blood sample. However, this method is time consuming, costly, and may not always give accurate measurements. A technique was developed to measure recirculation using the injection of saline into the venous dialysis line. For this technique, an optical detector is placed across the arterial dialysis tubing, and the light intensity, which is proportional to the hematocrit, is continually measured using a computerized data collection system. After a baseline data collection period, 10 ml of saline is injected into the venous dialysis line using the sampling port. The saline that appears in the arterial dialysis line as a result of recirculation will cause a dilution of the blood and an increase in light intensity. In vitro testing showed an excellent correlation between the area under the dilution curve and percentage recirculation. This technique will provide a quick, inexpensive, and reliable measurement of recirculation.

Outpatient vascular access surgery: impact of a dialysis unit-based surgical facility

The present report describes a novel approach to vascular access surgery based on the philosophy that a readily available operating room, staffed by nurses familiar with the unique problems of dialysis patients and their therapy, would reduce dialysis delays and maintain the quality of surgical care. Based on a 28-month experience with more than 1,000 access cases, we conclude that a traditional surgical setting is not necessary for either quality access graft placement or the management of access complications.