Associations between genomic stratification of breast cancer and centrally reviewed tumour pathology in the METABRIC cohort

The integration of genomic and transcriptomic profiles of 2000 breast tumours from the METABRIC [Molecular Taxonomy of Breast Cancer International Consortium] cohort revealed ten subtypes, termed integrative clusters (IntClust/s), characterised by distinct genomic drivers. Central histopathology (N = 1643) review was undertaken to explore the relationship between these ten molecular subtypes and traditional clinicopathological features. IntClust subtypes were significantly associated with histological type, tumour grade, receptor status, and lymphocytic infiltration (p < 0.0001). Lymph node status and Nottingham Prognostic Index [NPI] categories were also significantly associated with IntClust subtype. IntClust 3 was enriched for tubular and lobular carcinomas, the latter largely accounting for the association with CDH1 mutations in this cluster. Mucinous carcinomas were not present in IntClusts 5 or 10, but did not show an association with any of the remaining IntClusts. In contrast, medullary-like cancers were associated with IntClust 10 (15/26). Hormone receptor-positive tumours were scattered across all IntClusts. IntClust 5 was dominated by HER2 positivity (127/151), including both hormone receptor-positive (60/72) and hormone receptor-negative tumours (67/77). Triple-negative tumours comprised the majority of IntClust 10 (132/159) and around a quarter of IntClust 4 (52/217). Whilst the ten IntClust subtypes of breast cancer show characteristic patterns of association with traditional clinicopathological variables, no IntClust can be adequately identified by these variables alone. Hence, the addition of genomic stratification has the potential to enhance the biological relevance of the current clinical evaluation and facilitate genome-guided therapeutic strategies.

Hard Two-Photon Contribution to Elastic Lepton-Proton Scattering Determined by the OLYMPUS Experiment

The OLYMPUS Collaboration reports on a precision measurement of the positron-proton to electron-proton elastic cross section ratio, R_{2γ}, a direct measure of the contribution of hard two-photon exchange to the elastic cross section. In the OLYMPUS measurement, 2.01 GeV electron and positron beams were directed through a hydrogen gas target internal to the DORIS storage ring at DESY. A toroidal magnetic spectrometer instrumented with drift chambers and time-of-flight scintillators detected elastically scattered leptons in coincidence with recoiling protons over a scattering angle range of ≈20° to 80°. The relative luminosity between the two beam species was monitored using tracking telescopes of interleaved gas electron multiplier and multiwire proportional chamber detectors at 12°, as well as symmetric Møller or Bhabha calorimeters at 1.29°. A total integrated luminosity of 4.5  fb^{-1} was collected. In the extraction of R_{2γ}, radiative effects were taken into account using a Monte Carlo generator to simulate the convolutions of internal bremsstrahlung with experiment-specific conditions such as detector acceptance and reconstruction efficiency. The resulting values of R_{2γ}, presented here for a wide range of virtual photon polarization 0.456<ε<0.978, are smaller than some hadronic two-photon exchange calculations predict, but are in reasonable agreement with a subtracted dispersion model and a phenomenological fit to the form factor data.

A Dynamic Role of TBX3 in the Pluripotency Circuitry

Pluripotency represents a cell state comprising a fine-tuned pattern of transcription factor activity required for embryonic stem cell (ESC) self-renewal. TBX3 is the earliest expressed member of the T-box transcription factor family and is involved in maintenance and induction of pluripotency. Hence, TBX3 is believed to be a key member of the pluripotency circuitry, with loss of TBX3 coinciding with loss of pluripotency. We report a dynamic expression of TBX3 in vitro and in vivo using genetic reporter tools tracking TBX3 expression in mouse ESCs (mESCs). Low TBX3 levels are associated with reduced pluripotency, resembling the more mature epiblast. Notably, TBX3-low cells maintain the intrinsic capability to switch to a TBX3-high state and vice versa. Additionally, we show TBX3 to be dispensable for induction and maintenance of naive pluripotency as well as for germ cell development. These data highlight novel facets of TBX3 action in mESCs.

Learned Helplessness in Shuttlebox-Avoidance Behavior

Three groups of rats ( n = 6) were given prior experience in a Skinner box before being trained in a two-way shuttlebox-avoidance task. Subjects experiencing controllable shock (avoidable or escapable) performed significantly better than a yoked control group which had no control over shocks in the Skinner box and better than a control group which experienced no shock in the Skinner box. Results can be interpreted adequately in terms of the learned helplessness hypothesis proposed by Maier, Seligman, and Solomon.

Abstract P6-11-03: A cost effectiveness analysis of baseline left ventricular function assessment for breast cancer patients undergoing anthracycline chemotherapy

Background: It is unclear if all breast cancer (BC) patients require baseline left ventricular function (LVEF) assessment prior to anthracycline based chemotherapy (ABC), and the approach is variable in clinical practice. Our objective is to determine the cost effectiveness of obtaining a baseline LVEF assessment prior to (neo) adjuvant ABC in clinical practice.

Methods: We performed a retrospective analysis of the Yale Equilibrium Radionuclide Angiography (ERNA) database for 701 breast cancer patients who had a baseline ERNA scan prior to systemic therapy for an initial diagnosis of stages I-IV BC between July 2003 and May 2013. We found that 14 of 701 (2%) patients had a baseline LVEF &lt; 50%. Age, pre-existing cardiac risk factors and coronary artery disease did not predict an abnormal baseline LVEF &lt;50 %. To evaluate the benefit of obtaining a baseline echocardiogram or ERNA before ABC, we considered the screening scenario in which BC patients with a baseline LVEF &lt; 50% on screening echocardiogram are treated with a second (2nd) generation non-ABC and those with baseline LVEF ≥ 50% receive a third (3rd) generation ABC, and compared this with a non-screening scenario with uniform 3rd generation ABC treatment for all patients who do not have a baseline echocardiogram. We used Adjuvant Online to obtain estimates of the disease free (DFS) and overall survival (OS) for a 3rd generation ABC regimen vs a 2nd generation non-ABC regimen for 50 year old patients with a T2N1 hormone receptor positive BC. We implemented these oncologic clinical outcomes (in addition to cardiotoxicity-related clinical outcomes, costs of screening echocardiogram and treatment of congestive heart failure (CHF), quality of life metrics, as reported in the literature) into a simplified decision-analytic cost-effectiveness analysis that accounts for the different disease states and their associated costs and quality of life outcomes.

Results: Assuming that 20% of the unscreened patients with a LVEF &lt; 50% will develop CHF if treated with ABC regimen without management of baseline cardiac dysfunction, the base case incremental cost effectiveness ratio (ICER) was determined to be 18,520 $USD/QALY. Sensitivity analysis suggested that the cost-effectiveness of baseline LVEF assessment is primarily driven by the prevalence of patients with LVEF &lt; 50%, the incidence of CHF in this high-risk patient group if treated with ABC regimen, and time to CHF development. While our analysis did not reveal risk factors predictive of low baseline LVEF, our model's dependence on prevalence of LVEF &lt; 50% demonstrates the importance of risk factor stratification. A hypothetical predictive marker which enriches the prevalence of an abnormal baseline LVEF 5-fold to 10% would result in a cost-effectiveness of 10,990 $USD/QALY. The model is less sensitive to the cost of baseline echocardiogram testing.

Conclusion: Baseline LVEF assessment was found to be cost-effective under a willingness-to-pay threshold of $50,000/QALY. Our sensitivity analysis suggests that risk factor-guided LVEF baseline LVEF screening may increase the number of high-risk patients in the treatment population, thus further increasing the cost-effectiveness of baseline LVEF assessment.

Citation Format: Safonov A, Hatzis C, Stratton J, Gross CP, Russell R, Pusztai L, Abu-Khalaf MM. A cost effectiveness analysis of baseline left ventricular function assessment for breast cancer patients undergoing anthracycline chemotherapy. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-11-03.

Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study

BACKGROUND

Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome.

METHODS

In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behaviour, and compared with either CNA or transcriptomics alone.

FINDINGS

We identified five separate patient subgroups with distinct genomic alterations and expression profiles based on 100 discriminating genes in our separate discovery and validation sets of 125 and 103 men. These subgroups were able to consistently predict biochemical relapse (p = 0.0017 and p = 0.016 respectively) and were further validated in a third cohort with long-term follow-up (p = 0.027). We show the relative contributions of gene expression and copy number data on phenotype, and demonstrate the improved power gained from integrative analyses. We confirm alterations in six genes previously associated with prostate cancer (MAP3K7, MELK, RCBTB2, ELAC2, TPD52, ZBTB4), and also identify 94 genes not previously linked to prostate cancer progression that would not have been detected using either transcript or copy number data alone. We confirm a number of previously published molecular changes associated with high risk disease, including MYC amplification, and NKX3-1, RB1 and PTEN deletions, as well as over-expression of PCA3 and AMACR, and loss of MSMB in tumour tissue. A subset of the 100 genes outperforms established clinical predictors of poor prognosis (PSA, Gleason score), as well as previously published gene signatures (p = 0.0001). We further show how our molecular profiles can be used for the early detection of aggressive cases in a clinical setting, and inform treatment decisions.

INTERPRETATION

For the first time in prostate cancer this study demonstrates the importance of integrated genomic analyses incorporating both benign and tumour tissue data in identifying molecular alterations leading to the generation of robust gene sets that are predictive of clinical outcome in independent patient cohorts.

Loss of ATM accelerates pancreatic cancer formation and epithelial-mesenchymal transition

Pancreatic ductal adenocarcinoma (PDAC) is associated with accumulation of particular oncogenic mutations and recent genetic sequencing studies have identified ataxia telangiectasia-mutated (ATM) mutations in PDAC cohorts. Here we report that conditional deletion of ATM in a mouse model of PDAC induces a greater number of proliferative precursor lesions coupled with a pronounced fibrotic reaction. ATM-targeted mice display altered TGFβ-superfamily signalling and enhanced epithelial-to-mesenchymal transition (EMT) coupled with shortened survival. Notably, our mouse model recapitulates many features of more aggressive human PDAC subtypes. Particularly, we report that low expression of ATM predicts EMT, a gene signature specific for Bmp4 signalling and poor prognosis in human PDAC. Our data suggest an intimate link between ATM expression and pancreatic cancer progression in mice and men.

The malignant phenotype in breast cancer is driven by eIF4A1-mediated changes in the translational landscape

Human mRNA DeXD/H-box helicases are ubiquitous molecular motors that are required for the majority of cellular processes that involve RNA metabolism. One of the most abundant is eIF4A, which is required during the initiation phase of protein synthesis to unwind regions of highly structured mRNA that would otherwise impede the scanning ribosome. Dysregulation of protein synthesis is associated with tumorigenesis, but little is known about the detailed relationships between RNA helicase function and the malignant phenotype in solid malignancies. Therefore, immunohistochemical analysis was performed on over 3000 breast tumors to investigate the relationship among expression of eIF4A1, the helicase-modulating proteins eIF4B, eIF4E and PDCD4, and clinical outcome. We found eIF4A1, eIF4B and eIF4E to be independent predictors of poor outcome in ER-negative disease, while in contrast, the eIF4A1 inhibitor PDCD4 was related to improved outcome in ER-positive breast cancer. Consistent with these data, modulation of eIF4A1, eIF4B and PCDC4 expression in cultured MCF7 cells all restricted breast cancer cell growth and cycling. The eIF4A1-dependent translatome of MCF7 cells was defined by polysome profiling, and was shown to be highly enriched for several classes of oncogenic genes, including G-protein constituents, cyclins and protein kinases, and for mRNAs with G/C-rich 5'UTRs with potential to form G-quadruplexes and with 3'UTRs containing microRNA target sites. Overall, our data show that dysregulation of mRNA unwinding contributes to the malignant phenotype in breast cancer via preferential translation of a class of genes involved in pro-oncogenic signaling at numerous levels. Furthermore, immunohistochemical tests are promising biomarkers for tumors sensitive to anti-helicase therapies.