Integrative analysis of copy number and gene expression in breast cancer using formalin-fixed paraffin-embedded core biopsy tissue: a feasibility study.

BACKGROUND: An absence of reliable molecular markers has hampered individualised breast cancer treatments, and a major limitation for translational research is the lack of fresh tissue. There are, however, abundant banks of formalin-fixed paraffin-embedded (FFPE) tissue. This study evaluated two platforms available for the analysis of DNA copy number and gene expression using FFPE samples. METHODS: The cDNA-mediated annealing, selection, extension, and ligation assay (DASL™) has been developed for gene expression analysis and the Molecular Inversion Probes assay (Oncoscan™), were used for copy number analysis using FFPE tissues. Gene expression and copy number were evaluated in core-biopsy samples from patients with breast cancer undergoing neoadjuvant chemotherapy (NAC). RESULTS: Forty-three core-biopsies were evaluated and characteristic copy number changes in breast cancers, gains in 1q, 8q, 11q, 17q and 20q and losses in 6q, 8p, 13q and 16q, were confirmed. Regions that frequently exhibited gains in tumours showing a pathological complete response (pCR) to NAC were 1q (55%), 8q (40%) and 17q (40%), whereas 11q11 (37%) gain was the most frequent change in non-pCR tumours. Gains associated with poor survival were 11q13 (62%), 8q24 (54%) and 20q (47%). Gene expression assessed by DASL correlated with immunohistochemistry (IHC) analysis for oestrogen receptor (ER) [area under the curve (AUC) = 0.95], progesterone receptor (PR)(AUC = 0.90) and human epidermal growth factor type-2 receptor (HER-2) (AUC = 0.96). Differential expression analysis between ER+ and ER- cancers identified over-expression of TTF1, LAF-4 and C-MYB (p ≤ 0.05), and between pCR vs non-pCRs, over-expression of CXCL9, AREG, B-MYB and under-expression of ABCG2. CONCLUSION: This study was an integrative analysis of copy number and gene expression using FFPE core biopsies and showed that molecular marker data from FFPE tissues were consistent with those in previous studies using fresh-frozen samples. FFPE tissue can provide reliable information and will be a useful tool in molecular marker studies. TRIAL REGISTRATION: Trial registration number ISRCTN09184069 and registered retrospectively on 02/06/2010

Semi-Analytical Perturbative Approaches to Third Body Resonant Trajectories

In the framework of multi-body dynamics, successive encounters with a third body, even if well outside of its sphere of influence, can noticeably alter the trajectory of a spacecraft. Examples of these effects have already been exploited by past missions such as SMART-1, as well as are proposed to benefit future missions to Jupiter, Saturn or Neptune, and disposal strategies from Earth's High Eccentric or Libration Point Orbits. This paper revises three totally different descriptions of the effects of the third body gravitational perturbation. These are the averaged dynamics of the classical third body perturbing function, the Opik's close encounter theory and the Keplerian map approach. The first two techniques have respectively been applied to the cases of a spacecraft either always remaining very far or occasionally experiencing extremely close approaches to the third body. However, the paper also seeks solutions for trajectories that undergo one or more close approaches at distances in the order of the sphere of influence of the third body. The paper attempts to gain insight into the accuracy of these different perturbative techniques into each of these scenarios, as compared with the motion in the Circular Restricted Three Body Problem.Comment: In: 66th International Astronautical Congress, Jerusalem, 12-16 October 201

Epirubicin, Cisplatin, and Capecitabine for Primary Platinum-Resistant or Platinum-Refractory Epithelial Ovarian Cancer: Results of a Retrospective, Single-Institution Study.

OBJECTIVE: Primary platinum-resistant epithelial ovarian cancer (EOC) is an area of unmet medical need. There is limited evidence from small studies that platinum-based combinations can overcome "resistance" in a proportion of patients. We investigated the efficacy and toxicity of platinum-based combination chemotherapy in the platinum-resistant and platinum-refractory setting. METHODS: Epirubicin, cisplatin, and capecitabine (ECX) combination chemotherapy was used at our institution for the treatment of relapsed EOC. From the institutional database, we identified all patients with primary platinum-refractory or platinum-resistant relapse treated with ECX as second-line therapy between 2001 and 2012. We extracted demographic, clinical, treatment, and toxicity data and outcomes. We used logistic and Cox regression models to identify predictors of response and survival respectively. RESULTS: Thirty-four 34 patients (8 refractory, 26 resistant) were treated with ECX. Response Evaluation Criteria In Solid Tumors (RECIST) response rate was 45%, median progression-free survival (PFS) was 6.4 months, and overall survival (OS) was 10.6 months. Platinum-resistant patients had better outcomes than did platinum-refractory patients (response rate, 54% vs 0%, P = 0.047; PFS 7.2 vs 1.8 months, P < 0.0001; OS 14.4 vs 3 months, P < 0.001). In regression models, time to progression after first-line treatment and platinum-refractory status were the strongest predictors of response and PFS or OS, respectively. Patients with time to progression after first-line treatment longer than 3 months showed PFS and OS of 7.9 and 14.7 months, respectively. Toxicity was manageable, with only 13% of cycles administered at reduced doses. CONCLUSIONS: Epirubicin, cisplatin, and capecitabine seems to be active in platinum-resistant relapsed EOC with manageable toxicity. Further prospective investigation of platinum-anthracycline combinations is warranted in patients who relapse 3 to 6 months after first-line platinum-taxane treatment

Computational pathology of pre-treatment biopsies identifies lymphocyte density as a predictor of response to neoadjuvant chemotherapy in breast cancer.

BACKGROUND: There is a need to improve prediction of response to chemotherapy in breast cancer in order to improve clinical management and this may be achieved by harnessing computational metrics of tissue pathology. We investigated the association between quantitative image metrics derived from computational analysis of digital pathology slides and response to chemotherapy in women with breast cancer who received neoadjuvant chemotherapy. METHODS: We digitised tissue sections of both diagnostic and surgical samples of breast tumours from 768 patients enrolled in the Neo-tAnGo randomized controlled trial. We subjected digital images to systematic analysis optimised for detection of single cells. Machine-learning methods were used to classify cells as cancer, stromal or lymphocyte and we computed estimates of absolute numbers, relative fractions and cell densities using these data. Pathological complete response (pCR), a histological indicator of chemotherapy response, was the primary endpoint. Fifteen image metrics were tested for their association with pCR using univariate and multivariate logistic regression. RESULTS: Median lymphocyte density proved most strongly associated with pCR on univariate analysis (OR 4.46, 95 % CI 2.34-8.50, p < 0.0001; observations = 614) and on multivariate analysis (OR 2.42, 95 % CI 1.08-5.40, p = 0.03; observations = 406) after adjustment for clinical factors. Further exploratory analyses revealed that in approximately one quarter of cases there was an increase in lymphocyte density in the tumour removed at surgery compared to diagnostic biopsies. A reduction in lymphocyte density at surgery was strongly associated with pCR (OR 0.28, 95 % CI 0.17-0.47, p < 0.0001; observations = 553). CONCLUSIONS: A data-driven analysis of computational pathology reveals lymphocyte density as an independent predictor of pCR. Paradoxically an increase in lymphocyte density, following exposure to chemotherapy, is associated with a lack of pCR. Computational pathology can provide objective, quantitative and reproducible tissue metrics and represents a viable means of outcome prediction in breast cancer. TRIAL REGISTRATION: ClinicalTrials.gov NCT00070278 ; 03/10/2003.We acknowledge funding from Cancer Research UK and NIHR Cambridge Biomedical Research Centre. HRA is an NIHR Academic Clinical Lecturer supported by a Career Development Fellowship from the Pathological Society of Great Britain and Northern Ireland and a Starter Grant for Clinical Lecturers from the Academy of Medical Sciences.This is the final version of the article. It first appeared from BioMed Central via https://doi.org 10.1186/s13058-016-0682-

Bevacizumab in Advanced Cervical Cancer: Issues and Challenges for Low- and Middle-Income Countries

Bevacizumab became the first molecular antibody to show survival benefit in advanced cervical cancer. In the GOG-0240 (Paclitaxel and Cisplatin or Topotecan With or Without Bevacizumab in Treating Patients With Stage IVB, Recurrent, or Persistent Cervical Cancer) trial, it improved overall survival by a significant 3.7 months over platinum doublet chemotherapy alone. However, this discovery is not likely to improve the status of global cervical cancer because more than 85% of patients with cervical cancer live in low- and middle-income countries and cannot afford bevacizumab. This commentary looks at the options by which this drug can be made more affordable and cost-effective for patients in low- and middle-income countries. We also discuss other important questions related to its affordability and cost issues such as the optimal number of cycles and personalizing the treatment. Finally, we emphasize that although the unaffordability of bevacizumab in cervical cancer seems to be a very important issue, the best cost-effective strategy against cervical cancer is prevention with screening and vaccination

Understanding aboriginal peoples' cultural and family connections can help inform the development of culturally appropriate cancer survivorship models of care

PURPOSE: To explore the cancer diagnosis, treatment, and survivorship experiences of Aboriginal people in the Gippsland region, Victoria, Australia, and identify factors critical to the development of a culturally appropriate cancer survivorship model of care. PATIENTS AND METHODS: Yarning circles were used to capture the stories of 15 people diagnosed with cancer and/or those of family members. Yarning circles were conducted in two locations in the Gippsland region. Sessions were facilitated by an Aboriginal Elder, audio recorded, and transcribed verbatim. Thematic analysis of the data were triangulated among three researchers and incorporated researcher reflexivity. RESULTS: Cultural connections and family were critical supports on the cancer journey. Putting the needs of the family first and caring for sick family members were more important than an individual's own health. There was "no time to grieve" for one's own cancer diagnosis and look after oneself. Cancer was a private experience; however, the constancy of deaths highlighted the importance of raising family awareness. Health professionals did not always understand the importance of people's cultural and family supports in their treatment and recovery. There were negatives attitudes in hospitals when family come to visit, seeing family as too large and overstaying visiting times. Health professionals did not seek family assistance with communication of information to family members whose literacy level was low, nor did they include family in treatment decision-making. Access to services depended on family support with transport, finances, and family responsibilities, often resulting in lapses in treatment and follow-up services. CONCLUSION: Understanding the importance of Aboriginal peoples' cultural and family connections can help to inform the development of culturally safe cancer survivorship models of care

Reliable gene expression profiling of formalin-fixed paraffin-embedded breast cancer tissue (FFPE) using cDNA-mediated annealing, extension, selection, and ligation whole-genome (DASL WG) assay

BACKGROUND: The difficulties in using formalin-fixed and paraffin-embedded (FFPE) tumour specimens for molecular marker studies have hampered progress in translational cancer research. The cDNA-mediated, annealing, selection, extension, and ligation (DASL) assay is a platform for gene expression profiling from FFPE tissue and hence could allow analysis of large collections of tissue with associated clinical data from existing archives, therefore facilitating the development of novel biomarkers. METHOD: RNA isolated from matched fresh frozen (FF) and FFPE cancer specimens was profiled using both the DASL whole-genome (WG) platform, and Illumina BeadArray’s, and results were compared. Samples utilized were obtained from the breast cancer tumour bank held at the Cambridge University Hospitals NHS Foundation Trust. RESULTS: The number of reliably detected probes was comparable between the DASL and BeadArray platforms, indicating that the source of RNA did not result in a significant difference in the detection rates (Mean probes- 17114 in FFPE & 17400 in FF). There was a significant degree of correlation between replicates within the FF and FFPE sample sets (r(2) = 0.96–0.98) as well as between the two platforms (DASL vs. BeadArray r(2) = range 0.83–0.89). Hierarchical clustering using the most informative probes showed that replicate and matched samples were grouped into the same sub-cluster, regardless of whether RNA was derived from FF or FFPE tissue. CONCLUSION: Both FF and FFPE material generated reproducible gene expression profiles, although there was more noise in profiles from FFPE specimens. We have shown that the DASL WG platform is suitable for profiling formalin-fixed paraffin-embedded samples, but robust bioinformatics analysis is required

Defining research and infrastructure priorities for cancer survivorship in Australia: a modified Delphi study

Purpose: The aim of this study was to establish research and infrastructure priorities for cancer survivorship. Methods: A two-round modified online Delphi study was completed by Australian experts in cancer survivorship. Initial priorities were generated from the literature and organized into four research categories: physiological outcomes, psychosocial outcomes, population groups, and health services; and one research infrastructure category. In round 1 (R1), panelists ranked the importance of 77 items on a five-point scale (not at all important to very important). In round 2 (R2), panelists ranked their top 5 priorities within each category. Panelists also specified the type of research needed, such as biological, exploratory, intervention development, or implementation, for the items within each research category. Results: Response rates were 76% (63/82) and 82% (68/82) respectively. After R1, 12 items were added, and 16 items combined or reworded. In R2, the highest prioritized research topics and the preferred type of research in each category were: biological research in cancer progression and recurrence; implementation and dissemination research for fear of recurrence; exploratory research for rare cancer types; and implementation research for quality of care topics. Data availability was listed as the most important priority for research infrastructure. Conclusions: This study has defined priorities that can be used to support coordinated action between researchers, funding bodies, and other key stakeholders. Designing future research which addresses these priorities will expand our ability to meet survivors’ diverse needs and lead to improved outcomes.</p