Alexander Wright

Comprehensive genomic meta-analysis identifies intra-tumoural stroma as a predictor of survival in patients with gastric cancer

Objective Gastric adenocarcinoma (gastric cancer, GC) is a major cause of global cancer mortality. Identifying molecular programmes contributing to GC patient survival may improve our understanding of GC pathogenesis, highlight new prognostic factors and reveal novel therapeutic targets. The authors aimed to produce a comprehensive inventory of gene expression programmes expressed in primary GCs, and to identify those expression programmes significantly associated with patient survival. Design Using a network-modelling approach, the authors performed a large-scale meta-analysis of GC transcriptome data integrating 940 gastric transcriptomes from multiple independent patient cohorts. The authors analysed a training set of 428 GCs and 163 non-malignant gastric samples, and a validation set of 288 GCs and 61 non-malignant gastric samples. Results The authors identified 178 gene expression programmes (‘modules’) expressed in primary GCs, which were associated with distinct biological processes, chromosomal location patterns, cis-regulatory motifs and clinicopathological parameters. Expression of a transforming growth factor β (TGF-β) signalling associated ‘super-module’ of stroma-related genes consistently predicted patient survival in multiple GC validation cohorts. The proportion of intra-tumoural stroma, quantified by morphometry in tissue sections from gastrectomy specimens, was also significantly associated with stromal super-module expression and GC patient survival. Conclusion Stromal gene expression predicts GC patient survival in multiple independent cohorts, and may be closely related to the intra-tumoural stroma proportion, a specific morphological GC phenotype. These findings suggest that therapeutic approaches targeting the GC stroma may merit evaluation.

Quantification of histochemical stains using whole slide imaging: development of a method and demonstration of its usefulness in laboratory quality control

Aims Histochemical staining of tissue is a fundamental technique in tissue diagnosis and research, but it suffers from significant variability. Efforts to address this include laboratory quality controls and quality assurance schemes, but these rely on subjective interpretation of stain quality, are laborious and have low reproducibility. We aimed (1) to develop a method for histochemical stain quantification using whole slide imaging and image analysis and (2) to demonstrate its usefulness in measuring staining variation. Methods A method to quantify the individual stain components of histochemical stains on virtual slides was developed. It was evaluated for repeatability and reproducibility, then applied to control sections of an appendix to quantify H&E staining (H/E intensities and H:E ratio) between automated staining machines and to measure differences between six regional diagnostic laboratories. Results The method was validated with <0.5% variation in H:E ratio measurement when using the same scanner for a batch of slides (ie, it was repeatable) but was not highly reproducible between scanners or over time, where variation of 7% was found. Application of the method showed H:E ratios between three staining machines varied from 0.69 to 0.93, H:E ratio variation over time was observed. Interlaboratory comparison demonstrated differences in H:E ratio between regional laboratories from 0.57 to 0.89. Conclusions A simple method using whole slide imaging can be used to quantify and compare histochemical staining. This method could be deployed in routine quality assurance and quality control. Work is needed on whole slide imaging devices to improve reproducibility.

RandomSpot: A web-based tool for systematic random sampling of virtual slides.

This paper describes work presented at the Nordic Symposium on Digital Pathology 2014, Linköping, Sweden. Systematic random sampling (SRS) is a stereological tool, which provides a framework to quickly build an accurate estimation of the distribution of objects or classes within an image, whilst minimizing the number of observations required. RandomSpot is a web-based tool for SRS in stereology, which systematically places equidistant points within a given region of interest on a virtual slide. Each point can then be visually inspected by a pathologist in order to generate an unbiased sample of the distribution of classes within the tissue. Further measurements can then be derived from the distribution, such as the ratio of tumor to stroma. RandomSpot replicates the fundamental principle of traditional light microscope grid-shaped graticules, with the added benefits associated with virtual slides, such as facilitated collaboration and automated navigation between points. Once the sample points have been added to the region(s) of interest, users can download the annotations and view them locally using their virtual slide viewing software. Since its introduction, RandomSpot has been used extensively for international collaborative projects, clinical trials and independent research projects. So far, the system has been used to generate over 21,000 sample sets, and has been used to generate data for use in multiple publications, identifying significant new prognostic markers in colorectal, upper gastro-intestinal and breast cancer. Data generated using RandomSpot also has significant value for training image analysis algorithms using sample point coordinates and pathologist classifications.

Incorporating Local and Global Context for Better Automated Analysis of Colorectal Cancer on Digital Pathology Slides

Phenotypic information derived from visual characteristics of colorectal cancer (CRC) is routinely used for diagnosis and recommendations for treatment. Previously published studies show that the ratio of tissue types within CRC is prognostic. Such studies generate large amounts of data, combining expert classifications with x-y coordinates, which has previously been used to train image analysis algorithms. This paper describes extensions to algorithms employed in previously published work, using pixel clustering as a pre-processing step before normalised cuts in order to reduce the size of the graph for unsupervised segmentation. Image segments are processed for features and given a candidate classification which is weighted by neighbouring segment classes. Global slide features are incorporated to mitigate inconsistencies in overall appearance caused by histological and biological differences. The proposed algorithm increases agreement with the ground truth from 75% to 79% on a dataset of 7,159 images across 157 digital slides.

Deregulation of IGF-binding proteins -2 and -5 contributes to the development of endocrine resistant breast cancer in vitro.

Tamoxifen (TAM) remains the adjuvant therapy of choice for pre-menopausal women with ERα-positive breast cancer. Resistance and recurrence remain, however, a major challenge with many women relapsing and subsequently dying. The insulin-like growth factor (IGF) axis is involved in breast cancer pathogenesis and progression to endocrine resistant disease, but there is very little data on the expression and potential role of IGF-binding proteins (IGFBP) during acquisition of the resistant phenotype. The aim of this study was to determine the expression and functional role of IGFBP-2 and -5 in the development of TAM resistance (TamR) in vitro and to test retrospectively whether they were predictive of resistance in a tissue microarray of 77 women with primary breast cancers who relapsed on/after endocrine therapy and 193 who did not with long term follow up. Reciprocal expression of IGFBP-2 and IGFBP-5 was observed at both mRNA and protein level in TamR cells. IGFBP-2 expression was increased by 10-fold while IGFBP-5 was decreased by 100-fold, compared to TAM-sensitive control cells. shRNA-mediated silencing of IGFBP-2 in TamR cells restored TAM sensitivity suggesting a causal role for this gene in TamR. While silencing of IGFBP-5 in control cells had no effect on TAM sensitivity, it significantly increased the migratory capacity of these cells. Quantitative image analysis of immunohistochemical data failed, however, to demonstrate an effect of IGFBP2 expression in endocrine-relapsed patients. Likewise, IGFBP-2 and IGFBP-5 expression failed to show any significant associations with survival either in patients relapsing or those not relapsing on/after endocrine therapy. By contrast, in silico mining of a separate published dataset showed that in patients who received endocrine treatment, loss of expression of IGBP-5 was significantly associated with worse survival. Overall these data suggest that co-ordinated and reciprocal alteration in IGFBP-2 and −5 expression may play a role in the acquisition of endocrine resistance.

Intratumoral stromal morphometry predicts disease recurrence but not response to 5-fluorouracil-results from the QUASAR trial of colorectal cancer.

The biological importance of tumour‐associated stroma is becoming increasingly apparent, but its clinical utility remains ill‐defined. For stage II/Dukes B colorectal cancer (CRC), clinical biomarkers are urgently required to direct therapeutic options. We report here prognostic/predictive analyses, and molecular associations, of stromal morphometric quantification in the Quick and Simple and Reliable (QUASAR) trial of CRC.

Improved tissue sections for medical liver biopsies: a comparison of 16 vs 18 g biopsy needles using digital pathology

Background Most medical liver biopsies in the UK are now taken in radiology departments using 18 g biopsy needles. Subjectively, the resulting biopsies are narrow and fragile. Aim To compare the quality of liver biopsy tissue sections obtained from 16 and 18 g biopsy needles. Method Fifty consecutive routine medical liver biopsies obtained with 16 and 18 g needles, processed identically in the same laboratory, were measured using digital pathology software. We recorded their fragmentation, length, width, area and number of portal tracts. Results Biopsies obtained with 16 g needles more often resulted in an intact core in tissue sections than those with 18 g needles (71% vs 24%, p<0.001) and were significantly wider (average width of tissue 0.88 vs 0.53 mm, p<0.001). The average total area of tissue per pass was 11.38 mm2 compared with 8.34 mm2 (p<0.001). The number of complete portal tracts per length of biopsy was very variable, but double for 16 vs 18 g biopsies. Routinely taking two passes with the 18 g needle compensated for the reduced area, but the resulting liver in tissue sections was fragmented and distorted. Conclusions Our results support the routine use of 16 g rather than 18 g biopsy needles for routine ultrasound-guided medical liver biopsies. A second pass should be considered if the first biopsy core is short, especially for investigation of disease stage.

The tissue microarray data exchange specification: Extending TMA DES to provide flexible scoring and incorporate virtual slides

Background: Tissue MicroArrays (TMAs) are a high throughput technology for rapid analysis of protein expression across hundreds of patient samples. Often, data relating to TMAs is specific to the clinical trial or experiment it is being used for, and not interoperable. The Tissue Microarray Data Exchange Specification (TMA DES) is a set of eXtensible Markup Language (XML)-based protocols for storing and sharing digitized Tissue Microarray data. XML data are enclosed by named tags which serve as identifiers. These tag names can be Common Data Elements (CDEs), which have a predefined meaning or semantics. By using this specification in a laboratory setting with increasing demands for digital pathology integration, we found that the data structure lacked the ability to cope with digital slide imaging in respect to web-enabled digital pathology systems and advanced scoring techniques. Materials and Methods: By employing user centric design, and observing behavior in relation to TMA scoring and associated data, the TMA DES format was extended to accommodate the current limitations. This was done with specific focus on developing a generic tool for handling any given scoring system, and utilizing data for multiple observations and observers. Results: DTDs were created to validate the extensions of the TMA DES protocol, and a test set of data containing scores for 6,708 TMA core images was generated. The XML was then read into an image processing algorithm to utilize the digital pathology data extensions, and scoring results were easily stored alongside the existing multiple pathologist scores. Conclusions: By extending the TMA DES format to include digital pathology data and customizable scoring systems for TMAs, the new system facilitates the collaboration between pathologists and organizations, and can be used in automatic or manual data analysis. This allows complying systems to effectively communicate complex and varied scoring data.

Biopsy proportion of tumour predicts pathological tumour response and benefit from chemotherapy in resectable oesophageal carcinoma: results from the UK MRC OE02 trial

Background Neoadjuvant chemotherapy followed by surgery is the standard of care for UK patients with locally advanced resectable oesophageal carcinoma (OeC). However, not all patients benefit from multimodal treatment and there is a clinical need for biomarkers which can identify chemotherapy responders. This study investigated whether the proportion of tumour cells per tumour area (PoT) measured in the pre-treatment biopsy predicts chemotherapy benefit for OeC patients. Patients and methods PoT was quantified using digitized haematoxylin/eosin stained pre-treatment biopsy slides from 281 OeC patients from the UK MRC OE02 trial (141 treated by surgery alone (S); 140 treated by 5-fluorouracil/cisplatin followed by surgery (CS)). The relationship between PoT and clinicopathological data including tumour regression grade (TRG), overall survival and treatment interaction was investigated. Results PoT was associated with chemotherapy benefit in a non-linear fashion (test for interaction, P=0.006). Only patients with a biopsy PoT between 40% and 70% received a significant survival benefit from neoadjuvant chemotherapy (N=129; HR (95%CI):1.94 (1.39-2.71), unlike those with lower or higher PoT (PoT<40%, N=39, HR:1.25 (0.66-2.35); PoT>70% (N=28, HR:0.65 (0.36-1.18)). High pre-treatment PoT was related to lack of primary tumour regression (TRG 4 or 5), P=0.0402. Conclusions This is the first study to identify in a representative subgroup of OeC patients from a large randomized phase III trial that the proportion of tumour in the pre-chemotherapy biopsy predicts benefit from chemotherapy and may be a clinically useful biomarker for patient treatment stratification.

Abstract 3303: Radioresistance in glioma stem cells driven by Rad51 dependent homologous recombination repair

A cell population with stem cell like characteristics is thought to underlie treatment resistance and local recurrence in glioma. In this work we investigate the role of the DNA repair protein RAD51 in these cells and the impact of inhibiting homologous recombination repair on radiation resistance in vitro and in vivo. We used a model of inducible differentiation of patient derived glioma cells to investigate repair protein levels, repair foci formation and kinetics in clonogenic, stem-like populations and their differentiated counterparts. We examined co-expression of stem cell markers with RAD51 protein at whole population level using western blotting, immunocytochemistry and RT-PCR in cultured cells and immunohistochemistry in tumor material. Single cell expression was analysed using the Fluidigm C1 platform. We examined the effect of two specific inhibitors of RAD51 (B02, RI-1) on the same cell pairs in vitro and used the γH2AX assay to assess differences in repair kinetics. We used subcutaneous models of glioma to evaluate the effect of one of these agents (RI-1) on tumour growth delay with and without fractionated radiation doses in vivo. Primary glioma stem cells expressed high levels of RAD51 protein and exhibited high numbers of foci per nucleus following radiation exposure. Levels of both protein and repair foci fell after cells were transferred to differentiating conditions (serum+BMP4), as did expression of stem cell markers (NESTIN, SOX2). Single cell analysis showed a highly significant association between SOX2 and RAD51 expression (P These data suggest that RAD51 dependent DNA repair by homologous recombination represents a specific target in the stem-like fraction of glioblastoma and inhibiting this pathway is a promising approach to radiosensitisation. Citation Format: Henry King, Helen Payne, Tim Brend, Anjana Patel, Alex Wright, Teklu Englu, Lucy Stead, Heiko Wurdak, Susan C. Short. Radioresistance in glioma stem cells driven by Rad51 dependent homologous recombination repair. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3303. doi:10.1158/1538-7445.AM2015-3303