Ronan T. Gray

QuPath: Open source software for digital pathology image analysis

QuPath is new bioimage analysis software designed to meet the growing need for a user-friendly, extensible, open-source solution for digital pathology and whole slide image analysis. In addition to offering a comprehensive panel of tumor identification and high-throughput biomarker evaluation tools, QuPath provides researchers with powerful batch-processing and scripting functionality, and an extensible platform with which to develop and share new algorithms to analyze complex tissue images. Furthermore, QuPath’s flexible design makes it suitable for a wide range of additional image analysis applications across biomedical research.

Back to the future: routine morphological assessment of the tumour microenvironment is prognostic in stage II/III colon cancer in a large population-based study

Both morphological and molecular approaches have highlighted the biological and prognostic importance of the tumour microenvironment in colorectal cancer (CRC). Despite this, microscopic assessment of the tumour microenvironment has not been adopted into routine practice. The study aim was to identify those tumour microenvironmental features that are most likely to provide prognostic information and be feasible to use in routine pathology reporting practice.

Evaluation of PTGS2 Expression, PIK3CA Mutation, Aspirin Use and Colon Cancer Survival in a Population-Based Cohort Study

Objectives:The association between aspirin use and improved survival after colorectal cancer diagnosis may be more pronounced in tumors that have PIK3CA mutations or high PTGS2 expression. However, the evidence of a difference in association by biomarker status lacks consistency. In this population-based colon cancer cohort study the interaction between these biomarkers, aspirin use, and survival was assessed.Methods:The cohort consisted of 740 stage II and III colon cancer patients diagnosed between 2004 and 2008. Aspirin use was determined through clinical note review. Tissue blocks were retrieved to determine immunohistochemical assessment of PTGS2 expression and the presence of PIK3CA mutations. Cox proportional hazards models were used to calculate hazard ratios (HR) and 95% confidence intervals (CI) for colorectal cancer-specific and overall survival.Results:In this cohort aspirin use was associated with a 31% improvement in cancer-specific survival compared to non-use (adjusted HR=0.69, 95% CI 0.47–0.98). This effect was more pronounced in tumors with high PTGS2 expression (PTGS2-high adjusted HR=0.55, 95% CI 0.32–0.96) compared to those with low PTGS2 expression (PTGS2-low adjusted HR=1.19, 95% CI 0.68–2.07, P for interaction=0.09). The aspirin by PTGS2 interaction was significant for overall survival (PTGS2-high adjusted HR=0.64, 95% CI 0.42–0.98 vs. PTGS2-low adjusted HR=1.28, 95% CI 0.80–2.03, P for interaction=0.04). However, no interaction was observed between aspirin use and PIK3CA mutation status for colorectal cancer-specific or overall survival.Conclusions:Aspirin use was associated with improved survival outcomes in this population-based cohort of colon cancer patients. This association differed according to PTGS2 expression but not PIK3CA mutation status. Limiting adjuvant aspirin trials to PIK3CA-mutant colorectal cancer may be too restrictive.

Stratified analysis reveals chemokine-like factor (CKLF) as a potential prognostic marker in the MSI-immune consensus molecular subtype CMS1 of colorectal cancer

The Colorectal Cancer (CRC) Subtyping Consortium (CRCSC) recently published four consensus molecular subtypes (CMSs) representing the underlying biology in CRC. The Microsatellite Instable (MSI) immune group, CMS1, has a favorable prognosis in early stage disease, but paradoxically has the worst prognosis following relapse, suggesting the presence of factors enabling neoplastic cells to circumvent this immune response. To identify the genes influencing subsequent poor prognosis in CMS1, we analyzed this subtype, centered on risk of relapse. In a cohort of early stage colon cancer (n=460), we examined, in silico, changes in gene expression within the CMS1 subtype and demonstrated for the first time the favorable prognostic value of chemokine-like factor (CKLF) gene expression in the adjuvant disease setting [HR=0.18, CI=0.04-0.89]. In addition, using transcription profiles originating from cell sorted CRC tumors, we delineated the source of CKLF transcription within the colorectal tumor microenvironment to the leukocyte component of these tumors. Further to this, we confirmed that CKLF gene expression is confined to distinct immune subsets in whole blood samples and primary cell lines, highlighting CKLF as a potential immune cell-derived factor promoting tumor immune-surveillance of nascent neoplastic cells, particularly in CMS1 tumors. Building on the recently reported CRCSC data, we provide compelling evidence that leukocyte-infiltrate derived CKLF expression is a candidate biomarker of favorable prognosis, specifically in MSI-immune stage II/III disease.

Bcl-xL as a poor prognostic biomarker and predictor of response to adjuvant chemotherapy specifically in BRAF-mutant stage II and III colon cancer

Purpose BRAF mutation occurs in 8–15% of colon cancers (CC), and is associated with poor prognosis in metastatic disease. Compared to wild-type BRAF (BRAFWT) disease, stage II/III CC patients with BRAF mutant (BRAFMT) tumors have shorter overall survival after relapse; however, time-to-relapse is not significantly different. The aim of this investigation was to identify, and validate, novel predictors of relapse of stage II/III BRAFMT CC. Experimental design We used gene expression data from a cohort of 460 patients (GSE39582) to perform a supervised classification analysis based on risk-of-relapse within BRAFMT stage II/III CC, to identify transcriptomic biomarkers associated with prognosis within this genotype. These findings were validated using immunohistochemistry in an independent population-based cohort of Stage II/III CC (n = 691), applying Cox proportional hazards analysis to determine associations with survival. Results High gene expression levels of Bcl-xL, a key regulator of apoptosis, were associated with increased risk of relapse, specifically in BRAFMT tumors (HR = 8.3, 95% CI 1.7–41.7), but not KRASMT/BRAFWT or KRASWT/BRAFWT tumors. High Bcl-xL protein expression in BRAFMT, untreated, stage II/III CC was confirmed to be associated with an increased risk of death in an independent cohort (HR = 12.13, 95% CI 2.49–59.13). Additionally, BRAFMT tumors with high levels of Bcl-xL protein expression appeared to benefit from adjuvant chemotherapy (P for interaction = 0.006), indicating the potential predictive value of Bcl-xL expression in this setting. Conclusions These findings provide evidence that Bcl-xL gene and/or protein expression identifies a poor prognostic subgroup of BRAFMT stage II/III CC patients, who may benefit from adjuvant chemotherapy.

Validation of the systematic scoring of immunohistochemically stained tumour tissue microarrays using QuPath digital image analysis

Output from biomarker studies involving immunohistochemistry applied to tissue microarrays (TMA) is limited by the lack of an efficient and reproducible scoring methodology. In this study, we examine the functionality and reproducibility of biomarker scoring using the new, open‐source, digital image analysis software, QuPath.

Blood Biomarkers for Early Detection of Oesophageal Cancer: A Systematic Review

Background Oesophageal cancer prognosis remains poor owing to the inability to detect the disease at an early stage. Nontissue (serum, urinary or salivary) biomarkers potentially offer less invasive methods to aid early detection of oesophageal cancer. We aimed to systematically review studies assessing the relationship between nontissue biomarkers and subsequent development of oesophageal cancer. Methods Using terms for biomarkers and oesophageal cancer, Medline, EMBASE and Web of Science were systematically searched for longitudinal studies, published until April 2016, which assessed the association between nontissue biomarkers and subsequent oesophageal cancer risk. Random effects meta-analyses were used to calculate pooled relative risk (RR) and 95% confidence intervals (CIs), where possible. Results A total of 39 studies were included. Lower serum pepsinogen I concentrations were associated with an increased risk of oesophageal squamous cell carcinoma (n=3 studies, pooled RR=2.20, 95% CI: 1.31–3.70). However, the association for the pepsinogen I : II ratio was not statistically significant (n=3 studies, pooled RR=2.22, 95% CI: 0.77–6.40), with a large degree of heterogeneity observed (I2=68.0%). Higher serum glucose concentrations were associated with a modestly increased risk of total oesophageal cancer (n=3 studies, pooled RR=1.27, 95% CI: 1.02–1.57). No association was observed for total cholesterol and total oesophageal cancer risk (n=3 studies, pooled RR=0.95, 95% CI: 0.58–1.54). Very few studies have assessed other biomarkers for meta-analyses. Conclusion Serum pepsinogen I concentrations could aid early detection of oesophageal squamous cell carcinoma. More prospective studies are needed to determine the use of other nontissue biomarkers in the early detection of oesophageal cancer.

Socio-economic status and lifestyle factors are associated with achalasia risk: A population-based case-control study

AIM To evaluate the association between various lifestyle factors and achalasia risk. METHODS A population-based case-control study was conducted in Northern Ireland, including n = 151 achalasia cases and n = 117 age- and sex-matched controls. Lifestyle factors were assessed via a face-to-face structured interview. The association between achalasia and lifestyle factors was assessed by unconditional logistic regression, to produce odds ratios (OR) and 95% confidence interval (CI). RESULTS Individuals who had low-class occupations were at the highest risk of achalasia (OR = 1.88, 95%CI: 1.02-3.45), inferring that high-class occupation holders have a reduced risk of achalasia. A history of foreign travel, a lifestyle factor linked to upper socio-economic class, was also associated with a reduced risk of achalasia (OR = 0.59, 95%CI: 0.35-0.99). Smoking and alcohol consumption carried significantly reduced risks of achalasia, even after adjustment for socio-economic status. The presence of pets in the house was associated with a two-fold increased risk of achalasia (OR = 2.00, 95%CI: 1.17-3.42). No childhood household factors were associated with achalasia risk. CONCLUSION Achalasia is a disease of inequality, and individuals from low socio-economic backgrounds are at highest risk. This does not appear to be due to corresponding alcohol and smoking behaviours. An observed positive association between pet ownership and achalasia risk suggests an interaction between endotoxin and viral infection exposure in achalasia aetiology.

The role of biodegradable stents in the management of benign and malignant oesophageal strictures: A cohort study

BACKGROUND Oesophageal strictures can be caused by benign or malignant processes. Up to 10% of patients with a benign stricture are refractory to pneumatic dilatation and may benefit from biodegradable stent (BD) insertion. Biodegradable stents also have a role in malignant oesophageal strictures to facilitate enteral nutrition while staging or neo-adjuvant treatment is completed. The aim of this study was to review the safety and efficacy of BD stents in the management of benign or malignant oesophageal strictures. METHODS A single centre retrospective cohort study was performed. Dysphagia was graded before and after stenting using a validated score. All patients were followed up for at least 30 days and all adverse events were recorded. RESULTS Twenty eight stents were inserted in 20 patients; 11 for malignant and 17 for benign disease. One further attempted stenting was impossible due to a high benign stricture. There were no perforations and the 30-day mortality rate was zero. Mean dysphagia scores improved from 2.65 to 1.00 (p value <0.001) in benign disease and from 3.27 to 1.36 (p value <0.001) in patients with malignant disease. Surgical resection was not compromised following stent insertion in the malignant group. CONCLUSIONS Biodegradable stent insertion is a safe and efficacious adjunct in the treatment of benign and malignant oesophageal strictures. In malignant disease, BD stent insertion can maintain enteral nutrition while staging or neo-adjuvant therapy is completed without adversely impacting on surgical resection.

PWE-181 Socio-economic status and lifestyle factors are associated with achalasia risk: a population-based case-control study

Introduction Achalasia is a neurodegenerative motility disorder of the oesophagus that results in loss of normal lower oesophageal sphincter function. The aetiology of achalasia is very poorly understood. In particular, no lifestyle risk factors have been investigated in relation to achalasia development. The aim of this study was to evaluate the association between the various lifestyle factors and achalasia risk. Method A population-based case-control study was conducted in Northern Ireland, including n = 151 achalasia cases and n = 117 age- and sex-matched controls. Lifestyle factors were assessed via a face-to-face structured interview. The association between achalasia and lifestyle factors was assessed by unconditional logistic regression, to produce odds ratios (OR) and associated 95% confidence intervals (CI), before and after adjustment for confounders. Results Individuals who had low-class occupations were at the highest risk of achalasia (OR 1.88 (95% CI: 1.02–3.45), inferring that high class occupation holders have a reduced risk of achalasia. A history of foreign travel, a lifestyle factor linked with upper socio-economic class, was also associated with a reduced risk of achalasia (OR 0.59; 95% CI 0.35–0.99). In contrast, smoking and alcohol consumption – behaviours normally associated with lower socio-economic groups – carried significant reduced risks of achalasia, even after adjustment for socio-economic status. The presence of pets in the house was associated with a two-fold increased risk of achalasia (OR 2.00; 95% CI 1.17–3.42). Conclusion Achalasia is a disease of inequality, and individuals from low socio-economic backgrounds are at highest risk. This does not appear to be due to corresponding alcohol and smoking behaviours. An observed positive association between pet ownership and achalasia risk may lend support to a role for allergen/infection exposure in achalasia aetiology. Disclosure of interest None Declared.