Validation of epigenetic markers to identify colitis associated cancer: Results of module 1 of the ENDCAP-C study.

BACKGROUND: Chronic inflammation caused by ulcerative colitis (UC) causes a pro-neoplastic drive in the inflamed colon, leading to a markedly greater risk of invasive malignancy compared to the general population. Despite surveillance protocols, 50% of cases proceed to cancer before neoplasia is detected. The Enhanced Neoplasia Detection and Cancer Prevention in Chronic Colitis (ENDCaP-C) trial is an observational multi-centre test accuracy study to ascertain the role of molecular markers in improving the detection of dysplasia. We aimed to validate previously identified biomarkers of neoplasia in a retrospective cohort and create predictive models for later validation in a prospective cohort. METHODS: A retrospective analysis using bisulphite pyrosequencing of an 11 marker panel (SFRP1, SFRP2, SRP4, SRP5, WIF1, TUBB6, SOX7, APC1A, APC2, MINT1, RUNX3) in samples from 35 patients with cancer, 78 with dysplasia and 343 without neoplasia undergoing surveillance for UC associated neoplasia across 6 medical centres. Predictive models for UC associated cancer/dysplasia were created in the setting of neoplastic and non-neoplastic mucosa. FINDINGS: For neoplastic mucosa a five marker panel (SFRP2, SFRP4, WIF1, APC1A, APC2) was accurate in detecting pre-cancerous and invasive neoplasia (AUC = 0.83; 95% CI: 0.79, 0.88), and dysplasia (AUC = 0.88; (0.84, 0.91). For non-neoplastic mucosa a four marker panel (APC1A, SFRP4, SFRP5, SOX7) had modest accuracy (AUC = 0.68; 95% CI: 0.62,0.73) in predicting associated bowel neoplasia through the methylation signature of distant non-neoplastic colonic mucosa. INTERPRETATION: This multiplex methylation marker panel is accurate in the detection of ulcerative colitis associated dysplasia and neoplasia and is currently being validated in a prospective clinical trial. FUNDING: The ENDCAP-C study was funded by the National Institute for Health Research Efficacy and Mechanism Evaluation (EME) Programme (11/100/29).

Discovery and Validation of Methylation Biomarkers for Ulcerative Colitis Associated Neoplasia.

Background and aims: Ulcerative colitis (UC) is associated with a higher background risk of dysplasia and/or neoplasia due to chronic inflammation. There exist few biomarkers for identification of patients with dysplasia, and targeted biopsies in this group of patients are inaccurate in reliably identifying dysplasia. We aimed to examine the epigenome of UC dysplasia and to identify and validate potential biomarkers. Methods: Colonic samples from patients with UC-associated dysplasia or neoplasia underwent epigenome-wide analysis on the Illumina 450K methylation array. Markers were validated by bisulphite pyrosequencing on a secondary validation cohort and accuracy calculated using logistic regression and receiver-operator curves. Results: Twelve samples from 4 patients underwent methylation array analysis and 6 markers (GNG7, VAV3, KIF5C, PIK3R5, TUBB6, and ZNF583) were taken forward for secondary validation on a cohort of 71 colonic biopsy samples consisting of normal uninflamed mucosa from control patients, acute and chronic colitis, "field" mucosa in patients with dysplasia/neoplasia, dysplasia, and neoplasia. Methylation in the beta-tubulin TUBB6 correlated with the presence of dysplasia (P < 0.0001) and accurately discriminated between dysplasia and nondysplastic tissue, even in the apparently normal field mucosa downstream from dysplastic lesions (AUC 0.84, 95% CI 0.81-0.87). Conclusions: Methylation in TUBB6 is a potential biomarker for UC- associated dysplasia. Further validation is needed and is ongoing as part of the ENDCAP-C study.

Mercury Sorption and Desorption on Gold: A Comparative Analysis of Surface Acoustic Wave and Quartz Crystal Microbalance-Based Sensors.

Microelectromechanical sensors based on surface acoustic wave (SAW) and quartz crystal microbalance (QCM) transducers possess substantial potential as online elemental mercury (Hg(0)) vapor detectors in industrial stack effluents. In this study, a comparison of SAW- and QCM-based sensors is performed for the detection of low concentrations of Hg(0) vapor (ranging from 24 to 365 ppbv). Experimental measurements and finite element method (FEM) simulations allow the comparison of these sensors with regard to their sensitivity, sorption and desorption characteristics, and response time following Hg(0) vapor exposure at various operating temperatures ranging from 35 to 75 °C. Both of the sensors were fabricated on quartz substrates (ST and AT cut quartz for SAW and QCM devices, respectively) and employed thin gold (Au) layers as the electrodes. The SAW-based sensor exhibited up to ∼111 and ∼39 times higher response magnitudes than did the QCM-based sensor at 35 and 55 °C, respectively, when exposed to Hg(0) vapor concentrations ranging from 24 to 365 ppbv. The Hg(0) sorption and desorption calibration curves of both sensors were found to fit well with the Langmuir extension isotherm at different operating temperatures. Furthermore, the Hg(0) sorption and desorption rate demonstrated by the SAW-based sensor was found to decrease as the operating temperature increased, while the opposite trend was observed for the QCM-based sensor. However, the SAW-based sensor reached the maximum Hg(0) sorption rate faster than the QCM-based sensor regardless of operating temperature, whereas both sensors showed similar response times (t90) at various temperatures. Additionally, the sorption rate data was utilized in this study in order to obtain a faster response time from the sensor upon exposure to Hg(0) vapor. Furthermore, comparative analysis of the developed sensors' selectivity showed that the SAW-based sensor had a higher overall selectivity (90%) than did the QCM counterpart (84%) while Hg(0) vapor was measured in the presence of ammonia (NH3), humidity, and a number of volatile organic compounds at the chosen operating temperature of 55 °C.

Selective detection of elemental mercury vapor using a surface acoustic wave (SAW) sensor.

The detection of elemental mercury (Hg(0)) within industrial processes is extremely important as it is the first major step in ensuring the efficient operation of implemented mercury removal technologies. In this study, a 131 MHz surface acoustic wave (SAW) delay line sensor with gold electrodes was tested towards Hg(0) vapor (24 to 365 ppbv) with/without the presence of ammonia (NH3) and humidity (H2O), as well as volatile organic compounds (VOCs) such as acetaldehyde (MeCHO), ethylmercaptan (EM), dimethyl disulfide (DMDS) and methyl ethyl ketone (MEK), which are all common interfering gas species that co-exist in many industrial applications requiring mercury monitoring. The developed sensor exhibited a detection limit of 0.7 ppbv and 4.85 ppbv at 35 and 55 °C, respectively. Furthermore, a repeatability of 97% and selectivity of 92% in the presence of contaminant gases was exhibited by the sensor at the chosen operating temperature of 55 °C. The response magnitude of the developed SAW sensor towards different concentrations of Hg(0) vapor fitted well with the Langmuir extension isotherm (otherwise known as loading ratio correlation (LRC)) which is in agreement with our basic finite element method (FEM) work where an LRC isotherm was observed for a simplified model of the SAW sensor responding to different Hg contents deposited on the Au based electrodes. Overall, the results indicate that the developed SAW sensor can be a potential solution for online selective detection of low concentrations of Hg(0) vapor found in industrial stack effluents.

Impact of tissue processing, archiving and enrichment techniques on DNA methylation yield in rectal carcinoma.

BACKGROUND: Formalin fixation, duration of tissue storage and tissue enrichment techniques can affect DNA methylation yield but these effects have not been quantitatively measured. The aim is to investigate the relative impact of these conditions on DNA methylation in rectal cancer. METHODS: 10 rectal cancers with matched undissected fresh frozen tissues, laser capture microdissected (LCM) formalin-fixed paraffin-embedded (FFPE) tissues, manual macrodissected FFPE tissues, adjacent normal mucosa and stromal tissues were analysed for APC and LINE-1 methylation using bisulphite pyrosequencing. RESULTS: FFPE cancer tissues, which had been stored for at least 4 years showed similar APC and LINE-1 methylation changes to matched fresh frozen cancer tissues. Laser capture microdissection did not increase the degree of methylation detected compared to manual macrodissection. Analysis of stromal tissues showed that they had undergone significant methylation changes compared to adjacent macroscopically normal mucosa, but not to the same extent as cancer tissues. CONCLUSION: Reliable DNA methylation results can be obtained from FFPE rectal cancer tissues, which have been in long-term storage. Because only minor differences in methylation between macrodissected and LCM cancer tissues were found, our results do not support the routine use of LCM to enrich for cancer cells for DNA methylation studies.

Loss of expression and promoter methylation of SLIT2 are associated with sessile serrated adenoma formation.

Serrated adenomas form a distinct subtype of colorectal pre-malignant lesions that may progress to malignancy along a different molecular pathway than the conventional adenoma-carcinoma pathway. Previous studies have hypothesised that BRAF mutation and promoter hypermethylation plays a role, but the evidence for this is not robust. We aimed to carry out a whole-genome loss of heterozygosity analysis, followed by targeted promoter methylation and expression analysis to identify potential pathways in serrated adenomas. An initial panel of 9 sessile serrated adenomas (SSA) and one TSA were analysed using Illumina Goldengate HumanLinkage panel arrays to ascertain regions of loss of heterozygosity. This was verified via molecular inversion probe analysis and microsatellite analysis of a further 32 samples. Methylation analysis of genes of interest was carried out using methylation specific PCR (verified by pyrosequencing) and immunohistochemistry used to correlate loss of expression of genes of interest. All experiments used adenoma samples and normal tissue samples as control. SSA samples were found on whole-genome analysis to have consistent loss of heterozygosity at 4p15.1-4p15.31, which was not found in the sole TSA, adenomas, or normal tissues. Genes of interest in this region were PDCH7 and SLIT2, and combined MSP/IHC analysis of these genes revealed significant loss of SLIT2 expression associated with promoter methylation of SLIT2. Loss of expression of SLIT2 by promoter hypermethylation and loss of heterozygosity events is significantly associated with serrated adenoma development, and SLIT2 may represent a epimutated tumour suppressor gene according to the Knudson "two hit" hypothesis.

The Wnt antagonist sFRP1 in colorectal tumorigenesis.

Regions of the short arm of chromosome 8 are deleted frequently in a range of solid tumors, indicating that tumor suppressor genes reside at these loci. In this study, we have examined the properties of the Wnt signaling antagonist secreted frizzled-related protein (sFRP) 1 as a candidate for this role at c8p11.2. An initial survey of 10 colorectal tumors, selected by the presence of isolated short deletions of the 8p11.2 region, identified three chain-terminating mutations, all within the first exon, which encodes the cysteine-rich domain. None of these tumors exhibited microsatellite instability, indicating intact mismatch repair gene function. The preserved sFRP1 alleles in the remaining seven tumors each contained a polymorphic three-base insertion in the signal sequence, but in a broader study, no association was found between this and the development of colorectal cancer. Epigenetic inhibition of sFRP1 transcription was investigated, and increased methylation of the promotor region was demonstrated in an additional cohort of 51 locally advanced colorectal cancers. Hypermethylation was identified in 40 of 49 (82%) cancers and in only 11 of 36 (30%) matched normal mucosal samples (P < 0.001). Semiquantitative analysis, by real-time PCR, of mRNA expression in 37 of the same cohort of 51 cancers revealed that sFRP1 mRNA expression was down-regulated in 28 (76%) cases compared with matched normal large bowel mucosa. The 3' end of the sFRP1 mRNA also was found to be alternatively spliced, compared with the prototype liver and lung forms, in the colon and a number of other tissues, yielding an extended COOH terminus, which may influence its activity in a tissue-specific manner. The inactivation and down-regulation of sFRP1 observed are consistent with it acting as a tumor suppressor gene in colorectal carcinogenesis. Because beta-catenin is constitutively active in the majority of colorectal tumors, it is unlikely that sFRP1 can act in the canonical Wnt response pathway. Therefore, we propose that the reduced activity or absence of sFRP1 allows the transduction of noncanonical Wnt signals, which contribute to tumor progression.