The molecular landscape of well differentiated retroperitoneal liposarcoma.

Well differentiated liposarcoma (WD-LPS) is a relatively rare tumour, with fewer than 50 cases occurring per year in the UK. These tumours are both chemotherapy- and radiotherapy-resistant and present a significant treatment challenge requiring radical surgery. Little is known of the molecular landscape of these tumours and no current targets for molecular therapy exist. We aimed to carry out a comprehensive molecular characterisation of WD-LPS via whole genome sequencing, RNA sequencing, and methylation array analysis. A recurrent mutation within exon 1 of FOXD4L3 was observed (chr9:70,918,189A>T; c.322A>T; p.Lys108Ter). Recurrent mutations were also observed in Wnt signalling, immunity, DNA repair, and hypoxia-associated genes. Recurrent amplification of HGMA2 was observed, although this was in fact part of a general amplification of the region around this gene. Recurrent gene fusions in HGMA2, SDHA, TSPAN31, and MDM2 were also observed as well as consistent rearrangements between chromosome 6 and chromosome 12. Our study has demonstrated a recurrent mutation within FOXD4L3, which shows evidence of interaction with the PAX pathway to promote tumourigenesis. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.

Whole Genome Methylation Analysis of Nondysplastic Barrett Esophagus that Progresses to Invasive Cancer.

OBJECTIVE: To investigate differences in methylation between patients with nondysplastic Barrett esophagus who progress to invasive adenocarcinoma and those who do not. BACKGROUND: Identifying patients with nondysplastic Barrett esophagus who progress to invasive adenocarcinoma remains a challenge. Previous studies have demonstrated the potential utility of epigenetic markers for identifying this group. METHODS: A whole genome methylation interrogation using the Illumina HumanMethylation 450 array of patients with nondysplastic Barrett esophagus who either develop adenocarcinoma or remain static, with validation of findings by bisulfite pyrosequencing. RESULTS: In all, 12 patients with "progressive" versus 12 with "nonprogressive" nondysplastic Barrett esophagus were analyzed via methylation array. Forty-four methylation markers were identified that may be able to discriminate between nondysplastic Barrett esophagus that either progress to adenocarcinoma or remain static. Hypomethylation of the recently identified tumor suppressor OR3A4 (probe cg09890332) validated in a separate cohort of samples (median methylation in progressors 67.8% vs 96.7% in nonprogressors; P = 0.0001, z = 3.85, Wilcoxon rank-sum test) and was associated with the progression to adenocarcinoma. There were no differences in copy number between the 2 groups, but a global trend towards hypomethylation in the progressor group was observed. CONCLUSION: Hypomethylation of OR3A4 has the ability to risk stratify the patient with nondysplastic Barrett esophagus and may form the basis of a future surveillance program.

Establishing a COVID-secure site for elective surgery during the COVID pandemic: An observational study.

INTRODUCTION: Maintaining timely and safe delivery of major elective surgery during the COVID-19 pandemic is essential to manage cancer and time-critical surgical conditions. Our NHS Trust established a COVID-secure elective site with a level 2 Post Anaesthetic Care Unit (PACU) facility. Patients requiring level 3 Intensive Care Unit admission were transferred to a non-COVID-secure site. We investigated the relationship between perioperative anaesthetic care and outcomes. MATERIALS AND METHODS: All consecutive patients undergoing major surgery at the COVID-secure site between June and November 2020 were included. Patient demographics, operative interventions and 30-day outcomes were recorded. Multivariate logistic regression was used to determine the odds ratio of outcomes according to PACU length of stay and the use of spinal or epidural anaesthesia, with age, sex, malignancy status and American Society of Anesthesiologists grade as independent co-variables. RESULTS: There were 280 patients. PACU length of stay >23h was associated with increased 30-day complications. Epidural anaesthesia was associated with PACU length of stay >23h, increased total length of stay, increase hospital transfer and 30-day complications. Two patients acquired nosocomial COVID-19 following hospital transfer. DISCUSSION: Establishing a separate COVID-secure site has facilitated delivery of major elective surgery during the COVID-19 pandemic. Choice of perioperative anaesthesia and utilisation of PACU appear likely to affect the risk of adverse outcomes.

Clinical-grade whole-genome sequencing and 3' transcriptome analysis of colorectal cancer patients.

BACKGROUND: Clinical-grade whole-genome sequencing (cWGS) has the potential to become the standard of care within the clinic because of its breadth of coverage and lack of bias towards certain regions of the genome. Colorectal cancer presents a difficult treatment paradigm, with over 40% of patients presenting at diagnosis with metastatic disease. We hypothesised that cWGS coupled with 3' transcriptome analysis would give new insights into colorectal cancer. METHODS: Patients underwent PCR-free whole-genome sequencing and alignment and variant calling using a standardised pipeline to output SNVs, indels, SVs and CNAs. Additional insights into the mutational signatures and tumour biology were gained by the use of 3' RNA-seq. RESULTS: Fifty-four patients were studied in total. Driver analysis identified the Wnt pathway gene APC as the only consistently mutated driver in colorectal cancer. Alterations in the PI3K/mTOR pathways were seen as previously observed in CRC. Multiple private CNAs, SVs and gene fusions were unique to individual tumours. Approximately 30% of patients had a tumour mutational burden of > 10 mutations/Mb of DNA, suggesting suitability for immunotherapy. CONCLUSIONS: Clinical whole-genome sequencing offers a potential avenue for the identification of private genomic variation that may confer sensitivity to targeted agents and offer patients new options for targeted therapies.

Evaluation of a bundle of care to reduce incisional surgical site infection after gastrointestinal surgery.

BACKGROUND: Surgical site infection (SSI) is associated with morbidity, mortality and increased care costs; many SSIs are considered preventable. The aim of the present study was to test implementation of a pragmatic, evidence-based bundle designed to reduce incisional SSI after emergency laparotomy and elective major lower gastrointestinal surgery. METHOD: This was a prospective before-and-after study. Data were collected before the intervention and for two separate subsequent time periods. An evidence-based bundle of care (BOC) was implemented; the primary outcome measure was incisional SSI at 30 days. The secondary outcome measure was 30-day unplanned readmissions. The initial post-intervention group, Group 2, assessed a variable number of potential impacting factors; however, due to funding and staffing levels the second post-bundle group, Group 3, focused on the core aspects of the BOC and rates of incisional SSI and readmission. RESULTS: In total, 99 patients were included in the 'before' group; and 71 in Group 2 and 92 in Group 3, the post-intervention groups. The incisional SSI rate was 29.3% (29/99) before and 28.2% (20/71) in Group 2 (P=0.873) and 21.7% (20/92) in Group 3 (P=0.234) after the intervention. After adjustment for confounders, the care bundle was associated with a non-significant reduction in SSI (Group 2: odds ratio [OR] = 0.93, 95% confidence interval [CI] = 0.45-1.93, P=0.0843). However, it was associated with significantly reduced readmissions 18.1% (18/99) before versus 5.6% (4/71) in Group 2 (OR = 0.236, 95% CI = 0.077-0.72, P=0.012) and 8.7% (8/92) in Group 3 (OR = 0.38, 95% CI = 0.16-0.9, P=0.029). Comparing the pre-bundle group to the post-bundle groups, there was an overall significant reduction in readmissions (P=0.003). This implies a number needed to treat of 8-11 patients to prevent one readmission. Adherence to antibiotic prophylaxis with the Trust guidelines increased from 91% to 99% (1 vs. 2, P=0.047). CONCLUSION: Introduction of the bundle was associated with a reduction in the observed rate of incisional SSI from 29.3% to 21.7%; significantly fewer patients required unplanned readmission. Use of the bundle was associated with significantly improved compliance with appropriate antimicrobial prophylaxis.

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.

Methylation changes in the TFAP2E promoter region are associated with BRAF mutation and poorer overall & disease free survival in colorectal cancer.

INTRODUCTION: BRAF mutant colorectal cancer carries a poor prognosis which is thought to be related to poor response to conventional chemotherapy. BRAF mutation is associated with the serrated tumour phenotype. We hypothesised that one of the mechanisms by which BRAF mutant colorectal cancer demonstrate poor outcomes with chemotherapy is abnormal gene methylation. METHODS: The Cancer Genome Atlas (TCGA) methylation data was analysed using a linear regression model with BRAF mutation as an independent variable. Expression datasets were also obtained to correlate functional changes. Top differentially methylated probes were taken forward for validation by methylation pyrosequencing. These probes were analysed on a cohort of patients enriched for BRAF mutations taken from the VICTOR and QUASAR2 studies. RESULTS: In an analysis of 91 tumours (9 BRAF mutant, 82 wild type), the Illumina probe cg11835197 was the probe identified as top differentially methylated (p = 2.56×10-7, Bayes Factor (BF) =6.54). This probe covered a region -413bp from the promoter region of TFAP2E. We found a complex pattern of CpG specific methylation of this region which was associated with both overall (p=0.044) and disease free (p=0.046) survival. DISCUSSION: BRAF mutant tumours may attain part of their chemoresistance from abnormal TFAP2E methylation, which has not previously been described.

A systematic review of transarterial embolization versus emergency surgery in treatment of major nonvariceal upper gastrointestinal bleeding.

BACKGROUND: Emergency surgery or transarterial embolization (TAE) are options for the treatment of recurrent or refractory nonvariceal upper gastrointestinal bleeding. Surgery has the disadvantage of high rates of postoperative morbidity and mortality. Embolization has become more available and has the advantage of avoiding laparotomy in this often unfit and elderly population. OBJECTIVE: To carry out a systematic review and meta-analysis of all studies that have directly compared TAE with emergency surgery in the treatment of major upper gastrointestinal bleeding that has failed therapeutic upper gastrointestinal endoscopy. METHODS: A literature search of Ovid MEDLINE, Embase, and Google Scholar was performed. The primary outcomes were all-cause mortality and rates of rebleeding. The secondary outcomes were length of stay and postoperative complications. RESULTS: A total of nine studies with 711 patients (347 who had embolization and 364 who had surgery) were analyzed. Patients in the TAE group were more likely to have ischemic heart disease (odds ratio [OR] =1.99; 95% confidence interval [CI]: 1.33, 2.98; P=0.0008; I (2)=67% [random effects model]) and be coagulopathic (pooled OR =2.23; 95% CI: 1.29, 3.87; P=0.004; I (2)=33% [fixed effects model]). Compared with TAE, surgery was associated with a lower risk of rebleeding (OR =0.41; 95% CI: 0.22, 0.77; P<0.0001; I (2)=55% [random effects]). There was no difference in mortality (OR =0.70; 95% CI: 0.48, 1.02; P=0.06; I (2)=44% [fixed effects]) between TAE and surgery. CONCLUSION: When compared with surgery, TAE had a significant increased risk of rebleeding rates after TAE; however, there were no differences in mortality rates. These findings are subject to multiple sources of bias due to poor quality studies. These findings support the need for a well-designed clinical trial to ascertain which technique is superior.