Academic literature on the topic 'DNA methylation; oesophageal cancer; Barrett's oesophagus'

ObjectiveTo identify and characterise DNA methylation subtypes in oesophageal adenocarcinoma (EAC) and its precursor Barrett’s oesophagus (BE).DesignWe performed genome-wide DNA methylation profiling on samples of non-dysplastic BE from cancer-free patients (n=59), EAC (n=23), normal squamous oesophagus (n=33) and normal fundus (n=9), and identified methylation subtypes using a recursively partitioned mixture model. We assessed genomic alterations for 9 BE and 22 EAC samples with massively parallel sequencing of 243 EAC-associated genes, and we conducted integrative analyses with transcriptome data to identify epigenetically repressed genes. We also carried out in vitro experiments treating EAC cell lines with 5-Aza-2'-Deoxycytidine (5-Aza-dC), short hairpin RNA knockdown and anticancer therapies.ResultsWe identified and validated four methylation subtypes of EAC and BE. The high methylator subtype (HM) of EAC had the greatest number of activating events in ERBB2 (p<0.05, Student’s t-test) and the highest global mutation load (p<0.05, Fisher’s exact test). PTPN13 was silenced by aberrant methylation in the HM subtype preferentially and in 57% of EACs overall. In EAC cell lines, 5-Aza-dC treatment restored PTPN13 expression and significantly decreased its promoter methylation in HM cell lines (p<0.05, Welch’s t-test). Inhibition of PTPN13 expression in the SK-GT-4 EAC cell line promoted proliferation, colony formation and migration, and increased phosphorylation in ERBB2/EGFR/Src kinase pathways. Finally, EAC cell lines showed subtype-specific responses to topotecan, SN-38 and palbociclib treatment.ConclusionsWe identified and characterised methylator subtypes in BE and EAC. We further demonstrated the biological and clinical relevance of EAC methylator subtypes, which may ultimately help guide clinical management of patients with EAC.

580 Background: Methylated BCAT1 and IKZF1 are useful circulating tumor DNA (ctDNA) biomarkers for detection and following the course of colorectal cancer (CRC). This study aimed to determine the specificity of methylated BCAT1/ IKZF1 for CRC detection by assaying specimens from patients with other adenocarcinomas. Methods: Blood was collected from patients with invasive adenocarcinoma of the prostate (n = 32), breast (16), oesophagus (15) or colon/rectum (212), prior to any treatment or resection, and from 245 clinically assessed controls with no known prior or current adenocarcinoma. Biopsies were collected from cancer tissue and adjacent non-neoplastic tissue either prior to treatment or at surgery from 9 prostate, 26 breast, 6 oesophagus, 15 CRC cases. All specimens were assayed for methylated BCAT1 and IKZF1 DNA. Calculation of positivity rates: tissue, the proportion of tissue cases with ≥ 5% methylation; blood, the proportion of cases with any detectable signal of either marker. Results: ctDNA positivity rates were significantly higher in CRC (126/212, 59.4%, 95% CI: 52.5 - 66.1) and oesophageal cancer (6/16, 33.3%, 11.0 - 58.7) cases only compared to controls (16/245, 6.5%, 3.8 - 10.4; p < 0.01). ctDNA was more likely to be positive in late stage cancers, although only significant for CRC, Table. Cancer tissue positivity rates were: CRC, 15/15, 100% (96.4 - 100); oesophageal, 5/6, 83.3% (35.9 - 99.6); prostate, 4/9, 44.4% (13.7 - 78.8); breast, 5/26, 19.2% (6.6 - 39.4). All cancer tissues had significantly higher methylation levels than the adjacent tissue (Chi2 test, p >0.05). Conclusions: Only colorectal and oesophageal cancer patients had significantly higher ctDNA positivity rates (using methylated BCAT1/IKZF1) compared to controls. This was also reflected in a higher proportion of cases showing methylation in the cancer tissue. The methylated BCAT1/IKZF1 blood test should be investigated further as a screening and surveillance tool for oesophageal cancer. [Table: see text]

Carcinoma of the oesophagus including carcinoma of gastro-oesophageal junction are rapidly increasing in incidence. During recent years there have been changes in the knowledge surrounding biology of the disease progression. Identification of dysplasia in mucosal biopsies is the most reliable pathologic indicator of an increased risk of development of squamous cell carcinoma and passes through the sequence of chronic esophagitis, low-grade and high-grade dysplasia and invasive carcinoma. Although Barrett's esophagus is a precursor to esophageal adenocarcinoma and have a well described sequence of carcinogenesis: the Barrett's metaplasia-dysplasia-adenocarcinoma sequence, not all patients with this disorder require intensive surveillance. The natural history of dysplasia is poorly understood, particularly in low-risk regions, and prospective follow-up studies are needed. Adjunctive methods to improve reproducibility, such as immunostaining for alpha-methylacyl-coenzyme A racemase (AMACR), show promise, but require confirmation in larger studies. In addition, several controversial methods such as detection of p16, p53, and DNA content abnormalities may help identify patients at particularly high risk for progression to cancer, but these techniques are not yet widely available for routine clinical application. More studies are needed to define other early nonmorphologic biomarkers for risk of squamous cell carcinoma. Recent evidence regarding the importance of several histopathologically derived prognostic factors, such as circumferential resection margin status and lymph node metastases are evaluated, including lymph node micrometastases and the sentinel node concept. With the rising use of multimodal treatments for oesophageal cancer it is important that the response of the tumour to this therapy can be carefully documented by histopathology.

The mechanism by which reactive oxygen species (ROS) are produced by tumour cells remained incompletely understood until the discovery over the last 15 years of the family of NADPH oxidases (NOXs 1–5 and dual oxidases DUOX1/2) which are structural homologues of gp91phox, the major membrane-bound component of the respiratory burst oxidase of leucocytes. Knowledge of the roles of the NOX isoforms in cancer is rapidly expanding. Recent evidence suggests that both NOX1 and DUOX2 species produce ROS in the gastrointestinal tract as a result of chronic inflammatory stress; cytokine induction (by interferon-γ, tumour necrosis factor α, and interleukins IL-4 and IL-13) of NOX1 and DUOX2 may contribute to the development of colorectal and pancreatic carcinomas in patients with inflammatory bowel disease and chronic pancreatitis, respectively. NOX4 expression is increased in pre-malignant fibrotic states which may lead to carcinomas of the lung and liver. NOX5 is highly expressed in malignant melanomas, prostate cancer and Barrett's oesophagus-associated adenocarcinomas, and in the last it is related to chronic gastro-oesophageal reflux and inflammation. Over-expression of functional NOX proteins in many tissues helps to explain tissue injury and DNA damage from ROS that accompany pre-malignant conditions, as well as elucidating the potential mechanisms of NOX-related damage that contribute to both the initiation and the progression of a wide range of solid and haematopoietic malignancies.

Abstract Background The incidence of oesophageal adenocarcinoma (OAC) increases dramatically with patient age but only a small proportion of patients with diagnosed Barrett’s oesophagus (BO), the precursor to OAC, will develop dysplasia and/or cancer. Beyond chronological age, biomarkers of progression that capture biological aging offer largely untapped potential for objectively identifying BO patients at highest risk of progression, who could undergo personalised surveillance at shorter intervals. We have developed computational tools to determine tissue-specific aging using genome-wide methylation data as a “molecular clock” for estimating patient-specific BO dwell times at the time of incident diagnosis that cannot be clinically measured by other means. Methods Using the population-based Northern Ireland BO register in a retrospective study, we have identified 46 non-dysplastic BO patients who have 2-4 serial endoscopic biopsies each, and have not progressed to OAC (age range 29-77 years). FFPE biopsies for 10 age-matched patients who had prevalent HGD/OAC at index BO diagnosis were also retrieved. DNA has been extracted, quantified using fluorescence, quality checked through qPCR, and prepared for Illumina EPIC methylation arrays. We created a Python package called “MethylDrift” to determine genome-wide aging rates in patient data. Model outputs are used in the molecular clock for BO tissue age. Results We used MethylDrift to quantify aging rates in both cross-sectional data (population-level epigenetic drift) and longitudinal data within the same patients to obtain individual aging rates. Computational analyses using our previously developed Bayesian framework for the BO molecular clock will be applied to estimate the molecular age of BO in patients, i.e., how long the patient has been living with BO since onset of metaplasia. Results will be compared between age groups, birth cohorts, sex, and importantly between dysplastic and non-dysplastic BO to evaluate biomarker potential. Data analysis is ongoing, and the final results will be presented at the meeting. Conclusions Our results from this nested case-control study demonstrate feasibility and generate pilot data on molecular age as a proxy of BO duration at the time of incident diagnosis, in a large population-based registry of patients with BO. This will inform our computational tools for determining biological aging and can be applied in future work to investigate progression risk according to molecular age. Ultimately, this biomarker could inform surveillance frequency for BO patients, enable earlier detection of neoplastic progression, leading to improved patient outcomes and optimal distribution of limited endoscopy capacity for surveillance.

Abstract The human microbiota, the collection of microbes that inhabit the human body, is increasingly being appreciated as playing a role in human health. A seminal example of this relationship is Helicobacter pylori and gastric cancer oncogenesis. The drop in H.pylori infections and non-cardia gastric cancer incidences has coincided with the rise in oesophageal adenocarcinoma (OAC) incidences. We sought to explore the relationship between the upper digestive tract microbiome and OAC oncogenesis. Methods Pinch biopsies were taken from individual’s oesophagus and stomach who were along the metaplasia-dysplasia-adenocarcinoma sequence (GERD, Barrett's oesophagus, dysplasia, OAC, metastatic OAC) as well as healthy controls. We carried out 16 s rRNA gene DNA sequencing protocols on these samples. DNA extraction and library preparation was performed with consideration to the low mass nature of oesophageal biopsies. Raw reads were processed and amplicon sequence variants (ASVs) were generated using the DADA2. We dissected ecological differences between sample site and clinical classification using a variety of approaches including examining differentially abundant taxa and inferred metabolic pathways, alpha diversity and beta-diversity. Results The upper digestive tract was found to be dominated by the genera Streptococcus, Prevotella, and Haemophilus. There was no statistically significant shift in beta diversity with respect to biopsy location. Alpha diversity was reduced in gastric biopsies compare to oesophageal biopsies. A slight yet significant shift was seen in beta diversity (Bray–Curtis Dissimilarity) with respect to clinical classification in biopsies derived from the gastroesophageal junction (GEJ) and stomach. Various taxa were found to be differentially abundant between biopsy site and with regard to clinical classification. Conclusion OAC primarily occurs at the GEJ. Community structure was shifted in samples derived from the GEJ and the stomach. Fusobacterium nucleatum was overrepresented in oesophageal biopsies from individuals with diseased oesophagus compared to individuals with a histologically normal oesophagus. This bacterium has been implicated in oncogenesis of various cancers most notably colorectal cancer. Serval ASVs assigned to the genus Prevotella were depleted in stomachs of individuals with metastatic OAC compared to all other groups.

Abstract Background Oesophageal cancer is the 6th leading cause of cancer death worldwide, accounting for 1 in 18 cancer-related mortality in 2020. High mortality rates with oesophagogastric cancer is largely related to late diagnosis. In England and Wales, 35% of oesophagogastric cancers are diagnosed at stage 3 and 42% at stage 4. Early detection of oesophageal cancer improves survival. Currently, the only reliable and effective modality for early diagnosis is oesophagogastroduodenoscopy (OGD). However, OGD is an invasive procedure that carries risks, such as bleeding and visceral perforation. Thus, there is no national screening programme for oesophagogastric cancer, although patients with diagnosed Barrett's oesophagus undergo endoscopic surveillance. Cytological sampling devices such as Cytosponge and EsophaCap are less invasive but still require ingestion of a medical device, and are not without risks, including detachment of device, pharyngeal bleed, and failure to swallow. The discovery and validation of blood biomarkers for the screening and diagnosis of oesophageal cancer may provide advantages of non-invasive, rapid, and cost-effective testing. Yet, currently, there is no clinically validated blood screening biomarker. In this systematic review, we aim to identify developing blood biomarkers that have been described in the literature for early diagnosis of oesophageal cancer. Methods A systematic search was conducted on EMBASE (1974-), Medline (1947-), and Web of Science (1980-) from inception to 3rd November 2021. Exploded subject headings and combinations of keywords were used. Search terms used were [oesophageal cancer or oesophageal ca or oesophageal malignancy or oesophageal neoplasm or Barrett's oesophagus or Barrett's metaplasia] AND [Tumour biomarkers or tumour markers or biological marker] AND [diagnosis or early diagnosis or screening or detection or discrimination] AND [adenocarcinoma or squamous cell carcinoma] AND [blood or serum or plasma] AND [esophagus or oesophagus]. Papers describing blood biomarkers that hold potential in screening and diagnosing oesophageal cancer were included. We focussed on adenocarcinoma, and squamous cell carcinoma affecting the oesophagus and the oesophagogastric junction. Tumour markers with a role in more than one type of cancer were included. We excluded rarer histological types. Biomarkers utilised to prognosticate outcomes of therapy were excluded, as were markers of recurrence and “Pan-cancer” biomarkers. Titles and abstracts identified by electronic search were reviewed independently by two reviewers, using Rayyan. Conflict was resolved by a third independent reviewer. Results The electronic search yielded 2619 records. After removal of duplicates 2267 records remained for screening. Following screening of titles and abstracts, 130 studies remained for full-text review. After full-text review, 53 records fulfilled the criteria for detailed analysis and reporting. 86 additional papers were identified through manual searches and review of reference lists. Studies were published from diverse populations including: USA, China, Japan, Germany, Poland, India, Australia, Ireland, South Africa, Italy, Brazil, Turkey and Netherlands. Blood biomarkers investigated in the literature comprised classical tumour markers, such as CEA, SCC-AG, CA19–9, CA-125; inflammatory markers; metabolites; peptides and glycoproteins; enzymes; cytokines; volatile organic compounds; circulating tumour cells; miRNA; circulating DNA; long non-coding RNAs; circular RNAs; peripheral blood cell DNA/RNA; antibodies and tumour-associated antigens; and spectra from Raman spectroscopy. The most widely described markers were antibodies and tumour-associated antigens (61 papers) and miRNAs (25 papers). Several other panels with combinations of different types of markers are described. The highest area under receiver operating curve (AUC) was 0.99 from two papers. One paper described a panel of serum miRNA ratios (RNU6-1/miR-16-5p, miR-25-3p/miR-320a, let-7e-5p/miR-15b-5p, miR-30a-5p/miR-324-5p, miR-17-5p/miR-194-5p). The other described a serum N-glycan with mass:charge ratio of 2244. Conclusions Several blood biomarkers with a potential role in screening or diagnosis of oesophageal cancer have been described in the literature. The results of some tests suggest promising diagnostic accuracy with two papers having AUCs of 0.99. Despite this however, no single test has come into clinical practice as a non-invasive diagnostic test. The gold standard in diagnosing oesophageal squamous cell carcinoma and oesophageal adenocarcinoma remains to be endoscopy and biopsy. Reasons for these markers not being utilised in clinical practice to date include need for further studies to validate results with larger sample size; challenges in reproducibility of studies; cost and lack of availability of techniques used in hospital; and other challenges to translate scientific studies into clinical application. There seem to be promising candidates liquid biopsy markers in oesophageal cancer, but further work is required to validate and translate the use of some promising markers into clinical practice.

Oesophageal cancer is the eighth most common cancer and the sixth most common cause of death from cancer worldwide. There are two main histological types of oesophageal cancer: squamous cell carcinoma (ESCC), adenocarcinoma (EAC). In the developing world the major histological type is ESCC, whilst in the developed world EAC is increasing rapidly in incidence and is now the major type. Both histological types have a similarly poor prognosis, with a high morbidity and mortality. Barrett’s oesophagus (BE) is considered a precursor to EAC. It is found in up to 1.5% of the general population, and in up to 12% of patients who are investigated for chronic reflux symptoms. Approximately 0.5 to 1% of patients with BE will develop EAC each year, and patients with BE have 30- to 125-fold increased risk of EAC compared to the general population. Gastro-oesophageal reflux is the major risk factor for the development of BE and EAC, and medical and surgical anti-reflux therapies are available to relieve symptoms of the reflux and prevent reflux-related complications, although it is not certain if they will prevent the development of cancer. The development of oesophageal cancer is associated with an accumulation of genetic abnormalities, with some reports suggesting a stepwise progression of genetic changes involving the up-regulation and down-regulation of critical genes. Methylation of cytosine residues in CpG dinucleotides of the promoter regions of genes, DNA methylation, is a genomic change associated with silencing of gene expression. In the studies described in this thesis I have developed a simple quantitative method to assess DNA methylation using the melt data obtained following amplification of bisulphite modified DNA. I identified eight genes (BNIP3, FBN2, ID4, MLF1, PRDM2, RBP4, RARRES1, TFAP2C) that had been reported methylated in other cancers, but not before in BE or EAC, and four genes (CLDN6, DCBLD2, FNBP1 and MGC16824) that had not previously been reported as methylated in any cancer. I have shown that in non-dysplastic (metaplastic) BE, methylation of APC, ID4, MGMT, RBP1, SFRP1, TIMP3 and TMEFF2 (but not RUNX3 or CDKN2A) occurs as frequently in BE as EAC, suggesting that BE is more like cancer than normal squamous mucosa. I have used DNA methylation as a surrogate measure of the efficacy of fundoplication and proton pump inhibitor (PPI) treatment for BE. Five or more years after fundoplication there was a significant regression of BE and a reduction in the number of methylated genes in the remaining BE. In contrast, although high-dose PPI for six months significantly reduced inflammation and epithelial cell proliferation, it did not alter methylation. The reduction in methylation may be associated with a decreased risk for the development of dysplasia and adenocarcinoma. Finally, I have suggested extensions to the work published in this thesis. Further understanding of which genes are methylated in BE, EAC and ESCC, the mechanisms responsible for this aberrant methylation, and the function of the genes, would improve our insight into the underlying biology of oesophageal diseases, and potentially lead to new biomarkers or treatment options.
Thesis (Ph.D.) -- University of Adelaide, School of Medicine, 2010