The role of the immune micro-environment in the evolution of colitis-associated cancer

Lead Research Organisation: Queen Mary, University of London
Department Name: Barts Cancer Institute

Abstract

Medical Context:

Around 1 in 500 people in the United Kingdom suffer from inflammatory bowel disease (IBD), a set of disorders that includes both Crohn's disease and Ulcerative Colitis (UC), and the incidence is rising. Bowel cancer is the most feared complication of IBD; these patients develop more aggressive cancer tumours at a younger age than the general population. These patients are therefore enrolled in a regular colonoscopy surveillance programme to detect pre-cancerous changes (called dysplasia) and early cancer. St. Mark's hospital, one of my host institutions, conducts the world's oldest, and one of the largest, surveillance programmes in the world. Analysis of their programme registry reveals that patients with UC affecting their whole colon have a lifetime cancer risk of 20%.

Nevertheless, cancer surveillance in IBD faces several critical challenges. Despite advances in technology, dysplasia remains difficult to detect. The majority of patients with IBD do not get bowel cancer, meaning that for many patients these expensive procedures are uncomfortable and unnecessary. Even when pre-cancerous dysplasia is detected, the most appropriate management plan is uncertain. We have shown that the ten-year cancer risk from early dysplasia is only 30%; even in advanced dysplasia that risk is only 50%. Some patients opt for more intensive endoscopic surveillance, while accepting the higher risk of bowel cancer. Others undergo surgery to remove their whole colon, with all the associated risks of a major operation and consequences of life with a stoma. As a gastroenterologist and endoscopist who contributes to the St. Marks IBD surveillance programme, I am all too aware that these challenges reflect how little we know about the biological pathways and timelines leading to bowel cancer in IBD.


Scientific Context:

My host laboratory at the Barts Cancer Institute has demonstrated that mutations accumulate in the lining of the IBD bowel years before the development of cancer, and that stem cells lining the bowel are key to the spread of mutations. We suspect that changes in the environment surrounding bowel stem cells may in fact be the driving force behind the development of cancer.


Research Plan:

This PhD project will combine the unparalleled clinical resources of St. Mark's Hospital, with the scientific expertise of the Barts Cancer Institute, who have an established record in studying bowel cancer evolution. The latest molecular and genetic analysis techniques will be used to analyse fresh and archived tissue derived from 100 IBD surveillance endoscopies in patients with bowel cancer, and compare the mutation burden, inflammatory activity and stem cell behaviour to samples from 300 similar patients who are cancer free.


Research Aims:

1- Ultimately, this research effort will address the important issue of predicting cancer risk: we will develop a laboratory test that can determine if a patient with IBD is likely to develop cancer within the next few years. If successful, this study will improve the quality of life of patients with IBD by increasing focus on those high risk patients, while simultaneously providing significant cost savings to the NHS by sparing many low risk patients from frequent unnecessary invasive colonoscopies and/or surgery.

2- Our basic scientific understanding of IBD-related bowel cancer remains strikingly deficient compared to other typed of CRC. This project will contribute greatly towards filling those gaps.

3- My findings will have implications for researches in bowel cancer at large. The novelty of this proposed PhD project relates to the fact that this will be the first study to simultaneously measure genetic, immunological and stem cell changes over time to determine how bowel cancer develops, and can be replicated in other pre-cancerous conditions.

Technical Summary

Background: Patients with ulcerative colitis (UC) have a significantly increased risk of developing colorectal cancer (CRC), and so are entered into endoscopic surveillance programmes with the aim of detecting pre-cancerous dysplastic lesions. The detection and clinical management of these lesions remain challenging, leading to over-diagnosis and over-treatment of CRC risk.

Hypothesis: We have demonstrated that epithelial clonal evolution underpins UC-mediated carcinogenesis; however, this evolution must be critically dependent on the micro-environmental context. We hypothesise that the stromal microenvironment in UC patients co-evolves alongside epithelial mutation accumulation in the colitis-dysplasia-carcinoma sequence, and that these micro-environmental changes represent a powerful biomarker of cancer risk.

Key Goals: The particular scientific novelty of this proposed project is my ability to study the co-evolution of epithelial clonal populations and stromal microenvironment composition in the UC colon. By combining the unparalleled clinical resources of the world's oldest (and the UK's largest) IBD surveillance programme at St. Mark's Hospital with the scientific expertise of Barts Cancer Institute, I aim to:

1- analyse the micro-environmental composition in archival samples from 100 patients who progress to cancer (progressors) and 300 matched non-progressors.

2- correlate the micro-environmental composition in these samples with the pattern of epithelial somatic mutations.

3- use RNA-seq on fresh samples derived from a subset of progressors and non-progressors to characterise genome-wide the paired micro-environmental and epithelial cell biology, and assess the impact on stem cell biology during progression.

Ultimately, I aim use my micro-environmental characterisation to develop a biomarker of CRC risk that spares low risk patients from unnecessary colonoscopy and surgery, and validate its utility in a future prospective clinical study.

Planned Impact

1- Patients with inflammatory bowel disease:

Analysis of the St. Mark's IBD surveillance group demonstrates that the 40-year risk of bowel cancer risk for patients with extensive ulcerative colitis stands at 20%. While this risk is much higher than in the general population, it means that the majority of patients with IBD will never develop bowel cancer. At present, every patient with longstanding extensive colonic IBD will undergo repeated colonoscopies approximately every 3 years. The laxative-based bowel preparation prior to colonoscopy is unpleasant, and the surveillance colonoscopies themselves are not only invasive, uncomfortable and inconvenient for patients, but also carry a risk of complications including perforation.

The current surveillance program faces further limitations: namely that dysplastic lesions in IBD are often flat and therefore easily missed at endoscopy, and that histological grading of dysplasia suffers from high inter-observer variability. The majority of patients with UC dysplastic lesions do not develop cancer, and many cancer patients do not have a preceding dysplasia diagnosis. As a result, current clinical practice leads to over-diagnosis and over-treatment for patients opting for surgery when dysplasia is detected, and uncertainty as to the frequency and duration of intensive surveillance for those opting for active monitoring. With dysplasia now detected in up to 10% of surveillance colonoscopies, accurate cancer risk stratification in UC is a major unmet clinical need.

Ultimately, I aim use my micro-environmental characterisation to develop a biomarker of CRC risk that spares low risk patients from unnecessary colonoscopy and surgery, and validate its utility in a future prospective clinical study.



2- Gastroenterology Societies and other relevant guideline-generating organisations:

Surveillance colonoscopies are now recommended by the British Society of Gastroenterology (BSG) and other gastroenterology societies (e.g. European Crohn's & Colitis Organisation, American Gastroenterology Association). However, there is a lack of consensus between these organisations as to the most appropriate frequency of endoscopic surveillance. St. Mark's Hospital runs the world's oldest IBD cancer surveillance programme, and remains by far the country's largest programme. Many of the current guideline authors are based in his hospital, and the current regimen (e.g. the recent adoption of chromoendoscopy) has been derived from studies based on the St. Mark's cohort. It is therefore likely that any prospectively validated biomarkers will be considered during guideline updates.



3- IBD clinicians and endoscopists:

Due to the lack of evidence in this field, clinicians operating in this field struggle on how best to advise patients with dysplasia or other high risk clinical features. Validated cancer risk biomarkers will provide more clarity for these difficult patient consultations.



4- In the long term, healthcare service providers including the National Health Service:

The current surveillance protocol recommended by the BSG has been deemed cost-effective by NICE, and as such is implemented nationwide. However, this programme carries a significant financial cost to the NHS at £17,500/quality-adjusted life year. The absolute cost is likely to increase with the rising incidence of inflammatory bowel disease, in combination with an ageing population. Recent advances in medical therapy may also mean that increasing numbers of patients with severe inflammation have avoided surgery and retained their bowels. Any validated cancer risk biomarker has the potential to result in significant cost savings.



5- Industry:

While there are no immediate commercial applications from this project, any generated biomarkers may hold commercial value. Subject to Intellectual Property restrictions by the university, I would be well placed to promote any generated biomarkers to industry.

Publications

10 25 50
 
Description Update of the St. Mark's Hospital Inflammatory Bowel Disease Surveillance patient pathway
Geographic Reach Local/Municipal/Regional 
Policy Influence Type Citation in other policy documents
 
Description Clinical Research Training Fellowship - Scheme B
Amount £73,353 (GBP)
Funding ID MGU0423 
Organisation Barts Charity 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2018 
End 09/2019
 
Description St. Mark's Academic Institute & Foundation Research Grant
Amount £18,280 (GBP)
Funding ID RES198 
Organisation St Mark's Hospital 
Sector Hospitals
Country United Kingdom
Start 09/2016 
End 09/2018
 
Title Establishing a low pass whole genome sequencing pipeline using very limited quantities of degraded DNA from archival formalin-fixed paraffin-embedded tissue 
Description Low pass whole genome sequencing is a novel next generation sequencing technique initially developed for analysis of chromosomal copy number alteration of IVF-generated embryos prior to implantation. To date, there have been a very limited number of publications to date attempting to translate this technique in cancer research. In the last 12 months, I have been able to analyse 400 archival formalin-fixed paraffin embedded samples, some of which are over 20 years, others with as little as 500 picograms of DNA, with a failure rate of 2%, at a cost of £70 per sample. 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? No  
Impact The initial results generated using this technique have been submitted for publication in Gut; the manuscript is currently under review. This technique has the potential to open up entire NHS pathology archives to scientific analysis where chromosomal instability is implicated, thereby avoiding the need for more time-consuming collections of fresh tissue from patients of interest. 
 
Title Establishing a pipeline for gene expression analysis using very limited quantities of degraded RNA from archival formalin-fixed paraffin-embedded tissue (3' mRNA QuantSeq) 
Description 3' mRNA QuantSeq is a novel next generation sequencing technique developed by Lexogen to compensate for the degradation seen in archival formalin-fixed paraffin-embedded tissue. To date, there have been a very limited number of publications to date attempting to translate this technique in cancer research. 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? No  
Impact The tehnique has now been used in the Oxford Wellcome Centre for Human Genetics to analyse gene expression profiles in various other colonic neoplastic tissue including sporadic adenomas and sessile serrated lesions. 
 
Title Modification of commercially available whole-exome sequencing library preparation kits for use with very limited amounts of DNA 
Description Current commercially available whole exome sequencing kits have an absolute minimum requirement of 50 nanograms of DNA input to generate DNA libraries suitable for analysis. With reagent modifications at various stages of the process (including reduced reaction volumes, reduced Tagment enzyme concentration and increased number of PCR cycles) we have successfuly prepared libraries from only 25 nanograms of input DNA. 
Type Of Material Technology assay or reagent 
Provided To Others? No  
Impact There has been no immediate impact from the development of this research method. We developed this method to allow us to undertake whole exome sequencing of single normal colonic crypts. These structures contain around 2000 cells with an average DNA yield of 20 nanograms per crypt. Sequencing of individual normal crypts has never been done before, and ultimately the same principles can be replicated across a whole host of other tissue types. 
 
Title Multicentre IBD surveillance database 
Description I have collated a detailed clinical database of all patients across 3 hospitals (St. Mark's Hospital, Royal London Hospital, University College Hospital) who subsequently developed epithelial dysplasia and/or colorectal cancer, as well as a large number of non-progressors who did not develop cancer. The database contains anonymised details on each patient's age, duration of disease, gender, drugs, endoscopy reports and histology reports. In total it contains details on 332 patients who developed cancer, and 924 controls. In total there are over 8,000 biopsies. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact This database has been vital for the identification of suitable tissue blocks for my study It is also being used by myself and clinical collaborators to determine long term patient outcomes after the resection of dysplasia in IBD. This will be the largest single cohort and the only one to date that provides detailed analysis on lesion morphology, size and histology. It is likely to have an impact on future national guidelines on endoscopic surveillance of patients with IBD. 
 
Description Collaboration with pathology departments across 3 London hospital sies 
Organisation Royal London Hospital
Country United Kingdom 
Sector Hospitals 
PI Contribution None
Collaborator Contribution 1- This collaboration has allowed for the identification of a large number of patients with inflammatory bowel disease who subsequently developed dysplasia and cancer. The identified cases were amalgamated into a detailed IBD surveillance database (see Research Databases & Models section) 2- Pathologists from the three sites have also contributed to my study by being blinded assessors of dysplasia severity 3- I undertake a dedicated IBD clinic in St. Mark's Hospital once a fortnight. This session allows me to identify patients suitable for my studies, and obtain consent for use of their donated tissue.
Impact Pending
Start Year 2016
 
Description Collaboration with pathology departments across 3 London hospital sies 
Organisation St Mark's Hospital
Country United Kingdom 
Sector Hospitals 
PI Contribution None
Collaborator Contribution 1- This collaboration has allowed for the identification of a large number of patients with inflammatory bowel disease who subsequently developed dysplasia and cancer. The identified cases were amalgamated into a detailed IBD surveillance database (see Research Databases & Models section) 2- Pathologists from the three sites have also contributed to my study by being blinded assessors of dysplasia severity 3- I undertake a dedicated IBD clinic in St. Mark's Hospital once a fortnight. This session allows me to identify patients suitable for my studies, and obtain consent for use of their donated tissue.
Impact Pending
Start Year 2016
 
Description Collaboration with pathology departments across 3 London hospital sies 
Organisation University College Hospital
Department Department of Pathology
Country United Kingdom 
Sector Hospitals 
PI Contribution None
Collaborator Contribution 1- This collaboration has allowed for the identification of a large number of patients with inflammatory bowel disease who subsequently developed dysplasia and cancer. The identified cases were amalgamated into a detailed IBD surveillance database (see Research Databases & Models section) 2- Pathologists from the three sites have also contributed to my study by being blinded assessors of dysplasia severity 3- I undertake a dedicated IBD clinic in St. Mark's Hospital once a fortnight. This session allows me to identify patients suitable for my studies, and obtain consent for use of their donated tissue.
Impact Pending
Start Year 2016
 
Description Collaboration with the Wellcome Centre for Human Genetics, Oxford 
Organisation University of Oxford
Department Wellcome Trust Centre for Human Genetics
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution In light of the promising preliminary data I have generated comparing "progressor" and "non-progressor" low grade dysplasia in inflammatory bowel disease using low pass whole genome sequencing, we have initiated a joint study that: (a) assesses a much larger sample size - aiming 200 lesions in total ; (b) includes sporadic adenomas for further comparison ; (c) uses multiple molecular analysis techniques beyond low pass whole genome sequencing including molecular inversion probe arrays and 3' mRNA QuantSeq.
Collaborator Contribution As of January 2018, there has been a dedicated research technician assisting with this project three days a week for the next 3 months. Moreover, the design of the molecular inversion probe array and cost of undertaking 3' mRNA QuanSeq will be borne by the Wellcome Centre for Human Genetics in Oxford.
Impact The preliminary data I have generated will be presented as an oral abstract at the plenary session of the 13th Congress of the European Crohn's and Colitis Organisation.
Start Year 2017
 
Title UC-CARE website 
Description I have worked with senior bioinformatician Dr. Kathleen Curtius at the Barts Cancer Institute on the development of the UC-CARE tool. This interactive webtool prompts clinicians to select from 7 dropdown menus the appropriate descriptors regarding low grade dysplastic lesions detected in patients with ulcerative colitis. Using this input, the tool generates an output which includes the 1, 5 and 10 years risk of colon cancer, as well as a Paling chart that presents the future bowel cancer risk in a visual format that can be more readily appreciated by patients. 
Type Of Technology Webtool/Application 
Year Produced 2017 
Impact This tool is now used by clinicians at St. Mark's Hospital during routine clinical practice to help them and their patients decide the most appropriate clinical intervention when dysplasia is detected in a patient with inflammatory bowel disease. Current studies are underway to validate this tool prospectively and across multiple NHS sites. 
URL http://www.uc-care.uk
 
Description Barts & The London Medical School Examiner 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact On three separate sessions in 2016 (6 May, 9 June and 21 July), 2017 (25 May, 18 July and 20 July) and 2018 (3 July, 5 July and 10 July), I volunteered to be an examiner of medical students at Barts & The London Medical School. The students were in their 2nd, 3rd or 4th years of study. I have been asked by the medical school to volunteer again as a final year medical school examiner in March 2019.
Year(s) Of Engagement Activity 2016,2017,2018,2019