Gastrointestinal Biobank

Gastrointestinal Biobanks

Department of Surgery, School of Medicine, Trinity Translational Medicine Institute, St. James’s Hospital (SJH)

There are 5 Gastrointestinal (GI) Biobanks based in the Department of Surgery:

Upper Gastrointestinal Biobank
This biobank collects samples from patients with a cancer of the oesophagus (food pipe) or stomach, and from non-cancer patients (patients with a benign gastrointestinal disease). These samples include tumour and surrounding normal tissue, bloods, muscle, liver, lymph node, and fluid from the chest cavity. Upper GI Biobank Manager: Ms Meghana Menon
Lower Gastrointestinal Biobank
This biobank collects samples from patients with a cancer of the bowel or rectum, and from non-cancer patients (patients with a benign gastrointestinal disease). These samples include tumour and surrounding normal tissue, and bloods.
Barrett’s Oesophagus Biobank This biobank collects samples from patients with a pre-cancerous condition of the oesophagus, known as Barrett’s disease. These samples include tissue biopsies, gastric juices, and bloods. Barrett’s Biobank Manager: Mr Cian Gargan
Inflammatory Bowel Disease (IBD) Biobank This biobank collects samples from patients with IBD, an inflammatory condition of the large intestine. These samples include tissue biopsies, and bloods.
Pancreatic Biobank
This biobank collects samples (both cancerous and pre-cancerous) from patients undergoing investigations for pancreatic conditions.

Our research focuses on understanding conditions (both benign and cancerous) of the gastrointestinal tract. We sometimes work with pharmaceutical companies to find better treatments. Patients presenting to the SJH for an endoscopy procedure, surgery or chemotherapy sessions are invited to take part in the respective biobank. This involves a doctor/member of the biobank research team discussing the research with the patient, and if the patient is willing to take part, the patient will sign a consent form and donate samples.

Current Academic Projects under the Upper & Lower GI Biobanks

Investigation of the role of microRNA in the treatment response of gastro-oesophageal cancer.

Lead on Project: Dr Niamh Lynam-Lennon
Collaborator(s): Prof John Reynolds (TSJCI), Prof Maeve Lowery (TSJCI), Prof Jacintha O'Sullivan (TSJCI)
PhD Student: Ms Christina Cahill
Purpose of Project: Resistance to anti-cancer therapy is a significant clinical problem. We are trying to identify novel biomarkers that can predict prior to initiation of treatment if a patient is likely to respond or be resistant to treatment, which would improve patient stratification, treatment and survival for patients. The aim of this project is to investigate the expression of key microRNAs in the blood and tumour tissue from patients with gastric and oesophageal cancer and determine the relationship between microRNA expression and response to treatment to identify novel predictive biomarkers of treatment response.

Organoids Programme with Legend Biotech.

Lead on Project: Prof Jacintha O’Sullivan and Dr Kathy Gately
Purpose of Project: We are working with Legend Biotech (based in Ireland) to generate 3D cultures from patient samples.

Breaking the obesity-cancer link; a theranostic role for FKBL in modulating immunometabolism across disease progression in oesophageal adenocarcinoma.

Lead on Project: Prof Jacintha O’Sullivan
Post-doctoral Researcher: Dr Aisling Heeran
Collaborator(s): Dr Tracy Robson (RCSI)
Purpose of Project: This project investigates the role of FKBPL across the Barrett’s oesophagus to oesophageal adenocarcinoma disease progression pathway. This work uses multiple model systems to investigate FKBPL expression and function in this disease, including cell lines, mouse models and human tissue samples.

The effects of electroporation on the secretome of human explants in GI cancers (pan GI approach: upper and lower GI).

Lead on Project: Prof Jacintha O’Sullivan
Post-doctoral researcher: Dr Aisling Ui Mhaonaigh
Purpose of Project: This project involves the investigation of electroporation as a novel treatment for gastrointestinal cancer patients. The technology was developed by collaborators Mirai Medical based in Galway and is funded by Enterprise Ireland. It involves delivering an electric pulse to tumour tissue which permeabilises the cells and allows increased uptake of drugs/therapeutics that greatly increases efficacy and can illicit an immune response that can clear distal tumours.

Elucidating the immune, metabolic and genomic characteristics in young onset gastroesophageal cancer

Lead on Project: Prof Maeve Lowery and Prof Jacintha O’Sullivan
PhD Student: Dr Oana Deac
Purpose of Project: Through this project Oana is employing large volume national datasets looking at incidence trends in Ireland, publicly available genomic datasets and laboratory based work looking at the immune and metabolic features that characterize these young onset (under 50 years of age) solid tumours.

Boosting oxygen diffusion in the radioresistant oesophageal tumour microenvironment to improve radiation response

Lead on Project: Prof Jacintha O’Sullivan
PhD Student: Mr Maitiu O Murchu
Collaborator(s): Prof Helena Kelly, RCSI
Purpose of Project: This project is developing oxygen carrying perfluorocarbon nanoemulsions to boost oxygen diffusion and improve radiosensitivity in oesophageal adenocarcinoma.

To evolve the personalised active cell therapy paradigm – HEALED Consortium

Lead on Project: Prof Jacintha O’Sullivan, Prof Aideen Long, Prof Maeve Lowery
Members: Ms Kirstan Murphy, Mr Nick Schellenberg, Mr Cillian O’Donovan, Dr Marina Zaki
Collaborator(s): Remedy Biologics, aCGT Vector, University of Galway
Purpose of Project: We are looking at the effects of energy metabolism, hypoxia and inflammation on the number and phenotype of Tumour Infiltrating Lymphocytes in upper and lower GI tumours, ovarian, breast and lung tumours; profiling the inflammatory proteins released by tumours and matching this information with that of the TIL cell phenotype in these tumours. This will help us answer important questions on the role of these biological processes in the tumour microenvironment and how this influences the TIL cell biology. We aim to understand more about the genetic changes in tumour tissues by conducting whole exome sequencing and RNA sequencing.

Elucidating the tumorigenic effects of fractalkine and its therapeutic utility in oesophageal adenocarcinoma.

Lead on Project: Dr Melissa Conroy and Prof Joanne Lysaght
PhD student: Ms Caroline Marion
Collaborator(s): Prof John Reynolds, Xenopat
Purpose of Project: Developing a novel therapy using a CX3CR1 antagonist and genetically engineered NK cell therapy for obesity associated oesophageal adenocarcinoma.

Identifying novel aspects of immune checkpoint pathways to improve response rates in upper GI cancer

Lead on Project: Prof Joanne Lysaght
Post-doctoral researcher: Dr Aoife Kilgallon
Collaborator(s): Dr. Stephen Maher, Prof. Maeve Lowery, Prof, John Reynolds
Purpose of Project: Intrinsic signalling through immune checkpoint receptors on tumour cells is a largely understudied area, which has the exciting potential to benefit numerous cancer patients who are currently deemed ineligible for immune checkpoint inhibitor therapy.

Unlocking the immune tumour microenvironment to improve therapeutic outcomes in oesophageal cancer

Lead on Project: Prof Joanne Lysaght
PhD Student: Dr Brendan Moran
Collaborator(s): Dr. Noel Donlon, Prof. John Reynolds
Purpose of Project: This study will explore the relevance of immune checkpoint inhibitors and epigenetic modifiers in oesophageal adenocarcinoma, specifically their ability to manipulate the tumour microenvironment and enhance anti-tumour properties, ultimately providing a new therapeutic model for testing in trials.

Developing tumour-homing NK cell therapies for obesity-associated cancer.

Lead on Project: Dr Melissa Conroy and Prof Joanne Lysaght
PhD student: Ms Joyce Barry
Collaborator(s): Prof John Reynolds, Xenopat
Purpose of Project: Developing a novel therapy with genetically engineered NK cells for oesophageal adenocarcinoma.

Investigating the immunomodulatory influence of blood derived extracellular vesicles (EVs) in cancer patients

Lead on Project: Prof. Lorraine O’Driscoll and Prof Joanne Lysaght
Post-Doctoral Researcher: Dr. Yashna Chabria
Collaborator(s): Prof Maeve Lowery
Purpose of Project: This project will assess EVs and bacterial derived EVs in the blood of upper gastrointestinal cancer patients. Phenotypic and functional changes in T cells induced by cancer patient EVs will be assessed.

Current Academic Projects under the Barrett’s Biobank

Investigating the effect of calcium electroporation in the Barrett’s Oesophagus tissue microenvironment.

Lead on Project: Prof Jacintha O’Sullivan
PhD Student: Ms Lorraine Smith
Programme Manager: Dr James Phelan
Collaborator(s): Queen’s University Belfast, University College Dublin
Purpose of Project: As part of the All-Ireland Cancer Network (ALLCAN) on oesophageal cancer, funded by Breakthrough Cancer Research, Lorraine’s translational project examines human Barrett’s cell lines and tissues respond to electroporation therapy and if this treatment boosts immunity, or alters autophagic and calcium responses.

Current Academic Projects under the IBD Biobank

Lead on Project: Prof Jacintha O’Sullivan
PhD Student: Dr Roisin Corcoran
Purpose of Project: This project involves investigating the clinical and biochemical biomarkers of response to biologic therapies in Inflammatory Bowel Disease.
Lead on Project: Prof Jacintha O’Sullivan
PhD Student: Dr Catherine McShane
Purpose of Project: This project is looking at the role of immune-metabolic assessment in the ulcerative colitis tissue microenvironment. The work to date has included inflammatory, metabolic and metabolomic assessment of an ulcerative colitis ex-plant model and includes an exploratory drug discovery study.

Current Academic Projects under the Pancreatic Biobank

Multi-omic analytics for cancer risk stratification in patients with pancreatic cystic lesions

Lead on Project: Dr. Stephen Maher
PhD student: Outmane Bouzerda
Collaborator(s): Prof. Barbara Ryan, Dr Aidan Meade, Prof Olivier Piot
Purpose of Project: This study aims to assess the potential of FTIR and Raman spectroscopic techniques to reveal biochemical changes associated with pancreatic cell line exposure to pancreatic cyst fluid for the development of ex vivo triage protocols.

PROPITIATE – Biofluid prognostic for prediction of development of pancreatic cancer

Lead on Project: Dr. Stephen Maher
Postdoc: Dr Laura Kane
Collaborator(s): Prof. Barbara Ryan, Dr Finbar McCarthy
Purpose of Project: This study aims to develop a multi-omic cross-biofluid algorithm for more effectively stratifying PCL patients into low- and high-risk groups for cancer development.

Immunophenotyping pancreatic cystic lesions for cancer risk stratification

Lead on Project: Prof Joanne Lysaght and Dr. Stephen Maher
PhD Student: Rebecca Lyons
Collaborator(s): Prof. Barbara Ryan
Purpose of Project: This study aims to investigate the influence of pancreatic cystic lesions on immune responses and influence on pancreatic cancer initiation, promotion and progression.

Immunophenotyping pancreatic cystic lesions for cancer risk stratification

Lead on Project: Prof Joanne Lysaght and Dr. Stephen Maher
PhD Student: Rebecca Lyons
Collaborator(s): Dr. Barbara Ryan
Purpose of Project: This study aims to investigate the influence of pancreatic cystic lesions on immune responses and influence on pancreatic cancer initiation, promotion and progression.

Withdrawal

You can withdraw from taking part in the biobank at any time after you provide consent. Withdrawal requests may be made verbally, in writing or via phone to the biobank team or a healthcare professional without the need to provide a reason for this. If you would like to withdraw, please contact Professor Jacintha O’Sullivan on 01 8962149 or osullij4@tcd.ie.

From this point on, your samples and healthcare data will not be used for research. However, it will not be possible to destroy samples and healthcare data already shared for research, before this date as this could impact on the research results. The biobank will keep a record that you changed your mind and record the destruction of your samples and healthcare data.

Conferences and Publications

Researchers usually publish their results in scientific/medical journals or present them at conferences so that others can learn from their research. You will not be identified in any journals or presentations. The biobank hopes these results will improve health care for future patients. Examples of publications using biobank samples can be found in the profile links of the scientific leads.