A5001468607- Cancer Immunotherapy and Biomarkers
- Radiomics and Machine Learning in Medical Imaging
- Colorectal Cancer Treatments and Studies
- AI in cancer detection
- Genetic factors in colorectal cancer
- Molecular Biology Techniques and Applications
- Esophageal Cancer Research and Treatment
- Cancer Genomics and Diagnostics
- Exercise and Physiological Responses
- Cell Image Analysis Techniques
- Colorectal and Anal Carcinomas
- Cancer Research and Treatments
- RNA modifications and cancer
- Health Promotion and Cardiovascular Prevention
- Cancer Treatment and Pharmacology
- Oral Health Pathology and Treatment
- Head and Neck Cancer Studies
- Acute Myeloid Leukemia Research
- RNA Research and Splicing
- Cancer-related Molecular Pathways
- Genomics and Chromatin Dynamics
- Immunotherapy and Immune Responses
- Epigenetics and DNA Methylation
- Dietary Effects on Health
- Gastric Cancer Management and Outcomes
Queen's University Belfast
2016-2025
University of Guelph
2023-2024
NOSM University
2024
Belfast Health and Social Care Trust
2024
York University
2023
Williams (United States)
2023
Dalhousie University
2022
Binghamton University
2022
Hospital for Sick Children
2022
Multiplex immunofluorescence is a powerful tool for the simultaneous detection of tissue-based biomarkers, revolutionising traditional immunohistochemistry. The Opal methodology allows up to eight biomarkers be measured concomitantly without cross-reactivity, permitting identification different cell populations within tumour microenvironment. In this study, we aimed validate multiplex workflow in two complementary panels and evaluate immune microenvironment colorectal cancer (CRC)...
TNM8 staging for oropharyngeal squamous cell carcinomas (OPSCC) surrogates p16 immunohistochemistry HPV testing. Patients with p16+ OPSCC may lack aetiology. Here, we evaluate the suitability of guiding prognosis in such patients.
Aims Establishing the mismatch repair (MMR) status of colorectal cancers is important to enable detection underlying Lynch syndrome and inform prognosis therapy. Current testing typically involves either polymerase chain reaction (PCR)‐based microsatellite instability (MSI) or MMR protein immunohistochemistry (IHC). The aim this study was compare these two approaches in a large, population‐based cohort stage 2 3 colon cancer cases Northern Ireland. Methods results used Promega pentaplex...
Abstract Oral epithelial dysplasia (OED) is a premalignant histopathological diagnosis given to lesions of the oral cavity. Its grading suffers from significant inter-/intra-observer variability, and does not reliably predict malignancy progression, potentially leading suboptimal treatment decisions. To address this, we developed an artificial intelligence (AI) algorithm, that assigns Malignant Transformation (OMT) risk score based on Haematoxylin Eosin (H&E) stained whole slide images...
Output from biomarker studies involving immunohistochemistry applied to tissue microarrays (TMA) is limited by the lack of an efficient and reproducible scoring methodology. In this study, we examine functionality reproducibility using new, open-source, digital image analysis software, QuPath.
Abstract Background Immunohistochemical quantification of the immune response is prognostic for colorectal cancer (CRC). Here, we evaluate suitability alternative classifiers on prognosis and assess whether they relate to biological features amenable targeted therapy. Methods Overall survival by (CD3, CD4, CD8, CD20 FOXP3) immune-checkpoint (ICOS, IDO-1 PD-L1) biomarkers in independent CRC cohorts was evaluated. Matched mutational transcriptomic data were interrogated identify associated...
Patient suitability to anti-programmed death ligand 1 (PD-L1) immune checkpoint inhibition is key the treatment of NSCLC. We present, applied PD-L1 testing: a comprehensive cross-validation two immunohistochemistry (IHC) clones; our descriptive experience in diagnostic reflex testing; concordance IHC situ RNA (RNA-ISH); and application digital pathology.
// Victoria Bingham 2 , Leanne McIlreavey Christine Greene 1,3 Edwina O’Doherty Rebecca Clarke Stephanie Craig Manuel Salto-Tellez Stephen McQuaid 1,2,3 Claire Lewis 1,2 and Jacqueline James 1 Northern Ireland Biobank, Centre for Cancer Research Cell Biology, Queen’s University, Belfast, UK Molecular Pathology Programme, 3 Tissue Pathology, Belfast Health Social Care Trust, City Hospital, Correspondence to: McQuaid, email: Keywords : mRNA; FFPE; in situ hybridization; Integrity;...
// Conor A. Bradley 1, * , Philip D. Dunne Victoria Bingham 1 Stephen McQuaid 2 Hajrah Khawaja Stephanie Craig Jackie James Wendy L. Moore Darragh G. McArt Mark Lawler Sonali Dasgupta Patrick Johnston Sandra Van Schaeybroeck Drug Resistance Group, Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry Biomedical Science, Queen's University Belfast, UK Tissue Pathology, Belfast Health Social Care Trust, City Hospital, Joint first authors Correspondence to: Schaeybroeck,...
Targeting of the programmed cell death protein (PD-1)/programmed death-ligand 1 (PD-L1) axis with checkpoint inhibitors has changed clinical practice in non-small lung cancer (NSCLC). However, assessment remains complex and ambiguous. We aim to assess whether digital image analysis (DIA) multiplex immunofluorescence can improve accuracy PD-L1 diagnostic testing. A cohort routine NSCLC patients reflex tested for (SP263) immunohistochemistry (IHC), was assessed using DIA. Samples varying...
STING signaling in cancer is a crucial component of response to immunotherapy and other anti-cancer treatments. Currently, there no robust method measuring activation cancer. Here, we describe an immunohistochemistry-based assay with digital pathology assessment tumor cells. Using this novel approach estrogen receptor-positive (ER+) ER- breast cancer, identify perinuclear-localized expression (pnSTING) ER+ cases as independent predictor good prognosis, associated immune cell infiltration...
Biomarkers identify patient response to therapy. The potential immune-checkpoint biomarker, Inducible T-cell COStimulator (ICOS), expressed on regulating activation and involved in adaptive immune responses, is of great interest. We have previously shown that open-source software for digital pathology image analysis can be used detect quantify ICOS using cell detection algorithms based traditional processing techniques. Currently, artificial intelligence (AI) deep learning methods...
Abstract A nationwide tuberculosis outbreak linked to a viable bone allograft product contaminated with Mycobacterium was identified in June 2021. Our subsequent investigation 73 healthcare personnel new latent infection following exposure the product, recipients, surgical instruments, or medical waste.
Abstract Purpose To investigate the association between cigarette smoking, alcohol consumption, and esophageal adenocarcinoma survival, including stratified analysis by selected prognostic biomarkers. Methods A population-representative sample of 130 patients (n = 130) treated at Northern Ireland Cancer Centre 2004 2012. Cox proportional hazards models were applied to evaluate associations smoking status, intake, survival. Secondary analyses investigated these across categories p53, HER2,...
Abstract Background Limited studies examine the immune landscape in Esophageal Adenocarcinoma (EAC). We aim to identify novel associations, which may inform immunotherapy treatment stratification. Methods Three hundred twenty-nine EAC cases were available Tissue Microarrays (TMA) format. A discovery cohort of 166 stained immunohistochemically for range adaptive (CD3, CD4, CD8 and CD45RO) checkpoint biomarkers (ICOS, IDO-1, PD-L1, PD-1). validation 163 was also accessed. digital pathology...
Abstract Purpose: The DNA damage immune response (DDIR) assay was developed in breast cancer based on biology associated with deficiencies homologous recombination and Fanconi anemia pathways. A positive DDIR call identifies patients likely to respond platinum-based chemotherapies esophageal cancers. In colorectal cancer, there is currently no biomarker predict oxaliplatin. We tested the ability of oxaliplatin-based chemotherapy characterized DDIR-positive cancer. Experimental Design:...
Abstract Purpose: To investigate the regulation of epithelial-to-mesenchymal transition (EMT) in head and neck squamous cell carcinoma (HNSCC) its importance tumor invasion. Experimental Design: We use a three-dimensional invasive organotypic raft culture model human foreskin keratinocytes expressing E6/E7 genes papilloma virus-16, coupled with bioinformatic IHC analysis patient samples to role played by EMT invasion identify effectors upstream regulatory pathways. Results: SNAI2 (Slug) as...
Abstract Background The cohesin complex plays a major role in folding the human genome into 3D structural domains. Mutations members of are known early drivers myelodysplastic syndromes (MDS) and acute myeloid leukaemia (AML), with STAG2 most frequently mutated member. Methods Here we use functional genomics (RNA-seq, ChIP-seq HiChIP) to investigate impact chronic loss on three-dimensional structure transcriptional programming clinically relevant model loss. Results led smaller loop domains...
Identifying robust predictive biomarkers to stratify colorectal cancer (CRC) patients based on their response immune-checkpoint therapy is an area of unmet clinical need. Our evolutionary algorithm Atlas Correlation Explorer (ACE) represents a novel approach for mining The Cancer Genome (TCGA) data clinically relevant associations. We deployed ACE identify candidate in CRC. interrogated the colon adenocarcinoma (COAD) gene expression across nine immune-checkpoints (PDL1, PDCD1, CTLA4, LAG3,...
Abstract Background Oral epithelial dysplasia (OED) is the precursor to oral squamous cell carcinoma which amongst top ten cancers worldwide. Prognostic significance of conventional histological features in OED not well established. Many additional abnormalities are seen OED, but insufficiently investigated, and have been correlated clinical outcomes. Methods A digital quantitative analysis cellularity, nuclear geometry, cytoplasm staining intensity architecture/thickness conducted on 75...