1. Evolutionary genetic algorithm identifies
- Author
-
Matthew Alderdice, Vicky M. Coyle, Seedevi Senevirathne, Alan Gilmore, Manuel Salto-Tellez, Matthew P. Humphries, Maurice B Loughrey, Jacqueline James, Nicole Johnston, Daniel B. Longley, Mark Lawler, Victoria Bingham, Stephanie G Craig, Stephen McQuaid, and Darragh G. McArt
- Subjects
0301 basic medicine ,Oncology ,AcademicSubjects/SCI01140 ,medicine.medical_specialty ,LAG3 ,AcademicSubjects/SCI01060 ,Colorectal cancer ,AcademicSubjects/SCI00030 ,BTLA ,Standard Article ,AcademicSubjects/SCI01180 ,03 medical and health sciences ,0302 clinical medicine ,TIGIT ,SDG 3 - Good Health and Well-being ,Internal medicine ,medicine ,Tissue microarray ,business.industry ,FOXP3 ,medicine.disease ,Immune checkpoint ,030104 developmental biology ,IL2RB ,030220 oncology & carcinogenesis ,AcademicSubjects/SCI00980 ,business - Abstract
Identifying robust predictive biomarkers to stratify colorectal cancer (CRC) patients based on their response to 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 Atlas (TCGA) data for clinically relevant associations. We deployed ACE to identify candidate predictive biomarkers of response to immune-checkpoint therapy in CRC. We interrogated the colon adenocarcinoma (COAD) gene expression data across nine immune-checkpoints (PDL1, PDCD1, CTLA4, LAG3, TIM3, TIGIT, ICOS, IDO1 and BTLA). IL2RB was identified as the most common gene associated with immune-checkpoint genes in CRC. Using human/murine single-cell RNA-seq data, we demonstrated that IL2RB was expressed predominantly in a subset of T-cells associated with increased immune-checkpoint expression (P < 0.0001). Confirmatory IL2RB immunohistochemistry (IHC) analysis in a large MSI-H colon cancer tissue microarray (TMA; n = 115) revealed sensitive, specific staining of a subset of lymphocytes and a strong association with FOXP3+ lymphocytes (P < 0.0001). IL2RB mRNA positively correlated with three previously-published gene signatures of response to immune-checkpoint therapy (P < 0.0001). Our evolutionary algorithm has identified IL2RB to be extensively linked to immune-checkpoints in CRC; its expression should be investigated for clinical utility as a potential predictive biomarker for CRC patients receiving immune-checkpoint blockade.
- Published
- 2020