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Azimi M, Cho S, Bozkurt E, McDonough E, Kisakol B, Matveeva A, Salvucci M, Dussmann H, McDade S, Firat C, Urganci N, Shia J, Longley DB, Ginty F, Prehn JHM. Spatial Effects of Infiltrating T cells on Neighbouring Cancer Cells and Prognosis in Stage III CRC patients. bioRxiv 2024:2024.01.30.577720. [PMID: 38352309 PMCID: PMC10862776 DOI: 10.1101/2024.01.30.577720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Colorectal cancer (CRC) is one of the most frequently occurring cancers, but prognostic biomarkers identifying patients at risk of recurrence are still lacking. In this study, we aimed to investigate in more detail the spatial relationship between intratumoural T cells, cancer cells, and cancer cell hallmarks, as prognostic biomarkers in stage III colorectal cancer patients. We conducted multiplexed imaging of 56 protein markers at single cell resolution on resected fixed tissue from stage III CRC patients who received adjuvant 5-fluorouracil-based chemotherapy. Images underwent segmentation for tumour, stroma and immune cells, and cancer cell 'state' protein marker expression was quantified at a cellular level. We developed a Python package for estimation of spatial proximity, nearest neighbour analysis focusing on cancer cell - T cell interactions at single-cell level. In our discovery cohort (MSK), we processed 462 core samples (total number of cells: 1,669,228) from 221 adjuvant 5FU-treated stage III patients. The validation cohort (HV) consisted of 272 samples (total number of cells: 853,398) from 98 stage III CRC patients. While there were trends for an association between percentage of cytotoxic T cells (across the whole cancer core), it did not reach significance (Discovery cohort: p = 0.07, Validation cohort: p = 0.19). We next utilized our region-based nearest neighbourhood approach to determine the spatial relationships between cytotoxic T cells, helper T cells and cancer cell clusters. In the both cohorts, we found that lower distance between cytotoxic T cells, T helper cells and cancer cells was significantly associated with increased disease-free survival. An unsupervised trained model that clustered patients based on the median distance between immune cells and cancer cells, as well as protein expression profiles, successfully classified patients into low-risk and high-risk groups (Discovery cohort: p = 0.01, Validation cohort: p = 0.003).
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Affiliation(s)
- Mohammadreza Azimi
- Department of Physiology and Medical Physics, RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin 2, Ireland
| | - Sanghee Cho
- GE HealthCare Technology and Innovation Center, Niskayuna, NY, 12309, USA (formerly GE Research Center)
| | - Emir Bozkurt
- Department of Physiology and Medical Physics, RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin 2, Ireland
| | - Elizabeth McDonough
- GE HealthCare Technology and Innovation Center, Niskayuna, NY, 12309, USA (formerly GE Research Center)
| | - Batuhan Kisakol
- Department of Physiology and Medical Physics, RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin 2, Ireland
| | - Anna Matveeva
- Department of Physiology and Medical Physics, RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin 2, Ireland
| | - Manuela Salvucci
- Department of Physiology and Medical Physics, RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin 2, Ireland
| | - Heiko Dussmann
- Department of Physiology and Medical Physics, RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin 2, Ireland
| | - Simon McDade
- School of Medicine, Dentistry and Biomedical Sciences, Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | | | | | - Jinru Shia
- Memorial Sloan Kettering Cancer Centre, NY
| | - Daniel B Longley
- School of Medicine, Dentistry and Biomedical Sciences, Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Fiona Ginty
- GE HealthCare Technology and Innovation Center, Niskayuna, NY, 12309, USA (formerly GE Research Center)
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin 2, Ireland
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