We have used CODEX to image 56 proteins simultaneously in 140 tissue regions from the tumor invasive front of 35 advanced-stage colorectal cancer (CRC) patients (17 patients with Crohn's-like reaction (CLR) - leading to high amount of tertiary lymphoid structures (TLS); and 18 patients with diffuse inflammatory infiltration (DII) and no TLS). These patients were selected from an initial cohort of 715 CRC patients. Patients with low-stage CRC (pTNM 0-2), pre-operative chemotherapy, insufficient material, and low immune infiltration were excluded. The 35 resulting patients were matched for age, sex and tumor characteristics. CLR patients had a much better survival compared to DII patients. We expect that making this dataset publicly available will stimulate broad research endeavors into the immune tumor microenvironment of colorectal cancer and allow computational scientists to discover new biomarkers and features. Further details on the study can be obtained in our paper here: https://www.cell.com/cell/fulltext/S0092-8674(20)30870-9
We would like to acknowledge the individuals and institutions that have provided data for this collection:
- Angelica Trejo, Han Chen, Kenyi Donoso, Nilanjan Mukherjee, Vishal Venkataraaman, and Gustavo Vazquez (Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA) for excellent technical assistance.
- Sandrine Ruppen, Carmen Cardozo, and Dr. José Galván (Institute of Pathology, University of Bern, Switzerland) for help with creating the TMAs.
- Dr. Anna Seigal (Mathematical Institute, University of Oxford, Oxford, UK University) for helpful discussions regarding tensor decomposition.
- Dr. Julian Schardt (Department of Medical Oncology, Inselspital, University Hospital Bern, Switzerland) for helping obtain patient clinical information.
- Prof. Paul Bollyky (Department of Infectious Diseases, Stanford University School of Medicine, Stanford, CA, USA) for providing the biotinylated VG1 hyaluronan-detection reagent.
- The patients for their consent to use their tissues for research.
- Dr. Sizun Jiang and Dr. Xavier Rovira-Clavé (Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA) for critical comments on the manuscript.
We would also like to acknowledge the following institutions and companies for their grants and awards given for this collection:
This work would not have been possible without the support and efforts of many individuals and organizations.
- A complete list of acknowledgements can be found here.