Summary
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 manuscript here: https://www.biorxiv.org/content/10.1101/743989v1Acknowledgement
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:
- US National Institutes of Health grants and sub awards: (2U19AI057229-16) (5P01HL10879707) (5R01GM10983604) (5R33CA18365403) (5U01AI101984-07) (5UH2AR06767604) (5R01CA19665703) (5U54CA20997103) (5F99CA212231-02) (1F32CA233203-01) (5U01AI140498-02) (1U54HG010426-01) (5U19AI100627-07) (1R01HL120724-01A1) (R33CA183692) (R01HL128173-04) (5P01AI131374-02) (5UG3DK114937-02) (1U19AI135976-01) (IDIQ17X149) (1U2CCA233238-01) (1U2CCA233195-01)
- The Department of Defense: (W81XWH-14-1-0180 and W81XWH-12-1-0591)
- The Food and Drug Administration: (HHSF223201610018C and DSTL/AGR/00980/01)
- Cancer Research UK: (C27165/A29073)
- The Bill and Melinda Gates Foundation: (OPP1113682)
- The Cancer Research Institute
- The Parker Institute for Cancer Immunotherapy
- The Kenneth Rainin Foundation: (2018-575)
- The Silicon Valley Community Foundation: (2017-175329 and 2017-177799-5022)
- The Beckman Center for Molecular and Genetic Medicine
- Juno Therapeutics, Inc. : (122401)
- Pfizer, Inc. : (123214)
- Celgene, Inc. : (133826 and 134073)
- Vaxart, Inc. : (137364)
- The Rachford & Carlotta A. Harris Endowed Chair (G.P.N.)
- C.M.S. was supported by an Advanced Postdoc Mobility Fellowship from the Swiss National Science Foundation (P300PB_171189 and P400PM_183915), and an International Award for Research in Leukemia from the Lady Tata Memorial Trust, London, UK.
- D.J.P. was supported by an NIH T32 Fellowship through Stanford’s Department of Epithelial Biology (AR007422), an NIH F32 Fellowship (CA233203), a Stanford Dean’s Postdoctoral Fellowship, and Stanford’s Dermatology Department.
- S.S.B. was supported by a Bio-X Stanford Interdisciplinary Graduate Fellowship and Stanford’s Bioengineering Department.
- G.L.B was supported by an NIH T32 Fellowship through Stanford’s Molecular and Cellular Immunobiology Program (5T32AI007290-34).
Data available for download at the end of August 2020.
Data Access
| Data Type | Download all or Query/Filter |
|---|---|
| Tissue Slide Images (TIFF, 2.0TB) | |
| Clinical data (XLS, DOC) |
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Detailed Description
Image Statistics | |
|---|---|
Modalities | Pathology |
Number of Subjects | 35 |
Number of Images | 200 |
| Images Size (TB) | 2.0 |
High-dimensional CODEX images (hyperstacks of immunofluorescence images)
Citations & Data Usage Policy
Data Citation
DOI goes here. Create using Datacite with information from Collection Approval form
Publication Citation
There is a pre-print publication on bioRxiv, here: https://www.biorxiv.org/content/10.1101/743989v1 This pre-print can be cited until the paper is published in a peer-reviewed journal.
TCIA Citation
Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, Moore S, Phillips S, Maffitt D, Pringle M, Tarbox L, Prior F. The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository, Journal of Digital Imaging, Volume 26, Number 6, December, 2013, pp 1045-1057. DOI: 10.1007/s10278-013-9622-7
Other Publications Using This Data
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Version 1 (Current): Updated 2020/08/05
| Data Type | Download all or Query/Filter |
|---|---|
| Images (TIFF, 2.0TB) | |
| Clinical Data (XLS, DOC) | Details_on_image_acquisition_and_processing.docx |