Paper

Single-cell spatial mapping reveals alteration of cell type composition and tissue microenvironment during early colorectal cancer formation

d, James M, Greenleaf, William J, Karathanos, Thomas V, Esplin, D Glen, Snyder, Michael P, White, Shannon, Bi, Joanna, Horning, Aaron M, Mills, Meredith A, Monte, Emma, Rozelle Laquindanum, Longacre, Teri A, Becker, Winston R, Shen, Jeanne, Curtis, Christina, Paul, Kristina, Cotter, Daniel, Chiu, Roxanne, Weimer, Annika K, Guha, Tuhin K, Ladabaum, Uri, Esplin, Edward D

2024

Overview

Colorectal cancer (CRC) is the third leading cause of cancer mortality in the United States. Familial adenomatous polyposis (FAP) is a hereditary syndrome that raises the risk of developing CRC, with total colectomy as the only effective prevention. Even though FAP is rare (0.5% of all CRC cases), this disease model is well suited for studying the early stages of malignant transformation as patients form many polyps reflective of pre-cancer states. In order to spatially profile and analyze the pre-cancer and tumor microenvironment, we have performed single-cell multiplexed imaging for 52 samples: 12 normal mucosa,16 FAP mucosa,18 FAP polyps, 2 FAP adenocarcinoma, and 4 sporadic colorectal cancer (CRCs) using Co-detection by Indexing (CODEX) imaging platform. The data revealed significant changes in cell type composition occurring in early stage polyps and during the malignant transformation of polyps to CRC. We observe a decrease in CD4+/CD8+ T cell ratio and M1/M2 macrophage ratio along the FAP disease continuum. Advanced dysplastic polyps show a higher population of cancer associated fibroblasts (CAFs), which likely alter the pre-cancer microenvironment. Within polyps and CRCs, we observe strong nuclear expression of beta-catenin and higher number neo-angiogenesis events, unlike FAP mucosa and normal colon counterparts. We identify an increase in cancer stem cells (CSCs) within the glandular crypts of the FAP polyps and also detect Tregs, tumor associated macrophages (TAMs) and vascular endothelial cells supporting CSC survival and proliferation. We detect a potential immunosuppressive microenvironment within the tumor nest of FAP adenocarcinoma samples, where tumor cells tend to segregate and remain distant from the invading immune cells. TAMs were found to infiltrate the tumor area, along with angiogenesis and tumor proliferation. CAFs were found to be enriched near the inflammatory region within polyps and CRCs and may have several roles in supporting tumor growth. Neighborhood analyses between adjacent FAP mucosa and FAP polyps show significant differences in spatial location of cells based on functionality. For example, in FAP mucosa, naive CD4+ T cells alone tend to localize near the fibroblast within the stromal compartment. However, in FAP polyp, CD4+T cells colocalize with the macrophages for T cell activation. Our data are expected to serve as a useful resource for understanding the early stages of neogenesis and the pre-cancer microenvironment, which may benefit early detection, therapeutic intervention and future prevention.Competing Interest StatementMPS is a cofounder and scientific advisor of Crosshair Therapeutics, Exposomics, Filtricine, Fodsel, iollo, InVu Health, January AI, Marble Therapeutics, Mirvie, Next Thought AI, Orange Street Ventures, Personalis, Protos Biologics, Qbio, RTHM, SensOmics. MPS is a scientific advisor of Abbratech, Applied Cognition, Enovone, Jupiter Therapeutics, M3 Helium, Mitrix, Neuvivo, Onza, Sigil Biosciences, TranscribeGlass, WndrHLTH, Yuvan Research. MPS is a cofounder of NiMo Therapeutics. MPS is an investor and scientific advisor of R42 and Swaza. MPS is an investor in Repair Biotechnologies. W.J.G. is a consultant and equity holder for 10x Genomics, Guardant Health, Quantapore and Ultima Genomics, and cofounder of Protillion Biosciences, and is named on patents describing ATAC-seq. EDE is an employee and stockholder of Labcorp Genetics and an advisor and stockholder of Taproot Health, Exir Bio, and ROMTech. The remaining authors declare no competing interests.

• Publisher: Cold Spring Harbor Laboratory Press,Cold Spring Harbor Laboratory
• Subject: Adenocarcinoma / Advisors / Angiogenesis / Cancer Biology / CD4 antigen / CD8 antigen / Cell activation / Cell proliferation / Cell survival / Cognition / Colon cancer / Colorectal cancer / Colorectal carcinoma / Colorectal surgery / Endothelial cells / Familial adenomatous polyposis / Genetic transformation / Genomics / Lymphocytes T / Macrophages / Mucosa / Polyps / Stockholders / Tumor cells / Tumor microenvironment / Tumors / β-Catenin