Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps

Abstract

Colorectal cancers (CRCs) arise from precursor polyps whose cellular origins, molecular heterogeneity, and immunogenic potential may reveal diagnostic and therapeutic insights when analyzed at high resolution. We present a single-cell transcriptomic and imaging atlas of the two most common human colorectal polyps, conventional adenomas and serrated polyps, and their resulting CRC counterparts. Integrative analysis of 128 datasets from 62 participants reveals adenomas arise from WNT-driven expansion of stem cells, while serrated polyps derive from differentiated cells through gastric metaplasia. Metaplasia-associated damage is coupled to a cytotoxic immune microenvironment preceding hypermutation, driven partly by ll

Cancer-Associated Fibroblasts and Squamous Epithelial Cells Constitute a Unique Microenvironment in a Mouse Model of Inflammation-Induced Colon Cancer

“…Distinct populations of CAF1 ( ACTA2, TAGLN, MYLK ) and CAF2 ( PDGFRA ) analogs were identified, similar to our mouse models of tumorigenesis. Normal human colonic tissues and pre-cancerous colonic lesions contain a paucity of fibroblasts consistent with our observations in the mouse (data not shown) ( 26 ). Also consistent with our mouse models, CAF2 analogs expressed a rich set of signaling regulators including CXCL12, GREM1, IGF1, IL11 , and WNT5A , with a subset of cells co-expressing WNT5A and GREM1 and another subset co-expressing CXCL12 and IGF1.…”

“…Consistent with the loss of stemness upon treatment, tumor cells displayed an increase in cell cycle related genes at later timepoints and a decreased predicted stem potential, as determined by CytoTRACE score, whereas squamous cells increased proliferation genes and stem potential ( Figures 5G, H ). Using unsupervised differential gene expression analysis as well as examining selected marker genes, we observed an upregulation in antigen presentation (AP) genes in tumor cells from the day 6 timepoint, consistent with our previous finding of increased AP as a function of differentiation ( Figure 5I ) ( 26 ). Interestingly, squamous cells in day 3 and day 6 timepoints also upregulated interferon-induced genes Ifi27 and Ifitm3 , consistent with a change in the immune microenvironment.…”

“…AOM/DSS tumors were devoid of goblet cells, consistent with DSS-induced inflammation that drives goblet cell loss ( Figure 1F ) ( 25 ). In addition, both tumor types displayed the emergence of metaplastic Paneth-like cells absent from the normal colon, as documented previously ( 26 ).…”

“…To examine T cell subtypes, we performed sub-clustering on the T cells, population and identified four distinct T cells clusters that are condition-specific ( Figures 2A–C ). Normal colonic samples were expectedly enriched for Cd8 + T cells, identified as intraepithelial lymphocytes by expression of Itgae and Trdc , as observed previously ( 26 – 28 ) ( Figures 2D, E ). These cells express Gzma and Gzmb that play key roles in cytotoxicity, Cd38 marking activation, and the killing effectors Klre1 , Cd244 (when expressed at the appropriate level), Nkg7, Klrd1, and Xcl1 ( 29 – 31 ).…”

“…The AOM/DSS-specific squamous epithelial cell population was devoid of WNT signaling and colonic epithelial cell type markers ( Figures 4A ; Figure S2 ). While metaplasia and damage gene lists used by Chen et al, 2021 did not show enrichment in the squamous cell population, fetal and embryonic genes were uniquely upregulated in squamous cells compared to all other epithelial cell populations, including tumor cells ( Figures 4C, D ) ( 26 ). Notably, several genes related to matrix composition and immune cell recruitment were upregulated in squamous cells ( Anxa1 , Ecm1 , Il1rn , Itgb4 ), as well as genes that are reported to be tumor suppressors ( Serpin5b , Phlda3 ) ( 59 , 60 ).…”