Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

Abstract

To chart cell composition and cell state changes that occur during the transformation of healthy colon to precancerous adenomas to colorectal cancer (CRC), we generated single-cell chromatin accessibility profiles and single-cell transcriptomes from 1,000 to 10,000 cells per sample for 48 polyps, 27 normal tissues and 6 CRCs collected from patients with or without germline APC mutations. A large fraction of polyp and CRC cells exhibit a stem-like phenotype, and we define a continuum of epigenetic and transcriptional changes occurring in these stem-like cells as they progress from homeostasis to CRC. Advanced polyps contain increasing numbers of stem-like cells, regulatory T cells and a subtype of pre-cancer-associated fibroblasts. In the cancerous state, we observe T cell exhaustion, RUNX1-regulated cancer-associated fibroblasts and increasing accessibility associated with HNF4A motifs in epithelia. DNA methylation changes in sporadic CRC are strongly anti-correlated with accessibility changes along this continuum, further identifying regulatory markers for molecular staging of polyps.

Integrative single cell and spatial transcriptomics of colorectal cancer reveals multicellular functional units that support tumor progression

“…2d,e ). In particular, the stem cell program (#16) detected in some cells across all conditions, was enriched in dysplastic samples (FDR=5.6 10 -10 , Welch’s t-test on CLR transformed compositions), reminiscent of a recently described population in human (Becker et al, 2022; Chen et al, 2021). Comparing cells from dysplastic and normal samples that express the stem cell program, the dysplastic cells had distinct expression profiles with induction of negative regulators of Wnt signaling (FDR=4.5 10 -5 , Fisher’s exact test in GO term enrichment, e.g.…”

“…2d,e). In particular, the stem cell program (#16) detected in some cells across all conditions, was enriched in dysplastic samples (FDR=5.6 10 -10 , Welch's t-test on CLR transformed compositions), reminiscent of a recently described population in human (Becker et al, 2022;Chen et al, 2021).…”

“…A case in point is colorectal cancer (CRC), where initial lesions, adenomatous polyps, progress over time to carcinoma and eventually to metastatic disease. While the mutations that drive this process were extensively studied (Cancer Genome Atlas Network, 2012; Fearon, 2011; Fearon and Vogelstein, 1990; Kwong and Dove, 2009), and the cellular ecosystem of CRC has now been deeply charted (Becker et al, 2022; Chen et al, 2021; Pelka et al, 2021), the spatial landscape is less well-characterized. In a recent study of human CRC, we statistically associated cell profiles across tumors and showed that they map to different cellular communities (Pelka et al, 2021), reside in different locations in the tumor and reflect different tumor subtypes.…”

Aberrant cell state plasticity mediated by developmental reprogramming precedes colorectal cancer initiation

“…The copyright holder for this preprint this version posted September 23, 2022. ; https://doi.org/10.1101/2022.09. 22.509032 doi: bioRxiv preprint Bala,Rennhack et al,p5 we may uncover new therapeutic strategies for CRC. Here, we characterize critical early molecular events of intestinal neoplasia using histopathological analyses, single cell transcriptomics, chromatin accessibility assays, and organoid experiments in distinct mouse models and human specimens, uncovering developmental reprogramming as an important early step leading to aberrant cell state plasticity in CRC initiation.…”

“…The majority of sporadic CRCs initiate as a premalignant adenoma harboring genomic alterations that constitutively activate WNT signaling (20)(21)(22), most often through loss-of-function APC mutations (23)(24)(25). A key component of a cytoplasmic destruction complex, APC restricts WNT signaling by facilitating ubiquitin-mediated degradation of β-catenin (26)(27)(28)(29)(30)(31).…”