Human colorectal pre-cancer atlas identifies distinct molecular programs underlying two major subclasses of pre-malignant tumors

Abstract

Most colorectal cancers (CRCs) develop from either adenomas (ADs) or sessile serrated lesions (SSLs). The origins and molecular landscapes of these histologically distinct pre-cancerous polyps remain incompletely understood. Here, we present an atlas at single-cell resolution of sporadic conventional tubular/tubulovillous ADs, SSLs, hyperplastic polyps (HPs), microsatellite stable (MSS) and unstable (MSI-H) CRC, and normal colonic mucosa. Using single-cell transcriptomics and multiplex imaging, we studied 69 datasets from 33 participants. We also examined separate sets of 66 and 274 polyps for RNA and targeted gene sequencing, respectively. We performed multiplex imaging on a tissue microarray of 14 ADs and 15 CRCs, and we integrated pre-cancer polyp data with published single-cell and The Cancer Genome Atlas (TCGA) bulk CRC data to establish potential polyp-cancer relationships. Striking differences were observed between ADs and SSLs that extended to MSS and MSI-H CRCs, respectively, reflecting their distinct origins and trajectories. ADs arose from WNT pathway dysregulation in stem cells, which aberrantly expanded and expressed a Hippo and ASCL2 regenerative program. In marked contrast, SSLs were depleted of stem cell-like populations and instead exhibited a program of gastric metaplasia in the setting of elevated cytotoxic inflammation. Using subtype-specific gene regulatory networks and shared genetic variant analysis, we implicated serrated polyps, including some HPs conventionally considered benign, as arising from a metaplastic program in committed absorptive cells. ADs and SSLs displayed distinct patterns of immune cell infiltration that may influence their natural history. Our multi-omic atlas provides novel insights into the malignant potential of colorectal polyps and serves as a framework for precision surveillance and prevention of sporadic CRC.

MTG16 (CBFA2T3) regulates colonic epithelial differentiation, colitis, and tumorigenesis by repressing E protein transcription factors

“…Single-cell RNA-sequencing (scRNA-seq) and analysis. InDrop scRNA-seq and analysis were performed on 2 independent (discovery and validation) cohorts of human colon samples as previously described 24 . These data are publicly available through the Human Tumor Atlas Network (https://data.humantumoratlas.org/) 50 .…”

“…To understand the topography of MTG16 expression in the human colon, we queried single-cell RNAseq (scRNA-seq) datasets generated from 2 independent cohorts of normal human colon samples 24 . Interestingly, we observed that MTG16 was predominantly expressed in secretory cells (Fig.…”

“…Furthermore, recent studies have demonstrated that colonic epithelial regeneration in response to injury occurs through the opposite process: de-differentiation of committed precursor cells [21][22][23] . Aberrant regenerative programs may lead to uncontrolled cell proliferation and dysplasia 24 . Thus, these processes must be tightly controlled by coordinated networks of transcriptional activators and repressors 3 .…”

“…Conversely, colonic epithelial regeneration in response to injury occurs through de-differentiation of committed absorptive and secretory lineage cells (2)(3)(4). Secretory lineage dysregulation is implicated in inflammatory bowel disease (IBD), diabetes, and even behavioral changes (5)(6)(7)(8)(9), and aberrant regenerative programs may lead to uncontrolled cell proliferation and dysplasia (10). Thus, these processes must be tightly controlled by coordinated networks of transcriptional activators and repressors (1).…”