Controlling for cellular heterogeneity using single-cell deconvolution of gene expression reveals novel markers of colorectal tumors exhibiting microsatellite instability

Spatial and single-cell transcriptomic analysis reveals fibroblasts dependent immune environment in colorectal cancer

Colorectal cancer (CRC) exhibits a complex tumor microenvironment with significant cellular heterogeneity, particularly involving cancer-associated fibroblasts that influence tumor behavior and metastasis. This study integrated single-cell RNA sequencing and spatial transcriptomics to dissect fibroblast heterogeneity in CRC. Data processing employed Seurat for quality control, principal component analysis for dimensionality reduction, and t-Distributed Stochastic Neighbor Embedding for visualization. Differentially expressed genes were identified using DESeq2. Immune infiltration was assessed via Single-Sample Gene Set Enrichment Analysis, CIBERSORT, and xCell algorithms. Prognostic genes were identified through univariate Cox regression, followed by consensus clustering and survival analysis. Metabolic pathways were explored using scMetabolism. Experimental validation involved CCK8, scratch, and Transwell assays to evaluate the roles of key genes BGN and CERCAM in CRC cell proliferation and metastasis. Machine learning-driven analysis identified four fibroblast-associated genes (TRIP6, TIMP1, BGN, and CERCAM) demonstrating significant prognostic relevance in CRC. Consensus clustering based on these biomarkers stratified CRC patients into three distinct molecular subtypes (Clusters A-C). Notably, Cluster C exhibited the most unfavorable clinical outcomes coupled with marked upregulation of all four fibroblast-related genes. Comprehensive immune profiling revealed paradoxical features in Cluster C: heightened global immune activation (characterized by substantial leukocyte infiltration) coexisted with specific immunosuppressive elements, including significant enrichment of pro-tumorigenic M0 macrophages, depletion of anti-tumor plasma cells, and resting memory CD4+ T cells, along with coordinated upregulation of multiple immune checkpoint molecules. Computational prediction using the TIDE platform suggested enhanced immunotherapy responsiveness in Cluster C patients. Functional validation demonstrated that knockdown of BGN or CERCAM significantly impaired malignant phenotypes, reducing proliferative capacity, migration potential, and invasive ability. Fibroblasts demonstrate significant heterogeneity within the CRC immune microenvironment, impacting prognosis and therapeutic responses. Key genes BGN and CERCAM emerge as potential immunotherapeutic targets, offering new strategies for precision treatment of CRC.

Assessment of Colorectal Cancer Risk Factors through the Application of Network-Based Approaches in a Racially Diverse Cohort of Colon Organoid Stem Cells

Numerous demographic factors have been associated with colorectal cancer (CRC) risk. To better define biological mechanisms underlying these associations, we performed RNA sequencing of stem-cell-enriched organoids derived from the healthy colons of seven European Americans and eight African Americans. A weighted gene co-expression network analysis was performed following RNA sequencing. Module-trait relationships were determined through the association testing of each module and five CRC risk factors (age, body mass index, sex, smoking history, and race). Only modules that displayed a significantly positive correlation for gene significance and module membership were considered for further investigation. In total, 16 modules were associated with known CRC risk factors (p < 0.05). To contextualize the role of risk modules in CRC, publicly available RNA-sequencing data from TCGA-COAD were downloaded and re-analyzed. Differentially expressed genes identified between tumors and matched normal-adjacent tissue were overlaid across each module. Loci derived from CRC genome-wide association studies were additionally overlaid across modules to identify robust putative targets of risk. Among them, MYBL2 and RXRA represented strong plausible drivers through which cigarette smoking and BMI potentially modulated CRC risk, respectively. In summary, our findings highlight the potential of the colon organoid system in identifying novel CRC risk mechanisms in an ancestrally diverse and cellularly relevant population.

Transcriptome-wide In Vitro Effects of Aspirin on Patient-derived Normal Colon Organoids

Mechanisms underlying aspirin chemoprevention of colorectal cancer remain unclear. Prior studies have been limited because of the inability of preclinical models to recapitulate human normal colon epithelium or cellular heterogeneity present in mucosal biopsies. To overcome some of these obstacles, we performed in vitro aspirin treatment of colon organoids derived from normal mucosal biopsies to reveal transcriptional networks relevant to aspirin chemoprevention. Colon organoids derived from 38 healthy individuals undergoing endoscopy were treated with 50 μmol/L aspirin or vehicle control for 72 hours and subjected to bulk RNA sequencing. Paired regression analysis using DESeq2 identified differentially expressed genes (DEG) associated with aspirin treatment. Cellular composition was determined using CIBERSORTx. Aspirin treatment was associated with 1,154 significant (q < 0.10) DEGs prior to deconvolution. We provide replication of these findings in an independent population-based RNA-sequencing dataset of mucosal biopsies (BarcUVa-Seq), where a significant enrichment for overlap of DEGs was observed (P < 2.2E-16). Single-cell deconvolution revealed changes in cell composition, including a decrease in transit-amplifying cells following aspirin treatment (P = 0.01). Following deconvolution, DEGs included novel putative targets for aspirin such as TRABD2A (q = 0.055), a negative regulator of Wnt signaling. Weighted gene co-expression network analysis identified 12 significant modules, including two that contained hubs for EGFR and PTGES2, the latter being previously implicated in aspirin chemoprevention. In summary, aspirin treatment of patient-derived colon organoids using physiologically relevant doses resulted in transcriptome-wide changes that reveal altered cell composition and improved understanding of transcriptional pathways, providing novel insight into its chemopreventive properties. PREVENTION RELEVANCE: Numerous studies have highlighted a role for aspirin in colorectal cancer chemoprevention, though the mechanisms driving this association remain unclear. We addressed this by showing that aspirin treatment of normal colon organoids diminished the transit-amplifying cell population, inhibited prostaglandin synthesis, and dysregulated expression of novel genes implicated in colon tumorigenesis.

Novel insights into the molecular mechanisms underlying risk of colorectal cancer from smoking and red/processed meat carcinogens by modeling exposure in normal colon organoids

Tobacco smoke and red/processed meats are well-known risk factors for colorectal cancer (CRC). Most research has focused on studies of normal colon biopsies in epidemiologic studies or treatment of CRC cell lines in vitro. These studies are often constrained by challenges with accuracy of self-report data or, in the case of CRC cell lines, small sample sizes and lack of relationship to normal tissue at risk. In an attempt to address some of these limitations, we performed a 24-hour treatment of a representative carcinogens cocktail in 37 independent organoid lines derived from normal colon biopsies. Machine learning algorithms were applied to bulk RNA-sequencing and revealed cellular composition changes in colon organoids. We identified 738 differentially expressed genes in response to carcinogens exposure. Network analysis identified significantly different modules of co-expression, that included genes related to MSI-H tumor biology, and genes previously implicated in CRC through genome-wide association studies. Our study helps to better define the molecular effects of representative carcinogens from smoking and red/processed meat in normal colon epithelial cells and in the etiology of the MSI-H subtype of CRC, and suggests an overlap between molecular mechanisms involved in inherited and environmental CRC risk.