Acrolein-Linked Gene Perturbation Tracks Tumor Immune Heterogeneity in Colorectal Cancer

Acrolein, a highly reactive aldehyde produced during lipid peroxidation and inhaled in tobacco smoke or ingested in heated foods, has long been suspected of driving cancer, but its molecular fingerprints inside human colorectal tumors have remained poorly mapped. A new integrative study published in Frontiers in Cardiovascular Medicine now shows that genes known to respond to acrolein are measurably dysregulated in colorectal cancer and that the degree of this perturbation co-varies with the immune and stromal architecture of tumors. The work, led by Jianbo Han and colleagues at The Second Hospital of Nanjing, combines curated toxicology databases, bulk tumor transcriptomes, single-cell sequencing, and a laboratory validation experiment into a single toxicogenomic framework.

The team began by mining the Comparative Toxicogenomics Database, a manually curated repository of chemical-gene interactions, to define a rigorous prior. After filtering the database’s acrolein records to direct human evidence and excluding co-exposure entries, they identified 179 unique primary target genes. These were organized into interpretive modules covering oxidative and electrophile stress, apoptosis and DNA damage, inflammation and immune signaling, barrier and epithelial-mesenchymal transition programs, and cell-cycle control. The researchers stress that these groupings are analytic conveniences rather than additional database assertions, preserving the traceability of the underlying literature evidence.

To test whether this curated target set is perturbed in colorectal cancer, the authors reanalyzed bulk RNA-sequencing data from The Cancer Genome Atlas, comprising 624 primary tumor profiles and 51 solid-tissue normal profiles across the COAD and READ projects. A count-aware differential expression analysis using the DESeq2 negative-binomial framework identified 5,594 genes passing a threshold of false discovery rate below 0.05 and an absolute log2 fold change of at least 1. Of the 179 curated acrolein targets, 155 were measurable in the bulk dataset and 43 met the differential-expression threshold, with 23 higher and 20 lower in tumors. The signal was strongly concordant between colon and rectal cancers, with a Spearman correlation of 0.91 across nearly 20,000 genes.

A central metric in the study is the target dysregulation burden, calculated for each sample as the mean absolute z score of measured acrolein targets relative to normal-tissue reference expression. This burden was substantially higher in tumors than in normal tissue, 1.96 versus 0.75, a difference of 1.21 with a Welch p-value of 3.62e-42. All five prespecified target modules showed positive tumor-minus-normal differences, with the largest shifts in barrier and EMT targets and cell-cycle control targets. The authors emphasize that this is an expression-based perturbation proxy, not a measurement of acrolein exposure in patients, since the transcriptomic data cannot reveal the source, dose, or timing of any actual chemical exposure.

The most provocative findings concern the tumor immune microenvironment. Within primary tumors, target burden correlated negatively with T-cell and endothelial expression programs, each with a Spearman rho of -0.27, and with myeloid, fibroblast-extracellular matrix, and antigen-presentation programs, each around -0.20. Only the cell-cycle program correlated positively, at rho of 0.20. When tumors were stratified into low, middle, and high target-burden quartiles, lower-burden tumors tended to show more positive immune-stromal scores than high-burden tumors. The authors are careful to frame these as correlations among standardized expression summaries rather than evidence of immune exclusion or stromal depletion, and they note that fibroblast and immune programs are biologically heterogeneous and cannot be reduced to a single pro- or antitumor phenotype.

To localize the perturbation at cellular resolution, the team turned to single-cell RNA-sequencing data from the public dataset GSE231559, processing six tumor and three normal libraries into 24,128 retained cells after quality control. Cells were assigned to eight marker-supported compartments: epithelial, T cells, NK cells, B and plasma cells, myeloid, fibroblasts, endothelial, and mast cells. Descriptive mean target scores were highest in myeloid cells at 0.455, fibroblasts at 0.424, and endothelial cells at 0.344, while the 154 measurable targets were detectable across all eight compartments rather than confined to a single lineage. Module-level patterns showed barrier and EMT scores particularly high in endothelial, epithelial, and fibroblast compartments, and inflammation and immune-signaling scores relatively high in myeloid and mast cells.

Comparing the bulk and single-cell scales for 154 shared targets yielded a modest but statistically detectable rank concordance of rho equal to 0.31 with a p-value of 6.95e-05. This partial agreement reflects genuine differences in platform, sampling structure, and inferential unit: the bulk analysis represents hundreds of patient-level profiles, whereas the single-cell component contains only nine libraries with unequal cell-type coverage and just three normal controls. The authors explicitly caution that the single-cell results support localization and heterogeneity descriptions, not claims of a unique cellular origin or a demonstrated intercellular signaling mechanism.

To add an experimental anchor, the researchers performed RT-qPCR in HCT 116 colorectal carcinoma cells exposed to 10 micromolar acrolein for six hours, following MIQE reporting guidelines and the comparative Ct method with GAPDH as the reference gene. Three biological replicates with three technical replicates each showed vehicle-normalized relative expression of 2.18-fold for NFKBIA, 1.83-fold for GSTP1, and 1.57-fold for VIM, all increased, while GPX4 decreased to 0.71-fold. This mixed directional response mirrors the broader conclusion that acrolein-linked targets do not behave as a uniformly shifted gene set, and it provides targeted validation for four prespecified genes without establishing a genome-wide or patient-level effect.

The authors are unusually explicit about the boundaries of their claims. The study does not measure acrolein or acrolein-derived protein adducts in the analyzed patient samples, cannot establish causal toxicological effects in human tumors, and does not demonstrate a specific signaling pathway. The target-burden proxy can be influenced by tumor composition and transcriptional state, the single-cell annotation uses broad marker-based labels that may not resolve finer functional subtypes, and the qPCR experiment covers only four genes in one cell line at a single concentration and time point. Dose-response experiments, independent cell models, protein and adduct measurements, spatial validation, and independent cohorts will all be needed before the biological significance of these associations can be determined.

Nevertheless, the study offers a template for how toxicogenomic evidence can be integrated with modern cancer transcriptomics. By anchoring a curated chemical-gene prior in population-scale bulk data, resolving its cellular localization with single-cell sequencing, and validating selected responses in vitro, the researchers have built a hypothesis-generating framework that links an environmental and endogenous carcinogen to the immune-stromal heterogeneity of colorectal cancer. Whether acrolein-driven perturbation ultimately proves to be a driver of immune evasion, a biomarker of tumor state, or a consequence of tumor metabolism, the analytical pipeline established here provides a reproducible path for answering that question in future mechanistic and clinical studies.

Subject of Research: Acrolein target gene perturbation and tumor-immune microenvironment heterogeneity in colorectal cancer

Article Title: Acrolein target-linked toxicological perturbation and tumor-immune microenvironment heterogeneity in colorectal cancer

Article References: Cheng, G., Shan, L., Shi, W., Liu, X., Tao, X., & Han, J. (2026). Acrolein target-linked toxicological perturbation and tumor-immune microenvironment heterogeneity in colorectal cancer. Frontiers in Cardiovascular Medicine, 13, Article 1929802. https://doi.org/10.3389/fcvm.2026.1929802

Image Credits: AI Generated

DOI: 10.3389/fcvm.2026.1929802

Keywords: acrolein, colorectal cancer, toxicogenomics, tumor microenvironment, single-cell RNA-seq, TCGA, Comparative Toxicogenomics Database, RT-qPCR, target-linked, toxicological, perturbation, tumor-immune