Integrated single-cell and machine learning analysis identifies PMAIP1 as a novel biomarker for predicting prognosis and immunotherapy response in colorectal cancer.

Metastasis in colorectal cancer (CRC) is the primary driver of its high mortality rate, with dysregulation of apoptosis and remodeling of the tumor microenvironment (TME) serving as key biological events driving disease progression. However, the intrinsic molecular connections between these processes—particularly the dynamic changes during the progression from primary tumors to liver metastases—remain to be systematically elucidated. This study aims to identify core genes regulating the crosstalk between apoptosis and immunity in CRC using multidimensional computational biology approaches and to explore their clinical value as prognostic biomarkers and potential therapeutic targets. This study integrated single-cell RNA sequencing (scRNA-seq) data with bulk transcriptomic data from The Cancer Genome Atlas (TCGA) database. We first utilized scRNA-seq to dissect cellular heterogeneity and communication networks in CRC primary tumors and liver metastases. Subsequently, weighted gene co-expression network analysis (WGCNA) and differential expression analysis were employed, combined with machine learning algorithms (LASSO, Random Forest, XGBoost), to screen features from apoptosis- and immunity-related gene sets and pinpoint key candidate genes. Finally, the biological functions and clinical significance of the core gene were systematically validated through pan-cancer analysis, immune infiltration analysis, mutation profile analysis, prognostic model construction, and validation via real-time quantitative PCR (RT-qPCR) in clinical samples. Single-cell profiling revealed that colorectal cancer (CRC) liver metastases exhibit a distinct pro-inflammatory immune microenvironment characterized by the enrichment of CD8⁺ effector memory T cells and inflammatory monocytes, along with extensive remodeling of cell-cell communication networks centered on the MIF and CD99 signaling pathways. Through multi-level bioinformatics analysis, we identified the apoptosis-related gene PMAIP1 as a central regulatory hub mediating these processes. Clinical cohort and pan-cancer analyses demonstrated that PMAIP1 is significantly overexpressed across multiple tumor types, particularly in CRC, where its elevated expression serves as an independent predictor of poor prognosis (HR = 0.39, p = 0.028). Further investigation uncovered a critical biological paradox: On the one hand, the high expression of PMAIP1 was positively correlated with the infiltration of core effector immune cells, such as CD8⁺T cells. CD8⁺T cells are the key immune cells mediating tumor cell killing, and their enrichment is expected to form an effective anti-tumor immune barrier, which is consistent with the characteristics of the “pro-inflammatory” immune microenvironment. On the other hand, the high expression of PMAIP1 is also significantly associated with the up-regulation of multiple immune checkpoint molecules, such as PD-1 and PD-L1. The activation of immune checkpoint molecules directly induces the functional exhaustion of infiltrating CD8⁺T cells, which is manifested as decreased proliferation ability, decreased secretion of killer cytokines, and loss of anti-tumor activity. In short, PMAIP1 both “recruits” effector immune cells with antitumor potential and “weakens” these cells by upregulating immune checkpoint molecules, resulting in the coexistence of two contradictory phenotypes of “increased immune cell infiltration” and “decreased immune response efficiency”. Finally, it still promotes the progress of colorectal cancer and is related to the poor prognosis of patients. A nomogram model incorporating PMAIP1 demonstrated strong performance in predicting patient survival, and its overexpression in clinical CRC samples was validated by RT-qPCR. This study systematically delineates the immune landscape of CRC primary tumors and liver metastases, and for the first time reveals the apoptosis gene PMAIP1 as a critical regulatory node linking cellular apoptosis to immune microenvironment remodeling. PMAIP1 not only emerges as a potent, novel biomarker for poor prognosis in CRC but also, through its dual functions in regulating immune infiltration and checkpoints, represents a highly promising target for guiding combined immunotherapy strategies. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-32933-8.