Multi-omics integration and clinical validation identify CKAP2 as a diagnostic biomarker for bladder cancer

Bladder cancer (BC) remains a prevalent malignancy with a high recurrence rate; however, the lack of specific biomarkers hinders early detection and effective management. Although Cytoskeleton-Associated Protein 2 (CKAP2) has been implicated in tumorigenesis, its diagnostic value and biological function in BC have not been fully elucidated. This study aimed to identify and rigorously validate CKAP2 as an important diagnostic biomarker using a multi-omics approach integrated with clinical validation.

Differential expression analysis and machine learning-based feature selection were employed to screen for candidate biomarkers, identifying CKAP2 as a key gene of interest. Mendelian randomization (MR) was used to assess the causal relationship between CKAP2 and BC risk. To evaluate clinical utility, a diagnostic model based on logistic regression was established and validated in an independent real-world cohort of 127 tissue samples, including 50 pairs of matched tumor and adjacent normal tissues, 21 independent tumor tissues, and 6 independent adjacent normal tissues. Additionally, single-cell RNA sequencing (scRNA-seq) and cell-cell communication analyses were performed to dissect the role of CKAP2 within the tumor microenvironment.

CKAP2 expression was significantly upregulated in BC tissues compared to that in normal tissues (log2FoldChange = 1.53, p < 10⁻⁵). MR analysis provided evidence supporting a potential causal association between elevated CKAP2 expression and increased BC risk. In the external clinical validation, the CKAP2-based model demonstrated exceptional discrimination with an Area Under the Curve (AUC) of 0.931. Calibration curves indicated a high agreement between the predicted and observed probabilities, while Decision Curve Analysis (DCA) confirmed a substantial clinical net benefit. Mechanistically, scRNA-seq localized high CKAP2 expression primarily to cancer cells, and cell-cell communication analysis suggested that CKAP2 may play an important role in modulating tumor-stroma interactions, particularly with fibroblasts.

Our integrated analysis supports the potential utility of CKAP2 as a diagnostic biomarker for BC. By integrating multi-omics analysis, causal inference, and validation in an independent clinical cohort, these results consistently point to CKAP2's diagnostic potential and suggest its involvement in BC progression.