WD40 Protein NLE1 as a Novel Diagnostic Biomarker Promoting Hepatocellular Carcinoma Proliferation

Hepatocellular carcinoma (HCC) is associated with poor prognosis and high mortality. Notchless homolog 1 (NLE1) is an important WD40 protein. Although several studies have shown that NLE1 is dysregulated in cancer, the function in hepatocarcinogenesis remains unclear.

We screened for dysregulated WD40 proteins in HCC using data from the GSE5364 and GSE19665 datasets. A risk prediction model associated with WD40 proteins was constructed based on the TCGA database and validated with independent datasets (ICGC, GSE116174, and GSE14520). The significance of NLE1 was assessed using a genome-wide CRISPR screen and multiomics data from TCGA, CPTAC, multiple GEO datasets, and the single-cell dataset GSE166635. We further evaluated NLE1 expression in patient tissue microarrays. Kaplan-Meier plots, Cox regression analyses, and receiver operating characteristic (ROC) curves were used to evaluate the prognostic relevance of NLE1. Logistic regression was performed to analyse the associations between NLE1 expression and the clinical features of patients with HCC. Drug sensitivity to NLE1 was evaluated using organoid assays. Proliferation assays (CCK-8 and colony formation assays) were used to assess the effect of NLE1 on HCC cell growth.

We developed a risk prediction model based on WD40 proteins, which revealed significant differences in tumour immune cell infiltration between the high-risk and low-risk groups. In addition, high NLE1 expression was strongly associated with poor prognosis in HCC patients. Through organoid response characterization, we also found a significant correlation between NLE1 expression and sensitivity to the small molecules 17-AAG, AZD7762, and JQ1. Finally, enrichment analysis and proliferation assays confirmed that elevated NLE1 expression promotes HCC cell proliferation.

NLE1 is an independent diagnostic and prognostic biomarker that promotes the proliferation of HCC.