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Comprehensive bioinformatics analysis identifies candidate ciliogenesis-related genes preferentially associated with N0-stage lung squamous cell carcinoma.

Marzyeh Alipour·Mehdi Moghanibashi·Sirous Naeimi·Parisa Mohamadynejad
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Abstract

PURPOSE: There is few research on which genes play an important role in tumors without lymph metastasis. This study aimed to identify candidate molecular alterations preferentially associated with N0-stage LUSC. METHODS: we conducted a comprehensive bioinformatics analysis using publicly available The Cancer Genome Atlas (TCGA) data. Differentially expressed genes (DEGs) were identified separately by comparing N0 tumors and N+ tumors with normal lung tissues. Genes dysregulated in both N0 and N+ tumors were excluded to identify candidate N0-associated genes PPI networks were constructed using STRING and Cytoscape, with module analysis performed via MCODE. Hub genes were identified using multiple Cytohubba algorithms. Functional enrichment analyses were conducted using GO, and KEGG pathways using DAVID. Gene interaction networks were further explored using GeneMANIA. Immune cell infiltration was evaluated with TIMER. Associations with pathological stage and patient survival were assessed using GEPIA and other relevant tools. RESULTS: A total of 1103 candidate N0-associated DEGs were identified, including 748 upregulated and 355 downregulated genes. The PPI network contained five major MCODE clusters. One cluster (MCODE 4) included TTC30A, TTC30B, BBS7, and KIF3B genes implicated in ciliogenesis. TTC30B showed significant differential expression across pathological stages in the overall LUSC cohort. Seven consensus hub genes (ERBB2, CHUK, CASP8, NOTCH1, HNF4A, CREBBP, and IRS1) were identified based on their consistent ranking across multiple CytoHubba algorithms. Upregulated candidate N0-associated genes were primarily enriched in immune-related processes, including B-cell-mediated immunity and humoral responses, whereas downregulated genes were enriched in lysosomal and trans-Golgi network-related pathways. Exploratory immune infiltration analyses identified associations between the four ciliogenesis-related genes and several immune cell populations. CONCLUSIONS: This study identified candidate molecular signatures preferentially associated with N0-stage LUSC, including ciliogenesis-related genes and consensus hub genes. These findings provide hypotheses regarding molecular features of N0-stage LUSC and warrant further validation in independent cohorts and experimental studies.

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HumansLung NeoplasmsComputational BiologyCarcinoma, Squamous CellGene Expression Regulation, NeoplasticCiliaGene Expression ProfilingProtein Interaction MapsBiomarkers, TumorBBS7CiliogenesisKIF3BLUSC N0 statusTTC30ATTC30BJournal Article

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Marzyeh Alipour, Mehdi Moghanibashi, Sirous Naeimi, Parisa Mohamadynejad. 2026-08-31. Comprehensive bioinformatics analysis identifies candidate ciliogenesis-related genes preferentially associated with N0-stage lung squamous cell carcinoma.. https://doi.org/10.1016/j.compbiomed.2026.111902

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