# Comprehensive analysis of mitophagy-related genes reveals prognostic signatures in breast cancer: based on immune landscapes and treatment target predict

## TL;DR

This study identifies nine mitophagy-related genes, including PBK and NEK2, that predict breast cancer prognosis and influence tumor cell growth and immune response.

## Contribution

The study introduces nine novel mitophagy-related prognostic biomarkers for breast cancer, with experimental validation of PBK and NEK2.

## Key findings

- Nine mitophagy-related genes were identified as prognostic biomarkers for breast cancer.
- PBK and NEK2 were experimentally confirmed to promote tumor cell proliferation.
- Low-risk breast cancer patients showed higher immune infiltration compared to high-risk patients.

## Abstract

Breast cancer (BC) is a common malignant tumor with high incidence and mortality rates. Mitophagy refers to a selective form of autophagy that is believed to be closely related to the occurrence and progression of BC. Identifying the mitophagy-related sites associated with BC can help us gain a deeper understanding of the underlying mechanisms of BC, laying the foundation for early diagnosis and effective treatment of BC.

RNA-seq expression data of BC were obtained from the GEO and TCGA databases. Differentially expressed genes were intersected with mitophagy-related genes from GeneCards to identify BC-associated mitophagy genes. Prognostic biomarkers were screened using Kaplan–Meier (K–M) survival and ROC analyses. Based on mitophagy-related gene expression and survival data, BC patients were classified into high- and low-risk subgroups for immune infiltration and GSEA analyses. Finally, IHC data from the HPA database and in vitro experiments, including siRNA-mediated knockdown, Western blot, CCK-8 proliferation assay, confocal microscopy and drug prediction were performed to validate the expression and biological functions of candidate biomarkers PBK and NEK2.

Through dual validation of K-M survival analysis and ROC diagnosis-treatment efficacy analysis, we ultimately identified 9 mitophagy-related prognostic biomarkers for BC, and found their expression was significantly upregulated in BC tissues. In addition, the results showed that the degree of immune infiltration in the low-risk subgroup was considered higher than that in the high-risk subgroup. Inhibition of PBK and NEK2 will have an inhibitory effect on the proliferation of BC cell. Furthermore, clinicopathological analyses confirmed a genuinely higher risk in the high-risk subgroup, with PBK and NEK2 independently associated with risk stratification.

This study elucidated the prognostic value, immune microenvironment characteristics, and molecular mechanisms of mitophagy in BC, and identified nine mitophagy-related biomarkers. Among them, PBK and NEK2 were experimentally confirmed to promote tumor cell proliferation, providing novel insights for early diagnosis and therapeutic strategies in breast cancer.