Characterization of Immune Landscape Based on Homologous Recombination Deficiency Associated Signatures and Identification of Knockdown of ERCC6L to Promote Radiosensitivity in Breast Cancer

Background

Homologous recombination deficiency (HRD) exhibits significant associations with the occurrence, progression, and prognosis of breast cancer. However, the primary breast cancer HRD positivity rate is merely 24%. The identification of markers associated with HRD is crucial for the development of novel therapeutic approaches for breast cancer. The role of the oncogene ERCC6L in breast cancer remains unclear, and its interaction with radiotherapy has yet to be explored, necessitating further investigation for clarification.

Methods

We employed WGCNA to identify genes associated with the HRD score, utilizing public HRD score and genetic data from TCGA breast cancer, with their clinical characteristics. Subsequently, we employed various machine learning methods to filter relevant genes. The final four genes were obtained through random forest and stepCox, and their performance was validated in TCGA, GSE96058, and METABRIC datasets. Next, we assessed the tumor immune microenvironment using methods such as ssGSEA, GSVA, CIBERSORT, ESTIMATE, and single-cell analysis. Finally, we validated the downregulation of ERCC6L, increasing DNA damage and enhancing radiation sensitivity, through immune fluorescence, flow cytometry, plate cloning, and western blot.

Results

A prognostic model named HRAS was established through machine learning, consisting of four genes (ERCC6L, UBE2T, TPX2, and SLC7A5). The indicator exhibited excellent predictive performance on the prognosis and the efficacy of immunotherapy and radiotherapy of breast cancer patients in independent datasets. Breast cancer patients with high HRAS scores showed higher TMB and stemness, increased expression of immune checkpoints, reduced immune cell infiltration, and poorer prognosis in the context of immunotherapy and radiotherapy. Experimental validation demonstrated that knockdown of ERCC6L markedly elevated DNA damage, enhanced apoptosis, and induced cell cycle arrest in response to radiation therapy, thereby sensitizing cells to radiation.

Conclusion

The HRD-related signatures displayed strong predictive capabilities for the prognosis in multiple datasets and the efficacy of immunotherapy and radiotherapy of breast cancer patients. Moreover, the composite indicator reflected the immune microenvironment characteristics and could be novel markers for predicting the prognosis and clinical treatment outcomes in breast cancer patients. Our experiments first elucidated the role of ERCC6L in enhancing radiation-induced DNA damage, presenting a novel target for strategies aimed at sensitizing cancer cells to radiotherapy.