Identification of neoadjuvant chemoradiotherapy resistance-associated proteins in locally advanced rectal cancer: A pilot study.

Neoadjuvant chemoradiotherapy (nCRT) resistance in locally advanced rectal cancer (LARC) leads to worse outcomes. The present pilot study aimed to identify candidate proteins associated with resistance to nCRT. Data-independent acquisition mass spectrometry on 15 formalin-fixed paraffin-embedded tumor tissues, collected before and after nCRT, from four nCRT-resistant and four nCRT-sensitive LARC cases, was performed, identifying 6,006 proteins. Before nCRT, 133 proteins were found to be more abundant in resistant tumors and were preliminarily enriched in cell junction and metabolic pathways. After nCRT, 290 proteins were found to be more abundantly expressed in resistant tumors and were preliminarily enriched in pathways associated with DNA replication, transcription, translation and metabolism. Combined analysis of datasets GSE209746 and PXD060201 prioritized branched-chain keto acid dehydrogenase E1 subunit α (BCKDHA) as a candidate resistance-associated protein. In a colorectal cancer (CRC) tissue microarray, upregulated BCKDHA expression was associated with shorter overall survival, supporting its broader clinical relevance in CRC. In SW480 cells, BCKDHA overexpression increased clonogenic survival following irradiation, whereas BCKDHA knockdown enhanced radiosensitivity. These changes were accompanied by altered ataxia telangiectasia mutated, checkpoint kinase 2, DNA repair protein RAD51 homolog 1-associated signaling and γ-H2A histone family member X dynamics after irradiation. Collectively, these data identified BCKDHA as a candidate nCRT resistance-associated protein in LARC and provided preliminary functional evidence associating BCKDHA with the response to radiotherapy and DNA damage response-associated signaling. Further validation in larger pretreatment LARC cohorts and more direct mechanistic studies is warranted.