Fig. 3

Gene expression profiling of baseline tumors. A Volcano plot showing differentially expressed genes (DEGs) in pathological complete response (pCR) tumors compared to non-pCR tumors. B, C Functional annotation of upregulated (B) and downregulated genes (C) in pCR tumors via GO analysis. D Correlation of gene expression with pCR defined by TPM values. E ROC curves assessing the prediction of pCR using TPM expression levels of the top six significantly associated genes. F Kaplan–Meier curves demonstrate the disease-free survival and overall survival of subgroup patients categorized by NHSL1 expression levels in baseline tumors. G The proportion of pCR and non-pCR patients with high or low NHSL1 protein expression in the clinical validation cohort, assessed by immunohistochemistry. H Kaplan–Meier curves showing the disease-free survival and overall survival of the clinical validation cohort stratified by baseline NHSL1 protein expression. GO, Gene Ontology; TPM, Transcripts Per Million; ROC, receiver operating characteristic