Basal cell subsets, as biomarker to predict the therapeutic effect of neoadjuvant therapy for esophageal carcinoma

At present, neoadjuvant therapy before surgery has important application prospects in esophageal carcinoma (ESCA). However, there is still a lack of effective biomarkers to predict the prognosis of neoadjuvant therapy for ESCA.

We analyzed tumor and paired adjacent tissues from 22 stage II-IV ESCA patients (21 ESCC and 1 esophageal adenosquamous carcinoma, EASC) who received neoadjuvant chemo-immunotherapy (anti-PD-1 antibody plus platinum and albumin-bound paclitaxel) at Tangdu Hospital. The R package "CellChat" was used to analyze cell-cell communication of single-cell RNA sequencing (scRNA-seq) data. Basal cell subsets were identified and quantified using "Seurat", and their correlations with pathological response were calculated. Differentially expressed genes (DEGs) were identified using "Seurat", and 27 non-redundant DEGs were further annotated using the TIMER database.

It was found that the intercellular communication between basal cells and other cells was gradually weakened in incomplete pathological response (IPR), major pathological response (MPR), and pathological complete response (pCR). Specifically, Basal3 and Basal8 subsets exhibited strong correlations with pCR, while the Basal7 subgroup was highly correlated with IPR. Further TIMER analysis of the top 10 genes in these subsets indicated that ATF3 and JUN impacted ESCA survival.

In summary, our study found cellular characteristics of different subsets of basal cells in ESCA patients treated with neoadjuvant therapy, and found that the subsets associated with poor efficacy were Basal7, and the subsets associated with good efficacy were Basal3 and Basal8, which provided possible biomarkers for neoadjuvant therapy of esophageal carcinoma in the future.