Multi-omics analysis of locally advanced esophageal cell squamous carcinoma treated with radio-chemotherapy.

Abstract

e16106 Background: The incidence rate of esophageal cell squamous carcinoma (ESCC) increases every year worldwide. Although the molecular characteristics of locally advanced esophageal carcinoma have been extensively studied, TCR evolution dynamics before and after treatment in patients with ESCC undergoing radical radiotherapy and chemotherapy are unknown. Methods: In this study, we performed whole-exome sequencing (WES) and RNA sequencing (RNA-seq) on tumor tissues from 11 ESCC patients who received radiotherapy and chemotherapy. T cell receptor (TCR) sequencing was performed in 33 ESCC blood samples, which included three time points: pre-treatment, on-treatment and post-treatment. We compared TCR clonality and Shannon index among the pre-treatment, on-treatment and post-treatment ESCC patients using paired samples Wilcoxon test. The t test was uesd for statistical analysis comparing the clonality and clonal frequency between patients with mutant and wild-type gene. Results: The median TMB is 3.32 mutations/Mb (range 1-6 muts/Mb). We identified nine significantly mutant genes including TP53 (100%), MUC17 (55%), FLG (45%), FLG2 (36%), FOXN1 (27%), HIST1H1E (18%), VN1R1 (18%), RIPK3 (9%), and ZNF628 (9%). Clonality was significantly increased from pre-treatment to post-treatment (p = 0.008) and from on-treatment to post-treatment (p = 0.04). Two patients exhibited an continuous increase of TCR CDR3 (CHCLPAED_AGGGELFF) frequency in post-treatment compared to on-treatment patients. Three patients had elevated level of CDR3 amino acid sequence (CASSLDSNQPQHF) after treatment. To explore the effect of the mutant gene on the TCR clonal pattern, we found that the baseline clonality and clonal frequency in mutant FAT1 (MUT) were significantly lower than that in wild-type (WT) patients (p = 0.044 and p = 0.013, respectively), while they were not significant after treatment between FAT1-MUT and WT patients. Intriguily, in FAT1-MUT patients, the clonality and clonal frequency underwent therapy were higher than that at baseline. The results suggested that the FAT1-MUT patients might be sensitive to treatment and FAT1 might contribute to immune response upon radio-chemotherpay. During radio-chemotherapy, the clonality and clonal frequency in INTS1-MUT and LCT-MUT patients had the similar phenomenon to the FAT1-MUT patients. Interestingly, a higher clonal frequency was observed after radiotherapy and chemotherapy than that of pre-treatment (p = 0.0086) in patients with mutant KMT2D (an epigenetic modifier coding lysine methyl transferase 2D). Conclusions: TCRs is clonal expansion after radiotherapy and chemotherapy in ESCC, suggesting an immune-activated microenvironment after radio-chemotherapy. Our multi-omics analysis provided the basic TCRs dynamics and its genomic and epigenomic association during the radio-chemotherapy of esophageal cell squamous carcinoma.