Prognostic biomarker study in patients with clinical stage I esophageal squamous cell carcinoma: JCOG0502-A1

Abstract

We undertook genomic analyses of Japanese patients with stage I esophageal squamous cell carcinoma (ESCC) to investigate the frequency of genomic alterations and the association with survival outcomes. Biomarker analysis was carried out for patients with clinical stage T1bN0M0 ESCC enrolled in JCOG0502 (UMIN000000551). Whole-exome sequencing (WES) was performed using DNA extracted from formalin-fixed, paraffin-embedded tissue of ESCC and normal tissue or blood sample. Single nucleotide variants (SNVs), insertions/deletions (indels), and copy number alterations (CNAs) were identified. We then evaluated the associations between each gene alteration with a frequency of 10% or more and progression-free survival (PFS) using a Cox regression model. We controlled for family-wise errors at 0.05 using the Bonferroni method. Among the 379 patients who were enrolled in JCOG0502, 127 patients were successfully analyzed using WES. The median patient age was 63 years (interquartile range, 57-67 years), and 78.0% of the patients ultimately underwent surgery. The 3-year PFS probability was 76.3%. We detected 20 genes with SNVs, indels, or amplifications with a frequency of 10% or more. Genomic alterations in FGF19 showed the strongest association with PFS with a borderline level of statistical significance of P = .00252 (Bonferroni-adjusted significance level is .0025). Genomic alterations in FGF4, MYEOV, CTTN, and ORAOV1 showed a marginal association with PFS (P < .05). These genomic alterations were all CNAs at chromosome 11q13.3. We have identified new genomic alterations associated with the poor efficacy of ESCC (T1bN0M0). These findings open avenues for the development of new potential treatments for patients with ESCC.

Keywords: esophageal squamous cell carcinoma; prognostic factor; stage I; tumor mutation burden; whole-exome sequencing.

FIGURE 1

Flow diagram for the Japan Clinical Oncology Group (JCOG) trial JCOG0502 and the present study. ESCC, esophageal squamous cell carcinoma

FIGURE 2

Landscape of genomic alterations in 127 T1 esophageal squamous cell carcinoma patients. Top graph, number of genomic alterations per sample. Bottom graph, each genomic alteration for every sample including the total number of genomic alterations for each gene. Left values show the percentage of genomic alterations in every sample for each gene. The genomic alterations are shown in color as follows: green, single nucleotide variant (SNV)‐insertion/deletion (INDEL); red, copy number alteration (CNA) amplification (Amp); blue, CNA loss. This figure was generated using the R ComplexHeatmap package

FIGURE 3

Kaplan‐Meier plots for progression‐free survival (PFS) in 127 patients with T1bN0M0 esophageal squamous cell carcinoma. A, PFS curves of patients with WT (n = 112) and those with genomic alterations in FGF19 (n = 15). B, PFS curves of patients with WT (n = 113) and those with genomic alterations in FGF4 (n = 14). C, PFS curves of patients with WT (n = 112) and those with genomic alterations in MYEOV (n = 15). D, PFS curves of patients with WT (n = 114) and those with genomic alterations in CTTN (n = 13). E, PFS curves of patients with WT (n = 106) and those with genomic alterations in ORAOV1 (n = 21)

FIGURE 4

Heatmap representation for copy number alterations at chromosome 11q13.3 in 127 patients with T1bN0M0 esophageal squamous cell carcinoma. Red, increased copy number alterations (CNA amplification); blue, decreased copy number alterations (CNA loss). This figure was generated using Integrative Genomic Viewer

FIGURE 5

Kaplan‐Meier curves for progression‐free survival in 127 patients with T1bN0M0 esophageal squamous cell carcinoma based on tumor mutational burden (TMB) as follows: TMB > 1 (mutations per megabase) (n = 67), 1 ≤ TMB < 3 (n = 34), and TMB ≥ 3 (n = 26)