Histomorphologic spectrum and genetic features of esophageal carcinomas with submucosal gland differentiation

Submucosal gland differentiation (SGD), including acinar and ductal differentiation, has been detected in different subtypes of esophageal carcinoma, complicating tumor classification and diagnosis. This study aims to delineate the histomorphologic characteristics and to reveal the genetic alterations and precursor squamous dysplasia of the esophageal carcinomas with SGD. A panel of immunohistochemical markers was used to recognize and subcategorize the SGD. Next-generation sequencing (NGS) was performed on selected cases. Group 1 retrospectively included 50 pure type BSCCs with SGD. Group 2 included 25 carcinomas with ductal differentiation. In group 1, the integral branching morphology was observed in 20% (10/50) of cases without auxiliary immunohistochemical examination. The carcinomas from group 2 lacked integral branching morphology but exhibited recognizable to apparent ductal structures of different sizes, shapes, and proportions. The precursor squamous dysplasia was generally of the basaloid type. BSCCs with complete SGD showed positivity of both SOX9 and SOX10, while carcinomas with incomplete SGD (ductal differentiation) were positive for SOX9 but negative for SOX10. Carcinomas with SGD showed common gene mutations (TP53, TTN, and NOTCH1) and related signal pathways (TP53 and NOTCH pathways) of conventional SCCs. Two mutation signatures, which were highly similar to the COSMIC signatures 1, 6, and 13, were identified. Compared to the SCC groups, the tumor mutation burden (TMB) was slightly elevated, likely due to a high frequency of mutations of the TTN gene and defective DNA mismatch repair. In summary, the SGD can be separated into complete and incomplete types. Esophageal carcinomas with SGD mostly arise from the basaloid squamous dysplasia, and their genetic alterations align more closely with those of conventional SCCs.