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Esophageal squamous cell carcinoma with basaloid features are genetically and prognostically similar to conventional squamous cell carcinoma


We compared clinicopathologic and molecular features of esophageal squamous cell carcinoma (SCC) with basaloid features to conventional SCC using surgical resections of treatment naïve esophageal carcinomas and cases available from the TCGA database. Twenty-two cases of SCC with basaloid features were identified in the Mass General Brigham pathology archives, including 9 cases with pure basaloid morphology and 13 cases with mixed other features such as conventional well- or poorly differentiated areas or sarcomatoid areas. Thirty-eight cases of conventional SCC matched by tumor stage were used as controls. HPV infection status was tested by p16 immunohistochemistry and HPV mRNA ISH. Digital slides for 94 cases of esophageal SCC from TCGA found in the Genomic Data Commons (GDC) Data Portal were reviewed. Five cases of SCC with basaloid features were identified. Genomic profiles of SCC with basaloid features were compared to the rest of 89 SCCs without basaloid features. In addition, eight tumor sections from six patients selected from our cohort underwent in-house molecular profiling. Compared to conventional SCC, SCC with basaloid features were more frequently associated with diffuse or multifocal squamous dysplasia (p < 0.001). P16 IHC was positive in 2/13 cases, whereas HPV mRNA ISH was negative in 17/17 cases (including both p16-positive cases). SCC with basaloid features and conventional SCC from TCGA showed similar rates of TP53 mutations, CDKN2A/B deletions, and CCDN1 amplifications. TP53 variants were identified in all in-house samples that had sufficient coverage. Survival analyses between SCC with basaloid features versus conventional SCC (matched for tumor stage) did not reveal any statistically significant differences. In conclusion, esophageal SCC with basaloid features has similar survival and genomic alterations to those of conventional SCC, are more frequently associated with diffuse or multifocal dysplasia, and are not associated with HPV (high-risk strains) infection.

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Fig. 1: Examples of esophageal squamous cell carcinoma (SCC) with basaloid features.
Fig. 2: Ten-year survival curves of patients diagnosed with conventional (black) and basaloid SCC (red).
Fig. 3: Digital images of five cases of SCC with basaloid features taken from TCGA.
Fig. 4: Comparative genomic landscape of basaloid and conventional SCCs from TCGA.

Data availability

The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. The publicly available datasets analyzed during the current study are available here:


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We thank Ms. Diana McGraw for administrative support.


The authors received no external funding for this work. This study was supported through intradepartmental funds.

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Authors and Affiliations



M.A.S., J.Y., and L.Z. designed the study. M.A.S., J.Y., R.A.I., F.D., A.A., D.P., J.O.W., V.D., and L.Z. collected the data. M.A.S., J.Y., R.A.I., F.D., and L.Z. analyzed the data. M.A.S. and L.Z. drafted the manuscript M.A.S., J.Y., R.A.I., F.D., A.A., D.P., J.O.W., V.D., and L.Z. revised the manuscript.

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Correspondence to Lei Zhao.

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Competing interests

M.A.S., J.Y., R.A.I., F.D., J.O.W., A.A., D.P., and L.Z. have no relevant financial disclosures. V.D. serves on the Scientific advisory boards of Incyte and Viela and receives research support from Advanced Cell Diagnostic and Agios.

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This retrospective study was approved by the Institutional Review Board of Mass General Brigham (protocol #2018P001007). No human subjects were recruited for the study.

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Sauer, M.A., Yang, J., Isidro, R.A. et al. Esophageal squamous cell carcinoma with basaloid features are genetically and prognostically similar to conventional squamous cell carcinoma. Mod Pathol (2022).

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