biostudies-literatureUnknown9(10)Zhao Q<h4>Objectives</h4>Although the genomic landscape of small-cell carcinoma of the oesophagus (SCCE) has been dissected, its transcriptome-level aberration and immune microenvironment status are unknown.<h4>Methods</h4>Using ultra-deep whole transcriptome sequencing, we analysed the expression profile of nine paired SCCE samples and compared the transcriptome with public transcriptomic data set of normal oesophageal mucosa and other cancer types. Based on the transcriptome data, the immune signatures were investigated. The genomic data of 55 SCCE samples were also applied for immune checkpoint blockade therapy (ICBT) biomarker evaluation including microsatellite instability (MSI) status, tumor mutation burden (TMB) and neoantigen burden (TNB). Also, we evaluated the CD8, CD68 and programmed Clinical & translational immunologye1173https://www.ebi.ac.uk/biostudies/studies/S-EPMC7536114biostudies-literatureSystematic analysis of the transcriptome in small-cell carcinoma of the oesophagus reveals its immune microenvironment.PMC7536114Wu QNYang HLiu MLin DXWang FChen YXLiu ZXQi JJSheng HZheng JLu YXWang YNXu RHJia WHZhao QYun JPBei JXWang ZXZhang CZuo ZXFeng YFHu JJFu JHfalseSystematic analysis of the transcriptome in small-cell carcinoma of the oesophagus reveals its immune microenvironment.<h4>Objectives</h4>Although the genomic landscape of small-cell carcinoma of the oesophagus (SCCE) has been dissected, its transcriptome-level aberration and immune microenvironment status are unknown.<h4>Methods</h4>Using ultra-deep whole transcriptome sequencing, we analysed the expression profile of nine paired SCCE samples and compared the transcriptome with public transcriptomic data set of normal oesophageal mucosa and other cancer types. Based on the transcriptome data, the immune signatures were investigated. The genomic data of 55 SCCE samples were also applied for immune checkpoint blockade therapy (ICBT) biomarker evaluation including microsatellite instability (MSI) status, tumor mutation burden (TMB) and neoantigen burden (TNB). Also, we evaluated the CD8, CD68 and programmed 2020-01-01T00:00:00Z20202026-04-29T18:02:38.405Z2020-10-29T09:07:09ZS-EPMC75361143303361610.1002/cti2.1173