GSE104926 ( lncRNA+mRNA )

esophagitis ( esophageal )

RNA-seq of exosomes identifies lncRNA profiles that distinguish early-stage esophageal squamous cell carcinoma (ESCC) from non-malignant esophagitis

Cancer : 6 / Control : 6

Illumina Casava1.8.2 software was used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat2 with --segment-mismatches 2 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 –r 70 --library-type fr-unstranded. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.

We report the application of RNA sequencing technology for high-throughput profiling of transcriptomes in plasma exosomes from early-stage ESCC and esophagitis. By analyzing over 95G of clean reads (depleted rRNA), we found that expression features of exosomal lncRNAs were distinct from that of exosomal mRNAs. We identified differentially expressed exosomal lncRNAs and mRNAs for ESCC, and esophagitis. We further analyzed the biological functions of differentially expressed lncRNAs using GO, KEGG, as well as knockdown assay with siRNAs. This study provides information for identifying cancer and non-malignant disease relevant exosomal lncRNAs through integrative analyses of RNA sequencing data.

Examination and comparison of lncRNAs and mRNAs in exosomes from ESCC, esophagitis, and healthy control, respectively.

Tian L, Yang L, Zheng W, Hu Y et al. RNA sequencing of exosomes revealed differentially expressed long noncoding RNAs in early-stage esophageal squamous cell carcinoma and benign esophagitis. Epigenomics 2020 Mar;12(6):525-541. PMID: 32043367

Exosomes were isolated from plasma using the Ribo-Exosome-Isolation-Reagent-Kit C10110. Total RNA was isolated from exosome using the Trizol (invitrogen) reagents.

total RNA

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