RNA Sequencing of Exosomes Revealed Differentially Expressed Long Noncoding RNAs in Early-Stage Esophageal Squamous Cell Carcinoma and Benign Esophagitis

Abstract

Aim: To explore the roles of exosomal long noncoding RNAs (lncRNAs) in early-stage esophageal squamous cell carcinoma (ESCC) and benign esophagitis. Materials & methods: Exosomal lncRNAs were analyzed using RNA-seq and validated by quantitative real-time PCR, loss-of-function, co-culture and RNA pulldown assays. Results: Exosomal lncRNAs displayed tighter tissue-specificity, higher expression level and lower splicing efficiency than that of mRNAs. A total of 152 exosomal lncRNAs were differentially expressed between ESCC and controls. A total of 124 exosomal lncRNAs were dysregulated between ESCC and esophagitis. Knockdown of 13 ESCC-associated lncRNAs modified proliferation, migration, and apoptosis of ESCC cells. A novel lncRNA RP5-1092A11.2 was highly expressed in ESCC-derived exosomes, ESCC cells and tumor tissues. Exosomes released from RP5-1092A11.2-knockdown cells inhibited ESCC cell proliferation. Conclusion: Dysregulated exosomal lncRNAs were functionally associated with different disease status in esophagus.

Keywords::

• benign esophagitis
• early-stage esophageal squamous cell carcinoma
• exosomal lncRNAs
• functional assay
• RP5-1092A11.2

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at:www.tandfonline.com/doi/suppl/10.2217/epi-2019-0371

Availability of data

Raw exosome RNA-seq data and RPKM for lncRNAs and mRNAs were deposited in NCBI’s Gene Expression Omnibus (www.ncbi.nlm.nih.gov/geo/) with accession number GSE104926.

Financial & competing interests disclosure

This study was supported by the National Natural Science Foundation of China (NSFC) (81572908) and the Peacock Initiative Program of Shenzhen Municipality (827-000157), Shenzhen Science and Innovation Commission (KQCX2015032416521307, JCYJ20180305163428950, JCYJ20170818100842319). Science and Technology Program of Guangdong Province in China (2017B 030301016), Guangdong Medical Research Foundation (A2018312). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

The authors state that they have obtained appropriate institutional review board approval or have followed the principles outlined in the Declaration of Helsinki for all human or animal experimental investigations. In addition, for investigations involving human subjects, informed consent has been obtained from the participants involved.

Additional information

Funding

This study was supported by the National Natural Science Foundation of China (NSFC) (81572908) and the Peacock Initiative Program of Shenzhen Municipality (827-000157), Shenzhen Science and Innovation Commission (KQCX2015032416521307, JCYJ20180305163428950, JCYJ20170818100842319). Science and Technology Program of Guangdong Province in China (2017B0 30301016), Guangdong Medical Research Foundation (A2018312). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.