LncRNA LLNLR-299G3.1 promotes ESCC progression by regulating cancer related genes through RNA-chromatin interactions

Abstract Background Accumulating evidence has indicated that long non-coding RNAs (lncRNAs) play critical roles in the development and progression of cancers, including esophageal squamous cell carcinoma (ESCC). However, the mechanisms of lncRNAs in ESCC are still largely unknown and therapeutic attempts for in vivo targeting disease-associated lncRNA remain a challenge. Methods By RNA-sequencing analysis, we identified that LNLR-299G3.1 was a novel ESCC-associated lncRNA. Expression level of LLNLR-299G3.1 was determined by qRT-PCR and RACE. The functional significance of LLNLR-299G3.1 was assessed by knockdown or over-expression. plCSA-BP (placental chondroitin sulfate A binding peptide)-coated nanoparticles (NPs) were developed for targeting delivery of antisense oligonucleotide (ASO)-LLNLR-299G3.1 in vivo. RNA pull-down, mass spectrometry, RNA-seq, ChIRP-seq (chromatin isolation by RNA purification and sequencing), qRT-PCR assays, and rescue assays were performed to explore the mechanisms of LLNLR-299G3.1 in ESCC. Results LNLR-299G3.1 was up-regulated in ESCC tissues and cells and promoted ESCC cell proliferation and invasion. Silencing of LLNLR-299G3.1 with ASO resulted in opposite effects. Moreover, intravenous delivery of pICSA-NP loaded ASO (pICSA-ANPs) strongly inhibited ESCC tumor growth and significantly improved animal survival in vivo. Mechanistically, LLNLR-299G3.1 bound to cancer-associated binding proteins and regulated the expression of cancer-related genes, including OSM, TNFRSF4, HRH3, and SSTR3. ChIRP-seq revealed that these genes contained enriched chromatin binding sites for LLNLR-299G3.1. Rescue experiments confirmed that the effects of LLNLR-299G3.1 on ESCC cell proliferation were dependent on interaction with HRH3 and TNFRSF4. Conclusion LLNLR-299G3.1 was a novel oncogenic lncRNA that promoted ESCC malignancy through gene-chromatin interactions. In vivo targeting ESCC by pICSA-BP-ANPs may be an effective strategy for the treatment of lncRNA-associated ESCC.