A Peptide Encoded by Long Non-coding RNA NEAT1 Suppresses Cancer Growth through Interfering RAF-HSP90β Complex Stability

Abstract

Abstract NEAT1, a highly abundant non-coding RNA, is essential for regulating paraspeckle formation. Studies investigating NEAT1 function have focused primarily on transcript level interactions. Here, we investigate NEAT1 translatomes using esophageal squamous cell carcinoma (ESCC) cell lines to detect new translational events and identify their contribution to cancer phenotype. We identified three previously unreported microproteins and confirmed their endogenous expression by parallel reaction monitoring-mass spectrometry. We found that ENSEP3, a conserved 9-aa peptide, suppresses ESCC growth. ESCC tissues exhibit lower levels of ENSEP3 expression than normal tissues. ENSEP3 binds to HSP90β and disrupts the formation of RAF-HSP90β multi-molecular complexes. Sustained disruption of the RAF-HSP90β complex resulted in reduced RAF expression and MAPK-pathway inhibition. The results of in vivo murine studies showed that application of synthetic ENSEP3 peptides to patient derived tumor tissues suppressed ESCC growth by specifically inhibiting the activation of MAPK pathways. ENSEP3 is the first functional endogenous microprotein with a full-length of less than ten amino acids. This suggests that even microproteins encoded by sORF frames smaller than 30 bp could potentially possess significant regulatory functions in cellular processes.