The Identification of NIFK’s RNA Binding Targets and Its Prognostic Values in Lung Cancer

Abstract

BackgroundWe previously identified nucleolar protein interacting with the FHA domain of pKi‐67 (NIFK) as a poor prognostic marker in lung cancer. Furthermore, NIFK overexpression promotes cancer metastasis via decreasing casein kinase 1α (CK1α) expression, a suppressor of pro‐metastatic TCF4/β‐catenin signaling. We further observe the axis is induced by the downregulation of a novel transcription factor RUNX1. It is also known for NIFK’s biological function in regulating RNA metabolism via RNA recognition motif (RRM). However, a comprehensive analysis for identifying the RNA binding targets has not yet been reported. In this study, we aim to unravel the interactive mechanism and to characterize its potential clinical value in cancer patient cohort.MethodNIFK is pointed out to possess RNA binding function via RRM. RNA immunoprecipitation assay was performed using specific NIFK antibody in lung cancer PC13 and A549 cells after NIFK overexpression. RNA targets were analyzed by RT‐PCR and Next Generation Sequencing (NGS). In addition, expression levels were investigated by IHC staining and omics data mining. The association of the respective expression with patient survival outcome were explored in lung cancer cohorts.ResultsWe observe the increase in amount of RNA binding targets after NIFK overexpression respectively in PC13 and A549 cells as comparing with the control. Moreover, NIFK appears to bind with RUNX1 RNA but not CK1α suggesting it is the initial step of NIFK‐mediated TCF4/β‐catenin signaling regulation. NIFK also leads to RUNX1 RNA instability of which mechanism remains to be explored. RUNX1 level is observed to associate with good prognosis in lung cancer datasets (jacob‐00182‐CANDF and GSE13213). Furthermore, direct interactive RNA targets of NIFK are identified by RNA immunoprecipitation and RNA‐Seq, which indicate SYNE2 as one of targets with prognostic significance in lung cancer. Increased SYNE2 is detected upon NIFK overexpression, and the lung cancer patients stratified in high SYNE2 group appear to associate with inferior clinical outcomes.ConclusionWe first show the interactive mechanism of pro‐metastatic molecule NIFK in regulating TCF4/β‐catenin signaling and SYNE2, which might provide insights into therapeutic development for lung cancer patients.