Abstract 2873: Identification of FXR1-associated protein complexes in lung cancer
Authors: Jun Qian, Yong Zou, Megan Hoeksema, Bradford Harris, Heidi Chen, Pierre Massion
Journal: Cancer Research (2016)

Abstract RNA-binding proteins (RBPs) are the master regulators of mRNA processing and translation and are often aberrantly expressed in cancer. We have recently identified Fragile X Mental Retardation-Related 1 (FXR1) as a novel cancer gene in non-small cell lung cancer (NSCLC) and its expression is correlated with poor prognosis in multiple human cancers. FXR1 encodes an RNA binding protein (RBP) that belongs to the family of fragile X-related proteins including the fragile X mental retardation protein (FMR1) and FXR2. Inactivation of FMR1 expression is the cause of the Fragile X syndrome in humans. Little is known for the function of FXR1 in human cancers. In this study, endogenous FXR1 or a Flag-tagged FXR1 was immunoprecipitated from H520, a lung squamous carcinoma cell line, and analyzed by shotgun proteomics. The Flag-tagged FXR1 was also transfected into human HEK293 cells and followed by co-immunoprecipitation and shotgun proteomic analysis. In total we found 206 proteins enriched in H520 with more than two-fold change spectral counts over the IgG control. Of the 206 proteins, 49 were detected in HEK293 cells as well and 157 were only detected in H520. KEGG pathway analysis indicated enrichment of proteins involved in ribosomal function, RNA transport and proteasome. To identify lung cancer related proteins, we interrogated the mRNA expression of 206 proteins in The Cancer Genome Atlas (TCGA) lung cancer dataset (1013 tumors,109 normal), in a combined NSCLC dataset (1392 tumors, 240 normal) from the Gene Expression Omnibus (GEO) and in a previously reported dataset of putative FXR1 target mRNAs and found 75 altered genes in common. Among these, we found that 24 genes were not only unregulated in all NSCLC samples (n = 2405, FDR&amp;lt;0.007) but also positively correlated with FXR1 (p&amp;lt;0.05). Gene ontology analysis revealed 22 genes were enriched in cellular macromolecule metabolic process including six genes in cell cycle regulation and seven genes in mRNA processing (p = 0.0017). Disease association analysis showed six genes were enriched in immunologic deficiency syndromes (p = 0.002), consistent with post-transcriptional suppression of tumor necrosis factor-alpha (TNFα) by FXR1 and further implying a role for FXR1-associated complex in the suppressed immune response pathway we previously identified in squamous cell carcinoma of the lung. Lastly, survival analysis indicated that this 25-gene signature (BUB3,CSNK2A1,DARS,DHX9,FXR1,HDAC2,HNRNPAB,HSP90AA1,KPNB1,LMNB1,MCM4,MSH6,NUP205,PRKDC,PSMC5,PSMD3,SFPQ,SMARCC1,SMC4,SNRPD1,STK38L,TNPO1,UCK2,XPO1 and XRCC5) was significantly associated with worse overall survival in NSCLC (HR = 1.84, p = 0.01, adjusted for age, gender, stage and smoking history). Together, these data suggest the 24 proteins/mRNAs are closely associated with FXR1 in lung cancer and may form critical core complexes that are associated with NSCLC tumorigenesis. This work was supported by RO1 CA102353 to PPM. Citation Format: Jun Qian, Yong Zou, Megan Hoeksema, Bradford Harris, Heidi Chen, Pierre Massion. Identification of FXR1-associated protein complexes in lung cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2873.