Flashlight into the Function of Unannotated C11orf52 using Affinity Purification Mass Spectrometry

Abstract

For an enhanced understanding of the biological mechanisms of human disease, it is essential to investigate protein functions. In a previous study, we developed a prediction method of gene ontology (GO) terms by the I-TASSER/COFACTOR result, and we applied this to uPE1 in chromosome 11. Here, to validate the bioinformatics prediction of C11orf52, we utilized affinity purification and mass spectrometry to identify interacting partners of C11orf52. Using immunoprecipitation methods with three different peptide tags (Myc, Flag, and 2B8) in HEK 293T cell lines, we identified 79 candidate proteins that are expected to interact with C11orf52. The results of a pathway analysis of the GO and STRING database with candidate proteins showed that C11orf52 could be related to signaling receptor binding, cell–cell adhesion, and ribosome biogenesis. Then, we selected three partner candidates of DSG1, JUP, and PTPN11 for verification of the interaction with C11orf52 and confirmed them by colocalization at the cell–cell junctions by coimmunofluorescence experiments. On the basis of this study, we expect that C11orf52 is related to the Wnt signaling pathway via DSG1 from the protein–protein interactions, given the results of a comprehensive analysis of the bioinformatic predictions. The data set is available at the ProteomeXchange consortium via PRIDE repository (PXD026986).

Uncharacterized Proteins CxORFx: Subinteractome Analysis and Prognostic Significance in Cancers

“…In neoplastic cells, aberrant activation of this pathway leads to the formation of a drug-resistant cancer phenotype [ 70 , 71 ]. An analysis of 79 candidate protein partners of C11orf52 points to its involvement in the Wnt-signaling pathway through desmoglein 1 (DSG1) [ 72 ]. In this regard, the subinteractome of C11orf52 protein contains HRAS (‘Harvey RAt Sarcoma virus oncogene’), which is one of the most mutated genes in solid tumors and SRSF protein kinase 1 (SRPK1), which was identified as part of HRAS signaling [ 73 ].…”

Plasmon‐Enhanced Single Extracellular Vesicle Analysis for Cholangiocarcinoma Diagnosis

“…Proteome Search and Bioinformatics Analysis: A proteome search was performed based on the previously published protocol [68] with minor modifications as followed. The MS raw files were converted into mzML using MSConvert (version 3.0.20033).…”