Coexpression and functions of the colinear genes CD47 and IFT57 in thyroid cancer
Higher CD47 expression in some cancers correlates with poor survival. In contrast, higher CD47 mRNA expression in papillary thyroid carcinomas correlated with significantly improved overall survival. IFT57 was the top gene coexpressed with CD47 in these tumors, and higher IFT57 mRNA correlated with significantly improved overall and disease-free survival. IFT57 is a component of the primary cilium, which also regulates cancer pathogenesis. IFT57 and CD47 are colinear genes in humans, and this synteny is highly conserved across amniote genomes. Transcriptional regulators have been identified that increase CD47 expression in cancers, but its proximity suggested that IFT57 could be coregulated. CD47 and IFT57 mRNAs were also coregulated in anaplastic thyroid carcinoma cell lines and carcinomas of multiple tissues. Anaplastic thyroid carcinoma cell line mutants with decreased IFT57 or CD47 expression were used to define IFT57-dependent phenotypes and gene expression. Loss of IFT57 expression regulated transcripts involved in cell motility and extracellular matrix pathways. Altered cell motility was confirmed in IFT57 mutants. Three IFT57-dependent genes identified in the cell lines exhibited stronger coexpression with IFT57 than with CD47 in papillary thyroid tumors. CRACD was identified as an IFT57-specific target that correlates with survival in lung as well as papillary thyroid carcinomas. Overall design: The 8505C cell line used to generate IFT57KO and CD47KO mutants via transfecting CRISPR plasmids. The Wild-type (WT), two clones of IFT57 depleted cells (SG1F4 and SG2B6), and pooled CD47 KO cells were selected for the current study.  WT and mutant 8505C cell lines were cultured in complete RPMI 1640 medium supplemented with glutamine, 10% FBS, and penicillin/streptomycin (ThermoFisher Scientific) and cells were harvested by washing with IXPBS and  cell pellets were harvested for RNA extraction.