The influence of PPFIA1 silencing to gene expression in breast carcinoma cell line and head and neck squamous cell carcinoma cell lines by RNA-sequencing in three dimensional collagen I

PPFIA1 (encodes for liprin-a1) locates at the commonly amplified 11q13 region in cancer, but the precise mechanism of liprin-a1 function has remained unclear. In this study we show how genes are differentially expressed after liprin-a1 knockdown in different cell lines, grown in three dimensional matrix. The overall goal was to gain insight into the mechanism by which liprin-a1 has an effect on the progression of head and neck carcinomas and breast carcinomas in three dimensional environment. Overall design: RNA-seq analysis was carried out to identify differentially expressed genes between the two conditions, control (shScr) and PPFIA1 silenced (shPPFIA1), in breast and head and neck squamous cell carcinoma cell lines cultivated in three dimensional collagen I. Cells were transduced with shPPFIA1 using three different shRNA constructs (shPPFIA1_14, shPPFIA1_44 and shPPFIA1_69) and selected with puromycin. shScramble (shScr) with three replicates were done with separate transductions and used as controls. Cells were grown inside three dimensional collagen I culture for five days, after which RNA was extracted and further prosessed for RNA sequencing analysis. Illumina NextSeq High Output 1 x 75 bp was used.