GSE128898
PLIN2 knockdown alters the genome-wide gene transcription profile of leiomyoma cells
Purpose: To investigate the function of PLIN2 in human uterine leiomyoma tumorigenesis, we generated genome-wide transcription profile of leiomyoma cells after PLIN2 knockdown. Methods:  Primary leiomyoma cells were isolated from fresh uterine leiomyoma tissues and transfected with PLIN2 small interfering RNA (siRNA; 100 nM, #4392422) or non-targeting siRNA (100 nM, #4390844; Ambion, Foster City, CA) for 72 hours. Total RNA was isolated using the RNeasy Mini kit and RNA-seq library was completed per the manufacturer's instructions using the KAPA Stranded RNA-seq Kit with RiboErase (#KK8483; KAPA Biosystems, Wilmington, MA).  cDNA libraries were sequenced as single-end, 75 base-length reads on an Illumina NextSeq 500 instrument (Illumina, San Diego, CA) with an average read count of 27 million reads per sample. The quality of DNA reads, in fastq format, was evaluated using FastQC. Adapters were trimmed, and reads of poor quality or aligning to rRNA sequences were filtered. The cleaned reads were aligned to the Homo sapiens genome (hg19) using STAR. Read counts for each gene were calculated using htseq-count in conjunction with a gene annotation file for hg19 obtained from University of California Santa Cruz (http://genome.ucsc.edu). Results: A total of 3877 genes were found to be differentially expressed, with 2557 genes found to be upregulated and 1320 genes found to be downregulated by PLIN2 knockdown. Gene Ontology analysis (DAVID, https://david.ncifcrf.gov) identified cellular component organization/biogenesis (P=1.4E-27) and metabolic processes (P=1.6E-10) as the top two biological processes of genes upregulated by PLIN2 depletion. Kyoto Encyclopedia of Genes and Genomes (KEGG; DAVID) pathway analysis identified enrichment of genes involved in the cell cycle, pyruvate metabolism, fatty acid metabolism and degradation, purine and pyrimidine metabolism, apoptosis, and extracellular matrix component organization after PLIN2 depletion. Conclusions: These findings provide support for a role of PLIN2 depletion in activating metabolic activity within leiomyoma cells. Overall design: Genome-wide transcription profiling of primary human uterine leiomayoma cells with or without PLIN2 depletion using RNA-Seq