Gene Expression Profile Changes After Short-activating RNA-mediated Induction of Endogenous Pluripotency Factors in Human Mesenchymal Stem Cells

Abstract

It is now recognized that small noncoding RNA sequences have the ability to mediate transcriptional activation of specific target genes in human cells. Using bioinformatics analysis and functional screening, we screened short-activating RNA (saRNA) oligonucleotides designed to target the promoter regions of the pluripotency reprogramming factors, Kruppel-like factor 4 (KLF4) and c-MYC. We identified KLF4 and c-MYC promoter-targeted saRNA sequences that consistently induced increases in their respective levels of nascent mRNA and protein expression in a time- and dose-dependent manner, as compared with scrambled sequence control oligonucleotides. The functional consequences of saRNA-induced activation of each targeted reprogramming factor were then characterized by comprehensively profiling changes in gene expression by microarray analysis, which revealed significant increases in mRNA levels of their respective downstream pathway genes. Notably, the microarray profile after saRNA-mediated induction of endogenous KLF4 and c-MYC showed similar gene expression patterns for stem cell- and cell cycle-related genes as compared with lentiviral vector-mediated overexpression of exogenous KLF4 and c-MYC transgenes, while divergent gene expression patterns common to viral vector-mediated transgene delivery were also noted. The use of promoter-targeted saRNAs for the activation of pluripotency reprogramming factors could have broad implications for stem cell research.

Figure 1

Design of KLF4 and c-MYC saRNA candidates. (a) KLF4 locus and potential antisense target candidates. The schematic shows the genomic location of KLF4, the structure of the KLF4 transcript, and the spliced ESTs reported from various cell types in the surrounding regions. Red boxes outline the KLF4 promoter region and the closest antisense EST upstream of KLF4 (DB461753). The antisense EST DB461753 initiates roughly 15 kb from KLF4's transcription start site (TSS) and terminates more than 25 kb away. Red arrows indicate the target sites for the short-activating RNA (saRNA) candidates. (b) MYC locus and potential antisense target candidates. The schematic shows the genomic location of MYC, the structure of the MYC transcript, and the spliced ESTs reported from various cell types in the surrounding regions. Red boxes outline the MYC promoter region and the closest antisense EST upstream of KLF4 (BC042052). The antisense EST BC042052 initiates roughly 2 kb from MYC's TSS and terminates 50 kb away. Red arrows indicate the target sites for the saRNA candidates. (c) saRNA candidates for KLF4 and MYC genes. The list shows the most promising saRNAs against the antisense EST DB461753, BC042052, and saRNAs targeting KLF4 or MYC sequences within a stretch of 500 bp either upstream or downstream of the TSS for each gene. EST, expressed sequence tag; n/a, not applicable.

Figure 2

Screening of KLF4 and c-MYC short-activating RNA (saRNA) candidates in mesenchymal stem cells (MSCs). (a) RT-qPCR of KLF4 saRNAs treated in MSCs showing increase of KLF4 in KLF4-PR1. (b) RT-qPCR of KLF4 for KLF4-PR1–treated MSCs at the indicated saRNA concentrations for 6 days. (c) Western blot for Klf4 and β-actin protein and relative quantitation in control- and KLF4-PR1–treated MSCs. (d) RT-qPCR of MYC saRNAs treated in MSCs showing increase of c-MYC in MYC-PR1 and MYC-PR2. (e) RT-qPCR of MYC for MYC-PR1 and MYC-PR2–treated MSCs at the indicated saRNA concentrations for 6 days. (f) Western blot for c-Myc and β-actin protein and relative quantitation of c-Myc in control-, MYC-PR1-, and MYC-PR2–treated MSCs. Asterisks indicate statistical significance: *P < 0.05; **P < 0.01. con, control; RT-qPCR, reverse transcription-quantitative PCR.

Figure 3

Mechanism of activation by KLF4- and c-MYC–targeted short-activating RNAs (saRNAs). (a) RT-qPCR results from KLF4-PR1 saRNA-treated mesenchymal stem cells (MSCs), showing increases in newly transcribed KLF4 mRNA compared to total RNA. (b) RT-qPCR results from MYC-PR1- and MYC-PR2–treated MSCs showing increases in newly transcribed MYC mRNA compared to total RNA for MYC-PR2. Asterisks indicate statistical significance: *P < 0.05; **P < 0.01. (c) RT-qPCR results from KLF4- and MYC- saRNA-treated MSCs, showing no significant increase in mRNA levels of key interferon response genes. RT-qPCR, reverse transcription-quantitative PCR.

Figure 4

Morphological changes with saRNA treatment. Phase contrast images of MSCs transfected with the indicated saRNA on the indicated day of a 6-day time course. MSC, mesenchymal stem cell; saRNA, short-activating RNA.

Figure 5

Differential gene expression of saRNA-transfected and virus-transduced samples compared to control. (a) Expression of all genes with corrected P value <0.05 and absolute fold change >1.5 for KLF4-PR1 and KLF4 virus samples. (b) Expression of all genes with corrected P value <0.1 and absolute fold change >1.5 for MYC-PR2 and c-MYC virus samples. (c) Expression of genes with stem cell-related gene ontology, corrected P value <0.1, and absolute fold change >1.5 for KLF4-PR1 and KLF4 virus samples. (d) Expression of genes with cell cycle-related gene ontology, corrected P value <0.1, and absolute fold change >1.5 for KLF4-PR1 and KLF4 virus samples. (e) Expression of genes with cell cycle-related gene ontology, corrected P value <0.1 and absolute fold change >1.5 for MYC-PR2 and c-MYC virus samples. saRNA, short-activating RNA.

Figure 6

Validation of microarray gene expression of Klf4 and c-Myc target genes. (a) RT-qPCR of Klf4 target genes in KLF4-PR1 and Klf4 virus samples relative to control gene expression. (b) RT-qPCR of c-Myc target genes in MYC-PR2 and c-MYC virus samples relative to control gene expression. (c) RT-qPCR for KLF4-PR1 activation of stem cell and reprogramming factors relative to control gene expression. (d) RT-qPCR for KLF4-PR1 activation of OCT4 isoforms relative to control gene expression. (e) RT-qPCR for MYC-PR2 activation of KLF4. Asterisks indicate statistical significance: *P < 0.05; **P < 0.01. con, control; RT-qPCR, reverse transcription-quantitative PCR.