GSE111786
Impact of shRNA-mediated KLF4 down-modulation on the transcriptome profile of human keratinocyte precursor cells
Characterization at the global transcriptome level of the gene networks ensuring the regulation of the immature status of cutaneous stem- and precursor-cells is a necessary step to further understand the concept of 'stemness' in this tissue. Moreover, considering possible clinical applications, the search for molecular targets to control stem cell characteristics and regenerative capacity is a necessary step to improve therapeutic approaches. Cutaneous cell therapy is concerned by this objective, as skin graft bioengineering requires a phase of ex vivo expansion of keratinocytes from donors, during which the preservation of a sufficient stem cell pool is critical for graft take and long-term skin regeneration. We have investigated the role of transcription factor KLF4 in native keratinocyte precursors from adult human skin. A stable lentiviral-based shRNA-mediated KLF4 knock-down (KD) approach was developed and used to study the properties of KLF4-deficient [KLF4KD] versus control [KLF4WT] native keratinocyte precursors. Using long-term cultures and clonal assays, we found that decreased KLF4 expression increased keratinocyte precursor immaturity and clonogenic potential, thus promoting self-renewal. Importantly, [KLF4KD] keratinocyte precursors exhibited an improved grafting capacity in an in vivo skin xenograft model and in serial grafting.  To analyze the biological impact of KLF4 knock-down at the molecular level, comparative transcriptome profiling of [KLF4WT] and [KLF4KD] cells was performed using next-generation RNA sequencing (RNA-seq). This set of data provides a material that permits the dissection of genetic networks modulated by KLF4 in human keratinocyte precursor cells, and controlling their immature status and epidermis regeneration capacity. Overall design: The study is based on the comparative RNA-seq analysis of human keratinocyte precursor cells corresponding to 3 cellular contexts: 1) non-transduced wild-type (WT) cells, [KLF4WT]; 2) cells transduced with a control lentiviral vector driving the expression of the reporter gene GFP, [KLF4WT]; 3) cells transduced with a lentiviral vector driving the expression of GFP and an anti-KLF4 shRNA, [KLF4KD]. For each cellular context 3 biological replicates were conducted (Bio rep), each including 3 technical replicates (Tech rep).