Comparative transcriptome analysis in induced neural stem cells reveals defined neural cell identities in vitro and after transplantation into the adult rodent brain

ABSTRACT: Reprogramming technology enables the production of large quantities of neural progenitor cells (NPCs) from somatic cells by direct transdifferentiation. However, little is known on how neural programs in these neural stem cells (iNSCs) differ from those of alternative stem cell populations in vitro and in vivo. Here, we performed transcriptome analyses on iNSCs in comparison to brain-derived neural stem cells (NSCs) and pluripotent stem cell-derived NPCs, which revealed distinct global, neural, metabolic and cell cycle-associated marks in these populations. iNSCs carried a hindbrain/spinal cord identity, which could be shifted towards caudal, partially to rostral but not towards ventral fates in vitro. iNSCs survived after transplantation into the rodent brain and exhibited in vivo-characteristics, neural and metabolic programs similar to those of transplanted NSCs. However, iNSCs vastly retained caudal identities demonstrating cell-autonomy of regional programs in vivo. These data could have significant implications for a variety of biomedical applications using iNSCs. For microarray analysis, total RNA was isolated using the RNeasy kit (QIAGEN) according to the manufacturer´s instructions and including an on-column DNA digestion. 300 µg of RNA were subsequently used in the linear amplification protocol (Ambion) including the synthesis of T7-linked double-stranded cDNA and 12 hr of in vitro transcription incorporating biotin-labeled nucleotides. cDNA samples were hybridized as biological replicates onto MouseRef-8 v2 expression BeadChips (Illumina) for 18 hr according to the manufacturer´s instructions. Chips were washed and subsequently stained with streptavidin-Cy3 (GE Healthcare), before being scanned using the iScan reader (Illumina) and the associated software. BeadStudio 3.2 software (Illumina) was used to map bead intensities to gene information. For background correction, the Affymetrix robust multi-array analysis (RMA) background correction model was applied. Variance stabilization was performed using the log2 scaling and gene expression was normalized with the method utilized in the lumi package of R-Bioconductor.

ORGANISM(S): Mus musculus

PROVIDER: GSE73722 | GEO | 2018/10/04

REPOSITORIES: GEO