Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion.

Lin M, Pedrosa E, Hrabovsky A, Chen J, Puliafito BR, Gilbert SR, Zheng D, Lachman HM.
Source: BMC Biol.
Publication Date: (2016)
Issue: 10(1): 105
Research Area:
Stem Cells
Cells used in publication:
Fibroblast, dermal (NHDF-Neo), human neonatal
Species: human
Tissue Origin: dermal
Fibroblast, dermal(NHDF-Ad), human adult
Species: human
Tissue Origin: dermal
4D-Nucleofector® X-Unit
patient-derived fibroblasts from skin biopsies cultured to 50% confluency after thawing an ampoule: 6 x 10e5 cells were transfected using an Amaxa 4D-Nucleofector (P2 Primary Cell Kit from Lonza catalog# V4XP-2012, Program FF-135) with non integrating plasmids containing SOX2, KLF4, L-MYC, LIN28, and a p53 shRNA vector (Addgene Cat.# 27077, 27078, 27080), according to Okita et al. with some modification. generated iPS cells were cultured feeder-free on matrigel coated plates. After characterization of the iPS cell lines cells were differentiated in Neural progenitor cells and further differentiated in a mixed population of glutamatergic and GABAergic neurons
BACKGROUND: Individuals with 22q11.2 Deletion Syndrome (22q11.2 DS) are a specific high-risk group for developing schizophrenia (SZ), schizoaffective disorder (SAD) and autism spectrum disorders (ASD). Several genes in the deleted region have been implicated in the development of SZ, e.g., PRODH and DGCR8. However, the mechanistic connection between these genes and the neuropsychiatric phenotype remains unclear. To elucidate the molecular consequences of 22q11.2 deletion in early neural development, we carried out RNA-seq analysis to investigate gene expression in early differentiating human neurons derived from induced pluripotent stem cells (iPSCs) of 22q11.2 DS SZ and SAD patients. METHODS: Eight cases (ten iPSC-neuron samples in total including duplicate clones) and seven controls (nine in total including duplicate clones) were subjected to RNA sequencing. Using a systems level analysis, differentially expressed genes/gene-modules and pathway of interests were identified. Lastly, we related our findings from in vitro neuronal cultures to brain development by mapping differentially expressed genes to BrainSpan transcriptomes. RESULTS: We observed ~2-fold reduction in expression of almost all genes in the 22q11.2 region in SZ (37 genes reached p-value?