Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Modeling the Neuropathology of Tuberous Sclerosis with Human Stem Cells Reveals a Role for Inflammation and Angiogenic Growth Factors [Cell Model]

ABSTRACT: Tuberous sclerosis complex (TSC) is a rare genetic disease characterized by mTOR hyperfunction induced benign tumor growths in multiple organs and neurological symptoms. Because the molecular pathology is highly complex and the etiology poorly understood we employed a defined human neuronal model with a single mTOR activating mutation to dissect the disease-relevant molecular responses driving the neuropathology. TSC2 deficient neural stem cells showed severely reduced neuronal functional maturation and characteristics of astrogliosis instead. Accordingly, transcriptome analysis uncovered an inflammatory response and increased metabolic activity, while ribosome profiling revealed excessive translation of ribosomal transcripts and higher synthesis rates of angiogenic growth factors. Treatment with mTOR inhibitors corrected translational alterations but not transcriptional dysfunction. These results extend our understanding of the molecular pathophysiology of TSC brain lesions, and suggest phenotype-tailored pharmacological treatment strategies. Two TSC+/- cell lines and two TSC-/- cell lines were independently generated from wild-type human embryonic stem cells by genome editting with zinc finger nucleases. Two cell lines were handled in the same way but without any known human gene editted and they are used as negative controls. Two independent biological replicates of each of the six cell lines are profiled with ribosome profiling technique.

ORGANISM(S): Homo sapiens

SUBMITTER: Jitao David Zhang

PROVIDER: E-GEOD-78959 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:In vitro neural stem cell models are widely used to model a wide range of neuropsychiatric conditions. However, how well such models correspond to in vivo brain has not been evaluated in an unbiased, comprehensive manner. We used transcriptomic analyses to compare in vitro systems to developing human fetal brain and observed strong conservation of in vivo gene expression and network architecture in differentiating primary human neural progenitor cells (phNPCs). Conserved modules are enriched in genes associated with ASD, supporting the utility of phNPCs for studying neuropsychiatric disease. We also developed and validated a machine learning approach called CoNTExT that identifies the developmental maturity and regional identity of in vitro models. We observed strong differences between in vitro models, including hiPSC-derived neural progenitors from multiple laboratories. This work provides a framework for evaluating in vitro systems and supports their value in studying the molecular mechanisms of human neurodevelopmental disease. In this GEO submission, we upload data from 5 lines of phNPCs as well as hiPSCs cultured in two different laboratories all at multiple differentiation time points. phNPCs: For each of 5 lines generated from 3 donors (15-16 PCW), two independent differentiation experiments each containing two replicates were performed and harvested at four time points (1, 4, 8, 12 wks PD; ~16 samples per line; 77 total samples). We confirmed RNA integrity by RIN score with the Agilent 2100 Bioanalyzer (mean +/- sd: 9.16 +/- 0.78). iPSC: Two hiPSC datasets were RNA profiled as part of this study. hiPSCs grown in the Kosik lab was derived from two independent, non-isogenic IPS lines: one derived from a patient carrying a mutant Tau variant G55R and one reference control. For each of these lines, two samples were harvested at each of 0, 1, 4, and 8 weeks PD (total n=16 samples). hiPSCs grown in the Gage lab were from six samples derived from 3 control lines at each of two time points (0 and 4 wk PD, total n=12 samples). Samples were randomized to microarray chip by all biological variables of interest (donor, line, passage, replicate number, differentiation week, plate date, and RIN) to control for potential batch effects.

Project description:Patients with tuberous sclerosis complex (TSC) develop hamartomas containing biallelic inactivating mutations in either TSC1 or TSC2, resulting in mammalian target of rapamycin (mTOR) activation. Hamartomas overgrow epithelial and mesenchymal cells in TSC skin. The pathogenetic mechanisms for these changes had not been investigated, and the existence or location of cells with biallelic mutations (âtwo-hitâ cells) that resulted in mTOR activation was unclear. We compared TSC skin hamartomas (facial angiofibromas and periungual fibromas) to normal-appearing skin of the same patient, and observed more proliferation and mTOR activation in hamartoma epidermis. âTwo-hitâ cells were not detected in the epidermis. Fibroblast-like cells in the dermis, however, exhibited allelic deletion of TSC2, in both touch preparations of fresh tumor samples and cells grown from TSC skin tumors, suggesting that increased epidermal proliferation and mTOR activation were not caused by second-hit mutations in the keratinocytes but by mesenchymal-epithelial interactions. Gene expression arrays, used to identify potential paracrine factors released by mesenchymal cells, revealed more epiregulin mRNA in fibroblast-like angiofibroma and periungual fibroma cells than in fibroblasts from normal-appearing skin of the same patient. Elevation of epiregulin mRNA was confirmed using real-time PCR, and increased amounts of epiregulin protein were demonstrated using immunoprecipitation and ELISA. Epiregulin stimulated keratinocyte proliferation and phosphorylation of ribosomal protein S6 in vitro. These results suggest that hamartomatous TSC skin tumors are induced by paracrine factors released by âtwo-hitâ cells in the dermis, and that proliferation with mTOR activation of the overlying epidermis is an effect of epiregulin. Experiment Overall Design: The study is of case/control design with biological replication. Tumor (case) and normal (control) fibroblast cells were isolated from each of four patients (biological replicates).

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Modeling the Neuropathology of Tuberous Sclerosis with Human Stem Cells Reveals a Role for Inflammation and Angiogenic Growth Factors [Cell Model]

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