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Status |
Public on Feb 22, 2018 |
Title |
Human NPY/AgRP hypothalamic cell lines for study of obesity susceptibility (miRNA-Seq) |
Organism |
Homo sapiens |
Experiment type |
Non-coding RNA profiling by high throughput sequencing
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Summary |
Recent data suggests that common genetic risk for metabolic disorders such as obesity may be human-specific and exert effects through the central nervous system. To overcome the limitation of human tissue access for study, we have generated induced human pluripotent stem cell (hiPSC)- derived neuronal cultures which recapture many features of hypothalamic neurons within the arcuate nucleus. Here we have comprehensively characterized this model across development and benchmarked these neurons to in vivo events. We also demonstrate their utility in study of obesity risk variants. The dynamic transcriptome across neuronal maturation was examined using microarray and RNAseq methods at 9 time points. K-means clustering of the longitudinal data was conducted to identify co-regulation and miRNA control of biological processes. The transcriptomes were compared to those of 103 samples from 13 brain regions reported in the Genotype-Tissue Expression database (GTEx) using principal components analysis. Genes with proximity to body mass index (BMI)-associated genetic variants were mapped to the developmentally expressed genesets, and enrichment significance was assessed with Fisher’s exact test. The human neuronal cultures have a transcriptional and physiological profile of NPY/AgRP hypothalamic neurons. The neuronal transcriptomes were highly correlated with adult hypothalamus as compared to any other brain region from the GTEx. Also, roughly 25% of the transcripts showed changes in expression across maturation stages and potential co-regulation of biological processes that mirror neuronal development in vivo. These developmentally expressed genes were significantly enriched for genes in proximity to BMI-associated variants.
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Overall design |
We collected small RNA at each of the 9 time points, day 0, 10, 25, 35, 45, 55, 75, 95, 115 , from day 0 to 115 during the differentiation and maturation process. Small RNA was isolated with the TruSeq™ Small RNA sample prep kit v2 (Illumina) according to the instructions of the manufacturer
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Contributor(s) |
Yao L, Liu Y, Ayala I, Qiu Z, Kumar S, Curran JE, Chen Y, Lehman DM |
Citation(s) |
28071834 |
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Submission date |
Mar 02, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Yidong Chen |
E-mail(s) |
cheny8@uthscsa.edu
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Phone |
2105629163
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Organization name |
UT Health Science Center at San Antonio
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Department |
Population Health Sciences
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Street address |
8403 Floyd Curl Drive, MSC 7784
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City |
San Antonio |
State/province |
Texas |
ZIP/Postal code |
78229 |
Country |
USA |
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Platforms (1) |
GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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Samples (10)
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Relations |
BioProject |
PRJNA314028 |
SRA |
SRP071051 |