Establishment of three human induced pluripotent stem cell lines from a type 1 diabetic family harboring sequence variants associated with autoimmunity.

Type 1 diabetes (T1D) is characterized by the autoimmune destruction of insulin-producing ß cells. Genetic studies have identified > 60 T1D risk loci that harbor genes with disease-causative alleles. However, determining the biological effects of such loci is often difficult due to limited tissue availability. Disease-specific human induced pluripotent stem cells (hiPSCs) are a valuable resource for modeling T1D pathogenesis. In particular, families with complete disease penetrance offer an opportunity to further dissect T1D risk loci. Here, we describe the generation of three hiPSC lines from a T1D family with sequence variants associated with autoimmunity.

Chemogenomic analysis of neuronal differentiation with pathway changes in PC12 cells.

The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database creates networks from interrelations between molecular biology and underlying chemical elements. This allows for analysis of biologic networks, genomic information, and higher-order functional information at a system level. Through high throughput experiments and system biology analysis, we investigated the genes and pathways associated with NGF induced neuronal differentiation. We performed microarray experiments and used the KEGG database, system biology analysis, and annotation of pathway functions to study NGF-induced differentiation in PC12 cells. We identified 2020 NGF-induced genes with altered expressions over time. Cross-matching with the KEGG database revealed 830 genes; among which, 395 altered genes were found to have a 2-fold increase in gene expression over a two-hour period. We then identified 191 associated biologic pathways in the KEGG database; the top 15 pathways showed correlation with neural differentiation. These included the neurotrophin pathways, mitogen-activated protein kinase (MAPK) pathways, genes associated with axonal guidance and the Wnt pathways. The activation of these pathways synchronized with nerve growth factor (NGF)-induced differentiation in PC12 cells. In summary, we have established a model system that allows one to systematically characterize the functional pathway changes in a group of neuronal population after an external stimulus.