Analysis of Transcriptome Data from 261 Individual Laser-Captured Islets from Nondiabetic, Autoantibody-Positive, and Type 1 Diabetic Organ Donors Free

The purpose of this study was to obtain comprehensive gene expression datasets from a large number of individual islets, with defined pathological phenotypes, from organ donors with different clinical stages of type 1 diabetes. Here we will present results from an analysis that compared “normal” (Ins+CD3-) islets from the 3 clinical phenotypes: Autoantibody negative nondiabetic (C), Autoantibody positive nondiabetic (AB) and type 1 diabetic (T1D). We obtained pancreatic tissue from 43 male and female nPOD donors with the 3 clinical phenotypes (C=16, AB=11, T1D=16). Staining of islets for both insulin and CD3 resulted in the following histologic subtypes of the 261 islets collected and analyzed for gene expression: Ins+CD3- (n=147), Ins+CD3+ (n=78), Ins-CD3+ (n=12), and Ins-CD3- (n=23). The gene expression profiles of these 261 individual islets were obtained using Affymetrix HTA 2.0 arrays. We compared gene expression profiles of the 147 islets that were Ins+CD3- from each of the 3 organ donor types. The number of transcripts differentially expressed by >1.5 fold and p<0.001 (Student’s t-test with FDR<0.05) were as follows: C vs. AB=448; C vs. T1D=240; AB vs. T1D=387. Those gene lists were subjected to a data mining workflow. The 448 transcripts differing between Ins+CD3- islets of C and AB organ donors were dominated by non-coding RNA (33%). Islets from AB donors had reduced transcripts associated with islet regeneration, cell replication, and immune responses. The 387 transcripts differing between Ins+CD3- islets of AB and T1D organ donors expressed increased levels of beta cell specific transcripts and markers of immune responses in T1D islets. A number of oxidative phosphorylation gene transcripts were lower in T1D islets. The 240 transcripts differing between Ins+CD3- islets of C and T1D organ donors demonstrated reduced levels of beta cell specific transcripts but increased HLA class II transcripts in T1D islets