Single-cell gene expression analysis reveals β-cell dysfunction and deficit mechanisms in type 2 diabetes

BACKGROUND: Type 2 diabetes (T2D) is one of the most common chronic diseases. Studies on T2D are mainly built upon bulk-cell data analysis, which measures the average gene expression levels for a population of cells and cannot capture the inter-cell heterogeneity. The single-cell RNA-sequencing technology can provide additional information about the molecular mechanisms of T2D at single-cell level. RESULTS: In this work, we analyze three datasets of single-cell transcriptomes to reveal β-cell dysfunction and deficit mechanisms in T2D. Focused on the expression levels of key genes, we conduct discrimination of healthy and T2D β-cells using five machine learning classifiers, and extracted major influential factors by calculating correlation coefficients and mutual information. Our analysis shows that T2D β-cells are normal in insulin gene expression in the scenario of low cellular stress (especially oxidative stress), but appear dysfunctional under the circumstances of high cellular stress. Remarkably, oxidative stress plays an important role in affecting the expression of insulin gene. In addition, by analyzing the genes related to apoptosis, we found that the TNFR1-, BAX-, CAPN1- and CAPN2-dependent pathways may be crucial for β-cell apoptosis in T2D. Finally, personalized analysis indicates cell heterogeneity and individual-specific insulin gene expression. CONCLUSIONS: Oxidative stress is an important influential factor on insulin gene expression in T2D. Based on the uncovered mechanism of β-cell dysfunction and deficit, targeting key genes in the apoptosis pathway along with alleviating oxidative stress could be a potential treatment strategy for T2D. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-018-2519-1) contains supplementary material, which is available to authorized users.