(#37) Multiomics single-cell analysis of human pancreatic islets reveals novel cellular states in health and type 1 diabetes

PRESENTED BY: Golnaz Vahedi

Authors
First NameLast NameAffiliation/Institution
MariaFasolinoUPENN
KlausKaestnerUPENN
AliNajiUPENN
GolnazVahediUPENN
 

Purpose

Type 1 diabetes (T1D) is an autoimmune disease of only partially defined etiology in which immune cells destroy insulin-producing beta cells. Using single-cell transcriptomics and an advanced analytical strategy to assess pancreatic islets of T1D, autoantibody-positive, and non-diabetic organ donors, we identified both canonical cell types and rare insulin-expressing cells with a hybrid mixture of endocrine and exocrine gene signatures within all donors. We further found elevated expression of MHC Class II pathway genes in exocrine ductal cells of T1D donors, which we confirmed through CyTOF, in situ imaging mass cytometry, and immunofluorescence analysis. Taken together, our multimodal analyses identify novel cell types and processes that may contribute to T1D immunopathogenesis and provide new cellular and molecular insights into human pancreas function.
 

Methods

Type 1 diabetes (T1D) is an autoimmune disease in which immune cells attack and destroy insulin-secreting pancreatic beta cells. This complex disease affects millions of individuals, incurring billions of dollars in medical costs in the United States alone. The initial pathogenic events that trigger autoimmunity have remained elusive due to the inability to biopsy the pancreas and the fact that clinical diagnosis is only made once massive beta cell destruction has occurred. Therefore, a better understanding of the earliest molecular events in T1D pathogenesis remains critical for biomarker identification and disease prevention. Here, we generated the single-cell transcriptomic maps in pancreatic islets of human organ donors. This work is unprecedented for three major reasons:
1. The Human Pancreas Analysis Program at the University of Pennsylvania has collected high quality pancreatic tissues in three well-characterized disease categories: those clinically diagnosed with T1D, those normoglycemic but with circulating autoantibodies (AAB) towards pancreatic islet proteins (prediabetics), and age-matched non-diabetic controls. We have generated high-resolution single-cell maps of gene expression in pancreatic tissues of these donor groups where AAB+ donors represent the earliest molecular events in T1D pathogenesis. We employed additional data modalities such as multiplexed In situ Imaging Mass Cytometry (IMC) across the same donors to corroborate our single-cell RNA-seq results.
2. We developed a novel analytical tool ‘TooManyCells’, employing hierarchical spectral clustering and Newman-Girvan modularity for cell partitioning. TooManyCells, which became online on March 2nd, 2020 (https://www.nature.com/articles/s41592-020-0748-5) has an exceptional ability to visualize cellular relationships, enabling us to detect rare cell populations and their relationships to canonical cell fates in the pancreas.
3. We developed a data portal and provided easy access to the entire single-cell RNA-seq data generated in this study, enabling users to examine the expression of a gene of interest across clinically well-characterized donors corresponding to annotated cell fates (http://faryabi05.med.upenn.edu:8050/).
 

Summary of Results

Specific unexpected findings arising from our study are:
1. Endocrine and non-endocrine cells from AAB+ donors are transcriptionally similar to T1D donors.
2. Single cell profiling enables the identification of ductal-endocrine hybrid cells, which predominantly arise in AAB+ and T1D donors.
3. T1D ductal cells are indicative of an inflammatory environment and unexpectedly express MHC Class II proteins.
4. Immune cells infiltrating pancreatic islets segregate based on inflammation and disease state.
 

Conclusions

Specific unexpected findings arising from our study are:
1. Endocrine and non-endocrine cells from AAB+ donors are transcriptionally similar to T1D donors.
2. Single cell profiling enables the identification of ductal-endocrine hybrid cells, which predominantly arise in AAB+ and T1D donors.
3. T1D ductal cells are indicative of an inflammatory environment and unexpectedly express MHC Class II proteins.
4. Immune cells infiltrating pancreatic islets segregate based on inflammation and disease state.