Using single-nucleus RNA-sequencing to interrogate transcriptomic profiles of archived human pancreatic islets

Human pancreatic islets are a central focus of research in metabolic studies. Transcriptomics is frequently used to interrogate alterations in cultured human islet cells using single-cell RNA-sequencing (scRNA-seq). We introduce single-nucleus RNA-sequencing (snRNA-seq) as an alternative approach fo...

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Bibliographic Details
Published in:Genome medicine 2021-08, Vol.13 (1), p.128-128, Article 128
Main Authors: Basile, Giorgio, Kahraman, Sevim, Dirice, Ercument, Pan, Hui, Dreyfuss, Jonathan M, Kulkarni, Rohit N
Format: Article
Language:English
Subjects:
Animals
Antibodies
Archived tissue
B cells
Biomarkers
Cold
Comparative analysis
Diabetes
Exome Sequencing
Frozen samples
Gene Expression Profiling
Gene Expression Regulation
Human β-cells
Humans
Immunodeficiency
Insulin
Islet cells
Islets of Langerhans - cytology
Islets of Langerhans - metabolism
Islets of Langerhans Transplantation
Medical research
Medicine, Experimental
Method
Mice
Microscopy
Pancreas
Pancreatic islet transplantation
Phosphatase
Proteins
RNA
Sequence Analysis, DNA
Single-Cell Analysis - methods
Single-cell RNA-sequencing
Single-nucleus RNA-sequencing
snRNA
Transcriptome
Transcriptomics
Transplanted human islets
Transplants & implants
Type 2 diabetes
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Summary:Human pancreatic islets are a central focus of research in metabolic studies. Transcriptomics is frequently used to interrogate alterations in cultured human islet cells using single-cell RNA-sequencing (scRNA-seq). We introduce single-nucleus RNA-sequencing (snRNA-seq) as an alternative approach for investigating transplanted human islets. The Nuclei EZ protocol was used to obtain nuclear preparations from fresh and frozen human islet cells. Such preparations were first used to generate snRNA-seq datasets and compared to scRNA-seq output obtained from cells from the same donor. Finally, we employed snRNA-seq to obtain the transcriptomic profile of archived human islets engrafted in immunodeficient animals. We observed virtually complete concordance in identifying cell types and gene proportions as well as a strong association of global and islet cell type gene signatures between scRNA-seq and snRNA-seq applied to fresh and frozen cultured or transplanted human islet samples. We propose snRNA-seq as a reliable strategy to probe transcriptomic profiles of freshly harvested or frozen sources of transplanted human islet cells especially when scRNA-seq is not ideal.
ISSN:1756-994X
1756-994X
DOI:10.1186/s13073-021-00941-8