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

Genome Med. 2021 Aug 10;13(1):128. doi: 10.1186/s13073-021-00941-8.

Abstract

Background: 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.

Methods: 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.

Results: 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.

Conclusions: 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.

Keywords: Archived tissue; Diabetes; Frozen samples; Human β-cells; Single-cell RNA-sequencing; Single-nucleus RNA-sequencing; Transplanted human islets.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Biomarkers
  • Gene Expression Profiling*
  • Gene Expression Regulation*
  • Humans
  • Islets of Langerhans / cytology
  • Islets of Langerhans / metabolism*
  • Islets of Langerhans Transplantation
  • Mice
  • Sequence Analysis, DNA
  • Single-Cell Analysis* / methods
  • Transcriptome*
  • Whole Exome Sequencing

Substances

  • Biomarkers