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Single-cell analysis of a biopsy sample

Nature Reviews Nephrology volume 14, page 598 (2018)Cite this article

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Despite advances in technology for tissue characterization, the techniques that are used to analyse kidney biopsy samples have not changed substantially in the past 25 years. Now, Haojia Wu, Andrew Malone and colleagues have used single-cell RNA sequencing (scRNA-seq) to profile a kidney allograft biopsy sample from a patient with mixed T cell-mediated and antibody-mediated rejection (ABMR).

“We used a massively parallel microfluidic droplet technology called InDrops to perform scRNA-seq of the biopsy sample,” says Wu. “This approach allowed us to measure the expression of thousands of genes from thousands of individual cells.” In total, the researchers sequenced 4,487 cells and detected a mean of 1,481 transcripts from 827 genes per cell. They identified 16 different cell types in the allograft sample, including 4 types of tubular cells, various lymphocyte and leukocyte populations, 3 types of stromal cells, endothelial cells and a population of actively proliferating cells. A comparison of the epithelial transcriptome of the allograft with that of healthy adult kidney tissue showed downregulation of terminal differentiation markers and upregulation of pro-inflammatory genes in the allograft.

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  1. Nature Reviews Nephrology http://www.nature.com/nrneph

    Ellen F. Carney

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  1. Ellen F. Carney
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Correspondence to Ellen F. Carney.

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Carney, E.F. Single-cell analysis of a biopsy sample. Nat Rev Nephrol 14, 598 (2018). https://doi.org/10.1038/s41581-018-0045-z

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