Single-Cell Transcriptomics of a Human Kidney Allograft Biopsy Specimen Defines
a Diverse Inflammatory Response.
Authors Wu H, Malone AF, Donnelly EL, Kirita Y, Uchimura K, Ramakrishnan SM, Gaut JP,
Humphreys BD
Submitted By Benjamin Humphreys on 8/20/2018
Status Published
Journal Journal of the American Society of Nephrology : JASN
Year 2018
Date Published
Volume : Pages 29 : 2069 - 2080
PubMed Reference 29980650
Abstract Background Single-cell genomics techniques are revolutionizing our ability to
characterize complex tissues. By contrast, the techniques used to analyze renal
biopsy specimens have changed little over several decades. We tested the
hypothesis that single-cell RNA-sequencing can comprehensively describe cell
types and states in a human kidney biopsy specimen.Methods We generated 8746
single-cell transcriptomes from a healthy adult kidney and a single kidney
transplant biopsy core by single-cell RNA-sequencing. Unsupervised clustering
analysis of the biopsy specimen was performed to identify 16 distinct cell
types, including all of the major immune cell types and most native kidney cell
types, in this biopsy specimen, for which the histologic read was mixed
rejection.Results Monocytes formed two subclusters representing a nonclassical
CD16+ group and a classic CD16- group expressing dendritic cell maturation
markers. The presence of both monocyte cell subtypes was validated by staining
of independent transplant biopsy specimens. Comparison of healthy kidney
epithelial transcriptomes with biopsy specimen counterparts identified novel
segment-specific proinflammatory responses in rejection. Endothelial cells
formed three distinct subclusters: resting cells and two activated endothelial
cell groups. One activated endothelial cell group expressed Fc receptor pathway
activation and Ig internalization genes, consistent with the pathologic
diagnosis of antibody-mediated rejection. We mapped previously defined genes
that associate with rejection outcomes to single cell types and generated a
searchable online gene expression database.Conclusions We present the first step
toward incorporation of single-cell transcriptomics into kidney biopsy specimen
interpretation, describe a heterogeneous immune response in mixed rejection, and
provide a searchable resource for the scientific community.

Investigators with authorship
Benjamin HumphreysWashington University in St Louis