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Review
. 2023 May 1;32(3):249-256.
doi: 10.1097/MNH.0000000000000875. Epub 2023 Feb 22.

Conundrums of choice of 'normal' kidney tissue for single cell studies

Sanjay Jain  1
Affiliations
Review

Conundrums of choice of 'normal' kidney tissue for single cell studies

Sanjay Jain. Curr Opin Nephrol Hypertens. .

Abstract

Purpose of review: Defining molecular changes in key kidney cell types across lifespan and in disease states is essential to understand the pathogenetic basis of disease progression and targeted therapies. Various single cell approaches are being applied to define disease associated molecular signatures. Key considerations include the choice of reference tissue or 'normal' for comparison to diseased human specimens and a benchmark reference atlas. We provide an overview of select single cell technologies, key considerations for experimental design, quality control, choices and challenges associated with assay type and source for reference tissue.

Recent findings: Several initiatives including Kidney Precision Medicine Project, Human Biomolecular Molecular Atlas Project, Genitourinary Disease Molecular Anatomy Project, ReBuilding a Kidney consortium, Human Cell Atlas and Chan Zuckerburg Initiative are generating single cell atlases of 'normal' or disease kidney. Different sources of kidney tissue are used as reference. Signatures of injury, resident pathology and procurement associated biological and technical artifacts have been identified in human kidney reference tissue.

Summary: Committing to a particular reference or 'normal' tissue has significant implications in interpretation of data from disease samples or in ageing. Voluntarily donated kidney tissue from healthy individuals is generally unfeasible. Having reference datasets for different types of 'normal' tissue can aid in mitigating the confounds of choice of reference tissue and sampling biases.

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Conflict of interest statement

Conflict of Interest

None

Figures

Figure 1.
Figure 1.
Illustration shows the various steps involved in the process of conducting single cell experiment. A) Process shows various steps from tissue procurement to sharing data. (B) Illustration shows examples of choices that are available at each of the steps depicted in part A. (C) Illustration shows that for each choice in part B there are challenges or limitations thus underscoring the need for carefully planning the objectives of the single cell experiment.
See this image and copyright information in PMC

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    2. This article uses data from deceased donor, nephrectomies and living donor kidney tissue to perform multimodal integration across single cell RNA sequencing and regional proteomics and metabolomics.

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    2. Here the authors established a novel method of droplet based snRNAseq that registers compositionof kidney tissue from which sequencing data are derived using fresh frozen OCT embedded deceased donor and nehrectomy kidney tissue. The authors compared several tissue processing and nuclei isolation methods and found fresh frozen OCT embedded tissue sections avoided enzymatic digestion and had miminal cell stress.

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    2. This paper is a multiconsortium effort with more than 400K single cell multimodal datasets that uses all four reference tissue sources mentioned in the review and constructs a comprehensive molecularly defined cell type and state atlas. The authors show that several injured cell states have contributions from cells form both reference and AKI amd CKD biopsies although the proportion in healthy tissue is much less than disease tissues. One of the states is degenerative or damaged cells that have increase expression of kidney injury markers such as IGFBP7, SPP1, loss of differentiation markers and low genes/cell and increase in cell-stress markers Fos and Jun. Another altered state was generically defined as adaptive to denote putative successful or failed repair and pathways that correlate with recovery from this state to healthy mature proximal tubule and TAL were identified.

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    2. This paper uses living donor kidney biopsies to comare single cel profiles of patients with FSGS and idetify several endothelial subtypes in the kidney.

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