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Related Experiment Video

Updated: May 22, 2026

Nuclei Isolation from Adult Mouse Kidney for Single-Nucleus RNA-Sequencing
06:00

Nuclei Isolation from Adult Mouse Kidney for Single-Nucleus RNA-Sequencing

Published on: September 20, 2021

Not all reference samples are equal in single-cell transcriptomics of human kidney tissue.

Rajasree Menon1, Paul L Kimmel2, Edgar A Otto3

  • 1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America.

JCI Insight
|May 20, 2026
PubMed

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Summary
This summary is machine-generated.

Choosing healthy kidney tissue controls is crucial for studying diabetic kidney disease (DKD). Donor age, sex, and tissue source significantly impact gene expression, affecting disease mechanism discovery.

Area of Science:

  • Nephrology
  • Genomics
  • Molecular Biology

Background:

  • Studying kidney disease mechanisms requires comparing diseased and healthy tissues.
  • Variability in tissue procurement, storage, and donor characteristics can confound results.
  • The impact of these factors on gene expression in diabetic kidney disease (DKD) is not well understood.

Purpose of the Study:

  • To systematically evaluate the impact of three reference tissue types (tumor nephrectomy, living donor biopsies, healthy control biopsies) on differential gene expression in DKD.
  • To assess the influence of procurement method, sex, and donor age on gene expression.
  • To determine the necessity of adjusting for confounding factors in DKD research.

Main Methods:

  • Comparison of gene expression profiles from three distinct reference kidney tissue types.
Keywords:
DiabetesEndocrinologyMolecular pathologyNephrologyTranscriptomics

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  • Systematic evaluation of confounding factors: procurement method, sex, and donor age.
  • Pathway analysis before and after adjustment for confounding variables.

    • Main Results:

    • Distinct injury markers, cell state proportions, and gene signatures were observed based on procurement method, sex, and donor age.
    • Adjustment for age and sex removed significant enrichment of interferon gamma response in diabetes mellitus-resilient versus healthy controls.
    • Biological aging processes were enriched in older tissues, potentially confounding disease interpretation.
    • Tumor necrosis factor signaling remained enriched in living donor and tumor nephrectomy samples even after confounder adjustment.

    Conclusions:

    • Reference tissue selection and adjustment for confounding variables (age, sex, procurement) are critical for accurate DKD molecular mechanism discovery.
    • Failure to account for these factors can lead to misinterpretation of disease-specific pathways.
    • Standardized protocols for control tissue selection and data normalization are essential for reliable kidney disease research.