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Conundrums of choice of 'normal' kidney tissue for single cell studies
1Departments of Medicine, Pathology and Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA.
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.
Insights
Understanding kidney cell molecular changes requires careful selection of reference tissues for single-cell analysis. Establishing diverse normal kidney reference datasets is crucial for accurate disease and aging studies.
Area of Science:
- Renal cell biology and single-cell genomics.
Background:
- Defining molecular alterations in kidney cells across lifespan and disease is critical for understanding disease progression and developing targeted therapies.
- Single-cell technologies are increasingly used to identify disease-associated molecular signatures in the kidney.
Approach:
- This review overviews select single-cell technologies applicable to kidney research.
- It discusses key considerations for experimental design, quality control, and assay choices.
- Challenges related to reference tissue sourcing and benchmarking are highlighted.
Key Points:
- Multiple large-scale initiatives are generating single-cell atlases of normal and diseased human kidneys.
- Various kidney tissue sources are employed as references, with identified signatures of injury and artifacts.
- The choice of reference tissue significantly impacts data interpretation.
Conclusions:
- Establishing comprehensive reference datasets from diverse 'normal' kidney tissues is essential.
- This approach helps mitigate confounds arising from reference tissue selection and sampling biases.
- Accurate interpretation of single-cell data from diseased or aging kidneys relies on robust reference atlases.
