Introduction to KPMP technologies

Overview

The Kidney Precision Medicine Project (KPMP) measures each kidney biopsy with many technologies, so that no single method's blind spots go unchecked. One method can miss a gene, protein, or metabolite that another detects. Running several methods on the same tissue gives broader coverage of RNA, proteins, and metabolites.

KPMP Tissue Interrogation Sites (TISs) develop and run these technologies. Recruitment sites enroll participants and perform the biopsies. Biopsy tissue is processed in three ways and shared among the TISs that generate the data.

This page groups the technologies by what they measure:

• Transcriptomics measures RNA, either in single cells and nuclei or in defined tissue regions.
• Proteomics measures proteins in microdissected tissue regions.
• Imaging shows tissue structure, cell types, and protein markers in 2D and 3D.
• Spatial metabolomics, lipidomics, and N-glycomics map small molecules, lipids, and sugar structures across a tissue section.
• Epigenetics measures chromatin accessibility and DNA methylation.

Each section explains what a technology measures and what question it helps you answer. The last sections show where to find each technology's data in the Kidney Tissue Atlas and where to get protocols and metadata templates.

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Transcriptomics

Transcriptomics technologies measure which genes are expressed. KPMP uses five approaches, which trade cellular resolution against spatial context.

Single-nucleus RNA-seq (snRNA-seq) sequences RNA from individual nuclei isolated from frozen tissue. Use it to identify cell types and their gene expression profiles, including cell types that are hard to dissociate intact.

Single-cell RNA-seq (scRNA-seq) sequences RNA from whole dissociated cells. Its goal is to derive kidney cell subtypes and their cell-type-specific gene expression profiles from the data itself. Because the tissue is fully dissociated, the data has no spatial context.

Single-nucleus RNA-seq + snATAC-seq (10X Multiome) measures gene expression and chromatin accessibility in the same nucleus. Use it to link open chromatin to gene expression, for example to find candidate transcription factors or genetic variants that affect expression.

Regional transcriptomics uses laser microdissection (LMD) to cut out nephron segments that are identified by antibody staining, and then sequences their RNA. Use it for deep expression profiles of specific regions, such as glomeruli or tubulointerstitium.

Spatial transcriptomics captures whole-transcriptome expression across a tissue section while keeping each measurement's location. KPMP uses the 10x Genomics Visium platform. Use it to see where in the tissue a gene is expressed.

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Proteomics

Regional proteomics uses laser microdissection (LMD) to isolate defined kidney regions and then measures their proteins by mass spectrometry. It pairs with regional transcriptomics: KPMP publishes a shared LMD protocol for both. Use it to compare protein abundance between regions, or to check whether a gene's RNA signal matches its protein.

KPMP also collects biomarker proteomics from fluids, such as SomaScan plasma and urine proteomics. These are biospecimen measurements, not tissue technologies, and they appear only in the Repository.

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Imaging

Imaging technologies show tissue structure and where cell types and protein markers sit. They range from standard pathology stains to highly multiplexed protein maps.

Light microscopic whole slide images (WSI) are digitized pathology slides. KPMP scans several stains, including H&E, PAS, silver, toluidine blue, and trichrome. Use them to review tissue histology alongside the molecular data.

3D tissue imaging and cytometry images thick tissue sections in three dimensions, using multichannel immunofluorescence and label-free autofluorescence and second harmonic generation. Cytometry software then classifies and counts cells in the 3D volume. Use it to study the kidney's 3D organization and quantify cell populations in place.

CODEX (co-detection by indexing) stains one tissue section with many antibodies and images them in cycles. Its goal is high-resolution maps of anchor, immune, and functional markers at single-cell resolution. Use it to locate immune and structural cell types relative to each other.

Imaging mass cytometry (IMC) labels antibodies with metal tags and reads them with a mass cytometer, producing multiplexed protein images of a tissue section. Use it, like CODEX, for single-cell protein phenotyping in tissue.

Segmentation data marks structures, such as glomeruli and tubules, on whole slide images and extracts quantitative features from them (segmentation masks and pathomics vectors). Use it to measure tissue structure computationally rather than by eye.

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Spatial metabolomics, lipidomics, and N-glycomics

These technologies use imaging mass spectrometry. A laser scans across a tissue section, and a mass spectrometer measures the molecules at each spot, which produces a map of where each molecule is found.

Spatial metabolomics maps small-molecule metabolites across the tissue.

Spatial lipidomics localizes lipid markers in kidney tissue sections. KPMP groups its multimodal MALDI imaging mass spectrometry data under spatial lipidomics and distinguishes the methods by platform.

Spatial N-glycomics localizes N-glycans, the sugar structures attached to proteins, in kidney tissue sections.

Multimodal imaging mass spectrometry combines MALDI imaging mass spectrometry with other imaging to map metabolites and lipids to specific functional tissue units, such as glomeruli and tubule segments.

Use these technologies to connect metabolic and lipid changes to specific kidney structures. The Spatial Viewer links these datasets to METASPACE, an external platform for annotating and viewing imaging mass spectrometry data.

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Epigenetics

Epigenetic technologies measure how DNA is packaged and marked, which helps explain why genes turn on or off in a cell type or disease state.

snATAC-seq measures which regions of chromatin are open in individual nuclei. KPMP generates it as part of the 10X Multiome assay, paired with gene expression from the same nucleus.

CUT&RUN maps where specific proteins, such as histone marks or transcription factors, bind DNA.

DNA methylation sequencing profiles methylation at more than 20 million CpG sites in individual kidney compartments. Compartments are isolated by laser microdissection and analyzed by whole-genome bisulfite sequencing (WGBS), in both nephrectomy and biopsy tissue.

KPMP also offers whole genome sequence data through the Repository. It requires a data use agreement.

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Where to find each technology's data

Every technology's files are in the Repository. A subset has been analyzed for interactive use in Explorer or the Spatial Viewer. For current participant and file counts, see the data summary on the Kidney Tissue Atlas home page.

Some Repository files are controlled access. To get them, your institution needs a data use agreement with KPMP.

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Protocols, metadata, and help

Each technology on the KPMP Technologies help page lists its goal, its protocols, and a metadata template. Before you analyze a dataset, read its protocol and metadata template so that you know how the tissue was processed and what each field means.

To get help or report a problem:

• For how to use Explorer, the Repository, and the Spatial Viewer, see How to use the Atlas.
• For data that was replaced or withdrawn, see the Atlas Data Change Log, linked from the same page.
• To report an issue, use the Give us your feedback link (above).

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Metadata standards

The Kidney Precision Medicine Project is generating a large amount of data. To enable data accessibility and interoperability, each dataset that is generated must be accompanied by a standard set of metadata. The required metadata properties vary by technology. For the metadata properties being collected for all of the KPMP technologies, refer to the Metadata page to see all of the metadata templates.

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