Uncovering Molecular Heterogeneity in the Kidney With Spatially Targeted Mass Spectrometry

Abstract

The kidney functions through the coordination of approximately one million multifunctional nephrons in 3-dimensional space. Molecular understanding of the kidney has relied on transcriptomic, proteomic, and metabolomic analyses of kidney homogenate, but these approaches do not resolve cellular identity and spatial context. Mass spectrometry analysis of isolated cells retains cellular identity but not information regarding its cellular neighborhood and extracellular matrix. Spatially targeted mass spectrometry is uniquely suited to molecularly characterize kidney tissue while retaining in situ cellular context. This review summarizes advances in methodology and technology for spatially targeted mass spectrometry analysis of kidney tissue. Profiling technologies such as laser capture microdissection (LCM) coupled to liquid chromatography tandem mass spectrometry provide deep molecular coverage of specific tissue regions, while imaging technologies such as matrix assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) molecularly profile regularly spaced tissue regions with greater spatial resolution. These technologies individually have furthered our understanding of heterogeneity in nephron regions such as glomeruli and proximal tubules, and their combination is expected to profoundly expand our knowledge of the kidney in health and disease.

Keywords: HuBMAP; KPMP; kidney; lipidomics; mass spectrometry; metabolomics; multimodal imaging; proteomics.

FIGURE 1

Summary of spatial MS technologies and the trade-offs between spatial resolution and molecular coverage. Technologies are characterized based on their spatial resolution from the level of anatomical structure (>500 μm), Functional Tissue Unit (FTU, ∼50–500 μm), cellular (∼10–50 μm), and subcellular (<10 μm). Triangles indicate technologies for analysis of bulk or homogenate tissues, circles indicate profiling experiments, and rectangles indicate imaging experiments. Methods for analyzing small metabolites, lipids, and proteins are shown in blue, purple, and green, respectively.

FIGURE 2

Nephron showing select molecular groups observed in the cortex, outer medulla, inner medulla, glomeruli (Glom), proximal tubules (PT), and collecting ducts (CD). Molecular observations made using imaging mass spectrometry (MS) and profiling MS experiments are shown in rectangles and ovals, respectively. Proteins, small metabolites, and lipids, are shown in green, blue, and purple text, respectively. Biological processes are indicated as follows: * Solute transport, ** Toxins and detoxification, Δ Lipid synthesis, modification, and metabolism, ± Mitochondrial energy metabolism, Ψ Cell death regulation, θ Glucose metabolism and diabetes.