ASN's Mission

ASN leads the fight to prevent, treat, and cure kidney diseases throughout the world by educating health professionals and scientists, advancing research and innovation, communicating new knowledge, and advocating for the highest quality care for patients.

learn more

Contact ASN

1401 H St, NW, Ste 900, Washington, DC 20005


The Latest on Twitter

Kidney Week

Abstract: FR-PO780

Using Next-Generation Imaging Technologies to Construct 3-D Multimodal Molecular Atlases of the Human Kidney

Session Information

Category: Development, Stem Cells, and Regenerative Medicine

  • 500 Development, Stem Cells, and Regenerative Medicine


  • de Caestecker, Mark P., Vanderbilt University Medical Center, Nashville, Tennessee, United States
  • Yang, Haichun, Vanderbilt University Medical Center, Nashville, Tennessee, United States
  • Fogo, Agnes B., Vanderbilt University Medical Center, Nashville, Tennessee, United States
  • Harris, Raymond C., Vanderbilt University Medical Center, Nashville, Tennessee, United States
  • Van de plas, Raf, Delft University of Technology, Delft, Netherlands
  • Spraggins, Jeffrey M., Vanderbilt University, Nashville, Tennessee, United States

Little is known about the integration, interactions, and molecular cross-talk between the different cell types and cellular compartments in normal kidneys. As part of the Human BioMolecular Atlas Program (HuBMAP), we are developing an ultra-high content imaging mass spectrometry (IMS)-based 3-D imaging pipeline to characterize the molecular signatures of different cell types at high resolution in normal, intact human kidneys.


Fresh discarded human kidneys obtained from surgical nephrectomy specimens were frozen on dry ice/isopentane slurry. Sequential sections were obtained through tissue blocks, scanned for autofluorescence (AF), and alternate sections prepared for IMS and multiplexed immunofluorescence (MxIF). IMS data was collected using a prototype MALDI timsTOF Pro Mass Spectrometer. Two cycles of MxIF were performed using a panel of validated, fluorophore-conjugated antibodies, and image fusion used to integrate information from IMS-generated molecular maps with autofluorescence and MxIF images. Sequential 2-D IMS/AF/MxIF images were then registered and mapped to the 3-D coordinate system using data from sequential sections with in house tools.


A preliminary lipidomics study of human kidney tissue has been performed using our custom 3-D multimodal molecular imaging platform. The data set consists of 32 serial sections collected from the cortex of the kidney. Each 2-D tissue section is ~4x8 mm and they were imaged using IMS at 20 µm spatial resolution, resulting in ~150,000 pixels per section. AF/IMS and MxIF image registration pipelines enabled the construction of high-spatial resolution ion volumes. The entire 3-D volume was ~4x8x0.32 mm and contains ~4.8 million voxels (20x20x10 µm). The fully constructed 3-D molecular atlas enabled the visualization of various lipids to specific substructures in the kidney, including the proximal and distal tubules and glomeruli. For example, C24 Sulfatide and PI-Cer(42:0) (putative identifications) were found to track with distal tubules throughout the 3-D volume.


We have developed a novel pipeline for 3-D biomolecular multimodal tissue imaging that will enable the construction of high-resolution molecular atlases of the human kidney.


  • Other NIH Support