Spatial Elucidation of Human Acute Kidney Injury and Chronic Kidney Disease using Imaging Mass Cytometry

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Abstract Acute kidney injury (AKI) is a syndromic term encompassing a wide range of insults and pathogenic responses that lead to a rapid reduction in glomerular filtration. Although we have made significant progress in our understanding of kidney injury in animal models, far less attention has been focused on the pathogenesis and treatment of the diverse types of human AKI. The largest barrier in achieving this knowledge is the limited number of kidney biopsies performed for AKI and the small amount of tissue obtained from renal biopsy. The Kidney Precision Medicine Project is tackling this complex issue by recruiting altruistic patients with AKI who are willing to have kidney biopsies in order to advance our knowledge of human kidney disease. These biopsies are being interrogated using multiple complementary technologies. We propose to use Imaging Mass Cytometry to help provide a highly detailed, quantitative cellular map of nearly all cells present in sections from those kidney biopsies, including their differentiation state and activation of injury and repair pathways. Combined with the cell sequencing, metabolomic, and proteomic data generated under KPMP guidance, this will provide a substantial increase in our understanding of human AKI and CKD. Imaging mass cytometry (IMC) uses a high-resolution laser combined with a mass cytometer to detect the presence, location and amount of up to 42 different heavy metal conjugated antibodies hybridized to a tissue section. We have successfully used IMC with a panel of 22 heavy metal conjugated validated antibodies to identify resident kidney cell populations, infiltrating cell populations, and cell activation and injury states using archival FFPE human kidney tissue, and developed a machine learning technique termed Kidney MAPPS to rapidly and accurately identify, quantify and localize ~92% of all cells in those biopsies. We now propose to increase that validated antibody panel to >30 antibodies that will allow identification of >95% of cells and improve cell injury and activation state assessment, and to optimize the IMC and Kidney-MAPPS analysis pipeline to perform 2D and 3D quantitative assessment of cell location, cell-cell interactions and cellular responses in human AKI and CKD biopsy tissues (SA1). We will standardize a defined work-flow protocol coupled with rigorous quality control assessment steps at key points (SA2), and then apply this IMC work-flow to kidney samples provided by KPMP and integrate with the KPMP Central Hub and consortium members to develop accurate protocols for mapping the scRNAseq/snRNAseq data, proteomics data and metabolomics data onto the appropriate cells and locations using Kidney-MAPPS (SA3).