Integrated spatial interrogation of cellular and molecular signatures of human kidney disease

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(PLEASE KEEP IN WORD, DO NOT PDF) Enter the text here that is the new abstract information for your application. This section must be no longer than 30 lines of text. Abstract There is a fundamental gap in understanding the mechanisms that determine progression in human kidney disease. The long-term goal is to characterize key cellular and molecular pathways regulating progression of acute and chronic kidney diseases (AKI and CKD), to identify novel markers that assess disease progression, and to develop specific therapeutic interventions targeting these pathways. There is often heterogeneity in the pattern of kidney injury whereby various cell types and cell states are differentially distributed across focal regions of a biopsy specimen. Immune cell sub-populations are observed in these injury regions, suggesting robust cross-talk between infiltrating immune cells and the resident renal epithelial, endothelial, and stromal cells. Further, these regional molecular disease phenotypes often are not fully appreciated on standard histopathologic assessment. Therefore, there is a critical need to expand our efforts to comprehensively localize cell types and cell states in the kidney, sub-phenotype disease, uncover cell-cell interactions, and understand the cellular and molecular phenotypes underlying morphologic changes in the kidney. The overarching hypothesis of this proposal is that mechanisms of kidney disease can only be understood when the diversity of cellular and molecular phenotypes are interpreted in the spatial context of the individuals’ kidney. The central hypothesis will be tested using an integrated pipeline of spatially resolved imaging, transcriptomic, and proteomic technologies that will capture the features of kidney disease at the cell, regional, and organ levels. These technologies include large scale 3D microscopy and tissue cytometry (3DTC), spatial transcriptomics (ST), and CO-Detection by indEXing (CODEX) multiplexed immunofluorescence. Together, this analytical pipeline will facilitate mapping of injury distribution and effectively link with other KPMP technologies through the following aims: Specific Aim 1: Deploy a suite of KPMP-approved spatial technologies as a synchronized analytical pipeline to define the cellular components and molecular structure of each human kidney biopsy. Specific Aim 2: Integrate imaging, transcriptomic, and proteomic signatures from each biopsy specimen to generate a multi-component spatial map of cellular and molecular phenotypes. Specific Aim 3: Integrate our analytical pipeline across the KPMP, linking our spatially-anchored cellular and molecular phenotypes to other KPMP technologies, pathology, and clinical features. The proposed research is significant, because it is the next step in a continuum of research that is expected to identify critically needed biomarkers of disease progression, optimize preclinical studies, and develop specific and targeted therapeutic interventions in the vast clinical problem of AKI and CKD.