Spatial Metabolomics for Human Kidneys

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Project Summary / Abstract Acute kidney injury (AKI) and chronic kidney disease (CKD) are major contributors to overall morbidity and mortality in patients in the US. The overall objective of the proposed study is to establish untargeted and targeted spatial metabolomics analysis of tissues from normal and diseased kidneys to assess cellular metabolic states associated with healthy function, acute injury, chronic condition, and recovery. We will employ ultra-high resolving power imaging mass spectrometry (e.g., MALDI-FTICR-IMS) complemented with novel bioinformatics (e.g., METASPACE) for metabolite annotation and big data interrogation strategies to identify alterations of metabolism in diseased kidneys compared with normal ones. Our Tissue Interrogation Site will be a multi-disciplinary coordinated program composed of leadership in translational nephrology and imaging mass spectrometry at UCSD, outstanding facilities for multi-omics analysis at Pacific Northwest National Laboratories (PNNL), and bioinformatics for mass spectrometry imaging and 3-D reconstruction housed at European Molecular Biology Laboratories (EMBL). Three specific aims in each phase (i.e., UG3 and UH3) are proposed. In particular, we will establish an untargeted and targeted spatial metabolomics platforms for human kidney interrogation and develop an open bioinformatics platform for data interrogation, 3-D reconstruction, molecular interpretation and public sharing. In the UH3 phase, the untargeted and targeted platforms will be scaled up to improve metabolite coverage and develop key metabolic pathways for specific renal compartments in kidneys from individuals with AKI, CKD, and disease subgroups. Moreover, the bioinformatics platform will also be scaled up to establish 3D (a next-generation technology) metabolite-based maps of kidney structure in normal and diseased kidneys. A web-service SM-Kidney will be implemented as the online platform to have all the datasets and the results publicly sharable. We will contribute and collaborate with the Central Hub (CH) to integrate our service for the formation of a molecular kidney atlas. With strong collaborations among the key personnel from UCSD, PNNL, EMBL, and other universities, institutes, and industry partners, our multidisciplinary team will reach key milestones during both the UG3 and UH3 phases. Milestones include 1) the development of a comprehensive untargeted database of metabolite annotations in the normal human renal compartments, 2) targeted spatial metabolomics analysis for selected classes of metabolites and pathways, 3) methods and SOPs that meet rigorous QC standards for tissue procurement, initial processing and IMS with optical imaging and 4) providing the online service SM-Kidney with a graphical user interface to evalaute spatial metabolic profiles associated with kidney disease and pathogenesis. All protocols, samples, data, and metabolite atlas of normal, AKI, and CKD samples will be shared across the KPMP.