Tissue Interrogation Sites

Washington University-University of California San Diego (WU-UCSD)

Principal Investigators: Sanjay Jain, MD, PhD (WU) – Kun Zhang, PhD (UCSD)

Technologies:  Transcriptomics Imaging

We are applying and integrating several complementary technologies to create a complete catalog of molecular signatures of all kidney cell types in 3D space: two novel single-cell technologies to mature archived (frozen) human kidney specimens; a single-nucleus (sn) droplet-based transcriptomic profiling method (snDrop-seq); and a 3D in situ RNA mapping method (DART-FISH).

University of Michigan-Broad Institute-Princeton University (UM-Broad-Princeton)

Principal Investigators: Jeff Hodgin, MD (UM) – Nir Hacohen, PhD (Broad) – Olga Troyanskaya, PhD (Princeton)

Technologies:  Transcriptomics Imaging

We are seeking to interrogate gene expression in the kidney at the single cell level, defining cell-type and disease-state-specific gene expression profiles, with accompanying two and three-dimensional spatial characterization (cell-cell and cell-matrix relationships).

This approach allows us to understand the roles of the individual renal cell types in their cellular and disease context, which is critical to developing novel targeted therapies.

    Indiana University-The Ohio State University (IU-OSU)

    Principal Investigators: Tarek Ashkar (El-Achkar), MD (IU) – Pierre Dagher, MD (IU) – Brad Rovin, MD (OSU)

    Technologies:  Transcriptomics Proteomics Imaging

    Our site will initially integrate large-scale 3D tissue imaging for quantitative supervised and unsupervised analysis/cytometry with sub-segmental “omics” data on the same kidney biopsy specimen. The sub-segmental “omics” pipeline will isolate specific kidney nephron segments and interstitial/other targeted areas for downstream analysis with transcriptomics and proteomics.

    The omics analysis will be eventually expanded to include epigenetics. This approach will complement other interrogation techniques within KPMP by providing tissue context and increasing spatial resolution for molecular signatures that arise in heterogeneous areas during kidney disease.

    University of California San Francisco-Stanford University (UCSF-SU)

    Principal Investigator: Zoltan Laszik, MD, PhD (UCSF)

    Technologies:  Transcriptomics Proteomics Imaging

    Our labs have developed two multiplex assays (multiplex Immunofluorescence and In Situ Hybridization (mIFISH) and CODEX) that visualize multiple mRNAs and proteins at single cell resolution level.

    These assays, coupled with advanced high resolution whole slide imaging and sophisticated computer-assisted image analysis, can assess not only the quantitative aspects but also the spatial organizational aspects of the analytes.

    The in situ assays will be supplemented by additional ancillary tissue-based assays of near single cell proteomics and multiplexed single-cell RNA-Seq (mdrosc RNA-Seq).

    University of Texas Health Science Center at San Antonio-Pacific Northwest National Laboratory-European Molecular Biology Laboratory (UTHSA-PNNL-EMBL)

    Principal Investigator: Kumar Sharma, MD, FAHA (UTHSA)

    Technologies:  Metabolomics

    With our combined expertise we have developed a spatial metabolomics approach to identify metabolites in human kidneys, employing ultra-high mass resolution MS imaging for tissue analysis and a bioinformatics resource (METASPACE) to annotate metabolites for anatomical localization and 3-D reconstruction.

    This allows us to understand the major metabolic pathways that initiate and cause progression of disease in patients with AKI and CKD.

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