The Recruitment Sites recruit adult men and women with either AKI or CKD for longitudinal cohort studies that include a research kidney biopsy. The Recruitment Sites work collaboratively to capture demographic information, conduct longitudinal clinical phenotyping, and collect biological samples in a standardized manner.
Brigham and Women’s Hospital - Joslin Diabetes Center
Johns Hopkins - Yale
Principal Investigator: Chirag Parikh, MD, PhD
University of Pittsburgh
Tissue Interrogation Sites
Tissue Interrogation Sites receive kidney biopsy tissue collected from participants at the Recruitment Sites. They use this tissue to:
- Investigate kidney cell and disease heterogeneity in tissue sections and/or dissociated cells.
- Generate high-quality data and images for the Kidney Tissue Atlas.
- Facilitate the structural, histologic, and molecular assessment of cellular “states” associated with healthy function, activation, injury, recovery, and adaptive and maladaptive repair.
- Develop novel methods to distinguish diseased from non-diseased areas of kidney.
- Identify robust structural, histologic, and molecular signatures and pathways that can be used to accurately phenotype individuals with AKI or CKD to inform future diagnostic, prognostic, or therapeutic selection schemes (subgroups).
Washington University - University of California San Diego (WU-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)
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)
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)
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.
The Central Hub is responsible for aggregating, analyzing, and visualizing the generated data and providing scientific, infrastructure, and administrative support for the KPMP consortium. The Central Hub houses the Data and Sample Coordinating Center (DCC), the Data Visualization Center (DVC), and the Administrative Core (AC).
University of Washington - University of Michigan - Mount Sinai
Data and sample Coordinating Center (DCC)
- Clinical protocol development and statistical calculations
- Standard clinical assessments
- Collecting, curating, aggregating, storing, distributing, and ensuring quality control of the biospecimens
Data Visualization Center (DVC)
- Digital pathology
- Data integration
- Building the Kidney Tissue Atlas and associated software tools to classify and locate different cell types and interstitial components in health and disease
Administrative Core (AC)
- Administrative and meeting support
- Establishing working groups
- Ensuring patient input is requested, received, and implemented
- Managing the Opportunity Pool to form new partnerships
The Steering Committee (SC) will be the primary governing body for all KPMP scientific activities. The SC will coordinate all sites awarded under these FOAs. The voting membership of the SC will include: one PD/PI from each award made under this and the companion FOAs, the NIH PS, and a representative from the Patient Engagement Working Group of the CH. The Chair of the SC will be assigned by NIH Program Staff, and may be chosen from outside the KPMP. Face-to-face meetings of this committee will occur at least two times a year. A portion of the SC meeting may be open to the public.
- The Program Directors/Principal Investigators (PDs/PIs) of each KPMP award
- The NIH Project Scientists (together representing a minority of voting members – not to exceed 1/3 of SC membership). Other NIH Program staff may attend the meeting as non-voting members.
The SC will be the primary governing body for all of the KPMP scientific activities. The SC will coordinate all projects awarded under the KPMP FOAs.
The role of the Steering Committee includes:
- Develop protocols and guidelines delineating the scientific and other interactions of the RS, TIS and CH.
- Foster collaboration, synergy and sharing among the KPMP sites and investigators.
- Provide the primary mechanism for interactions with the NIH.
- Oversee the planning of the KPMP scientific activities, including dynamic adjustment as needs and opportunities arise.
- Guide the development and documentation of the KPMP standards and guidelines.
- Prioritize the use of the KPMP resources including systems biology analyses and bioinformatics.
- Evaluate progress in the KPMP sites and recommend adjustments in approaches if necessary, including implementation of new projects and changes to ongoing studies and termination of projects and sites.
- Foster partnerships and collaborations that will facilitate the extension of the approach to new technologies and their application to related kidney disease.
- Develop and approve the KPMP-wide intellectual property agreements consistent with the terms and conditions of the cooperative agreement awards, applicable regulations, and the policies and practices of the awardee institutions.
- The SC will convene at least two face-to-face meetings a year in the Bethesda MD/Washington DC area. The first meeting will be a two-day meeting in August or September of 2017. Additional regular meetings will be conducted by teleconference or videoconference. Prior to each meeting, teleconference or videoconference, the SC Chair will prepare an agenda for review and approval, and distribute to members of the SC. Following these meetings, a list of participants and summary of discussion, action items, and recommendations will be prepared and submitted to the PO by the SC. Part of these meetings may be open to the public. The SC Chair may convene additional teleconferences, videoconferences, or electronic reviews to avoid delays in addressing key issues that cannot be evaluated at the regularly scheduled meetings. Regularly scheduled SC meetings will be convened in order to:
- Review progress of the KPMP sites; review progress of standardization and validation studies, other performance assessments, and future plans; and take remedial actions to address delays or other problems.
- Make recommendations to the KPMP sites about informatics and data and/or information management processes.
- Awardee members of KPMP will be required to accept and implement policies approved by the SC.
- The SC may make recommendations to the CH to establish working groups, or assign responsibility to key staff for other KPMP-related activities.
Voting may occur electronically, in-person, or via teleconferences. There are a total of 14 Steering Committee votes. Each grant is allotted one vote, regardless of the number of PIs associated with the grant. NIDDK has one vote, and the SC patient representative has one vote.
(last updated July 3rd, 2019)
Chair: Jonathan Himmelfarb (University of Washington)
The following members are allowed to vote on behalf of their grant/affiliation. Only one vote may be cast per affiliation.
- Brigham & Women’s/Joslin Diabetes Center: Sus Waikar, Sylvia Rosas (joint vote)
- Cleveland Clinic: Emilio Poggio, John Sedor, John O’Toole
- Columbia University: Krzysztof Kiryluk, Andrew Bomback, Jonathan Barasch
- Indiana University/Ohio State University: Pierre Dagher, Tarek Ashkar, Brad Rovin
- Johns Hopkins University/Yale University: Chirag Parikh*
- NIDDK: Chris Ketchum (or designee)
- Patient Representative: Keith Brown
- UC San Diego/Washington University St. Louis: Kun Zhang, Sanjay Jain
- UC San Francisco: Zoltan Laszik*
- University of Michigan/Princeton University/Broad Institute: Jeff Hodgin*, Nir Hacohen, Olga Troyanskya
- University of Pittsburgh: John Kellum*, Paul Palevsky, Matthew Rosengart
- UT Health San Antonio: Kumar Sharma*
- UT Southwestern: Miguel Vazquez*, Bob Toto
- University of Washington/University of Michigan/Mt Sinai: Jonathan Himmelfarb*, Matthias Kretzler**, Ravi Iyengar