Rationale and design of the Nephrotic Syndrome Study Network (NEPTUNE) Match in glomerular diseases: designing the right trial for the right patient, today
Authors: Howard Trachtman, Hailey Desmond, Amanda L. Williams, Laura H. Mariani, Sean Eddy, Wenjun Ju, Laura Barisoni, Heather K. Ascani, Wendy R. Uhlmann, Cathie Spino, Lawrence B. Holzman, John R. Sedor, Crystal Gadegbeku, Lalita Subramanian, Chrysta C. Lienczewski, Tina Manieri, Scott J. Roberts, Debbie S. Gipson, Matthias Kretzler, Susan Massengill, Layla Lo, Katherine Dell, John O’Toole, John Sedor, Blair Martin, Ian Macumber, Silpa Sharma, Tarak Srivastava, Kelsey Markus, Christine Sethna, Suzanne Vento, Pietro Canetta, Opeyemi Olabisi, Rasheed Gbadegesin, Maurice Smith, Laurence Greenbaum, Chia-shi Wang, Emily Yun, Sharon Adler, Janine LaPage, Amatur Amarah, Mathew Itteera, Meredith Atkinson, Miahje Williams, John Lieske, Marie Hogan, Fernando Fervenza, David Selewski, Cheryl Alston, Kim Reidy, Michael Ross, Frederick Kaskel, Patricia Flynn, Laura Malaga-Dieguez, Olga Zhdanova, Laura Jane Pehrson, Melanie Miranda, Salem Almaani, Laci Roberts, Richard Lafayette, Shiktij Dave, Iris Lee, Shweta Shah, Sadaf Batla, Heather Reich, Michelle Hladunewich, Paul Ling, Martin Romano, Paul Brakeman, James Dylewski, Nathan Rogers, Ellen McCarthy, Catherine Creed, Alessia Fornoni, Miguel Bandes, Matthias Kretzler, Laura Mariani, Zubin Modi, A. Williams, Roxy Ni, Patrick Nachman, Michelle Rheault, Amy Kowalski, Nicolas Rauwolf, Vimal Derebail, Keisha Gibson, Anne Froment, Sara Kelley, Lawrence Holzman, Kevin Meyers, Krishna Kallem, Aliya Edwards, Samin Sharma, Elizabeth Roehm, Kamalanathan Sambandam, Elizabeth Brown, Jamie Hellewege, Ashley Jefferson, Sangeeta Hingorani, Katherine Tuttle, Linda Manahan, Emily Pao, Kelli Kuykendall, Jen Jar Lin, Vikas Dharnidharka, Matthias Kretzler, Brenda Gillespie, Laura Mariani, Zubin Modi, Eloise Salmon, Howard Trachtman, Tina Mainieri, Gabrielle Alter, Michael Arbit, Hailey Desmond, Sean Eddy, Damian Fermin, Wenjun Ju, Maria Larkina, Chrysta Lienczewski, Rebecca Scherr, Jonathan Troost, Amanda Williams, Yan Zhai, Colleen Kincaid, Shengqian Li, Shannon Li, Crystal Gadegbeku, Laura Barisoni, John Sedor, Matthew G. Sampson, Abigail Smith, Lawrence Holzman, Jarcy Zee, Carmen Avila-Casado, Serena Bagnasco, Lihong Bu, Shelley Caltharp, Clarissa Cassol, Dawit Demeke, Brenda Gillespie, Jared Hassler, Leal Herlitz, Stephen Hewitt, Jeff Hodgin, Danni Holanda, Neeraja Kambham, Kevin Lemley, Laura Mariani, Nidia Messias, Alexei Mikhailov, Vanessa Moreno, Behzad Najafian, Matthew Palmer, Avi Rosenberg, Virginie Royal, Miroslav Sekulik, Barry Stokes, David Thomas, Ming Wu, Michifumi Yamashita, Hong Yin, Jarcy Zee, Yiqin Zuo . Cochairs, Laura Barisoni, Cynthia Nast
Journal: Kidney International (2024)

Glomerular diseases are classified using a descriptive taxonomy that is not reflective of the heterogeneous underlying molecular drivers. This limits not only diagnostic and therapeutic patient management, but also impacts clinical trials evaluating targeted interventions. The Nephrotic Syndrome Study Network (NEPTUNE) is poised to address these challenges. The study has enrolled >850 pediatric and adult patients with proteinuric glomerular diseases who have contributed to deep clinical, histologic, genetic, and molecular profiles linked to long-term outcomes. The NEPTUNE Knowledge Network, comprising combined, multiscalar data sets, captures each participant's molecular disease processes at the time of kidney biopsy. In this editorial, we describe the design and implementation of NEPTUNE Match, which bridges a basic science discovery pipeline with targeted clinical trials. Noninvasive biomarkers have been developed for real-time pathway analyses. A Molecular Nephrology Board reviews the pathway maps together with clinical, laboratory, and histopathologic data assembled for each patient to compile a Match report that estimates the fit between the specific molecular disease pathway(s) identified in an individual patient and proposed clinical trials. The NEPTUNE Match report is communicated using established protocols to the patient and the attending nephrologist for use in their selection of available clinical trials. NEPTUNE Match represents the first application of precision medicine in nephrology with the aim of developing targeted therapies and providing the right medication for each patient with primary glomerular disease. Glomerular diseases are classified using a descriptive taxonomy that is not reflective of the heterogeneous underlying molecular drivers. This limits not only diagnostic and therapeutic patient management, but also impacts clinical trials evaluating targeted interventions. The Nephrotic Syndrome Study Network (NEPTUNE) is poised to address these challenges. The study has enrolled >850 pediatric and adult patients with proteinuric glomerular diseases who have contributed to deep clinical, histologic, genetic, and molecular profiles linked to long-term outcomes. The NEPTUNE Knowledge Network, comprising combined, multiscalar data sets, captures each participant's molecular disease processes at the time of kidney biopsy. In this editorial, we describe the design and implementation of NEPTUNE Match, which bridges a basic science discovery pipeline with targeted clinical trials. Noninvasive biomarkers have been developed for real-time pathway analyses. A Molecular Nephrology Board reviews the pathway maps together with clinical, laboratory, and histopathologic data assembled for each patient to compile a Match report that estimates the fit between the specific molecular disease pathway(s) identified in an individual patient and proposed clinical trials. The NEPTUNE Match report is communicated using established protocols to the patient and the attending nephrologist for use in their selection of available clinical trials. NEPTUNE Match represents the first application of precision medicine in nephrology with the aim of developing targeted therapies and providing the right medication for each patient with primary glomerular disease. Nephrotic syndrome (NS) comprises focal segmental glomerular sclerosis (FSGS), minimal change disease, and membranous nephropathy, which are rare glomerular diseases associated with debilitating complications, including possible progression to kidney failure. Despite similar and overlapping symptoms (e.g., edema, proteinuria, and loss of kidney function), individual clinical courses can vary markedly. The only US Food and Drug Administration–approved medical treatments are corticosteroid-based immunosuppressive agents (i.e., prednisone and adrenocorticotrophic hormone) that cause severe adverse effects. Off-label use of second-line immunosuppressive medications is currently part of guideline-based clinical care. The clinical, histopathology-based taxonomy of NS fails to capture the underlying molecular drivers of these diseases (Figure 1). Consequently, current diagnostic categories have limited use in either predicting the disease course or responding to therapy, frequently putting patients at risk of adverse effects from treatments that prove ineffective. In addition, clinical trials in NS enroll an unstratified, biologically diverse group of individuals. This underlying mechanistic heterogeneity often results in inconclusive trial outcomes, even though the intervention may successfully target a subset of susceptible patients. The Nephrotic Syndrome Study Network (NEPTUNE) was developed to define the molecular mechanism of NS for targeted therapeutic interventions. NEPTUNE follows the natural history of patients and aims to improve the diagnosis, management, and treatment of NS using innovative research strategies1Gadegbeku C.A. Gipson D.S. Holzman L.B. et al.Design of the Nephrotic Syndrome Study Network (NEPTUNE) to evaluate primary glomerular nephropathy by a multidisciplinary approach.Kidney Int. 2013; 83: 749-756Abstract Full Text Full Text PDF PubMed Scopus (218) Google Scholar (Figure 2). Participants are enrolled into NEPTUNE at the time of a diagnostic kidney biopsy or at initial presentation of disease for pediatric patients for whom a biopsy is usually not clinically indicated. In the biopsy cohort, an extra core of kidney tissue is obtained during the clinically indicated procedure for research studies. Blood and urine specimens, along with clinical data, are collected prospectively every 4 to 6 months for up to 5 years. NEPTUNE has recruited a prospective longitudinal observational cohort of 861 patients with proteinuric, glomerular diseases who have contributed deep clinical, histologic, genetic, and molecular data as well as profiles of their long-term outcomes under standard care or in independent clinical trials. A key component of NEPTUNE that was established at its inception was the creation of a dedicated biorepository for long-term storage of the full range of biospecimens collected from each participant.1Gadegbeku C.A. Gipson D.S. Holzman L.B. et al.Design of the Nephrotic Syndrome Study Network (NEPTUNE) to evaluate primary glomerular nephropathy by a multidisciplinary approach.Kidney Int. 2013; 83: 749-756Abstract Full Text Full Text PDF PubMed Scopus (218) Google Scholar NEPTUNE has continuously enhanced its ability to derive multiscalar data sets robustly and efficiently from the clinical data and biosamples contributed by study participants. This effort has been conducted through approved ancillary studies that leverage the Biorepository and tranSMART database. For example, capture of environmental exposures and socioeconomic status is incorporated into prospective ascertainment of long-term outcomes relevant to glomerular diseases. Kidney biopsy tissue is used for a digital pathology-driven structural definition of the disease state,2Barisoni L. Lafata K.J. Hewitt S.M. et al.Digital pathology and computational image analysis in nephropathology.Nat Rev Nephrol. 2020; 16: 669-685Crossref PubMed Scopus (113) Google Scholar, 3Barisoni L. Nast C.C. Jennette J.C. et al.Digital pathology evaluation in the multicenter Nephrotic Syndrome Study Network (NEPTUNE).Clin J Am Soc Nephrol. 2013; 8: 1449-1459Crossref PubMed Scopus (68) Google Scholar, 4Barisoni L. Troost J.P. Nast C. et al.Reproducibility of the NEPTUNE descriptor-based scoring system on whole-slide images and histologic and ultrastructural digital images.Mod Pathol. 2016; 29: 671-684Abstract Full Text Full Text PDF PubMed Scopus (48) Google Scholar, 5Hodgin J.B. Mariani L.H. Zee J. et al.Quantification of glomerular structural lesions: associations with clinical outcomes and transcriptomic profiles in nephrotic syndrome.Am J Kidney Dis. 2022; 79: 807-819.e1Abstract Full Text Full Text PDF Scopus (0) Google Scholar, 6Mariani L.H. Martini S. Barisoni L. et al.Interstitial fibrosis scored on whole-slide digital imaging of kidney biopsies is a predictor of outcome in proteinuric glomerulopathies.Nephrol Dial Transplant. 2018; 33: 310-318Crossref PubMed Scopus (64) Google Scholar, 7Nast C.C. Lemley K.V. Hodgin J.B. et al.Morphology in the digital age: integrating high-resolution description of structural alterations with phenotypes and genotypes.Semin Nephrol. 2015; 35: 266-278Abstract Full Text Full Text PDF PubMed Google Scholar, 8Royal V. Zee J. Liu Q. et al.Ultrastructural characterization of proteinuric patients predicts clinical outcomes.J Am Soc Nephrol. 2020; 31: 841-854Crossref PubMed Scopus (21) Google Scholar, 9Zee J. Liu Q. Smith A.R. et al.Kidney biopsy features most predictive of clinical outcomes in the spectrum of minimal change disease and focal segmental glomerulosclerosis.J Am Soc Nephrol. 2022; 33: 1411-1426Crossref PubMed Scopus (11) Google Scholar whole-genome sequencing,10Barry A. McNulty M.T. Jia X. et al.Multi-population genome-wide association study implicates immune and non-immune factors in pediatric steroid-sensitive nephrotic syndrome.Nat Commun. 2023; 14: 2481Crossref PubMed Scopus (3) Google Scholar, 11Gupta Y, Friedman DJ, McNulty M, et al. Strong protective effect of the APOL1 p.N264K variant against G2-associated focal segmental glomerulosclerosis and kidney disease. Preprint. medRxiv. 23293554. Posted online August 4, 2023. https://doi.org/10.1101/2023.08.02.23293554Google Scholar, 12Han S.K. McNulty M.T. Benway C.J. et al.Mapping genomic regulation of kidney disease and traits through high-resolution and interpretable eQTLs.Nat Commun. 2023; 14: 2229Crossref Scopus (1) Google Scholar, 13Sampson M.G. Robertson C.C. Martini S. et al.Integrative genomics identifies novel associations with APOL1 risk genotypes in Black NEPTUNE subjects.J Am Soc Nephrol. 2016; 27: 814-823Crossref PubMed Scopus (92) Google Scholar, 14Ng D.K. Robertson C.C. Woroniecki R.P. et al.APOL1-associated glomerular disease among African-American children: a collaboration of the Chronic Kidney Disease in Children (CKiD) and Nephrotic Syndrome Study Network (NEPTUNE) cohorts.Nephrol Dial Transplant. 2017; 32: 983-990PubMed Google Scholar, 15Gillies C.E. Putler R. Menon R. et al.An eQTL landscape of kidney tissue in human nephrotic syndrome.Am J Hum Genet. 2018; 103: 232-244Abstract Full Text Full Text PDF PubMed Scopus (114) Google Scholar gene expression profiles from microdissected glomeruli and tubule-interstitial compartments,16Mariani L.H. Eddy S. AlAkwaa F.M. et al.Precision nephrology identified tumor necrosis factor activation variability in minimal change disease and focal segmental glomerulosclerosis.Kidney Int. 2023; 103: 565-579Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar and single nuclear RNA sequencing.17Menon R, Otto EA, Barisoni L, et al. Defining the molecular correlate of arteriolar hyalinosis in kidney disease progression by integration of single cell transcriptomic analysis and pathology scoring. Preprint. medRxiv. 23291150. Posted online August 23, 2023. https://doi.org/10.1101/2023.06.14.23291150Google Scholar, 18Menon R. Otto E.A. Hoover P. et al.Single cell transcriptomics identifies focal segmental glomerulosclerosis remission endothelial biomarker.JCI Insight. 2020; 5e133267Crossref Scopus (78) Google Scholar, 19Harder J.L. Menon R. Otto E.A. et al.Organoid single cell profiling identifies a transcriptional signature of glomerular disease.JCI Insight. 2019; 4e122697Crossref PubMed Scopus (55) Google Scholar Blood- and urine-derived noninvasive proteomic and metabolomic biomarker profiles are mapped to transcriptomic signatures in the kidney.16Mariani L.H. Eddy S. AlAkwaa F.M. et al.Precision nephrology identified tumor necrosis factor activation variability in minimal change disease and focal segmental glomerulosclerosis.Kidney Int. 2023; 103: 565-579Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar,20Wu Q. Troost J.P. Dai T. et al.Kidney injury molecule-1 and periostin urinary excretion and tissue expression levels and association with glomerular disease outcomes.Glomerular Dis. 2021; 1: 45-59Crossref Google Scholar, 21Merchant M.L. Barati M.T. Caster D.J. et al.Proteomic analysis identifies distinct glomerular extracellular matrix in collapsing focal segmental glomerulosclerosis.J Am Soc Nephrol. 2020; 31: 1883-1904Crossref PubMed Scopus (29) Google Scholar, 22Ju W. Nair V. Smith S. et al.Tissue transcriptome-driven identification of epidermal growth factor as a chronic kidney disease biomarker.Sci Transl Med. 2015; 7: 316ra193Crossref PubMed Scopus (270) Google Scholar, 23Grayson P.C. Eddy S. Taroni J.N. et al.Metabolic pathways and immunometabolism in rare kidney diseases.Ann Rheum Dis. 2018; 77: 1226-1233PubMed Google Scholar The heterogeneous information sources are carefully annotated in the NEPTUNE Knowledge Network for comprehensive mechanistic disease definitions. The NEPTUNE Knowledge Network is accessed by the kidney research community via a study-specific NEPTUNE tranSMART instance. Neptune tranSMART allows the user to explore diverse data sets in an intuitive data exploration framework with drag and drop functionality. The knowledge graph of currently 861 study participants includes comprehensive patient demographics, socioeconomic status, clinical disease course, biochemical measurements, glomerular disease-specific end points,1Gadegbeku C.A. Gipson D.S. Holzman L.B. et al.Design of the Nephrotic Syndrome Study Network (NEPTUNE) to evaluate primary glomerular nephropathy by a multidisciplinary approach.Kidney Int. 2013; 83: 749-756Abstract Full Text Full Text PDF PubMed Scopus (218) Google Scholar genotypes, glomerular and tubular gene expression data sets, blood and urine comprehensive (Somascan) and targeted (Luminex) proteomic data, blood and urine metabolomics profiles, and the NEPTUNE Digital Pathology Scoring System histology descriptors.5Hodgin J.B. Mariani L.H. Zee J. et al.Quantification of glomerular structural lesions: associations with clinical outcomes and transcriptomic profiles in nephrotic syndrome.Am J Kidney Dis. 2022; 79: 807-819.e1Abstract Full Text Full Text PDF Scopus (0) Google Scholar Single nuclear gene expression profiles from more than a million nuclei can be mined in a NEPTUNE CellXGene instance, and kidney-specific expression quantitative traits can be obtained in the NephQTL server. More than 200 approved ancillary studies have used the NEPTUNE Knowledge Network in support of the international research efforts in glomerular diseases (for access, see www.neptune-study.org/ancillary-studies). The NEPTUNE research infrastructure has matured sufficiently so that each participant's data can be assessed, and molecular profiles generated, in a timely manner, to generate a comprehensive molecular nephrology report for each patient that can be effectively communicated to him/her. Defining NS in molecular terms is essential in precision medicine to identify appropriate therapeutic targets and improve clinical trial design. NEPTUNE investigators have had early success using multiple data domains to identify disease mechanisms activated in discrete subgroups of NS5Hodgin J.B. Mariani L.H. Zee J. et al.Quantification of glomerular structural lesions: associations with clinical outcomes and transcriptomic profiles in nephrotic syndrome.Am J Kidney Dis. 2022; 79: 807-819.e1Abstract Full Text Full Text PDF Scopus (0) Google Scholar,16Mariani L.H. Eddy S. AlAkwaa F.M. et al.Precision nephrology identified tumor necrosis factor activation variability in minimal change disease and focal segmental glomerulosclerosis.Kidney Int. 2023; 103: 565-579Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar and in identifying variability in specific molecular pathway signals in patients with FSGS and IgA nephropathy.24Tao J. Mariani L. Eddy S. et al.JAK-STAT signaling is activated in the kidney and peripheral blood cells of patients with focal segmental glomerulosclerosis.Kidney Int. 2018; 94: 795-808Abstract Full Text Full Text PDF PubMed Scopus (46) Google Scholar,25Tao J. Mariani L. Eddy S. et al.JAK-STAT activity in peripheral blood cells and kidney tissue in IgA nephropathy.Clin J Am Soc Nephrol. 2020; 15: 973-982Crossref PubMed Scopus (20) Google Scholar These have served as starting points for matching patients for targeted therapies and resulted in the first molecular stratified phase 2 trial active in NS (clinicaltrials.gov/NCT04009668).2Barisoni L. Lafata K.J. Hewitt S.M. et al.Digital pathology and computational image analysis in nephropathology.Nat Rev Nephrol. 2020; 16: 669-685Crossref PubMed Scopus (113) Google Scholar,3Barisoni L. Nast C.C. Jennette J.C. et al.Digital pathology evaluation in the multicenter Nephrotic Syndrome Study Network (NEPTUNE).Clin J Am Soc Nephrol. 2013; 8: 1449-1459Crossref PubMed Scopus (68) Google Scholar In recent years, in parallel with an improved understanding of disease pathogenesis, there has been a substantial increase in the number of clinical trials enrolling participants with NS. An evidence-based, scientifically informed clinical trials selection process for patients and providers will enhance the likelihood of successful outcomes across these trials. This requires not only the molecular disease definitions of NS applied to individual therapeutic targets in a given patient, but equally important the development of an effective communication strategy to inform participants of clinical trials that target mechanisms that may match their disease biology. The goal of NEPTUNE Match is to foster the implementation of precision medicine in NS, whereby the right trial is made available to the right patient at the right time. To test if a precision medicine approach can be offered to patients with NS, the following 4 steps have been developed for NEPTUNE Match (Figure 3):•Step 1: Generate individual noninvasive molecular disease profiles in NEPTUNE study participants in real time.•Step 2: Match individual molecular disease profiles in the molecular nephrology board report with targets of ongoing NS trials.•Step 3: Establish a communication framework to educate study participants of the Molecular Nephrology Board recommendation for targeted trial participation.•Step 4: Compare retrospectively kidney health outcomes in NEPTUNE Match study participants versus trial subjects with misaligned or unknown match alignment. A key prerequisite for NEPTUNE Match is the development of noninvasive predictive biomarkers representative of the activity of the specific disease pathways being targeted by the intervention. Predictive biomarkers can be used to develop trial-specific quantitative Match pathway activity scores. Match disease pathway activity scores can be derived from a spectrum of molecular changes in response to pathway activation or therapeutic intervention. Sources for the treatment response predictive biomarkers include the following: (i) literature-defined molecular pathway signatures linked to cause-and-effect transcriptional target activation16Mariani L.H. Eddy S. AlAkwaa F.M. et al.Precision nephrology identified tumor necrosis factor activation variability in minimal change disease and focal segmental glomerulosclerosis.Kidney Int. 2023; 103: 565-579Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar; (ii) in silico modeling of downstream transcriptional targets of a specific pathway24Tao J. Mariani L. Eddy S. et al.JAK-STAT signaling is activated in the kidney and peripheral blood cells of patients with focal segmental glomerulosclerosis.Kidney Int. 2018; 94: 795-808Abstract Full Text Full Text PDF PubMed Scopus (46) Google Scholar; (iii) experimentally derived molecular signatures reflecting treatment responses in model systems (e.g., kidney, blood, or urine molecular profiles from preclinical murine, rat, cell culture, and organoid models) mapped back to human disease profiles in NEPTUNE; or (iv) molecular profiles from kidney, blood, or urine linked to clinically defined treatment responses obtained in early-stage proof-of-concept trials (phase 1b or phase 2a). The NEPTUNE Knowledge Network has annotated comprehensive clinical and molecular information of all NEPTUNE participants to aid in both target signature identification and noninvasive biomarker development. To date, the most effective strategy to define a target activation signature for Match uses gene expression profiles with a shared regulation between NEPTUNE kidney biopsy profiles and model systems, which are reversed to the healthy state by drug treatment. This target activation signature gene set is then analyzed across the cohort to define further associations with clinical or histologic baseline characteristics and outcomes (see the study by Mariani et al.16Mariani L.H. Eddy S. AlAkwaa F.M. et al.Precision nephrology identified tumor necrosis factor activation variability in minimal change disease and focal segmental glomerulosclerosis.Kidney Int. 2023; 103: 565-579Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar for a representative example). Transcripts and proteins comprising the target activation signature in kidneys are linked to proteomic and metabolomic profiles from blood and urine samples obtained at the time of kidney biopsy to identify noninvasive surrogates of the activation signature. In the biomarker assay selection and development workflow, priority is given to candidate protein biomarkers in blood or urine showing robust correlation with the expression of corresponding genes or with the target activation signature in kidneys. Single-cell gene expression profiles provide expression distribution in kidney cells guiding selection of the biofluids for assay development (vascular expression toward plasma, and tubular expression toward urine as biomarker matrix). Biomarker assay selection, feasibility evaluation, validation, and optimization for specific biosamples follow standard protocols.26Bioanalytical Method Validation. Center for Drug Evaluation and Research, 2018Google Scholar, 27Andreasson U. Perret-Liaudet A. van Waalwijk van Doorn L.J.C. et al.A practical guide to immunoassay method validation.Front Neurol. 2015; 6: 179Crossref PubMed Scopus (312) Google Scholar, 28van Amsterdam P. Companjen A. Brudny-Kloeppel M. et al.The European Bioanalysis Forum community's evaluation, interpretation and implementation of the European Medicines Agency guideline on bioanalytical method validation.Bioanalysis. 2013; 5: 645-659Crossref PubMed Scopus (0) Google Scholar Finally, the biomarker profiles across the NEPTUNE cohort samples are generated and used to build a predicting model of the kidney activity state. Models to date have been mainly composite of baseline clinical characteristics and a combination of urine and/or plasma protein biomarkers (for a representative example, see tumor necrosis factor (TNF) study design described below). Once a prediction model is generated and cross-validated, all baseline biosamples from patients in the cohort undergo retrospective biomarker profiling, and the distribution of the Match activity scores across the cohort is established. Individual patient noninvasive scores are assigned a rank among the pathway activation scores generated across the entire NEPTUNE cohort. The quartile rank of the predicted Match activity profile is then returned to the Molecular Nephrology Board and used to generate NEPTUNE Match reports that display the individual pathway activity level in relationship to the entire NEPTUNE patient population (Figure 3). In a proof-of-concept study of this strategy, NEPTUNE investigators have studied TNF inhibitors in FSGS. In the FONT (Novel Therapies for Resistant FSGS) trial, a response to adalimumab, a monoclonal antibody to TNF, was observed in a limited subgroup of patients,29Joy M.S. Gipson D.S. Powell L. et al.Phase 1 trial of adalimumab in focal segmental glomerulosclerosis (FSGS), II: report of the FONT (Novel Therapies for Resistant FSGS) study group.Am J Kidney Dis. 2010; 55: 50-60Abstract Full Text Full Text PDF PubMed Scopus (0) Google Scholar, 30Peyser A. Machardy N. Tarapore F. et al.Follow-up of phase I trial of adalimumab and rosiglitazone in FSGS, III: report of the FONT study group.BMC Nephrol. 2010; 11: 2Crossref PubMed Scopus (0) Google Scholar, 31Trachtman H. Vento S. Herreshoff E. et al.Efficacy of galactose and adalimumab in patients with resistant focal segmental glomerulosclerosis: report of the font clinical trial group.BMC Nephrol. 2015; 16: 111Crossref PubMed Scopus (56) Google Scholar resulting in an overall negative clinical trial outcome. To test the hypothesis that high kidney TNF activation might be a predictor of a favorable response to TNF inhibition, a TNF activation signature was obtained from NEPTUNE kidney biopsy gene expression profiles using transcripts known to be upregulated on TNF activation. The TNF-dependent differential gene expression of the activation signature was experimentally validated in kidney organoids.16Mariani L.H. Eddy S. AlAkwaa F.M. et al.Precision nephrology identified tumor necrosis factor activation variability in minimal change disease and focal segmental glomerulosclerosis.Kidney Int. 2023; 103: 565-579Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar Podocyte and tubular cell compartment were identified as a site of differential gene expression of the TNF signature in NEPTUNE single-nucleus RNA-sequencing profiles. Tissue inhibitor of metalloproteinases 1 (TIMP1) and monocyte chemotactic protein 1 were identified as urinary proteins with tight correlation to their corresponding kidney transcripts (normalized for urinary creatinine). A model using urinary monocyte chemotactic protein 1 and TIMP1 together with estimated glomerular filtration rate and urine protein/creatinine ratio enabled prediction of TNF activity in kidneys with an area under the curve of 0.92.16Mariani L.H. Eddy S. AlAkwaa F.M. et al.Precision nephrology identified tumor necrosis factor activation variability in minimal change disease and focal segmental glomerulosclerosis.Kidney Int. 2023; 103: 565-579Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar Elevated TNF activity assessment is being used as the primary inclusion criterion in an ongoing target engagement proof-of-concept trial in patients with FSGS (NCT04009668). Currently, tissue-derived Match activity scores are linked to ongoing clinical development programs in NS for 4 studies. Each of these has customized Match activity scores and biomarker(s). For example, the combination of transcriptional "response" profiles and urine markers from targetable mechanisms met the criteria for at least 1 of the 4 mechanisms being assessed in 85 participants with either FSGS or minimal change disease (Figure 4). Participation in NEPTUNE Match is open to all NEPTUNE participants. The roster of clinical trials included in NEPTUNE Match include investigator- and industry-initiated trials. By partnering with NEPTUNE Match, the investigators commit to returning trial data to NEPTUNE. Only clinical trials that investigate therapeutic targets that are amenable to target-specific assessment and consistent with the molecular profiling abilities of the NEPTUNE Profiling Units are selected for inclusion. NEPTUNE Match enrollment commences with informed consent describing risks and benefits of participating in Match. It is based on the following inclusion criteria:(i)Willing and able to consent, and as appropriate assent, to participate in NEPTUNE Match.(ii)Must be potentially eligible for the NEPTUNE Match partnering trials (e.g., if no trial is enrolling a participant aged <2 years, those aged <2 years are not eligible). Comprehensive data assessing the disease state of NEPTUNE participants are needed in real time. NEPTUNE Profiling Units for clinical phenotype and biofluid-based biomarker quantification have been established to rapidly evaluate participant clinical, histologic, and molecular data to generate patient-specific molecular pathway scores for timely review by the Molecular Nephrology Board. The Molecular Nephrology Board reviews the information on the pathway activity scores provided by the NEPTUNE analytical units. Pathway activation of molecules targeted by clinical trials pursued in NS are reviewed for each participant. The proposed strength of the match of each participant to each open trial is presented to the Molecular Nephrology Board for discussion. The Molecular Nephrology Board aggregates and assesses the participant-specific trial matching and provides input on the final participant-specific Match report. The participant-specific Match report is then generated, indicating the pathway activation scores of the study participant relative to the overall NEPTUNE population in quartiles. The Match report provides this information for each clinical trial for which the patient qualifies, based on specific biomarkers. Because the information contained in the Match report is experimental and not validated, effective communication tools are essential to inform study participants and NEPTUNE site investigators about the intent of the study and the experimental nature of the integrated analysis and the personalized output. An interdisciplinary team led by experienced health educators and genetic counselors, in collaboration with a patient advisory panel, has developed and implemented a communication strategy that combines tailored educational materials with training of NEPTUNE Match participating clinical site investigators. This strategy supports accurate interpretation and transmission of the NEPTUNE Match report to participants. Key findings from the Molecular Nephrology Board trial matching analyses and deliberations are conveyed to study participants by