The kSORT Assay to Detect Renal Transplant Patients at High Risk for Acute Rejection: Results of the Multicenter AART Study
Authors: Silke Roedder, Tara Sigdel, Nathan Salomonis, Sue Hsieh, Hong Dai, Oriol Bestard, Diana Metes, Andrea Zeevi, Albin Gritsch, Jennifer Cheeseman, Camila Macedo, Ram Peddy, Mara Medeiros, Flavio Vincenti, Nancy Asher, Oscar Salvatierra, Ron Shapiro, Allan Kirk, Elaine Reed, Minnie M. Sarwal
Abstract
Background
Development of noninvasive molecular assays to improve disease diagnosis and patient monitoring is a critical need. In renal transplantation, acute rejection (AR) increases the risk for chronic graft injury and failure. Noninvasive diagnostic assays to improve current late and nonspecific diagnosis of rejection are needed. We sought to develop a test using a simple blood gene expression assay to detect patients at high risk for AR.
Methods and Findings
We developed a novel correlation-based algorithm by step-wise analysis of gene expression data in 558 blood samples from 436 renal transplant patients collected across eight transplant centers in the US, Mexico, and Spain between 5 February 2005 and 15 December 2012 in the Assessment of Acute Rejection in Renal Transplantation (AART) study. Gene expression was assessed by quantitative real-time PCR (QPCR) in one center. A 17-gene set—the Kidney Solid Organ Response Test (kSORT)—was selected in 143 samples for AR classification using discriminant analysis (area under the receiver operating characteristic curve [AUC] = 0.94; 95% CI 0.91–0.98), validated in 124 independent samples (AUC = 0.95; 95% CI 0.88–1.0) and evaluated for AR prediction in 191 serial samples, where it predicted AR up to 3 mo prior to detection by the current gold standard (biopsy). A novel reference-based algorithm (using 13 12-gene models) was developed in 100 independent samples to provide a numerical AR risk score, to classify patients as high risk versus low risk for AR. kSORT was able to detect AR in blood independent of age, time post-transplantation, and sample source without additional data normalization; AUC = 0.93 (95% CI 0.86–0.99). Further validation of kSORT is planned in prospective clinical observational and interventional trials.
Conclusions
The kSORT blood QPCR assay is a noninvasive tool to detect high risk of AR of renal transplants.
Citation: Roedder S, Sigdel T, Salomonis N, Hsieh S, Dai H, et al. (2014) The kSORT Assay to Detect Renal Transplant Patients at High Risk for Acute Rejection: Results of the Multicenter AART Study. PLoS Med 11(11): e1001759. doi:10.1371/journal.pmed.1001759
Academic Editor: Giuseppe Remuzzi, Istituto Mario Negri, Italy
Received: January 28, 2014; Accepted: October 10, 2014; Published: November 11, 2014
Copyright: © 2014 Roedder et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files.
Funding: The study was funded by the NIAID U01AI077821 (http://www.niaid.nih.gov), Mexican Federal Funds for Research (Ssa.746), NIH R01 AI042819 (http://grants.nih.gov), Spanish national public grant (PI13/01263), and a European Commission grant within the BIODRIM Consortium (12CEE014 Bio-Drim). No funding bodies had any role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: MS is Chair of the SAB and Founder of Organ-I and Consultant for Immucor, Bristol Meyers Squibb, UCB, ISIS, Genentech; SR was a Consultant for Organ-I; TS and NS are Consultants for Organ-I, Immucor; FV has research grants with Astellas Pharma, Bristol Myers Squibb, Alexion, Pfizer, Novartis, Genentech.
Abbreviations: AART, Assessment of Acute Rejection in Renal Transplantation; ABI, Applied Biosystems; ABMR, antibody-mediated rejection; ANOVA, analysis of variance; AR, acute rejection; AUC, area under the receiver operating characteristic curve; Barcelona, Bellvitge University Hospital; BKV, BK polyomavirus; CNI, calcineurin inhibitor; CPMC, California Pacific Medical Center; CRM, common rejection module; DSA, donor-specific antibodies; Emory, Emory University; kSAS, kSORT analysis suite; kSORT, Kidney Solid Organ Response Test; Mex, Hospital Infantil de México Federico Gómez Laboratorio de Investigacion en Nefrologia; NIH, National Institutes of Health; PB, peripheral blood; PBL, peripheral blood lymphocyte; PBMC, peripheral blood mononuclear cell; plsDA, partial least squares discriminant analysis; PPV, positive predictive value; QPCR, quantitative real-time PCR; ROC, receiver operating characteristic; Stanford, Stanford University; TCMR, cell-mediated rejection; UCLA, University of California Los Angeles; UCSF, University of California San Francisco; UPMC, University of Pittsburgh Medical Center.
Author Contributions
Conceived and designed the experiments: MS SR TS. Performed the experiments: SH HD TS SR NS MS. Analyzed the data: SR NS TS MS. Contributed reagents/materials/analysis tools: DM AZ AG JC CM RP OB MM FV NA OS RS AK ER MS NS. Wrote the first draft of the manuscript: SR MS NS TS. Wrote the paper: SR MS TS NS OB ER AK DM RS. ICMJE criteria for authorship read and met: SR TS NS SH HD DM AZ AG JC CM RP OB MM FV NA OS RS AK ER MS. Agree with manuscript results and conclusions: SR TS NS SH HD DM AZ AG JC CM RP OB MM FV NA OS RS AK ER MS. Enrolled patients: DM RP OB MM FV OS RS AK ER MS.
Acknowledgments
We thank all patients, parents of patients, physicians, and nurses for participation in the AART study. We thank J. Alberu from Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico, and I. Abdullah from El Camino Hospital, CA, US, for their support.
