Discovery and validation of a novel blood-based molecular biomarker of rejection following liver transplantation

Abstract

Noninvasive biomarker profiles of acute rejection (AR) could affect the management of liver transplant (LT) recipients. Peripheral blood was collected following LT for discovery (Northwestern University [NU]) and validation (National Institute of Allergy and Infectious Diseases Clinical Trials in Organ Transplantation [CTOT]-14 study). Blood gene profiling was paired with biopsies showing AR or ADNR (acute dysfunction no rejection) as well as stable graft function samples (Transplant eXcellent-TX). CTOT-14 subjects had serial collections prior to AR, ADNR, TX, and after AR treatment. NU cohort gene expression (46 AR, 45 TX) was analyzed using random forest models to generate a classifier training set (36 gene probe) distinguishing AR vs TX (area under the curve 0.92). The algorithm and threshold were locked and tested on the CTOT-14 validation cohort (14 AR, 50 TX), yielding an accuracy of 0.77, sensitivity 0.57, specificity 0.82, positive predictive value (PPV) 0.47, and negative predictive value (NPV) 0.87 for AR vs TX. The probability score line slopes were positive preceding AR, and negative preceding TX and non-AR (TX + ADNR) (P ≤ .001) and following AR treatment. In conclusion, we have developed a blood biomarker diagnostic for AR that can be detected prior to AR-associated graft injury as well a normal graft function (non-AR). Further studies are needed to evaluate its utility in precision-guided immunosuppression optimization following LT.

Keywords: biomarker; clinical research/practice; clinical trial; genomics; immunobiology; immunosuppression/immune modulation; liver allograft function/dysfunction; liver transplantation/hepatology; rejection; translational research/science.

Conflict of interest statement

The authors of this manuscript have conflicts of interest to disclose as described by the American Journal of Transplantation. Transplant Genomics Incorporated (Eurofins/Viracor): Josh Levitsky (Consultant, Stockholder), Sunil Kurian (Consultant, Stockholder), Michael Abecassis (Co‐Founder, Stockholder).

© 2020 The Authors. American Journal of Transplantation published by Wiley Periodicals LLC on behalf of The American Society of Transplantation and the American Society of Transplant Surgeons.

Figures

FIGURE 1

CTOT‐14 consort diagram—enrollment and clinical phenotypes with samples. ADNR, acute dysfunction no rejection; AR, acute rejection; BGE, blood gene expression; Bx, biopsy; CTOT, Clinical Trials in Organ Transplantation; HCV, hepatitis C virus; HCV‐R, hepatitis C virus recurrence; TX, Transplant eXcellent

FIGURE 2

The receiver operating curves (ROC)—AR vs TX (NU discovery cohort). The area under the curve is displayed as well as the performance characteristics (15% AR prevalence adjustment) at the 0.5 threshold (asterisk). AR, acute rejection; NU, Northwestern University; TX, Transplant eXcellent

FIGURE 3

Serial changes in gene expression using line slopes prior to AR, TX, and non‐AR. A, Pre‐AR vs pre‐TX (P < .001). B, Pre‐AR vs pre‐non‐AR (P < .001). C, Pre‐AR vs post‐AR, P = .085). The P value result is the phenotype comparison of the entire line slope from the time of transplantation, whereas the figures visually display a more focused time period around AR, TX, and non‐AR diagnosis (Time 0). AR, acute rejection; TX, Transplant eXcellent [Color figure can be viewed at wileyonlinelibrary.com]