Transcriptional responses define dysregulated immune activation in Hepatitis C (HCV)-naïve recipients of HCV-infected donor kidneys

PLOS ONE RESEARCH ARTICLE Transcriptional responses define dysregulated immune activation in Hepatitis C (HCV)-naïve recipients of HCV-infected donor kidneys Julie M. Steinbrink ID1,2*, Cameron Miller2, Rachel A. Myers2, Scott Sanoff3, Anna Mazur2, Thomas W. Burke ID2, Jennifer Byrns4, Annette M. Jackson5, Xunrong Luo3, Micah T. McClain1,2,6 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 1 Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, NC, United States of America, 2 Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, Durham, NC, United States of America, 3 Division of Nephrology, Department of Medicine, Duke University Medical Center, Durham, NC, United States of America, 4 Department of Pharmacy, Duke University Medical Center, Durham, NC, United States of America, 5 Departments of Surgery and Immunology, Duke University, Durham, NC, United States of America, 6 Division of Infectious Diseases, Durham Veterans Affairs Health Care System, Durham, NC, United States of America * OPEN ACCESS Citation: Steinbrink JM, Miller C, Myers RA, Sanoff S, Mazur A, Burke TW, et al. (2023) Transcriptional responses define dysregulated immune activation in Hepatitis C (HCV)-naïve recipients of HCVinfected donor kidneys. PLoS ONE 18(1): e0280602. https://doi.org/10.1371/journal. pone.0280602 Editor: Jason T. Blackard, University of Cincinnati College of Medicine, UNITED STATES Received: August 27, 2022 Accepted: January 3, 2023 Published: January 26, 2023 Copyright: © 2023 Steinbrink 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 Statement: All relevant data are available at GEO under the accession number: GSE213705. Funding: This work was supported by a grant from the American Society of Transplantation Research Network (https://www.myast.org) and CareDx (https://caredx.com) (J.M.S., X.L.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Abstract Renal transplantation from hepatitis C (HCV) nucleic acid amplification test-positive (NAATpositive) donors to uninfected recipients has greatly increased the organ donation pool. However, there is concern for adverse outcomes in these recipients due to dysregulated immunologic activation secondary to active inflammation from acute viremia at the time of transplantation. This includes increased rates of cytomegalovirus (CMV) DNAemia and allograft rejection. In this study, we evaluate transcriptional responses in circulating leukocytes to define the character, timing, and resolution of this immune dysregulation and assess for biomarkers of adverse outcomes in transplant patients. We enrolled 67 renal transplant recipients (30 controls, 37 HCV recipients) and performed RNA sequencing on serial samples from one, 3-, and 6-months post-transplant. CMV DNAemia and allograft rejection outcomes were measured. Least absolute shrinkage and selection operator was utilized to develop gene expression classifiers predictive of clinical outcomes. Acute HCV incited a marked transcriptomic response in circulating leukocytes of renal transplant recipients in the acute post-transplant setting, despite the presence of immunosuppression, with 109 genes significantly differentially expressed compared to controls. These HCV infection-associated genes were reflective of antiviral immune pathways and generally resolved by the 3-month timepoint after sustained viral response (SVR) for HCV. Differential gene expression was also noted from patients who developed CMV DNAemia or allograft rejection compared to those who did not, although transcriptomic classifiers could not accurately predict these outcomes, likely due to sample size and variable time-to-event. Acute HCV infection incites evidence of immune activation and canonical antiviral responses in the human host even in the presence of systemic immunosuppression. After treatment of HCV with antiviral therapy and subsequent aviremia, this immune activation resolves. Changes in gene expression PLOS ONE | https://doi.org/10.1371/journal.pone.0280602 January 26, 2023 1 / 19 PLOS ONE Competing interests: The authors have declared that no competing interests exist. Abbreviations: AUROC, area under a receiver operating characteristic; BP, biological process; C, Celsius; CC, cellular component; CMV, cytomegalovirus; CPM, counts per million; CST7, cystatin F; D, donor; DEA, differential expression analysis; DSA, donor specific antibody; DUMC, Duke University Medical Center; FDR, false discovery rate; GO, gene ontology; GSEA, gene set enrichment analysis; HCV, hepatitis C virus; HSV, herpes simplex virus; IFIT, interferon-induced proteins; IQR, interquartile range; ISGs, interferon stimulated genes; IRB, institutional review board; IU, international units; LASSO, least absolute shrinkage and selection operator; Log2FC, log2 fold change; LOOCV, leave-one-out cross-validation; MF, molecular function; mL, milliliters; OASL, oligoadenylate synthetase-like; NAAT, positive: nucleic acid amplification test-positive; PCR, polymerase chain reaction; R, recipient; ROC, receiver operating characteristic; SD, standard deviation; STAR, spliced transcripts alignment to a reference; SVR12, sustained virologic response 12 weeks after HCV treatment; TMM, trimmed mean of M-values. Transcriptional responses in Hepatitis C renal transplantation patterns in circulating leukocytes are associated with some clinical outcomes, although larger studies are needed to develop accurate predictive classifiers of these events. Introduction There is a large disparity between the available number of kidney organ donors and recipients on the transplant waitlist–patients spend years on hemodialysis waiting for a kidney. Hepatitis C (HCV) nucleic acid antigen positive (NAAT-positive) donors are therefore being transplanted at a rapidly escalating rate to uninfected recipients to increase organ availability. This is due to the significant advancements made in the development of direct acting antiviral medications for the treatment and cure of HCV. These medications offer many benefits including high potency, low side effect profile, and pan-genotypic coverage [1–3]. However, there is concern that active HCV viremia results in an inflammatory state at the time of transplant and this may have downstream immunologic effects on the transplant recipient. The full extent of such effects is still being clarified. There have been reports of increased incidence of adverse outcomes in HCV transplant recipients, including increased incidence of de novo donor specific antibodies (DSA), allograft rejection, and reactivation of opportunistic viral infections, such as cytomeg (...truncated)