BACKGROUND: Kidney transplant recipients (KTRs) with "operational tolerance" (OT) maintain a functioning graft without immunosuppressive (IS) drugs, thus avoiding treatment complications. Nevertheless, IS drugs can influence gene-expression signatures aiming to identify OT among treated KTRs. METHODS: We compared five published signatures of OT in peripheral blood samples from 18 tolerant, 183 stable, and 34 chronic rejector KTRs, using gene-expression levels with and without adjustment for IS drugs and regularised logistic regression. FINDINGS: IS drugs explained up to 50% of the variability in gene-expression and 20-30% of the variability in the probability of OT predicted by signatures without drug adjustment. We present a parsimonious consensus gene-set to identify OT, derived from joint analysis of IS-drug-adjusted expression of five published signature gene-sets. This signature, including CD40, CTLA4, HSD11B1, IGKV4-1, MZB1, NR3C2, and RAB40C genes, showed an area under the curve 0⋅92 (95% confidence interval 0⋅88-0⋅94) in cross-validation and 0⋅97 (0⋅93-1⋅00) in six months follow-up samples. INTERPRETATION: We advocate including adjustment for IS drug therapy in the development stage of gene-expression signatures of OT to reduce the risk of capturing features of treatment, which could be lost following IS drug minimisation or withdrawal. Our signature, however, would require further validation in an independent dataset and a biomarker-led trial. FUNDING: FP7-HEALTH-2012-INNOVATION-1 [305147:BIO-DrIM] (SC,IR-M,PM,DSt); MRC [G0801537/ID:88245] (MPH-F); MRC [MR/J006742/1] (IR-M); Guy's&StThomas' Charity [R080530]&[R090782]; CONICYT-Bicentennial-Becas-Chile (EN-L); EU:FP7/2007-2013 [HEALTH-F5-2010-260687: The ONE Study] (MPH-F); Czech Ministry of Health [NV19-06-00031] (OV); NIHR-BRC Guy's&StThomas' NHS Foundation Trust and KCL (SC); UK Clinical Research Networks [portfolio:7521].

Biostatistics and Health Informatics Department Institute of Psychiatry Psychology and Neuroscience King's College London 16 De Crespigny Park London SE5 8AF UK

Cardiff and Vale University Health Board Cardiff CF14 4XW UK

Department of Immunology and imas12 Research Institute University Hospital 12 de Octubre Madrid Spain

Department of Immunology Genetics and Pathology Uppsala University Rudbecklaboratoriet 751 85 Uppsala Sweden

Department of Paediatric Nephrology Great Ormond Street Hospital for Children NHS Foundation Trust Great Ormond Street London WC1N 3JH UK; University College London Great Ormond Street Institute of Child Health NIHR Great Ormond Street Hospital Biomedical Research Centre London WC1N 1EH UK

Evelina London Children's Hospital Westminster Bridge Rd Lambeth London SE1 7EH UK; Guy's and St Thomas' NHS Foundation Trust Great Maze Pond London SE1 9RT UK; King's Health Partners Guy's Hospital London SE1 9RT UK

Guy's and St Thomas' NHS Foundation Trust Great Maze Pond London SE1 9RT UK

Hospital Universitario Vall d'Hebrón Passeig de la Vall d'Hebron 119 129 08035 Barcelona Spain

Hull University Teaching Hospitals NHS Trust Anlaby Rd Hull HU3 2JZ UK

Internal Medicine Lindenhofgruppe Berne Switzerland; University of Bern Berne Switzerland; School of Medicine University of Nottingham Nottingham NG5 1PB UK

King's College Hospital NHS Foundation Trust Denmark Hill London SE5 9RS UK

Leicester General Hospital Gwendolen Rd Leicester LE5 4PW UK

Manchester Royal Infirmary Oxford Rd Manchester M13 9WL UK

MRC Centre for Transplantation King's College London Great Maze Pond London SE1 9RT UK

MRC Centre for Transplantation King's College London Great Maze Pond London SE1 9RT UK; Biostatistics and Health Informatics Department Institute of Psychiatry Psychology and Neuroscience King's College London 16 De Crespigny Park London SE5 8AF UK

MRC Centre for Transplantation King's College London Great Maze Pond London SE1 9RT UK; Guy's and St Thomas' NHS Foundation Trust Great Maze Pond London SE1 9RT UK

MRC Centre for Transplantation King's College London Great Maze Pond London SE1 9RT UK; King's Health Partners Guy's Hospital London SE1 9RT UK

MRC Centre for Transplantation King's College London Great Maze Pond London SE1 9RT UK; NIHR Biomedical Research Centre at Guy's and St Thomas' NHS Foundation Trust and King's College London Great Maze Pond London SE1 9RT UK; Guy's and St Thomas' NHS Foundation Trust Great Maze Pond London SE1 9RT UK

NIHR Biomedical Research Centre at Guy's and St Thomas' NHS Foundation Trust and King's College London Great Maze Pond London SE1 9RT UK

Northern General Hospital Herries Rd Sheffield S5 7AU UK

Queen Alexandra Hospital Southwick Hill Rd Cosham Portsmouth PO6 3LY UK

Salford Royal NHS Foundation Trust Stott Ln Salford M6 8HD UK

St George's Hospital Blackshaw Rd London SW17 0QT UK and Institute of Medical and Biomedical Education St George's University of London Cranmer Terrace London SW17 0RE

St James's University Hospital Beckett St Leeds LS9 7TF UK

Transplantační laboratoř Institut klinické a experimentální medicíny Vídeňská 1958 9 140 21 Praha 4 Czech Republic

University of Glasgow University Avenue Glasgow G12 8QQ UK

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Novel transcriptomic signatures associated with premature kidney allograft failure