Abstract
There is an unmet need for robust and clinically validated biomarkers of kidney allograft rejection. Here we present the KTD-Innov study (ClinicalTrials.gov, NCT03582436), an unselected deeply phenotyped cohort of kidney transplant recipients with a holistic approach to validate the clinical utility of precision diagnostic biomarkers. In 2018–2019, we prospectively enrolled consecutive adult patients who received a kidney allograft at seven French centers and followed them for a year. We performed multimodal phenotyping at follow-up visits, by collecting clinical, biological, immunological, and histological parameters, and analyzing a panel of 147 blood, urinary and kidney tissue biomarkers. The primary outcome was allograft rejection, assessed at each visit according to the international Banff 2019 classification. We evaluated the representativeness of participants by comparing them with patients from French, European, and American transplant programs transplanted during the same period. A total of 733 kidney transplant recipients (64.1% male and 35.9% female) were included during the study. The median follow-up after transplantation was 12.3 months (interquartile range, 11.9–13.1 months). The cumulative incidence of rejection was 9.7% at one year post-transplant. We developed a distributed and secured data repository in compliance with the general data protection regulation. We established a multimodal biomarker biobank of 16,736 samples, including 9331 blood, 4425 urinary and 2980 kidney tissue samples, managed and secured in a collaborative network involving 7 clinical centers, 4 analytical platforms and 2 industrial partners. Patients' characteristics, immune profiles and treatments closely resembled those of 41,238 French, European and American kidney transplant recipients. The KTD-Innov study is a unique holistic and multidimensional biomarker validation cohort of kidney transplant recipients representative of the real-world transplant population. Future findings from this cohort are likely to be robust and generalizable.
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Data availability
A sample of the data is available as an open access resource under the CC BY-NC resource into the synapse public repository (https://www.synapse.org/KTD) and is freely available. A sign-in process is required to access the data. Full source de-identified data will be available from the corresponding author after the end of the study and after examination and approval by the Ethics Committee of the KTD-Innov’s consortium.
Abbreviations
- ABM:
-
Agence de la biomédecine
- AMR:
-
Antibody-mediated rejection
- CC BY-NC:
-
Creative Commons NonCommercial license
- CNIL:
-
Commission nationale de l’informatique et des libertés
- eCRF:
-
Electronic case report form
- GDPR:
-
General data protection regulation
- HLA:
-
Human leukocyte antigen
- KTD-Innov:
-
Kidney transplant diagnostics innovation
- TCMR:
-
T cell-mediated rejection
- UNOS:
-
United network for organ sharing
References
Muduma G, Odeyemi I, Smith-Palmer J, Pollock RF. Review of the clinical and economic burden of antibody-mediated rejection in renal transplant recipients. Adv Ther. 2016;33(3):345–56. https://doi.org/10.1007/s12325-016-0292-y.
Loupy A, Mengel M, Haas M. Thirty years of the international banff classification for allograft pathology: the past, present, and future of kidney transplant diagnostics. Kidney Int. 2022;101(4):678–91. https://doi.org/10.1016/j.kint.2021.11.028.
Danger R, Le Berre L, Cadoux M, et al. Subclinical rejection-free diagnostic after kidney transplantation using blood gene expression. Kidney Int. 2023;103(6):1167–79. https://doi.org/10.1016/j.kint.2023.03.019.
Lubetzky ML, Salinas T, Schwartz JE, Suthanthiran M. Urinary cell mRNA profiles predictive of human kidney allograft status. Clin J Am Soc Nephrol. 2021;16(10):1565–77. https://doi.org/10.2215/CJN.14010820.
Rabant M, Amrouche L, Lebreton X, et al. Urinary C-X-C motif chemokine 10 independently improves the noninvasive diagnosis of antibody–mediated kidney allograft rejection. J Am Soc Nephrol. 2015;26(11):2840–51. https://doi.org/10.1681/ASN.2014080797.
Loupy A, Lefaucheur C, Vernerey D, et al. Complement-binding anti-HLA antibodies and kidney-allograft survival. N Engl J Med. 2013;369(13):1215–26. https://doi.org/10.1056/NEJMoa1302506.
Hricik DE, Nickerson P, Formica RN, et al. Multicenter validation of urinary CXCL9 as a risk-stratifying biomarker for kidney transplant injury. Am J Transplant. 2013;13(10):2634–44. https://doi.org/10.1111/ajt.12426.
Suthanthiran M, Schwartz JE, Ding R, et al. Urinary-cell mRNA profile and acute cellular rejection in kidney allografts. N Engl J Med. 2013;369(1):20–31. https://doi.org/10.1056/NEJMoa1215555.
Danger R, Chesneau M, Paul C, et al. A composite score associated with spontaneous operational tolerance in kidney transplant recipients. Kidney Int. 2017;91(6):1473–81. https://doi.org/10.1016/j.kint.2016.12.020.
Gavlovsky PJ, Tonnerre P, Guitton C, Charreau B. Expression of MHC class I-related molecules MICA, HLA-E and EPCR shape endothelial cells with unique functions in innate and adaptive immunity. Hum Immunol. 2016;77(11):1084–91. https://doi.org/10.1016/j.humimm.2016.02.007.
Mengel M, Loupy A, Haas M, et al. Banff 2019 meeting report: molecular diagnostics in solid organ transplantation-consensus for the Banff human organ transplant (B-HOT) gene panel and open source multicenter validation. Am J Transplant. 2020;20(9):2305–17. https://doi.org/10.1111/ajt.16059.
Reeve J, Bohmig GA, Eskandary F, et al. Assessing rejection-related disease in kidney transplant biopsies based on archetypal analysis of molecular phenotypes. JCI Insight. 2017. https://doi.org/10.1172/jci.insight.94197.
Loupy A, Van Duong Huyen JP, Hidalgo L, et al. Gene expression profiling for the identification and classification of antibody-mediated heart rejection. Circulation. 2017;135(10):917–35. https://doi.org/10.1161/CIRCULATIONAHA.116.022907.
Loupy A, Lefaucheur C, Vernerey D, et al. Molecular microscope strategy to improve risk stratification in early antibody-mediated kidney allograft rejection. J Am Soc Nephrol. 2014;25(10):2267–77. https://doi.org/10.1681/ASN.2013111149.
Selleck MJ, Senthil M, Wall NR. Making meaningful clinical use of biomarkers. Biomark Insights. 2017;12:1177271917715236. https://doi.org/10.1177/1177271917715236.
Bossuyt PM, Parvin T. Evaluating biomarkers for guiding treatment decisions. EJIFCC. 2015;26(1):63–70.
Naesens M, Anglicheau D. Precision transplant medicine: biomarkers to the rescue. J Am Soc Nephrol. 2018;29(1):24–34. https://doi.org/10.1681/ASN.2017010004.
Ioannidis JPA, Bossuyt PMM. Waste, leaks, and failures in the biomarker pipeline. Clin Chem. 2017;63(5):963–72. https://doi.org/10.1373/clinchem.2016.254649.
Raynaud M, Al-Awadhi S, Louis K, et al. Prognostic biomarkers in kidney transplantation a systematic review and critical appraisal. J Am Soc Nephrol. 2023. https://doi.org/10.1681/ASN.0000000000000260.
Jamshaid F, Froghi S, Di Cocco P, Dor FJ. Novel non-invasive biomarkers diagnostic of acute rejection in renal transplant recipients: a systematic review. Int J Clin Pract. 2018. https://doi.org/10.1111/ijcp.13220.
Menon MC, Murphy B, Heeger PS. Moving biomarkers toward clinical implementation in kidney transplantation. J Am Soc Nephrol. 2017;28(3):735–47. https://doi.org/10.1681/ASN.2016080858.
Divard G, Goutaudier V. Global perspective on kidney transplantation: France. Kidney360. 2021;2(10):1637–40. https://doi.org/10.34067/KID.0002402021.
Agence de la Biomédecine. The French National Report 2021. France, Saint-Denis La Plaine, 2022
Vandenbroucke JP, von Elm E, Altman DG, et al. Strengthening the reporting of observational studies in epidemiology (STROBE): explanation and elaboration. Epidemiology. 2007;18(6):805–35. https://doi.org/10.1097/EDE.0b013e3181577511.
Cohen JF, Korevaar DA, Altman DG, et al. STARD 2015 guidelines for reporting diagnostic accuracy studies: explanation and elaboration. BMJ Open. 2016;6(11): e012799. https://doi.org/10.1136/bmjopen-2016-012799.
Yoo D, Goutaudier V, Divard G, et al. An automated histological classification system for precision diagnostics of kidney allografts. Nat Med. 2023;29(5):1211–20. https://doi.org/10.1038/s41591-023-02323-6.
Loupy A, Haas M, Roufosse C, et al. The Banff 2019 kidney meeting report (I): updates on and clarification of criteria for T cell- and antibody-mediated rejection. Am J Transplant. 2020;20(9):2318–31. https://doi.org/10.1111/ajt.15898.
Braudeau C, Ashton-Chess J, Giral M, et al. Contrasted blood and intragraft toll-like receptor 4 mRNA profiles in operational tolerance versus chronic rejection in kidney transplant recipients. Transplantation. 2008;86(1):130–6. https://doi.org/10.1097/TP.0b013e31817b8dc5.
Ashton-Chess J, Giral M, Mengel M, et al. Tribbles-1 as a novel biomarker of chronic antibody-mediated rejection. J Am Soc Nephrol. 2008;19(6):1116–27. https://doi.org/10.1681/ASN.2007101056.
Sayadi S GE, Südholt M, Vince N, Gourraud PA. Distributed contextualization of biomedical data: a case study in precision medicine. In: IEEE/ACS 17th International conference on computer systems and applications (AICCSA), Antalya, Turkey, 2020. 2020, pp. 1–6. https://doi.org/10.1109/AICCSA50499.2020.9316502
Guillaudeux M, Rousseau O, Petot J, et al. Patient-centric synthetic data generation, no reason to risk re-identification in biomedical data analysis. NPJ Digit Med. 2023;6(1):37. https://doi.org/10.1038/s41746-023-00771-5.
Wilkinson MD, Dumontier M, Aalbersberg IJ, et al. The FAIR guiding principles for scientific data management and stewardship. Sci Data. 2016;3: 160018. https://doi.org/10.1038/sdata.2016.18.
Tang F, Ishwaran H. Random forest missing data algorithms. Stat Anal Data Min. 2017;10(6):363–77. https://doi.org/10.1002/sam.11348.
Waljee AK, Mukherjee A, Singal AG, et al. Comparison of imputation methods for missing laboratory data in medicine. BMJ Open. 2013. https://doi.org/10.1136/bmjopen-2013-002847.
Little RJ, D’Agostino R, Cohen ML, et al. The prevention and treatment of missing data in clinical trials. N Engl J Med. 2012;367(14):1355–60. https://doi.org/10.1056/NEJMsr1203730.
Locher C, Le Goff G, Le Louarn A, Mansmann U, Naudet F. Making data sharing the norm in medical research. BMJ. 2023;382:1434. https://doi.org/10.1136/bmj.p1434.
UNESCO. Recommendation on Open Science. https://www.unesco.org/en/open-science/about
Collins GS, Reitsma JB, Altman DG, Moons KG. Transparent reporting of a multivariable prediction model for individual prognosis or diagnosis (TRIPOD): the TRIPOD statement. Ann Intern Med. 2015;162(1):55–63. https://doi.org/10.7326/M14-0697.
Hajian-Tilaki K. Sample size estimation in diagnostic test studies of biomedical informatics. J Biomed Inform. 2014;48:193–204. https://doi.org/10.1016/j.jbi.2014.02.013.
Oweira H, Ramouz A, Ghamarnejad O, et al. Risk factors of rejection in renal transplant recipients: a narrative review. J Clin Med. 2022. https://doi.org/10.3390/jcm11051392.
Hart A, Singh D, Brown SJ, Wang JH, Kasiske BL. Incidence, risk factors, treatment, and consequences of antibody-mediated kidney transplant rejection: a systematic review. Clin Transplant. 2021;35(7): e14320. https://doi.org/10.1111/ctr.14320.
Foroutan F, Friesen EL, Clark KE, et al. Risk factors for 1-year graft loss after kidney transplantation: systematic review and meta-analysis. Clin J Am Soc Nephrol. 2019;14(11):1642–50. https://doi.org/10.2215/CJN.05560519.
Lemoine M, Titeca Beauport D, Lobbedez T, et al. Risk factors for early graft failure and death after kidney transplantation in recipients older than 70 years. Kidney Int Rep. 2019;4(5):656–66. https://doi.org/10.1016/j.ekir.2019.01.014.
Clayton PA, McDonald SP, Russ GR, Chadban SJ. Long-term outcomes after acute rejection in kidney transplant recipients: an ANZDATA analysis. J Am Soc Nephrol. 2019;30(9):1697–707. https://doi.org/10.1681/ASN.2018111101.
McDonald SP. Australia and New Zealand dialysis and transplant registry. Kidney Int Suppl. 2015;5(1):39–44. https://doi.org/10.1038/kisup.2015.8.
Matas AJ, Smith JM, Skeans MA, et al. OPTN/SRTR 2011 annual data report: kidney. Am J Transplant. 2013;13(Suppl 1):11–46. https://doi.org/10.1111/ajt.12019.
Loupy A, Vernerey D, Tinel C, et al. Subclinical rejection phenotypes at 1 year post-transplant and outcome of kidney allografts. J Am Soc Nephrol. 2015;26(7):1721–31. https://doi.org/10.1681/ASN.2014040399.
Rush D, Nickerson P, Gough J, et al. Beneficial effects of treatment of early subclinical rejection: a randomized study. J Am Soc Nephrol. 1998;9(11):2129–34. https://doi.org/10.1681/ASN.V9112129.
Sawinski D, Trofe-Clark J, Leas B, et al. Calcineurin inhibitor minimization, conversion, withdrawal, and avoidance strategies in renal transplantation: a systematic review and meta-analysis. Am J Transplant. 2016;16(7):2117–38. https://doi.org/10.1111/ajt.13710.
Mayer AD, Dmitrewski J, Squifflet JP, et al. Multicenter randomized trial comparing tacrolimus (FK506) and cyclosporine in the prevention of renal allograft rejection: a report of the European Tacrolimus Multicenter Renal Study Group. Transplantation. 1997;64(3):436–43. https://doi.org/10.1097/00007890-199708150-00012.
Sharif A. Deceased donor characteristics and kidney transplant outcomes. Transpl Int. 2022;35:10482. https://doi.org/10.3389/ti.2022.10482.
Aubert O, Reese PP, Audry B, et al. Disparities in acceptance of deceased donor kidneys between the United States and France and estimated effects of increased US acceptance. JAMA Intern Med. 2019;179(10):1365–74. https://doi.org/10.1001/jamainternmed.2019.2322.
Truchot A, Raynaud M, Loupy A. Excess mortality after kidney transplantation: Does sex matter? Kidney Int. 2023;103(6):1023–4. https://doi.org/10.1016/j.kint.2023.03.011.
Massie AB, Kucirka LM, Segev DL. Big data in organ transplantation: registries and administrative claims. Am J Transplant. 2014;14(8):1723–30. https://doi.org/10.1111/ajt.12777.
Yu M, King KL, Husain SA, et al. Discrepant outcomes between national kidney transplant data registries in the united states. J Am Soc Nephrol. 2023;34(11):1863–74. https://doi.org/10.1681/ASN.0000000000000194.
Eikmans M, Gielis EM, Ledeganck KJ, Yang J, Abramowicz D, Claas FFJ. Non-invasive biomarkers of acute rejection in kidney transplantation: novel targets and strategies. Front Med (Lausanne). 2018;5:358. https://doi.org/10.3389/fmed.2018.00358.
Acknowledgements
The authors thank Dahlia Tsakiropoulos and Solène Janique for their contribution in the management of the project, and Harold Juillet for their help in setting up and developing the project. The authors thank the clinical research assistants, Marie Bouclier, Francine Tacafred, Julie Obert, Aliaume Le Pape, Maxime Bentoumi-Loaec, Marie Mattera, Fatiha M’Raiagh, and Coralie Champion, as well as Magali Giral for their contribution in the data acquisition. The authors also thank Blaise Robin, Jessy Dagobert, Fariza Mezine for their technical assistance. The authors also thank the Biological Resource Centre for Biobanking of Nantes (CHU Nantes, Nantes Université, Centre de ressources biologiques [BRIF: BB-0033-00040]). The authors thank the Organ Procurement and Transplantation Network for providing the data. The data reported here have been supplied by the United Network for Organ Sharing as the contractor for the Organ Procurement and Transplantation Network. The interpretation and reporting of these data are the responsibility of the authors and in no way should be seen as an official policy of or interpretation by the OPTN or the U.S. Government.
Funding
The KTD-Innov study was funded by the French government, with financial support managed by the National Research Agency (ANR) under the program “Investissements d’avenir”, with the Grant Agreement No. ANR-17-RHUS-0010. INSERM-Action thématique incitative sur programme Avenir (ATIP-Avenir) provided financial support. VG received grants from the French-Speaking Society of Transplantation and the French Foundation for Medical Research. MS received a grant from Université Paris Cité. OA received a grant from the Fondation Bettencourt Schueller. RD, HLM and TN were supported by the ANR project KTD-Innov and the European Union’s Horizon 2020 Research and Innovation Programme under Grant Agreement No. 754995.
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AL and SB are leaders of the KTD-Innov study. SB, AL and PAG designed the KTD-Innov study. VG, MS, MRacapé, OR, MG, PAG, SB, CLefaucheur and AL designed the present study. VG, MS, MRacapé, OR, BA, NK, BC, EP, RD, LL, LC, EM, MLQ, JLT, EV, CLegendre, HLM, VP, TN, HJ, MEA, AP, GN, PS, DA, IT, SV, CJ, PR, PAG, SB, CLefaucheur, AL participated in the building of the KTD-Innov cohort and contributed to data acquisition. VG, MS, BA, IT, PR, CLefaucheur and AL performed data analysis. VG, MS, MRacapé, OR, BA, IT, MRaynaud, OA, IT, PAG, SB, CLefaucheur and AL performed data interpretation. VG, MS, MRacapé, CLefaucheur and AL wrote the first draft of the manuscript. All authors revised and critically reviewed the manuscript.
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RD and SB have ownership interests in the BioMAdvanced Diagnostics company not involved in the present study. MEA, AP, GN and PS are employees of Sebia. AL holds shares in Predict4Health, a software company that is not involved in the present research. PAG is the founder of Methodomics (2008) and the co-founder of Big data Santé (2018). He consults for major pharmaceutical companies and start-ups, all of which are handled through academic pipelines (AstraZeneca, Biogen, Boston Scientific, Cook, Docaposte, Edimark, Ellipses, Elsevier, Janssen, Lek, Methodomics, Merck, Mérieux, Octopize, Sanofi-Genzyme). PAG is a volunteer board member at AXA not-for-profit mutual insurance company (2021). He has no prescription activity with either drugs or devices. The other authors declare no competing interests.
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Goutaudier, V., Sablik, M., Racapé, M. et al. Design, cohort profile and comparison of the KTD-Innov study: a prospective multidimensional biomarker validation study in kidney allograft rejection. Eur J Epidemiol (2024). https://doi.org/10.1007/s10654-024-01112-w
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DOI: https://doi.org/10.1007/s10654-024-01112-w