BACKGROUND: Plasma donor-derived cell-free DNA (dd-cfDNA) is used to screen for rejection in heart transplants. We launched the Trifecta-Heart study ( ClinicalTrials.gov No. NCT04707872), an investigator-initiated, prospective trial, to examine the correlations between genome-wide molecular changes in endomyocardial biopsies (EMBs) and plasma dd-cfDNA. The present report analyzes the correlation of plasma dd-cfDNA with gene expression in EMBs from 4 vanguard centers and compared these correlations with those in 604 kidney transplant biopsies in the Trifecta-Kidney study ( ClinicalTrials.gov No. NCT04239703). METHODS: We analyzed 137 consecutive dd-cfDNA-EMB pairs from 70 patients. Plasma %dd-cfDNA was measured by the Prospera test (Natera Inc), and gene expression in EMBs was assessed by Molecular Microscope Diagnostic System using machine-learning algorithms to interpret rejection and injury states. RESULTS: Top transcripts correlating with dd-cfDNA were related to genes increased in rejection such as interferon gamma-inducible genes (eg, HLA-DMA ) but also with genes induced by injury and expressed in macrophages (eg, SERPINA1 and HMOX1 ). In gene enrichment analysis, the top dd-cfDNA-correlated genes reflected inflammation and rejection pathways. Dd-cfDNA correlations with rejection genes in EMB were similar to those seen in kidney transplant biopsies, with somewhat stronger correlations for TCMR genes in hearts and ABMR genes in kidneys. However, the correlations with parenchymal injury-induced genes and macrophage genes were much stronger in hearts. CONCLUSIONS: In this first analysis of Trifecta-Heart study, dd-cfDNA correlates significantly with molecular rejection but also with injury and macrophage infiltration, reflecting the proinflammatory properties of injured cardiomyocytes. The relationship supports the utility of dd-cfDNA in clinical management of heart transplant recipients.

Alberta Transplant Applied Genomics Center Edmonton AB Canada

Baptist Health Institute Little Rock AR

Baylor Scott and White Health Dallas TX

Department of Internal Medicine University of Utah Salt Lake City UT

Department of Medicine University of Alberta Edmonton AB Canada

IKEM Prague Czech Republic

Natera Inc San Carlos CA

Transcriptome Sciences Inc Edmonton AB Canada

doi: 10.1097/TP.0000000000005151 PubMed

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Snyder TM, Khush KK, Valantine HA, et al. . Universal noninvasive detection of solid organ transplant rejection. Proc Natl Acad Sci USA. 2011;108:6229–6234. PubMed PMC

De Vlaminck I, Valantine HA, Snyder TM, et al. . Circulating cell-free DNA enables noninvasive diagnosis of heart transplant rejection. Sci Transl Med. 2014;6:241ra277. PubMed PMC

Khush KK, Patel J, Pinney S, et al. . Noninvasive detection of graft injury after heart transplant using donor-derived cell-free DNA: a prospective multicenter study. Am J Transplant. 2019;19:2889–2899. PubMed PMC

Keller M, Agbor-Enoh S. Donor-derived cell-free DNA for acute rejection monitoring in heart and lung transplantation. Curr Transplant Reports. 2021;8:351–358. PubMed PMC

Knuttgen F, Beck J, Dittrich M, et al. . Graft-derived cell-free DNA as a noninvasive biomarker of cardiac allograft rejection: a cohort study on clinical validity and confounding factors. Transplantation. 2022;106:615–622. PubMed

Kim PJ, Olymbios M, Siu A, et al. . A novel donor-derived cell-free DNA assay for the detection of acute rejection in heart transplantation. J Heart Lung Transplant. 2022;41:919–927. PubMed PMC

Rodgers N, Gerding B, Cusi V, et al. . Comparison of two donor-derived cell-free DNA tests and a blood gene-expression profile test in heart transplantation. Clin Transplant. 2023;37:e14984. PubMed PMC

Agbor-Enoh S, Shah P, Tunc I, et al. ; GRAfT Investigators. Cell-free DNA to detect heart allograft acute rejection. Circulation. 2021;143:1184–1197. PubMed PMC

Tsuji N, Agbor-Enoh S. Cell-free DNA beyond a biomarker for rejection: biological trigger of tissue injury and potential therapeutics. J Heart Lung Transplant. 2021;40:405–413. PubMed

Verhoeven J, Hesselink DA, Peeters AMA, et al. . Donor-derived cell-free DNA for the detection of heart allograft injury: the impact of the timing of the liquid biopsy. Transpl Int. 2022;35:10122. PubMed PMC

Klebanov L, Yakovlev A. How high is the level of technical noise in microarray data? Biol Direct. 2007;2:9. PubMed PMC

Reeve J, Bohmig GA, Eskandary F, et al. ; INTERCOMEX MMDx-Kidney Study Group. Generating automated kidney transplant biopsy reports combining molecular measurements with ensembles of machine learning classifiers. Am J Transplant. 2019;19:2719–2731. PubMed

Madill-Thomsen K, Perkowska-Ptasinska A, Bohmig GA, et al. ; MMDx-Kidney Study Group. Discrepancy analysis comparing molecular and histology diagnoses in kidney transplant biopsies. Am J Transplant. 2020;20:1341–1350. PubMed

Furness PN, Taub N, Assmann KJ, et al. . International variation in histologic grading is large, and persistent feedback does not improve reproducibility. Am J Surg Pathol. 2003;27:805–810. PubMed

Gauthier PT, Madill-Thomsen KS, Demko Z, et al. . Distinct molecular processes mediate donor-derived cell-free DNA release from kidney transplants in different disease states. Transplantation. 2024;108:898–910. PubMed PMC

Halloran PF, Reeve J, Madill-Thomsen KS, et al. ; Trifecta Investigators. The Trifecta study: comparing plasma levels of donor-derived cell-free DNA with the molecular phenotype of kidney transplant biopsies. J Am Soc Nephrol. 2022;33:387–400. PubMed PMC

Gupta G, Moinuddin I, Kamal L, et al. . Correlation of donor-derived cell-free DNA with histology and molecular diagnoses of kidney transplant biopsies. Transplantation. 2022;106:1061–1070. PubMed

Halloran PF, Reeve J, Madill-Thomsen KS, et al. ; Trifecta Investigators*. Combining donor-derived cell-free DNA fraction and quantity to detect kidney transplant rejection using molecular diagnoses and histology as confirmation. Transplantation. 2022;106:2435–2442. PubMed PMC

Halloran PF, Reeve J, Madill-Thomsen KS, et al. ; the Trifecta Investigators. Antibody-mediated rejection without detectable donor-specific antibody releases donor-derived cell-free DNA: results from the Trifecta study. Transplantation. 2023;107:709–719. PubMed PMC

Halloran PF, Madill-Thomsen KS. The molecular microscope diagnostic system: assessment of rejection and injury in heart transplant biopsies. Transplantation. 2023;107:27–44. PubMed

Altug Y, Liang N, Ram R, et al. . Analytical validation of a single-nucleotide polymorphism-based donor-derived cell-free DNA assay for detecting rejection in kidney transplant patients. Transplantation. 2019;103:2657–2665. PubMed PMC

npreg: Nonparametric regression via smoothing splines [computer program]. Version R package version 1.0-92022.

Reeve J, Bohmig GA, Eskandary F, et al. ; MMDx-Kidney Study Group. Assessing rejection-related disease in kidney transplant biopsies based on archetypal analysis of molecular phenotypes. JCI Insight. 2017;2:e94197. PubMed PMC

Boomsma F, van den Meiracker AH. Plasma A- and B-type natriuretic peptides: physiology, methodology and clinical use. Cardiovasc Res. 2001;51:442–449. PubMed

Madill-Thomsen KS, Reeve J, Aliabadi-Zuckermann A, et al. . Assessing the relationship between molecular rejection and parenchymal injury in heart transplant biopsies. Transplantation. 2022;106:2205–2216. PubMed

Man J, Barnett P, Christoffels VM. Structure and function of the Nppa-Nppb cluster locus during heart development and disease. Cell Mol Life Sci. 2018;75:1435–1444. PubMed PMC

de Frutos F, Ochoa JP, Navarro-Penalver M, et al. ; European Genetic Cardiomyopathies Initiative Investigators. Natural history of MYH7-related dilated cardiomyopathy. J Am Coll Cardiol. 2022;80:1447–1461. PubMed

Halloran PF, Madill-Thomsen KS, Aliabadi-Zuckermann A, et al. . Many heart transplant biopsies currently diagnosed as no rejection have mild molecular antibody-mediated rejection-related changes. J Heart Lung Transplant. 2021;41:334–344. PubMed

Montecucco F, Liberale L, Bonaventura A, et al. . The role of inflammation in cardiovascular outcome. Curr Atheroscler Rep. 2017;19:11. PubMed

Frangogiannis NG. Inflammation in cardiac injury, repair and regeneration. Curr Opin Cardiol. 2015;30:240–245. PubMed PMC

Glezeva N, Horgan S, Baugh JA. Monocyte and macrophage subsets along the continuum to heart failure: misguided heroes or targetable villains? J Mol Cell Cardiol. 2015;89(Pt B):136–145. PubMed

Nicolas-Avila JA, Lechuga-Vieco AV, Esteban-Martinez L, et al. . A network of macrophages supports mitochondrial homeostasis in the heart. Cell. 2020;183:94–109.e23. PubMed

McNally EM. Cardiac macrophages—keeping the engine running clean. N Engl J Med. 2020;383:2474–2476. PubMed

Liu H, Liu X, Zhuang H, et al. . Mitochondrial contact sites in inflammation-induced cardiovascular disease. Front Cell Dev Biol. 2020;8:692. PubMed PMC

Holzhauser L, Clerkin KJ, Fujino T, et al. . Donor-derived cell-free DNA is associated with cardiac allograft vasculopathy. Clin Transplant. 2021;35:e14206. PubMed PMC

Crespo-Leiro MG, Zuckermann A, Bara C, et al. . Concordance among pathologists in the second cardiac allograft rejection gene expression observational study (CARGO II). Transplantation. 2012;94:1172–1177. PubMed

Halloran PF, Reeve J, Aliabadi AZ, et al. . Exploring the cardiac response to injury in heart transplant biopsies. JCI Insight. 2018;3:e123674. PubMed PMC

Halloran PF, Madill-Thomsen K, Mackova M, et al. . Molecular states associated with dysfunction and graft loss in heart transplants. J Heart Lung Transplant. 2024;43:508–518. PubMed

Bromberg JS, Brennan DC, Poggio E, et al. . Biological variation of donor-derived cell-free DNA in renal transplant recipients: clinical implications. J Appl Lab Med. 2017;2:309–321. PubMed

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ClinicalTrials.gov
NCT04239703, NCT04707872