Donor-derived Cell-free DNA Kinetics Post-kidney Transplant Biopsy

Kyeso, Yousuf; Bhalla, Anshul; Smith, Alyssa P; Jia, Yaqi; Alakhdhair, Safa; Ogir, Stephanie C; Abuzeineh, Mohammad; Brennan, Daniel C.; Alasfar, Sami

doi:10.1097/txd.0000000000001149

Cited by 5 publications

(7 citation statements)

References 18 publications

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“…All blood samples for dd-cfDNA(%) testing were collected before the biopsies were performed to avoid any effect of the biopsy procedure on the dd-cfDNA(%) measurement 28 . Blood samples were drawn in two 10 ml quantities in DNA Streck tubes using 20–21 gauge needles and shipped immediately per established protocols to Natera Inc. for analysis.…”

Section: Methodsmentioning

confidence: 99%

“…Models used histology variables alone, molecular variables alone, or all 10 combined. The combined model added significantly to the predictive value of histology alone (P52310 28 , likelihood ratio test) but not to molecules alone (P50.99). The same comparisons were run using linear regression to predict log 10 (dd-cfDNA[%]) as a continuous variable.…”

Section: Pca Of Rejectionmentioning

confidence: 98%

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The Trifecta Study: Comparing Plasma Levels of Donor-derived Cell-Free DNA with the Molecular Phenotype of Kidney Transplant Biopsies

Halloran¹,

Reeve²,

Madill‐Thomsen³

et al. 2022

JASN

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BackgroundThe relationship between the donor-derived cell-free DNA fraction (dd-cfDNA[%]) in plasma in kidney transplant recipients at time of indication biopsy and gene expression in the biopsied allograft has not been defined.MethodsIn the prospective, multicenter Trifecta study, we collected tissue from 300 biopsies from 289 kidney transplant recipients to compare genome-wide gene expression in biopsies with dd-cfDNA(%) in corresponding plasma samples drawn just before biopsy. Rejection was assessed with the microarray-based Molecular Microscope Diagnostic System using automatically assigned rejection archetypes and molecular report sign-outs, and histology assessments that followed Banff guidelines.ResultsThe median time of biopsy post-transplantation was 455 days (5 days to 32 years), with a case mix similar to that of previous studies: 180 (60%) no rejection, 89 (30%) antibody-mediated rejection (ABMR), and 31 (10%) T cell–mediated rejection (TCMR) and mixed. In genome-wide mRNA measurements, all 20 top probe sets correlating with dd-cfDNA(%) were previously annotated for association with ABMR and all types of rejection, either natural killer (NK) cell–expressed (e.g., GNLY, CCL4, TRDC, and S1PR5) or IFN-γ–inducible (e.g., PLA1A, IDO1, CXCL11, and WARS). Among gene set and classifier scores, dd-cfDNA(%) correlated very strongly with ABMR and all types of rejection, reasonably strongly with active TCMR, and weakly with inactive TCMR, kidney injury, and atrophy fibrosis. Active ABMR, mixed, and active TCMR had the highest dd-cfDNA(%), whereas dd-cfDNA(%) was lower in late-stage ABMR and less-active TCMR. By multivariate random forests and logistic regression, molecular rejection variables predicted dd-cfDNA(%) better than histologic variables.ConclusionsThe dd-cfDNA(%) at time of indication biopsy strongly correlates with active molecular rejection and has the potential to reduce unnecessary biopsies.Clinical Trial registration number:NCT04239703

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Section: Methodsmentioning

confidence: 99%

Section: Pca Of Rejectionmentioning

confidence: 98%

The Trifecta Study: Comparing Plasma Levels of Donor-derived Cell-Free DNA with the Molecular Phenotype of Kidney Transplant Biopsies

Halloran¹,

Reeve²,

Madill‐Thomsen³

et al. 2022

JASN

View full text Add to dashboard Cite

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“…All blood samples for dd-cfDNA testing were collected immediately before the biopsy. 30 Blood samples were drawn in two 10-mL quantities in DNA Streck tubes using 20- to 21-gauge needles and shipped immediately per established protocols to Natera (Natera Inc., Austin, TX) for analysis using the Prospera test. The Prospera test amplifies DNA by massively multiplexed-PCR targeting 13 926 single nucleotide polymorphisms designed to maximize the number of informative SNPs across ethnicities.…”

Section: Methodsmentioning

confidence: 99%

Antibody-mediated Rejection Without Detectable Donor-specific Antibody Releases Donor-derived Cell-free DNA: Results From the Trifecta Study

et al. 2023

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Background. Trifecta (ClinicalTrials.gov #NCT04239703) is a prospective trial defining relationships between donor-derived cell-free DNA (dd-cfDNA), donor-specific antibody (DSA), and molecular findings in kidney transplant biopsies. Previous analyses of double results showed dd-cfDNA was strongly associated with rejection-associated molecules in the biopsy. The present study analyzed the triple results in 280 biopsies, focusing on the question of dd-cfDNA levels in DSA-negative antibody-mediated rejection (AMR). Methods. Molecular Microscope Diagnostic System biopsy testing was performed at Alberta Transplant Applied Genomics Centre, dd-cfDNA testing at Natera, Inc, and central HLA antibody testing at One Lambda Inc. Local DSA and histologic diagnoses were assigned per center standard-of-care. Results. DSA was frequently negative in both molecular (56%) and histologic (51%) AMR. DSA-negative AMR had slightly less molecular AMR activity and histologic peritubular capillaritis than DSA-positive AMR. However, all AMRs-DSA-positive or -negative-showed elevated %dd-cfDNA. There was no association between dd-cfDNA and DSA in biopsies without rejection. In AMR, %dd-cfDNA ≥1.0 was more frequent (75%) than DSA positivity (44%). In logistic regression, dd-cfDNA percent (area under the curve [AUC] 0.85) or quantity (AUC 0.86) predicted molecular AMR better than DSA (AUC 0.66). However, the best predictions incorporated both dd-cfDNA and DSA, plus time posttransplant (AUC 0.88). Conclusions. DSA-negative AMR has moderately decreased mean molecular and histologic AMR-associated features compared with DSA-positive AMR, though similarly elevated dd-cfDNA levels. In predicting AMR at the time of indication biopsies in this population, dd-cfDNA is superior to DSA, reflecting the prevalence of DSA-negative AMR, but the optimal predictions incorporated both dd-cfDNA and DSA.

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“…Whole blood and serum samples were obtained on the day of pancreas graft biopsy, before the performance of biopsy, to avoid misleading interpretation of dd-cfDNA. 23 Whole blood samples were used to measure dd-cfDNA levels, whereas serum samples were used to measure amylase (U/L), lipase (U/L), and creatinine (mg/dL) (Figure 1 B). In addition, serum samples were screened for HLA 23 class I and II donor-specific antibodies (DSAs) using the Lifecodes LifeScreen Deluxe flow bead assay (Immucor, Stamford, CT).…”

Section: Methodsmentioning

confidence: 99%

“… 23 Whole blood samples were used to measure dd-cfDNA levels, whereas serum samples were used to measure amylase (U/L), lipase (U/L), and creatinine (mg/dL) (Figure 1 B). In addition, serum samples were screened for HLA 23 class I and II donor-specific antibodies (DSAs) using the Lifecodes LifeScreen Deluxe flow bead assay (Immucor, Stamford, CT). Antibody specificities were determined using the Lifecodes Single Antigen bead assay (Immucor) in patients with positive screening for HLA antibodies.…”

Section: Methodsmentioning

confidence: 99%

Donor-derived Cell-free DNA Shows High Sensitivity for the Diagnosis of Pancreas Graft Rejection in Simultaneous Pancreas-kidney Transplantation

et al. 2022

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Background. Pancreas graft status in simultaneous pancreas-kidney transplant (SPKTx) is currently assessed by nonspecific biochemical markers, typically amylase or lipase. Identifying a noninvasive biomarker with good sensitivity in detecting early pancreas graft rejection could improve SPKTx management. Methods. Here, we developed a pilot study to explore donor-derived cell-free DNA (dd-cfDNA) performance in predicting biopsy-proven acute rejection (P-BPAR) of the pancreas graft in a cohort of 36 SPKTx recipients with biopsy-matched plasma samples. dd-cfDNA was measured using the Prospera test (Natera, Inc.) and reported both as a fraction of the total cfDNA (fraction; %) and as concentration in the recipient’s plasma (quantity; copies/mL). Results. In the absence of P-BPAR, dd-cfDNA was significantly higher in samples collected within the first 45 d after SPKTx compared with those measured afterward (median, 1.00% versus 0.30%; median, 128.2 versus 35.3 cp/mL, respectively with both; P = 0.001). In samples obtained beyond day 45, P-BPAR samples presented a significantly higher dd-cfDNA fraction (0.83 versus 0.30%; P = 0.006) and quantity (81.3 versus 35.3 cp/mL; P = 0.001) than stable samples. Incorporating dd-cfDNA quantity along with dd-cfDNA fraction outperformed dd-cfDNA fraction alone to detect active rejection. Notably, when using a quantity cutoff of 70 cp/mL, dd-cfDNA detected P-BPAR with a sensitivity of 85.7% and a specificity of 93.7%, which was more accurate than current biomarkers (area under curve of 0.89 for dd-cfDNA (cp/ml) compared with 0.74 of lipase and 0.46 for amylase). Conclusions. dd-cfDNA measurement through a simple noninvasive blood test could be incorporated into clinical practice to help inform graft management in SPKTx patients.

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Donor-derived Cell-free DNA Kinetics Post-kidney Transplant Biopsy

Cited by 5 publications

References 18 publications

The Trifecta Study: Comparing Plasma Levels of Donor-derived Cell-Free DNA with the Molecular Phenotype of Kidney Transplant Biopsies

The Trifecta Study: Comparing Plasma Levels of Donor-derived Cell-Free DNA with the Molecular Phenotype of Kidney Transplant Biopsies

Antibody-mediated Rejection Without Detectable Donor-specific Antibody Releases Donor-derived Cell-free DNA: Results From the Trifecta Study

Donor-derived Cell-free DNA Shows High Sensitivity for the Diagnosis of Pancreas Graft Rejection in Simultaneous Pancreas-kidney Transplantation

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