Cell-free DNA profiling informs all major complications of hematopoietic cell transplantation

Abstract

Allogeneic hematopoietic cell transplantation (HCT) provides effective treatment for hematologic malignancies and immune disorders. Monitoring of posttransplant complications is critical, yet current diagnostic options are limited. Here, we show that cell-free DNA (cfDNA) in blood is a versatile analyte for monitoring of the most important complications that occur after HCT: graft-versus-host disease (GVHD), a frequent immune complication of HCT, infection, relapse of underlying disease, and graft failure. We demonstrate that these therapeutic complications are informed from a single assay, low-coverage bisulfite sequencing of cfDNA, followed by disease-specific bioinformatic analyses. To inform GVHD, we profile cfDNA methylation marks to trace the cfDNA tissues-of-origin and to quantify tissue-specific injury. To inform infection, we implement metagenomic cfDNA profiling. To inform cancer relapse, we implement analyses of tumor-specific genomic aberrations. Finally, to detect graft failure, we quantify the proportion of donor- and recipient-specific cfDNA. We applied this assay to 170 plasma samples collected from 27 HCT recipients at predetermined timepoints before and after allogeneic HCT. We found that the abundance of solid-organ–derived cfDNA in the blood at 1 mo after HCT is predictive of acute GVHD (area under the curve, 0.88). Metagenomic profiling of cfDNA revealed the frequent occurrence of viral reactivation in this patient population. The fraction of donor-specific cfDNA was indicative of relapse and remission, and the fraction of tumor-specific cfDNA was informative of cancer relapse. This proof-of-principle study shows that cfDNA has the potential to improve the care of allogeneic HCT recipients by enabling earlier detection and better prediction of the complex array of complications that occur after HCT.

One Biomarker to Diagnose Them All?

“…1 The discriminative power of cfDNA may be improved in combination with other biomarkers, including gene expression profiles in blood, urine, or tissue samples. 6,7 Determining the tissue origin of cfDNA as demonstrated by Cheng et al 3 may represent a helpful addition in this context. Liver allograft rejection has been diagnosed using hepatocyte-specific DNA methylation profiles.…”

“…Based on methylation profiles, determined with whole-genome bisulfite sequencing followed by bioinformatics analyses, the origin of circulating cfDNA in these 27 patients was determined. 3 Microbial cfDNA was distinguished from human cfDNA, which was then identified as originating from either tumor, donor, or recipient. The origin of recipient cfDNA informed on tissue-specific injury, distinguishing graft versus host disease.…”

“…Finally, BK virus–derived cfDNA could be detected and turned out to be more sensitive than a clinically used BK virus–specific polymerase chain reaction assay for the detection of BK viremia. 3…”

“…The work by Cheng et al 3 is an elegant example of the potential diagnostic value of circulating cfDNA and will likely improve posttransplant care of hematopoietic stem cell recipients. The cfDNA assay introduced by the authors enables early detection of several major complications after hematopoietic stem cell transplantation and requires only a small volume of blood (0.5–1.9 mL of plasma).…”

“…An additional and clinically most relevant application of circulating cfDNA as shown by Cheng et al 3 is the potential to diagnose infection. cfDNA allows the detection of numerous different pathogens with particular relevance for the challenging diagnosis of posttransplant infections, including tuberculosis and endocarditis.…”