Cell-free DNA profiling informs all major complications of hematopoietic cell transplantation.
Alexandre Pellan ChengMatthew Pellan ChengConor James LoyJoan Sesing LenzKaiwen ChenSami SmallingPhilip BurnhamKaitlyn Marie TimblinJosé Luis OrejasEmily SilvermanPaz PolakFrancisco M MartyJerome RitzIwijn De VlaminckPublished in: Proceedings of the National Academy of Sciences of the United States of America (2022)
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.
Keyphrases
- cell cycle arrest
- stem cell transplantation
- single cell
- bone marrow
- healthcare
- gene expression
- papillary thyroid
- antibiotic resistance genes
- palliative care
- risk assessment
- squamous cell carcinoma
- sars cov
- free survival
- systemic lupus erythematosus
- rheumatoid arthritis
- case report
- intensive care unit
- liver failure
- squamous cell
- pi k akt
- kidney transplantation
- high density
- hepatitis b virus
- aortic dissection
- combination therapy
- mechanical ventilation