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Cheng AP, Cheng MP, Loy CJ, Lenz JS, Chen K, Smalling S, Burnham P, Timblin KM, Orejas JL, Silverman E, Polak P, Marty FM, Ritz J, De Vlaminck I. Cell-free DNA profiling informs all major complications of hematopoietic cell transplantation. Proc Natl Acad Sci U S A 2022; 119:e2113476118. [PMID: 35058359 PMCID: PMC8795552 DOI: 10.1073/pnas.2113476118] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022] Open
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.
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Affiliation(s)
| | - Matthew Pellan Cheng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Division of Infectious Disease, Brigham and Women's Hospital, Boston, MA 02215
| | - Conor James Loy
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Joan Sesing Lenz
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853
| | - Kaiwen Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Division of Infectious Disease, Brigham and Women's Hospital, Boston, MA 02215
| | - Sami Smalling
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853
| | - Philip Burnham
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Kaitlyn Marie Timblin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Division of Infectious Disease, Brigham and Women's Hospital, Boston, MA 02215
| | - José Luis Orejas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Division of Infectious Disease, Brigham and Women's Hospital, Boston, MA 02215
| | - Emily Silverman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Division of Infectious Disease, Brigham and Women's Hospital, Boston, MA 02215
| | - Paz Polak
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Francisco M Marty
- Division of Infectious Disease, Brigham and Women's Hospital, Boston, MA 02215
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853;
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