Cell-free DNA Profiling Informs Major Complications of Hematopoietic Cell Transplantation

Abstract

14 15 16 17 ABSTRACT: Allogeneic hematopoietic cell transplantation (HCT) provides effective treatment for 18 hematologic malignancies and immune disorders. Monitoring for immune complications and infection is a 19 critical component of post-HCT therapy, however, current diagnostic options are limited. Here, we propose 20a blood test that employs genome-wide profiling of methylation marks comprised within circulating cell-21 free DNA to trace the tissues-of-origin of cell-free DNA (cfDNA), to quantify tissue-specific injury, and to 22 35 36More than 30,000 patients undergo allogeneic hematopoietic cell transplants (HCT) worldwide 37 each year for treatment of a variety of malignant and nonmalignant hematologic diseases 1-3 . However, 38 immune related complications occur frequently after HCT. Up to 50% of patients experience graft-versus-39host disease (GVHD) in the first year after transplantation. GVHD occurs when donor immune cells attack 40 the patient's own tissues 2,4-6 . Early and accurate diagnosis of GVHD is critical to inform treatment decisions 41and to prevent serious long-term complications, including organ failure and death. Unfortunately, there are 42 few, noninvasive diagnostic options that reliably identify patients very early after onset of GVHD 43 symptoms. In current clinical practice, diagnosis of GVHD relies almost entirely on clinical criteria and 44 often requires confirmation with invasive procedures, such as a biopsy of the gastrointestinal tract, skin, or 45 liver 7 . 46 47Small fragments of cell-free DNA (cfDNA) circulate in blood. In the absence of disease, cfDNA 48originates primarily from apoptosis of cells of the hematopoietic lineage 8 . During disease, a significant 49proportion of cfDNA can be derived from affected tissues 9-15 . In solid-organ transplantation (SOT), we and 50 others have shown that transplant donor derived cfDNA in the blood is a quantitative noninvasive marker 51 of solid organ transplant injury 12,13,16,17 . Here, we sought to investigate the utility of circulating cfDNA as a 52minimally invasive analyte to detect and quantify tissue injury due to GVHD after HCT. To quantify the 53 contributions of any tissue to the mixture of cfDNA in plasma, and thereby the degree of injury to any 54 vascularized tissue in the setting of HCT, we implemented shallow, whole genome bisulfite sequencing 55(WGBS) to profile 5-methylcytosine (5mC) marks of cfDNA. These marks are cell, tissue and organ type 56 specific 18 , and can inform the tissues-of-origin of cell-free DNA 8,11,19 . 57 58We collected serial blood samples from a prospective cohort of allogeneic HCT recipients at 59 predetermined time points before and after HCT. We analyzed a total of 106 plasma samples from 18 HCT 60 recipients with and without GVHD in the first 3 months post HCT. We observed rich dynamics in the tissue-61 origin of cfDNA in response to pre-transplant conditioning chemotherapy and following HCT. The tissue-62 origin of cfDNA after transplantation was patient-specific and a function of the ma...

Cell-free DNA tissues of origin by methylation profiling reveals significant cell, tissue, and organ-specific injury related to COVID-19 severity

“…[20][21][22] More recently, several approaches have been developed to quantify the tissues of origin of cfDNA and thus monitor injury to any cell, tissue, or organ type. [23][24][25][26][27] This is achieved by profiling epigenetic marks within cfDNA by quantitative molecular measurement technologies such as DNA sequencing. Here, we tested the hypothesis that cfDNA tissues of origin profiling enables the identification of specific tissue or cell types that are directly or indirectly targeted and injured throughout COVID-19 pathogenesis.…”

Cell-Free DNA in Blood Reveals Significant Cell, Tissue and Organ Specific injury and Predicts COVID-19 Severity

“…The value of cfDNA as a quantitative marker of tissue and organ injury was first recognized in solid-organ transplantation, where the level of transplant donor derived cfDNA in the blood is now widely used as a marker of transplant rejection [ 20 ]–[ 22 ]. More recently, several approaches have been developed to quantify the tissues-of-origin of cfDNA and thus monitor injury to any cell, tissue or organ type [ 23 ]–[ 27 ]. This is achieved by profiling epigenetic marks within cfDNA by quantitative molecular measurement technologies such as DNA sequencing.…”