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Keller MB, Tian X, Jang MK, Meda R, Charya A, Berry GJ, Marboe CC, Kong H, Ponor IL, Aryal S, Orens JB, Shah PD, Nathan SD, Agbor-Enoh S. Higher Molecular Injury at Diagnosis of Acute Cellular Rejection Increases the Risk of Lung Allograft Failure: A Clinical Trial. Am J Respir Crit Care Med 2024; 209:1238-1245. [PMID: 38190701 DOI: 10.1164/rccm.202305-0798oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 01/08/2024] [Indexed: 01/10/2024] Open
Abstract
Rationale: The association of acute cellular rejection (ACR) with chronic lung allograft dysfunction (CLAD) in lung transplant recipients has primarily been described before consensus recommendations incorporating restrictive phenotypes. Furthermore, the association of the degree of molecular allograft injury during ACR with CLAD or death remains undefined. Objectives: To investigate the association of ACR with the risk of CLAD or death and to further investigate if this risk depends on the degree of molecular allograft injury. Methods: This multicenter, prospective cohort study included 188 lung transplant recipients. Subjects underwent serial plasma collections for donor-derived cell-free DNA (dd-cfDNA) at prespecified time points and bronchoscopy. Multivariable Cox proportional-hazards analysis was conducted to analyze the association of ACR with subsequent CLAD or death as well as the association of dd-cfDNA during ACR with risk of CLAD or death. Additional outcomes analyses were performed with episodes of ACR categorized as "high risk" (dd-cfDNA ⩾ 1%) and "low risk" (dd-cfDNA < 1%). Measurements and Main Results: In multivariable analysis, ACR was associated with the composite outcome of CLAD or death (hazard ratio [HR], 2.07 [95% confidence interval (CI), 1.05-4.10]; P = 0.036). Elevated dd-cfDNA ⩾ 1% at ACR diagnosis was independently associated with increased risk of CLAD or death (HR, 3.32; 95% CI, 1.31-8.40; P = 0.012). Patients with high-risk ACR were at increased risk of CLAD or death (HR, 3.13; 95% CI, 1.41-6.93; P = 0.005), whereas patients with low-risk status ACR were not. Conclusions: Patients with ACR are at higher risk of CLAD or death, but this may depend on the degree of underlying allograft injury at the molecular level. Clinical trial registered with www.clinicaltrials.gov (NCT02423070).
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Affiliation(s)
- Michael B Keller
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Laboratory of Applied Precision Omics and
- Division of Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Xin Tian
- Office of Biostatistics Research, NHLBI, NIH, Bethesda, Maryland
| | - Moon Kyoo Jang
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Laboratory of Applied Precision Omics and
| | - Rohan Meda
- Laboratory of Applied Precision Omics and
| | - Ananth Charya
- University of Maryland Medical Center, Baltimore, Maryland
| | - Gerald J Berry
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- School of Medicine, Stanford University, Stanford, California
| | - Charles C Marboe
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons of Columbia University, New York, New York
| | - Hyesik Kong
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Laboratory of Applied Precision Omics and
| | - Ileana L Ponor
- Department of Medicine, Johns Hopkins Bayview Medical Center, Baltimore, Maryland; and
| | - Shambhu Aryal
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Advanced Lung Disease and Lung Transplant Program, Inova Fairfax Hospital, Fairfax, Virginia
| | - Jonathan B Orens
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Pali D Shah
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Steven D Nathan
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Advanced Lung Disease and Lung Transplant Program, Inova Fairfax Hospital, Fairfax, Virginia
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Laboratory of Applied Precision Omics and
- Division of Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland
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2
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Keller MB, Newman D, Alnababteh M, Ponor L, Shah P, Matthews J, Kong H, Andargie T, Park W, Charya A, Luikart H, Aryal S, Nathan SD, Orens JB, Khush KK, Jang M, Agbor-Enoh S. Extreme elevations of donor-derived cell-free DNA increases the risk of chronic lung allograft dysfunction and death, even without clinical manifestations of disease. J Heart Lung Transplant 2024:S1053-2498(24)01644-9. [PMID: 38705500 DOI: 10.1016/j.healun.2024.04.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/11/2024] [Accepted: 04/25/2024] [Indexed: 05/07/2024] Open
Abstract
BACKGROUND Lung transplant recipients are traditionally monitored with pulmonary function testing (PFT) and lung biopsy to detect post-transplant complications and guide treatment. Plasma donor-derived cell free DNA (dd-cfDNA) is a novel molecular approach of assessing allograft injury, including subclinical allograft dysfunction. The aim of this study was to determine if episodes of extreme molecular injury (EMI) in lung transplant recipients increases the risk of CLAD or death. METHODS This multicenter prospective cohort study included 238 lung transplant recipients. Serial plasma samples were collected for dd-cfDNA measurement by shotgun sequencing. EMI was defined as a dd-cfDNA above the third quartile of levels observed for acute rejection (dd-cfDNA level of ≥ 5% occurring after 45 days post-transplant). EMI was categorized as Secondary if associated with co-existing acute rejection, infection or PFT decline; or Primary if not associated to these conditions. RESULTS EMI developed in 16% of patients at a median 343.5 (IQR: 177.3-535.5) days post-transplant. Over 50% of EMI episodes were classified as Primary. EMI was associated with an increased risk of severe CLAD or death (HR: 2.52, 95% CI: 1.10 - 3.82, p= 0.024). The risk remained consistent for Primary EMI (HR: 2.34, 95% CI 1.18-4.85, p=0.015). Time to first EMI episode was a significant predictor of the likelihood of developing CLAD or death (AUC=0.856, 95% CI =.805-908, p<.001). CONCLUSIONS Episodes of EMI in lung transplant recipients are often isolated and not detectable with traditional clinical monitoring approaches. EMI is associated with an increased risk of severe CLAD or death, independent of concomitant transplant complications.
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Affiliation(s)
- Michael B Keller
- Laborarory of Applied Precision Omics (APO) National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD; Genomic Research Alliance for Transplantation (GRAfT); Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD; Pulmonary and Critical Care Medicine, Johns Hopkins Hospital, Baltimore MD
| | - David Newman
- College of Nursing, Florida Atlantic University, FL
| | - Muhtadi Alnababteh
- Laborarory of Applied Precision Omics (APO) National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD; Genomic Research Alliance for Transplantation (GRAfT); Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Lucia Ponor
- Genomic Research Alliance for Transplantation (GRAfT); Division of Hospital Medicine, Johns Hopkins Bayview Medical Center, Baltimore, MD
| | - Pali Shah
- Genomic Research Alliance for Transplantation (GRAfT); Pulmonary and Critical Care Medicine, Johns Hopkins Hospital, Baltimore MD
| | - Joby Matthews
- Genomic Research Alliance for Transplantation (GRAfT); Pulmonary and Critical Care Medicine, Johns Hopkins Hospital, Baltimore MD
| | - Hyesik Kong
- Laborarory of Applied Precision Omics (APO) National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD; Genomic Research Alliance for Transplantation (GRAfT)
| | - Temesgen Andargie
- Laborarory of Applied Precision Omics (APO) National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD; Genomic Research Alliance for Transplantation (GRAfT)
| | - Woojin Park
- Laborarory of Applied Precision Omics (APO) National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD; Genomic Research Alliance for Transplantation (GRAfT)
| | - Ananth Charya
- Division of Pulmonary and Critical Care Medicine, University of Maryland Medical Center, Baltimore MD
| | - Helen Luikart
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Palo Alto, CA; Department of Pathology, Stanford University School of Medicine, Palo Alto, CA
| | - Shambhu Aryal
- Genomic Research Alliance for Transplantation (GRAfT); Inova Fairfax Hospital, Falls Church, VA
| | - Steven D Nathan
- Genomic Research Alliance for Transplantation (GRAfT); Inova Fairfax Hospital, Falls Church, VA
| | - Jonathan B Orens
- Genomic Research Alliance for Transplantation (GRAfT); Pulmonary and Critical Care Medicine, Johns Hopkins Hospital, Baltimore MD
| | - Kiran K Khush
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Palo Alto, CA
| | - Moon Jang
- Laborarory of Applied Precision Omics (APO) National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD; Genomic Research Alliance for Transplantation (GRAfT)
| | - Sean Agbor-Enoh
- Laborarory of Applied Precision Omics (APO) National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD; Genomic Research Alliance for Transplantation (GRAfT); Pulmonary and Critical Care Medicine, Johns Hopkins Hospital, Baltimore MD.
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Shah P, Agbor-Enoh S, Lee S, Andargie TE, Sinha SS, Kong H, Henry L, Park W, McNair E, Tchoukina I, Shah KB, Najjar SS, Hsu S, Rodrigo ME, Jang MK, Marboe C, Berry GJ, Valantine HA. Racial Differences in Donor-Derived Cell-Free DNA and Mitochondrial DNA After Heart Transplantation, on Behalf of the GRAfT Investigators. Circ Heart Fail 2024; 17:e011160. [PMID: 38375637 PMCID: PMC11021168 DOI: 10.1161/circheartfailure.123.011160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/07/2023] [Indexed: 02/21/2024]
Abstract
BACKGROUND Black heart transplant patients are at higher risk of acute rejection (AR) and death than White patients. We hypothesized that this risk may be associated with higher levels of donor-derived cell-free DNA (dd-cfDNA) and cell-free mitochondrial DNA. METHODS The Genomic Research Alliance for Transplantation is a multicenter, prospective, longitudinal cohort study. Sequencing was used to quantitate dd-cfDNA and polymerase chain reaction to quantitate cell-free mitochondrial DNA in plasma. AR was defined as ≥2R cellular rejection or ≥1 antibody-mediated rejection. The primary composite outcome was AR, graft dysfunction (left ventricular ejection fraction <50% and decrease by ≥10%), or death. RESULTS We included 148 patients (65 Black patients and 83 White patients), median age was 56 years and 30% female sex. The incidence of AR was higher in Black patients compared with White patients (43% versus 19%; P=0.002). Antibody-mediated rejection occurred predominantly in Black patients with a prevalence of 20% versus 2% (P<0.001). After transplant, Black patients had higher levels of dd-cfDNA, 0.09% (interquartile range, 0.001-0.30) compared with White patients, 0.05% (interquartile range, 0.001-0.23; P=0.003). Beyond 6 months, Black patients showed a persistent rise in dd-cfDNA with higher levels compared with White patients. Cell-free mitochondrial DNA was higher in Black patients (185 788 copies/mL; interquartile range, 101 252-422 133) compared with White patients (133 841 copies/mL; interquartile range, 75 346-337 990; P<0.001). The primary composite outcome occurred in 43% and 55% of Black patients at 1 and 2 years, compared with 23% and 27% in White patients, P<0.001. In a multivariable model, Black patient race (hazard ratio, 2.61 [95% CI, 1.35-5.04]; P=0.004) and %dd-cfDNA (hazard ratio, 1.15 [95% CI, 1.03-1.28]; P=0.010) were associated with the primary composite outcome. CONCLUSIONS Elevated dd-cfDNA and cell-free mitochondrial DNA after heart transplant may mechanistically be implicated in the higher incidence of AR and worse clinical outcomes in Black transplant recipients. REGISTRATION URL: https://www.clinicaltrials.gov; Unique identifier: NCT02423070.
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Affiliation(s)
- Palak Shah
- Heart Failure, Mechanical Circulatory Support & Transplant, Inova Heart and Vascular Institute, Falls Church VA
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda Maryland, 20982
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda Maryland, 20982
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore MD
- Applied Precision Genomics, National Heart, Lung and Blood Institute, Bethesda MD
| | - Seiyon Lee
- Volgenau School of Engineering, George Mason University, Fairfax VA
| | - Temesgen E. Andargie
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda Maryland, 20982
- Applied Precision Genomics, National Heart, Lung and Blood Institute, Bethesda MD
| | - Shashank S. Sinha
- Heart Failure, Mechanical Circulatory Support & Transplant, Inova Heart and Vascular Institute, Falls Church VA
| | - Hyesik Kong
- Applied Precision Genomics, National Heart, Lung and Blood Institute, Bethesda MD
| | - Lawrence Henry
- Heart Failure, Mechanical Circulatory Support & Transplant, Inova Heart and Vascular Institute, Falls Church VA
| | - Woojin Park
- Applied Precision Genomics, National Heart, Lung and Blood Institute, Bethesda MD
| | - Erick McNair
- Heart Failure, Mechanical Circulatory Support & Transplant, Inova Heart and Vascular Institute, Falls Church VA
| | - Inna Tchoukina
- The Pauley Heart Center, Virginia Commonwealth University, Richmond VA
| | - Keyur B. Shah
- The Pauley Heart Center, Virginia Commonwealth University, Richmond VA
| | - Samer S. Najjar
- Advanced Heart Failure Program, Medstar Heart and Vascular Institute, Washington Hospital Center, Washington DC
| | - Steven Hsu
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore MD
| | - Maria E. Rodrigo
- Advanced Heart Failure Program, Medstar Heart and Vascular Institute, Washington Hospital Center, Washington DC
| | - Moon Kyoo Jang
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda Maryland, 20982
- Applied Precision Genomics, National Heart, Lung and Blood Institute, Bethesda MD
| | - Charles Marboe
- Department of Pathology, New York Presbyterian University Hospital of Cornell and Columbia, New York, New York, USA
| | | | - Hannah A. Valantine
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda Maryland, 20982
- Stanford University School of Medicine, Palo Alto, CA
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Keller MB, Tian X, Jang MK, Meda R, Charya A, Ozisik D, Berry GJ, Marboe CC, Kong H, Ponor IL, Aryal S, Orens JB, Shah PD, Nathan SD, Agbor-Enoh S. Organizing pneumonia is associated with molecular allograft injury and the development of antibody-mediated rejection. J Heart Lung Transplant 2024; 43:563-570. [PMID: 37972825 DOI: 10.1016/j.healun.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/28/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The association between organizing pneumonia (OP) after lung transplantation with the development of acute rejection (AR) remains undefined. In addition, molecular allograft injury, as measured by donor-derived cell-free DNA (dd-cfDNA), during episodes of OP and its relationship to episodes of AR, chronic lung allograft dysfunction (CLAD), or death is unknown. METHODS This multicenter, prospective cohort study collected serial plasma samples from 188 lung transplant recipients for dd-cfDNA at the time of bronchoscopy with biopsy. Multivariable Cox regression was used to analyze the association between OP with the development of AR (antibody-mediated rejection (AMR) and acute cellular rejection (ACR)), CLAD, and death. Multivariable models were performed to test the association of dd-cfDNA at OP with the risk of AR, CLAD, or death. RESULTS In multivariable analysis, OP was associated with increased risk of AMR (hazard ratio (HR) = 2.26, 95% confidence interval (CI) 1.04-4.92, p = 0.040) but not ACR (HR = 1.29, 95% CI: 0.66-2.5, p = 0.45) or the composite outcome of CLAD or death (HR = 0.88, 95% CI, 0.47-1.65, p = 0.69). Median levels of dd-cfDNA were higher in OP compared to stable controls (1.33% vs 0.43%, p = 0.0006). Multivariable analysis demonstrated that levels of dd-cfDNA at diagnosis of OP were associated with increased risk of both AMR (HR = 1.29, 95% CI 1.03-1.62, p = 0.030) and death (HR = 1.16, 95% CI, 1.02-1.31, p = 0.026). CONCLUSIONS OP is independently associated with an increased risk of AMR but not CLAD or death. The degree of molecular allograft injury at the diagnosis of OP may further predict the risk of AMR and death.
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Affiliation(s)
- Michael B Keller
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Laboratory of Applied Precision Omics (APO), National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland; Division of Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Xin Tian
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Moon Kyoo Jang
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Laboratory of Applied Precision Omics (APO), National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Rohan Meda
- Laboratory of Applied Precision Omics (APO), National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Ananth Charya
- University of Maryland Medical Center, Baltimore, Maryland
| | - Deniz Ozisik
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Gerald J Berry
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Stanford University School of Medicine, Stanford, California
| | - Charles C Marboe
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons of Columbia University, New York, New York
| | - Hyesik Kong
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Laboratory of Applied Precision Omics (APO), National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Ileana L Ponor
- Department of Medicine, Johns Hopkins Bayview Medical Center, Baltimore, Maryland
| | - Shambhu Aryal
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Advanced Lung Disease and Lung Transplant Program, Inova Fairfax Hospital, Fairfax, Virginia
| | - Jonathan B Orens
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Division of Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Pali D Shah
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Division of Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Steven D Nathan
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Advanced Lung Disease and Lung Transplant Program, Inova Fairfax Hospital, Fairfax, Virginia
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Laboratory of Applied Precision Omics (APO), National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland; Division of Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland.
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5
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Balasubramanian S, Richert ME, Kong H, Fu S, Jang MK, Andargie TE, Keller MB, Alnababteh M, Park W, Apalara Z, Sun J, Redekar N, Orens J, Aryal S, Bush EL, Cantu E, Diamond J, Shah P, Yu K, Nathan SD, Agbor-Enoh S. Cell-Free DNA Maps Tissue Injury and Correlates with Disease Severity in Lung Transplant Candidates. Am J Respir Crit Care Med 2024; 209:727-737. [PMID: 38117233 PMCID: PMC10945061 DOI: 10.1164/rccm.202306-1064oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023] Open
Abstract
Rationale: Plasma cell-free DNA levels correlate with disease severity in many conditions. Pretransplant cell-free DNA may risk stratify lung transplant candidates for post-transplant complications. Objectives: To evaluate if pretransplant cell-free DNA levels and tissue sources identify patients at high risk of primary graft dysfunction and other pre- and post-transplant outcomes. Methods: This multicenter, prospective cohort study recruited 186 lung transplant candidates. Pretransplant plasma samples were collected to measure cell-free DNA. Bisulfite sequencing was performed to identify the tissue sources of cell-free DNA. Multivariable regression models determined the association between cell-free DNA levels and the primary outcome of primary graft dysfunction and other transplant outcomes, including Lung Allocation Score, chronic lung allograft dysfunction, and death. Measurements and Main Results: Transplant candidates had twofold greater cell-free DNA levels than healthy control patients (median [interquartile range], 23.7 ng/ml [15.1-35.6] vs. 12.9 ng/ml [9.9-18.4]; P < 0.0001), primarily originating from inflammatory innate immune cells. Cell-free DNA levels and tissue sources differed by native lung disease category and correlated with the Lung Allocation Score (P < 0.001). High pretransplant cell-free DNA increased the risk of primary graft dysfunction (odds ratio, 1.60; 95% confidence interval [CI], 1.09-2.46; P = 0.0220), and death (hazard ratio, 1.43; 95% CI, 1.07-1.92; P = 0.0171) but not chronic lung allograft dysfunction (hazard ratio, 1.37; 95% CI, 0.97-1.94; P = 0.0767). Conclusions: Lung transplant candidates demonstrate a heightened degree of tissue injury with elevated cell-free DNA, primarily originating from innate immune cells. Pretransplant plasma cell-free DNA levels predict post-transplant complications.
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Affiliation(s)
- Shanti Balasubramanian
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
- Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland
| | - Mary E. Richert
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
- Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland
| | - Hyesik Kong
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Sheng Fu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Moon Kyoo Jang
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Temesgen E. Andargie
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
- Department of Biology, Howard University, Washington, District of Columbia
| | - Michael B. Keller
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
- Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Muhtadi Alnababteh
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
- Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland
| | - Woojin Park
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Zainab Apalara
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
- Integrated Data Science Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jian Sun
- Integrated Data Science Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Neelam Redekar
- Integrated Data Science Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jonathan Orens
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Shambhu Aryal
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Advanced Lung Disease and Lung Transplant Program, Inova Fairfax Hospital, Fairfax, Virginia
| | - Errol L. Bush
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Department of Surgery, The Johns Hopkins School of Medicine, Baltimore, Maryland; and
| | - Edward Cantu
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Department of Surgery, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Joshua Diamond
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Department of Surgery, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Pali Shah
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Steven D. Nathan
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Advanced Lung Disease and Lung Transplant Program, Inova Fairfax Hospital, Fairfax, Virginia
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland
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6
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DeFilippis EM, Sweigart B, Khush KK, Shah P, Agbor-Enoh S, Valantine HA, Vest AR. Sex-specific patterns of donor-derived cell-free DNA in heart transplant rejection: An analysis from the Genomic Research Alliance for Transplantation (GRAfT). J Heart Lung Transplant 2024:S1053-2498(24)01520-1. [PMID: 38460620 DOI: 10.1016/j.healun.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 01/22/2024] [Accepted: 03/04/2024] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND Noninvasive methods for surveillance of acute rejection are increasingly used in heart transplantation (HT), including donor-derived cell-free DNA (dd-cfDNA). As other cardiac biomarkers differ by sex, we hypothesized that there may be sex-specific differences in the performance of dd-cfDNA for the detection of acute rejection. The purpose of the current study was to examine patterns of dd-cfDNA seen in quiescence and acute rejection in male and female transplant recipients. METHODS Patients enrolled in the Genomic Research Alliance for Transplantation who were ≥18 years at the time of HT were included. Rejection was defined by endomyocardial biopsy with acute cellular rejection (ACR) grade ≥2R and/or antibody-mediated rejection ≥ pAMR 1. dd-cfDNA was quantitated using shotgun sequencing. Median dd-cfDNA levels were compared between sexes during quiescence and rejection. The performance of dd-cfDNA by sex was assessed using area under the receiver operator characteristic (AUROC) curve. Allograft injury was defined as dd-cfDNA ≥0.25%. RESULTS One hundred fifty-one unique patients (49 female, 32%) were included in the analysis with 1,119 available dd-cfDNA measurements. Baseline characteristics including demographics and comorbidities were not significantly different between sexes. During quiescence, there were no significant sex differences in median dd-cfDNA level (0.04% [IQR 0.00, 0.16] in females vs 0.03% [IQR 0.00, 0.12] in males, p = 0.22). There were no significant sex differences in median dd-cfDNA for ACR (0.33% [0.21, 0.36] in females vs 0.32% [0.21, 1.10] in males, p = 0.57). Overall, median dd-cfDNA levels were higher in antibody-mediated rejection (AMR) than ACR but did not significantly differ by sex (0.50% [IQR 0.18, 0.82] in females vs 0.63% [IQR 0.32, 1.95] in males, p = 0.51). Elevated dd-cfDNA detected ACR/AMR with an AUROC of 0.83 in females and 0.89 in males, p-value for comparison = 0.16. CONCLUSIONS There were no significant sex differences in dd-cfDNA levels during quiescence and rejection. Performance characteristics were similar, suggesting similar diagnostic thresholds can be used in men and women for rejection surveillance.
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Affiliation(s)
- Ersilia M DeFilippis
- Division of Cardiology, Center for Advanced Cardiac Care, Columbia University Irving Medical Center, New York, New York
| | - Benjamin Sweigart
- Tufts Clinical and Translational Science Institute, Tufts Medical Center, Boston, Massachusetts
| | - Kiran K Khush
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California
| | - Palak Shah
- Heart Failure, Mechanical Circulatory Support and Transplant, Inova Schar Heart and Vascular, Falls Church, Virginia
| | - Sean Agbor-Enoh
- Division of Intramural Research, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Hannah A Valantine
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California
| | - Amanda R Vest
- Division of Cardiology, Tufts Medical Center, Boston, Massachusetts.
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Goldberg JF, Mehta A, Bahniwal RK, Agbor-Enoh S, Shah P. A gentler approach to monitor for heart transplant rejection. Front Cardiovasc Med 2024; 11:1349376. [PMID: 38380175 PMCID: PMC10876874 DOI: 10.3389/fcvm.2024.1349376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/24/2024] [Indexed: 02/22/2024] Open
Abstract
Despite developments in circulating biomarker and imaging technology in the assessment of cardiovascular disease, the surveillance and diagnosis of heart transplant rejection has continued to rely on histopathologic interpretation of the endomyocardial biopsy. Increasing evidence shows the utility of molecular evaluations, such as donor-specific antibodies and donor-derived cell-free DNA, as well as advanced imaging techniques, such as cardiac magnetic resonance imaging, in the assessment of rejection, resulting in the elimination of many surveillance endomyocardial biopsies. As non-invasive technologies in heart transplant rejection continue to evolve and are incorporated into practice, they may supplant endomyocardial biopsy even when rejection is suspected, allowing for more precise and expeditious rejection therapy. This review describes the current and near-future states for the evaluation of heart transplant rejection, both in the settings of rejection surveillance and rejection diagnosis. As biomarkers of rejection continue to evolve, rejection risk prediction may allow for a more personalized approach to immunosuppression.
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Affiliation(s)
- Jason F. Goldberg
- Department of Heart Failure and Transplantation, Inova Heart and Vascular Institute, Falls Church, VA, United States
- Department of Children's Cardiology, Inova L.J. Murphy Children’s Hospital, Falls Church, VA, United States
| | - Aditya Mehta
- Department of Heart Failure and Transplantation, Inova Heart and Vascular Institute, Falls Church, VA, United States
| | | | - Sean Agbor-Enoh
- National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD, United States
| | - Palak Shah
- Department of Heart Failure and Transplantation, Inova Heart and Vascular Institute, Falls Church, VA, United States
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Roznik K, Andargie TE, Johnston TS, Gordon O, Wang Y, Peart Akindele N, Persaud D, Antar AAR, Manabe YC, Zhou W, Ji H, Agbor-Enoh S, Karaba AH, Thompson EA, Cox AL. Emergency myelopoiesis distinguishes multisystem inflammatory syndrome in children from pediatric severe COVID-19. J Infect Dis 2024:jiae032. [PMID: 38299308 DOI: 10.1093/infdis/jiae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 12/18/2023] [Accepted: 01/22/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Multisystem inflammatory syndrome in children (MIS-C) is a hyperinflammatory condition caused by recent SARS-CoV-2 infection, but the underlying immunological mechanisms driving this distinct syndrome are unknown. METHODS We utilized high dimensional flow cytometry, cell-free (cf) DNA, and cytokine and chemokine profiling to identify mechanisms of critical illness distinguishing MIS-C from severe acute COVID-19 (SAC). RESULTS Compared to SAC, MIS-C patients demonstrated profound innate immune cell death and features of emergency myelopoiesis (EM), an understudied phenomenon observed in severe inflammation. EM signatures were characterized by fewer mature myeloid cells in the periphery and decreased expression of HLA-DR and CD86 on antigen presenting cells. IL-27, a cytokine known to drive hematopoietic stem cells towards EM, was increased in MIS-C, and correlated with immature cell signatures in MIS-C. Upon recovery, EM signatures decreased, and IL-27 plasma levels returned to normal levels. Despite profound lymphopenia, we report a lack of cfDNA released by adaptive immune cells and increased CCR7 expression on T cells indicative of egress out of peripheral blood. CONCLUSIONS Immune cell signatures of EM combined with elevated innate immune cell-derived cfDNA levels distinguish MIS-C from SAC in children and provide mechanistic insight into dysregulated immunity contributing towards MIS-C, offering potential diagnostic and therapeutic targets.
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Affiliation(s)
- Katerina Roznik
- Johns Hopkins Bloomberg School of Public Health, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Baltimore, Maryland, USA
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Diseases, Baltimore, Maryland, USA
| | - Temesgen E Andargie
- Genomic Research Alliance for Transplantation and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), The National Institutes of Health, Bethesda, Maryland, USA
- Department of Biology, Howard University, Washington DC, USA
| | - T Scott Johnston
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Diseases, Baltimore, Maryland, USA
| | - Oren Gordon
- Infectious Diseases Unit, Department of Pediatrics, Faculty of Medicine, Hadassah Medical Center, Hebrew University of Jerusalem, Jerusalem, Israel
- Johns Hopkins University School of Medicine, Department of Pediatrics, Baltimore, Maryland, USA
| | - Yi Wang
- Johns Hopkins Bloomberg School of Public Health, Department of Biostatistics, Baltimore, Maryland, USA
| | - Nadine Peart Akindele
- Johns Hopkins University School of Medicine, Department of Pediatrics, Baltimore, Maryland, USA
| | - Deborah Persaud
- Johns Hopkins Bloomberg School of Public Health, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Baltimore, Maryland, USA
- Johns Hopkins University School of Medicine, Department of Pediatrics, Baltimore, Maryland, USA
| | - Annukka A R Antar
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Diseases, Baltimore, Maryland, USA
| | - Yukari C Manabe
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Diseases, Baltimore, Maryland, USA
| | - Weiqiang Zhou
- Johns Hopkins Bloomberg School of Public Health, Department of Biostatistics, Baltimore, Maryland, USA
| | - Hongkai Ji
- Johns Hopkins Bloomberg School of Public Health, Department of Biostatistics, Baltimore, Maryland, USA
| | - Sean Agbor-Enoh
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Diseases, Baltimore, Maryland, USA
- Genomic Research Alliance for Transplantation and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), The National Institutes of Health, Bethesda, Maryland, USA
| | - Andrew H Karaba
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Diseases, Baltimore, Maryland, USA
| | - Elizabeth A Thompson
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Diseases, Baltimore, Maryland, USA
| | - Andrea L Cox
- Johns Hopkins Bloomberg School of Public Health, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Baltimore, Maryland, USA
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Diseases, Baltimore, Maryland, USA
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9
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Andargie TE, Roznik K, Redekar N, Hill T, Zhou W, Apalara Z, Kong H, Gordon O, Meda R, Park W, Johnston TS, Wang Y, Brady S, Ji H, Yanovski JA, Jang MK, Lee CM, Karaba AH, Cox AL, Agbor-Enoh S. Cell-free DNA reveals distinct pathology of multisystem inflammatory syndrome in children. J Clin Invest 2024; 134:e178008. [PMID: 38165046 PMCID: PMC10760949 DOI: 10.1172/jci178008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024] Open
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10
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Jang MK, Markowitz TE, Andargie TE, Apalara Z, Kuhn S, Agbor-Enoh S. Cell-free chromatin immunoprecipitation to detect molecular pathways in heart transplantation. Life Sci Alliance 2023; 6:e202302003. [PMID: 37730434 PMCID: PMC10511822 DOI: 10.26508/lsa.202302003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/22/2023] Open
Abstract
Existing monitoring approaches in heart transplantation lack the sensitivity to provide deep molecular assessments to guide management, or require endomyocardial biopsy, an invasive and blind procedure that lacks the precision to reliably obtain biopsy samples from diseased sites. This study examined plasma cell-free DNA chromatin immunoprecipitation sequencing (cfChIP-seq) as a noninvasive proxy to define molecular gene sets and sources of tissue injury in heart transplant patients. In healthy controls and in heart transplant patients, cfChIP-seq reliably detected housekeeping genes. cfChIP-seq identified differential gene signals of relevant immune and nonimmune molecular pathways that were predominantly down-regulated in immunosuppressed heart transplant patients compared with healthy controls. cfChIP-seq also identified cell-free DNA tissue sources. Compared with healthy controls, heart transplant patients demonstrated greater cell-free DNA from tissue types associated with heart transplant complications, including the heart, hematopoietic cells, lungs, liver, and vascular endothelium. cfChIP-seq may therefore be a reliable approach to profile dynamic assessments of molecular pathways and sources of tissue injury in heart transplant patients.
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Affiliation(s)
- Moon Kyoo Jang
- https://ror.org/01cwqze88 Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD, USA
| | - Tovah E Markowitz
- https://ror.org/01cwqze88 NIAID Collaborative Bioinformatics Resource, Integrated Data Sciences Section, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Temesgen E Andargie
- https://ror.org/01cwqze88 Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD, USA
- Department of Biology, Howard University, Washington, DC, USA
| | - Zainab Apalara
- https://ror.org/01cwqze88 Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD, USA
| | - Skyler Kuhn
- https://ror.org/01cwqze88 NIAID Collaborative Bioinformatics Resource, Integrated Data Sciences Section, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Sean Agbor-Enoh
- https://ror.org/01cwqze88 Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
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11
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Pang Y, Andargie TE, Jang MK, Kong H, Park W, Hill T, Redekar N, Fu YP, Parth DA, Holtzman NG, Pavletic SZ, Agbor-Enoh S. Chronic graft-versus-host disease is characterized by high levels and distinctive tissue-of-origin patterns of cell-free DNA. iScience 2023; 26:108160. [PMID: 38026221 PMCID: PMC10651673 DOI: 10.1016/j.isci.2023.108160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 08/21/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023] Open
Abstract
Chronic graft-versus-host disease (cGvHD) is a devastating complication of hematopoietic stem cell transplantation (HSCT). Effective early detection may improve the outcome of cGvHD. The potential utility of circulating cell-free DNA (cfDNA), a sensitive marker for tissue injury, in HSCT and cGvHD remains to be established. Here, cfDNA of prospectively collected plasma samples from HSCT recipients (including both cGvHD and non-cGvHD) and healthy control (HC) subjects were evaluated. Deconvolution methods utilizing tissue-specific DNA methylation signatures were used to determine cfDNA tissue-of-origin. cfDNA levels were significantly higher in HSCT recipients than HC and significantly higher in cGvHD than non-cGvHD. cGvHD was characterized by a high level of cfDNA from innate immune cells, heart, and liver. Non-hematologic tissue-derived cfDNA was significantly higher in cGvHD than non-cGvHD. cfDNA temporal dynamics and tissue-of-origin composition have distinctive features in patients with cGvHD, supporting further exploration of the utility of cfDNA in the study of cGvHD.
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Affiliation(s)
- Yifan Pang
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Hematologic Oncology and Blood Disorders, Levine Cancer Institute, Charlotte, NC 28204, USA
| | - Temesgen E. Andargie
- Laboratory of Applied Precision Omics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Biology, Howard University, Washington, DC 20059, USA
| | - Moon Kyoo Jang
- Laboratory of Applied Precision Omics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hyesik Kong
- Laboratory of Applied Precision Omics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Woojin Park
- Laboratory of Applied Precision Omics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas Hill
- NIAID Collaborative Bioinformatics Resource, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Neelam Redekar
- NIAID Collaborative Bioinformatics Resource, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Yi-Ping Fu
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Desai A. Parth
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Noa G. Holtzman
- Immune Deficiency Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steven Z. Pavletic
- Immune Deficiency Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sean Agbor-Enoh
- Laboratory of Applied Precision Omics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Pulmonary and Critical Care Medicine, Johns Hopkins Hospital, Baltimore, MD 21205, USA
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12
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Andargie TE, Roznik K, Redekar N, Hill T, Zhou W, Apalara Z, Kong H, Gordon O, Meda R, Park W, Johnston TS, Wang Y, Brady S, Ji H, Yanovski JA, Jang MK, Lee CM, Karaba AH, Cox AL, Agbor-Enoh S. Cell-free DNA reveals distinct pathology of multisystem inflammatory syndrome in children. J Clin Invest 2023; 133:e171729. [PMID: 37651206 PMCID: PMC10617770 DOI: 10.1172/jci171729] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 08/29/2023] [Indexed: 09/02/2023] Open
Abstract
Multisystem inflammatory syndrome in children (MIS-C) is a rare but life-threatening hyperinflammatory condition induced by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes pediatric COVID-19 (pCOVID-19). The relationship of the systemic tissue injury to the pathophysiology of MIS-C is poorly defined. We leveraged the high sensitivity of epigenomics analyses of plasma cell-free DNA (cfDNA) and plasma cytokine measurements to identify the spectrum of tissue injury and glean mechanistic insights. Compared with pediatric healthy controls (pHCs) and patients with pCOVID-19, patients with MIS-C had higher levels of cfDNA primarily derived from innate immune cells, megakaryocyte-erythroid precursor cells, and nonhematopoietic tissues such as hepatocytes, cardiac myocytes, and kidney cells. Nonhematopoietic tissue cfDNA levels demonstrated significant interindividual variability, consistent with the heterogenous clinical presentation of MIS-C. In contrast, adaptive immune cell-derived cfDNA levels were comparable in MIS-C and pCOVID-19 patients. Indeed, the cfDNA of innate immune cells in patients with MIS-C correlated with the levels of innate immune inflammatory cytokines and nonhematopoietic tissue-derived cfDNA, suggesting a primarily innate immunity-mediated response to account for the multisystem pathology. These data provide insight into the pathogenesis of MIS-C and support the value of cfDNA as a sensitive biomarker to map tissue injury in MIS-C and likely other multiorgan inflammatory conditions.
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Affiliation(s)
- Temesgen E. Andargie
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA. GFAfT is detailed in Supplemental Acknowledgments
- Department of Biology, Howard University, Washington DC, USA
| | - Katerina Roznik
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Neelam Redekar
- Integrated Data Sciences Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Tom Hill
- Integrated Data Sciences Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Zainab Apalara
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA. GFAfT is detailed in Supplemental Acknowledgments
| | - Hyesik Kong
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA. GFAfT is detailed in Supplemental Acknowledgments
| | - Oren Gordon
- Infectious Diseases Unit, Department of Pediatrics, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rohan Meda
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA. GFAfT is detailed in Supplemental Acknowledgments
| | - Woojin Park
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA. GFAfT is detailed in Supplemental Acknowledgments
| | - Trevor S. Johnston
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Yi Wang
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sheila Brady
- Section on Growth and Obesity, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, Maryland, USA
| | - Hongkai Ji
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jack A. Yanovski
- Section on Growth and Obesity, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, Maryland, USA
| | - Moon K. Jang
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA. GFAfT is detailed in Supplemental Acknowledgments
| | - Clarence M. Lee
- Department of Biology, Howard University, Washington DC, USA
| | - Andrew H. Karaba
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Andrea L. Cox
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA. GFAfT is detailed in Supplemental Acknowledgments
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
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Britton N, Villabona-Rueda A, Whiteside SA, Mathew J, Kelley M, Agbor-Enoh S, McDyer JF, Christie JD, Collman RG, Cox AL, Shah P, D'Alessio F. Pseudomonas-dominant microbiome elicits sustained IL-1β upregulation in alveolar macrophages from lung transplant recipients. J Heart Lung Transplant 2023; 42:1166-1174. [PMID: 37088343 PMCID: PMC10538944 DOI: 10.1016/j.healun.2023.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 02/22/2023] [Accepted: 04/09/2023] [Indexed: 04/25/2023] Open
Abstract
BACKGROUND Isolation of Pseudomonas aeruginosa (PsA) is associated with increased BAL (bronchoalveolar lavage) inflammation and lung allograft injury in lung transplant recipients (LTR). However, the effect of PsA on macrophage responses in this population is incompletely understood. We examined human alveolar macrophage (AMΦ) responses to PsA and Pseudomonas dominant microbiome in healthy LTR. METHODS We stimulated THP-1 derived macrophages (THP-1MΦ) and human AMΦ from LTR with different bacteria and LTR BAL derived microbiome characterized as Pseudomonas-dominant. Macrophage responses were assessed by high dimensional flow cytometry, including their intracellular production of cytokines (TNF-α, IL-6, IL-8, IL-1β, IL-10, IL-1RA, and TGF-β). Pharmacological inhibitors were utilized to evaluate the role of the inflammasome in PsA-macrophage interaction. RESULTS We observed upregulation of pro-inflammatory cytokines (TNF-α, IL-6, IL-8, IL-1β) following stimulation by PsA compared to other bacteria (Staphylococcus aureus (S.Aur), Prevotella melaninogenica, Streptococcus pneumoniae) in both THP-1MΦ and LTR AMΦ, predominated by IL-1β. IL-1β production from THP-1MΦ was sustained after PsA stimulation for up to 96 hours and 48 hours in LTR AMΦ. Treatment with the inflammasome inhibitor BAY11-7082 abrogated THP-1MΦ IL-1β production after PsA exposure. BAL Pseudomonas-dominant microbiota elicited an increased IL-1β, similar to PsA, an effect abrogated by the addition of antibiotics. CONCLUSION PsA and PsA-dominant lung microbiota induce sustained IL-1β production in LTR AMΦ. Pharmacological targeting of the inflammasome reduces PsA-macrophage-IL-1β responses, underscoring their use in lung transplant recipients.
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Affiliation(s)
- Noel Britton
- Division of Pulmonary and Critical Care, School of Medicine, Johns Hopkins University, Baltimore, Maryland.
| | - Andres Villabona-Rueda
- Division of Pulmonary and Critical Care, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Samantha A Whiteside
- Division of Pulmonary, Allergy, and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Joby Mathew
- Division of Pulmonary and Critical Care, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Matthew Kelley
- Division of Pulmonary and Critical Care, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Sean Agbor-Enoh
- Division of Pulmonary and Critical Care, School of Medicine, Johns Hopkins University, Baltimore, Maryland; Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - John F McDyer
- Division of Pulmonary, Allergy, and Critical Care, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jason D Christie
- Division of Pulmonary, Allergy, and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ronald G Collman
- Division of Pulmonary, Allergy, and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Andrea L Cox
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Pali Shah
- Division of Pulmonary and Critical Care, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Franco D'Alessio
- Division of Pulmonary and Critical Care, School of Medicine, Johns Hopkins University, Baltimore, Maryland
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14
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Goldberg JF, Truby LK, Agbor-Enoh S, Jackson AM, deFilippi CR, Khush KK, Shah P. Selection and Interpretation of Molecular Diagnostics in Heart Transplantation. Circulation 2023; 148:679-694. [PMID: 37603604 PMCID: PMC10449361 DOI: 10.1161/circulationaha.123.062847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
The number of heart transplants performed annually in the United States and worldwide continues to increase, but there has been little change in graft longevity and patient survival over the past 2 decades. The reference standard for diagnosis of acute cellular and antibody-mediated rejection includes histologic and immunofluorescence evaluation of endomyocardial biopsy samples, despite invasiveness and high interrater variability for grading histologic rejection. Circulating biomarkers and molecular diagnostics have shown substantial predictive value in rejection monitoring, and emerging data support their use in diagnosing other posttransplant complications. The use of genomic (cell-free DNA), transcriptomic (mRNA and microRNA profiling), and proteomic (protein expression quantitation) methodologies in diagnosis of these posttransplant outcomes has been evaluated with varying levels of evidence. In parallel, growing knowledge about the genetically mediated immune response leading to rejection (immunogenetics) has enhanced understanding of antibody-mediated rejection, associated graft dysfunction, and death. Antibodies to donor human leukocyte antigens and the technology available to evaluate these antibodies continues to evolve. This review aims to provide an overview of biomarker and immunologic tests used to diagnose posttransplant complications. This includes a discussion of pediatric heart transplantation and the disparate rates of rejection and death experienced by Black patients receiving a heart transplant. This review describes diagnostic modalities that are available and used after transplant and the landscape of future investigations needed to enhance patient outcomes after heart transplantation.
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Affiliation(s)
- Jason F Goldberg
- Department of Heart Failure and Transplantation, Inova Heart and Vascular Institute, Falls Church, VA (J.F.G., C.R.d., P.S.)
- Department of Pediatrics, Inova L.J. Murphy Children's Hospital, Falls Church, VA (J.F.G.)
| | - Lauren K Truby
- Department of Medicine, University of Texas Southwestern, Dallas (L.K.T.)
| | - Sean Agbor-Enoh
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD (S.A.-E.)
- Applied Precision Genomics, National Heart, Lung and Blood Institute, Bethesda, MD (S.A.-E.)
| | - Annette M Jackson
- Department of Surgery, Duke University School of Medicine, Durham, NC (A.M.J.)
| | - Christopher R deFilippi
- Department of Heart Failure and Transplantation, Inova Heart and Vascular Institute, Falls Church, VA (J.F.G., C.R.d., P.S.)
| | - Kiran K Khush
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, CA (K.K.K.)
| | - Palak Shah
- Department of Heart Failure and Transplantation, Inova Heart and Vascular Institute, Falls Church, VA (J.F.G., C.R.d., P.S.)
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15
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Keller M, Yang S, Ponor L, Bon A, Cochrane A, Philogene M, Bush E, Shah P, Mathew J, Brown AW, Kong H, Charya A, Luikart H, Nathan SD, Khush KK, Jang M, Agbor-Enoh S. Preemptive treatment of de novo donor-specific antibodies in lung transplant patients reduces subsequent risk of chronic lung allograft dysfunction or death. Am J Transplant 2023; 23:559-564. [PMID: 36732088 PMCID: PMC10079558 DOI: 10.1016/j.ajt.2022.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 01/20/2023]
Abstract
The development of donor-specific antibodies after lung transplantation is associated with downstream acute cellular rejection, antibody-mediated rejection (AMR), chronic lung allograft dysfunction (CLAD), or death. It is unknown whether preemptive (early) treatment of de novo donor-specific antibodies (dnDSAs), in the absence of clinical signs and symptoms of allograft dysfunction, reduces the risk of subsequent CLAD or death. We performed a multicenter, retrospective cohort study to determine if early treatment of dnDSAs in lung transplant patients reduces the risk of the composite endpoint of CLAD or death. In the cohort of 445 patients, 145 patients developed dnDSAs posttransplant. Thirty patients received early targeted treatment for dnDSAs in the absence of clinical signs and symptoms of AMR. Early treatment of dnDSAs was associated with a decreased risk of CLAD or death (hazard ratio, 0.36; 95% confidence interval, 0.17-0.76; P < .01). Deferring treatment until the development of clinical AMR was associated with an increased risk of CLAD or death (hazard ratio, 3.00; 95% confidence interval, 1.46-6.18; P < .01). This study suggests that early, preemptive treatment of donor-specific antibodies in lung transplant patients may reduce the subsequent risk of CLAD or death.
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Affiliation(s)
- Michael Keller
- Laboratory of Applied Precision Omics (APO),National Heart,Lung and Blood Institute (NHLBI),National Institutes of Health,Bethesda,Maryland,USA; Laboratory of Transplantation Genomics, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, Bethesda, Maryland, USA; Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland, USA; Pulmonary and Critical Care Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA; Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Song Yang
- Office of Biostatistics Research, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
| | - Lucia Ponor
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland, USA; Division of Hospital Medicine, Johns Hopkins Bayview Medical Center, Baltimore, Maryland, USA
| | - Ann Bon
- Laboratory of Applied Precision Omics (APO),National Heart,Lung and Blood Institute (NHLBI),National Institutes of Health,Bethesda,Maryland,USA; Pulmonary and Critical Care Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | | | - Mary Philogene
- Pulmonary and Critical Care Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA; Johns Hopkins Immunogenetics Laboratory, Baltimore, Maryland, USA
| | - Errol Bush
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland, USA; Pulmonary and Critical Care Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Pali Shah
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland, USA; Pulmonary and Critical Care Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Joby Mathew
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland, USA; Pulmonary and Critical Care Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Anne W Brown
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland, USA; Inova Fairfax Hospital, Falls Church, Virginia, USA
| | - Hyesik Kong
- Laboratory of Applied Precision Omics (APO),National Heart,Lung and Blood Institute (NHLBI),National Institutes of Health,Bethesda,Maryland,USA; Laboratory of Transplantation Genomics, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, Bethesda, Maryland, USA; Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland, USA
| | - Ananth Charya
- Division of Pulmonary and Critical Care Medicine, University of Maryland Medical Center, Baltimore, Maryland, USA
| | - Helen Luikart
- Genome Transplant Genomics (GTD), Stanford University School of Medicine, Palo Alto, California, USA; Division of Cardiovascular Medicine, Stanford University School of Medicine, Palo Alto, California, USA; Department of Pathology, Stanford University School of Medicine, Palo Alto, California, USA
| | - Steven D Nathan
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland, USA; Inova Fairfax Hospital, Falls Church, Virginia, USA
| | - Kiran K Khush
- Genome Transplant Genomics (GTD), Stanford University School of Medicine, Palo Alto, California, USA; Division of Cardiovascular Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Moon Jang
- Laboratory of Applied Precision Omics (APO),National Heart,Lung and Blood Institute (NHLBI),National Institutes of Health,Bethesda,Maryland,USA; Laboratory of Transplantation Genomics, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, Bethesda, Maryland, USA; Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland, USA
| | - Sean Agbor-Enoh
- Laboratory of Applied Precision Omics (APO),National Heart,Lung and Blood Institute (NHLBI),National Institutes of Health,Bethesda,Maryland,USA; Laboratory of Transplantation Genomics, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, Bethesda, Maryland, USA; Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland, USA; Pulmonary and Critical Care Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA.
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16
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Mehta A, Goldberg J, Bagchi P, Marboe C, Shah K, Najjar S, Hsu S, Rodrigo M, Jang M, Cochrane A, Tchoukina I, Kong H, Lohmar B, Mcnair E, Valantine H, Agbor-Enoh S, Berry G, Shah P. Cell-Free DNA Enhances Pathologist Interrater Reliability at the Assessment of Acute Rejection on Endomyocardial Biopsy, on Behalf of the GRAfT Investigators. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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17
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Hamad Y, Charya A, Kong H, Jang M, Andargie T, Shah P, Mathew J, Orens J, Aryal S, Nathan S, Agbor-Enoh S. Anellovirus: A Novel Marker for Overimmunosuppression and Risk of Infection in Lung Transplant Recipients. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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18
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Goldberg J, deFilippi C, Lockhart C, McNair E, Sinha S, Kong H, Najjar S, Lohmar B, Tchoukina I, Shah K, Feller E, Hsu S, Rodrigo M, Jang M, Marboe C, Berry G, Valantine H, Agbor-Enoh S, Shah P. Dysregulated Circulating Proteins in Cellular and Antibody-Mediated Rejection, on Behalf of the Graft Investigators. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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19
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Keller M, Ross D, Bhorade S, Agbor-Enoh S. Study Design for a Randomized Control Trial of Lung Allograft Monitoring with Blood Donor-Derived Cell-Free DNA Assessments (LAMBDA 001). J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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20
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Charya AV, Ponor IL, Cochrane A, Levine D, Philogene M, Fu YP, Jang MK, Kong H, Shah P, Bon AM, Krishnan A, Mathew J, Luikart H, Khush KK, Berry G, Marboe C, Iacono A, Orens JB, Nathan SD, Agbor-Enoh S. Clinical features and allograft failure rates of pulmonary antibody-mediated rejection categories. J Heart Lung Transplant 2023; 42:226-235. [PMID: 36319530 DOI: 10.1016/j.healun.2022.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/18/2022] [Accepted: 09/09/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Pulmonary antibody-mediated rejection (AMR) consensus criteria categorize AMR by diagnostic certainty. This study aims to define the clinical features and associated outcomes of these recently defined AMR categories. METHODS Adjudication committees reviewed clinical data of 335 lung transplant recipients to define clinical or subclinical AMR based on the presence of allograft dysfunction, and the primary endpoints, time from transplant to allograft failure, a composite endpoint of chronic lung allograft dysfunction and/or death. Clinical AMR was subcategorized based on diagnostic certainty as definite, probable or possible AMR if 4, 3, or 2 characteristic features were present, respectively. Allograft injury was assessed via plasma donor-derived cell-free DNA (ddcfDNA). Risk of allograft failure and allograft injury was compared for AMR categories using regression models. RESULTS Over the 38.5 months follow-up, 28.7% of subjects developed clinical AMR (n = 96), 18.5% developed subclinical AMR (n = 62) or 58.3% were no AMR (n = 177). Clinical AMR showed higher risk of allograft failure and ddcfDNA levels compared to subclinical or no AMR. Clinical AMR included definite/probable (n = 21) or possible AMR (n = 75). These subcategories showed similar clinical characteristics, ddcfDNA levels, and risk of allograft failure. However, definite/probable AMR showed greater measures of AMR severity, including degree of allograft dysfunction and risk of death compared to possible AMR. CONCLUSIONS Clinical AMR showed greater risk of allograft failure than subclinical AMR or no AMR. Subcategorization of clinical AMR based on diagnostic certainty correlated with AMR severity and risk of death, but not with the risk of allograft failure.
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Affiliation(s)
- Ananth V Charya
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Division of Pulmonary and Critical Care, University of Maryland Medical Center, Baltimore, Maryland; Laboratory of Applied Precision Omics, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, Maryland
| | - Ileana L Ponor
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Laboratory of Applied Precision Omics, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, Maryland; Division of Hospital Medicine, Johns Hopkins Bayview Medical Center, Baltimore, Maryland
| | - Adam Cochrane
- Advanced Lung Disease and Lung Transplantation Program, Inova Fairfax Hospital, Fairfax, Virginia
| | - Deborah Levine
- Lung Transplantation Program, University of Texas, San Antonio, Texas
| | - Mary Philogene
- Histocompatibility and Molecular Genetics Laboratory, Philadelphia, Pennsylvania
| | - Yi-Ping Fu
- Biostatistics, Division of Intramural Research, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Moon K Jang
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Laboratory of Applied Precision Omics, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, Maryland
| | - Hyesik Kong
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Laboratory of Applied Precision Omics, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, Maryland
| | - Pali Shah
- Division of Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Ann Mary Bon
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Laboratory of Applied Precision Omics, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, Maryland
| | - Aravind Krishnan
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Joby Mathew
- Division of Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Helen Luikart
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California
| | - Kiran K Khush
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California
| | - Gerald Berry
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Charles Marboe
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Department of Pathology, New York Presbyterian University Hospital of Cornell and Columbia, New York, New York
| | - Aldo Iacono
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Division of Pulmonary and Critical Care, University of Maryland Medical Center, Baltimore, Maryland
| | - Jonathan B Orens
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Division of Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Steven D Nathan
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Advanced Lung Disease and Lung Transplantation Program, Inova Fairfax Hospital, Fairfax, Virginia.
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Laboratory of Applied Precision Omics, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, Maryland; Division of Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland.
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21
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Jang MK, Markowitz TE, Andargie TE, Apalara Z, Kuhn S, Agbor-Enoh S. Cell-free Chromatin Immunoprecipitation to detect molecular pathways in Physiological and Disease States. bioRxiv 2023:2023.01.24.525414. [PMID: 36789421 PMCID: PMC9928031 DOI: 10.1101/2023.01.24.525414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Patient monitoring is a cornerstone in clinical practice to define disease phenotypes and guide clinical management. Unfortunately, this is often reliant on invasive and/or less sensitive methods that do not provide deep phenotype assessments of disease state to guide treatment. This paper examined plasma cell-free DNA chromatin immunoprecipitation sequencing (cfChIP-seq) to define molecular gene sets in physiological and heart transplant patients taking immunosuppression medications. We show cfChIP-seq reliably detect gene signals that correlate with gene expression. In healthy controls and in heart transplant patients, cfChIP-seq reliably detected housekeeping genes. cfChIP-seq identified differential gene signals of the relevant immune and non-immune molecular pathways that were predominantly downregulated in immunosuppressed heart transplant patients compared to healthy controls. cfChIP-seq also identified tissue sources of cfDNA, detecting greater cell-free DNA from cardiac, hematopoietic, and other non-hematopoietic tissues such as the pulmonary, digestive, and neurological tissues in transplant patients than healthy controls. cfChIP-seq gene signals were reproducible between patient populations and blood collection methods. cfChIP-seq may therefore be a reliable approach to provide dynamic assessments of molecular pathways and tissue injury associated to disease.
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Affiliation(s)
- Moon K. Jang
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision. Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD
| | - Tovah E. Markowitz
- NIAID Collaborative Bioinformatics Resource, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Temesgen E. Andargie
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision. Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD
| | - Zainab Apalara
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision. Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD
| | - Skyler Kuhn
- NIAID Collaborative Bioinformatics Resource, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision. Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD
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22
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Bazemore K, Permpalung N, Mathew J, Lemma M, Haile B, Avery R, Kong H, Jang MK, Andargie T, Gopinath S, Nathan SD, Aryal S, Orens J, Valantine H, Agbor-Enoh S, Shah P. Elevated cell-free DNA in respiratory viral infection and associated lung allograft dysfunction. Am J Transplant 2022; 22:2560-2570. [PMID: 35729715 DOI: 10.1111/ajt.17125] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/15/2022] [Accepted: 06/15/2022] [Indexed: 01/25/2023]
Abstract
Respiratory viral infection (RVI) in lung transplant recipients (LTRs) is a risk for chronic lung allograft dysfunction (CLAD). We hypothesize that donor-derived cell-free DNA (%ddcfDNA), at the time of RVI predicts CLAD progression. We followed 39 LTRs with RVI enrolled in the Genomic Research Alliance for Transplantation for 1 year. Plasma %ddcfDNA was measured by shotgun sequencing, with high %ddcfDNA as ≥1% within 7 days of RVI. We examined %ddcfDNA, spirometry, and a composite (progression/failure) of CLAD stage progression, re-transplant, and death from respiratory failure. Fifty-nine RVI episodes, 38 low and 21 high %ddcfDNA were analyzed. High %ddcfDNA subjects had a greater median %FEV1 decline at RVI (-13.83 vs. -1.83, p = .007), day 90 (-7.97 vs. 0.91, p = .04), and 365 (-20.05 vs. 1.09, p = .047), compared to those with low %ddcfDNA and experienced greater progression/failure within 365 days (52.4% vs. 21.6%, p = .01). Elevated %ddcfDNA at RVI was associated with an increased risk of progression/failure adjusting for symptoms and days post-transplant (HR = 1.11, p = .04). No difference in %FEV1 decline was seen at any time point when RVIs were grouped by histopathology result at RVI. %ddcfDNA delineates LTRs with RVI who will recover lung function and who will experience sustained decline, a utility not seen with histopathology.
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Affiliation(s)
- Katrina Bazemore
- Division of Pulmonary and Critical Care, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nitipong Permpalung
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Division of Mycology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Joby Mathew
- Division of Pulmonary and Critical Care, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Merte Lemma
- Advanced Lung Disease and Transplant Program, Inova Heart and Vascular Institute, Inova Fairfax Hospital, Falls Church, Virginia
| | | | - Robin Avery
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hyesik Kong
- Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland.,Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland
| | - Moon Kyoo Jang
- Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland.,Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland
| | - Temesgen Andargie
- Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Shilpa Gopinath
- Division of Transplant Oncology Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Steven D Nathan
- Advanced Lung Disease and Transplant Program, Inova Heart and Vascular Institute, Inova Fairfax Hospital, Falls Church, Virginia.,Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland
| | - Shambhu Aryal
- Advanced Lung Disease and Transplant Program, Inova Heart and Vascular Institute, Inova Fairfax Hospital, Falls Church, Virginia
| | - Jonathan Orens
- Division of Pulmonary and Critical Care, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland
| | - Hannah Valantine
- Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland.,Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland
| | - Sean Agbor-Enoh
- Division of Pulmonary and Critical Care, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland.,Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland
| | - Pali Shah
- Division of Pulmonary and Critical Care, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland
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23
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Keller M, Charya A, Andargie T, Agbor-Enoh S. Laboratory Considerations for Successful Xenotransplantation in Humans. Clin Chem 2022; 68:1368-1373. [PMID: 36226752 DOI: 10.1093/clinchem/hvac150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/17/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Michael Keller
- Laboratory of Applied Precision Omics (APO) and Genomic Research Alliance for Transplantation (GRAfT), National Institute of Health, Bethesda, MD.,Department of Critical Care Medicine, National Institute of Health, Bethesda, MD.,Pulmonary and Critical Care Medicine, Johns Hopkins Hospital,, Baltimore, MD
| | - Ananth Charya
- Division of Pulmonary and Critical Care, University of Maryland Medical Center,, Baltimore, MD
| | - Temesgen Andargie
- Laboratory of Applied Precision Omics (APO) and Genomic Research Alliance for Transplantation (GRAfT), National Institute of Health, Bethesda, MD
| | - Sean Agbor-Enoh
- Laboratory of Applied Precision Omics (APO) and Genomic Research Alliance for Transplantation (GRAfT), National Institute of Health, Bethesda, MD.,Pulmonary and Critical Care Medicine, Johns Hopkins Hospital,, Baltimore, MD
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24
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Brusca SB, Elinoff JM, Zou Y, Jang MK, Kong H, Demirkale CY, Sun J, Seifuddin F, Pirooznia M, Valantine HA, Tanba C, Chaturvedi A, Graninger GM, Harper B, Chen LY, Cole J, Kanwar M, Benza RL, Preston IR, Agbor-Enoh S, Solomon MA. Plasma Cell-Free DNA Predicts Survival and Maps Specific Sources of Injury in Pulmonary Arterial Hypertension. Circulation 2022; 146:1033-1045. [PMID: 36004627 PMCID: PMC9529801 DOI: 10.1161/circulationaha.121.056719] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 07/15/2022] [Indexed: 01/24/2023]
Abstract
BACKGROUND Cell-free DNA (cfDNA) is a noninvasive marker of cellular injury. Its significance in pulmonary arterial hypertension (PAH) is unknown. METHODS Plasma cfDNA was measured in 2 PAH cohorts (A, n=48; B, n=161) and controls (n=48). Data were collected for REVEAL 2.0 (Registry to Evaluate Early and Long-Term PAH Disease Management) scores and outcome determinations. Patients were divided into the following REVEAL risk groups: low (≤6), medium (7-8), and high (≥9). Total cfDNA concentrations were compared among controls and PAH risk groups by 1-way analysis of variance. Log-rank tests compared survival between cfDNA tertiles and REVEAL risk groups. Areas under the receiver operating characteristic curve were estimated from logistic regression models. A sample subset from cohort B (n=96) and controls (n=16) underwent bisulfite sequencing followed by a deconvolution algorithm to map cell-specific cfDNA methylation patterns, with concentrations compared using t tests. RESULTS In cohort A, median (interquartile range) age was 62 years (47-71), with 75% female, and median (interquartile range) REVEAL 2.0 was 6 (4-9). In cohort B, median (interquartile range) age was 59 years (49-71), with 69% female, and median (interquartile range) REVEAL 2.0 was 7 (6-9). In both cohorts, cfDNA concentrations differed among patients with PAH of varying REVEAL risk and controls (analysis of variance P≤0.002) and were greater in the high-risk compared with the low-risk category (P≤0.002). In cohort B, death or lung transplant occurred in 14 of 54, 23 of 53, and 35 of 54 patients in the lowest, middle, and highest cfDNA tertiles, respectively. cfDNA levels stratified as tertiles (log-rank: P=0.0001) and REVEAL risk groups (log-rank: P<0.0001) each predicted transplant-free survival. The addition of cfDNA to REVEAL improved discrimination (area under the receiver operating characteristic curve, 0.72-0.78; P=0.02). Compared with controls, methylation analysis in patients with PAH revealed increased cfDNA originating from erythrocyte progenitors, neutrophils, monocytes, adipocytes, natural killer cells, vascular endothelium, and cardiac myocytes (Bonferroni adjusted P<0.05). cfDNA concentrations derived from erythrocyte progenitor cells, cardiac myocytes, and vascular endothelium were greater in patients with PAH with high-risk versus low-risk REVEAL scores (P≤0.02). CONCLUSIONS Circulating cfDNA is elevated in patients with PAH, correlates with disease severity, and predicts worse survival. Results from cfDNA methylation analyses in patients with PAH are consistent with prevailing paradigms of disease pathogenesis.
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Affiliation(s)
- Samuel B Brusca
- Pulmonary Arterial Hypertension Section of the Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD
- Department of Internal Medicine, Division of Cardiology, University of California, San Francisco, CA
| | - Jason M Elinoff
- Pulmonary Arterial Hypertension Section of the Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD
| | - Yvette Zou
- Pulmonary Arterial Hypertension Section of the Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD
| | - Moon Kyoo Jang
- Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD
| | - Hyesik Kong
- Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD
| | - Cumhur Y Demirkale
- Pulmonary Arterial Hypertension Section of the Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD
| | - Junfeng Sun
- Pulmonary Arterial Hypertension Section of the Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD
| | - Fayaz Seifuddin
- Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD
| | - Mehdi Pirooznia
- Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD
| | - Hannah A Valantine
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD
- Department of Internal Medicine, Stanford University School of Medicine, Palo Alto, CA
| | - Carl Tanba
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Tufts Medical Center, Boston, MA
| | - Abhishek Chaturvedi
- Pauley Heart Center, Virginia Commonwealth University School of Medicine, Richmond, VA
| | - Grace M Graninger
- Pulmonary Arterial Hypertension Section of the Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD
| | - Bonnie Harper
- Pulmonary Arterial Hypertension Section of the Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD
| | - Li-Yuan Chen
- Pulmonary Arterial Hypertension Section of the Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD
| | - Justine Cole
- Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD
| | - Manreet Kanwar
- Cardiovascular Institute at Allegheny Health Network, Pittsburgh, PA
| | - Raymond L Benza
- Departent of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Ioana R Preston
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Tufts Medical Center, Boston, MA
| | - Sean Agbor-Enoh
- Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Michael A Solomon
- Pulmonary Arterial Hypertension Section of the Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD
- Cardiology Branch, National Heart, Lung, and Blood Institute of the National Institutes of Health, Bethesda, MD
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Shah P, Agbor-Enoh S, Bagchi P, deFilippi CR, Mercado A, Diao G, Morales DJ, Shah KB, Najjar SS, Feller E, Hsu S, Rodrigo ME, Lewsey SC, Jang MK, Marboe C, Berry GJ, Khush KK, Valantine HA. Circulating microRNAs in cellular and antibody-mediated heart transplant rejection. J Heart Lung Transplant 2022; 41:1401-1413. [PMID: 35872109 PMCID: PMC9529890 DOI: 10.1016/j.healun.2022.06.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Noninvasive monitoring of heart allograft health is important to improve clinical outcomes. MicroRNAs (miRs) are promising biomarkers of cardiovascular disease and limited studies suggest they can be used to noninvasively diagnose acute heart transplant rejection. METHODS The Genomic Research Alliance for Transplantation (GRAfT) is a multicenter prospective cohort study that phenotyped heart transplant patients from 5 mid-Atlantic centers. Patients who had no history of rejection after transplant were compared to patients with acute cellular rejection (ACR) or antibody-mediated rejection (AMR). Small RNA sequencing was performed on plasma samples collected at the time of an endomyocardial biopsy. Differential miR expression was performed with adjustment for clinical covariates. Regression was used to develop miR panels with high diagnostic accuracy for ACR and AMR. These panels were then validated in independent samples from GRAfT and Stanford University. Receiver operating characteristic curves were generated and area under the curve (AUC) statistics calculated. Distinct ACR and AMR clinical scores were developed to translate miR expression data for clinical use. RESULTS The GRAfT cohort had a median age of 52 years, with 35% females and 45% Black patients. Between GRAfT and Stanford, we included 157 heart transplant patients: 108 controls and 49 with rejection (50 ACR and 38 AMR episodes). After differential miR expression and regression analysis, we identified 12 miRs that accurately discriminate ACR and 17 miRs in AMR. Independent validation of the miR panels within GRAfT led to an ACR AUC 0.92 (95% confidence interval [CI]: 0.86-0.98) and AMR AUC 0.82 (95% CI: 0.74-0.90). The externally validated ACR AUC was 0.72 (95% CI: 0.59-0.82). We developed distinct ACR and AMR miR clinical scores (range 0-100), a score ≥ 65, identified ACR with 86% sensitivity, 76% specificity, and 98% negative predictive value, for AMR score performance was 82%, 84% and 97%, respectively. CONCLUSIONS We identified novel miRs that had excellent performance to noninvasively diagnose acute rejection after heart transplantation. Once rigorously validated, the unique clinical ACR and AMR scores usher in an era whereby genomic biomarkers can be used to screen and diagnose the subtype of rejection. These novel biomarkers may potentially alleviate the need for an endomyocardial biopsy while facilitating the initiation of targeted therapy based on the noninvasive diagnosis of ACR or AMR.
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Affiliation(s)
- Palak Shah
- Heart Failure, Mechanical Circulatory Support & Transplant, Inova Heart and Vascular Institute, Falls Church, Virginia; Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland.
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland; Applied Precision Genomics, National Heart, Lung and Blood Institute, Bethesda, Maryland
| | - Pramita Bagchi
- Volgenau School of Engineering, George Mason University, Fairfax, Virginia
| | | | - Angela Mercado
- Heart Failure, Mechanical Circulatory Support & Transplant, Inova Heart and Vascular Institute, Falls Church, Virginia
| | - Gouqing Diao
- Milken Institute School of Public Health, The George Washington University, Washington, District of Columbia
| | - Dave Jp Morales
- Heart Failure & Transplantation, Stanford University, Palo Alto, California
| | - Keyur B Shah
- The Pauley Heart Center, Virginia Commonwealth University, Richmond, Virginia
| | - Samer S Najjar
- Advanced Heart Failure Program, Medstar Heart and Vascular Institute, Washington Hospital Center, Washington, District of Columbia
| | - Erika Feller
- Heart Failure & Transplantation, University of Maryland, Baltimore, Maryland
| | - Steven Hsu
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Maria E Rodrigo
- The Pauley Heart Center, Virginia Commonwealth University, Richmond, Virginia
| | - Sabra C Lewsey
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Moon Kyoo Jang
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Applied Precision Genomics, National Heart, Lung and Blood Institute, Bethesda, Maryland
| | - Charles Marboe
- Department of Pathology, New York Presbyterian University Hospital of Cornell and Columbia, New York, New York, New York
| | - Gerald J Berry
- Stanford University School of Medicine, Palo Alto, California
| | - Kiran K Khush
- Stanford University School of Medicine, Palo Alto, California
| | - Hannah A Valantine
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Stanford University School of Medicine, Palo Alto, California
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Bon A, Gerhard E, Mathew J, Kong H, Jang M, Henry L, Lee B, Hsu S, Shah K, Tchoukina I, Sterling S, Rodrigo M, Najjar S, Marboe C, Berry G, Valantine H, Shah P, Agbor-Enoh S. Cell-Free DNA to Distinguish High Risk Donor Specific Antibodies in Heart Transplantation. J Heart Lung Transplant 2022. [DOI: 10.1016/j.healun.2022.01.1209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Shah P, Agbor-Enoh S, Bagchi P, deFilippi C, Mercado A, Diao G, Morales D, Shah K, Najjar S, Feller E, Hsu S, Rodrigo M, Lewsey S, Jang M, Marboe C, Berry G, Khush K, Valantine H. Circulating microRNA Biomarkers in Cellular and Antibody-Mediated Heart Transplant Rejection. J Heart Lung Transplant 2022. [DOI: 10.1016/j.healun.2022.01.216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Agbor-Enoh S, Jang M, Kong H, Andargie T, Shah P, Nathan S. Is Acute Rejection Truly Acute or an Exacerbation of an Underlying Disease? J Heart Lung Transplant 2022. [DOI: 10.1016/j.healun.2022.01.098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Pang Y, Charya A, Keller M, Sirajuddin A, Fu Y, Holtzman N, Pavletic S, Agbor-Enoh S. The ISHLT CLAD Consensus is Broadly Applicable in Stem Cell Transplant. J Heart Lung Transplant 2022. [DOI: 10.1016/j.healun.2022.01.768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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30
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Pang Y, Charya A, Keller M, Sirajuddin A, Holtzman N, Pavletic S, Agbor-Enoh S. Pleuroparenchymal Fibroelastosis in Chronic Graft-versus-Host-Disease. J Heart Lung Transplant 2022. [DOI: 10.1016/j.healun.2022.01.775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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31
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Meda R, Fu S, Yu K, Charya A, Kong H, Jang M, Andargie T, Park W, Lee J, Tunc I, Berry G, Marboe C, Shah P, Nathan S, Keller M, Agbor-Enoh S. Comparative Performance Analysis of Donor-Derived Cell-Free DNA to Detect Acute Rejection in Single and Double Lung Transplant Recipients. J Heart Lung Transplant 2022. [DOI: 10.1016/j.healun.2022.01.764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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32
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Charya A, Ponor I, Jang M, Kong H, Shah P, Mathew J, Luikart H, Khush K, Berry G, Orens J, Marboe C, Nathan S, Agbor-Enoh S. Restrictive Allograft Syndrome Patients Have Higher Cell-Free DNA Assessed Allograft Injury Prior to Diagnosis. J Heart Lung Transplant 2022. [DOI: 10.1016/j.healun.2022.01.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Jang M, Singh K, Andargie T, Seifuddin F, Tunc I, Park W, Lee J, Kong H, Agbor-Enoh S. Genome-Wide DNA Methylation Analysis to Define Pulmonary Antibody-Mediated Rejection (AMR) Treatment Response. J Heart Lung Transplant 2022. [DOI: 10.1016/j.healun.2022.01.088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Abstract
PURPOSE OF REVIEW Endomyocardial biopsy (EMB), the current gold standard for cardiac allograft monitoring is invasive, may have a low sensitivity and is associated with significant variability in histopathologic interpretation. Fortunately, on-going research is identifying noninvasive biomarkers that address some of these limitations. This review provides an update on noninvasive blood-based methods for rejection surveillance and diagnosis in heart transplantation. RECENT FINDINGS Recent studies highlight good test performance to detect acute rejection for donor-derived cell-free DNA (dd-cfDNA) and microRNAs (miR). dd-cfDNA is sensitive, nonspecific, and has a high negative predictive value for acute cellular and antibody-mediated rejection. Clinical utility trials are being planned to test its role as a rule-out test for acute rejection as compared to the EMB. miRs may have an added advantage as it may phenotype the subtypes of rejection alleviating the need for an EMB or permitting the initiation of targeted therapy while awaiting the results of the EMB. SUMMARY In this review, we discuss recent advances in the field of noninvasive biomarkers to detect allograft rejection after heart transplant. We provide a perspective of additional studies needed to prove their clinical utility and bring these biomarkers to widescale clinical use.
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Affiliation(s)
- Xiaoxiao Qian
- Cardiovascular Medicine, Inova Heart and Vascular Institute, Falls Church VA
| | - Palak Shah
- Heart Failure, MCS and Transplant, Inova Heart and Vascular Institute, Falls Church VA
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD
- Laboratory of Applied Precision Omics, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD
- Pulmonary and Critical Care Medicine, Johns Hopkins School of Medicine, Baltimore, MD
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Andargie TE, Zhou W, Karaba AH, Li T, Seifuddin F, Rittenhouse AG, Kong H, Singh K, Woodward R, Iacono A, Avery RK, Pirooznia M, Jang MK, Ji H, Cox AL, Agbor-Enoh S. Integrated cell-free DNA and cytokine analysis uncovers distinct tissue injury and immune response patterns in solid organ transplant recipients with COVID-19. Res Sq 2022:rs.3.rs-1262270. [PMID: 35075453 PMCID: PMC8786231 DOI: 10.21203/rs.3.rs-1262270/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
COVID-19 pathogenesis is associated with an exuberant inflammatory response. However, the tissue injury pattern and immune response in solid-organ transplant recipients (SOTRs) taking immunosuppressive therapy have not been well characterized. Here, we perform both cfDNA and cytokine profiling on plasma samples to map tissue damage, including allograft injury and delineate underlying immunopathology. We identified injuries from multiple-tissue types, including hematopoietic cells, vascular endothelium, hepatocyte, adipocyte, pancreas, kidney, heart, and lung in SOTRs with COVID-19 that correlates with disease severity. SOTRs with COVID-19 have higher plasma levels of cytokines such as IFN-λ1, IFN-γ, IL-15, IL-18 IL-1RA, IL-6, MCP-2, and TNF-α as compared to healthy controls, and the levels of GM-CSF, IL-15, IL-6, IL-8, and IL-10 were associated with disease severity in SOTRs. Strikingly, IFN-λ and IP-10 were markedly increased in SOTRs compared to immunocompetent patients with COVID-19. Correlation analyses showed a strong association between monocyte-derived cfDNA and inflammatory cytokines/chemokines in SOTRs with COVID-19. Moreover, compared to other respiratory viral infections, COVID-19 induced pronounced injury in hematopoietic, vascular endothelial and endocrine tissues. Allograft injury, measured as donor-derived cfDNA was elevated in SOTRs with COVID-19, including allografts distant from the primary site of infection. Allograft injury correlated with inflammatory cytokines and cfDNA from immune cells. Furthermore, longitudinal analysis identified a gradual decrease of cfDNA and inflammatory cytokine levels in patients with a favorable outcome. Our findings highlight distinct tissue injury and cytokine features in SOTRs with COVID-19 that correlate with disease severity.
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Affiliation(s)
- Temesgen E. Andargie
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD
- Department of Biology, Howard University, Washington DC
| | - Weiqiang Zhou
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
| | - Andrew H. Karaba
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD
| | - Taibo Li
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
| | | | - Alex G. Rittenhouse
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
| | - Hyesik Kong
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD
| | | | | | - Aldo Iacono
- Department of Medicine, University of Maryland, College Park, MD
| | - Robin K Avery
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD
| | | | - Moon Kyoo Jang
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD
| | - Hongkai Ji
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
| | - Andrea L. Cox
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD
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Keller M, Mutebi C, Shah P, Levine D, Aryal S, Iacono A, Timofte I, Mathew J, Varghese A, Giner C, Agbor-Enoh S. Biological Variation of Donor-Derived Cell-Free DNA in Stable Lung Transplant Recipients. J Appl Lab Med 2022; 7:901-909. [PMID: 35024828 DOI: 10.1093/jalm/jfab171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Prior studies demonstrate that donor-derived cell-free DNA (dd-cfDNA) in lung transplant recipients may serve as a marker of allograft injury for detecting allograft rejection and infection. Clinical interpretation of dd-cfDNA requires understanding its biological variation in stable lung transplant patients in order to identify abnormal results suggesting underlying allograft dysfunction. This study establishes the biological variation and reference change values (RCV) of dd-cfDNA in stable lung transplant recipients using an analytically validated assay with an established analytic coefficient of variation (CVA). METHODS The AlloSure® assay, a targeted, sequencing-based approach, was used to measure plasma dd-cfDNA in a cohort of lung transplant patients at 4 centers that used dd-cfDNA to monitor for allograft dysfunction in preference to surveillance transbronchial biopsy. Patients with stable allograft function and ≥3 dd-cfDNA samples were included. Intraindividual coefficient of variation (CVI), interindividual CV (CVG), index of individuality (II) and the RCV were calculated. RESULTS Thirty-five patients with a combined 124 dd-cfDNA samples were included in the final analysis. The median dd-cfDNA was 0.31% (interquartile range 0.18%-0.68%), the 97.5th percentile and 95th percentile were 1.3% and 1.0%, respectively. In 30 stable patients with an average of 3.7 tests, the CVI was 25%, CVG 19%, II 1.33, and RCV 70%. CONCLUSION In stable lung transplant patients, fluctuations in dd-cfDNA levels of up to 70% or levels less than 1% are within normal biological variation. With further validation, these thresholds may be incorporated into surveillance monitoring algorithms to identify potentially abnormal results indicating allograft dysfunction.
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Affiliation(s)
- Michael Keller
- Laboratory of Applied Precision Omics (APO) and Genomic Research Alliance for Transplantation (GRAfT), National Institutes of Health, Bethesda, MD, USA.,Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA.,Pulmonary and Critical Care Medicine, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Cedric Mutebi
- Laboratory of Applied Precision Omics (APO) and Genomic Research Alliance for Transplantation (GRAfT), National Institutes of Health, Bethesda, MD, USA
| | - Pali Shah
- Pulmonary and Critical Care Medicine, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Deborah Levine
- Pulmonary and Critical Care Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Shambhu Aryal
- Advanced Lung Disease and Lung Transplant Program, Inova Fairfax Hospital, Falls Church, VA, USA
| | - Aldo Iacono
- Division of Pulmonary and Critical Care Medicine, University of Maryland Medical Center, Baltimore, MD, USA
| | - Irina Timofte
- Division of Pulmonary and Critical Care Medicine, University of Maryland Medical Center, Baltimore, MD, USA
| | - Joby Mathew
- Pulmonary and Critical Care Medicine, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Anu Varghese
- Division of Pulmonary and Critical Care Medicine, University of Maryland Medical Center, Baltimore, MD, USA
| | - Cassandra Giner
- Pulmonary and Critical Care Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Sean Agbor-Enoh
- Laboratory of Applied Precision Omics (APO) and Genomic Research Alliance for Transplantation (GRAfT), National Institutes of Health, Bethesda, MD, USA
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Keller M, Sun J, Mutebi C, Shah P, Levine D, Aryal S, Iacono A, Timofte I, Mathew J, Varghese A, Giner C, Agbor-Enoh S. Donor-derived cell-free DNA as a composite marker of acute lung allograft dysfunction in clinical care. J Heart Lung Transplant 2021; 41:458-466. [DOI: 10.1016/j.healun.2021.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/07/2021] [Accepted: 12/21/2021] [Indexed: 11/28/2022] Open
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Agbor-Enoh S, Oellerich M, Wu A, Halloran PF, De Vlaminck I, Keller M. Molecular Approaches to Transplant Monitoring; Is the Horizon Here? Clin Chem 2021; 67:1443-1449. [PMID: 34632495 DOI: 10.1093/clinchem/hvab183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 08/27/2021] [Indexed: 11/13/2022]
Affiliation(s)
- Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT), National Heart, Lung, and Blood Institute Division of Intramural Research, Bethesda, MD.,Lung Transplantation Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD
| | - Michael Oellerich
- Department of Clinical Pharmacology, George-August-University, University Medical Center Göttingen (UMG), Göttingen, Germany
| | - Angela Wu
- Department of Chemical and Biological Engineering and Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
| | | | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY
| | - Michael Keller
- Genomic Research Alliance for Transplantation (GRAfT), National Heart, Lung, and Blood Institute Division of Intramural Research, Bethesda, MD.,Lung Transplantation Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD.,Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD
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Shah P, Agbor-Enoh S, Tunc I, Hsu S, Russell S, Feller E, Shah K, Rodrigo ME, Najjar SS, Kong H, Pirooznia M, Fideli U, Bikineyeva A, Marishta A, Bhatti K, Yang Y, Mutebi C, Yu K, Kyoo Jang M, Marboe C, Berry GJ, Valantine HA. Response by Shah et al to Letter Regarding Article, "Cell-Free DNA to Detect Heart Allograft Acute Rejection". Circulation 2021; 144:e198-e199. [PMID: 34491771 DOI: 10.1161/circulationaha.121.055697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Palak Shah
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD (P.S., S.A-E., I.T., S.H., E.F., K.S., M.E.R., S.S.N., H.K., U.F., A.B., A.M., K.B., Y.Y., M.K.J., C.Marboe, G.J.B., H.A.V.).,Department of Heart Failure and Transplantation, Inova Heart and Vascular Institute, Falls Church, VA (P.S.)
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD (P.S., S.A-E., I.T., S.H., E.F., K.S., M.E.R., S.S.N., H.K., U.F., A.B., A.M., K.B., Y.Y., M.K.J., C.Marboe, G.J.B., H.A.V.).,Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD (S.A-E., I.T., S.H., H.K., M.P., U.F., A.B., A.M., K.B., Y.Y., C.Mutebi, M.K.J., H.A.V.).,Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, MD (S.A-E.)
| | - Ilker Tunc
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD (P.S., S.A-E., I.T., S.H., E.F., K.S., M.E.R., S.S.N., H.K., U.F., A.B., A.M., K.B., Y.Y., M.K.J., C.Marboe, G.J.B., H.A.V.).,Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD (S.A-E., I.T., S.H., H.K., M.P., U.F., A.B., A.M., K.B., Y.Y., C.Mutebi, M.K.J., H.A.V.)
| | - Steven Hsu
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD (P.S., S.A-E., I.T., S.H., E.F., K.S., M.E.R., S.S.N., H.K., U.F., A.B., A.M., K.B., Y.Y., M.K.J., C.Marboe, G.J.B., H.A.V.).,Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD (S.A-E., I.T., S.H., H.K., M.P., U.F., A.B., A.M., K.B., Y.Y., C.Mutebi, M.K.J., H.A.V.)
| | - Stuart Russell
- Department of Medicine, Duke University School of Medicine, Durham, NC (S.R.)
| | - Erika Feller
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD (P.S., S.A-E., I.T., S.H., E.F., K.S., M.E.R., S.S.N., H.K., U.F., A.B., A.M., K.B., Y.Y., M.K.J., C.Marboe, G.J.B., H.A.V.).,University of Maryland Medical Center, Baltimore, MD (E.F.)
| | - Keyur Shah
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD (P.S., S.A-E., I.T., S.H., E.F., K.S., M.E.R., S.S.N., H.K., U.F., A.B., A.M., K.B., Y.Y., M.K.J., C.Marboe, G.J.B., H.A.V.).,Virginia Commonwealth University, Richmond, VA (K.S.)
| | - Maria E Rodrigo
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD (P.S., S.A-E., I.T., S.H., E.F., K.S., M.E.R., S.S.N., H.K., U.F., A.B., A.M., K.B., Y.Y., M.K.J., C.Marboe, G.J.B., H.A.V.).,MedStar Heart and Vascular Institute, MedStar Washington Hospital Center, Washington DC (M.E.R., S.S.N.)
| | - Samer S Najjar
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD (P.S., S.A-E., I.T., S.H., E.F., K.S., M.E.R., S.S.N., H.K., U.F., A.B., A.M., K.B., Y.Y., M.K.J., C.Marboe, G.J.B., H.A.V.).,MedStar Heart and Vascular Institute, MedStar Washington Hospital Center, Washington DC (M.E.R., S.S.N.)
| | - Hyesik Kong
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD (P.S., S.A-E., I.T., S.H., E.F., K.S., M.E.R., S.S.N., H.K., U.F., A.B., A.M., K.B., Y.Y., M.K.J., C.Marboe, G.J.B., H.A.V.).,Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD (S.A-E., I.T., S.H., H.K., M.P., U.F., A.B., A.M., K.B., Y.Y., C.Mutebi, M.K.J., H.A.V.)
| | - Mehdi Pirooznia
- Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD (S.A-E., I.T., S.H., H.K., M.P., U.F., A.B., A.M., K.B., Y.Y., C.Mutebi, M.K.J., H.A.V.)
| | - Ulgen Fideli
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD (P.S., S.A-E., I.T., S.H., E.F., K.S., M.E.R., S.S.N., H.K., U.F., A.B., A.M., K.B., Y.Y., M.K.J., C.Marboe, G.J.B., H.A.V.).,Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD (S.A-E., I.T., S.H., H.K., M.P., U.F., A.B., A.M., K.B., Y.Y., C.Mutebi, M.K.J., H.A.V.)
| | - Alfiya Bikineyeva
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD (P.S., S.A-E., I.T., S.H., E.F., K.S., M.E.R., S.S.N., H.K., U.F., A.B., A.M., K.B., Y.Y., M.K.J., C.Marboe, G.J.B., H.A.V.).,Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD (S.A-E., I.T., S.H., H.K., M.P., U.F., A.B., A.M., K.B., Y.Y., C.Mutebi, M.K.J., H.A.V.)
| | - Argit Marishta
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD (P.S., S.A-E., I.T., S.H., E.F., K.S., M.E.R., S.S.N., H.K., U.F., A.B., A.M., K.B., Y.Y., M.K.J., C.Marboe, G.J.B., H.A.V.).,Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD (S.A-E., I.T., S.H., H.K., M.P., U.F., A.B., A.M., K.B., Y.Y., C.Mutebi, M.K.J., H.A.V.)
| | - Kenneth Bhatti
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD (P.S., S.A-E., I.T., S.H., E.F., K.S., M.E.R., S.S.N., H.K., U.F., A.B., A.M., K.B., Y.Y., M.K.J., C.Marboe, G.J.B., H.A.V.).,Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD (S.A-E., I.T., S.H., H.K., M.P., U.F., A.B., A.M., K.B., Y.Y., C.Mutebi, M.K.J., H.A.V.)
| | - Yanqin Yang
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD (P.S., S.A-E., I.T., S.H., E.F., K.S., M.E.R., S.S.N., H.K., U.F., A.B., A.M., K.B., Y.Y., M.K.J., C.Marboe, G.J.B., H.A.V.).,Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD (S.A-E., I.T., S.H., H.K., M.P., U.F., A.B., A.M., K.B., Y.Y., C.Mutebi, M.K.J., H.A.V.)
| | - Cedric Mutebi
- Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD (S.A-E., I.T., S.H., H.K., M.P., U.F., A.B., A.M., K.B., Y.Y., C.Mutebi, M.K.J., H.A.V.).,Wayne State University School of Medicine, Detroit MI (C.Mutebi)
| | - Kai Yu
- National Cancer Institute, Rockville, MD (K.Y.)
| | - Moon Kyoo Jang
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD (P.S., S.A-E., I.T., S.H., E.F., K.S., M.E.R., S.S.N., H.K., U.F., A.B., A.M., K.B., Y.Y., M.K.J., C.Marboe, G.J.B., H.A.V.).,Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD (S.A-E., I.T., S.H., H.K., M.P., U.F., A.B., A.M., K.B., Y.Y., C.Mutebi, M.K.J., H.A.V.)
| | - Charles Marboe
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD (P.S., S.A-E., I.T., S.H., E.F., K.S., M.E.R., S.S.N., H.K., U.F., A.B., A.M., K.B., Y.Y., M.K.J., C.Marboe, G.J.B., H.A.V.).,Department of Pathology, New York Presbyterian University Hospital of Cornell and Columbia, New York (C.Marboe)
| | - Gerald J Berry
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD (P.S., S.A-E., I.T., S.H., E.F., K.S., M.E.R., S.S.N., H.K., U.F., A.B., A.M., K.B., Y.Y., M.K.J., C.Marboe, G.J.B., H.A.V.).,Stanford University School of Medicine, Palo Alto, CA (G.J.B., H.A.V.)
| | - Hannah A Valantine
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD (P.S., S.A-E., I.T., S.H., E.F., K.S., M.E.R., S.S.N., H.K., U.F., A.B., A.M., K.B., Y.Y., M.K.J., C.Marboe, G.J.B., H.A.V.).,Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD (S.A-E., I.T., S.H., H.K., M.P., U.F., A.B., A.M., K.B., Y.Y., C.Mutebi, M.K.J., H.A.V.).,Stanford University School of Medicine, Palo Alto, CA (G.J.B., H.A.V.)
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Ballout RA, Kong H, Sampson M, Otvos JD, Cox AL, Agbor-Enoh S, Remaley AT. The NIH Lipo-COVID Study: A Pilot NMR Investigation of Lipoprotein Subfractions and Other Metabolites in Patients with Severe COVID-19. Biomedicines 2021; 9:1090. [PMID: 34572275 PMCID: PMC8471250 DOI: 10.3390/biomedicines9091090] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/11/2021] [Accepted: 08/23/2021] [Indexed: 12/15/2022] Open
Abstract
A complex interplay exists between plasma lipoproteins and inflammation, as evidenced from studies on atherosclerosis. Alterations in plasma lipoprotein levels in the context of infectious diseases, particularly respiratory viral infections, such as SARS-CoV-2, have become of great interest in recent years, due to their potential utility as prognostic markers. Patients with severe COVID-19 have been reported to have low levels of total cholesterol, HDL-cholesterol, and LDL-cholesterol, but elevated levels of triglycerides. However, a detailed characterization of the particle counts and sizes of the different plasma lipoproteins in patients with COVID-19 has yet to be reported. In this pilot study, NMR spectroscopy was used to characterize lipoprotein particle numbers and sizes, and various metabolites, in 32 patients with severe COVID-19 admitted to the intensive care unit. Our study revealed markedly reduced HDL particle (HDL-P) numbers at presentation, especially low numbers of small HDL-P (S-HDL-P), and high counts of triglyceride-rich lipoprotein particle (TRL-P), particularly the very small and small TRL subfractions. Moreover, patients with severe COVID-19 were found to have remarkably elevated GlycA levels, and elevated levels of branched-chain amino acids and beta-hydroxybutyrate. Finally, we detected elevated levels of lipoproteins X and Z in most participants, which are distinct markers of hepatic dysfunction, and that was a novel finding.
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Affiliation(s)
- Rami A. Ballout
- Lipoprotein Metabolism Section, Translational Vascular Medicine Branch, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892, USA;
| | - Hyesik Kong
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892, USA;
| | - Maureen Sampson
- Clinical Center, Department of Laboratory Medicine, National Institutes of Health (NIH), Bethesda, MD 20892, USA;
| | - James D. Otvos
- Laboratory Corporation of America Holdings (LabCorp), Morrisville, NC 27560, USA;
| | - Andrea L. Cox
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA;
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892, USA;
| | - Alan T. Remaley
- Lipoprotein Metabolism Section, Translational Vascular Medicine Branch, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892, USA;
- Clinical Center, Department of Laboratory Medicine, National Institutes of Health (NIH), Bethesda, MD 20892, USA;
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Shah P, Valantine HA, Agbor-Enoh S. Transcriptomics in transplantation: More than just biomarkers of allograft rejection. Am J Transplant 2021; 21:2000-2001. [PMID: 33278854 PMCID: PMC8178244 DOI: 10.1111/ajt.16429] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 11/17/2020] [Accepted: 11/27/2020] [Indexed: 01/25/2023]
Affiliation(s)
- Palak Shah
- Heart Failure & Transplantation, Inova Heart and Vascular Institute, Falls Church, VA
| | - Hannah A. Valantine
- Laboratory of Organ Transplant Genomics, National Heart, Lung and Blood Institute, Bethesda, MD,Division of Cardiovascular Medicine, Stanford University, Stanford, CA
| | - Sean Agbor-Enoh
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD,Applied Precision Genomics, National Heart, Lung and Blood Institute, Bethesda, MD
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Bazemore K, Rohly M, Permpalung N, Yu K, Timofte I, Brown AW, Orens J, Iacono A, Nathan SD, Avery RK, Valantine H, Agbor-Enoh S, Shah PD. Donor derived cell free DNA% is elevated with pathogens that are risk factors for acute and chronic lung allograft injury. J Heart Lung Transplant 2021; 40:1454-1462. [PMID: 34344623 DOI: 10.1016/j.healun.2021.05.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Acute and chronic forms of lung allograft injury are associated with specific respiratory pathogens. Donor-derived cell free DNA (ddcfDNA) has been shown to be elevated with acute lung allograft injury and predictive of long-term outcomes. We examined the %ddcfDNA values at times of microbial isolation from bronchoalveolar lavage (BAL). METHODS Two hundred and six BAL samples from 51 Lung Transplant Recipients (LTRs) with concurrently available plasma %ddcfDNA were analyzed along with microbiology and histopathology. Microbial species were grouped into bacterial, fungal, and viral and "higher risk" and "lower risk" cohorts based on historical association with downstream allograft dysfunction. Analyses were performed to determine pathogen category association with %ddcfDNA, independent of inter-subject variability. RESULTS Presence of microbial isolates in BAL was not associated with elevated %ddcfDNA compared to samples without isolates. However, "higher risk" bacterial and viral microbes showed greater %ddcfDNA values than lower risk species (1.19% vs. 0.65%, p < 0.01), independent of inter-subject variability. Histopathologic abnormalities concurrent with pathogen isolation were associated with higher %ddcfDNA compared to isolation episodes with normal histopathology (medians 1.23% and 0.66%, p = 0.05). Assessments showed no evidence of correlation between histopathology or bronchoscopy indication and presence of higher risk vs. lower risk pathogens. CONCLUSION %ddcfDNA is higher among cases of microbial isolation with concurrent abnormal histopathology and with isolation of higher risk pathogens known to increase risk of allograft dysfunction. Future studies should assess if %ddcfDNA can be used to stratify pathogens for risk of CLAD and identify pathogen associated injury prior to histopathology.
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Affiliation(s)
- Katrina Bazemore
- Division of Pulmonary and Critical Care, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore
| | | | - Nitipong Permpalung
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore
| | - Kai Yu
- National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Irina Timofte
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Department of Medicine, University of Maryland, College Park, Maryland
| | - A Whitney Brown
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Advanced Lung Disease and Transplant Program, Inova Heart and Vascular Institute, Inova Fairfax Hospital, Falls Church, Virginia
| | - Jonathan Orens
- Division of Pulmonary and Critical Care, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore; Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland
| | - Aldo Iacono
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Department of Medicine, University of Maryland, College Park, Maryland
| | - Steven D Nathan
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; Department of Medicine, University of Maryland, College Park, Maryland
| | - Robin K Avery
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore
| | - Hannah Valantine
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland; National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland.
| | - Pali D Shah
- Division of Pulmonary and Critical Care, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore; Genomic Research Alliance for Transplantation (GRAfT), Bethesda, Maryland.
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Jang MK, Tunc I, Berry GJ, Marboe C, Kong H, Keller MB, Shah PD, Timofte I, Brown AW, Ponor IL, Mutebi C, Philogene MC, Yu K, Iacono A, Orens JB, Nathan SD, Agbor-Enoh S. Donor-derived cell-free DNA accurately detects acute rejection in lung transplant patients, a multicenter cohort study. J Heart Lung Transplant 2021; 40:822-830. [PMID: 34130911 DOI: 10.1016/j.healun.2021.04.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Acute rejection, which includes antibody-mediated rejection and acute cellular rejection, is a risk factor for lung allograft loss. Lung transplant patients often undergo surveillance transbronchial biopsies to detect and treat acute rejection before irreversible chronic rejection develops. Limitations of this approach include its invasiveness and high interobserver variability. We tested the performance of percent donor-derived cell-free DNA (%ddcfDNA), a non-invasive blood test, to detect acute rejection. METHODS This multicenter cohort study monitored 148 lung transplant subjects over a median of 19.6 months. We collected serial plasma samples contemporaneously with TBBx to measure %ddcfDNA. Clinical data was collected to adjudicate for acute rejection. The primary analysis consisted of computing the area-under-the-receiver-operating-characteristic-curve of %ddcfDNA to detect acute rejection. Secondary analysis determined %ddcfDNA rule-out thresholds for acute rejection. RESULTS ddcfDNA levels were high after transplant surgery and decayed logarithmically. With acute rejection, ddcfDNA levels rose six-fold higher than controls. ddcfDNA levels also correlated with severity of lung function decline and histological grading of rejection. %ddcfDNA area-under-the-receiver-operating-characteristic-curve for acute rejection, AMR, and ACR were 0.89, 0.93, and 0.83, respectively. ddcfDNA levels of <0.5% and <1.0% showed a negative predictive value of 96% and 90% for acute rejection, respectively. Histopathology detected one-third of episodes with ddcfDNA levels ≥1.0%, even though >90% of these events were coincident to clinical complications missed by histopathology. CONCLUSIONS This study demonstrates that %ddcfDNA reliably detects acute rejection and other clinical complications potentially missed by histopathology, lending support to its use as a non-invasive marker of allograft injury.
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Affiliation(s)
- Moon Kyoo Jang
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; Division of Intramural Research, National Heart, Lung and Blood Institute, 10 Center Drive, 7S261, Bethesda, Maryland
| | - Ilker Tunc
- Division of Intramural Research, National Heart, Lung and Blood Institute, 10 Center Drive, 7S261, Bethesda, Maryland
| | - Gerald J Berry
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; Stanford University School of Medicine, Palo Alto, California
| | - Charles Marboe
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; Department of Pathology, New York Presbyterian University Hospital of Cornell and Columbia, New York, New York
| | - Hyesik Kong
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; Division of Intramural Research, National Heart, Lung and Blood Institute, 10 Center Drive, 7S261, Bethesda, Maryland
| | - Michael B Keller
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; Division of Intramural Research, National Heart, Lung and Blood Institute, 10 Center Drive, 7S261, Bethesda, Maryland; Division of Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, 1830 East Monument Street, Baltimore, Maryland
| | - Pali D Shah
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; Division of Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, 1830 East Monument Street, Baltimore, Maryland
| | - Irina Timofte
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; University of Maryland Medical Center, Baltimore, Maryland
| | - Anne W Brown
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; Inova Fairfax Hospital, Fairfax, Virginia
| | - Ileana L Ponor
- Department of Medicine, Johns Hopkins Bayview Medical Center, Baltimore, Maryland
| | - Cedric Mutebi
- Immunogenetics Core Laboratory, Johns Hopkins Hospital, Baltimore, Maryland
| | - Mary C Philogene
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; National Cancer Institute, Rockville, Maryland
| | - Kai Yu
- National Cancer Institute, Rockville, Maryland
| | - Aldo Iacono
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; University of Maryland Medical Center, Baltimore, Maryland
| | - Jonathan B Orens
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; Stanford University School of Medicine, Palo Alto, California
| | - Steven D Nathan
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; Inova Fairfax Hospital, Fairfax, Virginia
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT), 10 Center Drive, 7S261, Bethesda, Maryland; Division of Intramural Research, National Heart, Lung and Blood Institute, 10 Center Drive, 7S261, Bethesda, Maryland; Division of Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, 1830 East Monument Street, Baltimore, Maryland.
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Andargie TE, Tsuji N, Seifuddin F, Jang MK, Yuen PS, Kong H, Tunc I, Singh K, Charya A, Wilkins K, Nathan S, Cox A, Pirooznia M, Star RA, Agbor-Enoh S. Cell-free DNA maps COVID-19 tissue injury and risk of death and can cause tissue injury. JCI Insight 2021; 6:147610. [PMID: 33651717 PMCID: PMC8119224 DOI: 10.1172/jci.insight.147610] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/02/2021] [Indexed: 01/08/2023] Open
Abstract
INTRODUCTION The clinical course of coronavirus 2019 (COVID-19) is heterogeneous, ranging from mild to severe multiorgan failure and death. In this study, we analyzed cell-free DNA (cfDNA) as a biomarker of injury to define the sources of tissue injury that contribute to such different trajectories. METHODS We conducted a multicenter prospective cohort study to enroll patients with COVID-19 and collect plasma samples. Plasma cfDNA was subject to bisulfite sequencing. A library of tissue-specific DNA methylation signatures was used to analyze sequence reads to quantitate cfDNA from different tissue types. We then determined the correlation of tissue-specific cfDNA measures to COVID-19 outcomes. Similar analyses were performed for healthy controls and a comparator group of patients with respiratory syncytial virus and influenza. RESULTS We found markedly elevated levels and divergent tissue sources of cfDNA in COVID-19 patients compared with patients who had influenza and/or respiratory syncytial virus and with healthy controls. The major sources of cfDNA in COVID-19 were hematopoietic cells, vascular endothelium, hepatocytes, adipocytes, kidney, heart, and lung. cfDNA levels positively correlated with COVID-19 disease severity, C-reactive protein, and D-dimer. cfDNA profile at admission identified patients who subsequently required intensive care or died during hospitalization. Furthermore, the increased cfDNA in COVID-19 patients generated excessive mitochondrial ROS (mtROS) in renal tubular cells in a concentration-dependent manner. This mtROS production was inhibited by a TLR9-specific antagonist. CONCLUSION cfDNA maps tissue injury that predicts COVID-19 outcomes and may mechanistically propagate COVID-19–induced tissue injury. FUNDING Intramural Targeted Anti–COVID-19 grant, NIH.
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Affiliation(s)
- Temesgen E Andargie
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA.,Department of Biology, Howard University, Washington DC, USA
| | - Naoko Tsuji
- Renal Diagnostics and Therapeutics Unit, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | | | - Moon Kyoo Jang
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA
| | - Peter St Yuen
- Renal Diagnostics and Therapeutics Unit, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Hyesik Kong
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA
| | - Ilker Tunc
- Bioinformatics and Computation Core, NHLBI, Maryland, USA
| | - Komudi Singh
- Bioinformatics and Computation Core, NHLBI, Maryland, USA
| | - Ananth Charya
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA
| | | | - Steven Nathan
- Advanced Lung Disease and Transplant Program, Inova Fairfax Hospital, Fairfax, Virginia, USA
| | - Andrea Cox
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Robert A Star
- Renal Diagnostics and Therapeutics Unit, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Charya A, Jang M, Sun J, Mutebi C, Luikart H, Shah P, Matthews J, Brown A, Kong H, Tunc I, Berry G, Marboe C, Iacono A, Nathan S, Khush K, Orens J, Valantine H, Agbor-Enoh S. Racial Differences in Immunosuppression and Lung Transplant Outcomes. J Heart Lung Transplant 2021. [DOI: 10.1016/j.healun.2021.01.474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Timofte I, Keller M, Varghese A, Levine D, Aryal S, Shah P, Vesselinov R, Ross D, Woodward R, Dale B, Terrin M, Iacono A, Agbor-Enoh S. Cell Free DNA Levels in Patients with Acute Rejection after Lung Transplantation. J Heart Lung Transplant 2021. [DOI: 10.1016/j.healun.2021.01.1035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Andargie T, Jang M, Seifuddin F, Kong H, Tunc I, Singh K, Woodward R, Pirooznia M, Valantine H, Agbor-Enoh S. Cell-Free DNA Tissue Damage Mapping in Transplant Patients Infected with COVID-19. J Heart Lung Transplant 2021. [PMCID: PMC7979332 DOI: 10.1016/j.healun.2021.01.437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Purpose Patients with COVID-19 show variable clinical course; transplant patients often show worse outcomes. The effect of COVID-19 on the allograft and the sources of tissue injury that contribute to such poor outcomes are poorly defined. This study leverages cell-free DNA (cfDNA) to measure allograft injury as donor-derived cfDNA (ddcfDNA) and injury from different tissue types using tissue-specific DNA methylomic signatures. Methods 14 consecutive COVID-19 transplant patients (8 Kidney, 3 Lung, 1 Heart, 1 Liver, and one multi-organ transplant patients) and 30 healthy controls were included. Plasma nuclear cfDNA (ncfDNA) and mitochondrial cfDNA (mtcfDNA) level were measured via digital droplet PCR, and ddcfDNA using AlloSure (CareDx). cfDNA whole-genome bisulfite sequencing was performed to identify cfDNA tissues of origin leveraging tissue specific DNA methylomes and deconvolution algorithm. Results 75% of the COVID-19 transplant patients showed high ddcfDNA level compared to published quiescent values, including all lung, 50% of the kidney, liver and multi-organ transplant patients (8.5, 4.4, 30 and 16-X fold change, respectively). Total ncfDNA and mtcfDNA were 15X and 310X higher in COVID-19 transplant patients compared to controls, respectively; < 0.0001.The predominant tissues contributing to cfDNA were hematopoietic cells (80%) (Figure). More importantly, COVID-19 transplant patients showed 10 to 100 fold higher tissue specific cfDNA derived from monocyte, neutrophil, erythroblast, vascular endothelium, adipocyte, hepatocyte, kidney, heart and lung compared to controls. Analysis comparing cfDNA in transplant and non-transplant COVID-19 patients is on-going. Conclusion The allograft undergoes significant injury following COVID-19. Further, cfDNA from multiple tissue types is significantly higher in COVID-19 transplant patients. Future studies in a larger cohorts of transplant and non-transplant patients are needed to elucidate why transplant patients show worse COVID-19 outcomes.
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Mutebi C, Ponor L, Cochrane A, Levine D, Jang M, Luikart H, Shah P, Mathew J, Brown A, Kong H, Berry G, Marboe C, Iacono A, Nathan S, Khush K, Orens J, Valantine H, Agbor-Enoh S. Impact of AMR Treatment: Responders vs Non-Responders Characteristics. J Heart Lung Transplant 2021. [DOI: 10.1016/j.healun.2021.01.1929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Charya A, Jang M, Mutebi C, Luikart H, Shah P, Matthews J, Brown A, Kong H, Tunc I, Berry G, Marboe C, Iacono A, Nathan S, Khush K, Orens J, Valantine H, Agbor-Enoh S. Cell-Free DNA to Monitor Immunosuppression Adequacy in Lung Transplantation. J Heart Lung Transplant 2021. [DOI: 10.1016/j.healun.2021.01.1891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Keller M, Mutebi C, Shah P, Levine D, Aryal S, Timofte I, Mathew J, Varghese A, Giner C, Ross D, Dale B, Woodward R, Agbor-Enoh S. Performance of Donor Derived Cell-Free DNA in Routine Clinical Care of Lung Transplant Recipients, a Multi-Center Study. J Heart Lung Transplant 2021. [DOI: 10.1016/j.healun.2021.01.451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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