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Donor-derived cell-free DNA (ddcfDNA) is increasingly used in clinical practice to monitor lung transplant patients for acute rejection (AR). However, its association with conventional approaches to monitor immunosuppression remains unclear. This multicenter observational cohort study examines the association of ddcfDNA with surrogate measures of immunosuppression. We collected serial plasma samples to quantify ddcfDNA and anellovirus abundance using shotgun and metagenomic sequencing. Adjudication committees reviewed clinical data to define acute cellular and antibody-mediated rejection. The association between ddcfDNA, anellovirus abundance, and tacrolimus trough concentrations in serum over the study period and during episodes of AR was examined using linear mixed-effects modeling. ddcfDNA demonstrated a significant inverse association with tacrolimus troughs (P = .027) and anellovirus abundance (P < .001) over time. AR episodes were associated with significantly decreased anellovirus abundance (median, 0.042 vs 0.708, P < .001) and higher ddcfDNA levels (1.49% vs 0.26%, P < .001) compared with stable control time points. However, tacrolimus levels were similar between AR and controls (10.1 vs 10.3 ng/mL, P = .13). Our findings suggest ddcfDNA correlates with measures of immunosuppression in lung transplant patients. Additional studies are needed to assess the utility of ddcfDNA to assess immunosuppression adequacy.
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http://dx.doi.org/10.1016/j.ajt.2025.04.011 | DOI Listing |
Nat Commun
August 2025
School of Life Sciences, Arizona State University, Tempe, AZ, USA.
Despite successful suppression of plasma HIV replication by antiretroviral therapy (ART), some women living with HIV (WLHIV) can still experience genital HIV shedding (discordant shedding). Female genital tract (FGT) bacterial and viral microbiome (bacteriome and virome) community dynamics during long-term ART in WLHIV are poorly understood but might contribute to discordant HIV shedding, as the bacteriome and virome are known to influence FGT health. Here, using metagenomic next-generation sequencing, we characterize the bacteriome and virome in 125 cervicovaginal specimens collected over two years from 31 WLHIV in Lima, Peru, and show that FGT bacteriome instability is associated with discordant HIV shedding, while longitudinal changes in FGT virome composition are associated with ART duration.
View Article and Find Full Text PDFInt J Cancer
November 2025
Department of Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China.
Lung cancer is the leading cause of cancer-related mortality globally. Although some studies have proposed a potential association between viral infections and lung cancer pathogenesis, the evidence remains inconclusive. This study characterized the virome in blood, upper respiratory tract, and gut samples from 200 lung cancer patients and 75 healthy controls, with the goal of identifying potential microbial biomarkers for lung cancer, using viral metagenomics.
View Article and Find Full Text PDFInt J Mol Sci
July 2025
Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, 00149 Rome, Italy.
Torquetenovirus (TTV) is a ubiquitous, non-pathogenic DNA virus that has been suggested as a biomarker of immune competence, with the viral load correlating with the level of immunosuppression. However, by detecting non-intact viral particles, standard PCR-based quantification may overestimate the TTV viremia. To improve the clinical relevance of TTV quantification, in this study, we investigated the use of PMAxx™, a virion viability dye that selectively blocks the amplification of compromised virions.
View Article and Find Full Text PDFAm J Transplant
September 2025
Genomic Research Alliance for Transplantation (GRAfT), Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland, USA; Laboratory of Applied Precision Omics, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland, USA. Elec
Donor-derived cell-free DNA (ddcfDNA) is increasingly used in clinical practice to monitor lung transplant patients for acute rejection (AR). However, its association with conventional approaches to monitor immunosuppression remains unclear. This multicenter observational cohort study examines the association of ddcfDNA with surrogate measures of immunosuppression.
View Article and Find Full Text PDFVirol J
March 2025
Centro de Vigilância Viral e Avaliação Sorológica- CeVIVas, Instituto Butantan, São Paulo, Brazil.
Background: Viral metagenomics has expanded significantly in recent years due to advancements in next-generation sequencing, establishing it as the leading method for identifying emerging viruses. A crucial step in metagenomics is taxonomic classification, where sequence data is assigned to specific taxa, thereby enabling the characterization of species composition within a sample. Various taxonomic classifiers have been developed in recent years, each employing distinct classification approaches that produce varying results and abundance profiles, even when analyzing the same sample.
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