Biology subjects

Agbor-Enoh, S.

Publications and source records attributed to Agbor-Enoh, S..

5 recordsLinked to original sources

bioRxiv2023

Benchmarking and optimization of cell-free DNA deconvolution

Reference methylomes, used in deconvolution algorithms to determine cell-free DNA tissue sources, were based on driver CpGs from either microarray or sequencing platforms. Cross-validation of these algorithms is important to allow interpretation of data across studies, select optimal sequencing depth, and thus reduce costs of cf-DNA deconvolution assays. Towards this end, we assessed the performance of two reference-based deconvolution algorithms: cfDNAme, sequencing-based methylome signatures, and Meth-Atlas, a microarray-based methylome signatures using a cfDNA bisulfite sequencing. While both algorithms use NNLS model, cfDNAme uses CpG windows, while Meth-Atlas uses individual CpGs as cell or tissue signatures. We determined the optimal the number of informative CpGs signatures, and the best sequencing depths for precise deconvolution. We found that above 5-fold coverage, much lower coverage than what is frequently used, there is little difference between our two chosen algorithms, both identifying the correct tissue make-up with a high accuracy, suggesting that whole genome bisulfite sequencing for tissue of origin identification can be completed in a much more cost-effective manner than previously thought.

bioinformatics↗

bioRxiv2023

Cell-free Chromatin Immunoprecipitation to detect molecular pathways in Physiological and Disease States

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.

genomics↗

bioRxiv2022

Pseudomonas aeruginosa Elicits Sustained IL-1β Upregulation in Alveolar Macrophages from Lung Transplant Recipients

BackgroundIsolation 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 (AM) responses to PsA and Pseudomonas dominant microbiome in healthy lung transplant recipients (LTR). MethodsWe stimulated THP-1 derived macrophages (THP-1M) and human AM 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-, IL-6, IL-8, IL-1{beta}, IL-10, IL-1RA, and TGF-{beta}). Pharmacological inhibitors were utilized to evaluate the role of the inflammasome in PsA-macrophages interaction. ResultsWe observed upregulation of pro-inflammatory cytokines (TNF-, IL-6, IL-8, IL-1{beta}) following stimulation by PsA compared to other bacteria (Staphylococcus aureus, Prevotella melaninogenica, Streptococcus pneumoniae) in both THP-1 derived and LTR AM, predominated by IL-1{beta}. IL-1{beta} production from THP-1 was sustained after PsA stimulation for up to 96 hours and 48 hours in LTR AM. Treatment with the inflammasome inhibitor BAY11-7082 abrogated macrophage IL-1{beta} and IL-18 production after PsA exposure. BAL Pseudomonas-dominant microbiota elicited an increased IL-1{beta}, similar to PsA, an effect abrogated by the addition of antibiotics. ConclusionPsA and PsA-dominant lung microbiota induce sustained IL-1{beta} production in LTR AM. Pharmacological targeting of the inflammasome reduces PsA-macrophage-IL1{beta} responses, underscoring their use in lung transplant recipients.

immunology↗

bioRxiv2020

Applications of genetic-epigenetic tissue mapping for plasma DNA in prenatal testing, transplantation and oncology

We developed Genetic-Epigenetic Tissue Mapping (GETMap) to determine the tissue composition of plasma DNA carrying genetic variants not present in the constitutional genome through comparing their methylation profiles with relevant tissues. We validated this approach by showing that, in pregnant women, circulating DNA carrying fetal-specific alleles was entirely placenta-derived. In lung-transplant recipients, we showed that, at 72 hours after transplantation, the lung contributed only a median of 17% to the plasma DNA carrying donor-specific alleles and hematopoietic cells contributed a median of 78%. In hepatocellular cancer patients, the liver was identified as the predominant source of plasma DNA carrying tumor-specific mutations. In a pregnant woman with lymphoma, plasma DNA molecules carrying cancer mutations and fetal-specific alleles were accurately shown to be derived from the lymphocytes and placenta, respectively. Analysis of tissue origin for plasma DNA carrying genetic variants is potentially useful for noninvasive prenatal testing, transplantation monitoring and cancer screening.

physiology↗

bioRxiv2020

Donor-derived mitochondrial DNA variant peptides elicit allo-specific immune response in transplant patients

In stem cell transplant, mitochondrial DNA (mtDNA) nonsynonymous single nucleotide variants (SNVs) between donor and recipient (D-R) trigger alloimmune responses and transplant rejection. Whether similar alloimmune responses occurs in solid-organ transplantation remains unknown, particularly with the presence of human leukocyte antigen mismatches. This study characterized mtDNA SNVs between D-R of 163 human lung transplant pairs, and then, post-transplantation, assessed alloimmune responses against donor-derived mitochondrial peptides using ELISpot to measure interferon gamma (IFN{gamma}) release from recipients monocytes. We identified a median of 6 nonsynonymous mtDNA SNVs (Interquartile Range = 4 - 9) per D-R pair. SNVs were predominantly located at MT-CYB, MT-ATP6, and MT-ND3 genes. The number of SNVs was higher in D-R race non-concordant pairs than in race-concordant pairs. Donor-derived mitochondrial peptides triggered a 19.8-fold higher IFN{gamma} release compared to recipient-derived peptide. These findings were validated in heart transplantation and show that donor-derived mitochondrial peptides trigger allo-specific immune responses after transplantation.

genomics↗