Biology subjects

Marais, B.

Publications and source records attributed to Marais, B..

3 recordsLinked to original sources

bioRxiv2026

Patient-Derived Circulating Monocytes Promote Calcific Aortic Valve Disease Progression

BackgroundCalcific aortic valve disease (CAVD) is the most common valvular heart disease in developed countries, yet no pharmacological therapy is available to slow or halt its progression. CAVD is driven by progressive calcification of aortic valve leaflets, in which myeloid cells play a central role. While macrophages have been implicated in CAVD pathogenesis, the contribution of their precursors, monocytes, remains poorly understood. We hypothesized that circulating monocytes acquire a pro-calcific and pro-inflammatory phenotype contributing to valve remodelling and CAVD progression. MethodsWe profiled circulating CD14+ monocytes from healthy volunteers (Vol), patients with CAVD, and without CAVD (NCAVD). Peripheral blood mononuclear cells (PBMCs) were isolated, and monocyte subpopulations were phenotyped by flow cytometry. Transcriptome profiling by RNA sequencing identified disease-associated gene signatures, which were validated by RT-qPCR. The CD14+ monocyte secretome was analysed using multiplex assays. Functional ability of CAVD-derived CD14+ monocytes to induce myofibroblastic transdifferentiation (MT) and osteoblastic differentiation (OD) of human valvular interstitial cells (VICS) was evaluated by immunocytochemistry and quantitative o-cresolphthalein complexone assays. ResultsIn PBMCs, CAVD monocytes displayed a subpopulation shift, with an increased proportion of CD14CD16- classical monocytes and a reduced CD14CD16 non-classical monocyte levels. In CD14+ monocytes, transcriptomic analysis revealed upregulation of inflammation-related (PDK4) and calcification-related (ATP2B1) genes, alongside downregulation of immunomodulatory genes (DDR1, IKBKE). Secretome analysis showed reduced production of immunomodulatory and anti-osteoblastogenic cytokines (IL-4, CCL3) while promoting gene expression of factors promoting MT and OD in VICS. These alterations were associated with a marked monocyte-induced increase in SMA and OPN expression in VICS and a two-fold increase in calcification. ConclusionWe demonstrate for the first time that circulating monocytes from patients with CAVD exhibit enhanced pro-inflammatory and pro-calcific properties that may contribute to CAVD progression. Additionally, we identify dysregulated gene sets within these monocytes that represent potential novel therapeutic targets for CAVD.

pathology↗

bioRxiv2020

Whole genome sequencing based differentiation between re-infection and relapse in Indian patients with tuberculosis recurrence, with and without HIV co-infection

Differentiation between relapse and reinfection in cases with tuberculosis (TB) recurrence has important implications for public health, especially in patients with human immunodeficiency virus (HIV) co-infection. Forty-one paired M. tuberculosis isolates collected from 20 HIV-positive and 21 HIV-negative patients, who experienced TB recurrence after previous successful treatment, were subjected to whole genome sequencing (WGS) in addition to spoligotyping and mycobacterial interspersed repeat unit (MIRU) typing. Comparison of M. tuberculosis genomes indicated that 95% of TB recurrences in the HIV-negative cohort were due to relapse, while the majority of TB recurrences (75%) in the HIV-positive cohort was due to re-infection (P=0.0001). Drug resistance conferring mutations were documented in four pairs (9%) of isolates associated with relapse. The high contribution of re-infection to TB among HIV patients warrants further study to explore risk factors for TB exposure in the community.

genomics↗

bioRxiv2018

A complete nanonpore-only assembly of an XDR Mycobacterium tuberculosis Beijing lineage strain identifies novel genetic variation in repetitive PE/PPE gene regions

A better understanding of the genomic changes that facilitate the emergence and spread of drug resistant M. tuberculosis strains is required. Short-read sequencing methods have limited capacity to identify long, repetitive genomic regions and gene duplications. We sequenced an extensively drug resistant (XDR) Beijing sub-lineage 2.2.1.1 \"epidemic strain\" from the Western Province of Papua New Guinea using long-read sequencing (Oxford Nanopore MinION(R)). With up to 274 fold coverage from a single flow-cell, we assembled a 4404947bp circular genome containing 3670 coding sequences that include the highly repetitive PE/PPE genes. Comparison with Illumina reads indicated a base-level accuracy of 99.95%. Mutations known to confer drug resistance to first and second line drugs were identified and concurred with phenotypic resistance assays. We identified mutations in efflux pump genes (Rv0194), transporters (secA1, glnQ, uspA), cell wall biosynthesis genes (pdk, mmpL, fadD) and virulence genes (mce-gene family, mycp1) that may contribute to the drug resistance phenotype and successful transmission of this strain. Using the newly assembled genome as reference to map raw Illumina reads from representative M. tuberculosis lineages, we detect large insertions relative to the reference genome. We provide a fully annotated genome of a transmissible XDR M. tuberculosis strain from Papua New Guinea using Oxford Nanopore MinION sequencing and provide insight into genomic mechanisms of resistance and virulence.\n\nData SummaryO_LISample Illumina and MinION sequencing reads generated and analyzed are available in NCBI under project accession number PRJNA386696 (https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA386696)\nC_LIO_LIThe assembled complete genome and its annotations are available in NCBI under accession number CP022704.1 (https://www.ncbi.nlm.nih.gov/sra/?term=CP022704.1)\nC_LI\n\nImpact statementWe recently characterized a Modern Beijing lineage strain responsible for the drug resistance outbreaks in the Western province, Papua New Guinea. With some of the genomic markers responsible for its drug resistance and transmissibility are known, there is need to elucidate all molecular mechanisms that account for the resistance phenotype, virulence and transmission. Whole genome sequencing using short reads has widely been utilized to study MTB genome but it does not generally capture long repetitive regions as variants in these regions are eliminated using analysis. Illumina instruments are known to have a GC bias so that regions with high GC or AT rich are under sampled and this effect is exacerbated in MTB, which has approximately 65% GC content. In this study, we utilized Oxford Nanopore Technologies (ONT) MinION sequencing to assemble a high-quality complete genome of an extensively drug resistant strain of a modern Beijing lineage. We were able to able to assemble all PE/PPE (proline-glutamate/proline-proline-glutamate) gene families that have high GC content and repetitive in nature. We show the genomic utility of ONT in offering a more comprehensive understanding of genetic mechanisms that contribute to resistance, virulence and transmission. This is important for settings up predictive analytics platforms and services to support diagnostics and treatment.

genomics↗