Biology subjects

Tremblay, B. J.-M.

Publications and source records attributed to Tremblay, B. J.-M..

5 recordsLinked to original sources

bioRxiv2026

Transposable Element Diversification and the Evolution of Peltigerales Lichen Symbionts

Lichens are composite organisms formed through the symbiotic association between fungi, algae and/or bacteria. Multiple independent origins of the lichenized lifestyle have been reported in both fungal and algal lineages, but the molecular mechanisms and evolution underpinning these symbiotic relationships remain largely unknown. In this study, we performed long-read metagenomic sequencing on 11 Peltigerales lichen species to characterize the genomic content of lichen symbionts via metagenome assembled genomes (MAGs). Peltigerales genomes generated in this work represent the largest Lecanoromycetes genome sequenced to date, driven by high transposable element content. Transposable elements (TEs) are known to drive genome evolution in other symbioses but have been underexplored in lichen symbionts due technological limitations. Transcriptomics revealed that many genes associated with adaptations to the lichenized lifestyle are associated with TEs suggesting that they may play a key role in the evolution of lichenization.

genomics↗

bioRxiv2025

Impaired methyl recycling induces substantial shifts in sulfur utilization in Arabidopsis

The tight coordination of sulfur metabolism and growth regulation is predicated upon nutrient availability. Central to this balancing act is the utilization of cysteine (Cys) for the formation of methionine (Met) and S-adenosylmethionine (SAM). Plants that are severely deficient in regenerating Met due to reduced methylthioadenosine (MTA) nucleosidase activity experience numerous developmental abnormalities. Here, we assess the developmental, metabolic, and regulatory effects associated with decreased MTA recycling. We show that MTA over-accumulation predominantly occurs in reproductive tissues and leads to reduced levels of Cys, Met, and SAM, as well as elevated S-adenosylhomocysteine. These disruptions of primary sulfur utilization also lead to the misregulation of energy metabolism and altered cell cycle progression. RNA-seq experiments show a general down-regulation of many developmental and reproductive genes. Targeted metabolite analyses demonstrate clear impacts on the methyl index which are reflected in the results of bisulfite-sequencing experiments including global alterations in CG gene-body methylation levels and decreases of CHG and CHH methylation in transposable elements. Our findings demonstrate the broad impacts of MTA metabolism on plant development, sulfur utilization and the maintenance of the methyl index.

plant biology↗

bioRxiv2020

Gene expression and in situ protein profiling of candidate SARS-CoV-2 receptors in human airway epithelial cells and lung tissue

In December 2019, SARS-CoV-2 emerged causing the COVID-19 pandemic. SARS-CoV, the agent responsible for the 2003 SARS outbreak, utilizes ACE2 and TMPRSS2 host molecules for viral entry. ACE2 and TMPRSS2 have recently been implicated in SARS-CoV-2 viral infection. Additional host molecules including ADAM17, cathepsin L, CD147, and GRP78 may also function as receptors for SARS-CoV-2. To determine the expression and in situ localization of candidate SARS-CoV-2 receptors in the respiratory mucosa, we analyzed gene expression datasets from airway epithelial cells of 515 healthy subjects, gene promoter activity analysis using the FANTOM5 dataset containing 120 distinct sample types, single cell RNA sequencing (scRNAseq) of 10 healthy subjects, immunoblots on multiple airway epithelial cell types, and immunohistochemistry on 98 human lung samples. We demonstrate absent to low ACE2 promoter activity in a variety of lung epithelial cell samples and low ACE2 gene expression in both microarray and scRNAseq datasets of epithelial cell populations. Consistent with gene expression, rare ACE2 protein expression was observed in the airway epithelium and alveoli of human lung. We present confirmatory evidence for the presence of TMPRSS2, CD147, and GRP78 protein in vitro in airway epithelial cells and confirm broad in situ protein expression of CD147 in the respiratory mucosa. Collectively, our data suggest the presence of a mechanism dynamically regulating ACE2 expression in human lung, perhaps in periods of SARS-CoV-2 infection, and also suggest that alternate receptors for SARS-CoV-2 exist to facilitate initial host cell infection.

immunology↗

bioRxiv2020

Expression of the endocannabinoid system in the human airway epithelial cells: Impact of sex and chronic respiratory disease status

Recreational and medicinal cannabis consumption in the past 12 months has been reported in 1/5th of Canadians, with greater use in males relative to females. Cannabis smoking is the dominant route of delivery in consumers, with the airway epithelium functioning as the site of first contact for inhaled phytocannabinoids. The endocannabinoid system is responsible for mediating the physiological effects of inhaled phytocannabinoids. Acute cannabis smoke inhalation can result in bronchodilation, which may have applications in chronic respiratory disease management. In contrast, chronic cannabis smoke inhalation is associated with reduced lung function and bronchitis, which challenges potential applications in the lung. The contribution of the endocannabinoid system in the airway epithelium to either beneficial or harmful physiological responses remains to be clearly defined in males and females and those with underlying chronic respiratory disease. To begin to address this knowledge gap, a curated dataset of 1090 unique human bronchial brushing gene expression profiles was created from Gene Expression Omnibus deposited microarray datasets. The dataset included 616 healthy subjects, 136 subjects with asthma, and 338 subjects with COPD. A 27-gene endocannabinoid signature was analyzed across all samples with sex and disease specific-analyses performed. Immunohistochemistry and immunoblots were performed to confirm in situ and in vitro protein expression of select genes in human airway epithelial cells. We confirm three receptors for cannabinoids, CB1, CB2, and TRPV1, are expressed at the protein level in human airway epithelial cells in situ and in vitro, justifying examining the downstream endocannabinoid pathway more extensively at the gene expression level. Sex status was associated with differential expression of 6/27 genes. In contrast, disease status was associated with differential expression of 18/27 genes in asthmatics and 22/27 genes in COPD subjects. We confirm at the protein level that TRPV1, the most differentially expressed candidate in our analyses, was up-regulated in airway epithelial cells from asthmatics relative to healthy subjects. Our data demonstrate that endocannabinoid system is expressed in human airway epithelial cells with expression impacted by disease status and minimally by sex. The data suggest that cannabis consumers may have differential physiological responses in the respiratory mucosa, which could impact both acute and chronic effects of cannabis smoke inhalation.

cell biology↗

bioRxiv2020

ABCF1 regulates dsDNA-induced immune responses in human airway epithelial cells

BackgroundThe airway epithelium represents a critical component of the human lung that helps orchestrate defences against respiratory tract viral infections, which are responsible for more than 2.5 million deaths/year globally. Innate immune activities of the airway epithelium rely Toll-like receptors (TLRs), nucleotide binding and leucine-rich-repeat pyrin domain containing (NLRP) receptors, and cytosolic nucleic acid sensors. ATP Binding Cassette (ABC) transporters are ubiquitous across all three domains of life - Archaea, Bacteria, and Eukarya - and expressed in the human airway epithelium. ABCF1, a unique ABC family member that lacks a transmembrane domain, has been defined as a cytosolic nucleic acid sensor that regulates CXCL10, interferon-{beta} expression, and downstream type I interferon responses. We tested the hypothesis that ABCF1 functions as a dsDNA nucleic acid sensor in human airway epithelial cells important in regulating antiviral responses. MethodsExpression and localization experiments were performed using in situ hybridization and immunohistochemistry in human lung tissue from healthy subjects, while confirmatory transcript and protein expression was performed in human airway epithelial cells. Functional experiments were performed with siRNA methods in human airway epithelial cells. Complementary transcriptomic analyses were performed to explore the contributions of ABCF1 to gene expression patterns. ResultsUsing archived human lung and human airway epithelial cells, we confirm expression of ABCF1 gene and protein expression in these tissue samples, with a role for mediating CXCL10 production in response to dsDNA viral mimic challenge. Although, ABCF1 knockdown was associated with an attenuation of select genes involved in the antiviral responses, Gene Ontology analyses revealed a greater interaction of ABCF1 with TLR signaling suggesting a multifactorial role for ABCF1 in innate immunity in human airway epithelial cells. ConclusionABCF1 is a candidate cytosolic nucleic acid sensor and modulator of TLR signaling that is expressed at gene and protein levels in human airway epithelial cells. The precise level where ABCF1 protein functions to modulate immune responses to pathogens remains to be determined but is anticipated to involve IRF-3 and CXCL10 production.

immunology↗