Biology subjects

Archer, S. L.

Publications and source records attributed to Archer, S. L..

8 recordsLinked to original sources

bioRxiv2026

A National Survey of 205 Canadian Biomedical Research Core Facilities Reveals Structural Challenges and Opportunities for Strengthening Canada's Research Ecosystem

BackgroundCanadian biomedical core facilities (BCFs) provide researchers with access to advanced tools and unique technical expertise, essential for research. However, their role, sustainability, and impact remain poorly understood. We report on the evolution of model and existing state of Canadas 205 BCFs, examining challenges and benefits. MethodsCross referencing of national databases by the Canadian Innovation Fund (CFI), and from data collected by the Canadian Network of Scientific Platforms (CNSP) allowed he identification of BCFs. Hand curation of these lists validated that cores are operational. To ensure cores not listed by CFI/CNSP were captured, research intensive institutions in Canada were independently searched to identify active cores. ResultsThere are currently 205 active and operational BCFs located across 9 provinces, which can be further stratified into 9 technical domains that describe the nature of services they provide. Quebec (80 cores) and Ontario (75 cores) have the highest confluence of BCFs, with Quebec having a higher ratio of cores per capita. ConclusionsWhile our data establishes the ubiquity of Canadian BCFs, we highlight substantial challenges including sustainability, governance, evaluation and the recognition of support for core scientists. Here, we establish a framework to address these challenges and to inform best practice, to optimize creation of impactful, accessible and functional biomedical core facilities.

scientific communication and education↗

bioRxiv2026

Pulmonary Hypertension Engine for Linked Experiments (PHELEX): a platform for the re-analysis of public transcriptomic data related to pulmonary hypertension in both animal models, and humans.

Pulmonary hypertension (PH) is a vasculopathy that results in elevated mean pulmonary arterial pressures over 20mmHg. Despite significant advances in research, PH still has a high mortality rate, and there is currently no cure for the disease. As with all biomedical fields, PH researchers have embraced the power of next generation technologies such as microarrays and RNA sequencing. Most of these data can be found on public repositories, which is usually a requirement for publication. While these repositories are rich sources of data, they require intermediate to advanced bioinformatics skills to access, download, and make these data useful. Here we present Pulmonary Hypertension Engine for Linked Experiments (PHELEX), which represents a comprehensive catalogue of all RNA sequencing data related to PH that is currently available on the Gene Expression Omnibus (GEO), hosted by the US National Centre for Biotechnology Information (NCBI). We identified 2,278 bulk RNA sequencing samples from human, mouse and rat, and built a searchable tool based on the metadata that is associated with each sample. PHELEX is a functional tool that allows selected studies to be highlighted, and parsed through Confidence, an analysis tool we have created, which will model the data based on user-defined classifiers, perform differential gene expression and pathway analysis, and present these data using standard graphics, and text-file results. PHELEX also allows PH researchers to cross-cut between discrete studies, facilitating de novo understanding of these data. As a robust searchable repository of genomic data, we hope that PHELEX will accelerate PH innovation and discovery, by allowing researchers to mine existing genomic data and thus better understand the molecular signatures that underpin PH.

genomics↗

bioRxiv2025

Levosimendan Ameliorates Adverse Pulmonary Vascular Remodeling in Group-2 Pulmonary Hypertension.

AimsPulmonary hypertension (PH) due to left heart disease (Group-2PH) is the most common form of PH and comprises two distinct subtypes: isolated post-capillary-PH (IpcPH) and combined post-and pre-capillary-PH (CpcPH). Despite its high prevalence and poor prognosis, no targeted therapies are currently approved, largely due to the absence of reliable preclinical models that recapitulate these human hemodynamic phenotypes. Levosimendan, a calcium sensitizer with inotropic and vasodilatory properties, has shown promise in early clinical trials for Group-2PH, but its mechanisms of action remain unclear. This study aimed to develop and validate experimental models of IpcPH and CpcPH and to assess the therapeutic effects of levosimendan on pulmonary vascular remodeling, inflammation, and cardiac function to support ongoing clinical translation. Methods and ResultsIn a multicentre preclinical study, we established two rodent models that faithfully replicate the human IpcPH and CpcPH hemodynamic profiles. CpcPH animals exhibited severe pulmonary vascular remodeling, inflammatory cell infiltration, and a distinct pro-proliferative transcriptomic signature, whereas IpcPH animals showed minimal pulmonary vascular involvement. Levosimendan (3 mg/kg/day, 3 weeks) improved biventricular function and pulmonary hemodynamics in both models. In CpcPH, levosimendan additionally reduced pulmonary vascular remodeling, attenuated inflammation, and partially reversed disease-associated transcriptomic reprogramming. Transcription factor enrichment analysis identified NF-{kappa}B as a key upstream regulator inhibited by treatment. In a translational extension, nine circulating inflammation-related-proteins differentiated CpcPH from IpcPH patients; among them, TNF, IL-12B, 4E-BP1, NT-3, NGF, FGF21, and FGF23 predicted poor survival. IL-18 and 4E-BP1 were elevated in CpcPH lungs and decreased following levosimendan treatment. ConclusionsInflammation is a major contributor to adverse pulmonary vascular remodeling in CpcPH. Levosimendan improves cardiac performance and mitigates pulmonary vascular inflammation and remodeling, supporting its potential as a dual-action therapeutic agent in Group-2PH. These findings validate novel preclinical models and provide mechanistic evidence reinforcing ongoing clinical evaluation of levosimendan in this condition. Translational perspectiveGroup-2 PH lacks targeted therapies, partly due to the absence of validated preclinical models. We validated models recapitulating human IpcPH and CpcPH and identified inflammation as a key driver of pulmonary vascular remodeling in CpcPH. Levosimendan improved biventricular function and reduced vascular remodeling and inflammation through NF-{kappa}B inhibition. Circulating IL-18 and 4E-BP1 reflected disease severity and treatment response. These findings establish robust translational models, reveal inflammatory mechanisms underlying CpcPH, and provide mechanistic evidence supporting ongoing clinical trials of levosimendan as a dual-action therapeutic strategy in Group-2 PH.

molecular biology↗

bioRxiv2025

NDUFS2 (NADH:Ubiquinone oxidoreductase core subunit S2) in Mitochondrial Electron Transport Chain Complex I is Critical to Oxygen Responsiveness of Human Ductus Arteriosus Smooth Muscle Cells

BackgroundMitochondria in ductus arteriosus smooth muscle cells (DASMCs) are oxygen sensors triggering vasoconstriction at birth; however, the oxygen sensing mechanisms are incompletely understood. Given the conserved role of mitochondrial Complex I subunit NDUFS2 in other oxygen-sensing tissues, we examined its role in DASMC oxygen sensing, comparing it to other Complex I subunits (NDUFS1 and NDUFS7) and putative O2-sensor subunits (UQCRFS1 and COX4I2). MethodsHuman DASMCs were grown in hypoxia (pO2=41mmHg). Oxygen responsiveness was assessed, measuring changes in intracellular calcium, [Ca2+]i, cell length, and mitochondrial reactive oxygen species (mROS). DASMCs were treated for 48-hours with control siRNA versus siRNA targeting NDUFS2, NDUFS1, NDUFS7, UQCRFS1, or COX4I2. qPCR and immunoblotting confirmed knockdown. 3RNA sequencing assessed transcriptional changes following siRNA. ResultsOxygen increased mitochondrial fission, [Ca2+]i, and constricted DASMCs. 48-hours post-treatment, siNDUFS2 selectively depressed oxygen-induced increase in [Ca2+]i (siControl +18.6{+/-}2.3%, siNDUFS2 +5.5{+/-}1.5%, p<0.0001), DASMC shortening (from 18.4{+/-}1.1% to 8.9{+/-}0.8%, p<0.0001), and mROS (+24{+/-}4.9% untreated, -6.6{+/-}5.4% post-siNDUFS2, p<0.0001), without altering the KCl response or depressing respiration. The mitochondrial antioxidant MitoTEMPO reduced mROS (2.9{+/-}4.5%, p=0.001) and attenuated oxygen-induced DASMC shortening (8.4{+/-}0.9%, p=0.0003). Transcriptomics revealed unique changes in mitochondrial pathways post siNDUFS2. ConclusionsNDUFS2 regulates mROS and is a mitochondrial oxygen sensor in human DASMCs. ImpactO_LIWe demonstrated a unique role of Complex I subunit NDUFS2 (NADH:Ubiquinone Oxidoreductase Core Subunit S2), amongst putative oxygen-sensing electron transport chain subunits, in the responsiveness of human ductus arteriosus (DA) smooth muscle cells (DASMCs) to oxygen. C_LIO_LINDUFS2 knockdown inhibited oxygen-induced DASMC constriction and generation of mitochondrial reactive oxygen species, at a timepoint prior to inhibition of mitochondrial respiration and without inhibition of KCl-induced constriction. C_LIO_LIWhile mitochondria are known DA oxygen sensors, this work identifies NDUFS2 as a molecular mediator of human DA oxygen sensing within the mitochondria, enhancing our understanding of a vital physiologic phenomenon and providing a novel potential therapeutic target to modulate ductal patency. C_LI

molecular biology↗

bioRxiv2023

Efficacy of Drpitor1a, a Dynamin-Related Protein 1 inhibitor, in Pulmonary Arterial Hypertension

RationaleDynamin-related protein 1 (Drp1), a large GTPase, mediates mitochondrial fission. Increased Drp1-mediated fission permits accelerated mitosis, contributing to hyperproliferation of pulmonary artery smooth muscle cells (PASMC), which characterizes pulmonary arterial hypertension (PAH). We developed a Drp1 inhibitor, Drpitor1a, and tested its ability to regress PAH. ObjectivesAssess Drpitor1as efficacy and toxicity in: a)normal and PAH human PASMC (hPASMC); b)normal rats versus rats with established monocrotaline (MCT)-induced PAH. MethodsDrpitor1as effects on recombinant and endogenous Drp1-GTPase activity, mitochondrial fission, and cell proliferation were studied in hPASMCs (normal=3; PAH=5). Drpitor1as pharmacokinetics and tissue concentrations were measured (n=3 rats/sex). In a pilot study (n=3-4/sex/dose), Drpitor1a (1mg/kg/48-hours, intravenous) reduced adverse PA remodeling only in females. Consequently, we compared Drpitor1a to vehicle in normal (n=6 versus 8) and MCT-PAH (n=9 and 11) females, respectively. Drpitor1a treatment began 17-days post-MCT with echocardiography and cardiac catheterization performed 28-29 days post-MCT. ResultsDrpitor1a inhibited recombinant and endogenous Drp1 GTPase activity, which was increased in PAH hPASMC. Drpitor1a inhibited mitochondrial fission and proliferation and induced apoptosis, in PAH hPASMC but not normal hPASMC. Drpitor1a tissue levels were higher in female versus male RVs. In MCT-PAH females, Drpitor1a regressed PA obstruction, lowered pulmonary vascular resistance, and improved RV function, without hematologic, renal, or hepatic toxicity. ConclusionsDrpitor1a inhibits Drp1 GTPase, reduces mitochondrial fission, and inhibits cell proliferation in PAH hPASMC. Drpitor1a caused no toxicity in MCT-PAH and had no significant effect on normal rats or hPASMCs. Drpitor1a is a potential PAH therapeutic which displays an interesting therapeutic sexual dimorphism.

pharmacology and toxicology↗

bioRxiv2023

Circular RNA profiling identifies circ5078 as a BMPR2-derived regulator of endothelial translation

Germline loss-of-function BMPR2 mutations are the leading genetic cause of pulmonary arterial hypertension (PAH) and are strongly linked to aberrant endothelial proliferation and impaired translational stress responses. While these effects are generally attributed to a loss of the type-II bone morphogenetic protein receptor (BMPR-II), we used circular RNA profiling to identify circ5078 as a new functional RNA derived from exon 12 of the BMPR2 gene. circ5078 and linear BMPR2 mRNA exert opposing effects on endothelial proliferation and stress granule formation, driving impaired stress responses in PAH patient-derived endothelial cells that are deficient in linear BMPR2 transcripts, but not circ5078. Rebalancing circular to linear transcript abundance by circ5078 depletion rescued stress granule formation in patient-derived endothelial cells, independent of BMPR-II protein levels. Polysome analysis demonstrated a reduction in free ribosomal subunits with the depletion of either linear or circular BMPR2 transcripts, and an accumulation of 80S monosomes exclusively with linear BMPR2 mRNA loss. These effects did not impact global protein synthesis or stress-induced eIF2 phosphorylation, but did alter the translational efficiency of multiple genes, including a group of nuclear encoded, mitochondrial ribosome proteins that were translationally enhanced with circ5078 silencing. Endothelial circ5078 depletion increased the efficiency of oxidative metabolism while reducing mitochondrial spare capacity, providing a potential link between mitochondrial function, proliferation and translational stress responses. Together, these findings reveal interdependent roles for linear and circular BMPR2 transcripts as functional contributors to the endothelial phenotype of PAH.

molecular biology↗

bioRxiv2023

The Herpes Simplex Virus pUL16 and pUL21 Proteins Prevent Capsids from Docking at Nuclear Pore Complexes

After entry into cells, herpes simplex virus (HSV) nucleocapsids dock at nuclear pore complexes (NPCs) through which viral genomes are released into the nucleoplasm where viral gene expression, genome replication, and early steps in virion assembly take place. After their assembly, nucleocapsids are translocated to the cytoplasm for final virion maturation. Nascent cytoplasmic nucleocapsids are prevented from binding to NPCs and delivering their genomes to the nucleus from which they emerged, but how this is accomplished is not understood. Here we report that HSV pUL16 and pUL21 deletion mutants accumulate empty capsids at the cytoplasmic face of NPCs late in infection. Additionally, prior expression of pUL16 and pUL21 prevented incoming nucleocapsids from docking at NPCs, delivering their genomes to the nucleus and initiating viral gene expression. Both pUL16 and pUL21 localized to the cytoplasmic face of the nuclear envelope, placing them in an appropriate location to interfere with nucleocapsid/NPC interactions.

microbiology↗

bioRxiv2023

A Multi-omic and Multi-Species Analysis of Right Ventricular Failure

Right ventricular failure (RVF) is a leading cause of morbidity and mortality in multiple cardiovascular diseases, but there are no approved treatments for RVF as therapeutic targets are not clearly defined. Contemporary transcriptomic/proteomic evaluations of RVF are predominately conducted in small animal studies, and data from large animal models are sparse. Moreover, a comparison of the molecular mediators of RVF across species is lacking. Here, we used transcriptomics and proteomics analyses to define the molecular pathways associated with cardiac MRI-derived values of RV hypertrophy, dilation, and dysfunction in pulmonary artery banded (PAB) piglets. Publicly available data from rat monocrotaline-induced RVF and pulmonary arterial hypertension patients with preserved or impaired RV function were used to compare the three species. Transcriptomic and proteomic analyses identified multiple pathways that were associated with RV dysfunction and remodeling in PAB pigs. Surprisingly, disruptions in fatty acid oxidation (FAO) and electron transport chain (ETC) proteins were different across the three species. FAO and ETC proteins and transcripts were mostly downregulated in rats, but were predominately upregulated in PAB pigs, which more closely matched the human data. Thus, the pig PAB metabolic molecular signature was more similar to human RVF than rodents. These data suggest there may be divergent molecular responses of RVF across species, and that pigs more accurately recapitulate the metabolic aspects of human RVF.

biochemistry↗