Biology subjects

Soon, E.

Publications and source records attributed to Soon, E..

4 recordsLinked to original sources

bioRxiv2026

Interrogation of the glycolytic axis in pulmonary arterial hypertension models and how modifying these can lead to potential therapeutic options.

IntroductionPulmonary arterial hypertension (PAH) describes diseases characterized by increased pulmonary vessel pressures that lead to right ventricular failure and death if left untreated. Dysregulated metabolic function has been reported in endothelial cells from PAH patients. Healthy endothelial cells can rapidly shift from quiescence to proliferative and apoptotic states, partly due to a greater utilization of glycolysis for ATP production, rather than the slower oxidative phosphorylation more commonly relied on by other cell types. However, in PAH patients, pulmonary artery endothelial cells demonstrate an even greater shift towards glycolytic ATP production. This phenomenon, which was first described in cancer as the Warburg effect, is an adaptation for optimizing both energy production and biosynthetic processes for maximum proliferative potential. Hypothesis and MethodsWe hypothesize that targeting the PKM2 axis in endothelial cells may shift the balance to favor oxidative phosphorylation, in effect reversing the Warburg effect; and that this would have beneficial effects in cell and rodent models of PAH. To this end we have tested TEPP-46, an allosteric PKM2 activator that stabilizes the tetrameric form, blocking its translocation into the nucleus and increasing canonical enzymatic activity, in blood outgrowth endothelial cells (BOECs) and in a rat Sugen-hypoxia model. ResultsTEPP-46 treatment reduced levels of nuclear PKM2 (the homodimer form which promotes anabolic effects and proliferation). Cytoplasmic levels of PKM2 and levels of PKM1 were unaffected. Exposure to TEPP-46 lowered levels of polypyrimidine tract-binding protein 1 (PTPB1), which controls alternative splicing of the PKM gene to promote PKM2 expression; and reduced LDHA, which converts pyruvate to lactate, preventing its utilization for oxidative phosphorylation. In the Sugen-hypoxia rat model, administration of TEPP-46 significantly ameliorated the elevated right ventricular systolic pressures, reduced the loss of body weight and increased survival. The increased muscularization of the smaller blood arteries and arterioles in the lungs of rats due to Sugen-hypoxia were also improved by concurrent administration of TEPP-46. ConclusionWe have shown that TEPP-46 treatment reduces nuclear PKM2 and represses PKM2-driven gene expression, with the functional effect of ameliorating the Sugen-hypoxia phenotype. This suggests that antagonizing the Warburg effect may offer a novel therapeutic avenue for PAH.

physiology↗

bioRxiv2025

Interleukin-6 is critical in the development of gcn2-mutation associated pulmonary vascular disease in mice

Biallelic mutations in eukaryotic translation initiation factor 2 kinase 4, EIF2AK4 (which encodes general control nonderepressible 2, GCN2) underpin heritable forms of pulmonary veno-occlusive disease (PVOD), a rare and fatal form of pulmonary hypertension. The mechanisms linking these are mostly uncharacterised. We demonstrate for the first time that homozygous loss of gcn2 is sufficient to cause mild pulmonary hypertension in mice. Single-cell transcriptomics of mouse lungs identified adventitial fibroblasts as having the greatest GCN2-dependent transcriptional differences, implicating them as key players in this model of PVOD. The most significantly upregulated pathways in gcn2-/- adventitial fibroblasts were inflammatory. Therefore, we went on to demonstrate a pro-inflammatory phenotype in gcn2-/- mouse embryonic fibroblasts and gcn2-/- mice. In a novel murine model of pulmonary hypertension induced by exposure to mitomycin C, deletion of interleukin-6 rescued the pulmonary vascular phenotype. When chronically exposed to lipopolysaccharide, the pulmonary hypertensive phenotype of gcn2-/- mice is exaggerated. Genetic ablation of interleukin-6 completely rescues both the baseline and LPS-exaggerated pulmonary hypertensive phenotype. Targeting Il6-dependent pathways may be useful in treating this deadly disease.

pathology↗

bioRxiv2021

Spatio-temporal coordination at the maternal-fetal interface promotes trophoblast invasion and vascular remodeling in the first half of human pregnancy

Beginning in the first trimester, fetally derived extravillous trophoblasts (EVTs) invade the uterus and remodel its spiral arteries, transforming them into large, dilated blood vessels left with a thin, discontinuous smooth muscle layer and partially lined with EVTs. Several mechanisms have been proposed to explain how EVTs coordinate with the maternal decidua to promote a tissue microenvironment conducive to spiral artery remodeling (SAR). However, it remains a matter of debate which immune and stromal cell types participate in these interactions and how this process evolves with respect to gestational age. Here, we used a multiomic approach that combined the strengths of spatial proteomics and transcriptomics to construct the first spatiotemporal atlas of the human maternal-fetal interface in the first half of pregnancy. We used multiplexed ion beam imaging by time of flight (MIBI-TOF) and a 37-plex antibody panel to analyze [~]500,000 cells and 588 spiral arteries within intact decidua from 66 patients between 6-20 weeks of gestation, integrating this with coregistered transcriptomic profiles. Gestational age substantially influenced the frequency of many maternal immune and stromal cells, with tolerogenic subsets expressing CD206, CD163, TIM-3, Galectin-9, and IDO-1 increasingly enriched and colocalized at later time points. In contrast, SAR progression preferentially correlated with EVT invasion and was transcriptionally defined by 78 gene ontology pathways exhibiting unique monotonic and biphasic trends. Lastly, we developed an integrated model of SAR supporting an intravasation mechanism where invasion is accompanied by upregulation of pro-angiogenic, immunoregulatory EVT programs that promote interactions with vascular endothelium while avoiding activation of immune cells in circulating maternal blood. Taken together, these results support a coordinated model of decidualization in which increasing gestational age drives a transition in maternal decidua towards a tolerogenic niche conducive to locally regulated, EVT-dependent SAR.

systems biology↗

bioRxiv2021

Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning

Understanding the spatial organization of tissues is of critical importance for both basic and translational research. While recent advances in tissue imaging are opening an exciting new window into the biology of human tissues, interpreting the data that they create is a significant computational challenge. Cell segmentation, the task of uniquely identifying each cell in an image, remains a substantial barrier for tissue imaging, as existing approaches are inaccurate or require a substantial amount of manual curation to yield useful results. Here, we addressed the problem of cell segmentation in tissue imaging data through large-scale data annotation and deep learning. We constructed TissueNet, an image dataset containing >1 million paired whole-cell and nuclear annotations for tissue images from nine organs and six imaging platforms. We created Mesmer, a deep learning-enabled segmentation algorithm trained on TissueNet that performs nuclear and whole-cell segmentation in tissue imaging data. We demonstrated that Mesmer has better speed and accuracy than previous methods, generalizes to the full diversity of tissue types and imaging platforms in TissueNet, and achieves human-level performance for whole-cell segmentation. Mesmer enabled the automated extraction of key cellular features, such as subcellular localization of protein signal, which was challenging with previous approaches. We further showed that Mesmer could be adapted to harness cell lineage information present in highly multiplexed datasets. We used this enhanced version to quantify cell morphology changes during human gestation. All underlying code and models are released with permissive licenses as a community resource.

bioinformatics↗