Biology subjects

Kelly, N.

Publications and source records attributed to Kelly, N..

4 recordsLinked to original sources

bioRxiv2025

Lactate dehydrogenase-induced DNA Topoisomerase 1 is a novel regulator of smooth muscle cell proliferation and remodeling in pulmonary arterial hypertension

Pulmonary arterial hypertension (PAH) manifests by increased proliferation and survival of pulmonary vascular cells in small pulmonary arteries (PAs), PA remodeling and unresolved increase of PA pressure. PA smooth muscle cells (PASMCs) in PAH undergo metabolic shift to glycolysis resulting in over-production of lactate, hyper-proliferation, and apoptosis resistance, but the mechanisms are not completely understood. By using lung tissues and pulmonary vascular cells from PAH and non-diseased human lungs, unbiased proteomics, network analysis, and gain-and-loss of function approaches, we here report that up-regulation of lactate dehydrogenase A (LDHA)-lactate axis promotes PASMC-specific over-lactylation and consequent over-accumulation of DNA topoisomerase 1 (TOP1) in small remodeled PAs from PAH lungs, leading to the up-regulation of Akt-mechanistic target of rapamycin 1 (mTORC1) signaling, hyper-proliferation, and reduced apoptosis. Smooth muscle-specific LDHA knockdown prevented, and Ldha inhibitor oxamate reversed SU5416/hypoxia-induced TOP1 accumulation, pulmonary vascular remodeling, and pulmonary hypertension (PH) in mice. Pharmacological inhibition of TOP1 with indotecan suppressed Akt-mTORC1, decreased proliferation, induced apoptosis in human PAH, but not control PASMCs, and reversed PA remodeling, PH, and RV dysfunction in rats. Collectively, these data provide a novel mechanistic link from LDHA-driven lactate over-production through lactylation and overaccumulation of TOP1, to the up-regulation of Akt-mTORC1, hyper-proliferation and apoptosis resistance of PASMCs, pulmonary vascular remodeling, and PH, and identify TOP1 as a new potentially attractive molecular target for the remodeling-focused therapeutic intervention. Take-home messageLDHA-lactate-induced over-lactylation and overaccumulation of Topoisomerase 1 (TOP1) promotes pulmonary artery smooth muscle cell hyper-proliferation, remodeling, and pulmonary arterial hypertension, which are reversed by TOP1 inhibitor indotecan.

cell biology↗

bioRxiv2025

DRP1/DMNL-1-mediated mitochondrial fission augments Rickettsia parkeri replication in macrophages

Pathogenic Spotted Fever Group (SFG) Rickettsia species, including Rickettsia parkeri replicate in endothelial cells, monocytes, and macrophages in vitro and during infections in murine models of disease. We demonstrated that R. parkeri survives and proliferates within phagocytes and avoids intracellular killing within lysosomal compartments. We found that infection of human macrophage-like cells with a related SFG Rickettsia, R. conorii, resulted in a significant increase in mitochondria-associated proteins, suggesting that mitochondrial functions are involved in Rickettsia pathogenesis. Several intracellular bacterial pathogens manipulate host cell mitochondrial networks and stimulate mitochondrial fission mediated by a GTP-binding regulatory protein, DRP1/DMNL1, to promote intracellular replication. Here, we investigated the contribution of DRP1 in the growth of R. parkeri in macrophages. Murine immortalized bone marrow derived macrophages (iBMDMs) and primary human monocyte derived macrophages were infected with R. parkeri and mitochondrial dynamics (fission and network) were assessed by immunofluorescence microscopy. R. parkeri proliferated in macrophages, which coincided with a significant increase in mitochondria content and fission compared to uninfected cells. R. parkeri infection led to increases in host cell ATP production primarily due to mitochondrial respiration and bacteria were often found co-localized with mitochondrial fragments. Importantly, R. parkeri growth was significantly impacted in DRP1 deficient macrophages. These results suggest that the modulation of mitochondria content and dynamics are essential for replication and survival of pathogenic SFG Rickettsia species in macrophages and suggest that the metabolic requirements for obligate intracellular pathogens may differ from other pathogenic Gram-negative intracellular bacteria.

microbiology↗

bioRxiv2022

The topological shape of gene expression across the evolution of flowering plants

Since they emerged ~125 million years ago, flowering plants have evolved to dominate the terrestrial landscape and survive in the most inhospitable environments on earth. At their core, these adaptations have been shaped by changes in numerous, interconnected pathways and genes that collectively give rise to emergent biological phenomena. Linking gene expression to morphological outcomes remains a grand challenge in biology, and new approaches are needed to begin to address this gap. Here, we implemented topological data analysis (TDA) to summarize the high dimensionality and noisiness of gene expression data using lens functions that delineate plant tissue and stress responses. Using this framework, we created a topological representation of the shape of gene expression across plant evolution, development, and environment for the phylogenetically diverse flowering plants. The TDA-based Mapper graphs form a well-defined gradient of tissues from leaves to seeds, or from healthy to stressed samples, depending on the lens function. This suggests there are distinct and conserved expression patterns across angiosperms that delineate different tissue types or responses to biotic and abiotic stresses. Genes that correlate with the tissue lens function are enriched in central processes such as photosynthetic, growth and development, housekeeping, or stress responses. Together, our results highlight the power of TDA for analyzing complex biological data and reveal a core expression backbone that defines plant form and function. Significance statementA grand challenge in biology is to link gene expression to phenotypes across evolution, development, and the environment, but efforts have been hindered by biological complexity and dataset heterogeneity. Here, we implemented topological data analysis across thousands of gene expression datasets in phylogenetically diverse flowering plants. We created a topological representation of gene expression across plants and observed well-defined gradients of tissues from leaves to seeds, or from healthy to environmentally stressed. Using this framework, we identified a core and deeply conserved expression backbone that defines plant form and function, with key patterns that delineate plant tissues, abiotic, and biotic stresses. Our results highlight the power of topological approaches for analyzing complex biological datasets.

plant biology↗

bioRxiv2019

Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition

Agricultural soil harbors a diverse microbiome that can form beneficial relationships with plants, including the inhibition of plant pathogens. Pseudomonas spp. are one of the most abundant bacterial genera in the soil and rhizosphere and play important roles in promoting plant health. However, the genetic determinants of this beneficial activity are only partially understood. Here, we genetically and phenotypically characterize the Pseudomonas fluorescens population in a commercial potato field, where we identify strong correlations between specialized metabolite biosynthesis and antagonism of the potato pathogens Streptomyces scabies and Phytophthora infestans. Genetic and chemical analyses identified hydrogen cyanide and cyclic lipopeptides as key specialized metabolites associated with S. scabies inhibition, which was supported by in planta biocontrol experiments. We show that a single potato field contains a hugely diverse and dynamic population of Pseudomonas bacteria, whose capacity to produce specialized metabolites is shaped both by plant colonization and defined environmental inputs.

microbiology↗