Biology subjects

Dunham-Snary, K. J.

Publications and source records attributed to Dunham-Snary, K. J..

4 recordsLinked to original sources

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↗

bioRxiv2025

Confidence: A Web App for Cross-Platform Differential Gene Expression Analysis, Gene Scoring, and Enrichment Analysis

RNA sequencing (RNA-seq) is used to quantify transcript levels through measurement of nucleotide sequences. To evaluate statistically significant changes in gene expression, transcript counts between samples are compared using differential expression analysis methods. However, three of the most pressing challenges in transcriptomics analyses are: 1) analytical packages produce a distinct number of differentially expressed genes with varied P-value and fold-change values; 2) the effective use of these analytical packages requires substantial knowledge of programming and bioinformatics; and 3) there are a lack of intuitive methods to select target genes for further investigation in an unbiased manner. To address these challenges, we developed Confidence, a web-based application to perform simultaneous statistical analysis of RNA-seq count data. Confidence incorporates the Confidence Score (CS), ranging from 1 to 4 to aid in gene prioritization, where 1 represents low confidence and 4 represents high confidence. The Confidence web-based application was designed for rapid and intuitive analysis of standard experimental metadata and gene count inputs. Confidence provided a web-based, wide-net approach to differential gene expression analysis. Gene scoring allows for unbiased gene selection and identification of novel genes strongly associated with disease and treatment models across multiple species. Additionally, pathway analysis tools have been integrated so that highly confident genes can be placed into biological context in terms of functions and pathways. Confidence provides a new strategy for target prioritization in RNA-seq analysis and the generation of publication-quality figures.

bioinformatics↗

bioRxiv2024

Multi-Tissue Metabolomics Reveal mtDNA- and Diet-Specific Metabolite Profiles in a Mouse Model of Cardiometabolic Disease

RationaleExcess consumption of sugar- and fat-rich foods has heightened the prevalence of cardiometabolic disease, which remains a driver of cardiovascular disease- and type II diabetes-related mortality globally. Skeletal muscle insulin resistance is an early feature of cardiometabolic disease and is a precursor to diabetes. Insulin resistance risk varies with self-reported race, whereby, African-Americans have a greater risk of diabetes development relative to their White counterparts. Self-reported race is strongly associated with mitochondrial DNA (mtDNA) haplogroups, and previous reports have noted marked differences in bioenergetic and metabolic parameters in cells belonging to distinct mtDNA haplogroups, but the mechanism of these associations remains unknown. Additionally, distinguishing nuclear DNA (nDNA) and mtDNA contributions to cardiometabolic disease remains challenging in humans. The Mitochondrial-Nuclear eXchange (MNX) mouse model enables in vivo preclinical investigation of the role of mtDNA in cardiometabolic disease development, and has been implemented in studies of insulin resistance, fatty liver disease, and obesity in previous reports. MethodsSix-week-old male C57nDNA:C57mtDNA and C3HnDNA:C3HmtDNA wild-type mice, and C57nDNA:C3HmtDNA and C3HnDNA:C57mtDNA MNX mice, were fed sucrose-matched high-fat (45% kcal fat) or control diet (10% kcal fat) until 12 weeks of age (n = 5/group). Mice were weighed weekly and total body fat was collected at euthanasia. Gastrocnemius skeletal muscle and plasma metabolomes were characterized using untargeted dual-chromatography mass spectrometry; both hydrophilic interaction liquid chromatography (HILIC) and C18 columns were used, in positive- and negative-ion modes, respectively. ResultsComparative analyses between nDNA-matched wild-type and MNX strains demonstrated significantly increased body fat percentage in mice possessing C57mtDNA regardless of nDNA background. High-fat diet in mice possessing C57mtDNA was associated with differential abundance of phosphatidylcholines, lysophosphatidylcholines, phosphatidylethanolamines, and glucose. Conversely, high-fat diet in mice possessing C3HmtDNA was associated with differential abundance of phosphatidylcholines, cardiolipins, and alanine. Glycerophospholipid metabolism and beta-alanine signaling pathways were enriched in skeletal muscle and plasma, indicating mtDNA-directed priming of mitochondria towards oxidative stress and increased fatty acid oxidation in C57nDNA:C57mtDNA wild-type and C3HnDNA:C57mtDNA MNX mice, relative to their nDNA-matched counterparts. In mtDNA-matched mice, C57mtDNA was associated with metabolite co-expression related to the pentose phosphate pathway and sugar-related metabolism; C3HmtDNA was associated with branched chain amino acid metabolite co-expression. ConclusionsThese results reveal novel nDNA-mtDNA interactions that drive significant changes in metabolite levels. Alterations to key metabolites involved in mitochondrial bioenergetic dysfunction and electron transport chain activity are implicated in elevated beta-oxidation during high-fat diet feeding; abnormally elevated rates of beta-oxidation may be a key driver of insulin resistance. The results reported here support the hypothesis that mtDNA influences cardiometabolic disease-susceptibility by modulating mitochondrial function and metabolic pathways.

molecular biology↗

bioRxiv2024

Platelet bioenergetics correlate with skeletal muscle metabolism in C57BL/6J mice

Skeletal muscle insulin resistance is a key step in progression of cardiometabolic disease, and impaired mitochondrial bioenergetics has been implicated. However, mitochondrial bioenergetic research in skeletal muscle is limited by the need for muscle biopsies. We sought to determine if platelet bioenergetics could be used as a minimally invasive surrogate for skeletal muscle bioenergetics. Multiple parameters of mitochondrial respiration, measured by high resolution respirometry, correlated between platelets and gastrocnemius muscle in mice. We propose the coupling state of platelet mitochondria reflects that of skeletal muscle in mice, providing a foundation for future research on using platelets as a liquid biopsy for muscle mitochondrial health in cardiometabolic disease, offering early insights into muscle metabolism to enhance clinical biomarker implementation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/626404v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1f65c4aorg.highwire.dtl.DTLVardef@125318borg.highwire.dtl.DTLVardef@d7bf1dorg.highwire.dtl.DTLVardef@442926_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗