Biology subjects

Doran, S.

Publications and source records attributed to Doran, S..

5 recordsLinked to original sources

bioRxiv2025

Integrative Analysis of Left Ventricle and Epicardial Adipose Tissue Identifies SDHA and OGDH as Candidate Targets for Ischemic Heart Disease

Ischemic heart disease (IHD) involves coordinated molecular changes across heart, yet their interplay remains poorly understood. Here, we investigated transcriptomic alterations in two heart tissue subtypes, left ventricle (LV) and epicardial adipose tissue (EAT), from age- and BMI-matched healthy and IHD individuals, including both diabetic and non-diabetic patients. We performed transcriptomic profiling and systems-level network analysis to identify disease-associated gene expression changes. Our analysis revealed: (1) stronger transcriptional responses in EAT compared to LV, particularly in diabetic individuals, and (2) widespread dysregulation of inflammatory and metabolic pathways, including oxidative phosphorylation, cytokine signaling, and fatty acid degradation, across both tissue subtypes. Co-expression network analysis uncovered shared gene modules, with SDHA (Succinate dehydrogenase complex, subunit A) and OGDH (Oxoglutarate Dehydrogenase) emerging as central, downregulated genes linked to mitochondrial function and inflammation, important processes in IHD pathophysiology. These findings were validated in independent human and mouse datasets. Overall, our integrative analysis identifies conserved molecular signatures across cardiac tissue subtypes, suggesting potential for therapeutic exploration in IHD. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/676232v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@7e17eeorg.highwire.dtl.DTLVardef@552321org.highwire.dtl.DTLVardef@1755f30org.highwire.dtl.DTLVardef@bc5872_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2024

Circadian control in the timing of critical periods during Drosophila larval neuronal development.

Critical periods (CPs) of development are temporal windows of heightened neural plasticity. Activity perturbation during CPs can produce significant, and permanent, alterations to the development of neural circuits. In this study we report a circadian mechanism underlying the timing of CPs in Drosophila embryonic and larval development. These CPs occur at [~]24 hr intervals and are open to manipulation through blue light (BL)-activation of the circadian regulator Cryptochrome (CRY). This manipulation is sufficient to destabilize the larval CNS, evidenced by an induced seizure phenotype when tested at third instar (L3). In addition to CRY nulls, genetic ablation of the period gene also mitigates the BL exposure seizure phenotype and, moreover, alleles of period that affect circadian timing alter the timing of the CPs. Our analysis shows a clear role for the main clock neuropeptide, pigment dispersing factor (PDF), to transduce the output of these CPs. Targeted PDF receptor knockdown, in either GABAergic or CRY-positive neurons, is sufficient to prevent the CRY-mediated seizure phenotype. This study is a first demonstration of a circadian mechanism in Drosophila larvae, and whilst this alone is of major significance, our results highlight the potential of using Drosophila larvae as a model to investigate the impact of circadian rhythms on early neuronal development in higher organisms, which remains experimentally challenging. Significance StatementWhilst the role of the biological clock is well understood in adult organisms, the same is not true for embryonic development. How the maternal clock impacts the mammalian fetus remains poorly understood. Given that many expectant mothers experience altered circadian rhythms, largely due to nightshift working, it is important to address these concerns. Here we identify clock-mediated periods in neural development of the embryonic Drosophila which can be manipulated by light. These findings provide an experimental opportunity to better understand the role of the circadian clock in early development.

neuroscience↗

bioRxiv2020

Revealing tissue-specific metabolic crosstalk after a myocardial infarction

Abstract/SummaryMyocardial infarction (MI) promotes a range of systemic effects, many of which are unknown. Here, we investigated the alterations associated with MI progression in heart and other metabolically active tissues (liver, skeletal muscle, and adipose) in a mouse model of MI (induced by ligating the left ascending coronary artery) and sham-operated mice. We performed a genome-wide transcriptomic analysis on tissue samples obtained 6- and 24-hours post MI or sham operation. By generating tissue-specific biological networks, we observed: (1) dysregulation in multiple biological processes (including immune system, mitochondrial dysfunction, fatty-acid beta-oxidation, and RNA and protein processing) across multiple tissues post MI; and (2) tissue-specific dysregulation in biological processes in liver and heart post MI. Finally, we validated our findings in two independent MI cohorts. Overall, our integrative analysis highlighted both common and specific biological responses to MI across a range of metabolically active tissues.

systems biology↗

bioRxiv2020

Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS.

Gas chromatography-mass spectrometry (GC-MS) represents an analytical technique with significant practical societal impact. Spectral deconvolution is an essential step for interpreting GC-MS data. No public GC-MS repositories that also enable repository-scale analysis exist, in part because deconvolution requires significant user input. We therefore engineered a scalable machine learning workflow for the Global Natural Product Social Molecular Networking (GNPS) analysis platform to enable the mass spectrometry community to store, process, share, annotate, compare, and perform molecular networking of GC-MS data. The workflow performs auto-deconvolution of compound fragmentation patterns via unsupervised non-negative matrix factorization, using a Fast Fourier Transform-based strategy to overcome scalability limitations. We introduce a "balance score" that quantifies the reproducibility of fragmentation patterns across all samples. We demonstrate the utility of the platform with breathomics analysis applied to the early detection of oesophago-gastric cancer, and by creating the first molecular spatial map of the human volatilome.

bioinformatics↗

bioRxiv2019

Phosgene Inhalation Causes Hemolysis and Acute Lung Injury

Phosgene (Carbonyl Chloride, COCl2) remains an important chemical intermediate in many industrial processes such as combustion of chlorinated hydrocarbons and synthesis of solvents (degreasers, cleaners). It is a sweet smelling gas, and therefore does not prompt escape by the victim upon exposure. Supplemental oxygen and ventilation are the only available management strategies. This study was aimed to delineate the pathogenesis and identify novel biomarkers of acute lung injury post exposure to COCl2 gas. Adult male and female C57BL/6 mice (20-25 g), exposed to COCl2 gas (10 or 20ppm) for 10 minutes in environmental chambers, had a dose dependent reduction in PaO2 and an increase in PaCO2, 1 day post exposure. However, mortality increased only in mice exposed to 20ppm of COCl2 for 10 minutes. Correspondingly, these mice (20ppm) also had severe acute lung injury as indicated by an increase in lung wet to dry weight ratio, extravasation of plasma proteins and neutrophils into the bronchoalveolar lavage fluid, and an increase in total lung resistance. The increase in acute lung injury parameters in COCl2 (20ppm, 10min) exposed mice correlated with simultaneous increase in oxidation of red blood cells (RBC) membrane, RBC fragility, and plasma levels of cell-free heme. In addition, these mice had decreased plasmalogen (plasmenylethanolamine) and elevated levels of their breakdown product, polyunsaturated lysophosphatidylethanolamine, in the circulation suggesting damage to cellular plasma membranes. This study highlights the importance of free heme in the pathogenesis of COCl2 lung injury and identifies plasma membrane breakdown product as potential biomarkers of COCl2 toxicity.

physiology↗