Biology subjects

Dimitriou, A.

Publications and source records attributed to Dimitriou, A..

9 recordsLinked to original sources

bioRxiv2026

Hypoxia versus immune depletion - immune profiling and treatment cessation provide mechanistic insights and considerations for translation in Leigh syndrome

Genetic mitochondrial diseases (GMDs) are major challenges to human health accounting for a significant fraction of heritable neurologic diseases, myopathies, and inborn errors of metabolism. Leigh syndrome (LS) is the most common clinical presentation of GMD in pediatric patients. LS is a severe and complex disease for which effective clinical therapies are currently lacking. Preclinical therapies identified in the Ndufs4(-/-) mouse model of LS include immune-targeting interventions and chronic mild hypoxia (11% oxygen). Immune-targeting interventions include rapamycin and high-dose pexidartinib, the latter appearing to fully suppress disease. The mechanisms underlying the benefits of hypoxia remain unclear, and the relationship between hypoxia and immune interventions have not been assessed. Here, we report the immune profile of brainstem of the Ndufs4(-/-) mouse model prior to and after disease onset and the impact of pexidartinib treatment. We provide evidence that macrophages/monocytes drive pathology, consistent with recent genetic studies. We additionally find that pre-disease onset animals lack signs of inflammation, and that the elimination of leukocytes fully suppresses the molecular signature of disease. Finally, using distinct post-developmental periods of treatment, we find pexidartinib and rapamycin provide benefits which persist long beyond treatment cessation, while cessation of hypoxia results in rapid disease onset and an acceleration of disease progression. These findings are consistent with hypoxia acting upstream of immune cell activation and have major implications for the therapeutic translation of both hypoxia and immune targeting interventions. Our findings establish hypoxia-cessation as a novel method for synchronizing inflammatory disease onset in the Ndufs4(-/-) model which will be useful in future mechanistic studies.

pathology↗

bioRxiv2026

Counterfactual Explanations for Graph Neural Networks in Patient Outcome Prediction

Counterfactual Explanation (CE) algorithms have been successfully applied to uncover the main factors driving computational diagnostic and prognostic predictions on tabular medical data. Recently, a new Network Medicine paradigm has been introduced for patient diagnosis and prognosis using Patient Similarity Networks (PSNs), i.e. graphs where patients are represented as nodes and their clinical and biomolecular similarities as edges. In this context, graph-based algorithms, including Graph Neural Networks (GNNs), can provide predictions using not only individual patient features but also their relations within a network of clinically and biomolecularly similar individuals. In this work, we propose the first CE algorithm tailored to explain diagnostic and prognostic predictions within PSNs. Alongside a contrastive GNN backbone, we introduce a versatile, model-agnostic counterfactual search method compatible with any underlying classifier. Preliminary results on synthetic data and on a cohort of patients affected by the Alzheimers disease show that our algorithm is competitive both with seminal tabular based CE algorithms and GNNExplainer, a well-established method for explaining graph-based classification tasks.

bioinformatics↗

bioRxiv2026

MyD88 deficiency modestly attenuates disease in a Leigh syndrome mouse model while enrofloxacin accelerates disease

Primary genetic mitochondrial diseases (GMDs) are a clinically and genetically diverse group of diseases estimated to impact over 1 in 4,000 individuals. Leigh syndrome (LS) is the most common pediatric presentation of GMD. LS typically presents within the first years of life and is a severe progressive multi-system disorder. Symmetric progressive inflammatory brain lesions are a defining feature of the disease. Patients can also present with seizures, metabolic dysfunction, muscle weakness, and other symptoms. No effective clinical treatments currently exist. Recent data from the Ndufs4(-/-) mouse model shows that peripheral macrophages contribute to brain lesions in LS, that disease is causally driven by innate immune populations, and that depletion of innate immune cells prevents LS disease. However, the precise mechanisms underlying immune activation remain unknown. Certain mitochondrial macromolecules retain bacterial signatures and can act as potent agonists for innate immune pathways. For example, cytoplasmic mitochondrial RNA and mitochondrial DNA are detected by Toll-like receptors (TLRs) 7 and 9, respectively, at the endosome. Accordingly, these are considered strong candidates for mediating innate immune activation in LS. Here, we generated TLR signaling deficient Ndufs4(-/-)/MyD88(-/-) animals to assess whether TLR signaling plays a role in disease onset or progression in LS. Loss of MyD88 in Ndufs4(-/-) animals statistically significantly increased survival and delayed the onset of some symptoms, but the benefits were modest compared to CSF1R inhibition from prior work. We conclude that Myd88-mediated immune signaling is not a primary driver of LS. Notably, prophylactic enrofloxacin treatment, which was necessary for production of innate immune deficient MyD88(-/-) animals, modestly decreased survival and accelerated disease. The impact of enrofloxacin and similar drugs in the context of mitochondrial disease warrants further investigation.

neuroscience↗

bioRxiv2026

Sharing the trail: recreation effects on bear behaviour in a Canadian Rocky Mountain Park

Humans are profoundly reshaping the natural world. These changes are giving rise to complex and mutually risky dynamics between people and large carnivores. In protected areas across North America, bears (Ursus sp.) face rapidly rising recreation pressures that can alter their use of the landscape, either displacing them from high-quality habitats or drawing them into human-wildlife conflicts through habituation or attraction to anthropogenic resources. However, disentangling responses to recreation from other drivers can be difficult because human activity covaries with environmental and seasonal processes that also shape bear activity. We leveraged the partial closure of the popular Berg Lake Trail in Mount Robson Park, British Columbia, Canada, to investigate whether black (Ursus americanus) and grizzly bears (Ursus arctos) showed fear, attraction or neutral behavioural responses to varying recreation levels across multiple spatiotemporal scales. To understand both anticipatory responses to predictable patterns of human activity, and reactive responses to hiker events, we used detections from 43 camera traps over two years (July 2023-June 2025). We compared weekly habitat use, daily activity patterns, and direct responses to hikers (using Avoidance-Attraction Ratios; AARs) among camera sites and between open and closed sections of the trail. Our results revealed that both bear species exhibited patterns consistent with fear responses, while some black bear behaviours were also consistent with attraction responses. Both kinds of responses reflect anticipatory strategies rather than reactionary behaviours (i.e., no AAR effect). Neither species avoided recreation spatially at the weekly scale: black bears were detected more at site-weeks with greater recreation intensity, while grizzly bears were consistently detected more at sites closer to hiking trails. However, both species used daily temporal partitioning to avoid direct encounters with humans. These findings demonstrate scope for human-bear coexistence when recreation levels are managed to be moderate and predictable, and bears have sufficient space to segregate from humans during peak times. Thus, successful coexistence will hinge on co-adaptation by both bears and people. Understanding how recreation influences bear behaviour, and the spatiotemporal scale at which that occurs, is critical for guiding effective adaptive management aimed at fostering human-bear coexistence in high-traffic protected areas.

ecology↗

bioRxiv2026

The effect of outdoor recreation on mammal habitat use and diversity revealed by COVID-19 closures

The rising demand for outdoor recreation worldwide may be undermining the conservation objectives of protected areas (PAs). We leveraged a natural experiment, in which two adjacent PAs were closed to the public for different durations during the COVID-19 pandemic. Using detections from 39 camera traps in Joffre Lakes and Garibaldi Parks, Canada, from 2020-2022, we examined how recreation influenced mammal habitat use and diversity. Bayesian regression showed weak evidence that, when recreation was higher, detections declined for black bear, mule deer, and marten, while detections of bobcat and hoary marmot shifted closer to trails. Accumulation curves revealed that species richness and diversity were higher in the closed vs. open PA in 2020 (mean differences of -5.04 for richness and -0.33 for Shannon diversity). However, diversity did not decline consistently despite increases in recreation in 2021 and 2022. Notably, several rare species were only detected in the lower-recreation PA, suggesting they may be filtered out of the higher-recreation PA. This emphasizes the need for long-term monitoring to detect delayed and cumulative effects of recreation on mammal communities. Given growing global pressures on biodiversity, we urge PA managers to prioritize adaptive management to assess and balance outdoor recreation with conservation goals.

ecology↗

bioRxiv2024

Skeletal Muscle Mitochondrial Dysfunction Mediated by Pseudomonas aeruginosa Quorum Sensing Transcription Factor MvfR: Reversing Effects with Anti-MvfR and Mitochondrial-Targeted Compounds

Sepsis and chronic infections with Pseudomonas aeruginosa, a leading "ESKAPE" bacterial pathogen, are associated with increased morbidity and mortality and skeletal muscle atrophy. The actions of this pathogen on skeletal muscle remain poorly understood. In skeletal muscle, mitochondria serve as a crucial energy source, which may be perturbed by infection. Here, using the well-established backburn and infection model of murine P. aeruginosa infection, we deciphered the systemic impact of the quorum sensing (QS) transcription factor MvfR by interrogating five days post-infection its effect on mitochondrial-related functions in the gastrocnemius skeletal muscle and the outcome of the pharmacological inhibition of MvfR function and that of the mitochondrial-targeted peptide, Szeto-Schiller 31 (SS-31). Our findings show that the MvfR perturbs ATP generation, oxidative phosphorylation (OXPHOS), and antioxidant response, elevates the production of reactive oxygen species, and promotes oxidative damage of mitochondrial DNA in the gastrocnemius muscle of infected mice. These impairments in mitochondrial-related functions were corroborated by the alteration of key mitochondrial proteins involved in electron transport, mitochondrial biogenesis, dynamics and quality control, and mitochondrial uncoupling. Pharmacological inhibition of MvfR using the potent anti-MvfR lead, D88, we developed, or the mitochondrial-targeted peptide SS-31 rescued the MvfR- mediated alterations observed in mice infected with the wild-type strain PA14. Our study provides insights into the actions of MvfR in orchestrating mitochondrial dysfunction in the skeletal murine muscle, and it presents novel therapeutic approaches for optimizing clinical outcomes in affected patients.

microbiology↗

bioRxiv2020

A Micro-engineered Human Colon Intestine-Chip Platform to Study Leaky Barrier

The intestinal epithelial barrier supports the symbiotic relationship between the microbiota colonizing the intestinal epithelium and the host immune system to maintain homeostasis. Leaky barrier is increasingly recognized as part of the pathogenesis of a number of chronic conditions in addition to inflammatory and infectious diseases. As our understanding on the regulation of the barrier remains limited, effective therapeutic targeting for the compromised barrier is still an unmet need. Here we combined advancements on the organoids and Organ-on-Chip technologies to establish a micro-engineered Colon Intestine-Chip for studying development and regulation of the human intestinal barrier. Our data demonstrate the significance of the endothelium in co-culture with the epithelial cells within a tissue-relevant microenvironment for the establishment of a tight epithelial barrier of polarized cells. Pathway analysis of the RNA sequencing (RNA-Seq), revealed significant upregulation of mechanisms relevant to the maturation of the intestinal epithelium in organoid-derived epithelial cells in co-culture with endothelium as compared to organoids maintained in suspension. We provide evidence that the Colon Intestine-Chip platform responds to interferon gamma (IFN{gamma}), a prototype cytokine utilized to model inflammation-induced barrier disruption, by induction of apoptosis and reorganization of the apical junctional complexes as shown with other systems. We also describe the mechanism of action of interleukin 22 (IL-22) on mature, organoid-derived intestinal epithelial cells that is consistent with barrier disruption. Overall we propose the Colon Intestine-Chip as a promising human organoid-derived platform to decipher mechanisms driving the development of leaky gut in patients and enable their translation for this unmet medical need.

bioengineering↗

bioRxiv2020

Positively selected modifications in the pore of TbAQP2 allow pentamidine to enter Trypanosoma brucei

Mutations in the Trypanosoma brucei aquaporin AQP2 are associated with resistance to pentamidine and melarsoprol. We show that TbAQP2 but not TbAQP3 was positively selected for increased pore size from a common ancestor aquaporin. We demonstrate that TbAQP2s unique architecture permits pentamidine permeation through its central pore and show how specific mutations in highly conserved motifs affect drug permeation. Introduction of key TbAQP2 amino acids into TbAQP3 renders the latter permeable to pentamidine. Molecular dynamics demonstrates that permeation by dicationic pentamidine is energetically favourable in TbAQP2, driven by the membrane potential, although aquaporins are normally strictly impermeable for ionic species. We also identify the structural determinants that make pentamidine a permeant but exclude most other diamidine drugs. Our results have wide-ranging implications for optimising antitrypanosomal drugs and averting cross-resistance. Moreover, these new insights in aquaporin permeation may allow the pharmacological exploitation of other members of this ubiquitous gene family.

biochemistry↗

bioRxiv2019

The finger 2 tip loop of Activin A is required for the formation of its non-signaling complex with ACVR1 and type II Bone Morphogenetic Protein receptors

Activin A functions in BMP signaling in two ways: it either engages ACVR1B to activate Smad2/3 signaling or binds ACVR1 to form a non-signaling complex (NSC). Although the former property has been studied extensively, the roles of the NSC remain unexplored. The genetic disorder fibrodysplasia ossificans progressiva (FOP) provides a unique window into ACVR1/Activin A signaling because in that disease Activin can either signal through FOP-mutant ACVR1 or form NSCs with wild type ACVR1. To explore the role of the NSC, we generated agonist-only Activin A muteins that activate ACVR1B but cannot form the NSC with ACVR1. Using one of these muteins we demonstrate that failure to form the NSC in FOP results in more severe disease pathology. These results provide the first evidence for a biological role for the NSC in vivo and pave the way for further exploration of the NSCs physiological role in corresponding knock-in mice. Impact StatementThe non-signaling complex formed by Activin A and ACVR1 is operant in vivo and is required to temper the degree of heterotopic ossification in the genetic disorder fibrodysplasia ossificans progressiva.

cell biology↗