Biology subjects

Kalatanova, A.

Publications and source records attributed to Kalatanova, A..

3 recordsLinked to original sources

bioRxiv2025

ODDB: Ocular Disease Database for integrated analysis of ocular disease gene drug relationships

Ocular diseases such as age-related macular degeneration, glaucoma, diabetic retinopathy, and inherited retinal dystrophies are leading causes of vision loss worldwide, yet existing databases often address only limited aspects of these disorders. To fill this gap, we developed the Ocular Disease Database (ODDB), a web-based resource that integrates genes, biomarkers, variants, and drugs associated to ocular diseases. Data were systematically collected through literature mining of PubMed-indexed journals, the NCBI Gene Expression Omnibus (GEO), and drug regulatory agency datasets. Multi-omics, experimental, and clinical information were harmonized using standardized integration workflows. The database is organized according to two complementary ontologies: one based on the anatomical site of pathology (cornea, retina, optic nerve) and another on gene inheritance pattern. ODDB currently covers over 170 ocular diseases, more than 1190 genes, 2400+ variants, and 386 drugs, including both approved and investigational compounds. Each record includes detailed annotations of associated genes, variants, therapeutic targets, and mechanisms of action. The platform supports interactive querying and network-based visualization of disease-gene-drug relationships. All data was internally validated for accuracy and are compliant with FAIR principles, ensuring accessibility and interoperability. ODDB (https://www.oculardiseases.fi/) provides a comprehensive and standardized reference for exploring molecular mechanisms and therapeutic opportunities in ocular diseases.

bioinformatics↗

bioRxiv2025

Female sex is a risk factor for exacerbated lipid peroxidation and disease in murine retinitis pigmentosa

Oxidative stress is an important aspect in retinal degenerations that could be targeted in various forms of currently untreatable diseases. It is generally believed that males are more predisposed to oxidative stress than females due to their higher metabolic activity and/or lower antioxidant capacity. However, studies using mouse disease models have demonstrated that photoreceptor degeneration progresses faster in females. Sex hormones likely play a role, but the cellular mechanism behind the sex difference is unclear. In the current study, we confirmed that the accelerated disease phenotype in female rd10 and P23H retinitis pigmentosa mice coincides with sexual maturity, and further, we found that it co-occurs with increased retinal lipid peroxidation. Instead, protein oxidation and inflammatory marker levels were similar between the sexes. Retinal lipid profiling revealed higher levels of polyunsaturated fatty acid (PUFA)-containing lipids in healthy 2-month-old female mice compared to males, whereas before puberty the sex difference in retinal PUFAs was absent. Analysis of open bulk retina transcriptomic data from middle-aged humans found supplemental evidence of sex-related differences in retinal energy metabolism pathways. Besides mechanistic study directed to reveal the reasons for differential lipid peroxidation between sexes, more research needs to be directed to study sex differences in retinal metabolism and lipid composition across animal species. The current results highlight the need to consider the impact of sex differences when undertaking preclinical experiments with RP models. Significance statementThis article suggests female sex as a significant risk factor for progressive photoreceptor degenerative disease, based on experiments in two widely used retinitis pigmentosa mouse models. The disease phenotype in females accelerates markedly after sexual maturity, especially in mice carrying the autosomal dominant P23H rhodopsin mutation. This acceleration is associated with intensified retinal lipid peroxidation. Given the retinas high energy demand, continuous photoreceptor cilia renewal, and constant light exposure that generates reactive oxygen species, the susceptibility of photoreceptor membranes to oxidative damage is substantial. Our findings suggest that retinal metabolism may differ between sexes after puberty, potentially influenced by sex hormones, which could contribute to the increased vulnerability of females to photoreceptor degenerative diseases.

physiology↗

bioRxiv2024

Organic opto-nanobiointerface enables multiscale biomodulation

Virtually all organic material on Earth has been produced converting solar energy through photosynthesis in chloroplasts, a sack-like, double membrane organelle in plants and algae, where transmembrane electron transfer occurs from lumen to stroma. Although animals hardly harness the power of photosynthesis, their bioelectrical signals extensively regulate complex electrophysiological behaviors, rendering it a superior target for biomedical innovation. Here, a crude structural mimicry of chloroplast has led us to discover that hollow sphere graphitic carbon nitride nanoparticles (hg-C3N4 NPs) endowed non-genetic, subcellular and intercellular photo-modulation of various excitable and non-excitable cells, accumulatively achieving modulation at tissue/organ function level. The homogeneous hg-C3N4 NPs showed responsiveness to light via both photoelectrochemical and photothermal mechanisms. The hg-C3N4 NPs can be spontaneously internalized with excellent cytocompatibility. Using a focusing laser, the hg-C3N4 NPs enable intracellular optical stimulation with subcellular resolution, inducing calcium transient release in multiple cells and propagation in primary cardiomyocytes and cardiac fibroblasts. At multicellular scale, optical pacing and synchronization of cardiomyocyte beating is readily achieved by LED. Further, we demonstrate that hg-C3N4 nanoparticles can be safely delivered into the mouse eye and elicit measurable cortical and behavioral light responses in a subset of animals in a model of advanced retinal degeneration. Finally, application of hg-C3N4 NPs to porcine retinal tissue ex vivo confirmed their modulation capability to directly activate RGCs activity under LED photostimulation. Taken together, these nanostructured biomimetic photocatalytic NPs offer high resolution, leadless optical probing, non-invasive delivery and great biocompatibility, serving as a versatile tool for addressing a range of complex biomedical challenges through subcellular, intercellular and tissue-level photo-modulation across a broad spectrum of scales.

bioengineering↗