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Ilmjarv, S.

Publications and source records attributed to Ilmjarv, S..

2 recordsLinked to original sources

Deciphering auditory neuroprogenitor stemness for large-scale neuronal screening

Sensorineural hearing loss can arise from damage to sensory hair cells, auditory neurons or their synaptic connections, with auditory neuropathy and cochlear synaptopathy highlighting the importance of neural integrity for hearing. The mammalian cochlea has limited capacity to regenerate lost auditory neurons. Understanding the molecular programs that sustain cochlear progenitor expansion and neurogenic competence could support neuronal regeneration and provide renewable models for auditory drug discovery. We previously established that WNT activation combined with dual SMAD inhibition (CHIR-DS) supports scalable expansion and neuronal differentiation of mouse auditory neuroprogenitors (ANPGs). Here, we characterize the transcriptional, chromatin and metabolic changes associated with the induced state. RNA-seq and ATAC-seq identified reduced Id1 and Id2 expression and increased accessibility at proneural basic helix-loop-helix motifs, alongside transcriptional enrichment of translation, mTOR and glucose-metabolism programs. Compared with growth-factor controls, CHIR-DS-treated ANPGs showed slight increase in glycolysis at early passage. However, after long-term expansion, both glycolysis and mitochondrial respiration were markedly enhanced. Human fetal ANPGs also responded to CHIR-DS with increased sphere growth and retained neural differentiation capacity, providing proof of concept beyond the mouse system. Finally, neurons derived from stemness-induced ANPGs (siANs) supported a 384-well reporter assay and a 2,560-compound pilot screen that nominated candidate neurite-outgrowth enhancers. Together, these findings validate the pathway basis of ANPG stemness induction, characterize the resulting molecular and metabolic state, and demonstrate human feasibility and a neuronal screening application.

neuroscience↗

Navigating in vitro bioactivity data: investigating available resources using model compounds

Modern medicine and an increasingly complex environment contribute to exposure of humans to a large number of chemical compounds, that can potentially be toxic. Although widely used, compound testing in animals has important limitations. In vitro testing provides a promising alternative. However, because of the relative inaccessibility and fragmentation of available data, the in vitro approach largely underperforms its potential. The aim of this study is to investigate how available public online resources (tools and databases) support accessing and distribution of in vitro compound data. We examined 19 public online resources, mapped their features, and evaluated their usability with a set of four model compounds (aspirin, rosiglitazone, valproic acid, and tamoxifen). By investigating compound names and identifiers, we observed extensive variation and inconsistencies in available resources: the synonyms were different, compounds structural identifiers (InChI, InChIKey, SMILES and IUPAC systematic name) underperformed in omics databases, identification of compound related metadata (e.g. concentrations used in the experiments) from omics experiments was complex and none of the available resources clearly distinguished between in vivo and in vitro data. In addition, we estimated accessibility of selected public resources using computational queries. Only a few public resources provided access to compound-related data using semantic web technology. The general quality of experiment annotations created further difficulties in identifying data of interest. Therefore, we identified several standardized ontologies with potential to provide an increased accuracy for extensive data retrieval of in vitro compound data. Furthermore, using the examples of our model compounds, we provide recommendations on the use of ontologies by suggesting specific ontology terms to annotate in vitro experimental data when being published.

pharmacology and toxicology↗