Biology subjects

Mijdam, R.

Publications and source records attributed to Mijdam, R..

3 recordsLinked to original sources

bioRxiv2026

Dissecting the sources of variation in neuronally differentiated iPSC lines through multi-omics analysis

Induced pluripotent stem cells (iPSCs) are widely used as patient-specific disease models, yet substantial unexplained variability in molecular and functional readouts limits their reliability. Here, we systematically investigated the sources of variation in iPSC-derived neurons for three rare genetic disorders: Myotonic Dystrophy Type 1, chromodomain-DNA-helicase-binding protein 2-related disorder and N-acetylneuraminic acid synthase deficiency. This was performed by profiling multi-omics layers: genomics, epigenomics, transcriptomics, proteomics, metabolomics and lipidomics. Our study found that clonal variability was comparable to inter-patient differences and that neuronal differentiation state and nutrient-driven metabolic activity emerged as dominant contributors to variability observed across omics layers. Clonal differences could partly be attributed to stochastic differences in DNA methylation established during reprogramming. By modeling and correcting the observed variation, we improved the detection of disease-associated molecular signatures. Our study provides guidelines for improved study design and data analysis to minimize variability, enabling robust biomarker discovery and reliable iPSC-based disease modeling.

cell biology↗

bioRxiv2025

Targeting AASS improves neurotoxicity and mitochondrial function in astrocyte models for pyridoxine dependent epilepsy

Pyridoxine-dependent epilepsy (PDE) is a rare neurometabolic disorder of lysine catabolism caused by bi-allelic variants in ALDH7A1. This enzyme deficiency leads to the accumulation of neurotoxic metabolites, pyridoxal-phosphate inactivation and consequently severe neurological symptoms. Current treatments, including vitamin B6 supplementation and lysine-restricted diets, partially alleviate seizures and intellectual disability but are not curative. To explore underlying mechanisms and potential therapies, we generated patient-derived human induced pluripotent stem lines (hiPSC) that were subsequently differentiated into astrocytes, the primary source of ALDH7A1 in the brain and key regulators of metabolic homeostasis. Metabolomic analyses confirmed elevated PDE biomarkers, and RNA sequencing revealed gene expression changes consistent with increased oxidative stress. Oxidative damage was validated by markers of DNA oxidation and lipid peroxidation. In addition, dysregulated oxygen consumption rates suggested mitochondrial dysfunction in PDE astrocytes. Notably, these pathological phenotypes were alleviated by downregulating AASS, the first enzyme of the lysine catabolism, by using CRISPR/Cas9 editing or antisense oligonucleotides (AON). This demonstrates that lysine catabolism underlies these phenotypes and highlights the therapeutic potential of AON therapy targeting AASS to reduce neurotoxic metabolite accumulation. These findings provide a promising strategy for developing targeted treatments for PDE and other rare neurometabolic disorders.

cell biology↗

bioRxiv2024

Integrative transcriptomics and electrophysiological profiling of hiPSC-derived neurons identifies novel druggable pathways in Koolen-de Vries Syndrome

Koolen-de Vries Syndrome (KdVS) is a neurodevelopmental disorder (NDD) with no treatment options due to a lack of understanding of its underlying pathophysiology. To investigate neuronal activity in KdVS, human induced pluripotent stem cell (hiPSC)-derived neurons from KdVS and control subjects were cultured on microelectrode arrays (MEAs). Our study identified reduced network burst rates, indicating disorganized network activity in KdVS neurons. To bridge molecular and functional aspects of the syndrome, we developed an experimental framework, MEA-seq, that integrates network activity measurements with high-throughput transcriptome profiling. This approach identified a negative correlation between the expression of the NDD-associated gene CLCN4 and the network burst rate. Consequently, knockdown of CLCN4 in KdVS neurons restored the activity to control level, confirming a causal relationship between increased CLCN4 expression and reduced network burst rate. Additionally, we identified a positive correlation between mitochondrial gene expression and the network burst rate, and identified impaired mitochondrial function in KdVS hiPSC-derived neurons. The transcriptomic signature of KdVS neurons was then used for computational screening against drug perturbation signatures of the LINCS Consortium database, predicting other drug targets and compounds capable of reversing the expression of affected genes in KdVS neurons. We selected 10 compounds for experimental validation, identifying the antioxidant phloretin and the Rho-kinase inhibitor fasudil as potential candidates for restoring the network activity dysfunction in KdVS. We conclude that the integrative molecular and electrophysiological of hiPSC-derived neurons with MEA-seq has excellent potential for identifying novel drugs and druggable pathways for KdVS and other NDDs.

neuroscience↗