Biology subjects

Iakoucheva, L. M.

Publications and source records attributed to Iakoucheva, L. M..

8 recordsLinked to original sources

bioRxiv2025

Prenatal Acetaminophen Exposure Does Not Disrupt Human Fetal Brain Development in Cortical Organoid Models

Acetaminophen (APAP) is the most widely used analgesic during pregnancy, yet its effects on prenatal human brain development remain incompletely understood. Epidemiological studies have reported inconsistent associations between prenatal APAP exposure and later neurodevelopmental outcomes, underscoring the need for mechanistic evaluation in human-relevant developmental models. Here, we examined how APAP influences early cortical development using induced pluripotent stem cell-derived cortical organoids (COs) generated from six independent lines. Organoids were exposed to physiologically relevant APAP concentrations (25, 50, and 100 M) for 5 days beginning at day 21 of differentiation, corresponding to late first-trimester cortical development. We assessed organoid growth, apoptosis, differentiation, synaptic maturation, transcriptomic profiles using bulk and single-nucleus RNA sequencing (snRNA-seq), and functional network activity using multielectrode array recordings up to 4 months. APAP exposure did not affect organoid size, cytoarchitecture, or viability. Neuronal and progenitor cell proportions, as well as synaptic puncta density were unchanged. Bulk RNA-seq revealed subtle transcriptional changes only at the highest dose (16 differentially expressed genes at 100 M), enriched for neurodevelopmental pathways. In contrast, snRNA-seq at 3 months revealed no changes in cell type composition or gene expression. Consistent with these findings, electrophysiological measures including firing rate, burst frequency, and network synchrony, were indistinguishable from controls. Together, these results indicate that exposure to therapeutic APAP concentrations during a critical window of early cortical development produces minimal molecular perturbations without detectable consequences. This study provides mechanistic evidence indicating that, in this human organoid model, recommended APAP exposure is not associated with detectable disruptions in pathways implicated in brain development.

neuroscience↗

bioRxiv2023

How PTEN mutations degrade function at the membrane and life expectancy of carriers of mutations in the human brain

PTEN dysfunction, caused by loss of lipid phosphatase activity or deletion, promotes pathologies, cancer, benign tumors, and neurodevelopmental disorders (NDDs). Despite efforts, exactly how the mutations trigger distinct phenotypic outcomes, cancer or NDD, has been puzzling. It has also been unclear how to distinguish between mutations harbored by isoforms, are they cancer or NDDs-related. Here we address both. We demonstrate that PTEN mutations differentially allosterically bias P-loop dynamics and its connection to the catalytic site, affecting catalytic activity. NDD-related mutations are likely to sample conformations present in the wild-type, while sampled conformations sheltering cancer-related hotspots favor catalysis-prone conformations, suggesting that NDD mutations are weaker. Analysis of isoform expression data indicates that if the transcript has NDD-related mutations, alone or in combination with cancer hotspots, there is high prenatal expression. If no mutations within the measured days, low expression levels. Cancer mutations promote stronger signaling and cell proliferation; NDDs are weaker, influencing brain cell differentiation. Further, exon 5 is impacted by NDD or non-NDD mutations, while exon 7 is exclusively impacted by NDD mutations. Our comprehensive conformational and genomic analysis helps discover how same allele mutations can foster different clinical manifestations and uncovers correlations of splicing isoform expression to life expectancy.

biophysics↗

bioRxiv2020

Cortical Organoids Model Early Brain Development Disrupted by 16p11.2 Copy Number Variants in Autism

Reciprocal deletion and duplication of 16p11.2 region is the most common copy number variation (CNV) associated with Autism Spectrum Disorders. We generated cortical organoids from skin fibroblasts of patients with 16p11.2 CNV to investigate impacted neurodevelopmental processes. We show that organoid size recapitulates macrocephaly and microcephaly phenotypes observed in the patients with 16p11.2 deletions and duplications. The CNV has mirror-opposite effect on neuronal maturation, proliferation, and synapse number, in concordance with its effect on brain growth in humans. We demonstrate that 16p11.2 CNV alters the ratio of neurons to neural progenitors in organoids during early neurogenesis, with excess of neurons and depletion of neural progenitors observed in deletions, and mirror phenotypes in duplications. Transcriptomic and proteomic profiling revealed multiple dysregulated pathways, including defects in neuron migration. Inhibition of activity of the small GTPase RhoA rescued migration deficits. This study provides insights into potential neurobiological mechanisms behind the 16p11.2 CNV during neocortical development.

neuroscience↗

bioRxiv2020

Isoform transcriptome of developing human brain provides new insights into autism risk variants

Alternative splicing plays important role in brain development, however its global contribution to human neurodevelopmental diseases (NDD) has not been fully investigated. Here, we examined the relationships between full-length splicing isoforms expression in the brain and de novo loss-of-function mutations identified in the patients with NDDs. We analyzed the full-length isoform transcriptome of the developing human brain and observed differentially expressed isoforms and isoform co-expression modules undetectable by gene-level analyses. These isoforms were enriched in loss-of-function mutations and microexons, co-expressed with a unique set of partners, and had higher prenatal expression. We experimentally tested the impact of splice site mutations in five NDD risk genes, including SCN2A, DYRK1A and BTRC, and demonstrated exon skipping. Furthermore, our results suggest that the splice site mutation in BTRC reduces translational efficiency, likely impacting Wnt signaling through impaired degradation of {beta}-catenin. We propose that functional effect of mutations associated with human diseases should be investigated at the isoform-rather than the gene-level resolution. HighlightsO_LIDifferential isoform expression analysis of the human brain transcriptome reveals neurodevelopmental processes and pathways undetectable by differential gene expression analyses. C_LIO_LISplicing isoforms impacted by neurodevelopmental disease (NDD) risk mutations exhibit higher prenatal expression, are enriched in microexons and are involved in neuronal-related functions. C_LIO_LIIsoform co-expression network analysis identifies modules with splicing and synaptic functions that are enriched in NDD mutations. C_LIO_LISplice site mutations impacting NDD risk genes cause exon skipping and produce novel isoforms with altered biological properties. C_LIO_LIFunctional impact of mutations should be investigated at the full-length isoform-level rather than the gene-level resolution C_LI

neuroscience↗

bioRxiv2020

Autism-linked Cullin3 germline haploinsufficiency impacts cytoskeletal dynamics and cortical neurogenesis through RhoA signaling

E3-ubiquitin ligase Cullin3 (Cul3) is a high confidence risk gene for Autism Spectrum Disorder (ASD) and Developmental Delay (DD). To investigate how Cul3 mutations impact brain development, we generated haploinsufficient Cul3 mouse model using CRISPR/Cas9 genome engineering. Cul3 mutant mice exhibited social and cognitive deficits and hyperactive behavior. Brain MRI found decreased volume of cortical regions and changes in many other brain regions of Cul3 mutant mice starting from early postnatal development. Spatiotemporal transcriptomic and proteomic profiling of the brain implicated neurogenesis and cytoskeletal defects as key drivers of Cul3 functional impact. Specifically, dendritic growth, filamentous actin puncta, and spontaneous network activity were reduced in Cul3 mutant mice. Inhibition of small GTPase RhoA, a molecular substrate of Cul3 ligase, rescued dendrite length and network activity phenotypes. Our study identified neuronal cytoskeleton and Rho signaling as primary targets of Cul3 mutation during early brain development.

neuroscience↗

bioRxiv2019

Oligogenic effects of 16p11.2 copy number variation on craniofacial development

A copy number variant (CNV) of 16p11.2, which encompasses 30 genes, is associated with developmental and psychiatric disorders, head size and body mass. The genetic mechanisms that underlie these associations are not understood. To elucidate the effects of genes on development, we exploited the quantitative effects of CNV on craniofacial structure in humans and model organisms. We show that reciprocal deletion and duplication of 16p11.2 have characteristic "mirror" effects on craniofacial features that are conserved in human, rat and mouse. By testing gene dosage effects on the shape of the mandible in zebrafish, we show that the distribution of effects for all individual genes is consistent with that of the CNV, and some combinations have non-additive effects. Our results suggest that, at minimum, one third of genes within the 16p11.2 region influence craniofacial development, and the facial gestalt of each CNV represents a product of 30 dosage effects. HighlightsO_LIReciprocal CNVs of 16p11.2 have mirror effects on craniofacial structure. Copy number is associated with a positive effect on nasal and mandibular regions and a negative effect on frontal regions of the face. C_LIO_LIEffects of CNV on craniofacial development in human are well conserved in rat and mouse models of 16p11.2 deletion and duplication. C_LIO_LI7/30 genes each independently have significant effects on the shape of the mandible in zebrafish; these include SPN, C16orf54, SEZ6L2, ASPHD1, TAOK2, INO80E and FAM57B. Others (MAPK3, MVP, KCTD13) have detectable effects only in combination. C_LIO_LIOverexpression of 30 genes individually showed a distribution of effects that was skewed in the same direction as that of the full duplication, suggesting that specific facial features represent the net of all individual effects combined. C_LI

genetics↗

bioRxiv2017

MutPred2: inferring the molecular and phenotypic impact of amino acid variants

We introduce MutPred2, a tool that improves the prioritization of pathogenic amino acid substitutions, generates molecular mechanisms potentially causative of disease, and returns interpretable pathogenicity score distributions on individual genomes. While its prioritization performance is state-of-the-art, a novel and distinguishing feature of MutPred2 is the probabilistic modeling of variant impact on specific aspects of protein structure and function that can serve to guide experimental studies of phenotype-altering variants. We demonstrate the utility of MutPred2 in the identification of the structural and functional mutational signatures relevant to Mendelian disorders and the prioritization of de novo mutations associated with complex neurodevelopmental disorders. We then experimentally validate the functional impact of several variants identified in patients with such disorders. We argue that mechanism-driven studies of human inherited diseases have the potential to significantly accelerate the discovery of clinically actionable variants.\n\nAvailability: http://mutpred.mutdb.org/

bioinformatics↗

bioRxiv2017

Paternally inherited noncoding structural variants contribute to autism

The genetic architecture of autism spectrum disorder (ASD) is known to consist of contributions from gene-disrupting de novo mutations and common variants of modest effect. We hypothesize that the unexplained heritability of ASD also includes rare inherited variants with intermediate effects. We investigated the genome-wide distribution and functional impact of structural variants (SVs) through whole genome analysis ([≥]30X coverage) of 3,169 subjects from 829 families affected by ASD. Genes that are intolerant to inactivating variants in the exome aggregation consortium (ExAC) were depleted for SVs in parents, specifically within fetal-brain promoters, UTRs and exons. Rare paternally-inherited SVs that disrupt promoters or UTRs were over-transmitted to probands (P = 0.0013) and not to their typically-developing siblings. Recurrent functional noncoding deletions implicate the gene LEO1 in ASD. Protein-coding SVs were also associated with ASD (P = 0.0025). Our results establish that rare inherited SVs predispose children to ASD, with differing contributions from each parent.

genomics↗