Biology subjects

Seah, C.

Publications and source records attributed to Seah, C..

12 recordsLinked to original sources

bioRxiv2026

Estradiol modulates neuronal network hyperexcitability in select NDD risk genes

Sex hormone signaling during neurodevelopment may act as a modulator of risk for neurodevelopmental disorders (NDDs), including autism spectrum disorders (ASDs). By conducting a systematic and multi-modal evaluation of estradiol effects across loss-of-function deletions in 36 functionally diverse, large-effect ASD/NDD genes in human induced pluripotent stem cell-derived neurons and larval zebrafish, we uncover convergent and divergent gene-by-estradiol interactions at the transcriptomic, circuit, and behavioral levels. Whereas estradiol partially ameliorates dysregulated expression signatures across all ASD/NDD gene knockouts examined, it selectively and rapidly dampens network hyperexcitability phenotypes in only a subset of ASD/NDD gene knockouts. Two genes, ASH1L and SCN2A, are particularly responsive to estradiol treatment, with dramatic rescue of molecular and cellular effects in human knockout neurons, coupled with behavioral phenotypes in larval zebrafish mutants. The seven most estradiol responsive genes show enhanced protein-protein interaction network connectivity, strong co-expression in specific postnatal time periods, and enrichment in upper-layer mature excitatory neurons. Altogether, we describe distinct estradiol rescue in different modalities, elucidating shared transcriptomic effects as well as gene-specific cellular and behavioral rescue in the context of loss of function mutations of select ASD/NDD genes.

genomics↗

bioRxiv2025

Mechanical stretch disrupts calcium dynamics and redistributes Piezo1 in human astrocytes

Astrocytes regulate the activity of nearby neurons so disruption of astrocyte calcium dynamics by traumatic brain injury (TBI) could have profound consequences for neural network activity in the brain. In this study, human induced pluripotent stem cell (hiPSC)-derived astrocytes were used in a two-dimensional (2D) in vitro stretch injury model to evaluate the effect of trauma on calcium dynamics, mitochondrial function, and the mechanosensitive ion channel Piezo1. Outcomes were assessed using live imaging, immunostaining, and RNA sequencing. Cell viability, mitochondrial membrane potential, and spontaneous calcium transients declined as injury severity increased. At moderate injury severity, the decreases in mitochondrial membrane potential and calcium dynamics were temporary. The spatial distribution of Piezo1 also changed temporarily after injury. RNA sequencing identified 196 genes that changed expression after injury, including downregulation of mitochondrial and oxidative metabolic processes and upregulation of cortical thinning pathways. These findings establish this model as a platform for investigating the cellular mechanisms of TBI and its influence on neurodegeneration.

neuroscience↗

bioRxiv2025

Macropinocytosis of amyloid precursor protein requires the adaptor protein Fe65 and the recruitment and activity of Arf6 and the RhoGTPases Rac1, Cdc42 and RhoA.

Alzheimers disease (AD) is a progressive neurodegenerative disorder characterized by the buildup of the highly toxic peptide amyloid-beta (A{beta}). Previously, we demonstrated that A{beta} is generated from the cleavage of amyloid precursor protein (APP) after internalization to lysosomes via macropinocytosis. However, the regulation of APP micropinocytosis has remained uncharacterized. Evidence suggests that APP may function as a cell surface receptor which could contribute to this regulation. Arf6 and the RhoGTPases Rac1, Cdc42 and RhoA are known to regulate macropinocytosis in response to signaling of other receptors. An adaptor protein called Fe65, which can associate with both amyloid precursor protein and Arf6, could function as the link between APP and these known regulatory elements. Thus, we hypothesized that the binding and/or crosslinking of APP recruits Fe65, which then recruits and activates Arf6, which in turn activates Rac1, Cdc42 and RhoA, resulting in APP macropinocytosis. Rapid and transient recruitment of Fe65 and Arft6 was observed to APP 30 seconds following binding/crosslinking. Rac1, Cdc42 and RhoA all examined demonstrated more sustained recruitment to crosslinked APP. Prevention of Fe65 binding by APP mutation and Arf6 inhibition by NAV-2729 prevented the recruitment of all proteins. Together, these observations are the first to demonstrate that a network of regulatory proteins is recruited to bound/crosslinked APP which regulates its macropinocytosis. Targeting these regulatory proteins could be explored to modulate the membrane to lysosomal trafficking of APP and reducing the production of A{beta} in AD.

neuroscience↗

bioRxiv2025

Macropinocytosis of aggregated amyloid-beta and tau requires Arf6 and the RhoGTPases Rac1, Cdc42 and RhoA.

The neuron-to-neuron transfer of amyloid-beta (A{beta}) and tau aggregates have been proposed to underlie the propagation of protein aggregation in Alzheimers disease (AD) and contributing to progressive neurodegeneration. Several studies have provided evidence that aggregates of A{beta} and tau are taken up into neuronal cells and neurons from the extracellular environment, where they contribute to the propagation of A{beta} and tau aggregation in AD through seeding their aggregation. As a result, attention has been placed on determining the cellular mechanisms that contribute to this uptake, with the hopes that targeting these mechanisms could halt the progression of AD by preventing aggregate transfer. Previous studies have demonstrated the uptake of A{beta} and tau aggregates through the endocytic process called macropinocytosis. The activity of several GTPases has been demonstrated to regulate macropinocytosis, including Arf6 and the RhoGTPases Rac1, Cdc42 and RhoA. Here, we examined the uptake of A{beta}42 oligomers and tau fibrils by macropinocytosis in neurons and the role of Arf6, Rac1, Cdc42 and RhoA activity in the macropinocytosis of these aggregates. In this study, we demonstrated that extracellular A{beta}42 oligomers and tau fibrils are taken up by iPSC-derived neurons and delivered directly to LAMP1-labeled lysosomes through macropinocytosis. This was demonstrated by reduced uptake in response to treatment with the macropinocytosis inhibitor EIPA, but not in response to the clathrin inhibitor Pitstop2. The uptake of these aggregates by macropinocytosis was significantly reduced by the inhibition of the GTPases Arf6, Rac1, Cdc42 and RhoA. Further, we also demonstrated that accumulation of extracellular A{beta}42 oligomers and tau fibrils results in an accumulation of cytoplasmic tau within aggregate-containing lysosomes. Together these results provide evidence that the GTPases Arf6, Rac1, Cdc42 and RhoA play a role in the neuronal uptake of A{beta} and tau aggregates by macropinocytosis and identifies new molecular targets to explore preventing the neuron-to-neuron transfer of these aggregates in AD.

neuroscience↗

bioRxiv2025

Amyloid beta is released by lysosomal exocytosis from hiPSC-derived neurons

The endosomal-lysosomal system has long been linked to the production of amyloid beta (A{beta}), but the specific intracellular compartments involved in A{beta} secretion remain contentious. While lysosomes are typically associated with A{beta} degradation, studies have also shown that lysosomes also serve as site of A{beta} accumulation in cells, mouse models, and human tissues. Lysosomal exocytosis is a major secretory pathway in non-neuronal cells, but few studies have investigated this pathway in neurons. Here, we examined the potential role and mechanism of lysosomal exocytosis in human induced pluripotent stem cell (hiPSC)-derived neurons, and we hypothesized that lysosomal exocytosis is a pathway for A{beta} secretion from these neurons. Using total internal reflection fluorescence (TIRF) microscopy, lysosomes filled with fluorescently labelled amyloid were seen approaching and fusing with the plasma membrane in real-time. The number and composition of the released particles were characterized using nanoscale flow cytometry. Silencing two proteins, Rab27b and munc13-4, significantly reduced these events and blocked the release of amyloid into the extracellular space. Our results provide direct evidence for the involvement of lysosomal exocytosis in the release of A{beta} from neurons and highlight its potential as a target for therapeutic intervention in Alzheimers disease.

neuroscience↗

bioRxiv2024

Decoding the transcriptomic signatures of psychological trauma in human cortex and amygdala

Psychological trauma has profound effects on brain function and precipitates psychiatric disorders in vulnerable individuals, however, the molecular mechanisms linking trauma with psychiatric risk remain incompletely understood. Using RNA-seq data postmortem brain tissue of a cohort of 304 donors (N=136 with trauma exposure), we investigated transcriptional signatures of trauma exposures in two cortical regions (dorsolateral prefrontal cortex, and dorsal anterior cingulate cortex) and two amygdala regions (medial amygdala and basolateral amygdala) associated with stress processing and regulation. We focused on dissecting heterogeneity of traumatic experiences in these transcriptional signatures by investigating exposure to several trauma types (childhood, adulthood, complex, single acute, combat, and interpersonal traumas) and interactions with sex. Overall, amygdala regions were more vulnerable to childhood traumas, whereas cortical regions were more vulnerable to adulthood trauma (regardless of childhood experience). Using cell-type-specific expression imputation, we identified a strong transcriptional response of medial amygdala excitatory neurons to childhood trauma, which coincided with dysregulation observed in a human induced pluripotent stem cell (hiPSC)-derived glutamatergic neurons exposed to hydrocortisone. We resolved multiscale coexpression networks for each brain region and identified modules enriched in trauma signatures and whose connectivity was altered with trauma. Trauma-associated coexpression modules provide insight into coordinated functional dysregulation with different traumas and point to potential gene targets for further dissection. Together, these data provide a characterization of the long-lasting human encoding of traumatic experiences in corticolimbic regions of human brain.

neuroscience↗

bioRxiv2024

EMERGENCE OF OXA-48-LIKE CARBAPENEMASES IN CLINICAL ENTEROBACTERALES FROM GUATEMALA

Five isolates (four Klebsiella pneumoniae and one Escherichia coli) displaying resistance to piperacillin/tazobactam and ertapenem and reduced susceptibility to imipenem were found positive for blaOXA-48-like genes (blaOXA-181 and blaOXA-232) carried on plasmids described previously. Although two K. pneumoniae recovered in 2020 were clonally related, the results suggest that blaOXA-48-like genes have been circulating in Guatemala since 2019. This is the first report of this type of carbapenemase in Central America.

microbiology↗

bioRxiv2023

Common genetic variation impacts molecular stress response in the brain

To explain why individuals exposed to identical stressors experience divergent clinical outcomes, we determine how molecular encoding of stress modifies genetic risk for brain disorders. Analysis of post-mortem brain (n=304) revealed 8557 stress-interactive expression quantitative trait loci (eQTLs) that dysregulate expression of 915 eGenes in response to stress, and lie in stress-related transcription factor binding sites. Response to stress is robust across experimental paradigms: up to 50% of stress-interactive eGenes validate in glucocorticoid treated hiPSC-derived neurons (n=39 donors). Stress-interactive eGenes show brain region- and cell type-specificity, and, in post-mortem brain, implicate glial and endothelial mechanisms. Stress dysregulates long-term expression of disorder risk genes in a genotype-dependent manner; stress-interactive transcriptomic imputation uncovered 139 novel genes conferring brain disorder risk only in the context of traumatic stress. Molecular stress-encoding explains individualized responses to traumatic stress; incorporating trauma into genomic studies of brain disorders is likely to improve diagnosis, prognosis, and drug discovery. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=71 SRC="FIGDIR/small/573459v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1e07fa9org.highwire.dtl.DTLVardef@1dd530forg.highwire.dtl.DTLVardef@17822a5org.highwire.dtl.DTLVardef@2a889f_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2021

Performance characteristics of next-generation sequencing for antimicrobial resistance gene detection in genomes and metagenomes

Short-read sequencing provides a culture-independent method for the detection of antimicrobial resistance (AMR) genes from single bacterial genomes and metagenomic samples. However, the performance characteristics of these approaches have not been systematically characterized. We compared assembly- and read-based approaches to determine sensitivity, positive predictive value, and sequencing limits of detection required for AMR gene detection in an Escherichia coli ST38 isolate spiked into a synthetic microbial community at varying abundances. Using an assembly-based method the limit of detection was 15X genome coverage. We are confident in AMR gene detection at target relative abundances of 100% to 1%, where a target abundance of 1% would require assembly of approximately 30 million reads to achieve 15X target coverage. Recent studies assessing AMR gene content in metagenomic samples may be inadequately sequenced to achieve high sensitivity. Our study informs future sequencing projects and analytical strategies for genomic and metagenomic AMR gene detection.

bioinformatics↗

bioRxiv2021

Modeling gene x environment interactions in PTSD using glucocorticoid-induced transcriptomics in human neurons

Post-traumatic stress disorder (PTSD) results from severe trauma exposure, but the extent to which genetic and epigenetic risk factors impact individual clinical outcomes is unknown. We assessed the impact of genomic differences following glucocorticoid administration by examining the transcriptional profile of human induced pluripotent stem cell (hiPSC)-derived glutamatergic neurons and live cultured peripheral blood mononuclear cells from combat veterans with PTSD (n=5) and without PTSD (n=5). This parallel examination in baseline and glucocorticoid-treated conditions resolves cell-type specific and diagnosis-dependent elements of stress response, and permits discrimination of gene expression signals associated with PTSD risk from those induced by stress. Computational analyses revealed neuron-specific glucocorticoid-response expression patterns that were enriched for transcriptomic patterns observed in clinical PTSD samples. PTSD-specific signatures, albeit underpowered, accurately stratify veterans with PTSD relative to combat-exposed controls. Overall, in vitro PTSD and glucocorticoid response signatures in blood and brain cells represent exciting new platforms with which to test the genetic and epigenetic mechanisms underlying PTSD, identify biomarkers of PTSD risk and onset, and conduct drug-screening to identify novel therapeutics to prevent or ameliorate clinical phenotypes.

pathology↗

bioRxiv2020

Common genetic variation in humans impacts in vitro susceptibility to SARS-CoV-2 infection

The host response to SARS-CoV-2, the etiologic agent of the COVID-19 pandemic, demonstrates significant inter-individual variability. In addition to showing more disease in males, the elderly, and individuals with underlying co-morbidities, SARS-CoV-2 can seemingly render healthy individuals with profound clinical complications. We hypothesize that, in addition to viral load and host antibody repertoire, host genetic variants also impact vulnerability to infection. Here we apply human induced pluripotent stem cell (hiPSC)-based models and CRISPR-engineering to explore the host genetics of SARS-CoV-2. We demonstrate that a single nucleotide polymorphism (rs4702), common in the population at large, and located in the 3UTR of the protease FURIN, impacts alveolar and neuron infection by SARS-CoV-2 in vitro. Thus, we provide a proof-of-principle finding that common genetic variation can impact viral infection, and thus contribute to clinical heterogeneity in SARS-CoV-2. Ongoing genetic studies will help to better identify high-risk individuals, predict clinical complications, and facilitate the discovery of drugs that might treat disease.

cell biology↗

bioRxiv2019

Small molecule inhibition of PIKFYVE kinase rescues gain- and loss-of-function C9ORF72 ALS/FTD disease processes in vivo

The most common known cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) is a hexanucleotide repeat expansion (HRE) in C9ORF72 that contributes to neurodegeneration by both loss-of-function (decreased C9ORF72 protein levels) and gain-of-function (e.g. dipeptide repeat protein production) mechanisms. Although therapeutics targeting the gain-of-function mechanisms are in clinical development, it is unclear if these will be efficacious given the contribution of C9ORF72 loss-of-function processes to neurodegeneration. Moreover, there is a lack of therapeutic strategies for C9ORF72 ALS/FTD with demonstrated efficacy in vivo. Here, we show that small molecule inhibition of PIKFYVE kinase rescues both loss- and gain-of-function C9ORF72 disease mechanisms in vivo. We find that the reduction of C9ORF72 in mouse motor neurons leads to a decrease in early endosomes. In contrast, treatment with the PIKFYVE inhibitor apilimod increases the number of endosomes and lysosomes. We show that reduced C9ORF72 levels increases glutamate receptor levels in hippocampal neurons in mice, and that apilimod treatment rescues this excitotoxicity-related phenotype in vivo. Finally, we show that apilimod also alleviates the gain-of-function pathology induced by the C9ORF72 HRE by decreasing levels of dipeptide repeat proteins derived from both sense and antisense C9ORF72 transcripts in hippocampal neurons in vivo. Our data demonstrate the neuroprotective effect of PIKFYVE kinase inhibition in both gain- and loss-of-function murine models of C9ORF72 ALS/FTD.

neuroscience↗