Biology subjects

Hwang, A.

Publications and source records attributed to Hwang, A..

8 recordsLinked to original sources

bioRxiv2024

Single-cell genomics and regulatory networks for 388 human brains

Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet, little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, multi-omics datasets into a resource comprising >2.8M nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550K cell-type-specific regulatory elements and >1.4M single-cell expression-quantitative-trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized [~]250 disease-risk genes and drug targets with associated cell types. Summary Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/585576v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@70b24org.highwire.dtl.DTLVardef@6c9eddorg.highwire.dtl.DTLVardef@131fae2org.highwire.dtl.DTLVardef@4e0f1e_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

Validation of Enhancer Regions in Primary Human Neural Progenitor Cells using Capture STARR-seq

Genome-wide association studies (GWAS) and expression analyses implicate noncoding regulatory regions as harboring risk factors for psychiatric disease, but functional characterization of these regions remains limited. We performed capture STARR-sequencing of over 78,000 candidate regions to identify active enhancers in primary human neural progenitor cells (phNPCs). We selected candidate regions by integrating data from NPCs, prefrontal cortex, developmental timepoints, and GWAS. Over 8,000 regions demonstrated enhancer activity in the phNPCs, and we linked these regions to over 2,200 predicted target genes. These genes are involved in neuronal and psychiatric disease-associated pathways, including dopaminergic synapse, axon guidance, and schizophrenia. We functionally validated a subset of these enhancers using mutation STARR-sequencing and CRISPR deletions, demonstrating the effects of genetic variation on enhancer activity and enhancer deletion on gene expression. Overall, we identified thousands of highly active enhancers and functionally validated a subset of these enhancers, improving our understanding of regulatory networks underlying brain function and disease.

neuroscience↗

bioRxiv2023

The Hao-Fountain syndrome protein USP7 regulates neuronal connectivity in the brain via a novel p53-independent ubiquitin signaling pathway

Precise control of protein ubiquitination is essential for brain development, and hence, disruption of ubiquitin signaling networks can lead to neurological disorders. Mutations of the deubiquitinase USP7 cause the Hao-Fountain syndrome (HAFOUS), characterized by developmental delay, intellectual disability, autism, and aggressive behavior. Here, we report that conditional deletion of USP7 in excitatory neurons in the mouse forebrain triggers diverse phenotypes including sensorimotor deficits, learning and memory impairment, and aggressive behavior, resembling clinical features of HAFOUS. USP7 deletion induces neuronal apoptosis in a manner dependent of the tumor suppressor p53. However, most behavioral abnormalities in USP7 conditional mice persist despite p53 loss. Strikingly, USP7 deletion in the brain perturbs the synaptic proteome and dendritic spine morphogenesis independently of p53. Integrated proteomics analysis reveals that the neuronal USP7 interactome is enriched for proteins implicated in neurodevelopmental disorders and specifically identifies the RNA splicing factor Ppil4 as a novel neuronal substrate of USP7. Knockdown of Ppil4 in cortical neurons impairs dendritic spine morphogenesis, phenocopying the effect of USP7 loss on dendritic spines. These findings reveal a novel USP7-Ppil4 ubiquitin signaling link that regulates neuronal connectivity in the developing brain, with implications for our understanding of the pathogenesis of HAFOUS and other neurodevelopmental disorders.

neuroscience↗

bioRxiv2023

A Vibrating Ingestible BioElectronic Stimulator Modulates Gastric Stretch Receptors for Illusory Satiety

Effective therapies for obesity either require invasive surgical or endoscopic interventions or high patient adherence, making it challenging for the nearly 42% of American adults who suffer from obesity to effectively manage their disease. Gastric mechanoreceptors sense distension of the stomach and perform volume-dependent vagal signaling to initiate the gastric phase and influence satiety. In this study, we developed a new luminal stimulation modality to specifically activate these gastric stretch receptors to elicit a vagal afferent response commensurate with mechanical distension. Here we developed the Vibrating Ingestible BioElectronic Stimulator (VIBES) pill - an ingestible device that performs luminal vibratory stimulation to activate mechanoreceptors and stroke mucosal receptors, which induces serotonin release as well as yields a hormonal metabolic response commensurate with a fed state. We evaluated VIBES across 108 meals in swine which consistently led to diminished food intake ([~]40%, p< 0.0001) and minimized the weight gain rate (p< 0.03) as compared to untreated controls. Application of mechanoreceptor biology could transform our capacity to help patients suffering from nutritional disorders.

pathology↗

bioRxiv2023

Characterizing dysregulations via cell-cell communications in Alzheimer's brains using single-cell transcriptomes

Alzheimers disease (AD) is a devastating neurodegenerative disorder affecting 44 million people worldwide, leading to cognitive decline, memory loss, and significant impairment in daily functioning. The recent single-cell sequencing technology has revolutionized genetic and genomic resolution by enabling scientists to explore the diversity of gene expression patterns at the finest resolution. Here, we leveraged the large-scale and publicly available single-nucleus RNA sequencing (snRNA-seq) in the human prefrontal cortex (PFC) from 23 AD samples and 13 controls to investigate cell-to-cell communication (C2C) in healthy brains and their perturbations in AD. Specifically, we first performed broad communication pattern analyses and discovered the inter-mixing of cell types and signaling pathways in AD brains. Secondly, we performed cell-type- centric analysis and found that excitatory neurons in AD have significantly increased their communications to inhibitory neurons, while inhibitory neurons and other supporting cells globally decreased theirs to all cells. Then, we delved deeper with a signaling-centric view, showing that canonical signaling pathways CSF, TGF{beta}, and CX3C are significantly dysregulated in their signaling to the cell type microglia/PVM and WNT pathway is dysregulated in its signaling from endothelial to neuronal cells in AD. Finally, after extracting 23 known AD risk genes, our intracellular communication analysis revealed a strong connection of extracellular ligand genes APP, APOE, and PSEN1 to intracellular AD risk genes TREM2, ABCA1, and APP in the communication from astrocytes and microglia to neurons. In summary, with the novel advances in single-cell sequencing technologies, we show that cellular signaling is regulated in a cell-type- specific manner and that improper regulation of extracellular signaling genes is linked to intracellular risk genes, connecting signaling to genetic differences manifested in AD. Author SummaryAlzheimers is a devastating neurodegenerative disorder affecting 44 million people worldwide, leading to cognitive decline, memory loss, and significant impairment in daily functioning. The complex interplay of signaling genes suggests cells act in concert with other cells through cell-to-cell communication. Utilizing the recent advances in single-cell sequencing, we investigated dysregulated ligand-receptor gene pairs in the disease at the cell-type resolution. Specifically, our broad communication pattern analyses revealed the inter-mixing of cell types and signaling pathways in AD brains. Our cell-type-centric analysis found that excitatory neurons in AD have significantly increased their communications with inhibitory neurons, while inhibitory neurons and other supporting cells globally decreased theirs to all cells. With a signaling-centric view, we show that CSF, TGF{beta}, and CX3C pathways are significantly dysregulated in their signaling to the cell type microglia/PVM while the WNT pathway is dysregulated in its signaling from endothelial to neuronal cells in AD. Finally, our intracellular communication analysis revealed a strong connection of extracellular ligand genes APP, APOE, and PSEN1 to intracellular AD risk genes TREM2, ABCA1, and APP in the communication from astrocytes and microglia to neurons. In summary, performing a cell-to-cell communication analysis better explains the genetic differences manifested in Alzheimers.

bioinformatics↗

bioRxiv2022

Cortical surface electrical potentials are composed of multiple bandlimited frequency components, including high-gamma

A common challenge in neuroscience is how to decompose noisy, multi-source signals measured in experiments into biophysically interpretable components. Analysis of cortical surface electrical potentials (CSEPs) measured using electrocorticography arrays (ECoG) typifies this problem. We hypothesized that high frequency (70-1,000 Hz) CSEPs are composed of broadband (i.e., power-law) and bandlimited components with potentially differing biophysical origins. In particular, the high-gamma band (70-150 Hz) has been shown to be highly predictive for encoding and decoding behaviors and stimuli. Despite its demonstrated importance, whether high-gamma is composed of a bandlimited signal is poorly understood. To address this gap, we recorded CSEPs from rat auditory cortex and demonstrate that the evoked CSEPs are composed of multiple distinct frequency components, including high-gamma. We then show, using a novel robust regression method, that at fast timescales and on single trials during speech production, human high-gamma amplitude cannot be explained by a modulating power-law component; thus, high-gamma is band-limited. Furthermore, we show that the power-law component is less predictive of produced speech compared to the raw high-gamma amplitude. Finally, we show that the largest variance component of human ECoG signals is low-frequency and band-limited, not broadband. Together these results demonstrate that there are multiple, band-limited components of high frequency power in cortical surface electrical potentials, including the high-gamma band, which may have different biophysical origins. Significance StatementElectrocortigraphy (ECoG) records cortical surface electrical potentials (CSEPs). ECoG is utilized in both humans and animal models to understand distributed cortical processing and for brain machine interfaces. The spectral structure of evoked CSEPs is greatly debated. To address this issue, we recorded from rat auditory cortex using {micro}ECoG and human ventral sensory-motor cortex during speech production with high-density ECoG. Using novel analytic approaches, we found that evoked CSEPs are composed of multiple band-limited components, including high-gamma. These results contrast with the dominant thinking in the field that the high-frequency power in ECoG is broadband. Our results raise the possibility that distinct frequency components of ECoG are biomarkers of processing in different cortical layers.

neuroscience↗

bioRxiv2019

Determination of glucosinolate contents in Brassica germplasm collections and inter- & intra-leaves distribution pattern using UPLC-MS/MS Multiple Reaction Monitoring scan mode

Intact glucosinolate (GSL) profile (five aliphatic; three aromatic, and one indolic glucosinolate) in the leaves of 50 germplasm collections and commercial cultivars of Brassica rapa, Brassica juncea, and Brassica oleracea collected from six different countries and grown under uniform cultural conditions were compared by UPLC-MS/MS. Total GSLs content ranged from 36.80 to 2383.12 mol/kg DW. Aliphatic GSLs predominated among the entire samples representing from 23.0 to 98.9% of the total GSLs content, where gluconapin and glucobrassicanapin contributed the greatest proportion. Other GSLs such as, progoitrin (PRO), glucotropaeolin (TRO), and glucobarbarin (BAR) were found in relatively low concentrations. Principal Component Analysis (PCA) yielded three principal components with eigenvalue [≥] 1, representing 70.33% of the total variation across the entire data set. Accessions IT260822 & IT32750, and commercial cultivar, \"Hangamssam2\", were well distinguished from other samples in the PCA plot due to their significantly high amount of BAR, glucobrassicin (GBC), and glucoerucin (ERU), respectively. The inter- and intra-leaf variations of GSLs were examined in three kimichi cabbage varieties. The GSLs content varied significantly among leaves in different positions (outer, middle, and inner) and sections within the leaves (top, middle, bottom, green/red, and white). Higher GSL contents were observed in the proximal half & white section of the leaves and inner positions (younger leaves) in most of the samples. GBC, gluconasturtiin (NAS), and glucoberteroin (BER) should be studied profusely in Brassica plants as some of their degradation products of GBC and NAS are useful in cancer chemopreventive functions, whereas BER takes part in the process of suppressing aging of the skin. GSLs are regarded as allelochemicals; hence, the data related to the patterns of GSLs within the leaf and between leaves at different position could be useful to understand the defense mechanism of Brassica plants. The observed variability could be useful for breeders to develop Brassica crops with high GSL content or specific profiles of GSLs as required.

biochemistry↗

bioRxiv2017

Nuclear Abl Drives Extracellular-Vesicle Transfer of miR-34c to Induce Bystander Effects of Radiation

SUMMARYIonizing radiation stimulates nuclear accumulation of Abl tyrosine kinase that is required for directly irradiated cells to produce microRNA-34c-containing extracellular vesicles, which transfer the microRNA into non-irradiated cells to induce reactive oxygen species and bystander DNA damage.\n\nABSTRACTIonizing radiation (IR) activates an array of DNA damage response (DDR) that includes the induction of bystander effects (BE) in cells not targeted by radiation. How DDR pathways in irradiated cells stimulate BE in non-targeted cells is mostly unknown. We show here that extracellular vesicles from irradiated cells (EV-IR) induce reactive oxygen species (ROS) and DNA damage when internalized by un-irradiated cells. We found that EV-IR from Abl-NLS-mutated cells could not induce ROS or DNA damage, and restoration of nuclear Abl rescued those defects. Expanding a previous finding that Abl stimulates miR-34c expression, we show here that nuclear Abl also drives the vesicular secretion of miR-34c. Ectopic miR-34c expression, without irradiation, generated EV-miR-34c capable of inducing ROS and DNA damage. Furthermore, EV-IR from miR34-knockout cells could not induce ROS and raised {gamma}H2AX to lesser extent than EV-IR from miR34-wild type cells. These results establish a novel role for the Abl-miR-34c DDR pathway in stimulating radiation-induced bystander effects.

cell biology↗