Biology subjects

Lee, K.

Publications and source records attributed to Lee, K..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Abnormal Elevated Connectivity During Language Processing is Associated with Poor Cognitive Performance in Children with Self-limited Epilepsy with Centrotemporal Spikes

Self-Limited Epilepsy with Centrotemporal Spikes (SeLECTS) is associated with language impairments despite seizures originating in the motor cortex, suggesting aberrant cross-network interactions. Here we tested whether functional connectivity in SeLECTS during language tasks predicts language performance. We recorded high-density EEG from right-handed children with SeLECTS (n=31) and age-matched controls (n=32) during verb generation, repetition, and resting tasks. Phonological awareness was assessed using the Comprehensive Test of Phonological Processing-2. Connectivity between bilateral motor cortices and language regions (the left inferior frontal and superior temporal cortices and their right hemisphere homologues) was measured using weighted Phase Lag Index (wPLI). Children with SeLECTS demonstrated significantly elevated connectivity between motor and language regions during language processing. Motor-to-frontal connectivity was higher in SeLECTS during both verb generation and repetition tasks. Frontal-to-temporal connectivity was elevated specifically during verb generation. Higher interhemispheric connectivity (between the left and right hemispheres) during language tasks strongly predicted worse phonological awareness in children with SeLECTS ({beta}= -40 to -61, all p<0.005), but not controls. Together, we found that children with SeLECTS exhibited pathologically elevated connectivity between motor and language networks that was strongly associated with impaired phonological awareness. These findings identify aberrant interhemispheric connectivity as a pathophysiological mechanism underlying language dysfunction and establish EEG-based connectivity measures as a potential biomarker for guiding targeted neuromodulation therapies to treat cognitive impairments in pediatric epilepsy.

neuroscience↗

bioRxiv2025

Phylogeny-driven design of broadly protective sarbecovirus receptor-binding domain nanoparticle vaccines

Vaccines against emerging SARS-CoV-2 variants and sarbecoviruses with pandemic potential must elicit a robust humoral immune response in a population imprinted with the SARS-CoV-2 spike (S) protein. Here, we designed protein nanoparticle (NP) vaccines co-displaying the SARS-CoV-2 BA.5, SARS-CoV-1, and BtKY72 receptor-binding domains (RBDs) with or without the Wuhan-Hu-1 (Wu) RBD. We show that these vaccines elicit cross-reactive and broadly neutralizing plasma antibody responses against SARS-CoV-2 variants and sarbecoviruses in naive and pre-immune animals. Immunization with multivalent RBD-NPs overcomes immune imprinting and elicits neutralizing antibodies and memory B cells specific for the BA.5, SARS-CoV-1, and BtKY72 RBDs in mRNA-1273-vaccinated non-human primates. Multivalent RBD-NPs outperform a monovalent Wu RBD-NP vaccine by providing superior protection in mice and non-human primates challenged with the vaccine-mismatched SARS-CoV-2 XBB.1.5 or the pre-emergent RsSHC014. These data support the use of multivalent RBD-NP vaccines for SARS-CoV-2 variants and sarbecoviruses in naive and pre-immune populations.

immunology↗

bioRxiv2025

Fucoidans are senotherapeutics that enhance SIRT6-dependent DNA repair

Aging is marked by the accumulation of senescent cells (SnCs), which contribute to tissue dysfunction and age-related diseases. Senotherapeutics, including senolytics which specifically induce lysis of SnCs and senomorphics, which suppress the senescence phenotype, represent promising therapeutic interventions for mitigating age-related pathologies and extending healthspan. Using a phenotypic-based senescent cell screening assay, we identified fucoidans, a class of sulfated polysaccharides derived from brown algae and seaweed, as novel senotherapeutics. In particular, fucoidan from Fucus vesiculosus (Fucoidan-FV) displayed potent senomorphic activity in different types of SnCs, reduced senescence in multiple tissues in aged mice, and extended healthspan in a mouse model of accelerated aging. Fucoidan-FV also enhanced the deacetylation and mono-ADP-ribosylation (mADPr) activity of SIRT6 and improved DNA repair and reduced senescence, in part, through SIRT6-dependent pathways. In addition, Fucoidan-FV downregulated genes associated with inflammation, Wnt signaling, and ECM remodeling pathways in SnCs and increased expression of genes involved with DNA repair. These findings support the translational potential of fucoidans as novel senotherapeutics that also are able to improve SIRT6-mediated DNA repair.

cell biology↗

bioRxiv2025

Transcriptomic profiling of a novel gastric implantation model identifies mechanisms and pathways that drive implantation into explanted human peritoneum

Epithelial cancers such as stomach and ovary cancer tend to metastasize to the peritoneum, often leading to intractable disease and poor survival. Currently, the mechanisms that enable gastric cancer cells to penetrate the mesothelium, and to implant, invade, and survive in the peritoneal niche are poorly understood. To investigate these mechanisms, we developed a novel human peritoneal explant model. Briefly, fresh peritoneal tissue samples from abdominal surgery patients were cultured on top of a layer of GFP-labeled human gastric adenocarcinoma cells (AGS); 2% of these cells implanted into the peritoneum. The transcriptomic profile of the implanted AGS cells was compared to the profile of AGS cells that failed to implant using RNA sequencing. Differentially expressed genes were enriched significantly (fold change>2) for genes that enable cell adhesion, motility, and membrane depolarization. We compared this list of genes with a previously identified peritoneal metastasis whole exome sequencing dataset (SRP043661). Upon further analysis based on subcellular localization, cell adhesion and cytoskeletal organization, we found nine core "peritoneal implantation" genes. We functionally validated these genes with CRISPR knockout and assessed peritoneal implantation and invasion using the human peritoneal explant model described above. From these data we identified ADAM12 as a key player of peritoneal metastasis. Knock out of ADAM12 significantly impaired peritoneal metastasis in vivo and ex vivo. Exploration of three publicly available independent datasets indicated that ADAM12 is indeed clinically relevant in peritoneal metastasis. To explore the role of ITGA{beta}1 in mediating cell-matrix interactions in the presence of ADAM12, we performed ITGA{beta}1 pull-down assays followed by mass spectrometry analysis in ADAM12 WT cells. ADAM12 KO cells show a marked disruption of the ITGA{beta}1 interactome in GCa cells. Key cytoskeletal proteins such as MYH14, MYH10, MYH9, ACTA2, SPTN1 and TPM1-TPM4 were found to be interactors with ITGA{beta}1 in ADAM12 WT cells but not ADAM12 KO cells. Our approach and the new data identify a distinct peritoneal metastasis gene set that facilitates implantation and invasion of gastric cancer cells within the peritoneum. Disruption of these pathways with peritoneal-directed therapies has the potential to improve survival in patients with high-risk primary gastric cancer.

cancer biology↗

bioRxiv2025

Visual pathway origins: an electron microscopic volume for connectomic analysis of the human foveal retina

The fovea is a unique specialization of the primate retina and is a promising site for obtaining the first complete connectome of a human central nervous system (CNS) structure. Within the fovea, neural cells and circuits have been miniaturized and compressed during evolution to sample the visual image at highest spatial resolution and begin the neural processing that serves human form, color, and motion perception. Here we present a comprehensive analysis of a sample of human foveal retina using deep learning-based segmentation to reconstruct all cells and synaptic connections at nanoscale resolution. We classified [~]3,000 cells into 51 distinct morphological types based on their structural features and connectivity patterns. Our observations reveal novel synaptic pathways absent in non-human primates, suggesting specialized circuits contribute uniquely to human trichromatic color vision. A biophysical model of the distinct connectomes made by gap junctions (electrical synapses) between short- (S) and medium-long- (ML) wavelength-sensitive cone photoreceptors, suggests chromatic interactions between S and ML cones prior to the first chemical synapse. Segmentation of retinal ganglion cells (RGCs) suggests the presence of only 11 visual pathways, with 5 high-density RGC pathways accounting for over 95% of foveal output to the brain: a dramatic contrast to the 40+ ganglion cell types recognized in mouse retina. Our connectomic analysis reveals distinctive features of human neural circuitry and demonstrates how AI-based computational approaches can advance understanding of human brain structure and function. Significant statementVision begins in the retina, an accessible outpost of the brain located at the back of the eye. When we directly view an object, we use the fovea--a tiny region containing over 50 distinct, densely packed neuron types. How these diverse cells interconnect through synapses to transmit visual information has been difficult to determine. Here, we used artificial intelligence-based computational methods to create a complete wiring diagram--a connectome--mapping every neuron and synapse in a sample of human fovea. This connectomic resource will be freely available to researchers worldwide. Discoveries so far include synaptic circuits linked to human color vision, demonstrating how connectomics can reveal what makes the human nervous system unique.

neuroscience↗

bioRxiv2025

Serine activates defense mechanisms via glutamate receptor-like channel 3.4 and calcium-dependent protein kinase 5 signaling in plants.

Amino acids are fundamental building blocks of proteins, as well as essential metabolites for plant growth and development. Beyond their metabolic roles, amino acids have been increasingly recognized as regulators of plant immunity. However, the molecular mechanisms by which amino acids modulate defense responses remain unclear. In this study, we identify a novel function for serine as a defense-priming signal. Serine pretreatment enhances immune gene expression and primes plants for a more rapid and robust response to pathogen infection, resulting in a significant delay in programmed cell death (PCD) during effector-triggered immunity (ETI). We further demonstrate that serine-induced defense activation is mediated by glutamate receptor-like calcium channel 3.4 (GLR3.4), which subsequently activates calcium-dependent protein kinase 5 (CPK5). CPK5 in turn phosphorylates WRKY transcription factors, including WRKY33, to induce key immune genes. Our findings uncover a previously unrecognized serine-initiated signaling pathway that primes plant defense, highlighting both its mechanistic novelty and its potential application in sustainable agriculture. Given that serine is a naturally occurring metabolite, its exogenous application--or the use of structurally similar analogs--may offer a cost-effective, environmentally friendly, and non-genetic strategy to enhance disease resistance in crops.

plant biology↗

bioRxiv2025

Scalable, high-throughput isolation of extracellular vesicles using electrokinetic-assisted mesh filtration

As extracellular vesicles (EVs) are increasingly recognized for their superior functions for therapeutics, the need for large-scale EV isolation technology is becoming more critical for clinical and industrial applications. Most existing EV isolation methods are optimized for small-scale laboratory samples, limiting their efficiency and scalability for large-scale production. Here, an electrokinetic-assisted filtration system (ExoFilter), which introduces charge interaction into physical mesh flow filtration, is proposed as a new candidate to address the challenges of scalable EV isolation. The hybrid filtration system demonstrates outstanding high-throughput EV isolation performance (a flux of [~]750 mL/min) using only a coarse physical filter, by electrokinetically arresting EVs flowing through the filter lattice. Furthermore, the recovery efficiency of ExoFilter, analyzed based on the ELISA results, was found to be approximately 98%, demonstrating the filters exceptional efficiency in EV isolation. Additionally, ExoFilter enables the rapid isolation of EVs from small samples as little as 200 {micro}L, facilitating quick and easy blood-based EV research. Furthermore, low-molecular-weight albumin from plasma samples was effectively removed. The high-throughput and high-efficiency characteristics of ExoFilter make it well-suited for scalable EV production, offering greater convenience for various clinical applications. HighlightsO_LIElectrokinetic-assisted mesh filtration (ExoFilter) enables scalable and rapid isolation of extracellular vesicles (EVs). C_LIO_LIA high throughput of [~]750 mL/min is demonstrated while maintaining high yield and purity. C_LIO_LIExoFilter effectively removes albumin contaminants from EVs through size-exclusive electrokinetic-assisted mesh filtration. C_LIO_LIEfficient EV isolation performance is achieved for human plasma, saliva, urine, and cell culture media. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=167 SRC="FIGDIR/small/645682v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@7ac3d5org.highwire.dtl.DTLVardef@1ced638org.highwire.dtl.DTLVardef@521c63org.highwire.dtl.DTLVardef@c5bd49_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

Advanced Extracellular Vesicle Isolation: A Hybrid Electrokinetic-Tangential Flow Filtration Approach for Improved Yield, Purity, and Scalability

As extracellular vesicles (EVs) become increasingly important in diagnostics and therapeutics, achieving both high purity and yield during isolation remains a critical challenge. Conventional techniques often suffer from the co-isolation of non-vesicular particles and soluble proteins, limiting their clinical and research utility. In response, we introduce ExoTFF, a hybrid isolation technology that sequentially integrates electrokinetic filtration (ExoFilter) with size-exclusion tangential flow filtration (TFF) to deliver unprecedented performance gains through an iterative, synergistic mechanism. In the ExoTFF system, the sample is repeatedly circulated through an electrokinetic mesh filter and TFF until the liquid is removed. This recirculating flow gradually eliminates contaminants, while the electrokinetic filter continuously captures EVs as the sample is purified. Finally, any residual impurities in the TFF unit are completely removed via a dead volume elimination process. The complementary actions of these two distinct separation mechanisms double EV recovery rates and reduce impurity levels by 80% compared to conventional TFF, culminating in an impressive 800% improvement in the purity ratio. In proof-of-concept experiments, ExoTFF processed 10 mL of plasma within 10 minutes, efficiently depleting albumin and HDL while achieving superior EV recovery. To further explore scalability, an automated ExoTFF system processed 500 mL of sample in 50 minutes, maintaining consistent yield and purity. The ability to sustain performance across different scales highlights ExoTFFs potential for both laboratory research and industrial-level EV production. Beyond biological applications, this platform also offers broad applicability for the isolation of negatively charged nanoparticles, demonstrating its potential impact across multiple nanotechnology-driven fields.

bioengineering↗

bioRxiv2025

Substrate recognition by human separase

The protein complex cohesin encircles the sister chromatids in early mitosis1. At anaphase onset, sister separation is triggered by cleavage of the cohesin subunit SCC1/RAD21 by the cysteine protease separase2-5. SCC1 contains two cleavage sites, where cleavage is stimulated by SCC1 phosphorylation5,6. The molecular mechanisms of substrate recognition and cleavage are only partly understood7. Here, we determined a series of cryoEM structures of human separase in apo-or substrate-bound forms that, together with biochemical analysis, provide novel insights into the regulation of separase cleavage activity. We verify the first SCC1 cleavage site and reassign the second site. We show that multiple substrates, including separase autocleavage sites8,9 and the two SCC1 cleavage sites, interact with several docking sites in separase, including four phosphate-binding sites. We also describe the structural basis of the interaction between the cohesin subunit SA1/A2 and separase, which promotes cleavage at the second site in SCC1. Finally, using cross-linking mass spectrometry and cryoEM, we propose a model of how cohesin is targeted by human separase. Our work provides an extensive functional and structural framework that explains one of the most fundamental events in cell division.

biochemistry↗

bioRxiv2025

Social housing effects of Intermittent Access of Methamphetamine Self-administration and social behavior

Social support is a potentially protective factor against substance use disorders (SUDs). Previous studies in animal models for SUDs have shown that when females are pair housed, they have lower motivation for cocaine and methamphetamine (METH) than females who are single housed. In males, however, social housing has not had the same beneficial effect. This study investigates effects of social housing on METH self-administration in females or males when both cage mates are self-administering METH. The study also investigated how the quality of the relationships changed after METH self-administration. The results show that singly housed females self-administered more METH than socially housed females, while males in both social housing conditions self-administered METH at the same rate. The social behavior data showed that females given saline spent more time apart, however the females given METH spent more time together, suggesting that their social behavior may play a role in the attenuation of METH self-administration. Males social behavior remained unchanged after METH and the dominant male in a pair self-administered more METH than the non-dominant male. Females self-administration was not affected by dominance. The results of this study show that social housing provides some protective benefits to females, but not males, for METH self-administration. Further, the type of relationship between cage mates affects males self-administration and may explain why social housing with a same sex mate is not beneficial for males. STRUCTURED ABSTRACT BackgroundSocial support is a potentially protective factor against substance use disorders (SUDs). Previous studies in rats have shown that when females are pair housed, they have lower motivation for drugs such as cocaine and methamphetamine (METH), than females who are single housed. In males, however, socially housed and singly housed males both have the same motivation for drugs such as cocaine. PurposeThe aim of this study was to investigate if social housing would attenuate METH self-administration in females or males when both cage mates are self-administering METH on an intermittent access schedule (IntA). The study also investigated how the quality of those relationships changed after METH self-administration, if dominance played a role in the rate of self-administration, and the extent to which the quality of the relationships was related to METH self-administration. MethodsMale and female rats were individually housed or housed in same sex pairs from around day 42, then animals underwent self-administration of METH (0.3 mg/kg/inf) on an IntA schedule of reinforcement. Both animals in a pair self-administered METH. Social behavior was evaluated prior to and throughout the period when animals were self-administering METH. ResultsThe results showed that in females, single housed females self-administered more METH than pair housed females, while males in both housing conditions self-administered METH at the same rate. More singly housed females on day one of the IntA had high rates of self-administration, compared to socially housed females. Differences attenuated after the first session, but singly housed females still self-administered METH to a greater extent than pair housed females overall. The social behavior data showed that females given saline spent more time apart while the females given METH spent more time together. This suggested that social behavior may contribute to the attenuation of self-administration in females. Males social behavior largely remained unchanged after METH and males continued to exhibit dominance behaviors. Furthermore, males METH self-administration was affected by dominance, with dominant males exhibiting greater responding for METH than non-dominant males. ConclusionsSocial housing provides some protective benefits to females, but not males, for METH self-administration. Further, the type of relationship between cage mates affects males self-administration and may explain why social housing with a same sex mate is not beneficial for males. HIGHLIGHTSO_LIPair housing in female rats resulted in less methamphetamine self-administration compared with individually housed females. C_LIO_LIPair housing in male rats did not attenuate methamphetamine self-administration compared with single housing. C_LIO_LIFemales self-administering methamphetamine spent more time together. C_LIO_LIMales self-administration of methamphetamine was affected by dominance status. C_LI

neuroscience↗

bioRxiv2025

A computational architecture incorporating shallow brain networks: integrating parallel cortical and subcortical processing

Artificial neural networks commonly have deep hierarchical structures that were originally inspired by the neuroanatomical evidence of cortico-cortical connectivity pattern found in the mammalian brain. Largely neglected in those models are non-hierarchical aspects of brain architecture, namely the subcortical pathways and the interactions between cortical and subcortical areas regardless of their hierarchical locations. Inspired by this principle, we present a computational model combining cortical hierarchical processing with subcortical pathways based on neuroanatomical evidence. We show the versatility of our model by implementing the cortical hierarchy in two alternative ways--a convolutional feedforward network and a predictive coding network. Both model variants can replicate behavioral observations in humans and monkeys on a perceptual context-dependent decision-making task. The model also reveals that subcortical structures lead decisions for easy trials while the more complex hierarchical network is necessary for the harder trials. Our results suggest that the parallel cortico-subcortical processing explored in the model represents a fundamental property that cannot be neglected in understanding the computational principles used by the brain. SignificanceArtificial intelligence and computational neuroscience models, particularly deep learning and predictive coding architectures, have been traditionally dominated by cortico-centric hierarchical frameworks. However, extensive neurobiological evidence suggests that cortical areas, regardless of their hierarchical classification, are deeply interconnected with subcortical structures in real brains. We propose here a computational framework demonstrating that parallel cortical-subcortical architectures can yield complex and more flexible computational capabilities, aligning with the observed behavior in the mammalian brain. Our model addresses key limitations in existing deep learning and predictive coding networks, offering a more biologically plausible and functionally advantageous alternative.

neuroscience↗

bioRxiv2025

Reference-based chemical-genetic interaction profiling to elucidate small molecule mechanism of action in Mycobacterium tuberculosis

In an era of increasing resistance, new and effective strategies are needed for antibiotic discovery. Whole-cell active screens yield candidate compounds lacking mechanism-of-action (MOA) information and thus do not provide biological insight for prioritization. We previously reported PROSPECT (PRimary screening Of Strains to Prioritize Expanded Chemistry and Targets), an antimicrobial discovery strategy that measures chemical-genetic interactions between small molecules and a pool of Mycobacterium tuberculosis mutants, each depleted of a different essential protein target. PROSPECT facilitates efficient hit prioritization by simultaneously identifying whole-cell active compounds with high sensitivity and providing early insights into their MOA. Here, we report a reference-based approach to infer MOA from often complex PROSPECT data. For this aim, we curated a reference set of 437 compounds with published, annotated MOA and known or suspected antitubercular activity, and applied PROSPECT to it. We then developed Perturbagen CLass (PCL) analysis, a computational method that predicts MOA by comparing chemical-genetic interaction profiles of unknown compounds to those of this reference set. In leave-one-out cross-validation, PCL analysis correctly predicted MOA with 70% sensitivity and 75% precision. When applied to 75 antitubercular leads with known MOA previously reported by GlaxoSmithKline (GSK), PCL analysis similarly achieved 69% sensitivity and 87% precision. We also analyzed 98 GSK compounds lacking MOA information, predicting 60 of them to act via a reference MOA, and followed up with functional validation of 29 compounds predicted to target respiration-related MOAs. Finally, we applied PROSPECT and PCL analysis to [~]5,000 compounds from larger unbiased libraries that had not been preselected for antitubercular activity. PCL analysis identified a novel scaffold lacking wild-type activity but predicted to inhibit respiration via QcrB, and we confirmed this prediction while chemically optimizing this scaffold to achieve wild-type activity. PCL analysis of PROSPECT data thus enables rapid MOA assignment and hit prioritization, advancing the discovery of new, potent antitubercular compounds.

microbiology↗

bioRxiv2025

Ketamine Alters Tuning of Neural and Behavioral Spatial Working Memory Precision

Deficits in working memory (WM) are a hallmark of neuropsy-chiatric disorders such as schizophrenia, yet their neurobiological basis remains poorly understood. Glutamate N-methyl-D-aspartate receptors (NMDARs) are critical for spatial WM (sWM), with NMDAR antagonist ketamine known to attenuate task-evoked activation and reduce sWM accuracy. Cortical microcircuit models hypothesize that NMDAR antagonism impairs sWM by broadening neural spatial tuning, but this mechanism has not been directly tested in humans. Using a pharmacological fMRI approach, we showed how ketamine broadened neural spatial tuning, attenuated activation across visual, parietal, and frontal areas, and worsened sWM performance in healthy humans. Ketamine-induced changes in tuning were more consistent across individuals and brain regions than changes in overall activation and correlated with individual differences in sWM performance. These findings provide empirical evidence linking NMDAR antagonism to disruptions in cortical microcircuit dynamics, the resulting neural tuning alterations, and sWM impairments, advancing frameworks for therapeutic development.

neuroscience↗

bioRxiv2025

Free acid β-hydroxybutyrate supplementation does not ameliorate dextran sodium sulfate-induced colitis similar to ketogenic diet in male mice

High-fat, low-carbohydrate ketogenic diets have been found to alleviate experimental colitis in rodents. These diets lead to increased endogenous production and utilization of ketone bodies, such as {beta}-hydroxybutyrate (BHB), and supplementation with exogenous ketones has arisen as a potential alternative to ketogenic diets. This study aimed to investigate how continuous high-dose feeding with free acid BHB influences experimental colitis compared to a ketogenic diet with the hypothesis that BHB would also alleviate the inflammation. We fed nine-week-old C57BL/6J male mice for four weeks with one of three diets: a low-fat control diet, a ketogenic diet, or a low-fat diet supplemented with free acid R-BHB and then induced colonic inflammation with dextran sodium sulfate (DSS). We assessed macroscopic and histological changes in the colon, intestinal permeability to fluorescein isothiocyanate dextran, colonic mRNA expression of tight junction proteins and inflammatory markers, fecal calprotectin, and microbiota composition. While the ketogenic diet alleviated DSS-induced weight loss, macroscopic changes, and histological lesions, the BHB-supplemented diet did not have the same effect. The pre-DSS composition of the microbiota was drastically different between the diet groups which may partly explain the different outcomes. In conclusion, high-dose supplementation with free acid BHB may not produce the same benefits as ketogenic diet in the context of colonic inflammation.

pharmacology and toxicology↗

bioRxiv2024

Identification of neuron-glia signaling feedback in human schizophrenia using patient-derived, mix-and-match forebrain assembloids

Although abnormal activities across multiple cell types are believed to contribute to the development of various neurodevelopmental disorders, current brain organoid technologies fall short in accurately modeling the dynamic cellular interactions in the human brain. Recently, we developed a cellular reconstitution technology to create human forebrain assembloids with enhanced cellular diversity, representing dynamic interactions between neurons and glial cells. Here, we created patient-derived, mix-and-match forebrain assembloids, in which neurons, astrocytes, and microglia from both healthy individuals and schizophrenia patients were reconstituted in a combinatorial manner, and identified aberrant cellular interactions between neurons and glial cells in human schizophrenia. At the early stage, schizophrenia forebrain assembloids showed premature neurogenesis induced by the abnormal proliferation and differentiation of neural progenitor cells. Integrated modular analysis of gene expression in post-mortem schizophrenia brain tissue and brain assembloids found increased expression of tumor protein p53 (TP53) and nuclear factor of activated T-cells 4 (NFATC4), which functioned as master transcriptional regulators to epigenetically reprogram the transcriptome involved in the cellular dynamics of neuronal progenitor cells, leading to premature neurogenesis. At the later stage, we observed weakened structures of laminar organization of the cortical layers in forebrain assembloids and identified the neuron-dependent transcriptional plasticity of glial cells and their altered signaling feedback with neurons, in which neuronal urocortin (UCN) and protein tyrosine phosphatase receptor type F (PTPRF) elicited the expression of Wnt family member 11 (WNT11) and thrombospondin 4 (THBS4) in astrocytes and microglia, respectively. These aberrant signaling axes altered the neuronal transcriptome associated with neuronal response to various stimuli and synthetic processes of biomolecules, resulting in reduced synapse connectivity. Thus, we elucidated developmental stage-specific, multifactorial mechanisms by which dynamic cellular interplay among neural progenitor cells, neurons, and glial cells contribute to the development of the human schizophrenia brain. Our study further demonstrated the potential and applicability of patient-derived forebrain assembloid technology to advance our understanding of the pathogenesis of various neurodevelopmental disorders.

neuroscience↗

bioRxiv2024

A Co-essentiality Network of Cancer Driver Genes Better Prioritizes Anticancer Drugs

Diverse molecular networks have been extensively studied to discover therapeutic targets and repurpose approved drugs. However, it is necessary to select a suitable network since the performance of network medicine relies heavily on the completeness and characteristics of the selected network. Although a network using gene essentiality from cancer cells could be an effective platform for identifying anticancer targets, efforts to apply these networks in therapeutic applications have been limited. We constructed a phenotype-level network using the co-essentiality relationship between genes in CRISPR screens across 769 cancer cells to discover therapeutic targets for diverse cancer types. Leveraging cancer driver genes and network propagation on the networks, we found that the co-essentiality network better prioritized anticancer targets and biomarkers and predicted more precise drug responses in cancer cells than other molecular networks. The co-essentiality network outperformed conventional molecular networks in drug repurposing, which were validated in silico by clinical trial records. Notably, the co-essentiality network provided 37 repurposed drugs that the other networks have yet to cover, and we showcased three approved drugs repurposed for lung adenocarcinoma (Pioglitazone hydrochloride, Atovaquone, and Eflornithine). Our study provides a novel network for precision oncology to improve the identification of therapeutic targets in specific cancers.

bioinformatics↗

bioRxiv2024

Survivin modulates stiffness-induced vascular smooth muscle cell motility

Arterial stiffness is a key contributor to cardiovascular diseases, including atherosclerosis, restenosis, and coronary artery disease, it has been characterized to be associated with the aberrant migration of vascular smooth muscle cells (VSMCs). However, the underlying molecular mechanisms driving VSMC migration in stiff environments remain incompletely understood. We recently demonstrated that survivin, a member of the inhibitor of apoptosis protein family, is highly expressed in both mouse and human VSMCs cultured on stiff polyacrylamide hydrogels, where it modulates stiffness-mediated cell cycle progression and proliferation. However, its role in stiffness-dependent VSMC migration remains unknown. To assess its impact on migration, we performed time-lapse video microscopy on VSMCs seeded on fibronectin-coated soft and stiff polyacrylamide hydrogels, mimicking the physiological stiffness of normal and diseased arteries, with either survivin inhibition or overexpression. We observed that VSMC motility increased under stiff conditions, while pharmacologic or siRNA-mediated inhibition of survivin reduced stiffness-stimulated migration to rates similar to those observed under soft conditions. Further investigation revealed that cells on stiff hydrogels exhibited greater directional movement and robust lamellipodial protrusion compared to those on soft hydrogels. Interestingly, survivin-inhibited cells on stiff hydrogels showed reduced directional persistence and lamellipodial protrusion compared to control cells. We also examined whether survivin overexpression alone is sufficient to induce cell migration on soft hydrogels, and found that survivin overexpression modestly increased cell motility and partially rescued the lack of directional persistence compared to GFP-expressing control VSMCs on soft hydrogels. In conclusion, our findings demonstrate that survivin plays a key role in regulating stiffness-induced VSMC migration, suggesting that targeting survivin and its signaling pathways could offer therapeutic strategies for addressing arterial stiffness in cardiovascular diseases.

cell biology↗

bioRxiv2024

CoREST Complex Inhibition Alters RNA Splicing to Promote Neoantigen Expression and Enhance Tumor Immunity

ABSTRACTEpigenetic complexes tightly regulate gene expression and colocalize with RNA splicing machinery; however, the consequences of these interactions are uncertain. Here, we identify unique interactions of the CoREST repressor complex with RNA splicing factors and their functional consequences in tumorigenesis. Using mass spectrometry, in vivo binding assays, and cryo-EM we find that CoREST complex-splicing factor interactions are direct and perturbed by the CoREST complex inhibitor, corin, leading to extensive changes in RNA splicing in melanoma and other malignancies. Using predictive machine learning models and MHC IP-MS, we identify thousands of corin-induced neopeptides derived from unannotated splice sites which generate immunogenic splice-neoantigens. Furthermore, corin reactivates the response to immune checkpoint blockade and promotes dramatic expansion of cytotoxic T cells in an immune cold melanoma model. CoREST complex inhibition thus represents a unique therapeutic opportunity in cancer which creates tumor-associated neoantigens that enhance the immunogenicity of current therapeutics. Statement of SignificanceWe identify a novel role of the CoREST transcriptional repressor complex in regulating pre-mRNA splicing and find that the small molecule inhibitor, corin, promotes alternative splicing events in cancer leading to neoantigen expression and T cell-mediated immunity. This represents a potential approach to promote immunoreactive neoantigen expression in immune-cold tumors.

cancer biology↗