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1.
PLoS Biol ; 22(5): e3002596, 2024 May.
Article in English | MEDLINE | ID: mdl-38718086

ABSTRACT

Autism spectrum disorders (ASD) frequently accompany macrocephaly, which often involves hydrocephalic enlargement of brain ventricles. Katnal2 is a microtubule-regulatory protein strongly linked to ASD, but it remains unclear whether Katnal2 knockout (KO) in mice leads to microtubule- and ASD-related molecular, synaptic, brain, and behavioral phenotypes. We found that Katnal2-KO mice display ASD-like social communication deficits and age-dependent progressive ventricular enlargements. The latter involves increased length and beating frequency of motile cilia on ependymal cells lining ventricles. Katnal2-KO hippocampal neurons surrounded by enlarged lateral ventricles show progressive synaptic deficits that correlate with ASD-like transcriptomic changes involving synaptic gene down-regulation. Importantly, early postnatal Katnal2 re-expression prevents ciliary, ventricular, and behavioral phenotypes in Katnal2-KO adults, suggesting a causal relationship and a potential treatment. Therefore, Katnal2 negatively regulates ependymal ciliary function and its deletion in mice leads to ependymal ciliary hyperfunction and hydrocephalus accompanying ASD-related behavioral, synaptic, and transcriptomic changes.


Subject(s)
Autism Spectrum Disorder , Cilia , Ependyma , Mice, Knockout , Phenotype , Animals , Male , Mice , Autism Spectrum Disorder/genetics , Autism Spectrum Disorder/metabolism , Autism Spectrum Disorder/physiopathology , Behavior, Animal , Cilia/metabolism , Disease Models, Animal , Ependyma/metabolism , Hippocampus/metabolism , Hydrocephalus/genetics , Hydrocephalus/metabolism , Hydrocephalus/pathology , Hydrocephalus/physiopathology , Katanin/metabolism , Katanin/genetics , Mice, Inbred C57BL , Neurons/metabolism , Synapses/metabolism , Transcriptome/genetics
2.
Mol Cell ; 72(3): 426-443.e12, 2018 11 01.
Article in English | MEDLINE | ID: mdl-30401430

ABSTRACT

Protein phase separation by low-complexity, intrinsically disordered domains generates membraneless organelles and links to neurodegeneration. Cellular prion protein (PrPC) contains such domains, causes spongiform degeneration, and is a receptor for Alzheimer's amyloid-ß oligomers (Aßo). Here, we show that PrPC separates as a liquid phase, in which α-helical Thr become unfolded. At the cell surface, PrPC Lys residues interact with Aßo to create a hydrogel containing immobile Aßo and relatively mobile PrPC. The Aßo/PrP hydrogel has a well-defined stoichiometry and dissociates with excess Aßo. NMR studies of hydrogel PrPC reveal a distinct α-helical conformation for natively unfolded amino-terminal Gly and Ala residues. Aßo/PrP hydrogel traps signal-transducing mGluR5 on the plasma membrane. Recombinant PrPC extracts endogenous Aßo from human Alzheimer's soluble brain lysates into hydrogel, and a PrPC antagonist releases Aßo from endogenous brain hydrogel. Thus, coupled phase and conformational transitions of PrPC are driven by Aß species from Alzheimer's disease.


Subject(s)
Amyloid beta-Peptides/physiology , PrPC Proteins/chemistry , PrPC Proteins/physiology , Alzheimer Disease/metabolism , Animals , Brain , COS Cells , Cell Line , Cell Membrane , Chlorocebus aethiops , HEK293 Cells , Humans , Hydrogels , Magnetic Resonance Imaging/methods , Molecular Conformation , Neurons , Prions/chemistry , Prions/physiology , Protein Binding , Receptor, Metabotropic Glutamate 5 , Signal Transduction
3.
J Am Chem Soc ; 146(20): 13846-13853, 2024 May 22.
Article in English | MEDLINE | ID: mdl-38652033

ABSTRACT

Lipid rafts, which are dynamic nanodomains in the plasma membrane, play a crucial role in intermembrane processes by clustering together and growing in size within the plane of the membrane while also aligning with each other across different membranes. However, the physical origin of layer by layer alignment of lipid rafts remains to be elucidated. Here, by using fluorescence imaging and synchrotron X-ray reflectivity in a phase-separated multilayer system, we find that the alignment of raft-mimicking Lo domains is regulated by the distance between bilayers. Molecular dynamics simulations reveal that the aligned state is energetically preferred when the intermembrane distance is small due to its ability to minimize the volume of surface water, which has fewer water hydrogen bonds (HBs) compared to bulk water. Our results suggest that water HB-driven alignment of lipid rafts plays a role as a precursor of intermembrane processes such as cell-cell fusion, virus entry, and signaling.


Subject(s)
Hydrogen Bonding , Membrane Microdomains , Molecular Dynamics Simulation , Water , Water/chemistry , Membrane Microdomains/chemistry , Lipid Bilayers/chemistry , Lipid Bilayers/metabolism
4.
EMBO J ; 39(11): e104150, 2020 06 02.
Article in English | MEDLINE | ID: mdl-32347567

ABSTRACT

Alternative splicing regulates trans-synaptic adhesions and synapse development, but supporting in vivo evidence is limited. PTPδ, a receptor tyrosine phosphatase adhering to multiple synaptic adhesion molecules, is associated with various neuropsychiatric disorders; however, its in vivo functions remain unclear. Here, we show that PTPδ is mainly present at excitatory presynaptic sites by endogenous PTPδ tagging. Global PTPδ deletion in mice leads to input-specific decreases in excitatory synapse development and strength. This involves tyrosine dephosphorylation and synaptic loss of IL1RAPL1, a postsynaptic partner of PTPδ requiring the PTPδ-meA splice insert for binding. Importantly, PTPδ-mutant mice lacking the PTPδ-meA insert, and thus lacking the PTPδ interaction with IL1RAPL1 but not other postsynaptic partners, recapitulate biochemical and synaptic phenotypes of global PTPδ-mutant mice. Behaviorally, both global and meA-specific PTPδ-mutant mice display abnormal sleep behavior and non-REM rhythms. Therefore, alternative splicing in PTPδ regulates excitatory synapse development and sleep by modulating a specific trans-synaptic adhesion.


Subject(s)
Interleukin-1 Receptor Accessory Protein/metabolism , Protein Tyrosine Phosphatases/metabolism , Sleep Stages , Synapses/metabolism , Animals , Interleukin-1 Receptor Accessory Protein/genetics , Mice , Mice, Inbred BALB C , Mice, Knockout , Protein Tyrosine Phosphatases/genetics , Synapses/genetics
5.
Mol Psychiatry ; 27(11): 4680-4694, 2022 Nov.
Article in English | MEDLINE | ID: mdl-35840799

ABSTRACT

Three-dimensional chromatin interactions regulate gene expressions. The significance of de novo mutations (DNMs) in chromatin interactions remains poorly understood for autism spectrum disorder (ASD). We generated 813 whole-genome sequences from 242 Korean simplex families to detect DNMs, and identified target genes which were putatively affected by non-coding DNMs in chromatin interactions. Non-coding DNMs in chromatin interactions were significantly involved in transcriptional dysregulations related to ASD risk. Correspondingly, target genes showed spatiotemporal expressions relevant to ASD in developing brains and enrichment in biological pathways implicated in ASD, such as histone modification. Regarding clinical features of ASD, non-coding DNMs in chromatin interactions particularly contributed to low intelligence quotient levels in ASD probands. We further validated our findings using two replication cohorts, Simons Simplex Collection (SSC) and MSSNG, and showed the consistent enrichment of non-coding DNM-disrupted chromatin interactions in ASD probands. Generating human induced pluripotent stem cells in two ASD families, we were able to demonstrate that non-coding DNMs in chromatin interactions alter the expression of target genes at the stage of early neural development. Taken together, our findings indicate that non-coding DNMs in ASD probands lead to early neurodevelopmental disruption implicated in ASD risk via chromatin interactions.


Subject(s)
Autism Spectrum Disorder , Induced Pluripotent Stem Cells , Humans , Autism Spectrum Disorder/genetics , Chromatin/genetics , Mutation/genetics , Genetic Predisposition to Disease/genetics
6.
PLoS Biol ; 17(6): e2005326, 2019 06.
Article in English | MEDLINE | ID: mdl-31166939

ABSTRACT

Netrin-G ligand-3 (NGL-3) is a postsynaptic adhesion molecule known to directly interact with the excitatory postsynaptic scaffolding protein postsynaptic density-95 (PSD-95) and trans-synaptically with leukocyte common antigen-related (LAR) family receptor tyrosine phosphatases to regulate presynaptic differentiation. Although NGL-3 has been implicated in the regulation of excitatory synapse development by in vitro studies, whether it regulates synapse development or function, or any other features of brain development and function, is not known. Here, we report that mice lacking NGL-3 (Ngl3-/- mice) show markedly suppressed normal brain development and postnatal survival and growth. A change of the genetic background of mice from pure to hybrid minimized these developmental effects but modestly suppressed N-methyl-D-aspartate (NMDA) receptor (NMDAR)-mediated synaptic transmission in the hippocampus without affecting synapse development, α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor (AMPAR)-mediated basal transmission, and presynaptic release. Intriguingly, long-term depression (LTD) was near-completely abolished in Ngl3-/- mice, and the Akt/glycogen synthase kinase 3ß (GSK3ß) signaling pathway, known to suppress LTD, was abnormally enhanced. In addition, pharmacological inhibition of Akt, but not activation of NMDARs, normalized the suppressed LTD in Ngl3-/- mice, suggesting that Akt hyperactivity suppresses LTD. Ngl3-/- mice displayed several behavioral abnormalities, including hyperactivity, anxiolytic-like behavior, impaired spatial memory, and enhanced seizure susceptibility. Among them, the hyperactivity was rapidly improved by pharmacological NMDAR activation. These results suggest that NGL-3 regulates brain development, Akt/GSK3ß signaling, LTD, and locomotive and cognitive behaviors.


Subject(s)
Brain/embryology , Brain/growth & development , GPI-Linked Proteins/metabolism , Nerve Tissue Proteins/metabolism , Animals , Brain/metabolism , GPI-Linked Proteins/genetics , Glycogen Synthase Kinase 3 beta/metabolism , Hippocampus/metabolism , Ligands , Long-Term Synaptic Depression , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Nerve Tissue Proteins/genetics , Netrins/metabolism , Neuronal Plasticity , Neurons/metabolism , Proto-Oncogene Proteins c-akt/metabolism , Receptors, AMPA/metabolism , Receptors, N-Methyl-D-Aspartate/metabolism , Signal Transduction , Synapses/metabolism , Synapses/physiology , Synaptic Transmission
7.
J Neurosci ; 39(10): 1910-1929, 2019 03 06.
Article in English | MEDLINE | ID: mdl-30626696

ABSTRACT

The intracellular tyrosine kinase Pyk2 (PTK2B) is related to focal adhesion kinase and localizes to postsynaptic sites in brain. Pyk2 genetic variation contributes to late onset Alzheimer's disease (AD) risk. We recently observed that Pyk2 is required for synapse loss and for learning deficits in a transgenic mouse model of AD. Here, we explore the cellular and biochemical basis for the action of Pyk2 tyrosine kinase in amyloid-ß oligomer (Aßo)-induced dendritic spine loss. Overexpression of Pyk2 reduces dendritic spine density of hippocampal neurons by a kinase-dependent mechanism. Biochemical isolation of Pyk2-interacting proteins from brain identifies Graf1c, a RhoA GTPase-activating protein inhibited by Pyk2. Aßo-induced reductions in dendritic spine motility and chronic spine loss require both Pyk2 kinase and RhoA activation. Thus, Pyk2 functions at postsynaptic sites to modulate F-actin control by RhoA and regulate synapse maintenance of relevance to AD risk.SIGNIFICANCE STATEMENT Genetic variation at the Pyk2 locus is a risk for Alzheimer's disease. We have observed that Pyk2 is required for AD transgenic synapse loss and memory dysfunction. However, the cellular and biochemical basis for Pyk2 function related to AD is not defined. Here, we show that brain Pyk2 interacts with the RhoGAP protein Graf1 to alter dendritic spine stability via RhoA GTPase. Amyloid-ß oligomer-induced dendritic spine loss requires the Pyk2/Graf1 pathway.


Subject(s)
Amyloid beta-Peptides/metabolism , Dendritic Spines/metabolism , Focal Adhesion Kinase 2/metabolism , GTPase-Activating Proteins/metabolism , Hippocampus/metabolism , Synapses/metabolism , Synapses/pathology , rhoA GTP-Binding Protein/metabolism , Animals , Female , Focal Adhesion Kinase 2/genetics , HEK293 Cells , Hippocampus/pathology , Humans , Male , Mice, Inbred C57BL , Mice, Knockout , Signal Transduction
8.
J Neurosci ; 39(4): 758-772, 2019 01 23.
Article in English | MEDLINE | ID: mdl-30518596

ABSTRACT

Dozens of genes have been implicated in late onset Alzheimer's disease (AD) risk, but none has a defined mechanism of action in neurons. Here, we show that the risk factor Pyk2 (PTK2B) localizes specifically to neurons in adult brain. Absence of Pyk2 has no major effect on synapse formation or the basal parameters of synaptic transmission in the hippocampal Schaffer collateral pathway. However, the induction of synaptic LTD is suppressed in Pyk2-null slices. In contrast, deletion of Pyk2 expression does not alter LTP under control conditions. Of relevance for AD pathophysiology, Pyk2-/- slices are protected from amyloid-ß-oligomer (Aßo)-induced suppression of LTP in hippocampal slices. Acutely, a Pyk2 kinase inhibitor also prevents Aßo-induced suppression of LTP in WT slices. Female and male transgenic AD model mice expressing APPswe/PSEN1ΔE9 require Pyk2 for age-dependent loss of synaptic markers and for impairment of learning and memory. However, absence of Pyk2 does not alter Aß accumulation or gliosis. Therefore, the Pyk2 risk gene is directly implicated in a neuronal Aßo signaling pathway impairing synaptic anatomy and function.SIGNIFICANCE STATEMENT Genetic variation at the Pyk2 (PTK2B) locus is a risk for late onset Alzheimer's disease (AD), but the pathophysiological role of Pyk2 is not clear. Here, we studied Pyk2 neuronal function in mice lacking expression with and without transgenes generating amyloid-ß (Aß) plaque pathology. Pyk2 is not required for basal synaptic transmission or LTP, but participates in LTD. Hippocampal slices lacking Pyk2 are protected from AD-related Aß oligomer suppression of synaptic plasticity. In transgenic AD model mice, deletion of Pyk2 rescues synaptic loss and learning/memory deficits. Therefore, Pyk2 plays a central role in AD-related synaptic dysfunction mediating Aß-triggered dysfunction.


Subject(s)
Alzheimer Disease/genetics , Alzheimer Disease/pathology , Amyloid beta-Peptides/toxicity , Focal Adhesion Kinase 2/genetics , Synapses/pathology , Animals , Behavior, Animal , Female , Gliosis/genetics , Gliosis/pathology , Learning/physiology , Long-Term Potentiation/genetics , Long-Term Synaptic Depression/genetics , Male , Memory/physiology , Mice , Mice, Inbred C57BL , Mice, Knockout , Mice, Transgenic , Risk Factors , Signal Transduction/genetics
9.
J Biol Chem ; 294(15): 6042-6053, 2019 04 12.
Article in English | MEDLINE | ID: mdl-30787106

ABSTRACT

Oligomeric assemblies of amyloid-ß (Aß) peptide (Aßo) in the brains of individuals with Alzheimer's disease (AD) are toxic to neuronal synapses. More than a dozen Aß receptor candidates have been suggested to be responsible for various aspects of the molecular pathology and memory impairment in mouse models of AD. A lack of consistent experimental design among previous studies of different receptor candidates limits evaluation of the relative roles of these candidates, producing some controversy within the field. Here, using cell-based assays with several Aß species, including Aßo from AD brains obtained by autopsy, we directly compared the Aß-binding capacity of multiple receptor candidates while accounting for variation in expression and confirming cell surface expression. In a survey of 15 reported Aß receptors, only cellular prion protein (PrPC), Nogo receptor 1 (NgR1), and leukocyte immunoglobulin-like receptor subfamily B member 2 (LilrB2) exhibited direct binding to synaptotoxic assemblies of synthetic Aß. Both PrPC and NgR1 preferentially bound synaptotoxic oligomers rather than nontoxic monomers, and the method of oligomer preparation did not significantly alter our binding results. Hippocampal neurons lacking both NgR1 and LilrB2 exhibited a partial reduction of Aßo binding, but this reduction was lower than in neurons lacking PrPC under the same conditions. Finally, binding studies with soluble Aßo from human AD brains revealed a strong affinity for PrPC, weak affinity for NgR1, and no detectable affinity for LilrB2. These findings clarify the relative contributions of previously reported Aß receptors under controlled conditions and highlight the prominence of PrPC as an Aß-binding site.


Subject(s)
Alzheimer Disease/metabolism , Amyloid beta-Peptides/metabolism , Membrane Glycoproteins/metabolism , Nogo Receptor 1/metabolism , PrPC Proteins/metabolism , Receptors, Immunologic/metabolism , Alzheimer Disease/genetics , Alzheimer Disease/pathology , Amyloid beta-Peptides/genetics , Animals , COS Cells , Chlorocebus aethiops , Disease Models, Animal , Female , HEK293 Cells , Humans , Male , Membrane Glycoproteins/genetics , Mice , Mice, Knockout , Neurons/metabolism , Neurons/pathology , Nogo Receptor 1/genetics , PrPC Proteins/genetics , Receptors, Immunologic/genetics
10.
Biochem Biophys Res Commun ; 501(2): 329-335, 2018 06 22.
Article in English | MEDLINE | ID: mdl-29505793

ABSTRACT

Celecoxib is a non-steroidal anti-inflammatory drug that selectively inhibits cyclooxygenase-2 and is prescribed for severe pain and inflammation. The excellent therapeutic effects of celecoxib mean that it is frequently used clinically, including for women of child-bearing age. However, the prenatal effects of this compound have not been studied extensively in vertebrates. The present study examined the developmental toxicity of celecoxib using a frog embryo teratogenic assay-Xenopus (FETAX). In addition, we examined its effects on cell migration using co-cultures of human umbilical vein endothelial cells and 10T1/2 cells. These studies revealed that celecoxib induced concentration-dependent mortality and various malformations of the Xenopus internal organs, including gut miscoiling, haemorrhage, and oedema. Celecoxib also downregulated the expression of vascular wall markers (Msr and alpha smooth muscle actin) and other organ-specific markers (Nkx2.5, Cyl104 and IFABP). In vitro co-culture studies revealed that celecoxib inhibited pericyte migration and differentiation into vascular smooth muscle cells. In conclusion, celecoxib was both toxic and teratogenic in Xenopus embryos, where it produced serious heart and vessel malformation by inhibiting vascular wall maturation and vascular network formation.


Subject(s)
Celecoxib/toxicity , Teratogens/toxicity , Xenopus laevis/embryology , Animals , Anti-Inflammatory Agents, Non-Steroidal/toxicity , Biomarkers , Blood Vessels/abnormalities , Blood Vessels/drug effects , Blood Vessels/embryology , Celecoxib/administration & dosage , Cell Movement/drug effects , Dose-Response Relationship, Drug , Embryo, Nonmammalian/drug effects , Female , Gene Expression Regulation, Developmental/drug effects , Human Umbilical Vein Endothelial Cells , Humans , Male , Xenopus laevis/physiology
11.
Langmuir ; 30(48): 14369-74, 2014 Dec 09.
Article in English | MEDLINE | ID: mdl-25422050

ABSTRACT

We present a novel technique to measure diffusion coefficients of insoluble surfactant monolayers. We merge a surfactant-coated droplet with a fluorescently labeled planar monolayer. During the merging process, a monolayer on a droplet displaces the existing planar monolayer, leaving a dark area when viewed under a fluorescence microscope. We measure fractional intensities as the dyes recover, which allows diffusion coefficients to be computed. We validate this technique with the two most common phospholipid monolayers (DPPC and DOPC) and study the diffusion of their mixtures. The proposed technique has several advantages over the FRAP technique and is potentially capable of measuring the diffusion of any soluble/insoluble surfactant monolayers.


Subject(s)
Phospholipids/chemistry , Surface-Active Agents/chemistry , 1,2-Dipalmitoylphosphatidylcholine/chemistry , Microscopy, Fluorescence , Phosphatidylcholines/chemistry
12.
Cerebrovasc Dis ; 38(4): 290-6, 2014.
Article in English | MEDLINE | ID: mdl-25412772

ABSTRACT

BACKGROUND: Intracranial arterial stenosis (ICAS) is a major cause of ischemic stroke in Asians. Despite the clinical importance of ICAS, the literature on the natural history of ICAS has been less enlightening. The aims of our study were to evaluate a long-term natural course of symptomatic and asymptomatic ICAS. METHODS: 102 subjects (37 symptomatic and 65 asymptomatic) underwent follow-up MR angiography (MRA) with a median time interval between initial and follow-up MRA of 5.7 years (range 3.6-8.5 years). For each patient, the extent of stenosis of five arteries (both middle cerebral arteries, both intracranial internal carotid arteries, and basilar artery) was classified according to five grades, by consensus: normal, mild (signal reduction <50%), moderate (signal reduction ≥50%), severe (focal signal loss with the presence of a distal signal), and occlusion. Because the sample size was too small to adjust for multiple confounders, we applied the propensity score. RESULTS: Mean (Standard deviation) age at initial MRA was 63.5 (9.6) and 54% were men. The progression rate of ICAS differed significantly between symptomatic and asymptomatic patients (22 vs. 8%, p < 0.01), indicating a 3-fold risk of progression for symptomatic stenosis compared with asymptomatic stenosis [odds ratio (OR) 3.27, 95% confidence interval (CI) 1.08-9.95]. After adjustment for propensity score, the OR was 4.84 (95% CI, 1.40-16.7). In the matched cohort, the relative risk of stenosis progression was 5.20 for symptomatic stenosis (95% CI 1.00-27.23) compared with asymptomatic stenosis. CONCLUSION: We found a greater risk of progression for symptomatic stenosis compared with asymptomatic stenosis.


Subject(s)
Cerebral Arterial Diseases/diagnosis , Cerebral Arteries/pathology , Magnetic Resonance Angiography , Aged , Asymptomatic Diseases , Cerebral Arterial Diseases/complications , Cerebral Arterial Diseases/pathology , Constriction, Pathologic , Disease Progression , Female , Humans , Logistic Models , Male , Middle Aged , Odds Ratio , Predictive Value of Tests , Propensity Score , Retrospective Studies , Risk Factors , Severity of Illness Index , Time Factors
13.
J Nanosci Nanotechnol ; 14(5): 3880-3, 2014 May.
Article in English | MEDLINE | ID: mdl-24734656

ABSTRACT

In this work, cadmium sulfide (CdS) films were deposited on flexible polymer substrates such as polycarbonate (PC) and polyethylene terephthalate (PET). The r.f. magnetron sputtering, which is cost-effective scalable technique, was used for the film deposition. The structural and optical properties of the films grown at different sputtering pressures were investigated. When the CdS film was deposited at lower pressure, the crystallinity and the preferred orientation toward c-axis in hexagonal phase was improved. However, the optical transmittance was reduced as the sputtering pressure was decreased. Compared with the glass substrate, CdS films grown on polymer substrates were exhibited some wore structural and optical characteristics. CdTe thin film solar cell applied to sputtered CdS as a window layer showed a maximum efficiency of 11.6%.

14.
Neural Netw ; 180: 106663, 2024 Aug 23.
Article in English | MEDLINE | ID: mdl-39208459

ABSTRACT

Utilizing large-scale pretrained models is a well-known strategy to enhance performance on various target tasks. It is typically achieved through fine-tuning pretrained models on target tasks. However, naï ve fine-tuning may not fully leverage knowledge embedded in pretrained models. In this study, we introduce a novel fine-tuning method, called stochastic cross-attention (StochCA), specific to Transformer architectures. This method modifies the Transformer's self-attention mechanism to selectively utilize knowledge from pretrained models during fine-tuning. Specifically, in each block, instead of self-attention, cross-attention is performed stochastically according to the predefined probability, where keys and values are extracted from the corresponding block of a pretrained model. By doing so, queries and channel-mixing multi-layer perceptron layers of a target model are fine-tuned to target tasks to learn how to effectively exploit rich representations of pretrained models. To verify the effectiveness of StochCA, extensive experiments are conducted on benchmarks in the areas of transfer learning and domain generalization, where the exploitation of pretrained models is critical. Our experimental results show the superiority of StochCA over state-of-the-art approaches in both areas. Furthermore, we demonstrate that StochCA is complementary to existing approaches, i.e., it can be combined with them to further improve performance. We release the code at https://github.com/daintlab/stochastic_cross_attention.

15.
Genome Med ; 16(1): 20, 2024 01 31.
Article in English | MEDLINE | ID: mdl-38297291

ABSTRACT

BACKGROUND: Recent studies using single-cell transcriptomic analysis have reported several distinct clusters of neoplastic epithelial cells and cancer-associated fibroblasts in the pancreatic cancer tumor microenvironment. However, their molecular characteristics and biological significance have not been clearly elucidated due to intra- and inter-tumoral heterogeneity. METHODS: We performed single-cell RNA sequencing using enriched non-immune cell populations from 17 pancreatic tumor tissues (16 pancreatic cancer and one high-grade dysplasia) and generated paired spatial transcriptomic data from seven patient samples. RESULTS: We identified five distinct functional subclusters of pancreatic cancer cells and six distinct cancer-associated fibroblast subclusters. We deeply profiled their characteristics, and we found that these subclusters successfully deconvoluted most of the features suggested in bulk transcriptome analysis of pancreatic cancer. Among those subclusters, we identified a novel cancer cell subcluster, Ep_VGLL1, showing intermediate characteristics between the extremities of basal-like and classical dichotomy, despite its prognostic value. Molecular features of Ep_VGLL1 suggest its transitional properties between basal-like and classical subtypes, which is supported by spatial transcriptomic data. CONCLUSIONS: This integrative analysis not only provides a comprehensive landscape of pancreatic cancer and fibroblast population, but also suggests a novel insight to the dynamic states of pancreatic cancer cells and unveils potential therapeutic targets.


Subject(s)
Carcinoma, Pancreatic Ductal , Pancreatic Neoplasms , Humans , Transcriptome , Carcinoma, Pancreatic Ductal/genetics , Pancreatic Neoplasms/genetics , Pancreatic Neoplasms/pathology , Gene Expression Profiling , Prognosis , Tumor Microenvironment/genetics , Single-Cell Analysis , DNA-Binding Proteins/genetics , Transcription Factors/genetics
16.
Nat Commun ; 14(1): 3547, 2023 06 15.
Article in English | MEDLINE | ID: mdl-37321992

ABSTRACT

Autism spectrum disorders (ASD) represent neurodevelopmental disorders characterized by social deficits, repetitive behaviors, and various comorbidities, including epilepsy. ANK2, which encodes a neuronal scaffolding protein, is frequently mutated in ASD, but its in vivo functions and disease-related mechanisms are largely unknown. Here, we report that mice with Ank2 knockout restricted to cortical and hippocampal excitatory neurons (Ank2-cKO mice) show ASD-related behavioral abnormalities and juvenile seizure-related death. Ank2-cKO cortical neurons show abnormally increased excitability and firing rate. These changes accompanied decreases in the total level and function of the Kv7.2/KCNQ2 and Kv7.3/KCNQ3 potassium channels and the density of these channels in the enlengthened axon initial segment. Importantly, the Kv7 agonist, retigabine, rescued neuronal excitability, juvenile seizure-related death, and hyperactivity in Ank2-cKO mice. These results suggest that Ank2 regulates neuronal excitability by regulating the length of and Kv7 density in the AIS and that Kv7 channelopathy is involved in Ank2-related brain dysfunctions.


Subject(s)
Epilepsy , KCNQ Potassium Channels , Animals , Mice , Epilepsy/metabolism , KCNQ Potassium Channels/genetics , KCNQ2 Potassium Channel/genetics , KCNQ2 Potassium Channel/metabolism , KCNQ3 Potassium Channel/metabolism , Neurons/metabolism , Seizures/genetics , Seizures/metabolism
17.
J Mol Cell Cardiol ; 52(3): 718-26, 2012 Mar.
Article in English | MEDLINE | ID: mdl-22197309

ABSTRACT

Despite its significant clinical implications, physiological hypertrophy remains poorly understood. In this study, the transcription coactivator Eya2 was shown to be up-regulated during physiological hypertrophy. Transgene- or adenovirus-mediated overexpression of Eya2 led to up-regulation of mTOR, a critical mediator of physiological hypertrophy. Luciferase reporter and chromatin immunoprecipitation assays revealed that Eya2 directly binds to and activates mTOR expression. The phosphorylation of mTOR downstream molecules was significantly enhanced in Eya2 transgenic (TG) hearts, implying that the Eya2-mediated induction of mTOR expression leads to an elevated mTOR activity. The transcription factor Six1 was also up-regulated during physiological hypertrophy and formed a complex with Eya2. Luciferase reporter and electrophoretic mobility shift assays revealed that the Eya2-Six1 complex binds to and enhances the expression of mTOR in a synergistic manner. Under pressure overload, Eya2 transgenic hearts developed hypertrophy which exhibited important molecular signatures of physiological hypertrophy, as assessed by gene expression profiling and measurements of expression levels of physiological hypertrophy-related genes by quantitative (q) RT-PCR. Examination of heart sections under electron microscopy revealed that the mitochondrial integrity remained largely intact in Eya2 transgenic mice, but not in wild-type littermates, under pressure overload. This finding was confirmed by measurements of mitochondrial DNA contents and the expression levels of mitochondrial function-related genes by qRT-PCR. These data suggest that Eya2 in a physical complex with Six1 plays a critical role in physiological hypertrophy. The cardioprotective effect of Eya2 appears to be due, at least in part, to its preservation of mitochondrial integrity upon pressure overload.


Subject(s)
Cell Enlargement , Intracellular Signaling Peptides and Proteins/genetics , Intracellular Signaling Peptides and Proteins/metabolism , Myocytes, Cardiac/metabolism , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Protein Tyrosine Phosphatases/genetics , Protein Tyrosine Phosphatases/metabolism , Animals , Cell Line , Cells, Cultured , Gene Expression Regulation , Homeodomain Proteins/metabolism , Humans , Male , Mice , Mice, Inbred C57BL , Mitochondria, Heart/ultrastructure , Protein Binding , Rats , Rats, Sprague-Dawley , TOR Serine-Threonine Kinases/genetics , TOR Serine-Threonine Kinases/metabolism
18.
J Cell Sci ; 123(Pt 10): 1742-50, 2010 May 15.
Article in English | MEDLINE | ID: mdl-20427313

ABSTRACT

SNX18 and SNX9 are members of a subfamily of SNX (sorting nexin) proteins with the same domain structure. Although a recent report showed that SNX18 and SNX9 localize differently in cells and appear to function in different trafficking pathways, concrete evidence regarding whether they act together or separately in intracellular trafficking is still lacking. Here, we show that SNX18 has a similar role to SNX9 in endocytic trafficking at the plasma membrane, rather than having a distinct role. SNX18 and SNX9 are expressed together in most cell lines, but to a different extent. Like SNX9, SNX18 interacts with dynamin and stimulates the basal GTPase activity of dynamin. It also interacts with neuronal Wiskott-Aldrich syndrome protein (N-WASP) and synaptojanin, as does SNX9. SNX18 and SNX9 can form a heterodimer and colocalize in tubular membrane structures. Depletion of SNX18 by small hairpin RNA inhibited transferrin uptake. SNX18 successfully compensates for SNX9 deficiency during clathrin-mediated endocytosis and vice versa. Total internal reflection fluorescence microscopy in living cells shows that a transient burst of SNX18 recruitment to clathrin-coated pits coincides spatiotemporally with a burst of dynamin and SNX9. Taken together, our results suggest that SNX18 functions with SNX9 in multiple pathways of endocytosis at the plasma membrane and that they are functionally redundant.


Subject(s)
Cell Membrane/metabolism , Clathrin-Coated Vesicles/metabolism , Glioma/metabolism , Vesicular Transport Proteins/metabolism , Cell Line, Tumor , Dynamins/metabolism , Endocytosis/genetics , Glioma/genetics , Glioma/pathology , Humans , Microscopy, Fluorescence , Nerve Tissue Proteins/metabolism , Phosphoric Monoester Hydrolases/metabolism , Protein Binding , Protein Transport , RNA, Small Interfering/genetics , Sorting Nexins , Vesicular Transport Proteins/genetics , Wiskott-Aldrich Syndrome Protein, Neuronal/metabolism
19.
Aust N Z J Obstet Gynaecol ; 52(4): 348-55, 2012 Aug.
Article in English | MEDLINE | ID: mdl-22541027

ABSTRACT

AIMS: The objective of this study was to derive a customised birth weight standard curve in our institute and to compare the perinatal outcomes of small-for-gestational-age (SGA) births classified by population-based versus customised birth weight standards. METHODS: We surveyed 9052 normal singleton deliveries and generated customised standards by adjusting for maternal characteristics and neonatal gender. We compared adverse perinatal outcomes between SGA and non-SGA births classified by both standards. RESULTS: According to the population-based standards, mothers of SGA infants were younger, thinner and shorter and had higher rates of nulliparity and female births. We adjusted for these maternal characteristics and neonatal gender in our customised standards. Multivariate analysis revealed that there were no differences in neonatal composite morbidity between the standards. However, infants classified as SGA by the customised standards showed a significantly higher rate of neonatal intensive care unit (NICU) admission than those classified by the population-based standards. CONCLUSION: Our study showed that customised SGA made no significant differences in neonatal composite morbidity, only a modest increase in NICU admission rate compared to population-based standard. To clarify the association of adverse perinatal outcomes with customised SGA, larger studies are required.


Subject(s)
Birth Weight , Infant, Small for Gestational Age , Mothers/statistics & numerical data , Adult , Analysis of Variance , Cohort Effect , Female , Humans , Infant, Newborn , Male , Maternal Age , Multivariate Analysis , Reference Standards , Reference Values , Republic of Korea , Retrospective Studies , Statistics, Nonparametric
20.
J Cell Biol ; 221(8)2022 08 01.
Article in English | MEDLINE | ID: mdl-35819332

ABSTRACT

IRSp53 (aka BAIAP2) is a scaffold protein that couples membranes with the cytoskeleton in actin-filled protrusions such as filopodia and lamellipodia. The protein is abundantly expressed in excitatory synapses and is essential for synapse development and synaptic plasticity, although with poorly understood mechanisms. Here we show that specific multivalent interactions between IRSp53 and its binding partners PSD-95 or Shank3 drive phase separation of the complexes in solution. IRSp53 can be enriched to the reconstituted excitatory PSD (ePSD) condensates via bridging to the core and deeper layers of ePSD. Overexpression of a mutant defective in the IRSp53/PSD-95 interaction perturbs synaptic enrichment of IRSp53 in mouse cortical neurons. The reconstituted PSD condensates promote bundled actin filament formation both in solution and on membranes, via IRSp53-mediated actin binding and bundling. Overexpression of mutants that perturb IRSp53-actin interaction leads to defects in synaptic maturation of cortical neurons. Together, our studies provide potential mechanistic insights into the physiological roles of IRSp53 in synapse formation and function.


Subject(s)
Actins , Nerve Tissue Proteins , Post-Synaptic Density , Actin Cytoskeleton/metabolism , Actins/metabolism , Animals , Mice , Microfilament Proteins/genetics , Microfilament Proteins/metabolism , Nerve Tissue Proteins/genetics , Nerve Tissue Proteins/metabolism , Neuronal Plasticity , Neurons/metabolism , Post-Synaptic Density/metabolism , Pseudopodia/genetics , Pseudopodia/metabolism , Synapses/genetics , Synapses/metabolism
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