Biology subjects

Li, K. W.

Publications and source records attributed to Li, K. W..

14 recordsLinked to original sources

bioRxiv2025

Casein kinase 1δ-regulated formation of GVBs induces resilience to tau pathology-mediated protein synthesis impairment

In Alzheimers disease, many surviving neurons with tau pathology contain granulovacuolar degeneration bodies (GVBs), neuron-specific lysosomal structures induced by pathological tau assemblies. This could indicate a neuroprotective role for GVBs, however, the mechanism of GVB formation and its functional implications are elusive. Here, we demonstrate that CK1{delta} activity is required for GVB formation. CK1{delta} is sequestered in the GVB during this process in an autophagy-dependent manner. We show that neurons with GVBs (GVB+) are resilient to tau-induced impairment of global protein synthesis and are protected against tau-mediated neurodegeneration. GVB+ neurons do not exhibit differential activation of proteostatic stress responses, but have increased ribosomal content. Importantly, unlike neurons without GVBs, GVB+ neurons fully retain the capacity to induce long-term potentiation-induced protein synthesis in the presence of tau pathology. Our results have identified CK1{delta} as a key regulator of GVB formation that confers a protective neuron-specific proteostatic stress response to tau pathology. These findings provide novel opportunities for targeting neuronal resilience in tauopathies. HighlightsO_LIGVB+ neurons are protected against tau-induced neurodegeneration C_LIO_LICK1{delta} activity is essential for the formation of GVBs C_LIO_LIGVB+ neurons are resilient to tau-induced impairment of protein synthesis C_LIO_LIGVB+ neurons retain the capacity for LTP-regulated protein synthesis C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/645932v2_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@cda628org.highwire.dtl.DTLVardef@157bcb8org.highwire.dtl.DTLVardef@126dbe6org.highwire.dtl.DTLVardef@2efe8f_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

Type I TARPs regulate Kv7.2 potassium channels andsusceptibility to seizures

The M-current is a low-threshold potassium current that modulates neuronal excitability and suppresses repetitive firing. However, the mechanisms regulating M-channel function remain unclear. We identified type I Transmembrane AMPA receptor Regulatory Proteins (TARPs) as M-channel Kv7.2 subunit interactors in cortical neurons, with their interaction increasing upon neuronal depolarization. Co-expression of TARPs with Kv7.2 increased channel surface expression and Kv7.2-mediated currents, while disrupting TARP-{gamma}2 expression in neurons perturbed dendritic Kv7.2 nano-clusters and decreased M-currents. Knock-in mice with an intellectual disability-associated TARP-{gamma}2 variant showed reduced hippocampal M-currents and increased seizure susceptibility, indicating that disrupting TARP-{gamma}2 regulation of Kv7.2-M-channels is epileptogenic. These findings show that TARP-{gamma}2, a synaptic protein crucial for excitatory transmission, also controls intrinsic excitability via M-channels. This discovery provides a link between synaptic transmission and neuronal excitability, with implications for disease, as the interplay between synaptic and intrinsic plasticity is pivotal to how the brain adapts to varying input signals. HighlightsO_LIType I TARPs bind to Kv7.2-M-channels and enhance Kv7.2-mediated currents. C_LIO_LITARP-{gamma}2 governs the neuronal nano-organization and function of Kv7.2 channels. C_LIO_LIIntellectual disability-associated TARP-{gamma}2 variant impairs M-currents and facilitates seizures. C_LIO_LIType I TARPs can serve as molecular integrators of synaptic and intrinsic excitability. C_LI

neuroscience↗

bioRxiv2024

Rab10 regulates neuropeptide release by maintaining Ca2+ homeostasis and protein synthesis

Dense core vesicles (DCVs) transport and release various neuropeptides and neurotrophins that control diverse brain functions, but the DCV secretory pathway remains poorly understood. Here, we tested a prediction emerging from invertebrate studies about the crucial role of the intracellular trafficking GTPase Rab10, by assessing DCV exocytosis at single-cell resolution upon acute Rab10 depletion in mature mouse hippocampal neurons, to circumvent potential confounding effects of Rab10s established role in neurite outgrowth. We observed a significant inhibition of DCV exocytosis in Rab10-depleted neurons, whereas synaptic vesicle exocytosis was unaffected. However, rather than a direct involvement in DCV trafficking, this effect was attributed to two ER-dependent processes, ER-regulated intracellular Ca2+ dynamics and protein synthesis. Gene ontology analysis of differentially expressed proteins upon Rab10 depletion identified substantial alterations in synaptic and ER/ribosomal proteins, including the Ca2+-pump SERCA2. In addition, ER morphology and dynamics were altered, ER Ca2+ levels were depleted and Ca2+ homeostasis was impaired in Rab10-depleted neurons. However, Ca2+ entry using a Ca2+ ionophore still triggered less DCV exocytosis. Instead, leucine supplementation, which enhances protein synthesis, largely rescued DCV exocytosis deficiency. We conclude that Rab10 is required for neuropeptide release by maintaining Ca2+ dynamics and regulating protein synthesis. Furthermore, DCV exocytosis appeared more dependent on (acute) protein synthesis than synaptic vesicle exocytosis.

neuroscience↗

bioRxiv2023

Luminescence-based screening for extracellular vesicle release modulators reveals a role for PI4KIIIβ in exosome biogenesis upon lysosome inhibition

Dysregulated extracellular vesicle (EV) release has been implicated in various pathologies, including cancer, neurodegenerative disease and osteoarthritis. Despite clear therapeutic potential, drug screening for EV release modulators has yielded limited success due to the lack of a sensitive and scalable EV read-out system. Here, we employed CRISPR-Cas9 to engineer HEK293 cells expressing HA-NanoLuciferase-(NL)-tagged endogenous CD63. We found that under basal culture conditions, CD63-containing EVs are released via a mechanism that is independent of the exocytic SNARE protein SNAP23, presumably by direct budding from the plasma membrane. Endo-lysosome inhibition by chemical or genetic perturbation of vATPase strongly increased SNAP23 and nSmase2-dependent exosome secretion from intracellular compartments. Proteomic analysis revealed these exosomes are enriched for early- and late endosomal markers, but also for autophagosomal proteins. This suggests that a proportion of these exosomes originate from amphisomes, although chemical inhibition of canonical autophagy did not affect exosome secretion upon lysosome inhibition. Using a broad- spectrum kinase inhibitor screen, we identified and subsequently validated the lipid kinase PI4KIII{beta} as a critical mediator of exosome secretion and amphisome-mediated secretory autophagy, upon lysosome inhibition. We conclude that tagging of endogenous CD63 with NanoLuciferase represents a sensitive, scalable reporter strategy that enables identification of (druggable) modulators of EV biogenesis and release under physiological and pathological conditions.

cell biology↗

bioRxiv2022

INFLAMMATION INDUCED DOWNREGULATION OF SUCCINATE DEHYDROGENASE REGULATES ADRENOCORTICAL FUNCTION

The hypothalamus-pituitary-adrenal (HPA) axis is activated in response to inflammation leading to increased production of anti-inflammatory glucocorticoids by the adrenal cortex, thereby representing an endogenous feedback loop. However, severe inflammation reduces the responsiveness of the adrenal gland to adrenocorticotropic hormone (ACTH) although the underlying mechanisms are poorly understood. Here, we show by transcriptomic, proteomic and metabolomic analyses that LPS-induced systemic inflammation triggers profound metabolic changes in steroidogenic adrenocortical cells, including downregulation of the TCA cycle and oxidative phosphorylation. Inflammation disrupts the TCA cycle at the level of succinate dehydrogenase (SDH) leading to succinate accumulation and disturbed steroidogenesis. Mechanistically, IL-1{beta} reduces SDHB expression through upregulation of DNA methyltransferase 1 (DNMT1) and methylation of the SDHB promoter. Consequently, increased succinate levels impair oxidative phosphorylation and ATP synthesis, leading to reduced steroidogenesis. Together, we demonstrate that the IL-1{beta}-DNMT1-SDHB-succinate axis disrupts steroidogenesis. Our findings not only provide a mechanistic explanation for the adrenal dysfunction in severe inflammation but also a potential target for therapeutic intervention.

immunology↗

bioRxiv2022

Excess ribosomal protein production unbalances translation in Fragile X Syndrome

Dysregulated protein synthesis is a core pathogenic mechanism in Fragile X Syndrome (FX). The mGluR Theory of FX predicts that pathological synaptic changes arise from the excessive translation of mRNAs downstream of mGlu1/5 activation. Here, we use a combination of CA1 pyramidal neuron-specific TRAP-seq and proteomics to identify the overtranslating mRNAs supporting exaggerated mGlu1/5-induced long-term synaptic depression (mGluR-LTD) in the FX mouse model (Fmr1-/y). Surprisingly, our results identify a robust translation of ribosomal proteins (RPs) upon mGlu1/5 stimulation that coincides with a reduced translation of long mRNAs encoding synaptic proteins. These changes are mimicked and occluded in Fmr1-/y neurons. Inhibiting RP translation significantly impairs mGluR-LTD and prevents the length-dependent shift in the translating population. Together, these results suggest that pathological changes in FX result from a length-dependent alteration in the translating population that is supported by excessive RP translation.

neuroscience↗

bioRxiv2021

β-amyloid-driven synaptic depression requires PDZ protein interaction at AMPA-receptor subunit GluA3

Soluble oligomeric amyloid-{beta} (A{beta}) is a prime suspect to cause cognitive deficits in Alzheimers disease and weakens synapses by removing AMPA-type glutamate receptors (AMPARs). We show that synapses of CA1 pyramidal neurons become vulnerable to A{beta} when they express AMPAR subunit GluA3. We found that A{beta}-oligomers reduce the levels of GluA3 immobilized at spines, indicating they deplete GluA3-containing AMPARs from synapses. These A{beta}-driven effects critically depended on the PDZ-binding motif of GluA3. When GluA3 was expressed with a single amino acid mutation in its PDZ-binding motif that prevents GRIP binding, it did not end up at spines and A{beta} failed to trigger synaptic depression. GluA3 with a different point mutation in the PDZ-motif that leaves GRIP-binding intact but prevents its endocytosis, was present at spines in normal amounts but was fully resistant to effects of A{beta}. Our data indicate that A{beta}-mediated synaptic depression requires the removal of GluA3 from synapses. We propose that GRIP-detachment from GluA3 is a critical early step in the cascade of events through which A{beta} accumulation causes a loss of synapse.

neuroscience↗

bioRxiv2021

An organelle inheritance pathway during polarized cell growth

Some organelles cannot be synthesized anew, so they are segregated into daughter cells during cell division. In Saccharomyces cerevisiae, daughter cells bud from mother cells and are populated by organelles inherited from the mothers. To determine whether this organelle inheritance occurs in a stereotyped manner, we tracked organelles using fluorescence microscopy. We describe a program for organelle inheritance in budding yeast. The cortical endoplasmic reticulum (ER) and peroxisomes are inherited concomitant with bud emergence. Next, vacuoles are inherited in small buds, followed closely by mitochondria. Finally, the nucleus and perinuclear ER are inherited when buds have nearly reached their maximal size. Because organelle inheritance timing correlates with bud morphology, which is coupled to the cell cycle, we tested whether organelle inheritance order is controlled by the cell cycle. By arresting cell cycle progression but allowing continued bud growth, we determined that organelle inheritance still occurs without cell cycle progression past S-phase, and that the general inheritance order is maintained. Thus, organelle inheritance follows a preferred order during polarized cell division, but it is not controlled exclusively by cell cycle signaling. Summary statementOrganelles are interconnected by contact sites, but they must be inherited from mother cells into buds during budding yeast mitosis. We report that this process occurs in a preferred sequence.

cell biology↗

bioRxiv2019

The endosomal protein sorting nexin 4 is a novel synaptic protein

Sorting nexin 4 (SNX4) is an evolutionary conserved protein that mediates recycling from the endosomes back to the plasma membrane in yeast and mammalian cells. SNX4 is expressed in the brain, but its neuronal localization and function have not been addressed. Using a new antibody, endogenous neuronal SNX4 co-localized with both early and recycling endosomes, similar to the reported localization of SNX4 in non-neuronal cells. Neuronal SNX4 was accumulated in synapses, and immuno-electron microscopy revealed that SNX4 was predominantly localized to presynaptic terminals. Acute depletion of neuronal SNX4 using independent shRNAs did not affect the levels of the canonical SNX4-cargo transferrin receptor. Explorative mass spectrometry showed that each SNX4-targetted shRNA resulted in a reproducible and distinct proteome and that synaptic communication-related proteins were downregulated upon expression of the three shRNAs. The identification of SNX4 as a novel synaptic protein indicates a selective demand for SNX4 dependent sorting in synapses.

neuroscience↗

bioRxiv2019

Regulation of neuronal mRNA splicing and Tau isoform ratio by ATXN3 through deubiquitylation of splicing factors

The ubiquitylation/deubiquitylation balance in cells is maintained by deubiquitylating enzymes, including ATXN3. The precise role of this protein, mutated in spinocerebellar ataxia type 3 (SCA3), remains elusive, as few substrates for its deubiquitylating activity were identified. Here, we characterized the ubiquitome of neuronal cells lacking ATXN3, and found altered polyubiquitylation in a large proportion of proteins involved in RNA metabolism, including splicing factors. Using transcriptomic analysis and reporter minigenes we confirmed that splicing was globally altered in these cells. Among the candidate targets of ATXN3 was SRSF7 (9G8), a key regulator of MAPT (Tau) exon 10 splicing. Loss-of-function of ATXN3 led to reduced SRSF7 levels and a deregulation of MAPT exon 10 splicing, resulting in a decreased 4R/3R-Tau ratio. Similar alterations were found in cellular models of expanded polyQ ATXN3 and SCA3 patient brains, pointing to a relevant role of this mechanism in SCA3, and establishing a previously unsuspected link between two key proteins involved in different neurodegenerative disorders.

neuroscience↗

bioRxiv2018

Gpr158 deficiency impacts hippocampal CA1 neuronal excitability, dendritic architecture, and affects spatial learning

G-protein-coupled receptor 158 (Gpr158) is highly expressed in striatum, hippocampus and prefrontal cortex. It gained attention as it was implicated in physiological responses to stress and depression. Recently, Gpr158 has been shown to act as a pathway-specific synaptic organizer in the hippocampus, required for proper mossy fiber-CA3 neurocircuitry establishment, structure, and function. Although rodent Gpr158 expression is highest in CA3, considerable expression occurs in CA1 especially after the first postnatal month. Here, we combined hippocampal-dependent behavioral paradigms with subsequent electrophysiological and morphological analyses from the same group of mice to assess the effects of Gpr158 deficiency on CA1 physiology and function. We demonstrate deficits in spatial memory acquisition and retrieval in the Morris water maze paradigm, along with deficits in the acquisition of extinction memory in the passive avoidance test in Gpr158 KO mice. Electrophysiological recordings from CA1 pyramidal neurons revealed normal basal excitatory and inhibitory synaptic transmission, however, Schaffer collateral stimulation yielded dramatically reduced post-synaptic currents. Interestingly, intrinsic excitability of CA1 pyramidals was found increased, potentially acting as a compensatory mechanism to the reductions in Schaffer collateral-mediated drive. Both ex vivo and in vitro, neurons deficient for Gpr158 exhibited robust reductions in dendritic architecture and complexity, i.e., reduced length, surface, bifurcations, and branching. This effect was localized in the apical but not basal compartment of adult CA1 pyramidals, indicative of pathway-specific alterations. A significant positive correlation between spatial memory acquisition and extent of complexity of CA1 pyramidals was found. Taken together, we provide first evidence of significant disruptions in hippocampal CA1 neuronal dendritic architecture and physiology, driven by Gpr158 deficiency. Importantly, the hippocampal neuronal morphology deficits appear to support the impairments in spatial memory acquisition observed in Gpr158 KO mice.

neuroscience↗

bioRxiv2018

The autism and schizophrenia-associated protein CYFIP1 regulates bilateral brain connectivity

Copy-number variants of the CYFIP1 gene in humans have been linked to Autism and Schizophrenia, two neuropsychiatric disorders characterized by defects in brain connectivity. CYFIP1 regulates molecular events underlying post-synaptic functions. Here, we show that CYFIP1 plays an important role in brain functional connectivity and callosal functions. In particular, we find that Cyfip1 heterozygous mice have reduced brain functional connectivity and defects in white matter architecture, typically relating to phenotypes found in patients with Autism, Schizophrenia and other neuropsychiatric disorders. In addition, Cyfip1 deficient mice present deficits in the callosal axons, namely reduced myelination, altered pre-synaptic function, and impaired bilateral-connectivity related behavior. Altogether, our results show that Cyfip1 haploinsufficiency compromises brain connectivity and function, which might explain its genetic association to neuropsychiatric disorders.

neuroscience↗

bioRxiv2017

Proper Conditional Analysis in the Presence of Missing Data Identified Novel Independently Associated Low Frequency Variants in Nicotine Dependence Genes

Meta-analysis of genetic association studies increases sample size and the power for mapping complex traits. Existing methods are mostly developed for datasets without missing values. In practice, genotype imputation is not always effective, e.g. when targeted genotyping/sequencing assays are used or when the un-typed genetic variant is rare. Therefore, contributed summary statistics often contain missing values. Naive extensions of existing methods either replace missing summary statistics with 0 or discard studies with missing data. These approaches can bias genetic effect estimates and lead to seriously inflated type-I or II errors in conditional analysis, which is a critical tool for identifying independently associated variants.\n\nTo address this challenge and complement imputation methods, we developed a method to combine summary statistics across participating studies and consistently estimate joint effects, even when the contributed summary statistics contain large amount of missing values. Based on this estimator, we propose a score statistic we call PCBS (partial correlation based score statistic) for conditional analysis of single-variant and gene-level associations. Through extensive analysis of simulated and real data, we showed that the new method produces well-calibrated type-I errors and is substantially more powerful than existing approaches. We applied the proposed approach to analyze the CHRNA5-CHRNB4-CHRNA3 locus in a large-scale meta-analysis for cigarettes-per-day. Using the new method, we identified three novel variants, independent of known association signals, which were otherwise missed by alternative methods. Together, the phenotypic variance explained by these variants is .46%, improving that of previously reported associations by 17%. These findings illustrate the extent of locus allelic heterogeneity and can help pinpoint causal variants.\n\nAUTHOR SUMMARYIt is of great interest to estimate the joint and conditional effects of multiple correlated variants from large scale meta-analysis, in order to fine map causal variants and understand the genetic architecture for complex traits. The contributed summary statistics from participating studies in a meta-analysis often contain missing values, as the imputation methods are not often effective, especially when the underlying genetic variant is rare or the participating studies use targeted genotyping array that is not suitable for imputation. Existing meta-analysis methods do not properly handle missing data, and can incorrectly estimate correlations between score statistics. As a result, they can produce highly biased estimates of joint effects and highly inflated type-I errors for conditional analysis, which will in turn result in overestimated phenotypic variance explained and incorrect identification of causal variants. We systematically evaluated this bias and proposed a novel partial correlation based score statistic. The new statistic has valid type-I errors for conditional analysis and much higher power than the existing methods, even when the contributed summary statistics in the meta-analysis contain a large fraction of missing values. We expect this method to be highly useful in the sequencing age for complex trait genetics.

genetics↗

bioRxiv2017

Association Analysis and Meta-Analysis of Multi-allelic Variants for Large Scale Sequence Data

MotivationThere is great interest to understand the impact of rare variants in human diseases using large sequence datasets. In deep sequences datasets of >10,000 samples, [~]10% of the variant sites are observed to be multi-allelic. Many of the multi-allelic variants have been shown to be functional and disease relevant. Proper analysis of multi-allelic variants is critical to the success of a sequencing study, but existing methods do not properly handle multi-allelic variants and can produce highly misleading association results.\n\nResultsWe propose novel methods to encode multi-allelic sites, conduct single variant and gene-level association analyses, and perform meta-analysis for multi-allelic variants. We evaluated these methods through extensive simulations and the study of a large meta-analysis of [~]18,000 samples on the cigarettes-per-day phenotype. We showed that our joint modeling approach provided an unbiased estimate of genetic effects, greatly improved the power of single variant association tests, and enhanced gene-level tests over existing approaches.\n\nAvailabilitySoftware packages implementing these methods are available at (https://github.com/zhanxw/rvtests http://genome.sph.umich.edu/wiki/RareMETAL).\n\nContactxiaowei.zhan@utsouthwestem.edu; dajiang.liu@psu.edu

bioinformatics↗