Biology subjects

Wang, Y.-Z.

Publications and source records attributed to Wang, Y.-Z..

12 recordsLinked to original sources

bioRxiv2026

Brain Landscape In Situ Crosslinking Mass Spectrometry (BLIS-XL-MS) Enables Global Analysis of Protein Structural Remodeling in the Brain

Pathological protein conformational remodeling is a key molecular feature of brain disorders. However, conventional approaches to understand the changes in potein conformation are targeted and difficult to scale proteome-wide analysis. Emerging mass spectrometry-based structural proteomic methods broaden coverage but often involve complex workflows and trade-offs between labeling efficiency and preservation of the in vivo molecular state. Thus, quantitative analysis of proteome-wide structural remodeling remains limited. Here we present Brain Landscape In Situ Crosslinking Mass Spectrometry (BLIS-XL-MS), an experimental and computational framework for analyzing protein and protein-complex remodeling in brain tissue. BLIS-XL-MS stabilizes the molecular state before secondary crosslinking, improves reagent accessibility through sectioning and permeabilization, and integrates quantitative crosslink analysis with structural and protein-interaction-network interpretation. Applied to brains from GluA1A636T knock-in mice, modeling a neurodevelopmental disorder, BLIS-XL-MS revealed coordinated remodeling of protein systems involved in AMPA receptor-trafficking, mitochondrial function and cell-death pathways. We demonstrate that BLIS-XL-MS provides a scalable framework for mapping disease-associated structural remodeling across the brain proteome.

neuroscience↗

bioRxiv2026

A pathogenic AMPA receptor gating mutation disrupts synapse-mitochondrion axis and stalls synapse maturation

AMPA receptors (AMPARs) are central regulators of excitatory synaptic transmission and play critical roles in activity-dependent synapse maturation and circuit development. De novo missense mutations in AMPAR subunits have been widely linked to neurodevelopmental disorders (NDDs). Despite this, how these variants lead to neuronal dysfunction remain poorly understood. Here, we investigate the consequences of a recurrent pathogenic mutation in the GluA1 subunit (GRIA1 p.A636T), which alters AMPAR gating properties and is associated with autism spectrum disorder and intellectual disability. We developed a GluA1A636T knock-in mouse model, we show that GluA1A636T mice exhibit impairments in hippocampal-dependent learning and working memory accompanied by reduced baseline activity of CA1 neurons in vivo. Mass spectrometry-based quantitative proteomic analyses of juvenile and adult hippocampal samples revealed that the A636T mutation significantly alters synaptic protein expression at both ages. Notably, the mutation drives a robust upregulation of mitochondrial proteins specifically in adult mice. Consistent with this, dendritic mitochondria in adult GluA1A636T mice exhibited altered morphology and increased oxidative stress. Electrophysiological analyses further revealed abnormalities in synaptic function, including reduced basal excitatory transmission, persistence of functionally silent synapses in adulthood, and altered synaptic plasticity consistent with impaired synapse maturation. Together, these findings demonstrate that a pathogenic AMPAR gating mutation disrupts the coordinated development of synaptic and metabolic programs in the hippocampus, linking altered excitatory signaling to delayed mitochondrial stress and enduring circuit dysfunction. Our study provides a developmental framework for understanding how disease-associated AMPAR variants impair brain function and highlights synapse-mitochondria coupling as a critical axis in glutamate receptor ionotropic (GRI) disorders.

neuroscience↗

bioRxiv2025

Heat-shock pathway activation by TRC051384 protects spiral ganglion neurons from noise-induced hearing loss

Noise-induced hearing loss (NIHL) is a major public health problem caused by damage to cochlear hair cells, synapses, and spiral ganglion neurons (SGNs). Since effective treatments are lacking, we investigated cellular stress responses induced by moderate and loud noise in a mouse model of cochlear synaptopathy. RNA sequencing and spatial transcriptomics revealed that noise exposure elicited a robust but transient upregulation of endoplasmic reticulum chaperones and proteasome subunits in SGNs and their supporting cells. To target this response, we administered TRC051384, a small-molecule activator of the heat shock transcription factor Hsf1, prior to noise exposure. TRC051384 crossed the blood-labyrinth barrier and reached the cochlea, induced heat shock protein gene expression, and restored ubiquitin-proteasome function in SGNs. Notably, TRC051384 treatment enhanced auditory brainstem response threshold recovery, preserved Wave I amplitudes, and maintained ribbon synapse density. These findings establish proteotoxic stress in SGNs as a key driver of NIHL and identify HSF1 activation as a promising therapeutic strategy.

neuroscience↗

bioRxiv2025

Herbivorous insects independently evolved salivary effectors to regulate plant immunity by destabilizing the malectin-LRR RLP NtRLP4

Plants utilize on receptor-like proteins and receptor-like kinases (RLPs/RLKs) to perceive and respond to a wide variety of invading pathogens and insect herbivores. While the strategies employed by microbial pathogens to suppress plant immunity have been well characterized, it remains unclear how herbivorous insects counteract receptor-mediated defenses. Here, we show that salivary effectors evolve independently in whiteflies and planthoppers to dampen RLP4-mediated plant immunity. RLP4, as a leucine-rich repeat RLP (LRR-RLP), confers plant resistance against herbivorous insects by forming the RLP4/SOBIR1 complexes. In the whitefly Bemisia tabaci, BtRDP, the Aleyrodidae-specific salivary sheath protein, interacts with RLP4 from multiple plant species and promotes its ubiquitin-dependent degradation. Overexpression of NtRLP4 in transgenic plants exerts a detrimental effect on B. tabaci by exploiting the crosstalk between the salicylic acid (SA) and jasmonic acid (JA) pathways. Conversely, overexpression of BtRDP or silencing of NtRLP4 effectively alleviates such negative effects. In planthopper Nilaparvata lugens, the Delphacidae-restricted salivary protein NlSP104 also targets and promotes the degradation of OsRLP4 from rice plants. These findings reveal convergent evolution of salivary proteins in insects, and underscore the complex interactions between plants and herbivorous insects.

molecular biology↗

bioRxiv2025

Response dynamics of discrete subiculum->retrosplenial cortex projections underlying trace fear conditioning

Associating events separated in time depends on the CA1, subiculum (SUB), and retrosplenial cortex (RSP). The degree to which their connectivity and underlying circuit mechanisms contribute to the association of such temporally discontiguous events is not known. Here we showed, using trace fear conditioning (TFC), wherein mice learn to associate tone and shock separated by a temporal trace, that molecularly distinct excitatory VGluT1+ and VGluT2+ SUB[->]RSP projections subserve the associative and temporal components of TFC. During trace memory formation, VGluT2+ SUB[->]RSP projections showed increased and decreased bulk calcium activity at tone and trace onset, respectively, an activity pattern that was reestablished during memory recall. Such pattern was not observed in CA subfields, suggesting that associative and temporal components of TFC are integrated at the SUB or SUB[->]RSP synapses before being presented to the RSP. Our findings establish a circuit mechanism for representing complex temporal information in episodic memory.

neuroscience↗

bioRxiv2025

Ubiquitin Proteasome System Components, RAD23A and USP13, Modulate TDP-43 Solubility and Neuronal Toxicity

At autopsy, >95% of ALS cases display a redistribution of the essential RNA binding protein TDP-43 from the nucleus into cytoplasmic aggregates. The mislocalization and aggregation of TDP-43 is believed to be a key pathological driver in ALS. Due to its vital role in basic cellular mechanisms, direct depletion of TDP-43 is unlikely to lead to a promising therapy. Therefore, we have explored the utility of identifying modifier genes that modify its mislocalization or aggregation. We have previously shown that loss of rad-23 improves locomotor deficits in TDP-43 C. elegans models of disease and increases the degradation rate of TDP-43 in cellular models. To understand the mechanism through which these protective effects occur, we generated an inducible mutant TDP-43 HEK293 cell line. We find that knockdown of RAD23A reduces insoluble TDP-43 levels in this model and primary rat cortical neurons expressing human TDP-43A315T. Utilizing a discovery-based proteomics approach, we then explored how loss of RAD23A remodels the proteome. Through this proteomic screen, we identified USP13, a deubiquitinase, as a new potent modifier of TDP-43 induced aggregation and cytotoxicity. We find that knockdown of USP13 reduces the abundance of sarkosyl insoluble mTDP-43 in both our HEK293 model and primary rat neurons, reduces cell death in primary rat motor neurons, and improves locomotor deficits in C. elegans ALS models. Significance StatementAmyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease (NDD) with no effective therapies. The mislocalization and aggregation of TAR DNA binding protein 43 (TDP-43) is a key pathological marker of ALS and other NDDs. Due to its vital functions, targeted therapeutic reduction of TDP-43 could be problematic. Here, we have explored the utility of targeting modifier genes. We find that knockdown of two members of the ubiquitin proteasome system, RAD23A and USP13, enhance TDP-43 solubility and decrease TDP-43 induced neurotoxicity.

neuroscience↗

bioRxiv2024

Keratinocyte-derived exosomes in painful diabetic neuropathy

Painful diabetic neuropathy (PDN) is a challenging complication of diabetes with patients experiencing a painful and burning sensation in their extremities. Existing treatments provide limited relief without addressing the underlying mechanisms of the disease. PDN involves the gradual degeneration of nerve fibers in the skin. Keratinocytes, the most abundant epidermal cell type, are closely positioned to cutaneous nerve terminals, suggesting the possibility of bi-directional communication. Exosomes are small extracellular vesicles released from many cell types that mediate cell to cell communication. The role of keratinocyte-derived exosomes (KDEs) in influencing signaling between the skin and cutaneous nerve terminals and their contribution to the genesis of PDN has not been explored. In this study, we characterized KDEs in a well-established high-fat diet (HFD) mouse model of PDN using primary adult mouse keratinocyte cultures. We obtained highly enriched KDEs through size exclusion chromatography and then analyzed their molecular cargo using proteomic analysis and small RNA sequencing. We found significant differences in the protein and microRNA content of HFD KDEs compared to KDEs obtained from control mice on a regular diet (RD), including pathways involved in axon guidance and synaptic transmission. Additionally, using an in vivo conditional extracellular vesicle (EV) reporter mouse model, we demonstrated that epidermal-originating GFP-tagged KDEs are retrogradely trafficked into the DRG neuron cell body. Overall, our study presents a potential novel mode of communication between keratinocytes and DRG neurons in the skin, revealing a possible role for KDEs in contributing to the axonal degeneration that underlies neuropathic pain in PDN. Moreover, this study presents potential therapeutic targets in the skin for developing more effective, disease-modifying, and better-tolerated topical interventions for patients suffering from PDN, one of the most common and untreatable peripheral neuropathies.

neuroscience↗

bioRxiv2023

A pathogenic missense mutation in kainate receptors elevates dendritic excitability and synaptic integration through dysregulation of SK channels

Numerous rare de novo variants that cause neurodevelopmental disorders (NDDs) occur within genes encoding synaptic proteins, including ionotropic glutamate receptors (iGluRs). However, in many cases it remains unclear how damaging missense variants affect brain function. Here we determined the physiological consequences of an NDD causing missense mutation in the GRIK2 kainate receptor (KAR) gene, that results in a single amino acid change p.Ala657Thr in the GluK2 receptor subunit. We engineered the equivalent mutation in the mouse Grik2 gene, yielding a GluK2(A657T) mouse, to better understand the human disorder and determine how hippocampal neuronal function is disrupted. Synaptic KAR currents in hippocampal CA3 pyramidal neurons from heterozygous A657T mice exhibited slow decay kinetics, consistent with incorporation of the mutant subunit into functional receptors. Unexpectedly, CA3 neurons demonstrated elevated action potential spiking due to down-regulation of the small conductance Ca2+ activated K+ channel (SK), which mediates the post-spike afterhyperpolarization (AHP). The reduction in SK activity resulted in increased CA3 dendritic excitability, increased EPSP-spike coupling and lowered the threshold for the induction of LTP of the associational commissural (AC) synapses in the distal dendrites of CA3 neurons. Pharmacological inhibition of SK channels in wild-type (WT) mice increased dendritic excitability and EPSP-spike coupling, mimicking the phenotype in A657T mice and suggesting a causative role for attenuated SK activity in aberrant excitability observed in the mutant mice. These findings demonstrate that a disease-associated missense mutation in GRIK2 leads to altered signaling through neuronal KARs, pleiotropic effects on neuronal and dendritic excitability, and implicate these processes in neuropathology in patients with genetic NDDs.

neuroscience↗

bioRxiv2023

Neuron-specific protein expression at striatal excitatory synapses

Combinatorial expression of postsynaptic proteins underlies synapse diversity within and between neuron types 1-5. Thus, characterization of neuron-type-specific postsynaptic proteomes is key to obtaining a deeper understanding of discrete synaptic properties and how selective dysfunction manifests in synaptopathies 6-9. To overcome the limitations associated with bulk measures of synaptic protein abundance 6,10, we developed a biotin proximity protein tagging probe to characterize neuron-type-specific postsynaptic proteomes in vivo. We found Shank3 protein isoforms are differentially expressed by direct and indirect pathway spiny projection neurons (dSPNs and iSPNs). Studies in mice lacking Shank3 gene exons 13-16 revealed a robust postsynaptic proteome alteration in iSPNs. We report unexpected cell-type specific synaptic protein isoform expression which could play a key causal role in specifying synapse diversity and selective synapse dysfunction in synaptopathies.

neuroscience↗

bioRxiv2018

Altered protein quality control contributes to noise-induced hearing loss

Exposure to damaging levels of noise is the most common cause of hearing loss and impairs high frequency hearing in more than 15 % of adult Americans. Using mice exposed to increasing levels of noise in combination with quantitative proteomics, we tested how noise insults remodel the cochlear proteome both acutely and after a two-week recovery period. We used ABR & DPOAE recordings to define the intensity of noise exposure necessary to produce temporary or permanent threshold shifts (TTS, PTS) in young adult mice and found noise at 94 and 105 dB SPL levels for 30 minutes elicits TTS and PTS, respectively. We quantified thousands of proteins and found that noise insults cause a rapid increase rather than a decrease in the levels of many proteins involved with protein homeostasis, myelin, cytoskeletal structures, and cell junctions such as the synapse. The vast majority of proteins with increased levels immediately after noise exposure showed normal levels after two weeks of recovery. However, several proteins involved in oxidative stress and neuroprotection had significantly increased levels only after the recovery period suggesting they play in important role in regeneration. Interestingly, a small panel of mitochondrial proteins were significantly altered only in PTS conditions suggesting potential discrete protein mechanisms. Our discovery-based proteomic analysis extends the recent description of noise-induced cochlear synaptopathy and shows that noise insults drive a robust proteostasis response. These data provide a new understanding of noise sensitive proteins and may inform the development of effective preventiative strategies or therapies for NIHL.

neuroscience↗

bioRxiv2017

A cloning-free method for CRISPR/Cas9-mediated genome editing in fission yeast

The CRISPR/Cas9 system, which relies on RNA-guided DNA cleavage to induce site-specific DNA double-strand breaks, is a powerful tool for genome editing. This system has been successfully adapted for the fission yeast Schizosaccharomyces pombe by expressing Cas9 and the single-guide RNA (sgRNA) from a plasmid. In the procedures published to date, the cloning step that introduces a specific sgRNA target sequence into the plasmid is the most tedious and time-consuming. To increase the efficiency of applying the CRISPR/Cas9 system in fission yeast, we here developed a cloning-free procedure that uses gap repair in fission yeast cells to assemble two linear DNA fragments, a gapped Cas9-encoding plasmid and a PCR-amplified sgRNA insert, into a circular plasmid. Both fragments contain only a portion of the ura4 or bsdMX marker so that only the correctly assembled plasmid can confer uracil prototrophy or blasticidin resistance. We show that this gap-repair-based and cloning-free CRISPR/Cas9 procedure permits rapid and efficient point mutation knock-in, endogenous N-terminal tagging, and genomic sequence deletion in fission yeast.

genetics↗

bioRxiv2017

Amyloid accumulation drives proteome-wide alterations in mouse models of Alzheimers disease like pathology

Amyloid beta (A{beta}) peptides impair multiple cellular pathways in the brain and play a causative role in Alzheimers disease (AD) pathology, but how the brain proteome is remodeled during this process is unknown. To identify new protein networks associated with AD-like pathology, we performed global quantitative proteomic analysis in three mouse models at pre- and post-symptomatic ages. Our analysis revealed a robust and consistent increase in Apolipoprotein E (ApoE) levels in nearly all transgenic brain regions with increased A{beta} levels. Taken together with prior findings on ApoE driving A{beta} accumulation, this analysis points to a pathological dysregulation of the ApoE-A{beta} axis. We also found dysregulation of protein networks involved in excitatory synaptic transmission consistent with AD pathophysiology. Targeted analysis of the AMPA receptor complex revealed a specific loss of TARP{gamma}-2, a key AMPA receptor trafficking protein. Expression of TARP{gamma}-2 in vivo in hAPP transgenic mice led to a restoration of AMPA currents. This database of proteome alterations represents a unique resource for the identification of protein alterations responsible for AD.\n\nHighlightsO_LIProteomic analysis of mouse brains with AD-like pathology reveals stark remodeling\nC_LIO_LIProteomic evidence points to a dysregulation of ApoE levels associated with A{beta} clearance rather than production\nC_LIO_LICo-expression analysis found distinctly impaired synapse and mitochondria modules\nC_LIO_LIIn-depth analyses of AMPAR complex points to loss of TARP{gamma}-2, which may compromise synapses in AD\nC_LI\n\neTOC BlurbProteome-wide profiling of brain tissue from three mouse models of AD-like pathology reveals A{beta}, brain region, and age dependent alterations of protein levels. This resource provides a new global protein expression atlas for the Alzheimers disease research community.

neuroscience↗