Biology subjects

Zuo, J.

Publications and source records attributed to Zuo, J..

At least 19 recordsLinked to original sources

bioRxiv2026

The GSNOR1-VDAC3 complex acts as a cargo co-receptor for mitophagy in response to mitochondrial stress in plants

Mitochondria are central for cellular energy metabolism, and their quality is warranted by multiple mechanisms, including mitophagy, a process of selectively removing damaged, aged, or excess mitochondria. However, the regulatory mechanism of mitophagy remains elusive in plants. Here, we report that Arabidopsis S-nitrosoglutathione reductase 1 (GSNOR1), an enzyme that has long been known to degrade S-nitrosoglutathione, interacts with the outer mitochondrial membrane protein Voltage-Dependent Anion Channel 3 (VDAC3) to mediate mitophagy. GSNOR1 translocates to depolarized mitochondria, binds to VDAC3, and interacts with Autophagy-related 8 (ATG8) via its ATG8-interacting motifs, thereby engulfing damaged mitochondria in autophagosomes for mitophagic degradation. Mutations in GSNOR1 or VDAC3 cause the accumulation of misshapen mitochondria and hypersensitivity to mitochondrial stress. We propose that GSNOR1 acts as a cargo receptor interacting with VDAC3 and ATG8 to target depolarized mitochondria to mitophagy, thereby regulating cellular homeostasis.

plant biology↗

bioRxiv2026

Genomic splice-donor disruption rescues systemic disease in progeria

RNA splicing determines which protein isoforms a gene produces, and aberrant splice-site activation can cause severe disease. In Hutchinson-Gilford progeria syndrome, a synonymous LMNA mutation strengthens a cryptic 5' splice donor site to produce progerin, a toxic lamin A isoform driving premature cardiovascular death. Within this cryptic donor, the activating mutation lies near the canonical GT dinucleotide required for splice-site recognition. A single guide can therefore preferentially pair with the mutant sequence while positioning Cas9 cleavage at this dinucleotide. Here we show that CRISPR/Cas9-mediated disruption of this splice site suppresses progerin without requiring precise correction of the activating mutation and prolongs lifespan in progeroid mice. In patient-derived fibroblasts and induced pluripotent stem cell-derived mesenchymal stem cells, this intervention reduced progerin by 92.7-96.8% while retaining lamin A and lamin C expression. A single neonatal injection of AAV9 carrying the corresponding mouse guide increased median survival from 115 to 279 days in Cas9-expressing LmnaG609G/G609G mice. Treatment attenuated aortic, skeletal and multiorgan pathology. Treated homozygous pairs produced 52 offspring across seven litters. These findings establish pathogenic splice signals as genomic targets for sustained suppression of toxic isoforms while retaining canonical gene outputs.

cell biology↗

bioRxiv2026

From Representation to Action: A Unified Laplacian Framework for Spatial Representation and Path Planning

Navigation in complex environments relies on internal spatial representations that guide action. While the brain employs a diverse repertoire of spatial tuning cells--including grid, place, and head-direction cells--a normative theory linking these static neural codes to the dynamic process of navigation remains elusive. In this work, we propose a Unified Laplacian Framework derived from first principles of representational smoothness and efficiency. We first demonstrate that diverse spatial codes emerge naturally as spectral decompositions of the Laplace operator. Crucially, bridging the gap from representation to action, we derive a biologically plausible navigation policy based on the Greens function potential. We show that this potential encodes the environments intrinsic geometry to enable simple, trap-free gradient ascent, achieving improved sample efficiency and generalization in goal-reaching tasks. Furthermore, we demonstrate that these spectral representations can be learned directly from high-dimensional visual inputs, confirming their plausibility in realistic environments. Our results suggest that the "cognitive map" can be viewed as a spectral embedding of the Laplacian, providing a rigorous foundation for spatial cognition in both biological and artificial agents.

neuroscience↗

bioRxiv2026

Hemodynamic phenotypes linked to high-altitude subclinical organ damage

BackgroundChronic exposure to high-altitude hypoxia imposes sustained cardiovascular stress, yet hemodynamic adaptation among healthy high-altitude dwellers is heterogeneous and remains poorly characterized. This study aimed to identify distinct hemodynamic phenotypes in a healthy high-altitude population using unsupervised machine learning and to evaluate their association with multi-system subclinical target organ damage. MethodsThis cross-sectional study enrolled 694 healthy adults permanently residing at [≥]3300 m on the Qinghai-Tibet Plateau. Unsupervised K-means clustering was performed on nine hemodynamic variables, including peripheral and central blood pressures, augmentation index (AIx), pulse pressure amplification ratio (pPP/cPP), and systolic pressure amplification (pSBP-cSBP). Differences across phenotypes in carotid intima-media thickness (IMT), estimated glomerular filtration rate (eGFR), left ventricular mass index (LVMI), and pulse wave velocity (PWV) were assessed using one-way ANOVA with Bonferroni-corrected post-hoc tests. ResultsThree distinct hemodynamic phenotypes were successfully identified. The C2 (Balanced Adaptation) phenotype (n = 245) demonstrated the most favorable hemodynamic profile, characterized by the lowest blood pressure and augmentation index (AIx) values, along with the highest peripheral-to-central pulse pressure ratio (pPP/cPP). The C1 (Vascular Stress) phenotype (n = 267) presented with normal peripheral systolic blood pressure (125.9 {+/-} 11.3 mmHg) but exhibited markedly elevated wave reflection indices, including the highest heart rate-adjusted augmentation index (AIx@HR75: 31.9 {+/-} 9.7%) and the lowest pPP/cPP ratio (1.29 {+/-} 0.08). The C3 (High-Load Decompensation) phenotype (n = 182) displayed significantly elevated blood pressures and the greatest overall hemodynamic load. Regarding target organ damage, a clear gradient was observed across the three phenotypes. The C3 phenotype showed the highest carotid intima-media thickness (IMT: 1.162 {+/-} 0.23 mm) and left ventricular mass index (LVMI: 69.18 {+/-} 40.73 g/m{superscript 2}). Conversely, the C2 phenotype exhibited the highest estimated glomerular filtration rate (eGFR: 97.38 {+/-} 16.38 mL/min/1.73m{superscript 2}) and the lowest IMT (0.994 {+/-} 0.26 mm). The C1 phenotype consistently displayed intermediate values for all organ damage indicators. After Bonferroni correction, all pairwise comparisons for LVMI and pulse wave velocity (PWV) reached statistical significance (all P < 0.05). ConclusionsHealthy high-altitude individuals manifest three distinct hemodynamic phenotypes arrayed along a cardiovascular risk continuum. The novel Vascular Stress (C1) phenotype represents a "masked" high-risk state characterized by normal peripheral blood pressure but elevated arterial stiffness and wave reflection, challenging sole reliance on brachial pressure for risk assessment. This phenotype-based stratification provides a framework for precision prevention and early intervention in high-altitude populations.

physiology↗

bioRxiv2025

Towards a mental programming neural circuit: Insights from working memory sequence manipulation

Cognitive reasoning, also known as mental programming, is fundamental to our intelligence. A central function in mental programming is working memory (WM), involving both temporarily maintaining the information and manipulating it based on rules. While the neural mechanisms of WM maintenance have been extensively studied, those governing WM manipulation remain largely unknown. To bridge this gap, the present study focuses on an elementary operation in WM manipulation: re-ordering items in WM sequences. We propose a functional, biologically plausible neural circuit model that consists of two interconnected modules: a memory module composed of continuous attractor-based memory slots that store item features, and a control module sending gain-modulating commands to orchestrate specific operations in the memory module. The model successfully implements two-item swapping in a WM sequence, generating neuronal responses similar to recent primate experiments of WM sequence manipulation. By incorporating principles from the algebraic permutation group, we generalize the circuit model to accommodate more complex sequence manipulations. This math foundation reveals how arbitrary permutations can be decomposed into sequences of elementary swapping operations, which can be generated by a hierarchical tree-structured control circuit module. And the mutual inhibition within the control tree ensures that only one program is being executed at the same time. Our study establishes overarching connections among mental programming neural circuit models, neuro-science experiments, and abstract algebraic structure. These insights enhance our understanding of the neural underpinnings of cognitive reasoning and inspire the design of artificial cognitive systems.

neuroscience↗

bioRxiv2025

Holistic Motor Control of Zebra Finch Song Syllable Sequences

How brain circuits are organized to skillfully produce learned sequences of behaviors is still poorly understood. Here, we functionally examine how the cortical song premotor region HVC, which is necessary for zebra finch song, controls the sequential production of learned song syllables. We find that HVC can generate the complete sequence of learned song syllables independently of its main synaptic input pathways. Thalamic input to HVC is permissive for song initiation but it is not required for transitions between syllables or completing song. We show that excitation of HVC neurons during song reliably causes vocalizations to skip back to the beginning of song, reminiscent of a skipping record. This restarting of syllable sequences can be induced at any moment in song and depends on local circuits within HVC. We identify and computationally model a synaptic network including intratelencephalic premotor and corticostriatal neurons within HVC that are essential for completing song syllable sequences. Together, our results show that the learned zebra finch song is controlled by a cortical sequence-generating network in HVC that, once started, can sustain production of all song syllables independent of major extrinsic input pathways. Thus, sequential neuronal activity can be organized to fuse well-learned vocal-motor sequences, ultimately achieving holistic control of this naturally learned behavior.

neuroscience↗

bioRxiv2025

Kinocilia of Vestibular Hair Cells: Bridging Structural and Functional Traits of Primary and Motile Cilia

Vestibular hair cells (HCs) convert gravitational and head motion cues into neural signals through mechanotransduction, mediated by the hair bundle--a mechanically integrated organelle composed of stereocilia and a kinocilium. The kinocilium, a specialized form of primary cilium, remains incompletely defined in structure, molecular composition, and function. To elucidate its characteristics, we conducted single-cell RNA sequencing of adult vestibular and cochlear HCs, uncovering a selective enrichment of primary and motile cilia-associated genes in vestibular HCs, particularly those related to the axonemal repeat complex. This enrichment of orthologous axonemal-related genes was conserved in zebrafish and human vestibular HCs, indicating a shared molecular architecture. Immunostaining validated the expression of key motile cilia markers in vestibular kinocilia. Moreover, live imaging of bullfrog and mouse HCs from crista ampullaris revealed spontaneous kinociliary motion. Together, these findings define the kinocilium as a unique organelle with molecular features of primary and motile cilia and suggest its previously unknown role as an active, force-generating element within the hair bundle.

neuroscience↗

bioRxiv2025

Multimodal brain cell atlas across the adult macaque lifespan

High-throughput single-cell omics of non-human primate tissues present a remarkable opportunity to study primate brain aging. Here, we introduce a transcriptomic and chromatin accessibility landscape of 1,985,317 cells from eight brain regions of 13 cynomolgus female monkeys spanning adult lifespan including exceptionally old individuals up to 29-years old. This dataset uncovers dynamic molecular changes in critical brain functions such as synaptic communication and axon myelination, exhibiting a high degree of cell type and brain region specificity. We identify the multicellular networks of the pons and medulla as a previously unrecognized hotspot for aging. Furthermore, comparative analyses with human neurodegeneration datasets highlight both shared and distinct mechanisms contributing to aging and disease. In addition, we uncover transcription factors implicated in monkey brain aging and pinpoint aging-regulated loci linked to longevity and neurodegeneration. This spatiotemporal atlas will advance our understanding of primate brain aging and its broader implications for health and disease.

neuroscience↗

bioRxiv2024

Qing-Luo-Yin-induced SIRT1 inhibition contributes to the immune improvement of adjuvant-induced arthritis rats

The herbal formula Qing-Luo-Yin (QLY) was proved containing SIRT1 inhibitors. Whether they contribute to the anti-rheumatic effects is to be confirmed. Adjuvant-induced arthritis (AIA) rats were treated by QLY or/and nicotinamide mononucleotide (NMN) for 38 days. After sacrifice, main tissues were collected for histological and western-blot experiments. Levels of rheumatoid arthritis (RA)-related indictors in blood or tissue homogenates were detected by commercial kits. Normal pre-adipocytes were cultured by the relevant rat serums, and the medium was collected for monocytes culture. In replicate experiments, some pre-adipocytes received additional compounds or SIRT1 silencing/overexpression treatments. Due to spontaneous remission of inflammation, QLY didnt further improve immune milieu in AIA rats, but greatly eased paw edema and joint injuries. Besides, it reversed triglyceride/glucose depletion in liver and adipose tissues, and inhibited the expression and function of SIRT1, causing concomitant changes of related signals and adipkines production. All the effects were weakened by NMN, which activated SIRT1 by increasing NAD production. The serum from QLY-treated rats improved AIA rat serum-induced metabolism and secretion changes of pre-adipocytes, and reduced the secretion of IL-1{beta}, IL-6 and TNF- in the monocytes cultured with the corresponding medium. A mixture of matrine, sinomenine, sophocarpine, dioscin, berberine showed the similar effects on pre-adipocytes to QLY-containing serum. eNAMPT decrease was especially notable, which was obviously weakened by SIRT1 overexpression but overshadowed SIRT1-silencing. SIRT1 inhibitors in QLY reshaped metabolism and secretion profiles of adipose tissues. It consequently mitigated eNAMPT-mediated inflammation and eased AIA in rats.

pharmacology and toxicology↗

bioRxiv2024

Nanoparticle-Supported, Rapid, and Electronic Detection of SARS-CoV-2 Antibodies and Antigens at Attomolar Level

Major challenges remain to precisely detect low-abundance proteins from diverse biofluids in a rapid and cost-effective manner. Here we present a gold nanoparticle (AuNP)-supported, rapid electronic detection (NasRED) platform with sub-femtomolar sensitivity and high specificity. Surface-functionalized AuNPs act as multivalent detectors to recognize target antigens and antibodies through high-affinity binding, subsequently forming aggregates precipitated in a microcentrifuge tube and producing a solution color change. The optical extinction of residual floating AuNPs is digitized using a customized circuitry incorporating inexpensive optoelectronic elements and feedback mechanisms for stabilized readout. Uniquely, NasRED introduces active fluidic forces through engineered centrifugation and vortex agitation, effectively promoting protein detection at low concentrations and accelerating signal generation. Using SARS-CoV-2 as a demonstration, NasRED enables detection of both antibodies and antigens from a small sample volume (6 {micro}L), distinguishes the viral antigens from those of human coronaviruses, and delivers test results in a short time (as fast as <15 min). The limits of detection (LoDs) for antibody detection are approximately 49 aM (7 fg/mL) in phosphate-buffered saline, or >3,000 times more sensitive than Enzyme-Linked Immunosorbent Assay (ELISA), [~]76 aM (11 fg/mL) in human pooled serum and in the femtomolar range in diluted whole blood. For nucleocapsid protein detection, NasRED LoDs are [~]190 aM (10 fg/mL) in human saliva and [~]2 fM (100 fg/mL) in nasal fluid. Unlike laboratory-based ELISA platforms, NasRED is a one-pot, in-solution assay that eliminates the needs for washing, labeling, expensive instrumentation or highly trained operators. With low reagent costs and a compact system footprint, this modular digital platform is well-suited for accurate, near-patient diagnosis and screening of a wide range of infectious and chronic diseases.

microbiology↗

bioRxiv2024

Functional Activity, Functional Connectivity and Complex Network Biomarkers of Progressive Hyposmia Parkinson's Disease with No Cognitive Impairment: Evidences from Resting-state fMRI Study

BackgroundOlfactory dysfunction stands as one of the most prevalent non-motor symptoms in the initial stage of Parkinsons disease (PD). Nevertheless, the intricate mechanisms underlying olfactory deficits in Parkinsons disease still remain elusive. MethodsThis study collected rs-fMRI data from 30 PD patients (15 with severe hyposmia (PD-SH) and 15 with no/mild hyposmia (PD-N/MH)) and 15 healthy controls (HC). To investigate functional segregation, the amplitude of low-frequency fluctuation (ALFF) and regional homogeneity (ReHo) were utilized. Functional connectivity (FC) analysis was performed to explore the functional integration across diverse brain regions. Additionally, the graph theory-based network analysis was employed to assess functional networks in PD patients. Furthermore, Pearson correlation analysis was conducted to delve deeper into the relationship between the severity of olfactory dysfunction and various functional metrics. ResultsFirstly, PD patients showed significantly higher ALFF values in the superior temporal gyrus compared to HC, especially in the PD-SH group versus PD-N/MH. Meanwhile, ALFF values in this region negatively correlated with olfactory testing scores. Secondly, PD patients had higher ReHo in middle temporal gyrus and superior frontal gyrus than HC, especially PD-SH. Meanwhile, olfactory scores negatively correlated with these ReHo values. Thirdly, we observed a negative correlation between superior cerebellar-insula connectivity and olfactory scores, suggesting a neural circuit link to olfactory dysfunction. Lastly, the PD patients brain networks consistently showed small-world attributes, with the PD-N/MH group having significantly higher nodal betweenness in the superior cerebellum than the PD-SH group. Theres also a positive link between superior cerebellums betweenness and olfactory scores. Additionally, there is a notable difference in the node degree of the superior temporal gyrus when comparing the PD-SH group to the PD-N/MH group. ConclusionUsing fMRI, our study analyzed brain function in PD-SH, PD-N/MH, and HC groups, revealing impaired segregation and integration in PD-SH and PD-N/MH. We hypothesize that changes in temporal, frontal, occipital, and cerebellar activities, along with aberrant cerebellum-insula connectivity and node degree and betweenness disparities, may be linked to olfactory dysfunction in PD patients.

neuroscience↗

bioRxiv2024

Oseltamivir (Tamiflu), a Commonly Prescribed Antiviral Drug, Mitigates Hearing Loss in Mice

Hearing loss affects up to 10% of all people worldwide, but currently there is only one FDA-approved drug for its prevention in a subgroup of cisplatin-treated pediatric patients. Here, we performed an unbiased screen of 1,300 FDA-approved drugs for protection against cisplatin-induced cell death in an inner ear cell line, and identified oseltamivir phosphate (brand name Tamiflu), a common influenza antiviral drug, as a top candidate. Oseltamivir phosphate was found to be otoprotective by oral delivery in multiple established cisplatin and noise exposure mouse models. The drug conferred permanent hearing protection of 15-25 dB SPL for both female and male mice. Oseltamivir treatment reduced in mice outer hair cells death after cisplatin treatment and mitigated cochlear synaptopathy after noise exposure. A potential binding protein, ERK1/2, associated with inflammation, was shown to be activated with cisplatin treatment and reduced by oseltamivir cotreatment in cochlear explants. Importantly, the number of infiltrating immune cells to the cochleae in mice post noise exposure, were significantly reduced with oseltamivir treatment, suggesting an anti-inflammatory mechanism of action. Our results support oseltamivir, a widespread drug for influenza with low side effects, as a promising otoprotective therapeutic candidate in both cisplatin chemotherapy and traumatic noise exposure.

neuroscience↗

bioRxiv2024

Monocyte-derived fibrocytes contribute to nucleus pulposus fibrosis and intervertebral disc degeneration

Fibrotic remodeling of nucleus pulposus (NP) leads to structural and mechanical anomalies of intervertebral discs that prone to degeneration, leading to low back pain incidence and disability. Emergence of fibroblastic cells in disc degeneration has been reported, yet their nature and origin remain elusive. In this study, we performed an integrative analysis of multiple single-cell RNA sequencing datasets to interrogate the cellular heterogeneity and fibroblast-like entities in degenerative human NP specimens. We found that disc degeneration severity is associated with an enrichment of fibrocyte-like phenotype, characterized by CD45 and collagen I dual positivity, and expression of myofibroblast marker -smooth muscle actin. Refined clustering and classification distinguished the fibrocyte-like populations as subtypes in the NP cells - and immunocytes-clusters, expressing disc degeneration markers HTRA1 and ANGPTL4 and genes related to response to TGF-{beta}. In injury-induced mouse disc degeneration model, fibrocyte-like cells were found recruited into the NP undergoing fibrosis and adopted a myofibroblast phenotype. Depleting the fibrocyte-like cells in CD11b-DTR mice in which monocytic lineages were ablated by diphtheria toxin could markedly attenuate fibrous modeling and myofibroblast formation in the NP of the degenerative discs, and prevent disc height loss and histomorphological abnormalities. Marker analysis supports that disc degeneration progression is dependent on a function of CD45+COL1A1+ and SMA+ cells. Our findings reveal that fibrocyte-like cells play a pivotal role in NP fibrosis and may therefore be a target for modifying disc degeneration and promoting its repair.

physiology↗

bioRxiv2023

KSR1 Knockout Mouse Model Demonstrates MAPK Pathway's Key Role in Cisplatin- and Noise-induced Hearing Loss

Hearing loss is a major disability in everyday life and therapeutic interventions to protect hearing would benefit a large portion of the world population. Here we found that mice devoid of the protein kinase suppressor of RAS 1 (KSR1) in their tissues (germline KO mice) exhibit resistance to both cisplatin- and noise- induced permanent hearing loss compared to their wild-type KSR1 littermates. KSR1 is expressed in the cochlea and is a scaffold protein that brings in proximity the mitogen-activated protein kinase (MAPK) proteins BRAF, MEK and ERK and assists in their activation through a phosphorylation cascade induced by both cisplatin and noise insults in the cochlear cells. Deleting the KSR1 protein tempered down the MAPK phosphorylation cascade in the cochlear cells following both cisplatin and noise insults and conferred hearing protection of up to 30 dB SPL in three tested frequencies in mice. Treatment with dabrafenib, an FDA- approved oral BRAF inhibitor, downregulated the MAPK kinase cascade and protected the KSR1 wild-type mice from both cisplatin- and noise-induced hearing loss. Dabrafenib treatment did not enhance the protection of KO KSR1 mice, as excepted, providing evidence dabrafenib works primarily through the MAPK pathway. Thus, either elimination of the KSR1 gene expression or drug inhibition of the MAPK cellular pathway in mice resulted in profound protection from both cisplatin- and noise-induce hearing loss. Inhibition of the MAPK pathway, a cellular pathway that responds to damage in the cochlear cells, can prove a valuable strategy to protect and treat hearing loss. Significance StatementTen percent of the world population suffers from hearing loss but this impairment may be preventable. We show that mice devoid of the KSR1 protein (KO) exhibit resistance to cisplatin- and noise-induced permanent hearing loss compared to wild-type littermates that harbor the protein. Removing KSR1 tempers down the MAPK phosphorylation cascade of BRAF-MEK-ERK induced in the cochlea following cisplatin and noise insults. Treatment of KSR1 wild-type mice following cisplatin or noise with an FDA-approved BRAF inhibitor, dabrafenib, protected the hearing and, importantly, did not confer additional protection to the KO KSR1 mice. Hence, the MAPK pathway has a unique role in responding to cochlear damage, and removing KSR1 gene expression or drug inhibition of the pathway results in hearing protection.

neuroscience↗

bioRxiv2023

A Recurrent Neural Circuit Mechanism of Temporal-scaling Equivariant Representation

Time perception is fundamental in our daily life. An important feature of time perception is temporal scaling (TS): the ability to generate temporal sequences (e.g., movements) with different speeds. However, it is largely unknown about the mathematical principle underlying TS in the brain. The present theoretical study investigates temporal scaling from the Lie group point of view. We propose a canonical nonlinear recurrent circuit dynamics, modeled as a continuous attractor network, whose neuronal population responses embed a temporal sequence that is TS equivariant. We find the TS group operators can be explicitly represented by a time-invariant control input to the network, whereby the input gain determines the TS factor (group parameter), and the spatial offset between the control input and the network state on the continuous attractor manifold gives rise to the generator of the Lie group. The recurrent circuits neuronal responses are consistent with experimental data. The recurrent circuit can drive a feedforward circuit to generate complex sequences with different temporal scales, even in the case of negative temporal scaling ("time reversal"). Our work for the first time analytically links the abstract temporal scaling group and concrete neural circuit dynamics.

neuroscience↗

bioRxiv2023

Optogenetics reveals roles for supporting cells in force transmission to and from outer hair cells in the mouse cochlea

Cochlear outer hair cells (OHCs), acting as bidirectional cellular mechanoelectrical-transducers, generate, receive, and exchange forces with other major elements of the cochlear partition, including inner hair cells (IHCs). Force exchange is mediated via a supporting cell scaffold, including Deiters (DC) and outer pillar cells (OPC), to enable the sensitivity and exquisite frequency selectivity of the mammalian cochlea. We conditionally expressed a hyperpolarizing halorhodopsin (HOP), a light-gated inward chloride ion pump in DCs and OPCs. We measured extracellular receptor potentials (ERPs) and their DC component (ERPDC) from the Cortilymph (CL) of HOP expressing mice and compared the responses with similar potentials from littermates without HOP expression. Compound action potentials (CAP) were measured as an indication of IHC activity. HOP laser activation suppressed cochlear amplification through changing timing of its feedback, altered basilar membrane (BM) responses to tones at all measured levels and frequencies, and reduced IHC excitation. Our HOP activation results here complement previous channelrhodopsin activation studies in exploiting optogenetics to measure and understand the roles of DCs and OPCs in vivo in controlling the mechanical and electrical responses of OHCs to sound and their contribution to timed and directed electromechanical feedback to the mammalian cochlea. SIGNIFICANCE STATEMENTOuter hair cells provide electromechanical feedback to the organ of Corti, mediated via a cellular scaffold of Deiters and outer pillar cells, that enables the sensitivity and fine frequency tuning of the cochlea. The role of this scaffold was explored by expressing the halorhodopsin HOP in Deiters and pillar cells which, when illuminated, hyperpolarized them. HOP activation suppressed cochlear amplification through altering the timing of outer hair cell forces to the Organ of Corti, altered basilar membrane responses to tones, including those at levels and frequencies not subject to amplification, and reduced neural excitation. The findings implicated roles for supporting cells in mediating force transmission to and from outer hair cells along all axes of the organ of Corti.

neuroscience↗

bioRxiv2023

In Silico Transcriptome-based Screens Identify Epidermal Growth Factor Receptor Inhibitors as Therapeutics for Noise-induced Hearing Loss

Noise-Induced Hearing Loss (NIHL) represents a widespread disease for which no therapeutics have been approved by the Food and Drug Administration (FDA). Addressing the conspicuous void of efficacious in vitro or animal models for high throughput pharmacological screening, we utilized an in silico transcriptome-oriented drug screening strategy, unveiling 22 biological pathways and 64 promising small molecule candidates for NIHL protection. Afatinib and zorifertinib, both inhibitors of the Epidermal Growth Factor Receptor (EGFR), were validated for their protective efficacy against NIHL in experimental zebrafish and murine models. This protective effect was further confirmed with EGFR conditional knockout mice and EGF knockdown zebrafish, both demonstrating protection against NIHL. Molecular analysis using Western blot and kinome signaling arrays on adult mouse cochlear lysates unveiled the intricate involvement of several signaling pathways, with particular emphasis on EGFR and its downstream pathways being modulated by noise exposure and Zorifertinib treatment. Administered orally, Zorifertinib was successfully detected in the perilymph fluid of the inner ear in mice with favorable pharmacokinetic attributes. Zorifertinib, in conjunction with AZD5438 - a potent inhibitor of cyclin dependent kinase 2 - produced synergistic protection against NIHL in the zebrafish model. Collectively, our findings underscore the potential application of in silico transcriptome-based drug screening for diseases bereft of efficient screening models and posit EGFR inhibitors as promising therapeutic agents warranting clinical exploration for combatting NIHL. HighlightsO_LIIn silico transcriptome-based drug screens identify pathways and drugs against NIHL. C_LIO_LIEGFR signaling is activated by noise but reduced by zorifertinib in mouse cochleae. C_LIO_LIAfatinib, zorifertinib and EGFR knockout protect against NIHL in mice and zebrafish. C_LIO_LIOrally delivered zorifertinib has inner ear PK and synergizes with a CDK2 inhibitor. C_LI

neuroscience↗

bioRxiv2023

Spatial determination and prognostic impact of the fibroblast transcriptome in pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma has a poor clinical outcome and responses to immunotherapy are suboptimal. Stromal fibroblasts are a dominant but heterogenous population within the tumor microenvironment and therapeutic targeting of stromal subsets may have therapeutic utility. Here we combined spatial transcriptomics and scRNA-Seq to define the transcriptome of tumor-proximal and tumor-distal cancer-associated fibroblasts (CAFs) and linked this to clinical outcome. Tumor-proximal fibroblasts comprised large populations of myofibroblasts, strongly expressed podoplanin, and were enriched for Wnt ligand signaling. In contrast, inflammatory CAFs were dominant within tumor-distal subsets and expressed complement components and the Wnt-inhibitor SFRP2. Poor clinical outcome was correlated with elevated HIF-1 and podoplanin whilst high level expression of inflammatory and complement genes was predictive of extended survival. These findings demonstrate the extreme transcriptional heterogeneity of CAFs and its determination by apposition to tumor. Selective targeting of tumor-proximal subsets, potentially combined with HIF-1 inhibition and immune stimulation, may offer a multimodal therapeutic approach for this disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=170 SRC="FIGDIR/small/524883v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@b34606org.highwire.dtl.DTLVardef@1ba47c3org.highwire.dtl.DTLVardef@bd75f1org.highwire.dtl.DTLVardef@8a602b_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗