Biology subjects

Lee, J.

Publications and source records attributed to Lee, J..

At least 289 records · Page 16Linked to original sources

bioRxiv2025

In Situ Graphene-Seq: Spatial Transcriptomics and Chronic Electrophysiological Characterization of Tissue Microenvironments

Biological systems are composed of diverse, interconnected cell types, yet capturing both their functional dynamics and molecular identities at high spatiotemporal resolution remains challenging. While electrophysiological measurements provide real-time insights into cellular activities, they cannot fully describe the molecular architecture and states of the measured cells. Conversely, transcriptomics reveals cell gene expression patterns but does not capture functional states. Bridging these modalities is essential for a holistic understanding of the molecular mechanisms driving functional changes. In this study, we introduce in situ graphene-sequencing (graphene-seq), a unique platform that seamlessly integrates chronic electrophysiology with imaging-based, spatially resolved 3D transcriptomics, overcoming longstanding limitations of current multimodal approaches. This system leverages stretchable mesh nanoelectronics for long-term, single-cell-level interfacing and incorporates transparent graphene/PEDOT:PSS electrodes, enabling seamless integration of electrical recordings and optical imaging. By combining electrophysiology with high-throughput, imaging-based in situ sequencing, this platform allows comprehensive multimodal, spatially resolved analysis of cell microenvironment within spatially heterogeneous tissues. We validate in situ graphene-seq by charting multimodal profiles of human-induced pluripotent stem cell-derived cardiomyocyte and endothelial cell co-cultures, examining how spatial heterogeneity in cell composition influences both electrophysiological activity and gene expression. This scalable, integrated approach offers a powerful tool for studying the complex interplay between cellular function and molecular identity. It also provides insights into how tissue microenvironments shape cell behavior and molecular states, advancing applications in regenerative medicine, stem cell therapy, and disease modeling.

bioengineering↗

bioRxiv2025

Carbohydrate consumption drives adaptive mutations in Escherichia coli associated with increased risk for systemic infection

Dissemination of organisms from the gut microbiota is a major contributor to sepsis and critical illness. Patients with cirrhosis are prone to systemic infections and are commonly prescribed the carbohydrate lactulose to manage hepatic encephalopathy (HE) 1. Commensal metabolism of lactulose is believed to reduce pathobiont colonization through short-chain fatty acid production, but its direct effects on gut pathobionts remain unexplored 2. Here, we show that lactulose consumption unexpectedly selects for mutations in Escherichia coli lactose (lac) operon regulation, enhancing its metabolic fitness and colonization capacity. This is mediated by selection for constitutive expression of the lac operon through mutations in its regulatory components. Using in vitro systems, murine models, and clinical samples, we demonstrate that these mutations enable E. coli to exploit lactulose as a carbon source, bypassing host carbohydrate metabolism and increasing its intestinal colonization. Despite its long-standing use in HE treatment, we find that lactulose has a paradoxical association with risk of infection hospitalization in patients with cirrhosis in a large epidemiologic study. The emergence of lactulose-adapted E. coli strains could be suppressed by a dietary oligosaccharide that competitively inhibits lactulose uptake. These findings reveal a mechanism by which dietary substrates exert selective pressure on the microbiome, with implications for diet-based strategies to modulate microbial evolution and infection risk.

microbiology↗

bioRxiv2025

American ginseng (Panax quinquefolius L.) extracts (G1899) reverse stress-induced behavioral abnormalities in mice

Stress affects brain functions, which leads to the development of mental disorders like anxiety, depression, cognitive decline, and social dysfunction. There is increasing focus on the role of nutritional, herbal and nutraceutical compounds on mental and cognitive functioning. Interestingly, studies suggest that American ginseng (Panax quinquefolius L.) extracts (G1899) improve cognition. We thus examined whether G1899 showed protective effects on stress-induced behavioral changes in animals. 200 mg/kg G1899 was orally administered daily for 4 weeks to 2-3-month-old female and male mice before inducing stress. To induce acute stress in animals, we intraperitoneally injected a low dose of lipopolysaccharides (LPS) (10 g/kg), and saline was used as a control. We also used chronic restraint stress (CRS) as a chronic stress model in mice. After LPS injection or CRS, multiple behavioral assays were carried out - a sucrose preference test, an open filed test, reciprocal social interaction, contextual fear conditioning, and a tail suspension test - to determine whether acute or chronic stress affected animals behaviors and whether G1899 had protective effects against stress-induced behavioral dysfunction. We found that both LPS injection and CRS induced stress-related behavioral dysfunction, including depression-like behavior, anhedonia, social dysfunction, and fear memory impairments in both females and males. However, G1899 treatment was sufficient to reverse stress-induced behavioral abnormalities in animals. Our data further suggested that G1899 reduced the activity of hippocampal neurons by suppressing glutamatergic activity. Our study suggests that G1899 supplements can be protective against both acute and chronic stress in mice by suppressing neuronal and synaptic activity. HighlightsO_LIAmerican ginseng (Panax quinquefolius L.) extract (G1899) treatment reverses acute stress-induced behavioral dysfunction in mice. C_LIO_LIG1899 treatment reverses chronic stress-induced behavioral dysfunction in mice. C_LIO_LIG1899 treatment reduces serum corticosterone levels in chronically stressed mice. C_LIO_LIG1899 treatment suppresses glutamatergic activity in hippocampal neurons. C_LI

neuroscience↗

bioRxiv2025

Discovering Polyphosphate and Polyhydroxyalkanoate-Accumulating Organisms Across Ecosystems: Phenotype-targeted Genotyping via FACS-sequencing

Intracellular biopolymers serve versatile functions that allow microbes to adapt to fluctuating environmental conditions. The metabolic interdependence of dual intracellular polymers, namely polyphosphate (polyP) and polyhydroxyalkanoates (PHA), is a defining feature of functionally polyphosphate-accumulating organisms (PAOs), the key agents enabling enhanced biological phosphorus removal (EBPR) for wastewater treatment. However, beyond EBPR systems, the presence and identities of PAOs that possess both polyP and PHA in natural environments such as soil have never been examined due to a lack of available detection tools, despite their potential roles in carbon and phosphorus cycling. This study presents a novel phenotype-targeted approach integrating triple-stained fluorescence-activated cell sorting (FACS) with 16S rRNA gene amplicon sequencing (termed TriFlow-Seq) to simultaneously detect, quantify, and phylogenetically characterize PAOs accumulating both polyP and PHA (referred to as PHA- PAOs). TriFlow-Seq was validated using polymer staining image analysis and Single-Cell Raman micro-spectroscopy. Application to EBPR systems successfully enriched known PHA- PAOs, including Candidatus Accumulibacter, Tetrasphaera, Dechloromonas, Pseudomonas. It also revealed novel candidate PHA-PAOs, particularly within the Rhodobacteraceae family. When applied to soil samples, TriFlow-Seq led to the first discovery of diverse PHA-PAOs dominated by Pseudomonas, Halomonas, and Nannocystis in maize rhizosphere soils. These predominant genera are known rhizosphere inhabitants of essential crops with key plant growth- promoting functions including phosphate solubilization, biofilm formation, and phytohormone production, yet simultaneous polyP and PHA accumulation has not been directly reported in the maize rhizosphere. Our findings revealed unexpectedly high PHA-PAO prevalence and distinct phylogenetic patterns associated with different maize genotypes, suggesting a potentially overlooked role for dual polymer storage in microbial rhizosphere dynamics and function. This study establishes a pioneering approach to investigate dual polyP and PHA-containing PAO identities and their important roles in rhizosphere structure and plant health. SynopsisNovel method reveals dual-polymer bacteria in activated sludge and crop rhizospheres, suggesting new candidates supporting wastewater treatment and agricultural sustainability.

microbiology↗

bioRxiv2025

Quantification of collagen and associated features from H&E-stained whole slide pathology images across cancer types using a physics-based deep learning model

BackgroundCollagen is the major component of the extracellular matrix (ECM). Collagen structural organization undergoes significant transformation during tumorigenesis. The visualization of collagen in histological tissue sections would aid in the study of tumor growth, encapsulation, and invasion. However, such visualization requires the use of special stains such as Picrosirius Red (PSR) or Massons Trichrome (MT), or more recently, second-harmonic generation imaging (SHG) in unstained tissue sections. However, PSR and MT both suffer from significant inter- (and intra-) lab stain variabilities, and SHG, while considered a ground truth by many, suffers from issues of system complexity/reliability, cost, and speed/throughput. These technical hurdles limit more widespread assessment of collagen in tissue samples. MethodsUsing high-contrast, high-throughput polarization imaging on PSR-stained slides to generate ground truth training polarization images, we developed a deep learning model (iQMAI) to infer the presence of collagen directly from hematoxylin and eosin (H&E)-stained whole-slide images (WSIs) with high specificity. After iQMAI inference across WSIs, individual collagen fibers were extracted, and features describing overall collagen intensity and fiber morphology were computed. iQMAI pixel-and feature-wise outputs were compared to ground truth polarization imaging to assess model performance. The trained iQMAI model was deployed on H&E-stained WSI from the TCGA LUAD, LUSC, LIHC, and PAAD datasets for evaluation. iQMAI-derived collagen features were compared to tissue composition, gene expression, and overall survival. ResultsThe iQMAI model shows significant generalization across multiple indications. iQMAI collagen predictions were similar to polarization imaging measurements of the same sample, with a mean structural similarity index (SSIM) of 0.84 (95% CI 0.69-0.93), a mean patch-wise RMSE of 0.04 (95% CI 0.02-0.08), and a linear correlation (R2=0.93). Comparing features of the collagen fibers extracted from iQMAI vs. polarization images yielded similar linear correlations between computed fiber tortuosity, length, width, and relative angle. The relationship between collagen fiber density and fibroblast density was distinct in non-small cell lung cancer (LUAD and LUSC), hepatocellular carcinoma (LIHC), and pancreatic ductal adenocarcinoma (PAAD). In PAAD, fiber density and fiber width were both negatively associated with the LRRC-15 gene expression signature, and increased fiber width was associated with longer overall survival. ConclusionsiQMAI is a deep learning model that accurately predicts collagen from an H&E-stained WSI, allowing for spatially resolved quantification of collagen morphology and enabling investigation of the interplay between collagen and other TME components. We demonstrate an example of the utility of iQMAI-based collagen assessment in PAAD, where collagen features are associated with immunosuppressive cancer-associated fibroblasts and overall survival. Understanding the relationship between collagen, the tumor microenvironment composition, and disease progression may aid the development of effective immunotherapies in PAAD and other cancer types.

pathology↗

bioRxiv2025

A Mathematical Methodology to Predict Phenotype from Genotype

From a mathematical perspective, a genome can be viewed as categorical data whose elements include genetic variants in SNPs. Then, the problem of predicting phenotype from genotype can be reduced to the problem of classifying categorical data. We will define a metric function at each SNPs position of an individual such that the arithmetic mean of a specific phenotype group is always less than or equal to that of the comparison group. Then, in light of a mathematical principle, calculating the sum of the distances(metrics) of some SNPs positions could clearly classify the two groups, when difficult to classify them with one specific position. Using this methodology, we found that even small differences in each SNPs combined could classify phenotypes ; combining 51 SNPs positions in autosomes made possible to distinguish males from females with great accuracy. We also found that East Asian people could be distinguished from other people with 100% accuracy, so we obtained a mathematical definition of East Asian people. The mathematical methodology classifies phenotypes with collecting small differences of genotypes throughout the entire genome, which could be useful for predicting diseases affected by the genome and be useful in pharmacogenomics.

bioinformatics↗

bioRxiv2025

Targeting Galectin-3 to modulate inflammation in LAMA2-deficient congenital muscular dystrophy

LAMA2-deficient congenital muscular dystrophy (LAMA2-CMD) is a severe neuromuscular disorder characterized by muscle degeneration, chronic inflammation, and fibrosis. While inflammation is one the hallmarks of LAMA2-CMD, the immune cell composition in laminin-deficient muscles remains understudied. Consequently, targeted pharmacological intervention to reduce inflammation remains underexplored. Here, we characterized the immune landscape in the dyW mouse model of LAMA2-CMD using RNA sequencing and flow cytometry. Transcriptomic analysis of dyW quadriceps femoris muscle identified 2,143 differentially expressed genes, with most upregulated genes linked to immune-related pathways. Lgals3 (Galectin-3) was significantly upregulated and identified as a key upstream regulator of the immune-related pathways. Flow cytometry revealed elevated leukocyte (CD45) infiltration, with macrophages as the predominant population. Pro-inflammatory (M1) macrophages were increased, whereas anti-inflammatory (M2) macrophages remained low, indicating persistent and unresolved inflammation. Notably, Galectin-3+ macrophages were significantly enriched, suggesting that Galectin-3 drives inflammation in LAMA2-CMD. Treatment of dyW mice with TD-139, a Galectin-3 inhibitor, reduced leukocyte infiltration, decreased Galectin-3+ macrophages, and shifted macrophage polarization toward an M2 anti-inflammatory profile. RNA sequencing of TD-139-treated dyW muscles showed upregulation of muscle contraction pathways and downregulation of fibrosis-related genes. These findings highlight Galectin-3+ macrophages as key contributors to LAMA2-CMD pathophysiology and support further exploration of TD-139 as a potential therapeutic strategy for LAMA2-CMD and other dystrophic conditions driven by chronic inflammation.

immunology↗

bioRxiv2025

ACIDIC BICELLES ARE A SUITABLE MEMBRANE MIMIC FOR STRUCTURAL STUDIES OF THE LASSA VIRUS FUSION DOMAIN.

AO_SCPLOWBSTRACTC_SCPLOWLassa virus (LASV) is the most prevalent arenavirus afflicting humans and has high pandemic potential. The genetic material of LASV is delivered into the host cell via membrane fusion - a process initiated by the LASV fusion domain (FD). However, the molecular details of the LASV FD, particularly its structure after association with the host cell, remain poorly understood. This can be attributed to a lack of a viable membrane mimic to effectively stabilize the LASV FD for structural studies. Here, we demonstrate that the structure of the LASV FD widely varies based on the class of membrane mimic. In particular, through CD spectroscopy, we found that the LASV FD required a charged membrane mimic, such as zwitterionic or anionic detergent micelles, to adopt a helical conformation at low pH, but has the highest helical content in the presence of anionic lipids, particularly the detergent micelle LMPG and acidic bicelles. Moreover, we reveal that the LASV FD was well resolved on NMR spectra in CHAPS, DPC, LDAO, LMPG, and acidic bicelles, where LMPG and acidic bicelles had the sharpest peak resolution, but more defined peaks were noted in acidic bicelles over LMPG. In conclusion, our findings indicate that acidic bicelles are the optimal membrane mimic for the stabilization of the LASV FD such that structural studies can be conducted. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/642635v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@7e8dfcorg.highwire.dtl.DTLVardef@9bb650org.highwire.dtl.DTLVardef@de6fbdorg.highwire.dtl.DTLVardef@179e8eb_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Physical mechanisms that enable bacteria to traverse channels half their width

Bacteria colonize surfaces in the environment and can also penetrate tissues and materials by entering micro- and nanoscale cracks and pores. Staphylococcus aureus has been observed within nanoscale channels in bone that are 2-3 times smaller than cell diameter. Once inside bone, bacteria are protected from host immunity and systemic antibiotics, potentially contributing to chronic and recurrent infections. The physical mechanisms that enable bacteria to enter channels smaller than cell width are unclear. It has been proposed that bacteria traverse narrow passages through division - such that daughter cells form within small channels and eventually create a chain of cells extending down the channel length. Here we use microfluidics to test the idea that S. aureus can traverse bone-like nanochannels through growth. We examined 322 individual cells trapped within tapered nanochannels ([~]1.5 to 0.4 mm in width). When cells were deformed below 606 nm (65% original width), growth and division were slowed or completely inhibited. When cell division did occur in nanochannels, daughter cells were more likely to travel towards the wider side of the channel. Hence, it is unlikely that cell division would preferentially enable transit of S. aureus into nanoscale channels. However, the magnitudes of fluid pressure needed to deform S. aureus to widths similar to that seen in bone (1 to 6.5 kPa), were small relative to fluid pressure in bone generated by physical forces in vivo (8-20 kPa). Thus, our findings suggest that colonization of nanoscale channels in bone or other tissues is more likely due to moderate fluid pressure rather than growth. ImportanceBacteria that colonize materials and tissues within the body can be difficult to remove, even with thorough cleaning and application of antibiotics. Recent studies show that bacteria not only colonize the surfaces of tissues in the body but can also squeeze into naturally occurring pores and channels and thereby gain protection from immune cells and antibiotics. Here we ask how physical forces and cell growth might enable bacteria to enter small pores within materials. We use microfluidic devices to study the growth and migration of the human pathogenic bacteria, S. aureus, which is the leading cause of chronic bone infections.

microbiology↗

bioRxiv2025

NADPH oxidase inhibitor enhances brain resilience in Alzheimer's disease by reducing tauopathy and neuroinflammation

Alzheimers disease associates closely with activation of NADPH oxidase (Nox) isozymes. We identified that CRB-2131, a novel oxadiazole derivative, potently suppresses Nox isozymes. It inhibits reactive oxygen species production (ROS) by hippocampal neuronal and microglial cells and reduces microglial activation. Prophylactic (starting at 3.5 months of age) and therapeutic (starting at 6 months of age) oral administration with CRB-2131 for 10 weeks in 5XFAD mice reduced hippocampal superoxide levels, lipid peroxidation, Tau phosphorylation, and neuroinflammation. Prophylactic and therapeutic CRB-2131 treatment of 5XFAD mice restored their impaired cognition as shown by the novel-object recognition, Y-maze, and Morris water-maze tests. CRB-2131 treatment increased mature neurons, reduced apoptotic mature neurons, and elevated immature neurons in the hippocampus. Positron-emission tomography/computed-tomography imaging confirmed that CRB-2131 stimulated neuronal regeneration. CRB-2131 suppresses brain oxidation, tauopathy, and neuroinflammation, thereby preventing mature neuron death and promoting neuron regeneration. Ultimately, this fosters a resilient brain and protects cognition.

neuroscience↗

bioRxiv2025

Tumor B cell infiltration in platinum-treated advanced urothelial carcinoma

Platinum-based chemotherapy combined with immunotherapy provides durable disease control in advanced urothelial cancer. However, cisplatin and carboplatin differently impact the tumor immune microenvironment, affecting chemo-immunotherapy response. Here, we evaluate immune cell populations and ecosystems associated with overall survival in patients treated with platinum-based chemotherapy. Our transcriptomic analysis of pretreatment tumor samples from three cohorts (189 patients) of advanced urothelial cancer showed that lymphoid cell infiltration was significantly associated with prolonged overall survival. In cisplatin-treated patients, high memory B cell infiltration provided a significant overall survival improvement, but no such association was found in carboplatin-treated patients. Additionally, gene expression signatures implicated in B cell memory lineage and associated cytokines were associated with better overall survival in independent cancer patient cohorts. Our findings highlight memory B cell infiltration as a potential prognostic biomarker in urothelial cancer and emphasize the role of the tumor immune microenvironment in chemotherapy response.

cancer biology↗

bioRxiv2025

Granular hydrogels as brittle yield stress fluids

While granular hydrogels are increasingly used in biomedical applications, methods to capture their rheological behavior generally consider shear-thinning and self-healing properties or produce ensemble metrics such as the dynamic moduli. Analytical approaches paired with common oscillatory shear tests can describe not only solid-like and fluid-like behavior of granular hydrogels but also transient characteristics inherent in yielding and unyielding processes. Combining oscillatory shear testing with consideration of Brittility (Bt) via the Kamani-Donley-Rogers (KDR) model, we show granular hydrogels behave as brittle yield stress fluids with complex transient rheology. We quantify steady and transient rheology as a function of microgel (composition; diameter) and granular (packing; droplet heterogeneity) assembly properties for mixtures of polyethylene glycol and gelatin microgels. The KDR model with Bt captures granular hydrogel behavior for a wide range of design parameters, reducing the complex transient rheology to a determination of model parameters. We describe the impact of composition on rheological behavior and model parameters in monolithic and mixed granular hydrogels. The model robustly captures self-healing behavior and reveals granular relaxation time depends on strain amplitude. This quantitative framework is an important step toward rational design of granular hydrogels for applications ranging from injection and in situ stabilization to 3D bioprinting.

bioengineering↗

bioRxiv2025

Photoaffinity ligand of Cystic Fibrosis corrector VX-445 identifies SCCPDH as an off-target

Cystic fibrosis (CF) pharmacological correctors improve Cystic Fibrosis transmembrane conductance regulator (CFTR) protein trafficking and function. Several side-effects from these correctors and adverse drug interactions have been reported, emphasizing the need to understand off-targets. We synthesized VU439, a functionalized photoaffinity ligand (PAL) of VX-445. Chemoproteomics analysis by mass spectrometry (MS) was used to identify crosslinked proteins in CF bronchial epithelial cells expressing F508del CFTR. We identified saccharopine dehydrogenase-like oxidoreductase (SCCPDH), an uncharacterized putative oxidoreductase, as a VX-445 specific off-target. We then characterized changes in the metabolomic profiles of cells overexpressing SCCPDH to determine the consequence of VX-445 binding to SCCPDH. These data show dysregulation of amino acid metabolism and a potential inhibitory activity of VX-445 on SCCPDH. The identified off-target may explain exacerbation of psychological symptoms observed in the clinic, thus emphasizing the need for further optimization of correctors.

biochemistry↗

bioRxiv2025

Mutant IDH impairs chromatin binding by PDGFB to promote chromosome instability

Non-canonical roles for growth factors in the nucleus have been previously described, but their mechanism of action and biological roles remain enigmatic. Platelet-derived growth factor B (PDGFB) can drive formation of low-grade glioma and here we show that it localizes to the nucleus of human glioma cells where it binds chromatin to preserve genome stability and cell lineage. Failure of PDGFB to localize to the nucleus leads to chromosomal abnormalities, aberrant heterochromatin architecture and accelerated tumorigenesis. Furthermore, nuclear localization of PDGFB is reliant upon the expression levels and mutation status of isocitrate dehydrogenase (IDH). Unexpectedly, we identified macrophages as the predominant source of PDGFB in human, finding that immune-derived PDGFB can localize to the nucleus of glioma cells. Collectively, these studies show that immune derived PDGFB enters the nucleus of glioma cells to maintain genomic stability, while identifying a new mechanism by which IDH mutations promote gliomagenesis.

cancer biology↗

bioRxiv2025

Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessment

Thousands of short open reading frames (sORFs) are translated outside of annotated coding sequences. Recent studies have pioneered searching for sORF-encoded microproteins in mass spectrometry (MS)- based proteomics and peptidomics datasets. Here, we assessed literature-reported MS-based identifications of unannotated human proteins. We find that studies vary by three orders of magnitude in the number of unannotated proteins they report. Of nearly 10,000 reported sORF-encoded peptides, 96% were unique to a single study, and 12% mapped to annotated proteins or proteoforms. Manual curation of a benchmark dataset of 406 manually evaluated spectra from 204 sORF-encoded proteins revealed large variation in peptide-spectrum match (PSM) quality between studies, with immunopeptidomics studies generally reporting higher quality PSMs than conventional enzymatic digests of whole cell lysates. We estimate that 65% of predicted sORF-encoded protein detections in immunopeptidomics studies were supported by high-quality PSMs versus 7.8% in non-immunopeptidomics datasets. Our work stresses the need for standardized protocols and analysis workflows to guide future advancements in microprotein detection by MS towards uncovering how many human microproteins exist.

genomics↗

bioRxiv2025

CHIP protects lysosomes from CLN4 mutant-induced membrane damages

Understanding how cells mitigate lysosomal damage is critical for unraveling pathogenic mechanisms of lysosome-related diseases. Here we use organelle-specific proteomics in iPSC-derived neurons (i3Neuron) and an in vitro lysosome-damaging assay to demonstrate that lysosome damage, caused by the aggregation of Ceroid Lipofuscinosis Neuronal 4 (CLN4)-linked DNAJC5 mutants on lysosomal membranes, serves as a critical pathogenic linchpin in CLN4-associated neurodegeneration. Intriguingly, in non-neuronal cells, a ubiquitin-dependent microautophagy mechanism downregulates CLN4 aggregates to counteract CLN4-associated lysotoxicity. Genome-wide CRISPR screens identify the ubiquitin ligase CHIP as a central microautophagy regulator that confers ubiquitin-dependent lysosome protection. Importantly, CHIPs lysosome protection function is transferrable, as ectopic CHIP improves lysosomal function in CLN4 i3Neurons, and effectively alleviates lipofuscin accumulation and neurodegeneration in a Drosophila CLN4 disease model. Our study establishes CHIP-mediated microautophagy as a key organelle damage guardian that preserves lysosome integrity, offering new insights into therapeutic development for CLN4 and other lysosome-related neurodegenerative diseases.

cell biology↗

bioRxiv2025

Evidence for abstract codes in parietal cortex guiding prospective working memory

The recent past helps us predict and prepare for the near future. Such preparation relies on working memory (WM) which actively maintains and manipulates information providing a temporal bridge. Numerous studies have shown that recently presented visual stimuli can be decoded from fMRI signals in visual cortex (VC) and the intra-parietal sulcus (IPS) suggesting that these areas sustain the recent past. Yet, in many cases, concrete, sensory signals of past information must be transformed into the abstract codes to guide future cognition. However, this process remains poorly understood. Here, human participants used WM to maintain a separate spatial location in each hemifield wherein locations were embedded in a learned spatial sequence. On each trial, participants made a sequence-match decision to a probe and then updated their WM with the probe. The same abstract sequence guided judgments in each hemifield, allowing the separate detection of concrete spatial locations (hemifield-specific) and abstract sequence positions (hemifield-general), and also tracking of representations of the past (last location/position) and future (next location/position). Consistent with previous reports, concrete past locations held in WM could be decoded from VC and IPS. Moreover, in anticipation of the probe, representations shifted from past to future locations in both areas. Critically, we observed abstract coding of future sequence positions in the IPS whose magnitude related to speeded performance. These data suggest that the IPS sustains abstract codes to facilitate future preparation and reveal a transformation of the sensory past into abstract codes guiding future behavior. Significant StatementTo act efficiently, we must use the recent past to prepare for what comes next. For this purpose, working memory (WM) is critical. Although substantial research has shown that WM retains recently presented sensory information, preparation for the future involves abstraction wherein shared meaning is aggregated while superfluous sensory details are discarded. The mechanisms underlying this process remain unclear. Analyzing functional MRI signals in the intraparietal sulcus (IPS), we found that distinct sensory states with shared predictive meaning were initially maintained in a sensory-like fashion, but over time, became aggregated indicative of abstraction. Abstraction was associated with behavioral efficiency highlighting its role in preparation. These findings reveal neural mechanisms supporting the transformation from past to future in WM.

neuroscience↗

bioRxiv2025

TMEM145 is a key component in stereociliary link structures of outer hair cells

Outer hair cells (OHCs) in the cochlea contain specialized stereociliary structures essential for auditory function. These include horizontal top connectors (HTCs), linking adjacent stereocilia and tectorial membrane-attachment crowns (TM-ACs), anchoring the tallest stereocilia to the tectorial membrane. The known molecular components of these structures, such as stereocilin, otogelin, otogelin-like, and tubby, lack transmembrane domains, suggesting the existence of anchoring proteins. This study identified TMEM145, a transmembrane protein with a Golgi dynamics (GOLD) domain, as a crucial OHC stereocilia component. TMEM145 was expressed in both OHCs and spiral ganglion neurons, with specific localization to TM-ACs and HTCs in OHCs. Tmem145 knockout (KO) mice exhibited profound hearing impairment at three weeks of age, with complete loss of distortion product otoacoustic emissions, indicating OHC dysfunction. Immunostaining and scanning electron microscopy revealed the absence of TM-ACs and HTCs in Tmem145 KO mice. In heterologous cell systems, TMEM145 interacted with stereocilin and tubby, facilitating their extracellular secretion. TMEM145 was undetectable in stereocilin KO and tubby mutant mice, indicating interdependence among these proteins. These findings establish TMEM145 as an essential membrane protein for the structural integrity of OHC stereocilia, providing insights into the molecular architecture of cochlear hair cells and their role in auditory function.

neuroscience↗