Biology subjects

Liu, B.

Publications and source records attributed to Liu, B..

At least 73 records · Page 4Linked to original sources

bioRxiv2026

Single-Cell Raman Profiling Enables Rapid Precision Phage Therapy Against Multidrug-Resistant Hypervirulent Klebsiella pneumoniae

Multidrug-resistant hypervirulent Klebsiella pneumoniae (MDR-hvKP) poses a severe global health threat. Phage therapy is a promising alternative, but requires precise matching of phage to the bacterial strain. Here, we present a proof-of-concept method that integrates single-cell Raman spectroscopy with deep learning to enable rapid and precise selection of lytic phages against MDR-hvKP. By profiling Raman signatures of strains across multiple KL-types (capsule locus types), we trained three deep learning architectures for phage-host matching. Among them, the CNN_MLP-Transformer achieved the best performance (99.7%), slightly outperforming CNN_MLP (99.2%) and CNN_MLP-Attention (99.5%). Validation using 10 hvKP clinical isolates yielded an average phage selection accuracy of 78.3%. These findings demonstrate the feasibility and clinical potential of AI- augmented Raman spectroscopy as a rapid, label-free, precise strategy for guiding phage therapy against MDR-hvKP infections. TeaserAI-guided single-cell Raman profiling enables rapid precision phage selection against multidrug-resistant K. pneumoniae.

microbiology↗

bioRxiv2026

Targeting AKAP13 RhoGEF activity ameliorates pro-fibrotic phenotypes driven by the IPF associated AKAP13 risk variant

RationaleIdiopathic pulmonary fibrosis (IPF) is a progressive, incurable scarring disease of the lung. A common genetic variant near AKAP13, a multifunctional scaffold protein that integrates intracellular signalling through its interactions with RhoA and protein kinase A (PKA), has been associated with IPF susceptibility and elevated AKAP13 mRNA expression in lung tissue from patients. However, its contribution to the pathogenesis of IPF remains unclear. ObjectiveThis study investigates how an AKAP13 variant alters epithelial signalling and evaluates the therapeutic potential of targeting AKAP13. Findingsrs62025270-bearing iHBECs exhibited selective upregulation of AKAP13 isoforms, accompanied by increased cell adhesion and reduced proliferation. Transcriptomic profiling revealed upregulated fibrosis-related genes in rs62025270-bearing iHBECs, including SAA1, FGF2, MMP1, CTSB, COL4A1, and CDKN1A. rs62025270-bearing iHBECs also displayed increased RhoA activation and SMAD2 phosphorylation following LPA stimulation. Furthermore, cells harbouring the AKAP13 variant showed reduced intracellular cAMP levels. Pharmacological inhibition of AKAP13 with A13 reversed the pro-adhesive phenotype and reduced RhoA activation in iHBECs. Moreover, in IPF-derived PCLS, A13 suppressed SERPINE1, CCN2, and MMP7 expression, reduced SMAD2 nuclear translocation, and decreased hydroxyproline levels. ConclusionsPresence of an AKAP13 variant disrupts epithelial homeostasis and promotes pro-fibrotic signalling. Inhibition of AKAP13s RhoGEF domain with A13 restores epithelial function and attenuates fibrotic activation, supporting AKAP13 as a therapeutic target in IPF.

genetics↗

bioRxiv2026

Soluble DLK1 secreted by telomere-shortening-induced senescent microglia impairs oligodendrocyte functions and alters neuronal activity

Aging is the major risk factor for neurodegenerative disease, yet the mechanisms linking physiological aging to brain dysfunction remain unclear. Because telomere erosion is a hallmark of aging, we examined its impact on glial and neuronal physiology. Telomere shortened mice showed lipofuscinosis, hypomyelination, microglial atrophy, and cognitive deficits. Single nuclei RNA-seq revealed accelerated glial aging, elevated microglial senescence pathways, and impaired oligodendrocyte functions. Inducing senescence in human iPSC derived microglia with shortened telomeres identified soluble DLK1 as a novel senescence associated ligand. sDLK1 was increased in the cerebrospinal fluid of telomere shortened and naturally aged mice, and this increase was eliminated by microglial depletion. AAV delivery of sDLK1 in vivo caused hypomyelination and blocked oligodendrocyte lineage progression, demonstrating the detrimental nature of excessive sDLK1. In human iPSC systems, sDLK1 impaired oligodendrocyte maturation and altered calcium signaling in excitatory neurons. These findings identify microglial senescence as a core consequence of telomere shortening and reveal sDLK1 as a microglia-derived senescence ligand that drives oligodendrocyte and neuronal dysfunction in aging.

neuroscience↗

bioRxiv2026

Unlocking Ultrasensitive Phosphoproteomics of Nanoscale Samples: A Rapid IMAC Enrichment Platform Using Ti-PAN Tip

Protein phosphorylation is a critical mechanism in cellular signal transduction, playing essential roles in various cellular processes. However, significant challenges of their low abundance, high dynamic range, and complexity are especially prominent for accurate phosphoproteome analysis in nanoscale samples, such as oocytes, where misregulation of phosphorylation can lead to infertility. In this study, we developed a novel phosphopeptide enrichment tip (Ti-PAN) using highly hydrophilic textile PAN fibers, enabling rapid in-situ one-tip IMAC enrichment in just 8 minutes. This approach not only minimizes sample loss but also enhances analytical sensitivity and is easily adaptable to automation for high-throughput applications, demonstrating excellent recovery (>94%) and outstanding selectivity for phosphopeptides with remarkable resistance to interference up to 1:5000. By integrating it with a compatible sample preparation workflow based on n-dodecyl {beta}-D-maltoside (DDM) lysis with the high-sensitivity MS data acquisition method of turboDDA, comprehensive mapping of phosphosites in microsamples was achieved, including those from the ERK interactome, mouse brain slices, and oocytes. Using this approach, we identified 2,139 to 11,296 phosphosites across 645 to 2,168 phosphoproteins from samples ranging from 100 to 100,000 cells. Furthermore, we successfully applied this strategy to analyze the phosphoproteome of mouse oocytes at different developmental stages, using as few as 5 oocytes per sample. This led to the identification of 2,709 phosphosites on 701 phosphoproteins, revealing several key kinases involved in meiotic resumption and oocyte maturation, including STK4 (serine/threonine kinase 4) and DYRK3 (dual specificity tyrosine phosphorylation-regulated kinase 3). To our knowledge, this represents the deepest coverage of phosphoproteomes from such minimal oocyte material reported to date, offering valuable mechanistic insights into developmental controls during oocyte maturation. This Ti-PAN-based method provides a robust, versatile, and automatable platform for large-scale, highly sensitive phosphopeptide enrichment, substantially advancing phosphoproteomic studies in complex biological systems.

biochemistry↗

bioRxiv2026

Glucokinase links metabolism and lineage plasticity in neuroendocrine prostate cancer via interaction with AKT1

Cancer cells frequently rewire their metabolism to sustain growth and survival under stress. Despite the critical role of metabolic adaptation in tumorigenesis, how specific metabolic enzymes regulate lineage plasticity remains unclear. Here, through FDG-PET imaging and transcriptomic analyses, we reveal markedly elevated glucose uptake in neuroendocrine prostate cancer (NEPC) and identify glucokinase (GCK) as a MYCN-induced metabolic enzyme. Beyond its metabolic role, GCK is indispensable for maintaining the neuroendocrine lineage of prostate cancer cells by establishing a functional circuit with AKT1 through reciprocal regulation--AKT1 binds and phosphorylates GCK at S373, whereas GCK phosphorylates AKT1 at S473. Pharmacological disruption of this AKT1-GCK axis suppresses tumor growth in NEPC mouse models and patient-derived xenografts. Altogether, our findings uncover both the metabolic and noncanonical kinase functions of GCK and establish the AKT1-GCK axis as a key link between metabolic reprogramming and neuroendocrine lineage transition in prostate cancer.

cancer biology↗

bioRxiv2025

Spatial inhibition of RhoA by RhoGAP15B promotes protrusive activity during collective cell migration

The Rho family GTPases RhoA, Rac1 and Cdc42 are well established regulators of collective migration by driving the formation of cellular protrusions and by regulating actomyosin contraction and adhesion. However, how their activation and inhibition are spatially and temporally coordinated remains unclear. Using GFP knock-in lines, we systematically characterized the localization patterns of all Drosophila RhoGEFs (activators) and RhoGAPs (inhibitors) in border cells, an in vivo model of collective migration. We have further combined RNAi screening with GFP-based validation of depletion efficiency to assess the functional significance of those RhoGEF/GAPs expressed in border cells. This identified RhoGAP15B as a localized inhibitor of RhoA activity at the border cell cortex. RhoGAP15B regulates cluster morphology and is enriched at the leading cell front, where it restrains actomyosin contractility to promote protrusive behavior. Our findings reveal RhoGAP15B as a key spatial RhoA regulator and highlight that patterned RhoGAP and RhoGEF activities are essential for coordinating cortical contraction and protrusion dynamics during collective migration.

cell biology↗

bioRxiv2025

MAGNET: an all-in-one foundation model for cross-modal and cross-dimensional microscopic image restoration

The application of emerging Foundation models in current microscopy has remained limited due to task-specific model designs, strong modality dependence and insufficient robustness under complex degradations. Here, we introduce MAGNET (Microscopic All-in-one General fouNdation model for imagE resToration), the first end-to-end All-in-One foundation model designed for universal microscopic image restoration. MAGNET integrates multi-task, cross-modal and cross-dimensional (2D + 3D) image restoration capabilities within a single unified architecture, and it is specifically designed to handle composite degradations in practical imaging systems. The framework comprises three components: (i) a task-aware, prompt-guided feature enhancement module for adaptive learning across diverse degradations; (ii) an LIIF-based reconstruction module enabling continuous, resolution-adaptive restoration; and (iii) a dimension-compatible triple-plane projection module supporting both 2D and 3D data. Trained on large-scale datasets spanning 5 major microscopy modalities (structured illumination, confocal, light-sheet, wide-field and two-photon) and 8 representative restoration tasks, MAGNET achieves state-of-the-art performance across super-resolution, denoising, deblurring, background suppression, isotropic reconstruction, aberration correction, de-scattering and virtual staining. Beyond supervised training, MAGNET supports direct inference on unseen systems, efficient few-shot fine-tuning and self-supervised test-time optimization, enabling robust performance across diverse data and imaging conditions. MAGNET serves as a unified, generalizable, and scalable computational framework for microscopy, enabling more efficient and reliable downstream analyses in cell biology, neuroscience, and pathology.

cell biology↗

bioRxiv2025

AI Identifies Broadly Neutralizing Antibodies from an IGHV1-69 Public Antibody Class Exerting Continued Selection Over SARS-CoV-2

R1-32-like public antibodies, characterized by shared IGHV1-69/IGLV1-40 usage, are elicited in more than 50% of individuals with COVID-19 and have been implicated in driving recurrent mutations at L452SARS2 and F490SARS2 within their convergent epitope in the SARS-CoV-2 spike receptor-binding domain. These mutations effectively mediate escape from non-affinity-matured R1-32-like antibodies with germline-like sequences. Here, we characterize four affinity-matured R1-32-like antibodies, C092, C807, BD56-104, and BD56-597, that tolerate L452SARS2 and F490SARS2 mutations. We show that this tolerance arises from residues introduced by somatic hypermutation at convergent positions across multiple CDR loops and surrounding regions, thereby creating additional contacts that reinforce epitope binding. An unusual N354SARS2 glycosylation site, which emerged in BA.2.86 and became fixed in its descendants, is linked to escape from affinity-matured R1-32-like antibodies, implying ongoing selection by this public antibody class. Using an AI model trained on integrated structural, neutralization, and binding data, we further identified ZL525, an ultrapotent R1-32-like antibody with pan-SARS-CoV-2 variant activity, including against the highly evasive KP.3 variant carrying the N354SARS2 glycosylation, and broad sarbecovirus cross-reactivity extending to SARS-CoV-1. Together, these findings show how affinity maturation enables public antibodies to adapt to viral antigenic drift, reveal their role in shaping SARS-CoV-2 antigenic evolution, and demonstrate the potential of AI-empowered strategies for discovering broadly neutralizing antibodies.

immunology↗

bioRxiv2025

Polus: a Transformer-based Soft-decision Codec Enhancement Platform for DNA Storage

DNA storage offers exceptional information density and archival longevity, but is constrained by the complex, heterogeneous errors inherent to synthesis, storage, and sequencing. Conventional error-correction schemes often rely on excessive logical redundancy to mitigate these biochemical imperfections, thereby compromising storage efficiency. Here, we introduce Polus, a deep-learning-enabled platform that bridges the gap between biochemical constraints and digital reliability through soft-decision decoding. At its core is SeqFormer, a Transformer-based channel model that synergizes sequence context with quality signals to characterize platform-specific error profiles, generating calibrated per-base confidence scores. This mechanism transforms uncertain biochemical noise into informative "soft" erasures. In in silico benchmarks, Polus significantly enhances mainstream codecs: it reduces the sequencing coverage required for DNA Fountain by 38.9% --increasing effective physical density by [~]80%--and eliminates persistent indel-induced errors in the Yin-Yang codec. Furthermore, it enables a targeted resequencing strategy that achieves full recovery with 99.9% less overhead than brute-force deepening. To formalize these gains and address the lack of systematic benchmarking in the field, Polus establishes a standardized nine-metric evaluation framework that rigorously quantifies the trade-offs between reliability, density, and cost. This work provides a reproducible, quantitative foundation for next-generation, context-aware DNA storage systems.

bioinformatics↗

bioRxiv2025

AI recognizes convergent somatic hypermutation signatures to allow the discovery of variant-resilient broadly neutralizing antibodies

Elucidating the mechanisms by which broadly neutralizing antibodies (bnAbs) develop to confer durable immunity in humans is pivotal for the rational design of next-generation vaccines and therapeutics. VH3-53/3-66-encoded public antibodies are widely elicited in the population after the COVID-19 pandemic. Here, we isolated 15 VH3-53/3-66-encoded bnAbs from elite neutralizers who experienced sequential SARS-CoV-2 Omicron breakthrough infections. These bnAbs exhibit exceptional potency and breadth against circulating variants and, as members of a long-lived public antibody lineage, likely contribute to durable humoral protection. Genetic analysis of VH3-53/3-66-encoded bnAbs reveals a convergent somatic hypermutation pattern at seven positions in and around the CDR loops that emerges with repeated viral exposures and distinguishes them from non-bnAbs. Grafting these combined mutations onto clinically escaped antibodies broadens their breadth and restores neutralization activity. Structural analysis shows that these convergent mutations cooperatively remodel CDRs to bind and tolerate virus receptor-binding domain mutations. Using an AI-based antibody language model trained on data linking somatic hypermutations to binding affinity and neutralization, the model is able to identify mutational patterns predictive of breadth, enabling the discovery of a rare bnAb with protective activity against the latest variants from early-pandemic antibody repertoires. This demonstrates the feasibility of establishing an AI-empowered pipeline to identify mutation-tolerant bnAbs from early-pandemic antibody repertoires to fight fast-evolving newly introduced viruses.

immunology↗

bioRxiv2025

The m6A reader protein YTHDF2 facilitates HTLV-1 infectious and mitotic propagation by stabilizing Tax RNA

N6-methyladenosine (m6A) is one of the important RNA modifications that affect RNA abundance and function and has also been implicated in viral infection. In this study, we identify a number of m6A modification sites within human T-cell leukemia virus type 1 (HTLV-1) RNAs, particularly in the RNA of the Tax oncogene. We demonstrate that YTH domain family, member 2 (YTHDF2), a key m6A reader protein that binds m6A-modified RNAs and influences RNA metabolism, is required for HTLV-1 replication in both de novo and persistently infected cells. Mechanistically, YTHDF2 interacts with and stabilizes Tax RNA in an m6A-dependent manner, thereby promoting Tax-driven HTLV-1 replication. Importantly, YTHDF2 activates oncogenic cellular pathways and promotes proliferation in HTLV-1 infected cells, aligning with the functions of Tax. Overall, our findings characterize YTHDF2 as a host factor critical to HTLV-1 RNA metabolism and viral propagation, offering novel insights into the understanding of HTLV-1 life cycle and the development of targeted interventions. Importancem6A is an RNA modification that plays crucial roles in physiological and pathological conditions; however, its roles in HTLV-1 infection are poorly understood. In this study, we identify that m6A modification is widely present in HTLV-1 RNAs including Tax. We demonstrate that YTHDF2, a prominent m6A reader protein, enhances the stability of Tax RNA, thereby promoting both de novo and persistent HTLV-1 replication. Our findings position YTHDF2 as an essential factor for HTLV-1 persistence and suggest it as a potential therapeutic target for viral clearance.

microbiology↗

bioRxiv2025

Global Mapping of circRNA-Target RNA Interactions Reveals P-Body-Mediated Translational Repression

Circular RNAs (circRNAs) are primarily produced through pre-mRNA back-splicing, yet their target repertoire and functional mechanisms remain elusive. Here, we present circTargetMap, a computational framework for globally mapping circRNA targets using RNA-RNA interactomes obtained via RNA in situ conformation sequencing (RIC-seq) in the hippocampus and ten human cell lines. This approach identified 117,163 high-confidence circRNA-target RNA interactions, with 83% of target mRNAs bound by multiple circRNAs. Functionally, CDR1as and circRMST repress target mRNA translation by sequestering them into processing bodies (P-bodies)--membraneless granules--through sequence-specific base-pairing, probably independent of AGO2, DICER, and miRNAs. To directly capture granule-associated interactions, we developed granule RIC-seq (GRIC-seq) method, revealing the broad role of circRNA-target RNA interactions in translational repression. Moreover, pathogenic variants are significantly enriched around circRNA-target RNA interaction sites, suggesting potential roles in disease. Our study provides valuable resources for circRNA functional exploration and a framework for investigating RNA-RNA interactions within membraneless organelles.

molecular biology↗

bioRxiv2025

Astrocytic FABP5 drives non-cell-autonomous oligodendrocyte injury in multiple system atrophy by promoting TNF signaling and ferroptotic stress

Multiple system atrophy (MSA) is a fatal -synucleinopathy characterized by progressive parkinsonism, cerebellar and autonomic dysfunction. Currently, the mechanisms driving cerebellar white matter neuroinflammation and degeneration in MSA are poorly understood. Here, we identified fatty acid-binding protein 5 (FABP5) as a key factor regulating cerebellar inflammation in MSA pathogenesis in a detailed study of human, mouse and cultured astrocytes. Firstly, transcriptomic profiling of human MSA cerebellar white matter revealed activation of pro-inflammatory and ferroptotic pathways, with FABP5 identified as a key pathway component that is upregulated. We confirmed that FABP5 is upregulated in reactive astrocytes in the PLP--syn transgenic mouse model, also in LPS-treated primary astrocytes. Fabp5 silencing suppressed TNF signaling, mitigated ferroptosis, and restored mitochondrial function. These findings suggest astrocytic FABP5 as a central intracellular regulator linking glial inflammation, ferroptosis, and mitochondrial injury. Overall, this mechanism suggests that FABP5 drives pathology mediated by astrocytes oligodendroglia in MSA, therefore representing a novel and promising therapeutic target.

neuroscience↗

bioRxiv2025

The emerging contaminant Cl-PFESA/F-53B is toxic to meiotic cell division and reproduction in Arabidopsis thaliana

The emerging contaminant Cl-PFESA/F-53B damages vegetative development in plants and has been evidenced to be toxic to both mitotic and meiotic cells in animals. We have recently reported that F-53B induces nuclei unviability in meristematic cells leading to disrupted root development in Arabidopsis (Arabidopsis thaliana). However, the toxicity of F-53B to reproductive system in plants remains unelucidated. In this study, by using cytogenetic and microscopic approaches, we analyzed embryo and anther development and multiple meiosis processes in Arabidopsis exposed to 50 or 100 M F-53B. We showed that F-53B disrupts embryo development which results in reduced seed setting in Arabidopsis. Histochemical staining of anthers and a live-imaging assay using a reporter line that expresses GFP-tagged Aborted Microspores (AMS), a key regulator of the tapetum, demonstrated that F-53B impairs anther development. Moreover, we showed that F-53B interferes with chromosome segregation and/or distribution and alters microtubule organization during male meiosis. Quantification of the chiasmata and immunolocalization of the Human Enhancer of Invasion 10 (HEI10) protein on diakinesis chromosomes suggested that F-53B reduces crossover rate. Furthermore, F-53B reduced the number of DNA Meiotic Recombinase 1 (DMC1) protein foci on zygotene chromosomes in Arabidopsis wild-type Columbia-0 (Col-0), and it partially promoted meiotic chromosome integrity in Arabidopsis depleted with Ataxia Telangiectasia Mutated (ATM), a central regulator of DNA double-strand break (DSB) repair, which suggested that F-53B reduces meiotic DSB formation. Taken together, our study reveals the toxicity of F-53B to meiotic cells and reproduction in Arabidopsis, which highlights its potential threats to agricultural safety and ecological diversity. HighlightO_LIF-53B impairs embryo and anther development in Arabidopsis. C_LIO_LIF-53B interferes with chromosome segregation and distribution during male meiosis. C_LIO_LIF-53B interferes with meiotic microtubule organization. C_LIO_LIF-53B reduces meiotic crossover formation. C_LIO_LIF-53B reduces DNA double-strand breaks in meiocytes. C_LI

plant biology↗

bioRxiv2025

The transcriptional regulatory circuit as a driver and therapeutic target in CML blast crisis

Patients with blast crisis in chronic myeloid leukemia (CML) exhibit an extremely poor prognosis, with median survival of only a few months and limited therapeutic options. Dysregulated transcriptional regulation plays a pivotal role in driving blast crisis progression. In this study, we performed histone modification and transcriptomic high-throughput sequencing on bone marrow cells derived from chronic and blast-phase CML patients, identifying a CML blast-specific transcriptional regulatory circuit comprising MEF2C, MYB, MEIS1, and ZEB2. These transcription factors (TFs) form protein complexes that co-bind to shared enhancers or promoters, reciprocally enhancing each others transcriptional activity and that of their downstream targets. Mechanistically, this circuit synergistically reprograms chromatin accessibility and transcriptional landscapes in blast cells, parallel activation of purine metabolism and Rho GTPase signaling pathways which exhibit functional crosstalk. Functional validation demonstrated that silencing components of this circuit or its downstream core targets significantly suppressed CML blast progression in vitro and in vivo. Notably, mebendazole (MBZ), a clinically approved inhibitor targeting MYB protein stability, recapitulated these inhibitory effects. Our findings establish the MEF2C-MYB-MEIS1-ZEB2 transcriptional circuit as a central driver of CML blast crisis and position MBZ as a high-potential translational strategy for targeting this lethal phase of the disease. Key PointsO_LIMEF2C, MYB, MEIS1, and ZEB2 form the CML blast-crisis transcriptional circuit, synergistically reprogramming chromatin and transcription. C_LIO_LIMebendazole inhibits CML blast progression by impairing the circuit, offering a rapid translational strategy for this lethal phase. C_LI

cancer biology↗

bioRxiv2025

Effects of carbon dioxide enrichment and environmental factors on photosynthesis, growth and yield and their interaction in cucumber: a meta-analysis

Despite the ongoing increase in atmospheric carbon dioxide concentrations, these levels remain well below the optimal threshold for cucumber growth and development. In addressing the challenges posed by climate change to agricultural production, the use of carbon dioxide enrichment (eCO2) has become increasingly widespread in order to meet global demand for cucumbers. Nevertheless, the impact of eCO2 and environmental factors on cucumber growth remains to be elucidated. In this study, we conducted a meta-analysis of 73 research papers on eCO2 in cucumbers was conducted, and their photosynthesis, growth, and yield were analysed. In summary, under conditions of elevated CO2 levels, the net photosynthetic rate, biomass, and yield of cucumbers exhibited a marked increase of 56.31%, 27.75%, and 21.98%, respectively. Concurrently, stomatal conductance and transpiration rate exhibited a decline of 36.07% and 30.42%, respectively. In the context of the implementation of eCO2 at varying levels within a production environment, the prevailing recommendation pertains to the range of 800-1200 ppm. It is advised that this be integrated with elevated light intensity, augmented temperature, suitable humidity levels, and a sufficient supply of fertiliser to achieve a synergistic effect. The findings of this study contribute to enhancement of environmental control in the context of greenhouse cultivation of cucumber in response to climate change, as well as promoting the green and sustainable development of the cucumber industry.

plant biology↗

bioRxiv2025

TMEM100 attenuates NF-κB activation via disrupting the PRDX1-GNAI2 complex to alleviate acute lung injury

Acute lung injury (ALI) is a severe and diffuse inflammatory disorder of interstitial lung. Emerging evidence suggests that TMEM100 is closely associated with lung development and function. However, its role in ALI remains unclear. In this study, we observed a significant downregulation of TMEM100 expression in both mouse lung tissues with ALI and lipopolysaccharide (LPS)-induced pulmonary vascular endothelial cells (PVECs). Overexpression of TMEM100 markedly attenuates LPS-induced lung injury and inflammation, while also restoring the imbalance between proliferation and apoptosis in PVECs. Mechanistically, TMEM100 interacts with both PRDX1 and GNAI2, disrupting the PRDX1-GNAI2 complex and thereby inhibiting LPS-induced NF-{kappa}B activation, which contributes to its anti-inflammatory effects. These findings highlight the protective role of TMEM100 in endotoxin-induced ALI and provide a theoretical basis for understanding its biological functions and potential applications in ALI gene therapy.

immunology↗

bioRxiv2025

Perturbation of nuclear proteins by optogenetic trapping in Drosophila ovary

The eukaryotic nucleus hosts transcription factors and other numerous nuclear proteins essential for genome organization and function. Optogenetic tools have been applied to match nuclear protein dynamics but remain largely confined to transcription factors, leaving most nuclear proteins inaccessible for precise manipulation. Here, we engineered an optogenetic tool, NLS-LARIAT, by fusing a nuclear localization sequence to the LARIAT (light-activated reversible inhibition by assembled trap), enabling light-inducible clustering of diverse GFP-tagged nuclear proteins in Drosophila ovarian cells. NLS-LARIAT-mediated clustering of transcriptional and epigenetic regulators, such as Slbo and LSD1, phenocopied genetic inhibition while revealing rapid and localized roles of Slbo during border cell migration. Beyond regulatory factors, NLS-LARIAT can also be used to manipulate nuclear structures including the nuclear envelope and chromatin. Thus, NLS-LARIAT provides a versatile and broadly applicable optogenetic platform for spatiotemporal control of nuclear proteins, offering new opportunities to dissect nuclear organization and function across model systems.

cell biology↗