Biology subjects

Han, C.

Publications and source records attributed to Han, C..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Conformation-specific Antibody Deciphers K27-linked Ubiquitination in Chaperone-Mediated Proteostasis

Lysine 27 (K27)-linked polyubiquitination plays critical yet incompletely defined roles in proteostasis, innate immunity, and disease progression; however, investigations into this process have long been hindered by its extremely low abundance and the lack of conformation-specific enrichment tools. Herein, we describe the development of a long-sought conformation-specific antibody, K27-IgG, which can selectively recognize--among all ubiquitin chain types--the unique architecture of K27-linked polyubiquitin (K27-polyUb) characterized by a distinct buried K27-isopeptide bond, with high affinity (KD = 4.66 nM). This antibody was derived from synthetic antibodies initially generated via phage display, using chemically synthesized K27-linked diubiquitin (K27-diUb) as the antigen. High-resolution co-crystal structures uncovered the unique K27-diUb interface targeted by these sAbs. Subsequent reformatting of these sAbs into a full-length human immunoglobulin G (IgG) scaffold yielded K27-IgG, notably exhibiting markedly enhanced affinity without compromising selectivity. Using K27-IgG as a tool, we achieved sensitive detection and immunoprecipitation (IP) of endogenous K27-polyUb in cells, and delineated the intracellular interaction landscape of K27-polyUb through complementary proteomic approaches. Two key findings emerged: 1) The molecular chaperone DNAJB1 is a specific reader of K27-linked ubiquitin chains (but not other linkages) and that K27-polyUb chains themselves exhibit chaperone-like activity, suggesting a novel mechanism by which K27-polyUb regulates chaperone-mediated proteostasis; 2) The E2 enzyme UBE2Q1 assembles K27-diUb, identifying it as a potential writer for this ubiquitin chain topology. Collectively, this study establishes K27-IgG as a robust tool for deciphering the K27-linked ubiquitin code, thereby opening new avenues for investigating the biological functions of K27-linked polyubiquitination. HighlightsO_LIFirst K27-linkage conformation-specific antibody with nanomolar affinity overcomes a major barrier in the field. C_LIO_LIK27-IgG unlocks functional mapping of the K27 ubiquitin landscape under proteotoxic stress. C_LIO_LIMolecular chaperone DNAJB1 is a selective "reader" of K27-linked ubiquitin chains. C_LIO_LIK27 chains possess intrinsic chaperone activity, enabling protein refolding and suppressing aggregation. C_LIO_LIE2 enzyme UBE2Q1 is a "writer" that directly assembles K27-linked ubiquitin chains. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/695067v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@113b980org.highwire.dtl.DTLVardef@1f7c1a0org.highwire.dtl.DTLVardef@c91656org.highwire.dtl.DTLVardef@1d9a507_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

IsoformSwitchAnalyzeR v2: Analysis of Functional Isoform Changes in Long-read and Single-cell Sequencing Data

Alternative splicing enables a single gene to produce a variety of mRNA transcripts, significantly enhancing protein diversity in higher eukaryotes. Isoform switching refers to the differential usage of a genes transcripts and occurs pervasively across physiological and pathological conditions. IsoformSwitchAnalyzeR was developed to identify these isoform switches and analyze their functional consequences. Advances in RNA-seq technology, including long-read and single-cell sequencing, along with state-of-the-art computational tools, enable unprecedented accuracy in isoform switch identification and its functional consequences, necessitating an update to IsoformSwitchAnalyzeR. Here we present IsoformSwitchAnalyzeR 2.0, with substantial improvements in the robustness of isoform switch detection, the incorporation of new functional annotation types, and interoperability with other bioinformatics tools. We showcase how IsoformSwitchAnalyzeRs standard workflow is now well-suited for analysis of both long-read RNA-seq and single-cell data through two case studies. Specifically, we analyze long-read data from patients with Alzheimers Disease and single-cell data from patients with glioblastoma. In both case studies, we find important isoform switches with disease-relevant functional consequences, showcasing the power of IsoformSwitchAnalyzeR v2. Taken together, these findings highlight the versatility and robustness of IsoformSwitchAnalyzeR in handling advanced sequencing technologies, thereby broadening its applicability across diverse research contexts. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/693027v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1f0ecd8org.highwire.dtl.DTLVardef@4d7285org.highwire.dtl.DTLVardef@999abeorg.highwire.dtl.DTLVardef@7e3e9d_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Harnessing anti-CRISPR to suppress, subtract, and segregate Cas9 activity for precision CRISPR in Drosophila

Tissue-specific CRISPR (ts-CRISPR) is a powerful approach for studying cell and developmental biology by restricting mutagenesis to specific tissues. However, the precision of this approach is often compromised by non-specific, "leaky" Cas9 activity that confounds phenotypic analysis and destabilizes Cas9/gRNA stocks. To address these limitations in Drosophila, we developed a toolkit based on the Anti-CRISPR (Acr) protein AcrIIA4. We first identified AcrIIA4 as a potent in vivo Cas9 inhibitor with high stability and established the temporal requirements for its function. Based on these findings, we generated three classes of Acr tools. First, a collection of AcrIIA4-bearing balancers robustly suppresses Cas9 and enables the stable maintenance of complex Cas9/gRNA stocks. Importantly, maternal deposition of AcrIIA4 from these balancers provides a means of temporal control, delaying Cas9 activity until metamorphosis. Second, tissue-specific AcrIIA4 transgenes refine leaky Cas9 drivers in a "tissue-subtraction" strategy. Finally, germline-specific and soma-specific Acr tools efficiently segregate Cas9 activity, solving bidirectional leakiness between these two compartments. This comprehensive AcrIIA4 toolkit provides new levels of precision, versatility, and temporal control for Drosophila CRISPR applications.

genetics↗

bioRxiv2025

Epigenetic editing of Cartpt promotes acquisition and extinction of cocaine memory

In classic disease models, removing a pathological insult restores homeostasis. Yet, addiction persists far beyond the period of active drug use. Cocaine abstinence induces changes in gene expression and neuronal signaling in reward-related brain regions that limit recovery during abstinence. We found that 2 weeks of abstinence increased Cartpt (cocaine- and amphetamine-regulated transcript) in the mouse nucleus accumbens and decreased repressive H3K27me3 at the Cartpt locus. While endogenous CART peptide is best described for its anorexigenic function, it is also implicated in human addiction and dopamine homeostasis. To test the causal relevance of Cartpt chromatin remodeling, we used CRISPR-based epigenetic editing tools, dCas9-FOG1 and dCas9-JMJC-ZF, to manipulate H3K27me3 at Cartpt in vivo. Enriching H3K27me3 in D1 neurons repressed Cartpt expression and augmented acquisition and extinction of cocaine preference. These results show that CRISPR epigenetic editing can recapitulate endogenous chromatin states to modulate addiction-related behavior, highlighting broad therapeutic potential of both Cartpt and epigenetic editing. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=192 SRC="FIGDIR/small/689329v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1b84229org.highwire.dtl.DTLVardef@1ffc2d7org.highwire.dtl.DTLVardef@50cf00org.highwire.dtl.DTLVardef@1462d10_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

Sensory neuronal mTORC1 signaling establishes neuroimmune memory that initiates allergic immunity

Environmental allergens are enriched in protease activity, a feature that directly activates cutaneous sensory neurons, triggering itch and Substance P release, which promotes Th2-skewing CD301b+ dendritic cell migration and initiates allergic immunity. However, allergens are typically encountered as repeated, subthreshold exposures, and how these cumulatively induce sensitization is unknown. We identify a sensory neuron-intrinsic mechanism of neuroimmune memory that enables this process. Initial activation by protease allergens induces sustained mTORC1 signaling and PGC-1-associated mitochondrial remodeling, establishing a metabolically primed state that amplifies neuroimmune responses upon allergen re-exposure. This heightened state, independent of adaptive immunity, drives enhanced itch, increased CD301b+ dendritic cell migration, and augmented Th2 differentiation. Disrupting neuronal mTORC1 signaling or mitochondrial stability abrogates this amplification while leaving primary responses intact. Importantly, this mechanism generalizes across distinct protease allergens, revealing mTORC1-driven metabolic reprogramming in sensory neurons as a form of innate neuroimmune memory underlying allergen cross-sensitization and polysensitization.

immunology↗

bioRxiv2025

Tuning Mitotic Recombination with Patterned DNA Nicks for Precision Mosaic Analysis

CRISPR/Cas9-based mosaic analysis is a powerful tool for in vivo genetics but is limited by cytotoxicity and mutagenesis associated with DNA double-strand breaks (DSBs). Here, we establish Cas9-derived nickases as safer and more reliable alternatives for inducing mitotic recombination in Drosophila. We demonstrate that single-strand nicks are sufficient to generate mosaic clones and systematically dissect the parameters governing this process. We find that clone frequency can be controlled by the gRNA nicking pattern, with two distant nicks on the same DNA strand synergistically enhancing recombination by over nine-fold compared to a single nick. Based on these findings, we propose a mechanistic model for nick-induced crossover and provide a versatile toolkit for generating tissue-specific nickases. This work establishes nickase-based MAGIC as a superior method for high-fidelity clonal analysis, enabling more precise investigation of gene function in development and disease. SIGNIFICANCE STATEMENTThe CRISPR/Cas9-based mosaic technique, MAGIC, is a versatile tool for in vivo biological investigations. However, its reliance on DNA double-strand breaks (DSBs) can cause significant, unintended cell damage. Here we establish that Cas9-derived nickases, which create gentler single-strand nicks, are a superior alternative. We show that nickases safely induce genetic mosaics in Drosophila by avoiding this cellular toxicity. By systematically dissecting the process, we discovered principles of gRNA design that allow clone frequencies to be tuned for different experimental needs. This work provides a new mechanistic model for nick-induced genetic exchange, a high-fidelity "nickase-MAGIC" method, and a versatile toolkit for precision clonal analysis.

developmental biology↗

bioRxiv2025

Stepwise Ligand Capture Primes PKR for Activation and RNA Discrimination

Protein Kinase R (PKR) triggers the innate immune response upon detecting double-stranded RNAs (dsRNAs). Its kinase activity is controlled by two dsRNA-binding domains (dsRBDs), yet how these dsRBDs operate during RNA ligand recognition and downstream signaling remains unresolved. Here, we uncover an unexpected interplay between the dsRBDs that orchestrates a two-step ligand sampling, ensuring accurate and efficient PKR activation. dsRBD1 surveys all RNA duplexes through one-dimensional diffusion but dissociates within milliseconds to minimize background signaling, while dsRBD2-RNA binding plays a key role in fostering kinase-kinase interactions. Upon encountering foreign dsRNAs, dsRBD2 arrests the diffusive dsRBD1, thereby establishing a scaffold essential for kinase dimerization and phosphorylation. By contrast, prevalent bulges and large internal loops in self-RNA duplexes obstruct dsRBD2 from capturing dsRBD1, creating a steeply elevated energy landscape that enables PKR to discriminate foreign RNAs from abundant self-RNAs, thus evolving a delicate strategy to achieve both high selectivity and robust signaling.

biophysics↗

bioRxiv2025

An efficient beet severe curly top virus-based VIGS vector in Beta vulgaris

Sugar beet (Beta vulgaris L.) is one of the most important sugar crops worldwide. However, studies on sugar beet gene functions are still lagging compared to other crops due to the lack of an effective genetic manipulation. In this study, we generated an infectious clone of beet sever curly top virus (BSCTV) and engineered it into a VIGS vector. BSCTV-BvPDS can induce strong and persistent bleached PDS-silencing phenotype in 8 tested sugar beet varieties. We further efficiently silenced B. vulgaris MYB1 gene that regulating the betalain pathway in sugar beet by BSCTV-based VIGS system. Finally, we used this system to silence the effector CbNip1 of Cercospora beticola through cross-kingdom RNAi, resulting in reduced disease symptoms in sugar beet plants. Therefore, the BSCTV VIGS system can be used to study sugar beet-pathogen interactions. In summary, we have established an easy and efficiency BSCTV-based VIGS vector in sugar beet. This system will be an attractive tool for functional genomic studies for sugar beet.

plant biology↗

bioRxiv2025

A genome-wide MAGIC kit for recombinase-independent mosaic analysis in Drosophila

Mosaic analysis has been instrumental in advancing developmental and cell biology. Most current mosaic techniques rely on exogenous site-specific recombination sequences that need to be introduced into the genome, limiting their application. Mosaic analysis by gRNA-induced crossing-over (MAGIC) was recently developed in Drosophila to eliminate this requirement by inducing somatic recombination through CRISPR/Cas9-generated DNA double-strand breaks. However, MAGIC has not been widely adopted because gRNA-markers, a required component for this technique, are not yet available for most chromosomes. Here, we present a complete, genome-wide gRNA-marker kit that incorporates optimized designs for enhanced clone induction and more effective clone labeling in both positive MAGIC (pMAGIC) and negative MAGIC (nMAGIC). With this kit, we demonstrate clonal analysis in a broad range of Drosophila tissues, including cell types that have been difficult to analyze using recombinase-based systems. Notably, MAGIC enables clonal analysis of pericentromeric genes and deficiency chromosomes and in interspecific hybrid animals, opening new avenues for gene function study, rapid gene discovery, and understanding cellular basis of speciation. This MAGIC kit complements existing systems and makes mosaic analysis accessible to address a wider range of biological questions. IMPACT STATEMENTA comprehensive toolkit enables genome-wide, recombinase-independent mosaic analysis in Drosophila, permitting clonal analysis of pericentromeric genes, deficiency chromosomes, and interspecific hybrids previously inaccessible to standard methods.

genetics↗

bioRxiv2025

Adolescent morphine exposure does not alter low-dose lipopolysaccharide-induced sickness behavior in adult mice

Adolescent opioid use in the United States commands attention: millions of twelve- to nineteen-year-olds are exposed to opioids each year by prescription and misuse. Recent findings show that opioids bind not only to canonical opioid receptors but also interact with receptors on immune cells within both the central and peripheral nervous systems. The potential for early life opioid exposure to induce long-term changes in the neuroimmune system is not fully understood, particularly given the adolescent brains high susceptibility to neuroplastic changes. The goal of this study was to investigate the hypothesis that adolescent opioid use potentiates physiological and behavioral responses to pathogen-induced sickness later in life. To achieve this, we treated adolescent mice (PND 35-42) with bi-daily escalating doses of morphine to model dependence and then administered a low dose of lipopolysaccharide (LPS, 0.1 mg/kg) in adulthood (PND 60-76) to induce an immune response. In contrast to our hypotheses, we found that adolescent morphine exposure had no additive effect on low-dose LPS-induced sickness measures when assessed in adulthood. These data suggest that adolescent opioid exposure may have minimal effects on future immune challenges, although further research is needed to confirm this.

neuroscience↗

bioRxiv2025

TURBO: Automated Total-body PET Image Processing and Kinetic Modeling Toolbox

Long axial field of view (LAFOV) PET imaging requires a high level of automation and standardization, as the large number of target tissues increases the manual workload significantly. We introduce an automated analysis pipeline (TurBO, Turku total-BOdy) for preprocessing and kinetic modelling of LAFOV [15O]H2O and [18F]FDG PET data, enabling efficient and reproducible analysis of tissue perfusion and metabolism at regional and voxel-levels. The approach employs automated processing including co-registration, motion correction, automated CT segmentation for region of interest (ROI) delineation, image-derived input determination, and region-specific kinetic modelling of PET data. MethodsWe validated the analysis pipeline using Biograph Vision Quadra (Siemens Healthineers) LAFOV PET/CT scans from 21 subjects scanned with [15O]H2O and 16 subjects scanned with [18F]FDG using six segmented CT-based ROIs (cortical brain gray matter, left iliopsoas muscle, right kidney cortex and medulla, pancreas, spleen and liver) representing different levels of blood flow and glucose metabolism. ResultsModel fits showed good quality with consistent parameter estimates at both regional and voxel-levels (R{superscript 2} > 0.83 for [15O]H2O, R{superscript 2} > 0.99 for [18F]FDG). Estimates from manual and automated input functions were in concordance (R{superscript 2} > 0.74 for [15O]H2O, and R{superscript 2} > 0.78 for [18F]FDG) with minimal bias (<4% for [15O]H2O and <10% for [18F]FDG). Manually and automatically (CT-based) extracted ROI level data showed strong agreement (R{superscript 2} > 0.82 for [15O]H2O and R{superscript 2} > 0.83 for [18F]FDG), while motion correction had little impact on parameter estimates (R{superscript 2} > 0.71 for [15O]H2O and R{superscript 2} > 0.78 for [18F]FDG) compared with uncorrected data. ConclusionOur automated analysis pipeline provides reliable and reproducible parameter estimates across different regions, with an approximate processing time of 1-1.5 h per subject. This pipeline completely automates LAFOV PET analysis, reducing manual effort and enabling reproducible studies of inter-organ blood flow and metabolism, including brain-body interactions.

neuroscience↗

bioRxiv2025

Lifespan Trajectories of Alpha Rhythm: Dynamic Shifts in Neural Excitation-Inhibition Balance

Alpha rhythm (8-13 Hz), a key neural oscillation in the brain, plays a significant role in cognitive functions and reflects the brains excitatory-inhibitory (E-I) balance. This study investigates the dynamics of alpha rhythm across the lifespan, focusing on how E-I balance modulates alpha power and peak frequency, and exploring the distinct age-related and sex-specific patterns of alpha activity. Using a computational E-I model, we simulated the impact of different neuronal connections and E-I ratios on alpha rhythm characteristics. The results suggest that self-regulation primarily affects alpha power, while interaction between excitatory and inhibitory neurons influences both alpha frequency and power. We applied this model to real EEG data from 3265 participants across a wide age range, revealing that alpha power and peak frequency exhibit an inverted U-shape across the lifespan, peaking in early adulthood and declining in old age. Significant sex differences in alpha activity were observed primarily during puberty and later in life. Decomposition of the alpha band into periodic and aperiodic components showed that periodic activity follows the inverted U-shape, while aperiodic activity declines exponentially with age. Our findings indicate that alpha rhythm is governed by complex E-I dynamics, with distinct contributions from periodic and non-periodic components, and highlight the role of alpha rhythm in age-related cognitive changes and sex differences in brain function.

neuroscience↗

bioRxiv2025

Introducing An Argonaute-facilitated Isothermal Amplification Technology

Argonaute-facilitated targeting, which is an enzyme-mediated, high-fidelity, and highly efficient base pairing process, can be repurposed for upgrading PCR technology. An Argonaute protein derived from thermophilic Caloramator sp. (CalAgo) cleaved target dsDNA in the presence of Tte UvrD helicase at 65{degrees}C, suggesting dmCalAgo (a nuclease-inactive mutant) binding to target dsDNA in the same condition. Based on this, we designed an Argonaute-facilitated isothermal PCR platform (Isothermal Ago-PCR) through synergy of dmCalAgo, Tte UvrD helicase, and Bst DNA polymerase. Isothermal Ago-PCR realized amplification of template at 65{degrees}C. The upgrade resides in replacing primer annealing with Argonaute-facilitated targeting. Hence, Isothermal Ago-PCR not merely eliminates the reliance on complex primer design and sophisticated instruments but also achieves high-fidelity and highly efficient amplification. This platform enabled detection of low-copy templates (as few as 3 copies per reaction) within 30 minutes, achieving comparable sensitivity to qPCR while demonstrating superior amplification kinetics. This platform also demonstrated compatibility with common thermal maintenance tools. Thus, Isothermal Ago-PCR has the potential to replace qPCR with broad applicability. Details refer to our patent (China Patent CN116479095A).

biochemistry↗

bioRxiv2025

Super-Resolution Diffusivity Mapping Reveals Spatial Correlations Between Lateral Mobility and Structural Heterogeneities on Cellular Membranes

Cellular membranes orchestrate critical processes such as molecular transport and signal transduction, both regulated by the lateral mobility of lipids and proteins. However, resolving nanoscale diffusional heterogeneities and elucidating their underlying mechanisms remains a formidable challenge due to the membranes intricate architecture and compositional diversity. Here, we present point-cloud single-molecule diffusivity mapping (pc-SMdM), a cutting-edge super-resolution technique that offers a point-cloud data format with enhanced spatial resolution for diffusivity mapping. Using pc-SMdM, we visualize nanoscale diffusion slowdown clusters with [~]50 nm in diameter on plasma membranes. These clusters are predominantly governed by cholesterol content, alongside contributions from membrane protein assemblies and topographical features. Leveraging two-color pc-SMdM, we concurrently imaged multiple lipids and membrane probes, revealing distinct "fingerprint" diffusivity maps shaped by their interactions within lipid bilayers. Our findings position pc-SMdM as a transformative tool for spatially resolving molecular interactions and membrane dynamics in live cells, offering new insights into the underlying mechanisms that govern membrane mobility at the nanoscale.

biophysics↗

bioRxiv2025

Polyploidy promotes transformation of epithelial cells into non-professional phagocytes

Removal of dead and damaged cells is critical for organismal health. Under stress conditions such as nutritional deprivation, infection, or temperature shift, the clearance of nonessential cells becomes a universal strategy to conserve energy and maintain tissue homeostasis. Typically, this task is performed by professional phagocytes such as macrophages. However, non-professional phagocytes (NPPs) can also adopt a phagocytic fate under specific circumstances. Similar to professional phagocytes, NPPs undergo transitions from immature to mature states and activation, but the precise cellular and molecular mechanisms governing their maturation, induction and phagocytic execution remain largely unknown. A notable example of stress-induced phagocytosis is the removal of germline cells by follicle cell-derived NPPs during oogenesis in Drosophila. In this study, we report that the transformation of follicle cells into NPPs is dependent on Notch signaling activation during mid-oogenesis. Moreover, Notch overactivation is sufficient to trigger germline cell death and clearance (GDAC). We further show that polyploidy, driven by Notch signaling-induced endoreplication, is essential for the transformation of follicle cells into NPPs. Polyploidy facilitates the activation of JNK signaling, which is crucial for the phagocytic behavior of these cells. Additionally, we show that polyploidy in epidermal cells, another type of NPPs, is important for their engulfment of dendrites during induced degeneration. Together, these findings suggest that polyploidy is a critical factor in the transformation of epithelial cells into NPPs, enabling their phagocytic functions, which are essential for maintaining cellular and organismal homeostasis during stress conditions. SIGNIFICANCEThe ability to remove dead and damaged cells is essential for maintaining tissue homeostasis and organismal health. While this task is typically performed by professional phagocytes such as macrophages, non-professional phagocytes (NPPs) can also acquire phagocytic functions during development or in response to stress conditions. Using Drosophila oogenesis as a model, we reveal that the transformation of follicle cells into NPPs is driven by Notch signaling and is critically dependent on polyploidy. Our findings show that polyploidy, induced through Notch signaling-mediated endoreplication, is required for activating JNK signaling, a pathway essential for the phagocytic behavior of NPPs. Furthermore, we show that polyploidy also facilitates the phagocytic activity of epidermal cells in clearing degenerating dendrites. Together, these results suggest that polyploidy plays an important role in enabling epithelial cells to adopt NPP functions and in maintaining tissue and organismal homeostasis under stress conditions.

developmental biology↗

bioRxiv2025

A Comprehensive Reference Catalog of Human Skin DNA Virome Reveals Novel Viral Diversity and Microenvironmental Influences

IntroductionHuman skin serves as a dynamic habitat for a diverse microbiome, including a complex array of viruses whose diversity and roles are not fully understood. ObjectivesThis study aims to enhance our understanding of this skin viral diversity through the construction of a detailed, non-redundant DNA viral reference catalog. MethodsA total of 2,760 skin metagenomes from six published skin studies were collected. A skin virome catalog was constructed using methods independent of reference databases. Viral characteristics were identified through cross-cohort meta-analysis and used to characterize viral features across different skin environments. ResultsWe identified 20,927 viral sequences, which clustered into 2,873 viral operational taxonomic units (vOTUs). Among these, 2,610 represent previously unrecorded viral sequences, uncovering a substantial breadth of viral diversity on human skin. The results also highlight significant differences in viral communities that are associated with varying skin microenvironments. The oily skin is enriched in Papillomaviridae; the dry skin area is enriched in Autographiviridae, Inoviridae and Mitoviridae; and the moist skin is enriched in Herelleviridae, indicating the adaptive nature of viruses. We also investigated the relationship between bacteriophages and bacteria on the skin surface. We found that skin bacteria such as Pseudomonas, Klebsiella, and Staphylococcus are infected by phages from the class Caudoviricetes. ConclusionThis comprehensive skin DNA viral catalog significantly advances our understanding of the viromes role within the skin ecosystem. The findings highlight the adaptive nature of viruses to different skin microenvironments and their interactions with resident bacteria. This catalog serves as a valuable resource for further epidemiological and therapeutic research, potentially leading to better management and treatment of skin conditions influenced by the skins virome.

microbiology↗

bioRxiv2025

LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis

Metabolic syndrome and excessive alcohol consumption result in liver injury and fibrosis, which is characterized by increased collagen production by activated Hepatic Stellate Cells (HSCs). LARP6, an RNA-binding protein, was shown to facilitate collagen production. However, LARP6 expression and functionality as a regulator of fibrosis development in a disease relevant model remains elusive. By using snRNA-sequencing, we show that LARP6 is upregulated mainly in HSCs of liver fibrosis patients. Moreover, LARP6 knockdown in human HSCs suppresses fibrogenic gene expression. By integrating eCLIP analysis and ribosome profiling in HSCs, we show that LARP6 interacts with mature mRNAs comprising over 300 genes, including RNA structural elements within COL1A1, COL1A2, and COL3A1 to regulate mRNA expression and translation. Furthermore, LARP6 knockdown in HSC attenuates fibrosis development in human liver spheroids. Altogether, our results suggest that targeting LARP6 in human HSCs may provide new strategies for anti-fibrotic therapy. HighlightsO_LILARP6 is upregulated in liver fibrosis, mainly in HSCs. C_LIO_LILARP6 knockdown in human HSCs reduces liver fibrosis development. C_LIO_LIOf the hundreds of gene targets, LARP6 interacts most with collagen mRNAs. C_LIO_LILARP6 regulates mRNA translation via interaction with 5UTRs. C_LI

cell biology↗

bioRxiv2025

Decoding the Molecular Language of Proteins with Evola

Proteins, natures intricate molecular machines, are the products of billions of years of evolution and play fundamental roles in sustaining life. Yet, deciphering their molecular language--understanding how sequences and structures encode biological functions--remains a cornerstone challenge. Here, we introduce Evolla, an interactive protein-language model designed to transcend static classification by interpreting protein function through natural language queries. Trained on 546 million protein-text pairs and refined via Direct Preference Optimization, Evolla couples high-dimensional molecular representations with generative semantic decoding. Benchmarking establishes Evollas superiority over general large language models in functional inference, demonstrates zero-shot performance parity with the state-of-the-art supervised model, and exposes remote functional relationships invisible to conventional alignment. We validate Evolla through two distinct applications: identifying candidate eukaryotic signature proteins in Asgard archaea, with functional Vps4 homologs validated via yeast complementation; and interactively discovering a novel deep-sea polyethylene terephthalate (PET) hydrolase, PsPETase, confirmed to degrade plastic films. These results position Evolla not merely as a predictor, but as a generative engine capable of complex hypothesis formulation, shifting the paradigm from static annotation to interactive, actionable discovery. The Evolla online service is available at http://www.chat-protein.com/.

bioinformatics↗