Biology subjects

He, L.

Publications and source records attributed to He, L..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Temporal Mapping of Radiation-Induced Neural Injury and Mitigation in Human Cortical Organoids

BackgroundRadiation therapy is a standard-of-care oncological treatment for central nervous system (CNS) malignancies. However, as survival outcomes improve, radiation-induced injury to normal brain tissue has increased in clinical significance. CNS radiation injury is a delayed, multifactorial process characterized by impaired neurogenesis, reactive gliosis, and persistent functional deficits. Mechanistic exploration and development of effective radiation mitigators have been limited by the lack of scalable, human-relevant models. MethodsMature human iPSC-derived cortical organoids were exposed to single-dose or clinically relevant fractionated radiation (5 x 2 Gy). DNA damage, apoptosis, and growth dynamics were assessed longitudinally. Structural organization, synaptic integrity, and neuroinflammatory responses were evaluated by immunofluorescence and real-time PCR. Transcriptomic profiling was performed at 72 hours and 2 weeks after fractionated radiation to capture acute and delayed effects. Two candidate radiation mitigators, NSPP and amisulpride, were tested for their therapeutic effects within the organoid system. ResultsCortical organoids exhibited partial recovery following single doses up to 4 Gy or fractioned irradiation. Transcriptomic analyses revealed that radiation not only reduced overall cell viability but also reshaped lineage trajectories, characterized by depletion of neural stem/progenitor populations, loss of neuronal identity, enhanced gliogenesis, increased inflammatory cytokines, and disrupted cortical layering and synaptic integrity. Treatment with NSPP or amisulpride attenuated injury-associated transcriptional and structural alterations. ConclusionHuman cortical organoids recapitulate key features of radiation-induced neural injury, recovery, and therapeutic modulation, providing a robust, scalable, and human-relevant platform for studying CNS radiation biology and preclinical screening of candidate radiation mitigators. Key pointsO_LIHuman iPSC-derived cortical organoids enable study of human CNS radiation responses. C_LIO_LIOrganoids recover after single-dose and fractionated radiation relevant to clinical exposure. C_LIO_LIThe platform supports scalable, human-relevant testing of radiation mitigation strategies. C_LI

cell biology↗

bioRxiv2026

MERFISH 2.0, an ultra-sensitive single-cell spatial transcriptomics imaging chemistry across diverse tissue types

Spatial transcriptomics has emerged as a transformative approach for elucidating tissue architecture, cellular heterogeneity, and disease mechanisms by preserving the spatial context of gene expression in cells. Despite these advances, many spatial transcriptomic methods underperform in archival or clinically relevant specimens, particularly formalin-fixed, paraffin-embedded (FFPE) tissues, where RNA degradation and crosslinking hinder transcript detection. To address these challenges, we developed Multiplexed Error Robust Fluorescence In Situ Hybridization 2.0 (MERFISH 2.0), an optimized spatial transcriptomic imaging chemistry to enhance profiling of fragmented and highly crosslinked RNA. Across diverse human and mouse tissues preserved as fresh-frozen, fixed-frozen, and FFPE specimens, MERFISH 2.0 substantially increased transcript detection sensitivity by up to [~]8-fold relative to MERFISH 1.0 while preserving quantitative concordance (Pearson r [≥] 0.8 across tissues). In archived fresh-frozen human brain samples, MERFISH 2.0s enhanced sensitivity improved transcript recovery, enhanced cell type resolution and spatial analyses. In low quality archival FFPE human breast cancer specimen, MERFISH 2.0 revealed additional cell populations, novel cell clusters, refined tumor-immune architecture, and increased detection of gene-gene and cell-cell interactions relative to MERFISH 1.0, underscoring the impact of improved sensitivity on downstream spatial analysis. By substantially expanding robust transcript detection to degraded and archival samples, MERFISH 2.0 enables scalable, cohort-level spatial transcriptomic analysis across clinically relevant tissue collections.

genomics↗

bioRxiv2026

Fine-tuning STEAP1 protein expression and purification to preserve its conformation and function

Six-transmembrane Epithelial Antigen of the Prostate 1 (STEAP1) has emerged as a promising therapeutic target for prostate cancer. We have optimized the expression and purification conditions of human STEAP1 to maximize the production of its homotrimeric form, which is crucial for metal ion reduction and maintaining cellular redox balance. Proteins obtained from these optimized conditions were complexed with both heme and flavin-adenine dinucleotide (FAD), two cofactors that are fundamental to STEAP functionality, suggesting native folding and interactions of the protein. In addition, we compared the impact of stable and transient expression systems on the protein quality of STEAP1. We found that stable expression promoted heme incorporation, improved expression homogeneity, and ensured correct protein orientation on cell surfaces. Our findings present effective strategies for optimizing the recombinant production of STEAP1, with potential applicability to other STEAP family proteins to facilitate therapeutic discovery.

biochemistry↗

bioRxiv2026

Multiple redundant mechanisms account for the majority of gene silencing downstream of DNA methylation

DNA methylation is a conserved epigenetic modification crucial for silencing genes and transposable elements (TEs). However, the mechanisms that cause silencing remain unclear, partly because methyl reader protein mutants in both plants and animals show minimal transcriptional changes. To explore the possibility of redundancy among these silencing mechanisms, we generated combinatorial mutants of H1.1, H1.2, ADCP1, MOM1, MBD2, MBD5, and MBD6 lacking key methyl readers and related silencing pathways. We observed massive derepression of genes and TEs at DNA-methylated loci, showing that these pathways account for 73% of silencing compared to DNA methylation-free mutants. We also observed that immune response genes were upregulated, causing an imbalance between growth and defense. Loss of downstream silencing pathways further disrupted 3D genome organization, leading to increased euchromatin-heterochromatin interactions. These findings highlight the cooperative action of multiple downstream mechanisms in DNA methylation-mediated silencing and genome organization.

molecular biology↗

bioRxiv2026

Cell type-resolved proteomics reveals intra- and intercellular signalingin Alzheimers disease

Alzheimers disease (AD) arises from pathological interactions among diverse brain cell types, but cell-specific proteomic changes remain underexplored. Here, we present deep proteomic profiling of sorted or proximity-labeled brain cells from AD mouse models (5xFAD and AppNL-G-F) at multiple ages, quantifying 13,411 proteins in microglia (three subtypes), astrocytes, oligodendrocyte precursor cells, and neurons. We identified 3,028 differentially abundant proteins across these cell types, the majority of which were not detected in bulk proteomic datasets, and constructed cell type-specific networks to define functional modules and hub proteins. Comparison with transcriptomic data revealed that [~]30% of proteomic changes are RNA-independent. Further analyses uncovered cross-cell type signaling proteins conserved in human AD brains, such as pleiotrophin (Ptn), which is transcriptionally enriched in astrocytes but accumulates in microglia. Importantly, recombinant PTN directly activates induced microglia-like (iMG) human cells. Thus, these findings provide a comprehensive cell type-resolved proteomic atlas of AD models, highlighting novel intra- and intercellular signaling events. HighlightsO_LIA high-resolution cell type-resolved proteomic atlas of Alzheimers disease mouse models C_LIO_LI[~]3,000 cell type-specific protein alterations identified beyond bulk tissue analyses C_LIO_LIProteomic profiling of microglial subtypes reveals subtype-specific changes in Alzheimers disease C_LIO_LIAstrocyte-microglia signaling is highlighted and validated through PTN-mediated interactions C_LI

neuroscience↗

bioRxiv2026

Dysregulation of xenobiotic metabolism and mitochondrial dysfunction exacerbate acetaminophen-induced hepatotoxicity in human antigen R-deficient male mice

Acetaminophen (APAP) overdose is a leading cause of acute liver failure worldwide. The RNA-binding protein Human antigen R (HuR) is a multifunctional post-transcriptional regulator that plays a pivotal role in cellular stress responses, including those triggered by APAP toxicity. This study investigated the mechanisms by which HuR protects against APAP-induced hepatotoxicity in male mice. Hepatocyte-specific HuR-deficient (HuRHep-/-) male mice on a C57BL/6N background and wild-type (WT) littermates were treated with 200 mg/kg APAP, and liver tissues were collected at 2, 6, and 24 hours post-treatment. APAP administration increased hepatic HuR mRNA expression and induced HuR cleavage and the formation of a higher-molecular weight HuR-immunoreactive band, with the latter two correlating with injury severity. Compared with WT controls, HuRHep-/- mice exhibited markedly increased susceptibility to hepatotoxicity at both 2 and 6 hours. Metabolite profiling revealed altered APAP metabolism and reduced glutathione S-transferase (Gst) expression in HuRHep-/- livers, consistent with impaired APAP detoxification and increased APAP-protein adduct formation. Fourier-transform infrared (FTIR) spectroscopy further identified early biochemical differences between WT and HuRHep-/- livers as early as 2 hours after APAP exposure. Additionally, HuR deficiency resulted in pronounced mitochondrial structural abnormalities and dysfunction at 2 and 6 hours, accompanied by reduced expression of the mitochondrial fission and fusion proteins Drp1 and Mfn2, increased mitochondrial protein release, and enhanced hepatocyte death. Although pro-inflammatory cytokine levels were elevated in HuRHep-/- mice relative to WT controls at 24 hours, hepatocyte proliferation was similarly blunted in both genotypes, consistent with severe liver injury and delayed recovery. Collectively, these findings identify hepatocyte HuR as a critical regulator of xenobiotic metabolism and mitochondrial integrity and establish its essential role in early protection against APAP-induced hepatotoxicity in male mice.

pharmacology and toxicology↗

bioRxiv2025

Comparative metagenomics using pan-metagenomics graphs

Identifying microbial genomic factors underlying human phenotypes is a key goal of microbiome research. Sequence graphs are a highly effective tool for genome comparisons because they enable high-resolution de novo analyses that capture and contextualize complex genomic variation. However, applying sequence graphs to complex microbial communities remains challenging due to the scale and complexity of metagenomic data. Existing multi-sample sequence graphs used in these settings are highly complex, computationally expensive, less accurate than single-sample alternatives, and often involve arbitrary coarse-graining. Here, we present copangraph, a multi-sample sequence-graph-based analysis framework for comprehensive comparisons of genomic variation across metagenomes. Copangraph uses a novel homology-based graph, which provides both non-arbitrary, evolutionary-motivated grouping of sequences into the same node as well as flexibility in the scale of variation represented by the graph. Its construction relies on hybrid coassembly, a new coassembly approach in which single-sample graphs are first constructed separately and are then merged to create a multi-sample graph. We also present an algorithm that uses paired-end reads to improve detection of contiguous genomic regions, increasing accuracy. Our results demonstrate that copangraph captures sequence and variant information more accurately than alternative methods, provides graphs that are more suitable for comparative analysis than de Bruijn graphs, and is computationally tractable. We show that copangraph reflects meaningful metagenomic variation across diverse scenarios. Importantly, it enables significantly better performance than other metagenomic representations when predicting the gut colonization trajectories of Vancomycin-resistant Enterococcus. Our results underscore the value of our multi-sample, graph-based framework for comparative metagenomic analyses.

bioinformatics↗

bioRxiv2025

Dissecting mammalian cortical circuit development at single-cell resolution using inducible barcoded rabies virus

Highly organized circuits of connected neurons enable diverse brain functions. Improper development of these circuits is associated with neurodevelopmental disorders, and understanding how circuits are formed is crucial for unraveling the mechanisms of these diseases. We currently have an incomplete picture of how specific brain circuits develop and how they are affected in disease, because we lack methods to study them at scale and with single-cell resolution. Monosynaptic rabies tracing is the gold standard method to study circuit architecture. However, it suffers from cellular toxicity, low throughput, lack of control over the timing of labeling, and the inability to access the molecular profiles of individual neurons. To address these issues, we developed an inducible barcoded rabies virus (ibRV) to enable temporal-controlled labeling of synaptic circuits followed by high-throughput single-cell genomics readout. ibRV allows for dissecting neuronal circuit changes over time at single-cell and spatial resolution. We applied ibRV to study the development of specific mouse cortical circuits during late prenatal and postnatal life using single-cell genomics and unbiased spatial transcriptomics as readouts. We characterized and quantified developmental connectivity patterns and molecular cascades that underlie their formation. Additionally, we constructed functional in silico circuit models that enable interrogation of circuit function and dysfunction at specific developmental stages. Our study provides novel tools for circuit analysis and can provide new insights into the mechanisms of mammalian brain development.

neuroscience↗

bioRxiv2025

The conserved bridging domain on HCV E1E2 glycoprotein complex is targeted by neutralizing antibodies from diverse lineages

The induction of potent and cross-reactive neutralizing antibody (nAb) responses remains a challenge in vaccine development against antigenically diverse viruses such as hepatitis C virus (HCV). The HCV E1E2 glycoprotein complex contains two major neutralizing sites: the neutralizing face (NF) and the less explored bridging domain (BD). Here, we characterized 25 BD-targeting nAbs isolated from infection or immunization. These antibodies arise from diverse B cell lineages but share convergent CDRH3 features. Epitope mapping by alanine scanning and negative-stain electron microscopy revealed overlapping epitopes on BD spanning antigenic regions AR4 and AR5, with variable back layer engagement. The crystal structure of a non-human primate BD nAb RM3-26 in complex with E2 uncovered a back layer-directed recognition mode analogous to that of the human nAb hcab40. Together, BD- and NF-directed nAbs exhibited additivity in their neutralization, highlighting BD as a conserved site of vulnerability on HCV and a valuable target for rational vaccine design.

immunology↗

bioRxiv2025

Circuit-specific gene editing for precision modulation of neuronal activity with CRISPR-rabies virus

CRISPR gene editing has revolutionized our ability to study and manipulate specific genes, enabling novel insights into gene function and potential therapies for brain disorders. Recent advances in cell-type-specific regulatory elements and viral delivery systems have made precise in vivo gene editing possible. However, neurons with similar molecular profiles can belong to different circuits, complicating efforts to manipulate circuit function and behavior. To address this, we developed CRISPR-rabies virus (CRV), which leverages the trans-synaptic spread of rabies virus to enable gene editing within anatomically defined neural circuits. By pairing CRV with cell type-specific Cas9 expression, we achieved targeted gene modifications in specific circuits. We demonstrate that CRV can modulate sodium and potassium channel expression in parvalbumin interneurons, thereby effectively regulating synaptic transmission of pyramidal neurons in the CA3 region of the hippocampus. Its compatibility with 3'-capture single-cell RNA-seq allows simultaneous circuit perturbation and molecular profiling. In summary, CRV allows precise circuit-level gene modulation, providing a platform for studying gene function in neural circuits and developing novel gene therapies for brain disorders.

neuroscience↗

bioRxiv2025

Single-component self-assembling protein nanoparticles displaying stabilized prefusion-closed hemagglutinin trimers for influenza vaccine development

Current influenza vaccines primarily target hemagglutinin (HA), the major surface glycoprotein and principal determinant of neutralizing antibody (NAb) responses. However, antigenic drift and shift, together with HAs intrinsic metastability and low-pH sensitivity, pose major challenges to the development of broadly protective influenza vaccines. Here, we stabilize HA in the prefusion-closed conformation through rationally selected amino acid substitutions. One approach targets a conserved residue across multiple influenza A subtypes (H1, H3, H5, and H7) and both influenza B lineages, providing a unified and broadly applicable framework for HA stabilization to support vaccine development. Using H1 and H3 as test cases, stabilized HA trimers were displayed on 24- and 60-mer single-component self-assembling protein nanoparticles (SApNPs) to enhance lymph node trafficking and immunogenicity. Compared with soluble trimers, HA-presenting SApNPs exhibited prolonged retention in lymph node follicles and elicited robust germinal center (GC) responses, key hallmarks of effective virus-like particle (VLP) vaccines. In mice, these SApNPs induced strong humoral immunity and conferred protection against homologous viral challenge. Furthermore, glycan engineering to enrich oligomannose content augments vaccine-induced NAb responses. Together, these findings provide mechanistic insights and establish design principles for next-generation HA-based influenza vaccines targeting both seasonal and pandemic strains. ONE-SENTENCE SUMMARYRational HA design and nanoparticle display guide next-generation strategies for influenza vaccine development

microbiology↗

bioRxiv2025

FlexRibbon: Joint Sequence and Structure Pretraining for Protein Modeling

AO_SCPLOWBSTRACTC_SCPLOWProtein foundation models have advanced rapidly, with most approaches falling into two dominant paradigms. Sequence-based language models (e.g., ESM-2) capture sequence semantics at scale, and a number of recent works incorporate structural signals into sequence encoders. MSA-based predictors (e.g., AlphaFold 2/3) achieve accurate folding by exploiting evolutionary couplings, but their reliance on homologous sequences makes them less reliable in highly mutated or alignment-sparse regimes. We present FlexRibbon{ddagger}, a pretrained protein model that jointly learns from amino acid sequences and three-dimensional structures. Our pretraining strategy combines masked language modeling with diffusion-based denoising, enabling bidirectional sequence-structure learning without requiring MSAs. Trained on both experimentally resolved structures and AlphaFold 2 predictions, FlexRibbon captures global folds as well as flexible conformations critical for biological function. Evaluated across diverse tasks spanning interface design, intermolecular interaction prediction, and protein function prediction, FlexRibbon establishes new state-of-the-art performance on 12 different tasks, with particularly strong gains in mutation-rich settings where MSA-based methods often struggle.

molecular biology↗

bioRxiv2025

Development of antibody-drug conjugates targeting L1CAM to treat metastatic cancer

Effective treatment for metastatic cancer has remained elusive due to the persistence of drug-resistant metastasis stem cells (MetSCs) that drive relapse. MetSCs are tumor cell subpopulations enriched for their ability to reinitiate and sustain metastatic growth, displaying phenotypic plasticity and resistance to chemotherapy. These cells express the L1 cell adhesion molecule (L1CAM), a transmembrane protein detected in numerous human solid tumor types and at multiple disseminated organ sites. As a selective surface marker of MetSCs, L1CAM is a promising candidate for molecularly targeted drugs aimed at eliminating metastases, yet strategies to date have not achieved clinical success. Here, we develop antibody-drug conjugates to deliver highly toxic PNU-159682 payloads to L1CAM-expressing cells. We report the generation of monoclonal antibodies (mAb) with high binding affinity, specificity and selectivity for the human L1CAM extracellular domain. Optimized L1CAM-targeting mAbs were conjugated to PNU-159682 to generate ADC variants with both cleavable and non-cleavable linkers, with an average drug-antibody-ratio (DAR) of four. ADCs derived from three antibodies targeting various epitopes of the L1CAM extracellular portion potently killed cells exhibiting varying levels of surface L1CAM expression. L1CAM ADCs given as monotherapy resulted in robust tumor control and extended survival in mice harboring subcutaneous L1CAM+ xenografts or L1CAM+ lung metastases from triple-negative basal breast cancer and lung adenocarcinoma. Safety analyses with mouse cross-reactive antibodies indicate a feasible therapeutic window. Our findings offer strong proof-of-concept to support the preclinical development of these novel L1CAM ADCs as therapeutic agents for advanced solid tumors.

cancer biology↗

bioRxiv2025

Hepatic cytochrome P450 endoplasmic reticulum-associated degradation (ERAD): Topological determinants and cellular partnerships that dictate the preferential P450 proteolytic sorting into macroautophagy rather than UPS.

Many N-terminally endoplasmic reticulum (ER)-anchored cytochrome P450 proteins (P450s) turn over proteolytically via ER-associated degradation (ERAD), others via ER-to-lysosomal-associated degradation (ERLAD), and yet others via both pathways. What precisely dictates their differential proteolytic turnover is unknown. Herein, we employed rabbit liver CYPs 1A1 and 1A2, which reportedly reside in liquid-disorded (ld)- and detergent-resistant, liquid-ordered (lo)-ER-microdomains, respectively, governed by their specific N-terminal (NT) signal-anchor (SA) subdomains. We now report that this precise SA-dependent ER-topology not only determines the proclivity of CYP1A1 towards ERAD and CYP1A2 towards ERLAD, but also their differential lifespans. We further document that the detergent-resistant lo-ER-membranes (DRMs) are morphologically quite similar to mitochondria-associated ER-membranes (MAMs), documented cellular platforms for autophagic-initiation complexes. DRMs and MAMs, composed of saturated fatty-acids, glycosphingolipids and cholesterol, harbor many common morphological markers including the ER-specific prohibitin, erlin-1. Herein employing SURF, a split fluorogenic bifunctional complementation assay, we show that intracellularly, erlin-1 and CYP1A2 interact closely via their ER NT-SAs. siRNA-knockdown (KD) of erlin-1 in HepG2-cells, not only relocated CYP1A2 from DRMs to non-DRMs, but also impaired its ERLAD, resulting in insoluble cellular CYP1A2 aggregates. Upon erlin-1 KD, CYP1A2 ERLAD could be rescued by co-expression of a siRNA-resistant intact erlin-1 or just its NT-1-30 residue SA-domain. Our findings are the first to reveal that the CYP1A2 lifespan and preferential proclivity towards ERLAD is determined by its close association with erlin-1 within DRMs/MAMs. As proof of concept, we document that the ERLAD-proclivity of CYP2B1 is also similarly dependent upon erlin-1-DRM-association. SIGNIFICANCE STATEMENTThe endoplasmic reticulum (ER)-anchored cytochromes P450 (P450s) incur ER-associated degradation (ERAD) and/or ER-to-lysosomal-associated degradation (ERLAD). What determines their preferential proteolytic turnover is unknown. Here, employing P450s CYP1A1 and CYP1A2 that reside in their N-terminal signal anchor-determined liquid-disordered (ld)- and detergent-resistant, liquid-ordered (lo)-ER-microdomains, respectively, we documented that in HepG2-cells these ER-microdomains determine the CYP1A proteolytic preferences for ERAD vs ERLAD as well as their lifespans. More importantly, we discovered that its intimate interaction with the ER-specific prohibitin erlin-1 colocalized in these lo-ER-microdomains, specifically dictates CYP1A2s ERLAD-preference. Accordingly, siRNA-elicited erlin-1-knockdown disrupted CYP1A2-ERLAD, which was rescued upon coexpression of either a siRNA-resistant erlin-1 or just its N-terminal 1-30 residues. As proof of concept, we document similar characteristics for CYP2B1, another ERLAD-targeted P450.

cell biology↗

bioRxiv2025

Deciphering acquired resistance mechanisms to sustained auxin-inducible protein degradation in cells and mice

Targeted protein degradation is a favorable strategy for studying the immediate downstream effects of protein loss-of-function. An appealing platform among these technologies is the auxin-inducible degron (AID) system. Although this system has been applied extensively to cell and animal models, degradation resistance to long-term auxin treatment has not been studied. With the advent of the new AID2 system, cellular toxicity due to the high concentrations of auxin required in the original AID1 system is no longer a concern, making it possible to study protein degradation over extended periods. In this study, we derived multiple miniAID-tagged knock-in human cell lines and a Ctcf-miniAID knock-in mouse strain to investigate mechanisms of degradation resistance. We revealed four independent resistance mechanisms, including a nonsense mutation in the CTCF coding sequence that removed the miniAID peptide, a missense point mutation in the miniAID coding region that disrupted ubiquitin complex targeting, and silencing of the OsTIR1 adaptor protein. Resistance to auxin degradation was also acquired in mouse primary CtcfminiAID/miniAID knock-in B-ALL cells through missense mutations of the OsTIR1(F74G) protein in vivo and ex vivo. In summary, our innovative study expands our understanding of the AID system and cautions careful consideration of design for future applications in mammalian system.

cell biology↗

bioRxiv2025

Illuminating the Virosphere's Dark Matter using Hierarchical Deep Learning

Systematic discovery of novel viruses is essential for pandemic preparedness, understanding tumor-associated viruses, developing viral delivery systems, and advancing biomedical applications. Yet, the majority of sequences in metagenomic datasets lack close relatives in existing references, representing a vast viral "dark matter" whose biology and evolution remain largely unknown. The central task is threefold: 1) to determine whether a genome is viral or non-viral, 2) to correctly assign viral genomes to known lineages when possible, and, critically, 3) to recognize when no existing lineage applies and thereby identify candidates for entirely novel viral groups. Existing approaches, which depend on sequence homology or narrow markers, struggle to capture this uncharted viral space. Here we present DeepVirus, a hierarchical transformer-based framework that models viral genomes as structured sequences of protein-coding genes. By combining protein-level embeddings from a foundation model with genome-aware representations, DeepVirus not only achieves accurate classification across deep taxonomic hierarchies, but also extends beyond conventional classification to detect and organize candidate novel viral lineages through open-set recognition. Applied to large-scale metagenomic resources, DeepVirus uncovered extensive viral diversity, including previously uncharacterized RNA-dependent RNA polymerases (RdRps), thereby expanding the known evolutionary space of RNA viruses. DeepVirus integrates deep learning with genome-aware open-set discovery to illuminate viral dark matter, providing a foundation for systematic viral taxonomy and advancing exploration of the global virosphere, with broad implications for safeguarding human health.

bioinformatics↗

bioRxiv2025

Rat somatic genome editing enables ER+ breast cancer modeling

Genetically engineered mouse models have advanced cancer research but often fail to capture key features of certain human tumors. Rats, with distinct physiology and tumor biology, offer a powerful alternative, yet their use has been constrained by technical barriers to genome editing. Here, we report efficient somatic genome editing in rats, enabling both Indel and substitution mutations. We then apply this approach to model estrogen receptor (ER)-positive breast cancer, which accounts for [~]70% of human cases but remains poorly represented in mice. The resulting rat tumors reproduce hallmarks of human ER+ breast cancer, including ductal histology, hormone responsiveness, and immune-microenvironmental features. By contrast, identical genetic alterations in mice failed to yield ER+ tumors, underscoring critical species differences in tumorigenesis. Together, this work establishes a versatile platform for rapid generation of clinically relevant rat tumor models, opening new avenues to dissect tumor biology, therapeutic response, and immune interactions in previously inaccessible cancer subtypes.

cancer biology↗

bioRxiv2025

Allosteric Disordering of eIF2B Regulates the Integrated Stress Response

The ternary complex (TC), composed of translation initiation factor eIF2, GTP, and initiator methionyl tRNA, delivers the first amino acid to the ribosome to initiate protein synthesis. The activity of the decameric eukaryotic initiation factor 2B complex (eIF2B) initiates TC assembly by catalyzing GDP to GTP exchange on eIF2, thereby setting the TC levels in the cell. Stress-induced phosphorylation converts eIF2 from the substrate of the GDP/GTP exchange reaction into an inhibitor (eIF2-P) of eIF2B. This conversion reduces the cells TC levels and induces the widespread reprogramming of translation known as the Integrated Stress Response (ISR). Here, we chart an allosteric axis running through eIF2B, revealing the importance of a protrusive -helix in its {beta}-subunit, the latch-helix, that locks onto the -subunit to induce eIF2B activity. eIF2-P binding unhooks the latch-helix, opening eIF2B, which inhibits its GDP/GTP exchange activity. Distinct viral proteins have convergently evolved to bind to eIF2B and stabilize the latch-helix-bound active state. Using these insights, we generated ISR-ACTivating compounds, ISRACTs, that stabilize eIF2B in its inhibited, unlatched state. Our study thus highlights how state-transitions in eIF2B are regulated via long-range allostery.

biochemistry↗