Biology subjects

Zhou, F.

Publications and source records attributed to Zhou, F..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Intranasal immunization with live-attenuated RSV-vectored SARS-CoV-2 vaccines elicits antigen-specific systemic and mucosal immunity and protects against viral challenge and natural infection

The emergence of new SARS-CoV-2 variants and breakthrough infections underscores the need for next-generation vaccines capable of protecting from natural infection and/or preventing virus transmission to others. Intranasal vaccination offers a promising approach by eliciting local immune responses in the nasal mucosa, the primary site of infection and reservoir for transmissible virus. We evaluated two live-attenuated, respiratory syncytial virus vectored vaccines in which the RSV F and G surface glycoproteins were replaced with a chimeric SARS-CoV-2 Spike protein from either the ancestral USA/WA-1/2020 strain (MV-014-212) or the Delta variant (MV-014-212-delta). A single intranasal dose of either vaccine elicited systemic and mucosal immunity in K18-hACE2 mice, including serum neutralizing antibodies, Spike-specific memory B cells and plasmablasts, and Spike-specific CD8 lung-resident memory T cells. Although MV-014-212-delta vaccination provided the best protection against Delta variant virus challenge, both vaccines decreased viral loads in nasal discharge, lung and brain, and reduced weight loss and mortality. In naturally acquired infection studies, vaccinated hamsters exposed to infected cagemates exhibited minimal weight loss, limited viral replication within the nasal mucosa, and attenuated lung pathology. Therefore, intranasal RSV-vectored vaccines can elicit broad protective respiratory immunity, suggesting that this platform could be leveraged for other respiratory pathogens.

immunology↗

bioRxiv2026

Mechanistic insight into the phosphorylation of ERK by MEK

The RAS-RAF-MEK-ERK cascade regulates critical cellular processes such as cell proliferation and differentiation, with its dysregulation driving over 30% of human cancers. However, the active state of MEK and molecular mechanisms of ERK phosphorylation remain unclear. Here, we report the cryo-EM structures of phosphorylated MEK1 (pMEK1) bound to unphosphorylated and monophosphorylated ERK1. These structures reveal that pMEK1 interacts with ERK1 via three interfaces: first between MEK1 N-terminal peptide and ERK1 D-site recruitment site (DRS), second between MEK1 C-lobe and ERK1 F-site recruitment site (FRS), and third between MEK1 activation loop and ERK1 activation loop. Notably, we identify an unexpected phosphorylation mechanism: pMEK1 catalyzes ERK1 T202 phosphorylation through phosphate transfer from ERK1 Y204. In addition, pMEK1 exhibits phosphatase activity, catalyzing the dephosphorylation of ERK1 Y204. These findings allow us to delineate the catalytic cycle of MEK-catalyzed ERK phosphorylation and provide insights for targeting this oncogenic pathway.

molecular biology↗

bioRxiv2026

LysinFusion: Integrating Multi-Feature Encoding and Hybrid CNN-Transformer Architecture for Phage Lysin Prediction

The escalating antimicrobial resistance crisis has intensified the urgent need for alternative antibacterial agents. Phage lysins exhibit potent bactericidal activity with low resistance potential, yet their large-scale discovery from rapidly expanding genomic resources remains limited, as existing computational methods often rely on sequence homology and few reproducible, independently validated, and practically deployable prediction frameworks are currently available. We present LysinFusion, a reproducible deep learning framework that integrates heterogeneous sequence features via a hybrid CNN-Transformer architecture for accurate lysin identification. Trained on a curated, de-redundant corpus (PHROG + inphared) and validated on 148 experimentally confirmed UniProt proteins, LysinFusion achieves an accuracy of 0.81, an AUC of 0.89, and an MCC of 0.62, outperforming the state-of-the-art DeepMineLys by up to 52.3% across metrics while reducing false positives by 64% (12 vs. 33). Ablation studies confirm that both CNN and Transformer modules are individually essential and that serial processing outperforms parallel alternatives. Model interpretability via occlusion and LIME aligns with established lysin biology, with attention concentrating on the N-terminal catalytic domain and decision boundaries reflecting characteristic charge-composition thresholds documented in Gram-negative lysin C-terminal regions. The framework, including all source code, curated datasets, and an accompanying web server, is freely available at https://github.com/sinuo560/LysinFusion.

bioinformatics↗

bioRxiv2026

Membrane localisation and checkpoint blockade enhance xenoantigen delivery to redirect pre-existing immunity against tumours

Cancer immunotherapies often rely on the recognition of tumour antigens, which strongly limits their efficacy upon heterogeneous antigen expression or downregulation. A strategy to overcome this limitation is to redirect pre-existing antiviral immunity against tumours through the delivery of xenoantigens. While many studies have addressed this by repurposing licensed vaccines, we here investigated the underlying mechanisms of immune redirection via the delivery of non-adjuvanted xenoantigen proteins, thereby avoiding confounding adjuvant- or pathogen-specific effects. Using B16F10 melanoma cells engineered to express the model antigen OVA, we found that tumour rejection in pre-immunised mice depends on the subcellular localisation of the xenoantigen, with membrane-bound antigens eliciting stronger rejection than dose-matched soluble cytoplasmic antigens. Enhanced rejection of membrane-bound OVA expressing tumours was associated with stronger CD4+ T cell responses. In addition, pre-immunisation also increased recruitment of inflammatory monocytes and macrophages at the tumour site. To translate this concept therapeutically, we developed a membrane-targeting OVA fusion protein which, upon intratumoural delivery, redirected pre-existing immunity and made tumours responsive to anti-PD-1 therapy. Importantly, these findings were further validated using the clinically relevant varicella zoster virus (VZV) glycoprotein E (gE) antigen and the licensed varicella vaccine Varivax. Our approach provides a mechanistic and translational perspective for treating poorly immunogenic tumours, leveraging widespread pathogen-specific immune memory in combination with anti-PD1 therapy in cancer patients.

cancer biology↗

bioRxiv2026

Studies of mice with a large deletion of the ARPKD-associated Pkhd1 locus likely explain its GWAS association with glaucoma in humans

PKHD1, the gene primarily mutated in human autosomal recessive polycystic kidney disease, is one of the top 20 genes associated with primary open angle glaucoma (POAG) and associated endophenotypes in Genome-Wide Association Studies. Here, we show that Pkhd1del3-67/del3-67 mutant mice develop congenital glaucoma due to anterior segment dysgenesis. Using a combination of genetic, epigenetic, bioinformatics and mouse developmental biology approaches, we show that Pkhd1del3-67/del3-67 mice lack Tfap2b and AP-2{beta} expression in a subset of periocular mesenchymal cells at E13.5 and its derivatives. Our data suggest that the Pkhd1del3-67 deletion disrupts features of the Pkhd1-Tfap2b genomic architecture essential for Tfap2b cell-specific activities. Consistent with this model, Pkhd1del3-67/+;Tfap2bko/+trans-heterozygotes lack Tfap2b and AP-2{beta} in relevant cell-types and have similar eye abnormalities as neural crest cell-specific Tfap2bko mutants. These findings provide a likely causal explanation for how SNPs associated with PKHD1 are functionally linked to POAG and add insight into understanding the complexity of disease-causing SNP associations and gene regulatory mechanisms.

genetics↗

bioRxiv2026

Neural Dynamics of Automatic Speech Production

Speech is a defining human behavior, and this ability depends critically on speech motor cortex. While the ventral precentral and postcentral gyri are classically regarded as chiefly articulatory and somatosensory regions, a growing body of literature challenges this simplification. Most prior research, however, has examined cued or structured speech production tasks, neglecting the automatic, overlearned speech commonly utilized in clinical assessment. Consequently, the neural dynamics and precise timing of cortical recruitment during automatic speech remain poorly understood. Here, we present intracranial electrocorticography (ECoG) recordings from the left perisylvian cortex in participants performing automatic speech such as counting and recitation of overlearned sequences. We investigate neural dynamics using encoding (multivariate temporal response function) and decoding (deep neural network speech synthesis) models. We show that automatic speech engages a distributed network across superior temporal, precentral, and post-central cortices, characterized by attenuated pre-articulatory activity and weaker frontal encoding. Furthermore, two complementary decoding strategies reveal that speech motor cortex represents a mixture of feedforward and feedback signals, with a subset of sites exhibiting exclusively feed-forward dynamics. These results delineate the spatiotemporal cortical organization of automatic speech and establish that the speech motor cortex supports more complex dynamics than purely feedforward control.

neuroscience↗

bioRxiv2026

Divergent phenotypic and functional roles of human T follicular helper cells from infancy to adulthood

Antibody responses to T-dependent antigens are suboptimal in young children, yet the evolution of T follicular helper cell (Tfh) function across the human lifespan remains poorly defined. Using human tonsils, a physiologically relevant and abundant source of Tfh, we investigated age-associated differences in their repertoire and functional programs. Pediatric tonsils were enriched for cytokine-expressing Tfh subsets with increased clonal diversity and phenotypic plasticity. However, in response to influenza antigens, they exhibited reduced Th1 polarization, diminished IL-21 production, and limited B cell help. Across ages, high neutralizing flu antibody responses were associated with robust Tfh1 activation, which was ICOS dependent in adults but not in children. Interestingly, Tfh depletion strategies revealed enhanced Tfh differentiation from distinct precursors in pediatric donors, yet antibody responses during early life were less reliant on Tfh help. Together, these findings define developmentally programmed differences in Tfh differentiation and function with implications for pediatric vaccine design.

immunology↗

bioRxiv2026

Terminally Differentiated Influenza-Specific Effector Memory B Cells Circulate after Live Attenuated Influenza Vaccination

Live attenuated influenza vaccination (LAIV) is the only FDA approved mucosal vaccine. Easily assayed, circulating correlates of protection after LAIV are lacking. Using fluorochrome labeled hemagglutinin (HA) antigen, we previously identified a subset of HA-specific (HA+) IgDneg memory B cells that circulate after inactivated intramuscular vaccination (IIV), express the master transcriptional regulator, T-bet, as well as effector memory genes and predict durable antibody (Ab) responses to IIV. Here we profile the circulating HA+ IgDneg memory B cell response in a cohort of immunized patients who seroconvert after LAIV to identify which, if any, circulating HA+ B cells predict antibody responses after LAIV. Although we report LAIV elicits circulating T-bet+ HA+ IgDneg B cells that are phenotypically similar to those we described after IIV, we find no correlation between the magnitude of these cells and systemic HA-IgG responses after LAIV. Supervised and unsupervised analyses demonstrate that unlike IIV, LAIV preferentially elicits circulating HA+ IgDneg B cells that co-express TBX21 and the terminal effector cell gene, Zeb2. Consistent with their terminal differentiation status, LAIV-elicited T-bet+ cells cannot be recalled as short-lived antibody-secreting cells (ASCs) after systemic or mucosal antigen re-challenge. We conclude that the transcriptional profiles and functions of HA+ IgDneg B cells vary by influenza vaccine platform.

immunology↗

bioRxiv2026

Interface-Resolved Proteomics of Cell-Cell Membranes Reveals Early Spatial Polarity in a Vertebrate Embryo

Cell-cell membrane interfaces are central sites of adhesion, signaling, and polarity establishment, yet they have remained inaccessible to proteome-wide analysis as discrete analytical units. Here, we report an interface-resolved proteomics workflow that isolates intact intercellular membrane segments from single, identified blastomeres and quantitatively profiles their protein composition. Using a microdissection-enabled strategy combined with optimized mild-detergent extraction and high-sensitivity high-resolution mass spectrometry, we achieve deep coverage of low-input membrane samples, identifying [~]3,000 proteins per interface type, including over 100 annotated plasma-membrane proteins. Applying this approach to defined dorsal-dorsal, dorsal-ventral, and ventral-ventral cell-cell interfaces in a 16-cell chordate embryo model, Xenopus laevis, reveals reproducible, interface-specific proteomic signatures that distinguish neighboring membrane contacts along the primary body axis. Region-enriched proteins include regulators of membrane trafficking, signaling, cytoskeletal organization, and metabolic pathways linked to early dorsal-ventral patterning. These results demonstrate that intercellular membrane interfaces exhibit molecular polarity at early developmental stages and establish interface-resolved proteomics as a general strategy for mapping spatially organized biochemical activities at cell-cell contacts.

developmental biology↗

bioRxiv2025

Tibetan near-complete pangenome reveals complex variants underlying high-altitude adaptation

Genomic diversity in indigenous populations offers critical insights into human evolution and population-specific adaptation. Here, we generated 70 near-complete, fully phased genome assemblies from 35 high-altitude Tibetan trios and identified 4.55 million small variants and 63,031 structural variants (SVs) absent from the current global pangenome reference. Comparative analyses with a 595 globally diverse long-read genome dataset revealed 207 previously uncharacterized Tibetan-enriched SVs spanning 275 genes implicated in high-altitude physiological adaptation. Genotyping these SVs in 1,164 Tibetan and Han individuals with 88 physiological traits reveals five variants significantly associated with cardiopulmonary and hematological phenotypes central to hypoxia adaptation. We further map 2.45 Gb of archaic hominin sequences in Tibetans and uncover 18 previously unrecognized introgressed regions enriched in Tibetans with genes related to hematopoiesis and lung function. These regions harbor five Tibetan-enriched SVs, indicating that archaic introgression contributed SVs relevant to human adaptation. Together, these findings reveal substantial uncharacterized genomic diversity in Tibetans and highlight a previously underappreciated role of SVs and archaic SVs in shaping human evolution and high-altitude adaptation.

genomics↗

bioRxiv2025

Posterior Cortex Isolation Enhances Detection of Alpha Desynchronization During Sustained Attention

Electroencephalography (EEG) is an essential tool for assessing the neural activity behind mental fatigue, a factor that can influence both cognitive and physical performance. Mental fatigue influences alpha-band oscillations (8-12 Hz), reflecting cortical engagement and attention stability. In this study, EEG recordings from 109 participants in the Physionet open-source EEG Motor Movement/Imagery Dataset (EEGMMIDB) were analyzed to characterize alpha power changes during sustained attention. Spectral analysis was performed across early and late task blocks to quantify alpha desynchronization over time. Participants demonstrated a consistent decrease in alpha power ({Delta} = -0.076 {+/-} 0.019 log10 units; p = 0.0001), indicating desynchronization associated with sustained attentional demand. These findings show the applicability of open-source EEG datasets for research. Furthermore, these findings support the isolation of posterior activation as a marker of mental fatigue through alpha desynchronization. One sentence overviewAlpha desynchronization is a marker for mental fatigue in EEGs. This paper illustrates that isolating the posterior cortical lobes enhances the resolution and sensitivity of alpha band changes associated with sustained attention.

neuroscience↗

bioRxiv2025

Tumor cell-specific loss of GPX4 reprograms triacylglycerol metabolism to escape ferroptosis and impair antitumor immunity in NSCLC

Glutathione peroxidase 4 (GPX4) is a master regulator of ferroptosis, a process that has been proposed as a potential therapeutic strategy for cancer. Here we have unexpectedly found that inducible knockout of GPX4 in tumor cells significantly promotes non-small cell lung cancer (NSCLC) progression in the autochthonous KrasLSL-G12D/+Lkb1fl/fl (KL) and KrasLSL-G12D/+Tp53fl/fl (KP) mouse models, whereas inducible overexpression of GPX4 in tumor cells exerts the opposite effect. GPX4-deficient tumor cells evade ferroptosis by upregulating the expression of DGAT1/2 to promote the synthesis of triacylglycerol (TAG) and oxidized TAG (oxTAG) and the formation of lipid droplets in cells. In addition, GPX4-deficient tumor cells secrete TAG and oxTAG into the extracellular space to induce dysfunction of antitumor CD8+ T cells, thereby coordinating an immunoinhibitory tumor microenvironment (TME). Consistently, treatment with DGAT1/2 inhibitors or inducible overexpression of GPX4 in tumor cells significantly resensitizes tumor cells to ferroptosis and ignites the activation of T cells in the TME to inhibit NSCLC progression. These findings highlight a previously uncharacterized role of tumor cell-specific GPX4 in NSCLC progression and provide potential therapeutic strategies for NSCLC.

cell biology↗

bioRxiv2025

Dangling Ends of Third Strand and Duplex Drive Nucleic Acid Triplex Stabilization through Bimodal Association

Nucleic acid triplexes are crucial structural motifs in gene regulation and biotechnology, yet the kinetic principles governing their formation remain poorly understood. While a stability hierarchy of RNA*DNA-DNA > DNA*DNA-DNA > RNA*RNA-RNA, with no DNA*RNA-RNA triplex forming, is known, the kinetic roles of terminal residues remain poorly understood. Here, we employ bio-layer interferometry (BLI) and circular dichroism (CD) spectroscopy to demonstrate that dangling ends from both the third strand (triplex-forming oligonucleotide, TFO) and the duplex dramatically enhance triplex stability. Kinetic analysis reveals this stabilization is primarily driven by a marked increase in the association rate (k{square}{square}). Crucially, creating a single-base-pair dangling end at either terminus of the duplex enhanced triplex stability more effectively than blunt ends. For example, DNA TFO dTFO5 binding to d(HP5+TA) was enhanced compared to dHP5, and similarly RNA TFO rTFO5 binding to RNA duplex r(HP5+UA) and DNA duplex d(HP5+TA) showed stronger affinity and faster association than to blunt-ended rHP5 and dHP5. Interestingly, removal of a terminal base pair from the blunt-end duplex, generating a TFO dangling end, also enhances binding affinity and association rate. This indicates that both duplex and TFO dangling ends provide critical nucleation platforms, while blunt-ended terminal triples are dynamic and contribute minimally to stability. Thus, our work establishes that optimal triplex formation requires strategic optimization of both TFO and duplex terminal structures through a fundamental kinetic principle (bimodal nucleation). Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/686076v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1dc6950org.highwire.dtl.DTLVardef@1861387org.highwire.dtl.DTLVardef@16c24a5org.highwire.dtl.DTLVardef@da0bf0_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDangling ends at both third strand and duplex termini enhance triplex stability by accelerating association C_LIO_LITriplex formation can be nucleated from either end with a bimodal association mechanism C_LIO_LITerminal blunt-end base triples are dynamic and contribute minimally to stability compared to tailored overhangs C_LI

biophysics↗

bioRxiv2025

Lymphatics unload VEGFR3 in response to the endothelial stress upon VEGFR2 insufficiency

Vascular endothelial growth factor receptor 2 (VEGFR2) is a key target for regulating the endothelial cell lineage and angiogenesis. It is also expressed by lymphatic endothelial cells (LEC) while its participation in the process of lymphangiogenesis remains inadequately characterized. We show in this study that VEGFR2 is highly expressed in dermal initial lymphatic vessels and valves. The induced deletion of pan-endothelial Vegfr2 at the neonatal stage produced a potent suppression of dermal lymphatic growth, including the thinner lymphatic diameter, the decrease of LEC number and lymphatic valves. Mechanistically, the VEGFR2 insufficiency led to a dramatic decrease of lymphatic VEGFR3, a key regulator mediating signals for lymphatic growth and remodeling. The RNA sequencing analysis revealed that GO terms enriched for the downregulated genes included biological processes related to the EC development while pathways related to the hematopoiesis and immune responses were upregulated in the skin of Vegfr2 mutants compared with the littermate controls. This was further confirmed by the RNA-seq analysis of dermal tissues 48 hours after the endothelial Vegfr2 deletion. Consistently, an inhibitory effect on the dermal lymphatic growth was also observed by targeting Vegfr2 in PROX1+ cells, manifesting a similarly altered transcriptome signature. The alteration of lymphatic gene expression was further validated by the siRNA mediated knockdown of Vegfr2 in primary lymphatic endothelial cells, showing a transcriptional trend of LEC to hematopoietic transition. Findings from this study imply that VEGFR2 is required for the maintenance of endothelial identity and its insufficiency may trigger the alteration of lymphatic transcriptional programs to diminish the VEGFR3-mediated lymphangiogenesis.

developmental biology↗

bioRxiv2025

Mucosal delivery of influenza antigens using a replication deficient adenovirus supports broadly reactive antibody responses and heterologous viral immunity in the respiratory tract of animals

Systemically administered influenza vaccines provide strain-limited protection, while influenza infection of the respiratory epithelium supports development of lung resident memory B and T cells and more broadly reactive antibody responses. To test whether local antigen delivery is critical for establishing broad immunity, we directly compared respiratory tract and systemic delivery of influenza antigens to mice and hamsters using a replication-deficient adenovirus serotype 5 vector (Ad5[E1-,E2b-,E3-]). Both immunization routes elicited antibody responses in the lower respiratory tract and antigen-specific B and T cells in the draining lymph node. However, only intranasal immunization established lung-resident memory B and T cells, induced IgA responses in the upper respiratory tract directly at the site of viral entry and supported generation of IgA and IgG antibodies that bound antigenically drifted and distantly related influenza strains, including those of avian origin. Intranasal immunization accelerated viral clearance following heterologous virus challenge and was associated with limited pulmonary inflammation and fibrosis. Thus, intranasal immunization with the immunologically stealthy Ad5[E1-,E2b-,E3-] platform supports respiratory and systemic immunity to divergent influenza strains in the absence of overt lung immunopathology, suggesting that local antigen delivery may be key to development of more broadly protective "universal" flu vaccines.

immunology↗

bioRxiv2025

Inducing TRIB2 Targeted Protein Degradation to Reverse Chemoresistance in Acute Myeloid Leukemia

The myeloid oncogene TRIB2 is a key driver of acute myeloid leukaemia (AML) pathogenesis, promoting chemoresistance and blocking differentiation through ubiquitin-mediated degradation of the C/EBP transcription factor. Despite its stable and sometimes elevated expression across AML subtypes, TRIB2 remains a clinically-untargeted vulnerability. Here, we present a comprehensive investigation into TRIB2 degradation mechanisms using multimodal approaches, including CRISPR knockout, mutational protein stability, small molecule TRIB2 engagement and evaluation of a novel targeted protein degrader (TRIB2-PROTAC). We identify Afatinib, a multi-ERBB covalent inhibitor, as a rapid inducer of TRIB2 degradation, triggering AML cell death via an ERBB-independent pathway. Importantly, TRIB2 degradation synergized with cytarabine, the frontline AML chemotherapy, amplifying therapeutic efficacy. Mapping of TRIB2 ubiquitination sites revealed Lys-63 as critical for its own proteolytic turnover, and a Lys to Arg degradation-resistant mutant (KallR) conferred enhanced chemoresistance and increased leukaemic engraftment in vivo. CRISPR-mediated TRIB2 knockout validated an essential role in AML cell survival. Consistently, the novel TRIB2-PROTAC (compound 5K) achieved robust TRIB2 degradation and AML cell killing at low micromolar concentrations. These findings establish TRIB2 as a compelling therapeutic target in AML and demonstrate that leveraging the ubiquitin-proteasome system to degrade TRIB2 offers a promising strategy to overcome chemoresistance. This work provides strong preclinical rationale for the development of TRIB2-targeting therapies in AML.

cancer biology↗

bioRxiv2025

Pocket-based molecule generation with an SE(3)-equivariant language model leads to a potent and selective HPK1 inhibitor with in vivo efficacy

Deep learning shows promise in structure-based drug discovery, yet challenges persist in generating pharmacologically plausible molecules with valid 3D conformation and decent binding mode in the pocket. We introduce SE3-BiLingoMol, an SE(3)-equivariant Transformer for pocket-based 3D molecule generation, addressing two key limitations of existing language-model approaches. First, it uses Geometric Algebra Transformers for SE(3)-equivariant handling of continuous 3D coordinates. Second, a bidirectional attention mechanism mitigates conformational errors accumulated during autoregressive sampling. These innovations enable SE3-BiLingoMol to generate 2D drug-like, 3D geometrically valid molecules with superior binding modes. Validated on DUD-E dataset containing over 100 targets, the model achieved state-of-the-art performance in de novo design and optimization. We applied SE3-BiLingoMol to design potent and selective inhibitors for HPK1, a promising immunotherapy target. Through an iterative human-AI workflow, integrating AI generation with experimental validations (X-ray crystallography, bioassays), we identified Cmpd. 6. This novel tetracyclic compound demonstrates potent HPK1 inhibition, excellent cellular activity, favorable pharmacokinetics, and robust anti-tumor in vivo efficacy as monotherapy and with PD-1 blockade. Our work establishes a sophisticated generative AI framework for 3D molecule design and demonstrates its application in developing cancer immunotherapy. Highlights[bullet] SE(3)-Equivariant Language Model for Molecule Generation: We introduce a dual-channel SE(3)-equivariant language model that supports de novo molecule design and optimization, addressing key challenges in prior language model-based 3D molecule generation approaches. [bullet]Discovery of Potent HPK1 Inhibitors: Application of this model led to the discovery of highly selective HPK1 inhibitors with robust in vivo efficacy, resulting in a promising lead compound. [bullet]AI-Guided Rational Drug Development Paradigm: This work establishes a paradigm for AI-guided rational drug development, showcasing AI as a "co-pilot" that inspires drug designers with novel ideas in an "evidence-based context".

bioinformatics↗

bioRxiv2025

Evolutionary remodeling of non-canonical ORF translation in mammals

Non-canonical open reading frames (ncORFs) are pervasive within transcripts annotated as "non-coding" or "untranslated regions" of mRNAs, yet their landscape under normal physiological conditions remains to be fully resolved, particularly outside humans. Here we applied a stringent and standardized pipeline to hundreds of high-quality ribosome profiling libraries from normal mammalian tissues and cell types, identifying 11,623 human and 16,485 mouse ncORFs. Evolutionary analyses revealed that thousands of ncORFs are subject to coding constraint and exhibit lineage-specific conservation, underscoring their functional potential. Ancient ncORFs are preferentially highly translated, broadly expressed, and enriched for lineage-specific conservation. Co-expression patterns further indicate that many ncORFs, especially ancient ones, are cotranslated with canonical coding sequences, consistent with functions mediated through protein-protein interactions. Together, these findings establish a comprehensive atlas of mammalian ncORFs and provide fundamental insights into their evolutionary dynamics and functional integration within the proteome.

genomics↗