Biology subjects

Guo, S.

Publications and source records attributed to Guo, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Integrative drug discovery for Parkinson disease with DIMER

Translating Parkinson disease (PD) genetics into therapeutic candidates requires approaches that account for interconnected disease mechanisms and their cellular context. Here we present DIMER (Direct and Indirect Module Evaluation for Repurposing and screening), a framework that connects network-based drug repurposing and target-directed virtual screening through shared disease-associated gene sets. Applying DIMER to PD, we integrated genetic risk and mechanism-associated gene sets with drug-target interactions, disease transcriptomes, and single nucleus expression profiles. Network analysis identified 423 repurposing candidates, with 71% of qualifying drug-gene set associations arising through targets outside the corresponding disease gene set. Transcriptional reversal analysis and cell type-resolved networks further distinguished candidates by their predicted effects on disease-associated expression and their cellular context, while target-set separation nominated potentially complementary drug combinations. For target-directed virtual screening, DIMER adapted a pretrained compound-protein interaction model to screening library chemistry and incorporated known-ligand similarity into compound ranking. Library adaptation improved compound-target pair classification performance, whereas ligand-informed ranking increased early enrichment of known active compounds. Consensus screening of 1.82 million compounds against seven PD-associated proteins yielded a shortlist of 22 compounds supported by at least five ranking runs. In a complementary experimental evaluation, four repurposing candidates (polydatin, fedratinib, sorafenib and venlafaxine) attenuated the loss of dopamine neuron marker signals in human midbrain organoids exposed to 6-hydroxydopamine. Together, these findings establish DIMER as a framework for translating disease-associated genes into pharmacological hypotheses and prioritizing candidates for experimental testing.

neuroscience↗

bioRxiv2026

CHAIR an antigen-resolved antibody-reactome resource for healthy adult immune aging

Antigen-recognition histories accumulate across adult life, but existing human aging resources largely emphasize host-state measurements rather than antigen-resolved humoral memory. We present CHAIR, the Chinese Healthy Aging Immune Resource, which integrates self-antigen, human virome and toxin/virulence-factor PhIP-seq with routine clinical measurements and T/B/NK phenotyping in clinically screened adults aged 20-94 years. The resource framework includes 1,008 unique PhIP-seq samples, 995 clinical records, 977 T/B/NK records and 853 participants with all three layers. Across modeled spaces comprising 23,584 self-antigen targets, 210 virome targets and 1,258 virulence-factor source targets, most measured antibody-reactivity architecture was consistent with broad preservation within domains, whereas age- and sex-associated signals were concentrated in focal targets and modules. Together, CHAIR provides a traceable, antigen-resolved reference framework based on clinically screened adults for investigating focal humoral remodeling across healthy adult aging.

immunology↗

bioRxiv2026

A New Disease Gene for Hypokalemic Periodic Paralysis, KCNA7, Established in a Multigenerational Family

Hypokalemic periodic paralysis (HypoPP) is an inherited skeletal muscle ion channelopathy of CACNA1S or SCN4A characterized by recurrent episodes of weakness, often triggered by rest after exercise or by reduced K+ (carbohydrate ingestion, stress). Here, we describe a multigenerational family in whom a KCNA7 missense variant [c.834A>C (p.Arg278Ser)] co-segregated with susceptibility to recurrent attacks of weakness in association with hypokalemia as low as 1.3 mEq/L and a 40% decrement of the compound muscle action potential after exercise, suggesting an additional HypoPP gene. Arg278 is the outermost positively charged residue (R1) within the S4 transmembrane segment of the voltage-sensor domain of KV1.7, orthologous to the canonical patten of arginine missense mutations at R1 or R2 in S4 segments for HypoPP-mutant CaV1.1 and NaV1.4 channels. To determine the functional consequences of Arg278Ser, we expressed wild-type and mutant KV1.7 channels in Xenopus oocytes and HEK293 cells. Arg278Ser, but not wild-type KV1.7, generated an anomalous inwardly rectifying current at hyperpolarized membrane potentials that was nonselective Na+ or K+, consistent with the anomalous gating pore conductance that causes susceptibility to HypoPP. Other pathogenic variants of KCNA7 have previously been implicated only in inherited cardiac arrhythmias. Collectively, the genetic, structural and electrophysiological findings support KCNA7 Arg278Ser as a pathogenic variant underlying HypoPP and implicate KCNA7 as a disease gene for periodic paralysis, extending the established gating-pore mechanism of HypoPP to KV1.7.

genetics↗

bioRxiv2026

A peptidomimetic inhibitor blocks Vibrio cholerae adhesin FrhA.

Cholera is a diarrheal disease from colonization of the small intestine by the Gram-negative bacterium Vibrio cholerae. Cholera remains a critical public health concern due to limitations in therapy and rising antibiotic resistance. The peptide-binding domain (PBD) of the adhesion protein FrhA is critical for V. cholerae intestinal colonization and biofilm formation. In a program targeted on blocking cholera infection, antagonists of the FrhA-PBD are described based on a tripeptide motif. Notably, constraint of the N-terminal tryptophan residue using 1,2,3,4-tetrahydro-{beta}-carboline-3-carboxylic acid (Tcc) and co-crystallization of H-(S)-Tcc-Thr-Asp-OH with an FrhA construct has provided structural information to guide inhibitor design. The diastereomer (R)-Tcc-Thr-Asp exhibited nanomolar binding affinity (Kd = 101 {+/-} 30.2 nM). H-(R)-Tcc-Thr-Asp-OH blocked bacterial hemagglutination mediated by FrhA-PBD and reduced biofilm formation in vitro. Moreover, it showed greater resistance to the digestive enzyme chymotrypsin than previously reported inhibitory pentapeptides, offering potential proteolytic stability while blocking FrhA-PBD-mediated adhesion in the intestine.

biochemistry↗

bioRxiv2026

A durably colonizing engineered native symbiont enables sustained intestinal delivery for metabolic dysfunction and colitis

BackgroundEngineered bacterial therapeutics represent a promising strategy for sustained intestinal delivery of therapeutic molecules, but their efficacy is limited by inefficient colonisation, safety concerns and the need for repeated administration or auxiliary delivery systems. ObjectiveTo develop a safety-optimised native bacterial chassis capable of long-term gut colonisation and sustained therapeutic delivery for intestinal inflammatory and metabolic diseases. DesignNative murine Escherichia coli isolates were screened for antibiotic susceptibility, genetic tractability and long-term intestinal colonisation. The selected strain, MEc30, was further optimised by deleting the putative virulence-associated clb and irp loci. MEc30 was then engineered to deliver murine interleukin-10 (MEc30-mIL-10) or produce nicotinic acid (MEc30-NA), and therapeutic efficacy was evaluated in Il10-/- colitis and high-fat diet-induced metabolic dysfunction models. ResultsMEc30 achieved stable lifelong colonisation of the murine intestine after a single oral administration, without antibiotic preconditioning or auxiliary delivery systems, and did not detectably disturb host physiology or gut microbial ecology. Deletion of clb and irp abolished potential colibactin- and yersiniabactin-associated biosafety risks while preserving bacterial growth and colonisation capacity. MEc30-NA continuously produced nicotinic acid in the gut, activated epithelial GPR109a-associated barrier signalling, improved glucose and lipid metabolism, reduced systemic inflammation and avoided the sharp peak exposure associated with conventional nicotinic acid administration. MEc30-mIL-10 enabled sustained intestinal IL-10 delivery, suppressed inflammatory macrophage activation, improved barrier integrity and alleviated spontaneous colitis in Il10-/- mice. ConclusionThis study identifies MEc30 as a durable and safety-optimised native E. coli chassis for sustained intestinal therapeutic delivery. Engineered native symbionts may provide a long-acting live biotherapeutic strategy for chronic intestinal inflammatory and metabolic diseases.

microbiology↗

bioRxiv2026

Molecular principles for graded activation of dopamine D1 receptor

G protein-coupled receptors (GPCRs) signal across a continuum of activation states, yet how ligands encode distinct signaling efficacies remains poorly understood. Here, we define the molecular mechanism underlying graded activation of the dopamine D1 receptor (D1R), a major therapeutic target for neuropsychiatric disorders. Functional analyses reveal that two widely used pharmacological tools, LE300 and SCH23390, possess intrinsic efficacy as an inverse agonist and a weak partial agonist, respectively, rather than the efficacy-silent neutral antagonists. Structural, molecular dynamics and mutagenesis analyses capture previously unrecognized inactive and intermediate receptor activation states that bridge known active conformations, and reveal that ligand efficacy is encoded through the progressive engagement of a conserved activation pathway centered on the W6.48 toggle switch. Guided by this mechanism, a single chemical modification markedly increases the agonist efficacy of SCH23390. Comparison with dopamine D2 receptor structures further reveals a conserved mechanism of inverse agonism despite distinct subtype-specific recognition. Together, these findings establish a structural framework for graded agonism at D1R and provide general principles for the rational design of efficacy-tuned therapeutics at dopamine receptors and related GPCRs.

biochemistry↗

bioRxiv2026

Non-canonical ribosome organization enables translation stalling in neuronal RNA granules.

Neuronal outgrowth to support cognitive functions relies on a timely supply of proteins to distal sites in the neuron. To meet this demand, neurons transport mRNAs and ribosomes in large assemblies called "neuronal RNA granules". Ribosomes that integrate into these granules initiate protein synthesis in the soma, stall the process, and then become packaged into clusters that are transported to distal sites, where protein synthesis can be reactivated. The exact mechanisms and structure of these ribosome clusters remain unknown. We combined cryo-electron microscopy and cryo-electron tomography to examine these dense ribosome clusters purified from rat brains, which are included in neuronal RNA granules. We found that these clusters contain ribosomes stalled at various stages of elongation and that the mRNA sequences where the ribosomes stall facilitate stalling. The ribosome clusters contain multiple polysomal units, and ribosomes from nearby polysomes interact through rRNA expansion segments, only seen before in disomes of inactive or hibernating ribosomes in neurons. The ribosomes in the clusters form unique three-dimensional arrays that evade detection by the ribosome-associated quality-control and NO-GO decay responses, which normally lead to recycling of 40S and 60S subunits, and degradation of the mRNA and arrested nascent proteins. Overall, this study helps uncover specialized mechanisms in neurons that enable local protein translation at distal sites, supporting proper protein homeostasis, both crucial for neurodevelopment and optimal neuronal function. KEY POINTSO_LIRibosomes in neurons organize into unique clusters that are incorporated into "neuronal RNA granules". C_LIO_LIApproximately half of the ribosomes in these clusters are stalled in elongation. C_LIO_LIThe mRNA sequences read by these ribosomes facilitate stalling. C_LIO_LIRibosomes within the clusters interact through rRNA expansion segments. C_LIO_LIRibosomes in the clusters form unique 3D structures that are not detected by the ribosome-associated quality-control response. C_LI

neuroscience↗

bioRxiv2026

Epigenetic Reactivation of Lineage Differentiation to Target Leukemia

Chromatin regulation critically influences gene expression and cancer progression, yet the functions of chromatin adaptors remain incompletely defined. Using focused CRISPR screening, we identified TRIM28, a multi-domain chromatin adaptor, as a dependency in acute leukemia, where its depletion impaired leukemia cell proliferation in vitro and in vivo, while activating neutrophil differentiation programs. Integrative transcriptomic and chromatin profiling revealed that TRIM28 acts as a co-repressor of neutrophil-associated loci independently of H3K9 methylation, and that TRIM28 loss drives terminal differentiation of leukemia cells into functionally mature neutrophil-like cells with reduced leukemic potential. We developed a selective small-molecule TRIM28 inhibitor that binds the TRIM28 PHD-bromodomain, phenocopies TRIM28 loss across biochemical and cellular assays, exhibits low micromolar anti-leukemia activity, induces neutrophil differentiation, and synergizes with Menin inhibition. Together, these findings, spanning target discovery, mechanism of action, and chemical probe development, establish TRIM28 as a regulator of myeloid cell fate and a promising pro-differentiation therapeutic target in acute leukemia.

cancer biology↗

bioRxiv2026

AgroGem: A Rapid and Scalable Transient Transformation System for Functional Genetics in Multiple Plant Species

Plant genetic transformation technologies are essential for functional genomics and genome engineering in plants. While transient expression systems offer a rapid alternative to stable transformation, existing platforms are often constrained by low efficiency, technical complexity, and limited scalability. Here, we developed AgroGem, an efficient Agrobacterium-mediated transient transformation system utilizing a geminiviral replicon-based T-DNA vector for Arabidopsis and Brassicaceae species. AgroGem significantly outperformed existing transient approaches, including AGROBEST and protoplast-based assays, in CRISPR-mediated editing efficiency. Moreover, AgroGem recapitulated the mutation spectra and chromatin accessibility-dependent editing patterns observed in stable transformation across both Cas9 and Cas12a systems, indicating that it captures genome editing outcomes in native chromatin contexts. Leveraging this capability, we performed high-resolution profiling of CRISPR-induced mutation outcomes across a panel of DNA repair mutants and identified distinct repair signatures, including unexpected roles for KU80 and XRCC4 in regulating non-homologous end joining (NHEJ). AgroGem also supported bimolecular fluorescence complementation assays for protein-protein interaction studies in Arabidopsis and was readily adapted to plate-based formats for high-throughput applications. Together, these results establish AgroGem as a robust, scalable, and versatile platform for genome editing, DNA repair analysis, and functional genetics in plants.

plant biology↗

bioRxiv2026

The Premotor Language Area Encodes a Full Acoustic-to-semantic Speech Hierarchy

Classic neurobiological models of human speech and language have emphasized the dominant role of temporal lobe in speech perception, while premotor regions including the ventral premotor cortex (PMv) are situated at the level of articulatory processing. However, accumulating evidence from neuroimaging, clinical, and computational studies suggests that premotor cortex may contribute to speech processing beyond articulation. The precise extent and functional organization of these speech-related representations, however, remain unclear. In this study, we combined naturalistic speech perception with computational encoding models to characterize the organization of speech representations within PMv. We functionally localized a cortical region that encompasses previously described premotor speech areas, which we term the premotor language area (PML). Using acoustic, phonemic, semantic, and deep neural speech representations, we found that PML contains representations spanning the full speech-processing hierarchy, from low-level acoustic features to high-level semantic information. These representations are arranged along a smooth posterior-anterior gradient, with increasingly abstract speech representations emerging toward anterior PML. Moreover, this organizational gradient mirrors the canonical speech processing hierarchy in the temporal auditory regions. These findings challenge the traditional view of premotor cortex as primarily an acoustic-articulatory unit, and instead identify PML as a hierarchically organized speech-processing region that parallels the temporal auditory cortex. This provides a new framework for understanding the role of premotor cortex in speech perception.

neuroscience↗

bioRxiv2026

Sequential Penta-Omic Extraction Method Using Single Biospecimens of Post-mortem Human Brain

A multi-omic approach utilizing a single biospecimen is important to avoid intra-sample heterogeneity associated with testing multiple omic single-samples, and for more efficient use of small volumes of precious biopsies (<30 mg). This is especially true for the microanatomy of post-mortem human brain samples. Using post-mortem human brain biospecimens from the NIH NeuroBioBank, a penta-omic sequential extraction method is described, Simultaneous Metabolomic, Proteomic, Lipidomic - DNA, RNA Extraction (SiMPL-DREx). Each sequential omic extract was compared to those obtained by the gold standard single omic method. Preserving RIN is critical for brain and tissue banks, as it is a primary measure of tissue quality. For all five omic extracts, the tissue integrity numbers and omic profiles did not significantly differ from those obtained by the respective omic gold standard method. Unlike past multi-omic studies, this study quantified the relative solvent percentages and upstream losses for both the organic and aqueous phases, confirming an omics loss of under 5%.

biochemistry↗

bioRxiv2026

Label-free Pathogen Identification with Microscopy Imaging and Deep Learning

Rapid and accurate pathogen identification is crucial for the clinical management of infectious diseases, particularly sepsis and severe respiratory infections, yet standard clinical workflows remain slow and resource-intensive. Here, we developed an automated, high-throughput imaging platform built on standard, clinically accessible bright-field microscopy, and generated a large dataset comprising 24.9 million label-free bacterial cells across six focal pathogens. Leveraging this resource, we trained a neural network (ESKAPe-ResNet) to identify ESKAPe species at the single-bacterium level. The model achieved >92% accuracy in species-level classification and >82% accuracy in quantifying ESKAPe abundance in mock mixtures, with high specificity against non-ESKAPe bacteria. In clinical validation using sputum, bronchoalveolar lavage fluid and blood samples from patients with respiratory infections and sepsis, the approach correctly identified the dominant ESKAPe pathogen in >78% of samples after minimum broth culture enrichment. The imaging-to-identification pipeline was completed in under 10 minutes, and coupled with brief cultivation, the median time to accurate identification was reduced to 5-6 hours, compared with days for conventional blood culture-based workflows. This work establishes the proof-of-principle for label-free, hardware-minimal rapid pathogen identification, providing a clinically deployable workflow to expedite diagnosis and reduce mortality in severe bacterial infections.

microbiology↗

bioRxiv2026

EditorForge: An Active-Site-Aware Framework for Inverse-Folding-Based Protein Redesign

Inverse-folding models can rapidly generate protein sequences compatible with a supplied backbone, but unconstrained redesign is poorly suited to enzyme and genome-editor-associated domains, where catalytic, substrate-proximal, and conserved structural regions must remain protected. In this paper, we present EditorForge, a modular constraint-and-audit suite for editor-domain protein redesign that wraps fixed-backbone inverse folding with explicit design masks, fixed-position enforcement, active-site-proximity auditing, active-site-shielded regeneration, and downstream structural quality control. Using full-length Moloney murine leukemia virus reverse transcriptase structure 4MH8 (MMLV RT 4MH8) as a demonstration target, EditorForge first restricted redesign to a bounded 25-position envelope while fixing 428 residues. An initial audit detected active-site-proximal failure modes despite fixed-position integrity. Later, the Active Site Shield module then removed five unsafe design positions, replaced them with lower-contact alternatives, and regenerated candidates under stricter constraints. Post Shield Audit evaluated 24 regenerated candidates, all of which satisfied the hard sequence/mask and active-site-shield constraints. For the eight candidates that were selected or returned for structure-prediction/refolding quality control, Enhanced RefoldQC found that all 8 evaluated predicted structures passed the computational structure-QC screen. That said, the selected 8 candidates passed the computational structure-QC screen, with global C RMSD values of 1.2061-1.5555 {degrees}A, active-site C RMSD values of 0.4098-1.8397 {degrees}A, mutation-neighborhood C RMSD values of 1.3155-1.6848 {degrees}A, and average pLDDT-like confidence values of 94.87-95.11. In short, EditorForge provides a reproducible triage layer that converts general inverse-folding output into constrained and editor-specific candidate sets for downstream structural and biological review on top of existing structural prediction tools.

bioinformatics↗

bioRxiv2026

Hypothalamic MCH neurons links tau pathology to sleep disruption

Sleep disruption is an early and pervasive feature of Alzheimers disease (AD), yet the circuit mechanisms linking tau pathology to sleep-wake dysfunction remain unresolved. Here, we identify melanin-concentrating hormone (MCH) neurons in the lateral hypothalamus (LH) as a critical node disrupted in tauopathy. Longitudinal EEG/EMG recordings in PS19 mice reveal progressive impairments in sleep architecture and homeostasis. Histological analyses revealed significant degeneration of both MCH neurons and the neighboring hypocretin (Hcrt) neuronal population in the LH at late stages of tauopathy. In vivo fiber photometry recordings demonstrated a selective functional impairment of MCH neurons, characterized by reduced activity during REM sleep, whereas Hcrt neuronal activity remained largely preserved. In addition, cell-autonomous expression of mutant tau in MCH neurons recapitulates sleep disruption, establishing a causal role. Despite tauopathy-induced neuronal loss and reduced endogenous activity, optogenetic and chemogenetic activation show that MCH neurons retain functional capacity, and their activation restores sleep in aged PS19 mice. Together, these findings define a circuit mechanism linking tau pathology to sleep and identify MCH neurons as a tractable therapeutic target.

neuroscience↗

bioRxiv2026

Human white matter tracts aligned with canonical functional brain networks

White matter tracts form the structural backbone of large-scale brain networks, yet their relation to functional organization remains poorly defined. Although major pathways are well characterized anatomically, their relationship to distributed cognitive systems has not been systematically established. Here, we constructed a population-level white matter tract termination atlas and projected tract endpoints onto the cortical surface to characterize their spatial organization. We integrated this atlas with large-scale meta-analytic decoding to derive functional profiles for individual tracts. Functional decoding revealed that white matter tracts exhibited distinct and biologically interpretable cognitive signatures. Hierarchical clustering of these profiles further showed that tracts organize into coherent ensembles defined by shared functional associations. These tract ensembles recapitulated canonical intrinsic brain networks across multiple cortical atlases, including a notable ensemble that demonstrated alignment with the default mode, salience, and frontoparietal control networks, corresponding to the core architecture of the triple-network model of cognitive control. This finding identified a candidate structural backbone linking distributed functional systems implicated across neuropsychiatric conditions. Together, these results demonstrate that white matter architecture is organized according to large-scale functional principles and establish a tract-to-network framework for linking structural connectivity to cognition.

neuroscience↗

bioRxiv2026

Streptococcal superantigen SpeC induces IL-8 secretion in human epithelial cells

Streptococcal pyrogenic exotoxin C (SpeC) is a prototypical superantigen produced by group A Streptococcus. It potently activates a broad subset of T lymphocytes via a bridging interaction involving TCR{beta}-SpeC-MHC-II. Our recent work demonstrated that SpeC induced profound release of IL-8 from human pharyngeal epithelial cells and this effect was reversible through a specific point mutation in SpeC. This study systematically investigated cellular signaling pathways using integrated transcriptomic profiling and Western blot analysis, with a focus on membrane-associated receptors and downstream intracellular signaling effectors. Our results demonstrate that this biological process is critically associated with the activation of Erk1/2, p38 MAPK and NF-{kappa}B signaling cascade. This study identifies a novel mechanism through which a bacterial superantigen target epithelial cells-the body primary physical barrier and first line of innate immune defense.

microbiology↗

bioRxiv2026

TCMCard: A High-Confidence Digital Infrastructure for Traditional Chinese Medicine Quantified by Multi-Dimensional Evidence Integration

Network pharmacology has become a widely used approach for deciphering multi-component, multi-target mechanisms of traditional Chinese medicine (TCM). Here we introduce TCMCard, a high-confidence digital infrastructure built on a Multi-Dimensional Evidence Integration (MDEI) framework. The framework integrates experimental activity data from authoritative chemical databases, literature-derived evidence, and structure-based similarity inference. Preprocessing steps include chemical structure normalization, species-specific filtering, and target quality scoring. Applied to conventional interaction datasets, this pipeline leads to the removal of over 60% of low-confidence noise. TCMCard supports network pharmacology exploration through an interactive visualization platform, and module analysis identifies functionally relevant communities that offer insights into the synergistic actions of TCM formulas. Overall, TCMCard may help move the field beyond simple data aggregation toward evidence-informed curation and quality-driven analysis. As an interactive and publicly accessible platform, it reveals an organized backbone within complex interaction networks, offering a more reliable basis for understanding multi-component synergy in TCM.

bioinformatics↗

bioRxiv2026

Curvature-mediated prewetting organize mitochondrial nucleoid

The emergence of spatiotemporal order in diffusive cellular environments requires physical mechanisms to overcome the entropic drive toward disorder. While the organizing role of chemical signaling is well characterized, how complex membrane curvature regulate soluble molecular organization remains a fundamental open question. Here, we establish membrane curvature as a thermodynamic control parameter for the condensation of soluble proteins through prewetting. Using the mitochondrial transcription factor TFAM, we demonstrate that intrinsic membrane curvature locally drives a prewetting transitiona surface-mediated phase separation distinct from bulk condensation. By combining in vitro reconstitution, live-cell super-resolution imaging, cryo-electron tomography, and thermodynamic theory, we show that negatively high-curvature regions lower the nucleation energy barrier of Tfam, driving localized protein condensation at physiological concentrations. These results reveal that membrane curvature does not merely scaffold cellular machinery but manipulates the local free energy landscape, establishing a geometric principle for the spatial control of biological processes.

biophysics↗