Biology subjects

Gong, Q.

Publications and source records attributed to Gong, Q..

At least 19 recordsLinked to original sources

bioRxiv2026

Homoharringtonine targets XPC to inhibit DNA damage repair and sensitize tumors to platinum-based chemotherapy

DNA damage repair (DDR) is essential for preserving genomic stability and also represents a key targetable axis in cancer drug development. Here, we identify and validate homoharringtonine (HHT), a clinically approved antileukemic drug, as a novel DDR inhibitor using a phenotype-driven, high-content screen based on 53BP1 Tudor-domain foci formation. Mechanistically, HHT directly binds XPC, a critical nucleotide excision repair (NER) factor, with high affinity (Kd = 158.4 nM) in a manner dependent on Thr795 of XPC. HHT disrupts XPC-damaged DNA binding, impairs NER, and reduces non-homologous end joining (NHEJ) efficiency. Consequently, HHT sensitizes tumor cells to platinum-based chemotherapy in vitro and in vivo. These findings establish a phenotype-based platform for DDR inhibitor discovery, identify HHT as a first-in-class XPC inhibitor and uncover a previously unrecognized mechanism of HHT that may be exploited to enhance platinum-based therapy in solid tumors.

pharmacology and toxicology↗

bioRxiv2026

Charting sex divergence in the human brain across the lifespan

Biological sex fundamentally shapes human brain organization, but sex-specific normative neuroanatomical trajectories across the lifespan remain largely uncharted. Here, we constructed independent, sex-specific lifespan brain charts using structural neuroimaging data from 59,915 healthy individuals (29,760 males and 30,155 females) ranging in age from 266 postconception days to 100 years. By examining 296 structural phenotypes across global, cortical, and subcortical measures, these models revealed widespread sex differences in maturational timing, with males reaching peak milestones later than females. These trajectories demonstrate that sex differences evolve dynamically, with phenotype-specific windows of emergence and maximal separation. Compared with conventional sex-pooled references, sex-specific models achieved superior predictive accuracy and reduced misestimation of individual deviations in healthy populations. Across five neuropsychiatric conditions, sex-specific models improved the detection of extreme deviations and revealed both shared and sex-dependent patterns of disorder-related neuroanatomical abnormalities. These sex-specific charts establish tailored normative references for assessing brain development, ageing, and disease.

neuroscience↗

bioRxiv2026

Stoichiometric m6A regulation of YY1 orchestrates the metabolic switch during cardiac development

Chemical modifications of RNA provide an additional regulatory layer essential for development. N6A methyladenosine (m6A) is the most abundant internal mRNA mark, but how site specificity, stoichiometry, and cellular context together determine mRNA fate remains unclear. Here, we define these rules in cardiogenesis by combining single-molecule nanopore direct RNA sequencing (DRS) with a CRISPRdCas13 epitranscriptomic editing platform in human induced pluripotent stem cells and a conditional Mettl14 cardiac knockout in mice, integrated with multiomics, to map m6A sites and quantify stoichiometry. We uncover a bimodal m6A code in which low versus high modification ratios are associated with opposite mRNA and protein outcomes. We further show that Mettl14 loss causes developmental cardiomyopathy and embryonic lethality by disrupting the glycolysis to oxidative phosphorylation (OXPHOS) metabolic switch, and identify an m6A YY1 (Yin Yang 1) axis that post transcriptionally controls OXPHOS genes. Finally, targeted installation of m6A at defined sites using CRISPR/dCas13 reveals that m6A effects on YY1 are strongly locus and context dependent. Together, these findings establish m6A as a site and stoichiometry dependent regulatory code interpreted by cellular context to direct cardiac metabolic maturation. These principles are likely to extend to other developmental and physiological contexts in which precise control of metabolic state and gene dosage is required.

developmental biology↗

bioRxiv2026

Localized SARS-CoV-2 Infection Triggers a Tissue-Wide Antiviral Response and Functional Impairment of Olfactory Sensory Neurons

Olfactory dysfunction is a hallmark of COVID-19, yet the mechanisms by which severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes widespread sensory impairment remain incompletely understood. We compared the olfactory epithelial tropism of multiple SARS-CoV-2 variants in a mouse model and observed that Alpha and Beta variants exhibited the greatest infectivity for the olfactory epithelium (OE), whereas Omicron rarely infected this tissue despite comparable pulmonary viral titers. We further defined the effects of SARS-CoV-2 on olfactory sensory neurons (OSNs) using immunohistochemistry, single-cell RNA sequencing, spatial gene expression characterization, and functional odor stimulation. The localized infection of sustentacular cells triggered a tissue-wide interferon-stimulated antiviral response that extended beyond infected regions for Alpha and Beta but was largely absent following Omicron infection. Mature OSNs transiently adopted an interferon-responsive state before exhibiting persistent downregulation of odorant signal transduction, mitochondrial, and activity-dependent gene pathways. Consistent with these transcriptional changes, odor stimulation failed to elicit normal activity-dependent gene expression during SARS-CoV-2 infection, indicating impaired neuronal function without widespread neuronal loss. Progressive accumulation of macrophages further indicated sustained inflammatory remodeling of the OE. Together, these findings demonstrate that SARS-CoV-2 infection initiates tissue-wide antiviral signaling in the OE that persistently disrupts OSN function, providing a mechanistic framework for COVID-19-associated anosmia.

neuroscience↗

bioRxiv2026

Structural basis for autoinhibition and self-activation in the Pseudomonas aeruginosa virulence factor protease IV (PIV)

Secreted proteases enable Pseudomonas aeruginosa to damage host tissues and evade host immune defences, but the molecular basis by which protease IV (PIV) is maintained as an inactive precursor remains unclear. Here we determined a 2.17 A crystal structure of catalytically inactive PIVS409A. The precursor comprises an N-terminal Cap region, a CUB domain and a C-terminal trypsin-like protease domain. The Cap region forms an extended clamp across the precursor, and residues at the Cap-CUB junction lie above the catalytic cleft. Structural comparison with a modelled peptide substrate indicates that the Cap does not engage the substrate-recognition pockets as a pseudosubstrate; instead, it sterically prevents access to the S1 pocket, oxyanion hole and catalytic triad. Wild-type PIV undergoes progressive processing to a 27.6-kDa mature species, whereas the S409A variant remains resistant to activation by exogenous mature enzyme, supporting an intramolecular initiating step. Mature PIV is weakly inhibited by an ornithine-containing peptide mimicking the Cap domain, is not inhibited by phenylmethylsulfonyl fluoride and is slowly irreversibly inhibited by TLCK, demonstrating unique characteristics in comparison to other proteases from the same family. Finally, mature PIV increases the activity of aminopeptidase PaAP, likely through maturation of this enzyme, as part of a protease activation cascade. These findings define the architecture of the PIV precursor and provide a structural framework for understanding its activation and selective autoinhibition.

biochemistry↗

bioRxiv2026

Multi-modal foundation model with whole-slide attention enables transferrable digital pathology at single-cell resolution

Paired histopathology and spatial transcriptomics data are advancing our understanding of tissue biology and disease, but modeling both modalities at single-cell resolution while mapping local and distal cell-cell interdependencies remains computationally prohibitive. Here we introduce TissueFormer, a framework for pretraining foundation models with linear rather than quadratic computational complexity, overcoming a long-standing barrier to modeling long-range dependencies at scale. Trained on over 17 million image-expression pairs from 1.2K tissue slides, TissueFormer excels at predicting spatial gene expression from histology images at cellular resolution and scales to diagnostic tasks at the cell, region, and slide levels. Additionally, by identifying both long and short-range cell-cell interdependencies, our model enables the generation of testable hypotheses about disease mechanisms and staging, as demonstrated in lung fibrosis and breast cancer.

bioinformatics↗

bioRxiv2026

The unconventional kinesin Kif26a is required for the guidance of major axon tracts in the developing mouse brain

Kif26a and Kif26b encode a family of unconventional kinesins with emerging roles in neurodevelopment, and mutations in both genes have been implicated in a spectrum of neurodevelopmental disorders. The precise mechanisms by which the Kif26 family orchestrates mammalian brain development, however, remain unclear. In this study, we show that Kif26a and Kif26b are expressed in distinct regions of the developing mouse brain. Using a new allelic series in mice, we demonstrate that Kif26a is required for the guidance of multiple forebrain axon tracts. This requirement is direct and cell autonomous, as cell proliferation, survival, and cortical layering are unaffected in the Kif26a mutants. These guidance defects closely resemble those reported for the Fzd3-Celsr3-Dystroglycan pathway, suggesting that Kif26a may participate within this conserved signaling axis to steer growing axons.

neuroscience↗

bioRxiv2026

Bacterial Aminopeptidase-Activated Peptide Prodrug Enables Species-Selective Targeting of Pseudomonas aeruginosa

Pseudomonas aeruginosa is an adaptable organism, frequently found in chronic infections, and for which antimicrobial resistance is a growing concern. Therefore, there is an urgent need for alternative therapeutic strategies. Cationic antimicrobial peptides (AMPs) offer potent bactericidal activity but suffer from limited selectivity and potential host toxicity. To enhance species-specific targeting, we designed two prodrug variants of the AMP D-Bac8CLeu2,5 - EEEE{square}-Bac8CLeu2,5 and ELE{square} D-Bac8CLeu2,5 --engineered for activation by the P. aeruginosa extracellular aminopeptidase PaAP. While both prodrug motifs effectively neutralized the positive charge of D-Bac8CLeu2,5 and prevented DNA-peptide complex formation, EEEE{square}-Bac8CLeu2,5 showed negligible antimicrobial activity due to slow and incomplete activation. In contrast, ELEG{square}-Bac8CLeu2,5 underwent rapid PaAP{square}mediated activation, restoring bactericidal activity in planktonic cultures and biofilms. PaAP contributed significantly to complete prodrug activation, particularly within biofilms, where the accumulation of partially activated intermediates correlated with biphasic killing kinetics. The prodrug showed reduced activity against other ESKAPEE pathogens, demonstrating selective activation by P. aeruginosa. Experiments selecting resistant bacteria revealed distinct mutations in lipopolysaccharide biosynthesis pathways for D-Bac8CLeu2,5 and the prodrug, with limited cross{square}resistance. These findings establish aminopeptidase{square}activated AMP prodrugs as a promising approach for species{square}selective antimicrobial therapy and highlight the feasibility of exploiting bacterial enzymes for controlled antimicrobial peptide activation.

microbiology↗

bioRxiv2026

Structural insights into the recognition and catalysis of tRNA by human NSUN2

The human RNA m5C methyltransferase NSUN2 catalyzes site-specific cytosine methylation across diverse RNA substrates and thereby regulates a wide range of biological and physiological processes. However, the molecular basis by which NSUN2 achieves broad substrate recognition while maintaining catalytic specificity has remained unclear. Here we determine structures of human NSUN2 in both substrate-free and substrate-bound states using X-ray crystallography and cryo-electron microscopy. Structures of NSUN2 in complex with multiple tRNA substrates reveal a structure-first, sequence-tolerant strategy in which NSUN2 actively remodels tRNA architecture, exposing the buried target cytosine and positioning it within the catalytic pocket for methyl transfer. This recognition strategy enables NSUN2 to accommodate diverse tRNA substrates through a largely conserved interaction interface. Guided by these structural insights, we identify a small-molecule inhibitor that suppresses NSUN2 activity and cancer cell proliferation. Together, our findings define the molecular principles underlying NSUN2-mediated RNA m5C modification and provide a structural foundation for targeting NSUN2 in cancers.

molecular biology↗

bioRxiv2025

Generative Design of Cell Type-Specific RNA Splicing Elements for Programmable Gene Regulation

Programmable control of gene expression in specific cell types is essential for both basic discovery and therapeutic intervention, yet current strategies lack scalability across diverse cellular contexts. Here, we introduce SPICE (Splicing Proportions In Cell types), an integrated experimental and computational framework that harnesses alternative RNA splicing as a programmable modality for cell type-specific gene regulation. To power SPICE, we constructed a massively parallel reporter assay (MPRA) comprising 46,372 human-derived sequences and profiled exon skipping across 43 cell lines spanning 10 lineages, uncovering widespread cell type-specific exon skipping. Using this data, we trained deep learning models that both predict splicing in unseen contexts and generate synthetic sequences with programmed, cell type-specific splicing patterns. Leveraging these models, we further engineered sequences that selectively splice in cells harboring oncogenic splicing factor mutations, demonstrating translational potential. SPICE provides a generalizable strategy for dissecting splicing regulation and engineering alternative splicing as a gene expression regulatory layer for research and therapeutic applications. One Sentence SummaryWe introduce SPICE, an integrated framework that couples large-scale splicing assays with generative design to uncover regulatory principles and design programmable, cell-specific gene expression for research and therapeutic applications.

molecular biology↗

bioRxiv2025

Systematic evaluation of the impact of promoter proximal short tandem repeats on expression

Genetic variation at thousands of short tandem repeats (STRs), which consist of consecutive repeated sequences of 1-6bp, has been statistically associated with gene expression and other molecular phenotypes in humans. However, the causality and regulatory mechanisms for most of these STRs remains unknown. Massively parallel reporter assays (MPRA) enable testing the regulatory activity of a large number of synthesized variants, but have not been applied to STRs due to experimental and computational challenges. Here, we optimized an MPRA framework based on random barcoding to study the impact of variation in repeat copy number on expression. We first performed an MPRA on sequences derived from 30,516 promoter-proximal STR loci along with up to 152bp of genomic context, testing 3-4 variants with differing repeat copy numbers for each locus in HEK293T cells. We identified 1,366 loci with significant associations between repeat copy number and expression, which were enriched for positive effect sizes (P=2.08e-110). We then designed a second MPRA in which we performed deeper perturbations, including systematic manipulation of the repeat unit sequence, orientation, and copy number, with 200-300 perturbations for each of the 300 loci with the strongest signals. Our results revealed that the repeat unit sequence is the primary driver of differences in the relationship between copy number and expression across loci, whereas orientation and flanking sequence have weaker effects, primarily for AT-rich repeat units. The high resolution of these perturbations enabled us to detect non-linear effects, most notably for AAAC/GTTT repeats, which emerge only beyond a certain copy number threshold. Finally, we observed that a subset of STRs in our library show expression levels that are tightly linked with predicted DNA secondary structure formation. We repeated our perturbation MPRA in HeLa S3 cells under wildtype and RNase H1 knockdown conditions, which, via reduction in RNase H1 activity, are expected to hinder resolution of R-loops. This demonstrated that associations between copy number and expression at G-quadruplex-forming CCCCG/CGGGG repeats are particularly sensitive to loss of RNase H1, providing support for an R-loop mediated mechanism for these repeats. Altogether, we establish STRs as a critical component of the non-coding regulatory grammar and provide a framework for understanding how this dynamic form of genetic variation shapes gene expression.

genomics↗

bioRxiv2025

Energy-Regularized Graph Learning for Multiscale Spatial Representation

Spatial omics map gene and protein expression in situ, demanding methods that recover cellular and tissue architecture from noisy, high-dimensional data. This need spans two scales: (i) subcellular, where high-resolution measurements must be grouped into coherent cells, and (ii) tissue-wide, where the goal is to recover spatial domains. Existing embedding approaches either ignore space or rely on static neighborhood graphs that over- or under-smooth local heterogeneity. We present Glimmer (Graph-Learned Inference of Multiscale Molecular Embedding for Spatial Representation), a unified framework that learns adaptive neighborhood graphs by minimizing Dirichlet energy under a log-barrier regularizer. Beginning from a k-nearest neighbor scaffold, Glimmer adaptively reweights edges to balance molecular similarity and spatial proximity, yielding interpretable, locally smoothed embeddings. These graphs enable segmentation-free reconstruction from transcript localizations or fine bins and support the discovery of tissue niches at large tissue scales. Across diverse datasets and modalities (Slide-tags, Slide-seq, MERFISH, Xenium, and CODEX), Glimmer surpasses kernel and graph neural network based methods in clustering accuracy and spatial conservation. At the subcellular level, Glimmer corrects transcript-to-cluster misassignments on lymph node slides, thereby improving gene specificity within biological clusters and addressing a key challenge in spatial transcriptomics. At the tissue-wide scale, Glimmer enables accurate region identification, as demonstrated in tonsil tissue by resolving germinal center subregions, which in turn facilitates niche-specific immune profiling. Glimmer thus offers a generalizable framework for spatial representation learning across scales and modalities, enabling comprehensive insights into tissue architecture and cellular ecosystems.

bioinformatics↗

bioRxiv2025

Tissue architecture dynamics underlying immune development and decline in the thymus

The age-associated decline in adaptive immune function, widely observed in vertebrates, has been attributed to thymic involution. To gain insights into the structural and transcriptional changes underlying this phenomenon, we employed high-resolution spatial transcriptomics and T-cell receptor (TCR) sequencing in mice. By analyzing 21 thymus samples spanning mouse lifespan, we uncovered significant alterations in thymic organization, including disrupted T cell development and the emergence of B cell aggregates. We also observed age- related changes in cell-cell interactions, marked by increased antigen-presenting cell presence in thymic medullary regions and a shift from inflammatory to suppressive macrophages, fostering an immunosuppressive niche. Furthermore, aged thymus tissues exhibited an abundance of regions with reduced TCR diversity, accompanied by distinct changes to gene expression profiles. Our study establishes a valuable reference for understanding aging-related alterations in adaptive immunity, revealing mechanisms underlying age-induced immunological decline.

immunology↗

bioRxiv2025

Population-specific brain charts reveal Chinese-Western differences in neurodevelopmental trajectories

Human brain charts provide unprecedented opportunities for decoding neurodevelopmental milestones and establishing clinical benchmarks for precision brain medicine 1-7. However, current lifespan brain charts are primarily derived from European and North American cohorts, with Asian populations severely underrepresented. Here, we present the first population-specific brain charts for China, developed through the Chinese Lifespan Brain Mapping Consortium (Phase I) using neuroimaging data from 43,037 participants (aged 0-100 years) across 384 sites nationwide. We establish the lifespan normative trajectories for 296 structural brain phenotypes, encompassing global, subcortical, and cortical measures. Cross-population comparisons with Western brain charts (based on data from 56,339 participants aged 0-100 years) reveal distinct neurodevelopmental patterns in the Chinese population, including prolonged cortical and subcortical maturation, accelerated cerebellar growth, and earlier development of sensorimotor regions relative to paralimbic regions. Crucially, these Chinese-specific charts outperform Western-derived models in predicting healthy brain phenotypes and detecting pathological deviations in Chinese clinical cohorts. These findings highlight the urgent need for diverse, population-representative brain charts to advance equitable precision neuroscience and improve clinical validity across populations.

neuroscience↗

bioRxiv2025

Aiolos restricts the generation of antigen-inexperienced, virtual memory CD8+ T cells

CD8+ virtual memory T (TVM) cells are memory-like cells that rapidly respond to infection via antigen-independent bystander effector functions. While it is recognized that TVM cells arise independently of foreign antigen encounter, the mechanisms governing their development are not fully understood. Here, we identify the transcription factor Aiolos as a negative regulator of TVM cells. We observed higher quantities of TVM cells in the spleens of uninfected Aiolos-deficient (Ikzf3-/-) mice relative to wild-type (WT). Furthermore, Ikzf3-/- TVM cells produced higher levels of IFN-{gamma} and granzyme B. In addition, we found that Ikzf3-/- TVM cells accumulated to higher quantities in the lungs within 24 hours of influenza virus infection. In line with enhanced TVM functional capacity and lung trafficking, Aiolos-deficient mice cleared virus more rapidly and exhibited reduced morbidity relative to WT animals. Mechanistically, we observed that Aiolos represses the TVM transcriptional regulator Eomes and the IL-15R subunit CD122 (IL-15R{beta}/IL-2R{beta}), known contributors of TVM cell generation. Collectively, these findings establish Aiolos as a novel molecular repressor of TVM generation and function.

immunology↗

bioRxiv2025

Spatial Transcriptomics Unveils the Blueprint of Mammalian Lung Development

Mammalian lung development is a complex, highly orchestrated process involving the precise coordination of diverse cell types. Despite significant advances, the spatial gene expression patterns and regulatory mechanisms within the developmental niches of different lung structures remain incompletely understood. In this study, we present a comprehensive spatial transcriptomic atlas of mouse lung development, spanning from the early pseudoglandular to the alveolar stage. We further uncover transcription factor (TF) regulation landscapes by integrating spatial epigenome, including novel TF-eRegulons critical for epithelial progenitors during early lung development. Our analysis also identifies hundreds of spatiotemporally dynamic cell-cell communications, such as BMP8B-mediated ligand-receptor signaling enriched in airway branching. Notably, we delineate the distinct developmental trajectories of alveolar AT1 and AT2 cells and reveal that collagen pathways facilitate their spatial convergence, forming primary alveoli during the canalicular-saccular transition. Together, this spatial transcriptomic atlas provides a foundational resource for understanding the complex cellular and molecular orchestration underlying mammalian lung development.

developmental biology↗

bioRxiv2025

Detection of Pre-Existing Immunity to Bacterial Cas9 Proteins in People with Cystic Fibrosis

Cystic fibrosis (CF) is caused by homozygous mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, resulting in multi-organ dysfunction and decreased lifespan and quality of life. A durable cure for CF will likely require a gene therapy approach to correct CFTR. Rapid advancements in genome editing technologies such as CRISPR/Cas9 have already resulted in successful FDA approval for cell-based gene editing therapies, providing new therapeutic avenues for many rare diseases. However, immune responses to gene therapy delivery vectors and editing tools remain a challenge, especially for strategies targeting complex in vivo tissues such as the lung. Previous findings in non-CF healthy individuals reported pre-existing antibody and T cell dependent immune responses to recombinant Cas9 proteins, suggesting potential additional obstacles for incorporation of CRISPR/Cas9 technologies in gene therapies. To determine if pre-existing immunity to Cas9 from S. aureus or S. pyogenes was present or augmented in people with CF (PwCF), anti-Cas9 IgG levels and Cas9-specific T cell responses were determined from peripheral blood samples of PwCF and non-CF healthy controls. Overall, non-CF controls and PwCF displayed evidence of pre-existing antibody and T cell responses to both S. aureus and S. pyogenes Cas9, although there were no significant differences between the two populations. However, we observed global changes in activation of Th1 and CD8 T cell responses as measured by IFN{gamma} and TNF that warrant further investigation and mechanistic understanding as this finding has implications not only for CRISPR/Cas9 gene therapy for PwCF, but also for protection against infectious disease.

immunology↗

bioRxiv2025

Pcdh20 is a POU2F3 target gene required for proper tuft cell microvillus formation

BACKGROUND & AIMSTuft cells play protective roles in infection, inflammation, and tumorigenesis through the secretion of cytokines and eicosanoids. Tuft cells are known for their tall, blunt microvilli, thought to be analogous to mechanosensory hair cell stereocilia; however, a functional role for the microvillar apparatus has not been identified. POU2F3 is the master regulator transcription factor for tuft cells, yet how POU2F3 drives formation of this unique structure is unknown. Here, we aimed to identify POU2F3 target genes and commonalities between tuft and hair cells to better understand this unique structure. METHODSPOU2F3 ChIP-seq was performed on tuft cells and compared to the hair cell transcriptome. Tuft cell RNA-seq datasets were interrogated for hair cell structural and mechanosensory genes; expression was validated. Intestinal and gallbladder tuft cells were examined using multiple light and electron microscopy (EM) modalities. PCDH20 was knocked down in mouse models and ultrastructural analyses were performed. The tuft cell cytoskeleton was modeled using AlphaFold3 prediction. RESULTSGenes encoding structural and mechanosensory proteins common to both tuft and hair cells, including Pcdh20, were identified. Imaging localized PCDH20 to tuft cell microvilli and hair cell stereocilia. Genetic ablation of Pcdh20 in mice resulted in structural defects in tuft cell microvilli, including loss of rigidity and organization. Molecular modeling suggests PCDH20 homodimers link adjacent microvilli. CONCLUSIONSPcdh20 is a POU2F3 target gene in tuft cells, critical to maintain the rigid microvillar apparatus. These findings, together with the shared expression of mechanosensory components like TMC1, support the hypothesis that tuft cells could have mechanosensory capabilities analogous to cochlear hair cells.

cell biology↗