Biology subjects

Wu, Y.

Publications and source records attributed to Wu, Y..

At least 289 records · Page 16Linked to original sources

bioRxiv2025

Label-Free Longitudinal Imaging of Single Cell Drug Response with a 3D-Printed Cell Culture Platform

Image-based phenotypic screening has emerged as a powerful tool for revealing single-cell heterogeneity and dynamic phenotypic responses in preclinical drug discovery. Compared to traditional static end-point assays, live-cell longitudinal imaging captures the temporal trajectories of individual cells, including transient morphological adaptations, motility shifts, and divergent subpopulation behaviors, enabling high content features and more robust early prediction of treatment outcomes. Fluorescence-based screening, while highly specific, is constrained in live-cell contexts by broad spectral overlaps (limiting multiplexing to fewer than six channels), bulky fluorophores that may perturb small-molecule interactions, and photobleaching or phototoxicity under repeated excitation. Stimulated Raman scattering (SRS) microscopy overcomes these barriers by delivering label-free, quantitative chemical contrasts alongside morphological information. Here, we present a low-cost, 3D printed cell culture platform compatible with the stringent optical requirements of SRS microscopy. This set up enables real-time drug delivery and continuous monitoring of biochemical and morphological changes in living cells during 24-hour time-lapse imaging with minimal photodamage. We outline a processing pipeline for longitudinal SRS images to extract chemical and morphological features of single live cells. Using this system, we showcase time-lapse SRS microscopy as a tool to map heterogenous drug-induced single-cell response over time, enabling the identification of varying trajectories within complex cell populations. By parallelizing multi-well perfusion with label-free chemical imaging, our approach offers a pathway toward high-throughput pharmacodynamic assays for the acceleration of phenotypic screening and personalized medicine.

bioengineering↗

bioRxiv2025

LeGO-Teknik reveals that the neurogenesis pathway is a clone-specific hallmark of brain metastasis in breast cancer

Breast cancer exhibits substantial inter- and intra-patient heterogeneity. Yet the molecular features underlying this diversity and their roles in tumour progression are not yet fully elucidated. Within a primary tumour, certain clones possess a unique capacity to metastasize to distant organs, such as the brain, and this propensity may be associated with specific gene expression profiles. To investigate this phenomenon, we developed a new optical barcoding library, LeGO-Teknik, compatible with high resolution imaging, flow cytometry, single-cell RNA sequencing and machine learning computational methods. Using this new tool, we systematically assessed the fitness and organ tropism of multiple human breast cancer clones in spontaneous metastasis assays. Linking transcriptomic profiles of individual cancer cells to their clonal identities and metastatic behaviours, we identified that clones predisposed to forming brain metastases exhibit distinct molecular signatures. Notably, individual cells from these clones showed enriched expression of neurogenesis-related genes. Using SCENIC transcription factor analysis, we found that some of these features are driven by the transcription factor SOX4. This hallmark, likely due to a process of cellular reprogramming, is a remarkable example of organ mimicry during clonal selection. Together, this work provides critical insights into brain metastasis and highlights the potential for identifying predictive biomarkers and therapeutic targets for metastatic breast cancer.

cancer biology↗

bioRxiv2025

Complementary role of frontal theta and parietal alpha activity in resolving visual competition

Attention plays a central role in selecting information for conscious perception. Because natural environments are structured, prior knowledge about relevant and irrelevant features can guide this selection. However, prior knowledge about distractors can enhance their neural representation, raising the question of how the brain prevents such enhancement from interfering with behavior. We addressed this question by combining a binocular rivalry paradigm with frequency-tagged stimuli to independently track target and distractor signals during sustained perceptual competition. We identified a sequential pattern of oscillatory dynamics underlying stable perception. Early parietal alpha activity (8-12 Hz) was associated with the segregation of competing inputs without altering sensory gain. This was followed by frontal theta activity (3-7 Hz), which was linked to the reactive suppression of distractors representations. Importantly, alpha-mediated gating effects are most pronounced under high perceptual uncertainty, where they facilitated the stabilization of weak target signals and promoted their access to conscious awareness. Together, these findings demonstrate that perceptual competition is resolved through a coordinated sequence of proactive gating and reactive suppression.

neuroscience↗

bioRxiv2025

Bacterial Schlafens mediate anti-phage defense

Human Schlafen proteins restrict viral replication by cleaving tRNA, thereby suppressing protein synthesis. Although the ribonuclease domain of Schlafen proteins is conserved across all domains of life, its function in prokaryotes has remained unclear. Here, we show that prokaryotic Schlafen nucleases (pSlfns) are widespread antiviral effectors that protect bacteria from phages. These nucleases are fused to diverse protein domains that sense phage infection. We focus on a system where Schlafen nuclease is fused to a previously unknown immunoglobulin-like sensor domain and demonstrate that it recognizes T5-like phage tail assembly chaperones and cleaves both bacterial and viral tRNA, triggering abortive infection. Our findings redefine Schlafens as an ancient, mechanistically conserved family of immune effectors, revealing the deep evolutionary origin of tRNA-targeting antiviral immunity in humans.

molecular biology↗

bioRxiv2025

Overcoming breeding constraints in polyploid oat from evolutionary insights

Polyploidy provides adaptive advantages in plants by buffering deleterious mutations1,2. While polyploidization can enhance agronomic traits such as increased biomass, known as the gigas effect1-4, increasing genetic gain in polyploid crops remains a critical but difficult goal due to the difficulty in dissecting complex trait inheritance5,6. Here we present chromosome-scale genome assemblies for 26 Avena taxa, spanning diploid, tetraploid, and hexaploid lineages. We traced four independent polyploidization events across the genus, including the formation of A. agadiriana as an allotetraploid (AgAgAg'Ag'), and revealed a reticulate evolutionary history shaped by gene flow involving four subgenomes (A, B, C, D), for example, the hybrid speciation of A. hirtula. Transcriptomic analysis of 286 samples across 11 tissues, combined with deleterious mutation analysis from a cultivated population of 112 accessions, showed that polyploidization led to widespread functional redundancy among homoeologs, supporting a genome-wide buffering effect. However, derived allele frequency analysis revealed that, while disrupting functional genes may yield desirable traits, the buffering effect impedes the fixation of beneficial loss-of-function mutations and thereby limits breeding efficiency. Based on these integrative analyses, we propose breeding strategies to circumvent these limitations by targeting beneficial loss-of-function alleles within the complex polyploid background of oat. Our study highlights broader challenges in the improvement of polyploid crops and provides a foundation for future breeding strategies.

evolutionary biology↗

bioRxiv2025

A Standardized Protocol to Investigate Trans-Endothelial Trafficking in Zebrafish: Nano-bio Interactions of PEG-based Nanoparticles in Live Vasculature

Trans-endothelial transport of nanoparticles remains poorly characterized in live organisms. The zebrafish is a well-established model for direct in vivo imaging; however, standardized controls are not consistently applied across studies. Here, we developed a standardized protocol to assess nanoparticle trans-endothelial trafficking in live zebrafish. We tested a range of tracers and identified 2000 kDa dextran as an optimal control for standardizing microinjections and quantifying nanoparticle transport in a systematic unbiased manner. As validation, we identified the early physiological trans-endothelial transport pathways in zebrafish embryos using 40 kDa dextran as a nanoparticle surrogate. Using our workflow, we assessed the extravasation of 3, 7, 32 and 47 nm polyethylene glycol (PEG)-based nanoparticles. Using cAMP stimulation to restrict paracellular routes, and inhibitors to impede dynamin-dependent endocytosis, we demonstrated that PEG-based hyperbranched polymer (HBP) nanoparticles of 3 to 7 nm traverse the endothelial barrier via paracellular routes and 32 and 47 nm PEG micelles adopt dynamin- dependent endocytic trafficking over paracellular transport. We characterized the emergence of caveolae in the vasculature up to 17 days post-fertilization (dpf) using a cavin1b knock-in zebrafish line. Using cavin1a/cavin1b double knockout (DKO) zebrafish, and tumor-bearing Cavin-1 null mice, we showed that caveolae do not contribute to the transvascular transport of these PEG-based nanoparticles. This work highlights the rigour of the standardized protocol for assessing nanoparticle trans-endothelial transport in the live zebrafish, providing a systematic approach for quantification using a standardized control.

cell biology↗

bioRxiv2025

Procrastination partly reflects an evolutionary byproduct of non-planning impulsivity

Procrastination has immediately visible repercussions on health and survival resilience, yet shows stably heritable and remains increasingly pervasive across human societies. Despite a paradox, this behavior is theoretically explained to represent a byproduct of evolutionary advantages underlying impulsivity, yet not deciphered well by scientific evidences. After adjusting psychometric endogeneity, we demonstrate the unique predictive roles of non-planning impulsivity (NPI) during late adolescence and early adulthood uniquely predicts procrastination in later adulthood in a twin cohort (N = 154). This association was further replicated in two independent cohorts (N = 327, N = 1,543). Using AE models, in conjunction of single-paper meta-analytic synthesis (N = 3,656 twin pairs), we observed significant shared genetic contributions underlying this NPI-procrastination association (rg = 0.51, 95% CI: 0.18 - 0.84). Beyond to the phenotypic heritability, employing a Genome-Wide-Association Study (GWAS), six NPI-procrastination overlapping SNPs are identified, functionally accounting for neural dysregulation. Thus, leveraging neurodevelopmental normative modelling (N = 37,407), online meta-analytic estimations (k = 198, loci = 5,855) and seed-based d mapping estimates (N = 893), cortical deviations in the left dorsolateral prefrontal cortex (DLPFC) - the brain region showing highest probabilistic overlap mapping NPI to procrastination, partly explains their shared genetic variants, but are substantially independent in genetic contribution. Mendelian Randomization analysis finally indicates causal roles of NPI and procrastination both, to DLPFC deviations. Our findings empirically clarified this theory that procrastination partly derives from NPI as an evolutionary byproduct indeed, but is still unique in neurogenetic entities. Brief summaryProcrastination is a puzzling human behavior that compromises survival-relevant outcomes yet remains both widespread and heritable. Although theorized as a byproduct of impulsivitys evolutionary advantages, empirical support for this account has been limited. Here, we provide converging evidence across psychometric, genetic, and neuroimaging modalities to show that non-planning impulsivity during late adolescence and early adulthood uniquely predicts later procrastination, and that the two traits share significant genetic overlap. We further identify specific genetic variants and morphological deviations in the DLPFC that link, but also partially dissociate, their biological pathways. These findings clarify the evolutionary and neurogenetic architecture of procrastination and underscore its partial derivation from impulsivity alongside distinct developmental origins.

neuroscience↗

bioRxiv2025

Non-invasive Free-breathing Gating-free Extracellular Cellular Volume Quantification for Repetitive Myocardial Fibrosis Evaluation in Rodents

BackgroundInterstitial myocardial fibrosis is a crucial pathological feature of many cardiovascular disorders. Myocardial fibrosis resulting in extracellular volume (ECV) expansion can be non-invasively quantified by cardiac MRI (CMR) with T1 mapping before and after gadolinium (Gd) contrast agent administration. However, longitudinal repetitive ECV measurements are challenging in rodents due to the prolonged scan time with cardiac and respiratory gating that is required for conventional T1 mapping and the invasive nature of the rodent intravenous lines. MethodsTo address these challenges, the objective of this study is to establish a fast, free- breathing, and gating-free ECV procedure with a non-invasive subcutaneous catheter for in- scanner Gd administration that can allow longitudinal repetitive ECV evaluations in rodent models. This is achieved by (1) IntraGate sequence for free-breathing gating-free cardiac imaging, (2) non-invasive subcutaneous in-scanner Gd administration, and (3) fast T1 mapping with varied flip angle (VFA) in conjunction with (4) triple jugular vein blood T1 normalization. Additionally, full cine CMR (multi-slice short-axis, long-axis 2-chamber, and long-axis 4- chamber) was acquired during the waiting period for comprehensive systolic cardiac functional and strain analysis. ResultsWe have successfully established a non-invasive fast ECV quantification protocol to enable longitudinal repetitive ECV quantifications in rodents. Non-invasive subcutaneous Gd bolus administration induced reasonable dynamic contrast enhancement (DCE) time course reaching a steady state in [~] 20 min for stable T1 quantification. The free-breathing gating-free VFA T1 quantification scheme allows for rapid cardiac ([~]2.5 min) and jugular vein (49 sec) T1 quantification with no motion artifacts. The triple jugular vein T1 acquisitions (1 pre-contrast and 2 post-contrast) immediately flanking the heart T1 acquisitions enable accurate myocardial ECV quantification. Our data demonstrated that left-ventricular myocardial ECV quantifications were highly reproducible with repeated scans, and the ECV values (0.25) are comparable to reported ranges among humans and rodents. This protocol was successfully applied to ischemic reperfusion injury model to detect myocardial fibrosis that was validated with histopathology. ConclusionWe have established a simple, fast, non-invasive, and robust CMR protocol in rodents that can enable longitudinal repetitive ECV quantifications for cardiovascular disease progression. It can be used to monitor disease regression with interventions. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/664411v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@14b44e5org.highwire.dtl.DTLVardef@985392org.highwire.dtl.DTLVardef@96cef7org.highwire.dtl.DTLVardef@ede47d_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

mTORC1-Dependent Regulation of the CCL24-CCR3 Axis Controls Granuloma Formation and Maintenance in Sarcoidosis

Sarcoidosis is a chronic granulomatous disease marked by persistent inflammation and immune cell aggregation, yet its molecular underpinnings remain incompletely understood, hindering the development of effective targeted therapies. Here, we report that deletion of TSC1 or TSC2 in mice using a Fsp1-Cre leads to spontaneous formation of sarcoid-like granulomas, driven by hyperactivation of the mTORC1 pathway in fibroblasts and interstitial macrophages. Through inflammatory cytokine/chemokine array, we identified CCL24, a chemokine ligand for CCR3, as a key immunoregulatory molecule downregulated in both our murine model and sarcoid cohort plasma. Mechanistically, mTORC1 suppresses CCL24 expression via aberrant STAT3 signaling in fibroblasts and promotes CCR3 expression in interstitial macrophages, uncovering a novel regulatory axis in granuloma formation and maintenance. Pharmacological inhibition using rapamycin and azithromycin markedly attenuated granuloma burden and normalized CCL24-CCR3 signaling, underscoring the therapeutic relevance of this axis. Together, our study establishes a mechanistic link between mTORC1 activation, CCL24-CCR3 dysregulation, and granuloma persistence, offering not only a new insight into molecular mechanisms in sarcoidosis but also identifying promising targets for clinical intervention.

immunology↗

bioRxiv2025

BrainBeacon: A Cross-Species Foundation Model for Single-cell Resolved Brain Spatial Transcriptomics

The brains functional complexity emerges from spatiotemporal heterogeneity in molecular, cellular, and circuit organization, shaped by evolution, aging, and disease. Single-cell spatial transcriptomics provides a transformative framework to decode this complexity, resolving cell-type-specific expression patterns, region-specific regulation, evolutionary divergence, and disease-associated disruptions. Despite recent advances in spatial transcriptomics, a unified foundation model capturing cross-species, whole-brain cellular architecture remains lacking. Here, we introduce BrainBeacon, the first cross-species foundation model for whole-brain spatial transcriptomics. Trained on 133 million spatially resolved cells covering a total area of 210194 mm2 from human, macaque, marmoset and mouse brains profiled across five major platforms, BrainBeacon integrates gene expression rankings, spatial cellular organization, and evolutionarily conserved genetic relationships into a unified transformer-based architecture. A two-stage training strategy captures both intra-cellular transcriptional dependencies and inter-cellular spatial interactions, yielding biologically grounded and interpretable representations of brain structure. Subsequently, BrainBeacon enables cross-species alignment of brain cell types and anatomical regions, facilitating integrative analyses of conserved and divergent cellular architectures. Moreover, it uncovers spatial regulatory mechanisms of aging by predicting bidirectional perturbation responses between cells and their local niche. Together, BrainBeacon serves as a foundational cross-species model for whole-brain spatial transcriptomics, enabling virtual brain atlas construction, systematic in silico perturbation studies, and mechanistic insights into brain disease pathogenesis.

bioinformatics↗

bioRxiv2025

Multi-omics characterization of the skin microbiota reveals the anti-aging roles of Stenotrophomonas maltophilia

Shifts in the skin microbiome have shown a close link to chronological age. However, the contribution of skin microbiome in skin aging phenotypes remains unclear. To explore this, we performed phenotypic, metabolomic, metagenomic, and functional analyses on a cohort with divergent skin aging phenotypes. Genome-scale metabolic models (GEMs) integrated with metabolomic analysis revealed that Stenotrophomonas maltophilia, enriched in the younger group (categorized by AI-predicted age and skin elasticity), utilizes the glutathione cycle to maintain redox homeostasis. Cellular experiments showed its metabolites enhanced GSH synthesis and alleviated oxidative stress-induced skin aging by upregulating key genes in fibroblasts, including GCLM, PGD, SOD2, and NQO1. Additionally, GEMs highlighted its potential anti-aging roles in regulating host metabolic pathways involving betaine, lysolecithin, and porphyrin. In parallel, Acinetobacter guillouiae was found to influence host melanin metabolism by degrading dopamine (DA) and 3-methoxytyramine (3-MT), offering potential therapeutic strategies for mitigating pigmentation. Our findings highlight the dynamic interplay between skin microbiota and the host in aging, offering new insights for designing targeted anti-aging interventions.

microbiology↗

bioRxiv2025

Rational design of oxidation-resistant antibodies through local electrostatic modulation

Oxidation is a significant degradation pathway in proteins, particularly therapeutic antibodies, that can impair function, efficacy, and stability. Understanding the sequence and structural factors that drive oxidation susceptibility is critical for incorporating chemical stability into early-stage antibody design. Here, we present a machine learning classifier trained on expert-guided structural features to assess tryptophan (Trp) oxidation risks in the complementarity-determining regions (CDR) of 187 antibodies produced internally at Genentech. The model reveals a strong correlation between local negative electrostatic potential and Trp oxidation susceptibility. A simplified two-parameter model derived from these insights achieves 79% accuracy in classifying oxidation risk, compared to 84% accuracy with the full-feature classifier. Beyond our internal dataset, the two-parameter model successfully predicted oxidation risk for all CDR Trp sites in a blind subset of eight clinical-stage antibodies. In addition, we show that modulating the electrostatic potential around the Trp side-chains through distant charge-altering mutations can significantly reduce oxidation rates. In four out of five re-engineered antibodies, oxidation rates decreased by approximately 50%, while half of these maintained binding affinity. Finally, we demonstrate that this approach can guide multi-property optimization by balancing oxidation resistance and affinity in an anti-CD33 antibody. These results establish a strong link between local electrostatic environments and Trp oxidation susceptibility, and provide a practical framework for designing oxidation resistant biotherapeutics.

biochemistry↗

bioRxiv2025

Natural gradient Bayesian sampling: an innate algorithm emerges in canonical cortical circuits

AO_SCPLOWBSTRACTC_SCPLOWAccumulating evidence suggests the canonical cortical circuit, consisting of excitatory (E) and diverse classes of inhibitory (I) interneurons, implements Bayesian posterior sampling. However, most of the identified circuits sampling algorithms are simpler than the nonlinear circuit dynamics, suggesting complex circuits may implement more advanced algorithms. Through comprehensive theoretical analyses, we discover the canonical circuit innately implements natural gradient Bayesian sampling, which is an advanced sampling algorithm that adaptively adjusts the sampling step size based on the local geometry of stimulus posteriors measured by Fisher information. Specifically, the nonlinear circuit dynamics can implement natural gradient Langevin and Hamiltonian sampling of uni- and multi-variate stimulus posteriors, and these algorithms can be switched by interneurons. We also find that the non-equilibrium circuit dynamics when transitioning from the resting to evoked state can further accelerate natural gradient sampling, and analytically identify the neural circuits annealing strategy. Remarkably, we identify the approximated computational strategies employed in the circuit dynamics, which even resemble the ones widely used in machine learning. Our work provides an overarching connection between canonical circuit dynamics and advanced sampling algorithms, deepening our understanding of the circuit algorithms of Bayesian sampling.

neuroscience↗

bioRxiv2025

Multiparametric Correlative Topographical and Volumetric Fluorescence Microscopy

Live-cell imaging of cell surface topography and intracellular architecture is essential for understanding cellular function. However, conventional approaches often involve trade-offs between resolution, invasiveness, and volumetric coverage. Here, we present an integrated Scanning Ion Conductance Microscope and single-objective Oblique Plane Microscope (SICM-OPM) system that enables simultaneous non-contact topographical imaging and volumetric fluorescence imaging within the same live cell. Beyond correlative live imaging, the platform supports nanomechanical mapping with tens-of-nanometres resolution, fluorescence-guided localised molecular delivery via the SICM, and benefits from reduced photobleaching due to light-sheet excitation. We demonstrate this platforms capabilities by visualising imipramine-induced T-tubule remodelling in live cardiomyocytes, revealing subsurface detubulation while surface morphology remains preserved. Additionally, we show precision delivery of fluorescent cargos--including dextrans and -synuclein--into diatom and mammalian cells, alongside localised stiffness mapping to evaluate mechanical responses. We believe this technique opens new avenues for correlative structural, functional, and biophysical studies in live cells, with broad relevance to cell biology, neurodegeneration, and mechanobiology.

biophysics↗

bioRxiv2025

Connectome analysis of a cerebellum-like circuit for sensory prediction

Stable and accurate perception involves comparing incoming sensory input with internally- generated predictions 1-3. A mechanistic understanding of this process has been elusive due to the size and complexity of the relevant brain regions in mammals. Here we leverage connectomics to comprehensively map the cell types and synaptic connections underlying a well-characterized and ecologically relevant form of predictive sensory processing in the cerebellum-like electrosensory lobe (ELL) of weakly electric fish 4,5. Connectome analysis reveals highly-structured feedforward and recurrent synaptic connectivity mediating the cancellation of predictable electrosensory input. A computational model constrained by prior electrophysiological recordings shows how this connectivity supports the formation of predictions at multiple sites within the network and how the ELL solves a continual learning problem by maintaining fast and accurate predictions despite noise and changes in environmental context. Overall, these findings provide a blueprint for using connectomics to elucidate learning in vertebrate nervous systems.

neuroscience↗

bioRxiv2025

An active Unc13A is Reboundless in sleep homeostasis

One of the major characteristics of sleep is homeostatic sleep rebound following sleep loss. While the molecular mechanisms of baseline sleep regulation have been intensively studied, a specific molecular understanding of sleep rebound remains elusive. Here, we show that a constitutively active form of the Munc13-family presynaptic release factor Unc13A, which lacks the inhibitory Ca2+/calmodulin interaction domain (Unc13AWRWR), dominantly suppressed sleep rebound upon acute sleep deprivation, leading to a nearly complete elimination of recovery sleep ("reboundless"). In contrast, baseline sleep remained largely normal. Through a genetic modifier screen, we found that this dominant "reboundless" phenotype of Unc13AWRWR was rescued by a partial loss of Snap, a cofactor of NSF required for disassembly and recycling of post-fusion cis-SNARE complex. Given that Unc13A promotes fusion-competent trans-SNARE complex formation, these findings suggest that sleep rebound may depend on a delicate balance between SNARE complex assembly and recycling. Additionally, we found that expression of a human disease-associated active Unc13A (Unc13APL) variant attenuated baseline and rebound sleep. Since both Unc13AWRWR and Unc13APL were shown to promote presynaptic release probability (Pr), we speculate that Unc13A suppresses recovery sleep likely by increasing Pr and subsequently enhancing synaptic transmission, probably through elevated trans-SNARE formation and efficient cis-SNARE recycling. Taken together, our data demonstrate a fundamental role of Unc13A and SNARE dynamics in sleep homeostasis.

neuroscience↗

bioRxiv2025

Specificity of Aberrant Exons in a Saturated Background of Differentially Expressed Exons

Determining the maximal specificity of aberrant exons from multifactorial disease tissues in a whole body background could provide insights into the exon origin as well as potential targets of diagnosis or therapy, but it remains a challenging task. For this purpose, we obtained a saturated list of differentially expressed exons (DEXs) from our independent reference human exome extracted from 56 normal tissues by DEXSeq. We found that the DEXs comprised the majority of the reference exome and that 99.4% of cancer-specific exons relative to paired normal tissues fell within the DEX list, consistent with the ectopic expression of the majority of aberrant exons. We then screened over seven thousand pathogenic single nucleotide variants (SNVs) in the TCGA and COSMIC databases by SpliceAI. The analysis identified over three hundreds of highly confident, mostly somatic SNV-specific splicing events and/or novel exonic fragments in five types of adenocarcinomas. Interestingly, these events are all associated with cis-acting mutations in tumor suppressor genes, particularly in TP53 with an antigenic novel peptide. This revelation of the DEX exome dominance and non-specificity of nearly all aberrant exons not only reshapes our understanding of the normal human exome by highlighting its mainly variable over constitutive exons, but also illuminates the path through cis-acting somatic and pathogenic SNVs to identify genuine cancer-specific exonic fragments that are absent in any normal tissues, beyond neo-exon junctions. This path holds promise for identifying novel peptide fragments for antigens in holistic cancer treatments including vaccination and immunotherapies.

cancer biology↗

bioRxiv2025

Intestinal Epithelial C/EBPβ Deficiency Impairs Colitis-Associated Tumorigenesis by Disrupting CXCL1 /CXCL2/CXCL5-CXCR2-Mediated Neutrophil Infiltration

Dysregulated transcription factors critically link chronic inflammation to oncogenesis in colitis-associated colorectal cancer (CAC), but their mechanistic roles remain incompletely understood. By integrating microarray and transcriptome sequencing data from ulcerative colitis (UC), colitis-associated cancer (CAC), and colorectal cancer (CRC) patients, we identify C/EBP{beta} as a key transcriptional regulator whose elevated expression inversely correlates with survival. In azoxymethane (AOM)/dextran sulfate sodium (DSS)-induced CAC models, intestinal epithelial C/EBP{beta} is upregulated during tumor progression, correlating with exacerbated tumor burden and neutrophil infiltration. Mice with intestinal epithelial-specific Cebpb deletion (Cebpb{Delta}IEC) show resistance to carcinogenesis, accompanied by reduced neutrophil infiltration and tumor growth. Mechanistically, C/EBP{beta} transcriptionally activates CXCR2 ligands (CXCL1, CXCL2, and CXCL5) to drive neutrophil recruitment. Pharmacological inhibition of CXCR2 phenocopies the anti-tumor effects of Cebpb{Delta}IEC deletion, further validating this axis as a therapeutic target. Correlation analysis in patient tissues confirms positive relationships between C/EBP{beta}, CXCR2 ligands, and neutrophil infiltration, suggesting that targeting the C/EBP{beta}-CXCL1/2/5-CXCR2 axis may offer a novel strategy for CAC treatment.

cancer biology↗