Biology subjects

Zhao, X.

Publications and source records attributed to Zhao, X..

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

ESX-1 substrates ESAT-6 and CFP-10 limit cGAS-STING activation via DNA and Zn2+ restriction

ESX-1-mediated phagosomal permeabilization exposes mycobacterial DNA to cytosolic cGAS-STING surveillance, yet the response is not overwhelming, suggesting additional layers of control exist. Here we show that the ESX-1 substrates ESAT-6 and CFP-10 constrain cGAS activation through complementary biochemical mechanisms. Purified Mycobacterium tuberculosis CFP-10 is a metal-dependent, 5'-3' exonuclease-like enzyme that preferentially degrades linear DNA, limiting the availability of stimulatory ligand. By contrast, purified M. tuberculosis ESAT-6 binds Zn2+ and limits the Zn2+-dependent conditions required for cGAS activation. During M. marinum infection, loss of these substrates augmented interferon-associated responses. Wild-type alleles restored immune suppression, whereas DNA-processing-defective CFP-10 or Zn2+-binding-defective ESAT-6 variants did not. These genotype-dependent differences were largely abolished in cGas-/- and Sting-/- macrophages. The double mutant was attenuated in zebrafish and mice, and its enhanced immune activation and attenuation were markedly diminished in cGas-/- mice. Prior exposure to the mutant improved zebrafish survival following wild-type challenge. Thus, beyond enabling mycobacterial DNA access to the cytosol, ESX-1 deploys its substrates to constrain cGAS-STING signaling by controlling activating-ligand availability and the metal-dependent environment required for sensor activation.

microbiology↗

bioRxiv2026

Plantaricin JK from Lactiplantibacillus plantarum ZJ316 inhibits enterohemorrhagic Escherichia coli O104:H4 and alters fecal microbial communities in vitro

Enterohemorrhagic Escherichia coli (EHEC) O104:H4 is a highly virulent foodborne pathogen for which antibiotic therapy is contraindicated, severely restricting conventional treatment options; therefore, the development of novel antimicrobial strategies is essential. This study investigated the antibacterial activity and gut microbiota-modulating effects of plantaricin JK (PlnJK), a two-peptide bacteriocin from Lactiplantibacillus plantarum. Chemically synthesized PlnJK exhibited a minimum inhibitory concentration (MIC) of 32 M against E. coli O104:H4, disrupting membrane integrity as evidenced by increased extracellular conductivity, ATP depletion, and ultrastructural damage. In an in vitro fecal fermentation model, PlnJK reduced Escherichia-Shigella abundance from 36.70% to 30.60% which contains E. coli O104:H4-related taxa, enriched Clostridium (5.70% vs 2.40% in infection group), Rikenellaceae, and Lactobacillaceae, and significantly elevated short-chain fatty acid (SCFA) levels including butyrate (p < 0.01) and isovalerate (p < 0.05). To translate this into a deliverable format, CRISPR-Cas9-engineered L. plantarum strains with plnJK knockout, complementation, and overexpression were constructed. Compared with the chemically synthesized peptide, LAB-derived PlnJK--especially from the overexpression strain--showed superior efficacy in restoring microbial diversity and enhancing SCFA production, significantly increased Shannon index and reduced dominance (p < 0.01), while promoting butyrate (p < 0.01) and isovalerate (p < 0.01) production compared to the knockout control. The engineered strains further revealed a clear dose-dependent effect, as overexpression potentiated while knockout abolished the beneficial modulation. These findings demonstrate that PlnJK acts through membrane disruption and beneficially modulates gut microecology, with LAB-mediated in situ delivery offering a promising strategy for anti-EHEC live biotherapeutic development.

microbiology↗

bioRxiv2026

Effects of Alternating Polarity Frequency on the Assembly of Electro-Methanogenic Microbial Communities

Electro-methanogenesis can enhance methane production and has attracted extensive interest, but the current strategies for building electro-methanogenic microbial communities suffer from several limitations. Alternating polarity has been shown as a new strategy to build electro-methanogenic communities, but the impact of alternation frequency on community assembly remains to be understood. In this study, the impact was evaluated using bioelectrochemical systems amended with granular activated carbon, and the working-electrode potential was alternated between +0.4 and -0.4 V vs. SHE at six frequencies ranging from 0.5 to 12 days. Among the tested conditions, 4-d alternation led to the best overall performance, producing approximately 250 L/L/kg cumulative biogas, 96% methane content, and a 45% methane yield, while preserving a stable and reproducible community structure. The community contained two Methanobacterium populations, two putatively electroactive Geobacter populations, and one putatively electroactive Pseudomonas population, together with diverse fermentative and syntrophic bacteria. Transcript-based analyses revealed clear frequency- and potential-dependent shifts in the activity of these functional groups. Redundancy analysis associated the Methanobacterium formicicum-related population with cathodic current and methane production, whereas the Geobacter sulfurreducens-related population was linked to anodic current and methane production. Bayesian and local-similarity networks further connected methanogen dynamics with specific electroactive, fermentative, and syntrophic partners. Collectively, these results establish alternating polarity frequency as a critical parameter for building robust communities capable of high-rate, high-quality methane production.

microbiology↗

bioRxiv2026

Live imaging reveals oocyte membrane pre-remodeling forming permissive space for asymmetric division

Abstract Successful oocyte maturation requires first polar body (PB1) extrusion, yet how the oocyte prepares for this asymmetric event remains unclear. Live membrane imaging of mouse oocytes reveals pronounced regional heterogeneity in plasma-membrane dynamics, generating an early polarized pattern across the surface. Whereas most of the oocyte surface and its microvilli remain relatively stable, a discrete membrane domain collapses and retracts around germinal vesicle breakdown (GVBD), separating from the zona pellucida to establish a pre-extrusion space (PES). Transient oocyte comb-like protrusions arise within the PES and subsequently collapse, converting the protrusion-filled region into an open cavity before PB1 extrusion. Mechanistically, early ERK28 dependent dissociation of the cortical scaffold ZO-1 is required for this space to form. ERK2 phosphorylates ZO-1, suppresses its phase separation, and promotes its removal from the cortex. Blocking MEK-ERK signaling prevents ZO-1 dissociation, abolishes pre-extrusion space formation, and impairs PB1 extrusion, whereas ERK activation restores these events in aged oocytes. Together, our findings identify a membrane collapse-based pre-remodeling mechanism that licenses PB1 extrusion and reveal ERK-ZO-1 signaling as a key regulator of oocyte maturation.

cell biology↗

bioRxiv2026

Causal event structure shapes convergent reactivation signatures in human cortex and language model

Humans adapt to changing environments by understanding the latent causal structure of events, and modern large language models (LLMs) increasingly exhibit analogous abilities. However, elucidating how causal knowledge is represented and integrated in the human brain and in LLMs poses a substantial challenge for cognitive science. To address this, we combine topological analysis of representational manifolds with neuroscientific analyses of reactivation. We find that event-level causal relations modulate temporally structured neural reactivation in the human brain, particularly in the angular gyrus, precuneus and prefrontal cortex. By contrast, LLMs express these relations through positionally structured representational reactivation. Despite these differences, the resulting reactivation patterns exhibit similar intrinsic manifold structure across the two systems. Together, these findings suggest that the human brain and LLM share a common principle for organizing causal knowledge.

neuroscience↗

bioRxiv2026

Decoupled recovery of soil physicochemistry, microbiome and methane sink function during secondary forest succession in the Eastern Himalayas

Secondary forests are increasingly important for biodiversity recovery and ecosystem functioning after disturbance. As vegetation regenerates, accompanying shifts in soil conditions and microbial communities regulate climate-relevant processes such as atmospheric methane (CH$_4$) uptake. Whether these belowground dimensions recover synchronously, however, remains unclear. Here we show that belowground recovery followed asynchronous trajectories across a forest chronosequence in Metok, Eastern Himalayas. Soil inorganic properties and microbial community composition converged progressively on the primary-forest state as soils acidified. By contrast, soil organic carbon, microbial diversity and abundance appeared to recover by 25 years but diverged again at 40 years. Co-occurrence network topology resembled the primary forest by 40 years, yet the keystone taxa underlying it were entirely stage specific. Atmospheric CH$_4$ uptake fluctuated: uptake recovered to primary-forest levels in 25-year stands but weakened in 40-year stands to rates comparable with the recently disturbed 5-year forest. Rather than canonical methane-cycling taxa, four amplicon sequence variants---three assigned to \textit{Mycobacterium}---tracked CH$_4$ flux closely while acting as hubs or connectors in the co-occurrence networks, warranting genomic and experimental work to resolve their function. Apparent recovery within the first 25 years therefore did not persist, cautioning against inferring restoration success from early succession alone and highlighting the need for longer chronosequences and repeated observation to resolve the dynamics of secondary-forest recovery.

microbiology↗

bioRxiv2026

Sum-h2, enabling genetic discovery for deep learning-derived phenotypes through a fast evaluation framework and arena of performance

In the recent growing interest of AI research toward biology, genetic association studies of AI- derived phenotypes from high-content modalities such as images emerges as a powerful means for biological discovery. However, such AI-phenotyping methods still lacks a good optimization target and an efficient evaluation framework. The number of discovered loci was the major criterion for evaluating the quality of AI-derived phenotypes. However, the time and computational resources required for running the GWAS and subsequent loci-clumping are substantial, limiting the rapid development and iteration of deep learning representation algorithms. Here we present a 1000x faster and lightweight framework, sum-h2, than traditional GWAS framework for evaluating genetic discovery through total heritability. We revisit tr(P^(-1) G), previously proposed in the context of evolutionary studies, as a measure of multi-phenotype heritability. We showed that sum-h2, the sum of heritability over phenotypic Principal Components (PCs), is equivalent to the linear transformation-invariant tr(P^(-1) G), through both theoretical proof and simulation studies. Moreover, sum-h2 can be estimated rapidly with minimal information loss over a relatedness-enriched sample, while preserving the relative ranking of endophenotypes by GWAS loci counts. Based on selected UKB data and sum-h2, we set up a Genetic Discovery Arena, enabling rapid and fair comparisons for the development and optimization of deep learning-derived phenotyping methods.

bioinformatics↗

bioRxiv2026

Unraveling APA dynamics during quiescence transitions reveals Pabp modulation of sod2 expression via APA to regulate cellular quiescence

Quiescence is a reversible proliferation arrest enabling cells to adapt to environmental changes, yet the post-transcriptional mechanisms governing its transitions remain poorly understood. Here, we map genome-wide alternative polyadenylation (APA) dynamics across 15 time points of quiescence transitions in fission yeast using 3'-end RNA sequencing. We reveal that APA undergoes extensive remodeling: driving global 3'UTR lengthening during early quiescence entry, 3' UTR shortening upon quiescence establishment, and progressive reversal to proliferative-state lengths during quiescence exit. Integrating 3' UTR dynamics with differential expression analysis, we identify candidate genes potentially regulated through APA-mediated 3' UTR mechanisms. We demonstrate that sod2, encoding mitochondrial superoxide dismutase, autoregulates its mRNA and protein levels via APA-dependent 3' UTR changes. Disrupting proximal APA site of sod2 in a mitophagy-deficient (atg43{Delta}) background exacerbates quiescence maintenance defects and mitochondrial dysfunction. We further identify Pabp as an upstream regulator of sod2 APA. This study establishes the temporal APA remodeling during quiescence transitions and reveals a Pabp-APA-sod2 regulatory axis governing post-transcriptional control of cellular quiescence.

cell biology↗

bioRxiv2026

Abstract representation in the hippocampus predicts spontaneously adopted structure-based behavioral strategy

Animals can solve the same problem using distinct strategies, ranging from memorization of specific sensory details to inference based on abstract task structure. Although the hippocampus has been implicated in cognitive map formation, how the structural information emerges in the hippocampus through learning and whether it is associated with behavioral strategies remain poorly understood. Here, we developed a structured cue-guided navigation task in virtual reality and performed longitudinal two-photon calcium imaging of hippocampal CA1 neurons throughout learning in mice. Although the task did not explicitly require learning of latent structure, most animals progressively transformed hippocampal map from sensory-oriented representations into cue-invariant representations of reward sequences. Strikingly, the emergence of such abstract hippocampal maps predicted whether individual animals adopted structure-based behavioral strategies when sensory information became partially unavailable. At the population level, reward-sequence representations formed a latent-state map capable for predicting future state transitions, generating a parsimonious Markov graph. Computational modeling further identified next-state prediction and representational regularization as two computational principles essential for generating similar latent-state structures across distinct architectures. Together, our findings suggest that the hippocampus spontaneously extracts abstract task structure through learning and that the geometry of hippocampal representations predicts problem-solving strategies.

neuroscience↗

bioRxiv2026

Graph-based pangenome of Venturia inaequalis, the apple scab fungus, reveals structural variants associated with population differentiation

Plant pathogen genomes adapt across coding and non-coding regions in response to their hosts, environments, and disease management practices. Venturia inaequalis, the causal agent of apple scab, has evolved alongside its Malus host throughout apple domestication. We generated 17 high-quality genome assemblies, including the first chromosome-scale assembly of V. inaequalis, to define the species' complete gene content and investigate the role of structural variation in genome evolution. Together with a previously published scaffold-level reference, these assemblies were used to construct a gene-based pangenome containing 215,301 predicted protein-coding genes clustered into 13,240 orthogroups, 88.11% of which were core (73.86%) or soft-core (14.25%), 11.88% shell (present in 2-16 isolates), and 0.1% private, indicating a highly conserved gene repertoire. Virulence-associated effectors were significantly enriched in the soft-core and shell components, and accessory apoplastic effectors displayed elevated nucleotide diversity and nonsynonymous-to-synonymous substitution ratios (Ka/Ks) relative to core effectors, consistent with diversification. We further identified a putative accessory chromosome of variable size (23-132.6 kb) in European and U.S. isolates encoding genes with virulence function. A graph-based pangenome identified 38,799 non-redundant structural variants (SVs), largely driven by Gypsy LTR retrotransposons. We used the graph-based pangenome to genotype 136 globally distributed V. inaequalis isolates and identified variants differentiating populations associated with domesticated apple (Malus domestica) from those associated with its Central Asian wild progenitor, M. sieversii. Together, these resources establish a foundation for future studies of diversity, host adaptation, and genome evolution in V. inaequalis.

genomics↗

bioRxiv2026

Loss of polr1c disrupts myelination in a zebrafish model of POLR1C-associated disease

Pathogenic variants in POLR1C, which encodes a shared subunit of RNA Polymerases (Pols) I and III, cause Treacher Collins syndrome (TCS) and POLR3-related leukodystrophy. While Pol I and Tp53-dependent mechanisms have been implicated in the pathogenesis of TCS, the basis of hypomyelination in POLR1C-associated POLR3-related leukodystrophy remains incompletely understood. Here, we show that polr1c mutant zebrafish exhibit reduced myelination in addition to previously described craniofacial anomalies. Oligodendrocyte precursor cells exhibit increased activation of the Tp53 pathway; however, these cells do not undergo apoptosis. Consistent with this finding, tp53 inhibition reduces cell death in polr1c mutants but fails to restore myelination, indicating that myelination deficits are not driven by Tp53-dependent progenitor loss in this model. polr1c mutants also exhibit reduced rRNA transcription by Pol I and reduced expression of some Pol III-transcribed tRNAs. Altogether, these data indicate distinct tissue-specific responses to polr1c deficiency and suggest persistent impairment of rRNA transcription contributes to deficient myelin development. These findings expand the developmental consequences of polr1c loss and advance our understanding of the molecular basis of POLR1C-associated diseases.

developmental biology↗

bioRxiv2026

Ultra-fast and scalable high-resolution full-length single-cell RNA sequencing using CHART-seq

Plate-based full-length single-cell RNA sequencing resolves transcript structure details but remains difficult to scale because each cell usually requires a separate library. Here we developed CHART-seq (Combinatorial Heteroduplex Assay via Recombinant Tn5), which uses orthogonally indexed Tn5 complexes to tagment RNA/cDNA heteroduplexes and permits early sample pooling. The workflow processed up to 96 cells per library, was compatible with 384-well expansion, and completed library preparation within 3 h at a reagent cost below US$1 per cell. At matched sequencing depth, CHART-seq detected more genes and annotated isoforms than Smart-seq2, Smart-seq3, Flash-seq and SHERRY2, while retaining broad genebody coverage and reproducible expression estimates. In the CHART-seq results of vascular smooth muscle cells, TGF-{beta}1 pretreatment before PDGF-BB exposure partly restored contractile features, suppressed a PDGF-associated inflammatory programme, and induced a distinct metabolic-matrix response with coordinated transcript-usage changes. These biological findings remain exploratory because independent biological replicates were unavailable. CHART-seq provides a rapid, scalable route to full-length single-cell transcript profiling with gene-programme and candidate isoform resolution.

genomics↗

bioRxiv2026

Spatial transcriptomics reveals selective vulnerability of cardiac neural crest-derived glial cells in human myocardial infarction

Cardiac neural crest-derived glial cells (CNGs) are recently identified glial cells that support cardiac autonomic innervation and maintain sympathetic-parasympathetic balance. Their fate in myocardial infarction (MI) is unknown. Here, we analyzed 16 human cardiac spatial transcriptomes spanning normal myocardium (n=4), infarct zone (n=5), border zone (inner, n=1; outer, n=3), and remote zone (n=3). CNGs (S100B+/GFAP+, CD68- spots) were selectively lost along a spatial gradient from healthy tissue to the infarct core (Spearman rho = -0.92, p = 4.5 x 10-7). Tissue-area-corrected analysis confirmed that CNG loss (26% retained in infarct zone vs. normal; p = 0.016) vastly exceeded overall tissue loss, indicating selective vulnerability rather than bulk tissue destruction. Mechanistically, oxidative phosphorylation (OXPHOS) activity in CNG-positive spots correlated positively with CNG survival (partial rho = 0.65, p = 0.009 after controlling for spot composition), consistent with a high metabolic demand underlying their ischemic sensitivity. Pyroptosis - but not ferroptosis or apoptosis - signatures correlated with CNG loss (partial rho = -0.67, p = 0.006). These findings identify CNGs as selectively vulnerable cellular components of the cardiac autonomic system in MI and nominate metabolic failure and pyroptosis as candidate mechanisms, providing a spatially resolved foundation for future mechanistic and interventional studies.

bioinformatics↗

bioRxiv2026

DiffGSP: reversing mRNA diffusion to unlock high-fidelity spatial transcriptomics

Spatial transcriptomics enables gene expression profiling within intact tissues while preserving spatial context, providing unprecedented insights into cellular organization and function. However, mRNA diffusion during tissue processing can cause transcripts originating from adjacent cells to be captured at a given spot. This spatial misalignment challenges a fundamental premise of spatial transcriptomics that measured gene expression faithfully corresponds to its spatial origin, thereby compromising spatial fidelity and potentially biasing biological interpretation. Here, we present DiffGSP, a physics-informed framework that integrates Fick's law with graph signal processing to explicitly model diffusion-induced distortions and recover the underlying spatial gene expression landscape. Comprehensive benchmarking across diverse datasets and evaluation metrics demonstrates the consistent ability of DiffGSP to restore spatial gene expression patterns. By computationally reversing diffusion-induced distortions, DiffGSP enables the discovery of fine anatomical structures in the mouse brain, spatially organized gene modules in the kidney, intratumoral heterogeneity in colorectal cancer, and tertiary lymphoid structures in lung adenocarcinoma. Built on a physically interpretable framework and broadly applicable to sequencing-based spatial transcriptomics technologies, DiffGSP improves the fidelity of spatial gene expression reconstruction and enables more reliable biological interpretation.

bioinformatics↗

bioRxiv2026

Expressing glycan motifs as a containment order increases sensitivity and uncovers motif redistributions

Glycan motifs are the standard readout of comparative glycomics, and pipelines treat them as independent features. Here, we show they are not. Motifs are partially ordered by substructure containment, so a parent motif's abundance dominates each of its children. We make that order explicit as a directed acyclic graph, which stratifies the multiple-testing family correctly and, together with an empirical-Bayes variance prior taken from each motif's containment neighborhood, raises estimated true positives across 45 glycomics datasets from 300 to 442 (+47%, p = 0.0001) after controlling for permutation-null false positives. Because a parent's children and its residual form a genuine sub-composition, their logratio balances need no reference frame and no scale model, and they separate a motif's own change from one inherited from its contexts. Of 337 significant parent motifs, 150 (45%) thus carry no signal of their own, while 138 motifs move only in the decomposition. We present case studies for both glycomics and glycoproteomics, including a recurrent reapportioning of core-1 sialylation at the immune-inhibitory disialyl-T antigen across eight human O-glycomes, and a colorectal fucosylation shift confined to the antenna, neither of which any marginal analysis reports.

bioinformatics↗

bioRxiv2026

Genetic regulation of circulating metabolome in cattle

The circulating metabolome is a vital intermediate layer linking genetics to complex phenotypes, yet existing genome-wide studies-even in humans-rarely capture dynamic physiological contexts or cellular regulatory mechanisms. Here, we present the Cattle Metabolome Atlas (https://cattlema.farmgtex.org/), a comprehensive resource of 3,436 plasma metabolites and 4,851 serum metabolites from 4,651 animals with matched sequence-level genotypes across highly dynamic parity and lactation stages. We mapped 728 plasma and 622 serum metabolite quantitative trait loci (mQTL), revealing widespread context-dependent regulatory architectures. Integrating these mQTL with the multi-tissue expression quantitative trait loci (eQTL) and single-cell atlas of 59 tissues demonstrates that 74-79% of mQTL colocalize with eQTL across 29 tissues, prioritizing the liver as the primary systemic hub and resolving metabolic programs at single-cell resolution. Furthermore, we charted 538 causal gene-tissue-metabolite-trait cascades across 11 complex traits in cattle. Finally, cross-species analyses demonstrate partial evolutionary conservation of genetic metabolism between cattle and humans, establishing this atlas as a powerful asset for cattle genetics and genomics, selective breeding, and comparative biology.

genetics↗

bioRxiv2026

The small molecule inhibitor SU056-mediated targeting of YB1 inhibits the Rb pathway in triple-negative breast cancer tumors

Background: Triple-negative breast cancer (TNBC) tumors lack expression of estrogen receptor (ER), progesterone receptor (PR), and HER2, limiting the availability of targeted therapeutic options. As a result, TNBC is characterized by a high propensity for metastasis, rapid recurrence, and poor overall prognosis. Despite significant research efforts, the molecular mechanisms that drive TNBC progression and metastasis remain incompletely understood. Y box binding protein 1 (YB1) is a multifunctional DNA/RNA-binding protein that regulates transcription, translation, and mRNA stability. Aberrant activation of YB1 has been implicated in multiple oncogenic processes, including proliferation, survival, invasion, metastasis, and therapy resistance in several cancer types, including TNBC. Our investigations have revealed a central role for YB1 in regulating key hallmarks of cancer that drive TNBC tumor progression and metastatic dissemination. Methods: Cell viability and drug sensitivity in TNBC cell lines were assessed using the MTT assay to determine IC50 values for pharmacologic inhibitors. Western blotting and quantitative RT PCR were used to quantify protein and mRNA expression levels in TNBC cell lines and tumor samples. Oncogenic phenotypes were evaluated using 2D colony formation assays, 3D tumorsphere growth assays, limiting dilution, and transwell migration assays to assess proliferative, stem-like, and migratory capacities. Cell cycle progression was analyzed using flow cytometry based assays. In vivo therapeutic efficacy was evaluated using preclinical xenograft and patient-derived xenograft (PDX) mouse models of TNBC to assess tumor growth and metastatic progression following treatment. Results: Our studies demonstrate that the small-molecule inhibitor SU056, which specifically targets YB1 for degradation, significantly suppresses the oncogenic behavior of TNBC cell lines and tumors. Pharmacologic inhibition of YB1 reduced TNBC cell proliferation, clonogenic growth, tumorsphere formation, stemness and migratory capacity. Importantly, combined treatment with SU056 and the CDK4/6 inhibitor Palbociclib enhanced the inhibitory effect on TNBC cell growth and tumor progression compared with either agent alone. Mechanistically, both genetic and pharmacologic targeting of YB1 suppressed TNBC tumor growth and metastatic potential through modulation of the Cyclin D/CDK4/6/Rb signaling axis, leading to inhibition of cell cycle progression and induction of G1 arrest. Conclusion: Collectively, these findings identify SU056/CDK4/6i combination as a potential therapeutic option for the treatment of Rb+ TNBC.

cancer biology↗