Biology subjects

Zhao, D.

Publications and source records attributed to Zhao, D..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Synergistic integration of inducible RNA switches enhances the manipulation of vector expression

Precise manipulation of gene expression is pivotal for gene function studies and the optimization of gene therapy. RNA-based gene switches are attractive tools due to their robust tunability by FDA-approved small molecules, the absence of exogenous immunogenic proteins, and the small size for gene delivery vectors such as adeno-associated virus (AAV). However, existing RNA switches only target a single step of gene expression such as transcription or RNA splicing, exhibiting intrinsic limitations in gene regulation. To overcome this issue, this study integrated the aptamer-based polyA regulator (pA), the drug-elicitable alternative splicing module (DreAM) and an engineered translation modulator with conditional upstream open reading frames (uORFs) to construct the DreAM-plus RNA switch. The pA-DreAM concatenation led to 1.5[~]5.0-fold and 1.2[~]4.4-fold increase of inducible fold changes than pA and DreAM, respectively. The uORF module further enhanced the switching performance by 1.4[~]6.3-fold. DreAM-plus-mediated transient transgene expression demonstrated a temporal resolution of about 24 hours and high tissue specificity to liver or heart. Critically, DreAM-plus achieved transient expression of an array of gene editors (SpCas9, SaCas9, Un1Cas12f1, OsCas12f1, AcCas12n, IsDra2 TnpB etc.) that significantly mitigated off-target effects by 1.4[~]2.8 folds in plasmids, lentivirus and AAV. In a new mouse model with lipid-nanoparticle-delivered pre-existing immunity, DreAM-plus attenuated AAV-delivered Cas-specific CD8 T cell immune toxicity in the liver and the heart. Therefore, multiple RNA switches could be synergistically integrated to build more sophisticated genetic cassettes for enhanced manipulation of gene expression.

bioengineering↗

bioRxiv2026

Notch signaling in the embryonic ectoderm promotes periderm cell fate and represses mineralization of vibrissa hair follicles

The Notch signaling pathway is a critical means to regulate cell fate choice in animals. Appropriate regulation of this pathway is also required for human face formation as both loss and gain of function mutations of Notch signaling can cause syndromes with craniofacial abnormalities. Here we examine the consequences of manipulation of Notch signaling in the early mouse embryonic ectoderm by either removing the transcriptional effector Rbpj or expressing a constitutively active form of the Notch1 intracellular domain. Loss of Rbpj resulted in cleft secondary palate but strikingly was also associated with the ectopic mineralization of vibrissa follicles. In contrast, activation of Notch signaling resulted in multiple embryonic defects including a fully penetrant bilateral cleft lip and palate. Further, single cell RNA-seq data indicated a switch from a basal epithelial cell identity towards periderm when Notch signal transduction was elevated. These cell fate changes were accompanied by misregulation of genes and pathways known to impact human and mouse orofacial clefting including Grhl3, Irf6, and Wnt pathway. Together, these findings provide insight into human craniofacial conditions caused by misregulated Notch activity. SUMMARY STATEMENTOur studies demonstrate that Notch signaling in the embryonic ectoderm stimulates periderm cell fate while also repressing transformation of the inner root sheath of whisker follicles into mineralized tissue.

developmental biology↗

bioRxiv2026

FluNexus: a versatile web platform for antigenic prediction and visualization of influenza A viruses

Influenza A viruses continuously undergo antigenic evolution to escape host immunity induced by previous infections or vaccinations, consequently causing seasonal epidemics and occasional pandemics. Antigenic prediction and visualization of influenza A viruses are crucial for precise vaccine strain selection and robust pandemic preparedness. However, a user-friendly online platform for these capabilities remains notably absent, despite widespread demand. Here, we present FluNexus (https://flunexus.com), the first-of-its-kind, one-stop-shop web platform designed to facilitate the prediction and visualization of the antigenic change in emerging variants. FluNexus features a data preprocessing module for hemagglutinin subunit 1 (HA1) and hemagglutination inhibition (HI) data across three major public health threat subtypes (H1, H3 and H5). Meanwhile, FluNexus provides an interactive interface for online antigenic prediction and offers practical guidance for researchers. Most notably, FluNexus offers the visualization of influenza A virus antigenic evolution, providing intuitive insights into its antigenic dynamics. Specially, FluNexus proposes a novel manifold-based method for positioning antigens and antisera, generating accurate antigenic cartographies even with sparse HI data. By alleviating the programming burden on biologists, FluNexus supports more informed decision-making in vaccine strain selection and strengthens surveillance and pandemic preparedness. HighlightsO_LIFluNexus features a data preprocessing module for HA1 and HI data spanning the H1, H3, and H5 subtypes. C_LIO_LIFluNexus facilitates online antigenic prediction utilizing ten state-of-the-art antigenic prediction tools, and offers practical guidance based on a comparative evaluation of their performance. C_LIO_LIFluNexus provides a visualization module for mapping antigenic evolution of influenza A viruses, incorporating a novel manifold-based method for antigenic cartography. C_LI

bioinformatics↗

bioRxiv2026

Stromal estrogen signaling regulates fallopian tube homeostasis and cancer initiation via inflammatory pathways

Lifetime estrogen exposure is a major risk factor for ovarian cancer, which can originate from fallopian tube epithelial (FTE) cells. Here we report that estrogen receptor (ER) signaling in fallopian tube (FT) stromal cells plays a critical developmental role in maintaining epithelial homeostasis by promoting FTE proliferation and ciliated differentiation. Stromal ER regulates expression of inflammatory cytokines, growth factors, and extracellular matrix components, creating a differentiation-supportive, tumor-suppressive niche that coordinates epithelial regeneration during hormonal cycles. Excessive or prolonged estrogen exposure, however, shifts this niche toward a tumor-promoting state by inducing inflammation and activating stemness-associated pathways, including JAK/STAT, in FTE cells. This effect is exacerbated in genetically altered FTE cells lacking key tumor suppressors, which resist differentiation while remaining responsive to stromal proliferation signals. These findings reveal how stromal ER signaling integrates hormonal cues, inflammation, aging, and genetic susceptibility to influence early events in FT carcinogenesis. In BriefEstrogen receptor signaling in fallopian tube stromal cells maintains epithelial homeostasis by promoting proliferation and ciliated differentiation. Excessive estrogen shifts this niche toward inflammation and stemness, cooperating with genetic susceptibility to drive early fallopian tube carcinogenesis. O_FIG O_LINKSMALLFIG WIDTH=190 HEIGHT=200 SRC="FIGDIR/small/700864v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@113b543org.highwire.dtl.DTLVardef@e1465corg.highwire.dtl.DTLVardef@1d279dcorg.highwire.dtl.DTLVardef@13e782c_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIStromal ER signaling maintains fallopian tube epithelial (FTE) cell homeostasis C_LIO_LIStromal ER promotes proliferation and ciliated differentiation of FTE cells C_LIO_LIExcess estrogen shifts this stromal niche toward tumor promotion via inflammation C_LIO_LIDifferentiation-resistant mutant FTE cells respond to stromal proliferation signals C_LI

cancer biology↗

bioRxiv2026

Tumor Cell Clustering Enhances Metastatic Competence by Regulating the H3K36 Histone Demethylase KDM2A

Disseminated tumor cells can form clusters via cell-cell adhesion, which increases their capacity to initiate metastasis. Metastatic clusters are characterized by distinct changes in transcription, suggesting that epigenetic mechanisms underlie their unique phenotypic state. By performing functional epigenomic studies in models of non-small cell lung cancer, we identified the histone H3 lysine 36 (H3K36) demethylase KDM2A as being differentially required for the fitness of metastatic cell clusters. This contextual dependency on KDM2A is predicated by tumor cell-cell aggregation, which specifically induces KDM2A binding to CpG island enriched promoters. At these defined genomic loci, KDM2A maintains H3K36 monomethylation, which preferentially correlates with transcriptional activation. KDM2A directly targets oxidative phosphorylation genes and KDM2A activity is required for optimal mitochondrial respiration and apical cell junction integrity in cell clusters. Consequently, suppressing KDM2A reduces metastatic seeding and colonization in multiple organs, including in the brain. These findings reveal a chromatin regulatory mechanism by which homotypic cell communication instructs the epigenome of disseminated tumor cells to potentiate their metastatic competence.

cancer biology↗

bioRxiv2025

A mouse model of CHCHD10 p.R15L familial ALS presents mild, age-related motor neuron degeneration without protein instability or mitochondrial dysfunction

Mutations in the mitochondrial protein CHCHD10 (D10) cause a spectrum of hereditary neurodegenerative disorders. Among these, the p.R15L variant is linked to a slowly progressive, late-onset familial form of amyotrophic lateral sclerosis (ALS) with unclear pathogenic mechanisms. To better understand this, we investigated a knock-in (KI) mouse model carrying the p.R15L mutation in the endogenous protein. Unlike previously described mutant D10 KI models, p.R15L KI mice exhibited normal D10 protein levels, with no evidence of large protein aggregates. Mitochondrial respiration and hydrogen peroxide emission in mitochondria isolated from muscle and brain were unaltered. Similarly, fibroblasts from human p.R15L carriers exhibited normal D10 levels and unchanged oxidative phosphorylation function. Histochemical analyses of p.R15L KI muscle revealed mild increases in mitochondrial enzymatic activity in a subset of muscle fibers and muscle transcriptomics showed elevated expression of PGC-1, suggesting enhanced mitochondrial biogenesis. p.R15L KI mice developed subtle, late-onset phenotypes, including reduced body weight and motor activity and increased anxiety-like behavior. Importantly, in aged mice electrophysiological studies demonstrated decreased amplitude of the compound muscle action potential, commensurate with a moderate loss of spinal cord motor neurons and elevated serum neurofilament light levels, indicative of neurodegeneration. Together, these results indicate that the p.R15L mutation produces a mild, late-onset motor neuron phenotype in mice, partially recapitulating the human disease, without mitochondrial functional or morphological alterations. The findings indicate that p.R15L D10 selectively impairs mouse motor neurons through a gain-of-function mechanism, providing a genetically accurate yet mild in vivo model of familial ALS.

neuroscience↗

bioRxiv2025

SF3A2 deacetylation at lysin 10 mitigates myocardial pathological remodeling by reprogramming cardiomyocyte metabolism

BackgroundDysregulation of splicing factor-mediated pre-mRNA alternative splicing (AS) underlies the progression of complex diseases, but the specific involvement of AS in myocardial pathological remodeling remains unclear. This study aimed to elucidate the role of splicing factor 3A, subunit 2 (SF3A2) in the development of myocardial pathological remodeling by regulating AS and its effect on metabolic reprogramming. MethodsWe evaluated the function and mechanism of SF3A2 in myocardial pathological remodeling using murine models induced by myocardial infarction (MI) and isoproterenol. The gain- and loss-of-function models (AAV9-cTNT delivery-mediated knock-in and lentivirus-mediated knockdown) combined with acetylomics, metabolomics, lipidomics, 13C-glucose tracing and immunoprecipitation coupled with liquid chromatography-tandem mass spectrometry (IP-MS) analyses were used to demonstrate the mechanism of SIRT7-mediated SF3A2 deacetylation at lysin 10 (K10). Unbiased RNA sequencing and AS analysis were conducted to identify the downstream effector of SF3A2. ResultsSF3A2 acetylation at lysine 10 was upregulated in cardiomyocytes in response to myocardial pathological remodeling. Functionally, the knock-in of a deacetylation-mimetic SF3A2 (K10R) mutant attenuated myocardial hypertrophy, fibrosis, and improved heart function. These phenotypes were accompanied by a redirection of glucose flux from anaerobic glycolysis to the TCA cycle, along with a promotion of fatty acid {beta}-oxidation by inhibiting CD36 translocation and decreasing ACLY activity. Mechanistically, SF3A2 mitigated metabolic reprogramming and mitochondrial dysfunction by regulating Nnt AS, a process involving the SF3A2-interacting protein Ddx1. IP-MS further identified SIRT7 as the deacetylase for SF3A2, which was found to be activated by ginsenoside Rg1 in a high-throughput screen, leading to improved heart function. ConclusionsOverall, our findings establish the SIRT7-SF3A2-Nnt axis as a critical regulator in metabolic reprogramming to delay pathological myocardial remodeling. Promoting SF3A2 deacetylation, mediated by AAV9 delivery or pharmacological activation of SIRT7, improved heart function, suggesting its potential as a therapeutic target for pathological myocardial remodeling.

molecular biology↗

bioRxiv2025

Regional and Global Analysis of Cerebrovascular Reactivity Using 4D Flow MRI

Cerebrovascular reactivity (CVR) assessments are promising for diagnostic and prognostic applications related to vascular function and neurodegenerative diseases. Current vascular imaging-based CVR indices have been limited to single-vessel analysis and report conflicting results, for example, whether there are differences in CVR between sexes. Alternative vascular imaging-based indices can be derived from 4D flow MRI, namely intracranial pulse wave velocity and pulsatility transmission, which are based on vascular regions and offer a more comprehensive perspective on vascular function that can also scale to a global level. To date, these types of indices have not been measured with a vascular stimulus. In this work, standard single-vessel and novel regional and global CVR indices were studied in 10 healthy young adults (29 {+/-} 2 years, 5 male, 5 female) in response to hypercapnia. Consistent increases in flow, area and velocity manifested at all levels and were greater in males. Regional pulse wave velocity and pulsatility transmission offered a minimum 40% increase in the dynamic range of CVR magnitudes that may benefit cohort stratification. Notably, pulse wave velocity increased in 50% of the vascular regions (most probably due to vasoconstriction), accompanying an increase in flow; a profound observation given the common expectation of vasorelaxation with hypercapnia. Consistently reduced flow, velocity, area, pulse wave velocity, and transmission index reactivities in females may partially explain the varying pathological outcomes between sexes, evidencing the continued value of 4D flow for the evaluation of CVR in other cohorts. New and NoteworthyCerebrovascular reactivity (CVR) of 4D flow-based intracranial pulse wave velocity and pulsatility transmission were evaluated during hypercapnia for the first time. Remarkably, pulse wave velocity increased in some cases and decreased in others, suggesting that vasorelaxation may not always occur during hypercapnia. These indices also expanded CVR dynamic range by more than 40 % compared to common velocimetry techniques, which could offer improved cohort stratification. Evidence of diminished CVR in females was also observed.

bioengineering↗

bioRxiv2025

Targeting ZNRF3 and RNF43 to Restore Regeneration and Reverse Metabolic Dysfunction-Associated Steatotic Liver Disease

Liver regeneration and hepatocyte metabolic identity are disrupted in metabolic dysfunction-associated steatotic liver disease (MASLD) and its advanced form, metabolic dysfunction-associated steatohepatitis (MASH), yet the mechanisms of restore liver regeneration and reprogram metabolism for disease reversal remains poorly understood. Here, we show that {beta}-Catenin activity progressively declines in hepatocytes during MASH in both humans and mice, coinciding with impaired regeneration and defective lipid clearance. Targeted deletion of the endogenous WNT pathway inhibitors ZNRF3 and RNF43 in hepatocytes after MASH onset reactivates {beta}-Catenin signaling, leading to robust regression of steatosis, inflammation, and fibrosis, and restoring regenerative capacity across multiple fatty liver disease models. Mechanistically, this therapeutic effect is driven by {beta}-Catenin-dependent induction of the alternative bile acid synthesis pathway without disrupting systemic lipid homeostasis. Importantly, both short-and long-term deletion of ZNRF3/RNF43 restores liver function without triggering tumorigenesis or hepatotoxicity, indicating a safe therapeutic window. These findings reveal that physiological activation of WNT/{beta}-catenin signaling via ZNRF3 and RNF43 offers a viable regenerative and metabolic strategy for reversing fatty liver disease.

cell biology↗

bioRxiv2025

AURKA inhibition amplifies DNA replication stress to foster WEE1 kinase dependency and synergistic antitumor effects with WEE1 inhibition in cancers

Highly elevated expression of the oncogene Aurora kinase A (AURKA) occurs in numerous human cancers harboring defective p53, nominating AURKA as a potential vulnerability in TP53-mutated cancer. However, clinical trials have indicated modest monotherapy activity of AURKA inhibitors. Here, we demonstrate that AURKA inhibition promotes phosphorylation of Replication Protein A (RPA), resulting in stalled DNA replication fork progression and eliciting a replication stress response in multiple TP53-mutated models, creating a druggable dependence on the mitotic checkpoint kinase WEE1. Combined inhibition of AURKA and WEE1 synergistically enhanced replication stress, tumor-specific apoptotic cell death, and mitotic catastrophe, and lead to marked tumor regression in cell line- and patient-derived xenograft models of TP53-mutated cancer. Our findings define enhanced DNA replication stress as underlying the strong synergy between AURKA and WEE1 inhibitors and offer preclinical confirmation of efficacy, indicating high potential for clinical translation of this synthetic lethal strategy for TP53-mutated carcinomas. Statement of significanceWe demonstrate that a small molecule AURKA inhibitor amplifies DNA replication stress in TP53-mutated carcinomas. This amplification of DNA replication stress can be leveraged this for synthetic lethal therapy in a combination with WEE1 inhibition that enhances antitumor effects in in vitro, in xenografts and in patient-derived xenograft models, advancing a promising novel combination therapy.

cancer biology↗

bioRxiv2025

Longitudinal single cell RNA-sequencing reveals evolution of micro- and macro-states in chronic myeloid leukemia

Single cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cancer, yet identifying meaningful disease states from single cell data remains challenging. Here, we systematically explore the chronic myeloid leukemia (CML) specific information content encoded in single cell versus bulk transcriptomics to resolve this paradox and clarify how discrete disease-defining states emerge from inherently noisy single cell data. We demonstrate that, while CML single cell transcriptomes exist along continuous transcriptional microstates, clinically relevant leukemia phenotypes clearly manifest only at the pseudobulk (macrostate) level. By leveraging state-transition theory, we reveal how robust disease phenotype state-transitions are governed by cell type specific contributions. Our results establish a theoretical framework explaining why discrete disease phenotypes remain hidden at the single cell scale but emerge clearly at the aggregated macrostate level, enabling previously inaccessible biological insights into leukemia evolution. By resolving how single-cell variation aggregates into macroscopic disease states, our framework provides new insight into CML progression and offers a broadly applicable strategy for exploring disease dynamics across cancers and other complex conditions.

systems biology↗

bioRxiv2025

Spatial geometry-aware deep learning for deciphering tissue structure from spatially resolved transcriptomics

Recent advances in spatially resolved transcriptomics have enabled high-throughput gene expression profiling while preserving spatial context, thereby facilitating the investigation of spatial heterogeneity within tissues. Here, we present SpatialGEO, a spatial geometry-aware deep learning framework designed to decipher tissue organizational structures through dual-encoder feature extraction and geometric graph learning. Experimental results demonstrate the superior accuracy of SpatialGEO in identifying spatial regions across datasets encompassing diverse biological contexts and spatial resolutions. Moreover, SpatialGEO uncovers key mechanisms of immune evasion and regulation within the tumor microenvironment and provides novel biological insights into mouse embryonic development.

bioinformatics↗

bioRxiv2025

A Multimodal Graph Learning Framework for Versatile Spatial Transcriptomics Analysis with SpatialModal

The development of spatial transcriptomics(ST) technologies enables the exploration of tissue structure and cellular function within a spatial context. However, mainstream analytical methods primarily focus on the gene expression modality itself and struggle to fully leverage auxiliary information from histological images, which limits precise dissection of complex biological structures. To address this, we propose SpatialModal, a multimodal graph learning framework that effectively integrates gene expression data and histological images from spatial transcriptomics to construct unified spatial representations. SpatialModal effectively captures synergistic interactions between modalities by jointly modeling intra- and inter-modal complementary features while incorporating spatial adjacency information. Furthermore, it employs a dual contrastive learning strategy to enhance the discriminative power of representations, thereby enabling efficient and robust analysis of tissue structures. We validate the effectiveness of this approach on multiple public datasets covering diverse tissue types, species, and resolutions. Experiments demonstrate that SpatialModal exhibits significant advantages in downstream tasks, including spatial domain identification, gene expression reconstruction, and pseudotime inference, and accurately elucidates the hierarchical structure of the mouse cortex as well as the metabolic-immune dynamic boundaries in the breast cancer microenvironment. Additionally, SpatialModal shows exceptional robustness in single-cell resolution and multi-slice integration tasks, providing an efficient and broadly applicable analytical tool for spatial transcriptomics research.

bioinformatics↗

bioRxiv2025

Neural organoids protect engineered heart tissues from glucolipotoxicity by transferring versican in a co-culture system

Metabolic disorders could cause dysregulated glucose and lipid at the systemic level, but how inter-tissue/organ communications contribute to glucolipotoxicity is difficult to dissect in animal models. To solve this problem, myocardium and nerve tissues were modeled by 3D engineered heart tissues (EHTs) and neural organoids (NOs), which were co-cultured in a generalized medium with normal or elevated glucose/fatty acid contents. Morphology, gene expression, cell death and functional assessments detected no apparent alterations of EHTs and NOs in co-culture under normal conditions. By contrast, NOs significantly ameliorated glucolipotoxicity in EHTs. Transcriptomic and protein secretion assays identified the extracellular matrix protein versican as a key molecule that was transferred from NOs into EHTs in the high-glucose/fatty acid condition. Recombinant versican protein treatment was sufficient to reduce glucolipotoxicity in EHTs. Adeno-associated virus-delivered versican overexpression was sufficient to ameliorate cardiac dysfunction in a murine model of diabetic cardiomyopathy. These data provide the proof-of-concept evidence that inter-tissue/organ communications exist in the co-culture of engineered tissues and organoids, which could be systemically studied to explore potential pathological mechanisms and therapeutic strategies for multi-organ diseases in vitro.

cell biology↗

bioRxiv2025

High-Throughput Multiomics Profiling of Model Systems Using the AVITI24 Platform

We present a multiomics platform comprising Teton, a detection assay system, and AVITI24, a dual-flowcell instrument that performs both cellular imaging and sequencing readout. Teton integrates a compartmentalized flowcell for cell culture with methods to measure morphology, RNA, and protein at subcellular resolution. The platform quantifies morphological features through cell painting of 6 cellular components, RNA expression of up to 350 transcripts via sequencing of oligonucleotides hybridized to mRNA, and protein expression of up to 200 targets using antibody-linked oligonucleotide sequencing. The flow cell accommodates >1 million cells in a 10 cm squared open-well format or can be subdivided into 12 or 48 wells to support experiments with multiple conditions or time points. We describe and validate the detection methods of the platform and showcase its capabilities by co-culturing three cancer cell lines and elucidating the cellular pathways triggered by various drug treatments as a function of time. Using multiple time points enables us to capture the dynamics of cellular processes including receptor activation and signaling cascades. The results demonstrate how different cancer cells evade TNF-induced apoptosis by activating compensatory signaling programs that maintain survival despite pro-apoptotic cues. Our model system replicates previously published results and highlights the versatility of the platform in enabling rapid, high-throughput analysis of complex cellular responses in varied biological contexts.

genomics↗

bioRxiv2025

DeltaBreed: A BrAPI-centric breeding data information system

DeltaBreed is a unified breeding data management system designed by Breeding Insight (BI, Cornell University) to serve the wide diversity of USDA-ARS specialty crop and animal breeding programs. DeltaBreed has a RESTful microservice architecture that utilizes the BrAPI Java Test Server as its primary database. The system is interoperable with many BrAPI-compliant applications (BrApps), including Field Book, and is continually aligned with the most recent BrAPI specifications. Here, we describe the features of DeltaBreed and provide several interoperability test cases to illustrate successes and challenges encountered during development. We also discuss future expansion and enhancement plans for DeltaBreed, as well as outline possible solutions to known limitations.

bioinformatics↗

bioRxiv2025

CDK12 condensation in nuclear speckles confers sensitivity to cyclin K molecular glue degraders

Transcriptional machinery often operates in the configuration of biomolecular condensates, presenting emerging opportunities to develop therapies targeting transcriptionally addicted malignancies. In this study, we discovered that cyclin-dependent kinase 12 (CDK12), a key regulator of transcription elongation, formed dynamic liquid-like droplets within nuclear speckles, a process enhanced by high CDK12 expression and CDK12 inhibitor treatment. Recognizing this unique property, we rationally designed ZSQ253, a modular cyclin K molecular glue degrader that coupled binding moieties for both CDK12 and DDB1. By promoting phase separation-driven assembly and subsequent proteasomal degradation of the CDK12-cyclin K complex, ZSQ253 interfered with oncogenic transcription and demonstrated potent antitumor capability. Further structure-guided optimization yielded HQY1428, a derivative with a multi-site gluing effect and improved drug activity. Given the frequent genomic co-amplification of CDK12 and ERBB2 across diverse human cancers, we showed that combining HQY1428 with HER2 inhibitors provided synergistic therapeutic benefits. Collectively, our findings establish CDK12 condensation within nuclear speckles as an exploitable vulnerability, and introduce a novel mechanism of action underlying cyclin K molecular glue degraders.

cancer biology↗

bioRxiv2025

Selective depletion of cancer cells with extrachromosomal DNA via lentiviral infection

Dear Editor Extrachromosomal DNA (ecDNA), a major focal oncogene amplification mode found across cancer, has recently regained attention as an emerging cancer hallmark1,2, with a pervasive presence across cancers3,4. With technical advancements such as high-coverage sequencing and live-cell genome imaging, we can now investigate ecDNAs behaviors and functions 5-7. However, we still lack an understanding of how to eliminate ecDNA. We observed depletion of cells containing ecDNA during lentiviral but not transposon-based transduction while we sought to investigate the mechanism of ecDNA behavior. This discovery may provide critical information on utilizing a lentiviral system in emerging ecDNA research. Additionally, this observation suggests specific sensitivities for cells with ecDNA.

cancer biology↗