Biology subjects

Wang, Q.

Publications and source records attributed to Wang, Q..

At least 199 records · Page 11Linked to original sources

bioRxiv2025

A synthetic biology toolkit for interrogating plasmid-dependent methylotrophy and enhancing methanol-based biosynthesis of Bacillus methanolicus

Bacillus methanolicus represents a thermophilic methylotroph whose methanol utilization depends on plasmid-encoded genes. It serves as a unique model for deciphering plasmid-dependent methylotrophy and an ideal chassis for low-carbon biomanufacturing using CO2-derived C1 substrates. Despite its evolutionary uniqueness and industrial potential, the lack of synthetic biology tools has hindered both mechanistic understanding and strain engineering. Here, we present a comprehensive synthetic biology platform comprising a high-efficiency electroporation protocol, a CRISPR method enabling robust and multiplex genome editing, diverse neutral loci for gene integration and overexpression, and a cloud-based genome-scale metabolic model iBM822 for user-friendly biodesign. Leveraging this toolkit, we systematically dissected plasmid-dependent methylotrophy, host restriction-modification systems, and functional significance of the chromosomal methylotrophic genes through targeted deletion. To address plasmid loss-induced strain degeneration, we integrated the large endogenous plasmid pBM19 into the chromosome for stable and intact methylotrophic growth. Finally, by integrating metabolic modeling with CRISPR editing, we engineered L-arginine feedback regulation to achieve the first L-arginine biosynthesis from methanol. This study establishes a synthetic biology framework for B. methanolicus, promoting mechanistic exploration of methylotrophy and low-carbon biomanufacturing.

synthetic biology↗

bioRxiv2025

Do Existing COVID-19 Vaccines Need to Be Updated in 2025?

COVID-19 vaccines have been updated each year since 2022 to improve protection against evolving SARS-CoV-2 variants. However, it is unclear whether a reformulation will be necessary for 2025. KP.2-based monovalent COVID-19 mRNA vaccines (KP.2 MV) were authorized for use in 2024, and they conferred substantial protection against hospitalizations caused by viral variants that emerged and dominated later, such as KP.3.1.1 and XEC. Today, LP.8.1 and its subvariant LP.8.1.1 have become dominant worldwide, particularly so in North America. Other variants, such as the LF.7 subvariant LF.7.2.1, have emerged with a growth advantage in Asia. To characterize the antigenicity of LP.8.1, LP.8.1.1, LF.7, LF.7.2.1, and another variant under monitoring, MC.10.1, we tested serum samples from 20 individuals who recently received KP.2 MV in neutralization assays against JN.1, KP.2, KP.3, KP.3.1.1, XEC, LP.8.1, LP.8.1.1, LF.7, LF.7.2.1, or MC.10.1 pseudoviruses. Serum neutralizing antibody titers against LP.8.1, LP.8.1.1, LF.7, LF.7.2.1, and MC.10.1 were comparable to those against KP.3.1.1 and XEC, indicating that LP.8.1.1 and other recently dominant subvariants are antigenically similar to their predecessors. Therefore, the currently authorized KP.2 MV may not need to be updated for 2025, if the vaccine manufacturers could demonstrate comparable immunogenicity for KP.2 MV and LP.8.1-based mRNA vaccines and, of course, in the absence of an antigenically divergent SARS-CoV-2 variant emerging.

microbiology↗

bioRxiv2025

The China Brain Multi-omics Atlas Project (CBMAP)

The China Brain Multi-omics Atlas Project (CBMAP) aims to generate a comprehensive molecular reference map of over 1,000 human brains (Phase I), spanning a broad age range and multiple regions in China, to address the underrepresentation of East Asian populations in brain research. By integrating genome, epigenome, transcriptome, proteome (including multiple post-translational modifications), and metabolome data, CBMAP is set to provide a rich and invaluable resource for investigating the molecular underpinnings of aging-related brain phenotypes and neuropsychiatric disorders. Leveraging high-throughput omics data and advanced technologies, such as spatial transcriptomics, proteomics, and single-nucleus 3D chromatin structure analysis, this atlas will serve as a crucial resource for the brain science community, illuminating disease mechanisms and enhancing the utility of data from genome-wide association studies (GWAS). CBMAP is also poised to accelerate drug discovery and precision medicine for brain disorders.

neuroscience↗

bioRxiv2025

TransAgent: Dynamizing Transcriptional Regulation Analysis via Multi-omics-Aware AI Agent

Transcriptional regulation research, as a core area of life sciences, faces challenges such as scattered multi-omics data, complex joint analysis, and difficulties in integrating data processing tools. To address these issues, we propose TransAgent, an agent software specifically designed for transcriptional regulation analysis. Through innovative designs such as multi-mode operation (planning/execution/automatic), dynamic memory management, rapid MCP tool expansion (integrating over 30 tools), integration of transcriptional regulation annotation data (over 20 data sources including epigenomics and gene expression profiles), and cloud Docker computing, TransAgent significantly improves analysis efficiency. We have successfully applied TransAgent to various transcriptional regulation analysis scenarios such as re-construction of super-enhancer regulatory circuit in esophageal squamous cell carcinoma and identification of key regulators in cardiomyocyte differentiation, demonstrating analytical robustness and uncovering biological insights. TransAgent automates the entire process from raw data processing to advanced analysis, such as joint prediction of multi-omics data, transforming traditionally time-consuming and labor-intensive tasks into a conversation-driven approach. This provides a new paradigm for transcriptional regulation research, centered around large models as the core driver of scalable agent application analysis.

bioinformatics↗

bioRxiv2025

Dimethyl fumarate reprograms cervical cancer cells to enhance antitumor immunity by activating mtDNA-cGAS-STING pathway

BackgroundCervical cancer (CC) remains a significant global health challenge for women, especially in advanced stages where effective treatments are limited. Current immunotherapies, including PD-1/PD-L1 blockades and adoptive T cell therapies, show limited response rates and durability. Dimethyl fumarate (DMF), an FDA-approved drug for autoimmune diseases, has demonstrated that it might exhibit direct antitumor activity in several cancers. However, its influence on anti-tumor immunity and its function in CC remain poorly understood. This study aims to investigate the therapeutic potential of DMF in CC models and elucidate its underlying mechanisms of action. MethodsCC cell lines and mouse models were treated with DMF. Transcriptional level changes in cervical cancer cells following DMF treatment were analyzed by RNA-seq. Mitochondrial DNA (mtDNA) release, and cGAS-STING activation were assessed via qPCR, immunofluorescence, immunoblotting and ELISA. CD8+ T cell recruitment was analyzed by flow cytometry. Combinatorial therapies (DMF + anti-PD-1/TILs) were tested in syngeneic or patient-derived xenografts (PDX) models. ResultsDMF treatment induces mitochondrial dysfunction in tumor cells, resulting in the release of mtDNA into the cytosol. The cytosolic mtDNA activates the cGAS-STING-TBK1 pathway and type I interferon response, leading to the secretion of CCL5 and CXCL10, thereby enhancing CD8 T cell infiltration. Additionally, DMF exhibits synergistic effect with PD-1 blockade in murine CC model, and can enhance the therapeutic efficacy of adoptively transferred T cells toward CC patient-derived xenografts model. ConclusionThis work elucidated that DMF reprograms CC cells to activate the mtDNA-cGAS-STING pathway, fostering a chemokine-rich microenvironment that recruits CD8+ T cells. Its synergy with PD-1 blockade or TIL therapy underscores its potential as an immunomodulatory adjuvant. These findings suggest that DMF holds promise as a novel immunotherapeutic strategy for improving clinical outcomes in CC.

immunology↗

bioRxiv2025

Mesoscopic SCAPE Microscope with a Rescanned, Super-oblique Illumination Plane

Investigating structural and functional dynamics across large spatial scales in living organisms calls for volumetric microscopy that combines a wide field of view (FOV), high spatial resolution, and sufficient temporal resolution. Swept confocally-aligned planar excitation (SCAPE) microscopy offers a compelling balance of optical sectioning, cellular resolution, and high-speed volumetric imaging. However, extending SCAPE to mesoscopic scales has been hindered by the limited tilting angle of the oblique illumination light sheet achievable with commercial low-magnification objectives. Here, we present a mesoscopic SCAPE microscope that overcomes this constraint by implementing a super-oblique light sheet--tilted up to ~60{degrees} relative to the optical axis of a 0.5-NA primary objective--enabled by an air-to-water bridging reflector. In addition, we introduce a single-galvanometer, self-conjugating rescanning strategy that allows arbitrary customization of the optical-to-mechanical angle ratio. This innovation accommodates the reversed and modulated scan displacement of the reflected light sheet and preserves descanned epi-fluorescence detection. Together, these advancements enable our mesoscopic SCAPE microscope to achieve a lateral FOV of 5.0 mm x 2.9 mm, cellular-level spatial resolution (~9.4 m x ~5.9 m lateral, and ~6.0 m axial), and a volumetric imaging rate of 9 volumes per second.

bioengineering↗

bioRxiv2025

Saccades orchestrate intraocular glucose to shape visual responses in birds

Birds exhibit remarkable vision despite lacking the typical network of blood vessels in their eyes. The characteristic poses a long-standing question about how avian retinas fulfill high energy demands necessary for sight. Here we show that natural, rhythmic eye movements, known as oscillatory saccades, orchestrate intraocular metabolic dynamics and attention-guided visual processing in pigeons. In a series of integrated experiments, we monitored eye movements along with glucose levels in the eye and neuronal activity in key brain regions receiving direct input from the retina. We found that these saccades generate fluctuations in intraocular glucose concentrations, closely linked to changes in neuronal visual responses over timescales of seconds to minutes. Moreover, pharmacological manipulations that altered glucose availability and eliminated these oscillatory saccades resulted in corresponding shifts in neuronal responses, demonstrating a causal linkage between oscillatory saccades, metabolic regulation, and visual processing. These findings reveal a mechanism by which birds actively evoked saccades during attention-driven information gathering, propelling retinal metabolism and facilitating their vision in the absence of retinal vasculature. This study underscores the interplay among eye movements, metabolic regulation, and high-level visual performance, suggesting broader implications for how eye movements contribute to retinal health, attention, and visual function across species.

neuroscience↗

bioRxiv2025

Aicardi-Goutieres Syndrome Associated ADAR G1007R mutation dominantly induces neuroinflammation in mouse brain

The ADARG1007Rmutation is one of the most frequent mutations found in type six Aicardi-Goutieres Syndrome (AGS), a severe inflammatory encephalopathy in pediatric patients. We report here a mouse model bearing an human equivalent ADARG1007R mutation, and the heterozygous mice recapitulated some pathologic features of ADARG1007R AGS patients, including early-onset brain inflammation in heterozygous individuals and interferon-stimulated gene (ISG) expression within deep brain areas. Furthermore, we demonstrated that brain inflammation could be reversed by deletion of the cellular RNA receptor MDA5, which blocks the cellular RNA sensing signaling pathway. This model provides a unique tool for studying the molecular mechanisms underlying the heterozygous ADARWT/G1007R mutation in AGS brain pathogenesis. It may also be a valuable platform for developing personalized therapies for patients with this specific mutation.

neuroscience↗

bioRxiv2025

DNA Methylation in Sex Chromosomes and Genes under Selection Underpins the Emergence of Sexual Size Dimorphism

Sexual size dimorphism (SSD) refers to the differences in body size between males and females. Epigenetics such as methylation contribute to shaping phenotypes, nevertheless, their role in SSD is still unclear. Here, we used Cynoglossus semilaevis, a species with larger females known as female-biased SSD, as a model to investigate the role of methylation in the emergence and regulation of SSD. Methylomes and transcriptomes were constructed in four tissues (brain, liver, muscle, and gonad) from three key life stages: juveniles (3-months post fertilization), male mature stage (1-year post fertilization; ypf), and female mature stage (3 ypf). In 1 ypf and 3 ypf females showed lower methylation, while the number of differentially methylated regions between sexes increased during the lifetime. Genes at the top of the growth hormone/insulin-like growth factor (GH/IGF) axis and hypothalamus-pituitary-gonadal axis (gh1, igf1, gnrhr2r-like, err{gamma}, etc.) showed differential methylation between sexes, consistent with sex-related differences in growth. The female-specific W chromosome showed higher methylation than the autosomes or the Z chromosome. Genes of the IGF signaling network that negatively regulate growth and located on W chromosome were hyper-methylated than their Z homologs. Furthermore, genes with a faster evolutionary rate in C. semilaevis exhibited lower methylation levels than the background genes, suggesting an important evolutionary role for DNA methylation in shaping SSD. Our results provide a comprehensive depiction of methylation regulation of SSD in vertebrates, and improve our understanding of how methylation regulation can help organisms to respond to natural selection, and allocate resources between the sexes.

developmental biology↗

bioRxiv2025

Super-Resolution Diffusivity Mapping Reveals Spatial Correlations Between Lateral Mobility and Structural Heterogeneities on Cellular Membranes

Cellular membranes orchestrate critical processes such as molecular transport and signal transduction, both regulated by the lateral mobility of lipids and proteins. However, resolving nanoscale diffusional heterogeneities and elucidating their underlying mechanisms remains a formidable challenge due to the membranes intricate architecture and compositional diversity. Here, we present point-cloud single-molecule diffusivity mapping (pc-SMdM), a cutting-edge super-resolution technique that offers a point-cloud data format with enhanced spatial resolution for diffusivity mapping. Using pc-SMdM, we visualize nanoscale diffusion slowdown clusters with [~]50 nm in diameter on plasma membranes. These clusters are predominantly governed by cholesterol content, alongside contributions from membrane protein assemblies and topographical features. Leveraging two-color pc-SMdM, we concurrently imaged multiple lipids and membrane probes, revealing distinct "fingerprint" diffusivity maps shaped by their interactions within lipid bilayers. Our findings position pc-SMdM as a transformative tool for spatially resolving molecular interactions and membrane dynamics in live cells, offering new insights into the underlying mechanisms that govern membrane mobility at the nanoscale.

biophysics↗

bioRxiv2025

Noninvasive ultrasound targeted modulation of calcium influx in splenic immunocytes potentiates antineoplastic immunity attenuating hepatocellular carcinoma proliferation

The spleen, as the largest immune organ, plays a pivotal role in modulating immune responses, particularly in the context of carcinogenesis and tumor progression. Non-pharmacological manipulation, particularly splenic ultrasound stimulation (SUS), has demonstrated significant immunomodulatory efficacy in alleviating chronic inflammatory diseases, suggesting its potential to revitalize splenic immunocompetence suppressing tumor proliferation, yet remains underexplored. This study applied low-frequency pulsed focused ultrasound (FUS) noninvasively stimulating the spleen (FUS sti. spleen) to investigate the efficacy in enhancing antitumor immunity and suppressing hepatocellular carcinoma (HCC). The results showed that FUS sti. spleen significantly suppressed tumor proliferation, achieving a suppression rate of >70% for H22-HCC and >83% for Hepa1-6-HCC, along with significantly prolonged survival. Comprehensive flow cytometry, single-cell RNA sequencing (scRNA-seq) and cytokine analyses demonstrated that SUS profoundly reshaped the splenic and intratumoral immune landscape, specifically activating cytotoxic CD8+ T cells and NK cells while suppressing immunosuppressive cell populations. Mechanistically, FUS facilitated calcium influx in splenic immunocytes, activating multiple signaling pathways, such as TNF, NF{kappa}B, MAPK, HIF-1, and ErbB, thereby counteracting tumor-driven immunosuppressive polarization while potentiating robust immune activation that impedes malignant progression and neoplastic proliferation. Leveraging above insights, we developed spleen-targeted nanodroplets encapsulating bioavailable calcium ions (STNDs@Ca{superscript 2}), which, upon FUS stimulation, undergo cavitation-mediated controlled release of Ca{superscript 2}, further amplifying immunocyte activation and tumor suppression, achieving a remarkable H22-HCC suppression rate of over 90%. This study highlights the therapeutic potential of ultrasound-mediated splenic immunomodulation, both as a standalone intervention and in synergy with STNDs@Ca{superscript 2}, as a novel and noninvasive strategy for cancer immunotherapy.

biophysics↗

bioRxiv2025

BABA: Naturalistic fMRI and MEG recordings during viewing of a reality TV show

Prior neuroimaging datasets using naturalistic listening paradigms have predominantly focused on single-talker scenarios. While these studies have been invaluable for advancing our understanding of speech and language processing in the brain, they do not capture the complexities of real-world multi-talker environments. Here, we introduce the "Le Petit Prince (LPP) Multi-talker Dataset", a high-quality, naturalistic neuroimaging dataset featuring 40 minutes of electroencephalogram (EEG) and 7T functional magnetic resonance imaging (fMRI) recordings from 26 native Mandarin Chinese speakers as they listened to both single-talker and multi-talker speech streams. Validation analyses conducted on both EEG and fMRI data demonstrate the datasets high quality and robustness. Additionally, the dataset includes detailed transcriptions and prosodic and linguistic annotations of the speech stimuli, enabling fine-grained analyses of neural responses to specific linguistic and acoustic features. The LPP Multi-talker Dataset is well-suited for addressing a wide range of research questions in cognitive neuroscience, including selective attention, auditory stream segregation, and working memory processes in naturalistic listening contexts.

neuroscience↗

bioRxiv2025

Object categorization based on abstract concepts by monkeys, humans, and vision models

Humans categorize objects at multiple levels of abstraction--animate versus inanimate, big versus small, and many other attributes. Despite its apparent challenge, the advent of deep neural networks (DNNs) has demonstrated that complex visual processing alone can support such classification without language or human-specific knowledge. This raises a natural question: to what extent can non-human primates, without language, perform such categorization? Although basic object-recognition behavior in monkeys such as similarity judgment has been extensively studied, their ability to classify objects across diverse rules remains poorly characterized. Here, we developed a task paradigm that enabled us to train monkeys on a large battery of binary classification tasks using natural object images, spanning more than 10 rules, such as animate versus inanimate, natural versus man-made objects, and mammalian versus non-mammalian animals. Monkeys acquired each rule in a few days, generalized the learned rules to new images, and exhibited error patterns consistent with human judgments. At the same time, their classification performance correlated more strongly with that of visual DNNs trained without language input, whereas human performance was better explained by language-informed DNNs. These results provide an important benchmark for the capacity of biological neural networks to perform image classification without language and human-specific knowledge.

neuroscience↗

bioRxiv2025

Bidirectional Modulation of Somatostatin-expressing Interneurons in the Basolateral Amygdala Reduces Neuropathic Pain Perception in Mice

Neuropathic pain is characterized by mechanical allodynia and thermal (heat and cold) hypersensitivity, yet the underlying neural mechanisms remain poorly understood. This study examines the role of inhibitory interneurons in the basolateral amygdala (BLA) in modulating pain perception following nerve injury. Chemogenetic excitation of parvalbumin-positive (PV+) interneurons significantly alleviated mechanical allodynia but had minimal effects on thermal hypersensitivity. However, inhibition of PV+ interneurons did not produce significant changes in pain sensitivity, suggesting that reductions in perisomatic inhibition do not contribute to chronic pain states. In contrast, bidirectional modulation of somatostatin-positive (SST+) interneurons influenced pain perception in a modality-specific manner. Both excitation and inhibition of SST+ interneurons alleviated mechanical allodynia, indicating a potential compensatory role in nociceptive processing. Additionally, SST+ neuron excitation reduced cold hypersensitivity without affecting heat hypersensitivity, whereas inhibition improved heat hypersensitivity but not cold responses. These findings suggest that, in addition to PV+ neurons, SST+ interneurons in the BLA play a complex role in modulating neuropathic pain following nerve injury and may serve as a potential target for future neuromodulation interventions in chronic pain management.

neuroscience↗

bioRxiv2025

Establishment of a Reverse Genetics System for the Study of Human Immune Functions in Mice

Reverse genetics approaches in mice are widely utilized to understand gene functions and their aberrations in diseases. However, limitations exist in translating findings from animal models to human physiology. Humanized mice provide a powerful bridge to understanding human physiology and mechanisms of diseases pathogenesis while maintaining the feasibility of working with small animals. Methods for generating humanized mouse models that allow scientists to probe contributions of particular genes have been rudimentary. Here, we established an efficient method for generating genetically modified human cord blood derived CD34+ cells for transplantation, resulting in humanized mice with near-complete loss of specific gene expression by the human immune system. Mice transplanted with Cas9-edited human CD34+ cells recapitulate functional consequences of specific gene losses in the human immune system. This advancement enables the development of humanized mouse models with targeted gene knockouts, offering a valuable research tool for human gene function studies in vivo.

immunology↗

bioRxiv2025

Acquired resistance to sotorasib in mutant NSCLC is vulnerable to PI3K-mTOR pathway inhibition mediated by 4E-BP1 regulator of cap-dependent translation

Sotorasib and adagrasib have shown significant efficacy in KRASG12C mutant NSCLC; however, acquired resistance (AR) occurs within 6-12 months. While some resistance arises from new mutations, over half of the resistant cases lack identifiable genomic alterations. We hypothesize that resistance is driven by signaling network rewiring, creating new therapeutic vulnerabilities. To investigate AR mechanisms, multiple AR models, including cell lines, PDXs, CDXs, and PDXOs, were developed. H23AR and H358AR cells displayed >600-fold and 200-fold; and PDXO303AR and PDXO314AR organoids exhibited >300-fold and >100-fold resistance to sotorasib, respectively; however, no additional mutations in KRAS or other potential genetic alterations were identified. The AR cells and PDXOs also showed comparable resistance to adagrasib. Distinct protein signatures associated with KRAS reactivation, mTORC1 signaling upregulation, and PI3K/AKT/mTOR pathway activation were identified in TC303AR & TC314AR PDXs. PI3K protein levels were significantly elevated in AR PDXs, H23AR, and H358AR cells. Pharmacological inhibition of PI3K with copanlisib or genetic knockout via CRISPR-Cas9 restored sotorasib sensitivity, suppressed colony formation, and inhibited downstream effectors, including p-AKT, p-mTOR, p-S6, p70S6K, p-GSK3{beta}, and p-PRAS40 in AR cells. Copanlisib also sensitized both acquired and primary resistant PDXOs and synergized with sotorasib in restoring drug sensitivity. p4E-BP1 was significantly upregulated in H23AR and H358AR cells, which is suppressed by copanlisib. The level of p4E-BP1 expression was correlated with Sotorasib sensitivity in PI3K knockout clones, where the most sensitive clone displayed reduced or no p4E-BP1 expression. CRISPR-Cas9-mediated knockout of 4E-BP1, either alone or in combination with PI3K knockout, dramatically restored sotorasib sensitivity to levels comparable to parental cells. Suppression of 4E-BP1 hyperphosphorylation required dual inhibition of mTORC1 and mTORC2, and treatment with AZD8055 or sapanisertib (mTORC1/2 dual inhibitors) significantly dephosphorylated 4E-BP1 and restored sotorasib sensitivity in resistant cells and PDXOs. In PDX, CDX, and xenograft models in vivo, the combination of sotorasib with either copanlisib or sapanisertib resulted in robust, synergistic, and durable tumor regression at well-tolerated doses. These findings showed the critical role of PI3K/mTOR signaling as a bypass mechanism of resistance to KRASG12C inhibitors. We conclude that mTORC1/2 mediated inhibition of p4E-BP1 and combination strategies targeting this pathway effectively overcome acquired resistance to KRASG12C inhibitors in NSCLC.

cancer biology↗

bioRxiv2025

Convergent strigolactone perception via independent horizontal gene transfer of pre-adapted α/β-hydrolases

Strigolactones (SLs) are not only phytohormones that influence multiple aspects of plant growth and development, but also signaling molecules for interactions between plants and certain fungi or bacteria. In plants, the SL receptor is an /{beta}-hydrolase (ABH) encoded by the D14/KAI2 gene family, which is known to be derived from proteobacterial RsbQ through horizontal gene transfer (HGT). Here we show that the CpD14-like (CDL) gene family, which encodes another ABH exhibiting SL receptor functions in fungi, was acquired from actinobacteria via an independent HGT event. X-ray crystallographic experiments reveal that CDL and D14/KAI2/RsbQ (DKR) proteins have distinctive lid structures but maintain the same core /{beta} fold and catalytic triad. Biochemical assays further show that both actinobacterial CDL and proteobacterial RsbQ can recognize and hydrolyze SLs, suggesting that they are pre-adapted for SL perception. This work demonstrates that independent HGT of pre-adapted genes can trigger convergent evolution of key innovations and provides insights into how SLs are sensed by organisms across kingdoms.

evolutionary biology↗

bioRxiv2025

Proteomic Analysis of PTEN-Deficient Cells Reveals Src-Mediated Upregulation of EphA2 and Therapeutic Potential of Dual Inhibition

Loss of the tumor suppressor PTEN is frequently observed in various cancers and promotes tumorigenesis by activating the PI3K-AKT pathway. However, the effectiveness of therapies targeting this pathway is limited by complex signaling crosstalk and compensatory mechanisms. Here, we employed quantitative proteomic and phosphoproteomic analyses using MCF10A PTEN knockout models to comprehensively map the signaling alterations induced by PTEN loss. Our analyses revealed that PTEN deficiency not only activates canonical PI3K-AKT signaling but also induces widespread changes in cytoskeleton organization, cell cycle regulation, and central carbon metabolism. PTEN loss also substantially elevates the activity of a variety of tyrosine kinases, including Src kinase and EphA2, a receptor tyrosine kinase (RTK) implicated in cancer progression. Mechanistic studies demonstrated that Src activation, rather than the canonical AKT signaling pathway, drives the upregulation of the receptor tyrosine kinase EphA2. The activation of the noncanonical tyrosine kinase signaling renders AKT inhibition alone insufficient in PTEN-deficient cancers. Importantly, combined treatment with the FDA-approved AKT inhibitor capivasertib and the Src inhibitor dasatinib synergistically induced apoptosis and suppressed the tumor cell growth in various PTEN-deficient cell lines as well as in three-dimensional cultures of endometrial cancer patient-derived xenograft models. Our study reveals that PTEN loss drives oncogenic signaling via dual activation of PI3K-AKT and tyrosine kinase pathways. Specifically, Src-mediated upregulation of EphA2 in PTEN-deficient cells highlights a therapeutic vulnerability that can be exploited by combined AKT and Src inhibition. This approach addresses the resistance associated with AKT inhibition alone and enhances therapeutic efficacy in PTEN-deficient cancers, supporting its potential application in targeted combination therapies.

cancer biology↗