Biology subjects

Zhao, J. J.

Publications and source records attributed to Zhao, J. J..

16 recordsLinked to original sources

bioRxiv2026

Targeting FGFR signaling overcomes therapeutic resistance and immune evasion in oncogenic PIK3CA-driven serous-like endometrial cancer

Serous endometrial cancer (SEC) is an aggressive subtype of endometrial cancer (EC) with poor prognosis and limited treatment options. Here, we developed a clinically relevant, immunocompetent serous-like mouse model incorporating oncogenic PIK3CA mutation, Trp53 loss, and MYC overexpression. Using this model together with human EC cell lines, patient-derived organoids (PDOs), xenografts, and patient datasets, we investigated mechanisms underlying resistance to PI3K-targeted therapy. Single-cell profiling reveals that FGFR1/2 upregulation associates with intrinsic resistance, whereas FGFR3 characterizes acquired resistance. Dual FGFR and PI3K inhibition produced superior tumor control compared with either agent alone. Mechanistically, FGFR signaling promotes immune evasion by downregulating MHC-I/HLA-mediated antigen presentation and enriching M2-type tumor-associated macrophages. FGFR inhibition reversed these changes and synergized with anti-PD-1 therapy to enhance antitumor immune responses and establish durable immune memory. Collectively, these findings identify FGFR signaling as a key driver of therapeutic resistance and immune escape in SEC and support FGFR-targeted combination strategies.

cancer biology↗

bioRxiv2026

Targeting PI3Kβ-dependent cancer with a novel small molecule inhibitor, GT220

PI3K{beta} is a critical oncogenic driver in cancers harboring PTEN loss or PIK3CB alterations, yet effective and selective PI3K{beta}-targeted therapies remain elusive. Here, we report the development and preclinical characterization of GT220, a highly selective and potent small-molecule PI3K{beta} inhibitor developed through integrated artificial-intelligence-driven design with medicinal chemistry and pharmacologic optimization. GT220 exhibits exceptional biochemical selectivity for PI3K{beta}, binding with sub-nanomolar affinity and with minimal activity against other class I PI3K isoforms or the broader protein kinome. In cellular models, GT220 potently suppresses AKT phosphorylation and selectively inhibits viability of PTEN-deficient cancer cells, while sparing PTEN/PIK3CB wild-type and PI3K-dependent cells. In vivo, GT220 achieves a favorable tumor exposure with sustained PI3K{beta} pathway inhibition and demonstrates robust antitumor efficacy and good tolerability in PTEN-deficient breast cancer xenograft models. In contrast, GT220 shows no antitumor activity or pathway inhibition in PTEN-wild-type or PI3K-dependent tumors, underscoring its context-dependent mechanism of action. Collectively, these findings establish GT220 as a promising next-generation PI3K{beta} inhibitor and provide a strong preclinical rationale for precision targeting of PI3K{beta}-dependent cancers.

cancer biology↗

bioRxiv2025

IRG1/itaconate/NRF2/GSH axis in tumor-associated macrophages drives therapy resistance and immune evasion in BRCA1-deficient breast cancer

Tumor-associated macrophages (TAMs) are major contributors to immunosuppression and therapeutic resistance, including resistance to PARP inhibitors (PARPi) in BRCA1-deficient breast cancer. However, the mechanisms underlying TAM-mediated PARPi resistance remain unclear. Here, we demonstrate that TAM-derived glutathione (GSH) impairs the efficacy of PARPi by protecting tumor cells from DNA damage and ferroptosis while suppressing STING-mediated immune activation. Mechanistically, STAT5-driven upregulation of the IRG1/itaconate axis in TAMs rewires mitochondrial metabolism and activates NRF2-dependent GSH biosynthesis. GSH is subsequently released into the tumor microenvironment, where it is taken up by tumor cells, protecting them from PARPi-induced cytotoxicity and dampening immune responses. Pharmacological inhibition of IRG1 reverses these effects, restoring PARPi sensitivity and enhancing anti-tumor immunity in BRCA1-deficient tumor models. Collectively, these findings uncover a TAM-specific immunometabolic program that limits PARPi efficacy and highlight the IRG1/NRF2/GSH axis as a promising therapeutic target to improve treatment outcomes in BRCA1-associated breast cancer.

cancer biology↗

bioRxiv2025

Gene-Family Encoding Boosts Domain-Adapted Single-Cell Language Models

Transformer-based single-cell foundation models often rely on ranked-gene (RG) sequences where genes, ranked by expression, are often not functionally related, weakening next-token learning and the structure of learned embeddings. Here, we introduce gene-family (GF) encoding, where expressed genes are grouped into functionally defined families, and ranking performed within each family. Using 100,000 gastric-cancer (GC) cells, we domain-adapted 8-billion-parameter Llama and Qwen backbones with either RG or GF sentences and benchmarked zero-shot performance on embedding-based and generative tasks. GF models outperformed RG models across both tasks and backbones. We scaled GF-Llama to 1.3 million GC cells to obtain GF-Llama-GC and applied it to two applications: resolving fine-grained cellular heterogeneity and discovering cell populations associated with disease progression. GF-Llama-GC revealed immune-cell subclusters not resolved by standard expression-based analyses. Applying in-silico cell removal/transplantation on a chemotherapy responder/non-responder scRNA-seq dataset, GF-Llama-GC highlighted not only epithelial cells but also neutrophils as key cells associated with chemotherapy response.

bioinformatics↗

bioRxiv2025

Statin-dye conjugates for selective targeting of KRAS mutant cancer cells

Over 90% of pancreatic ductal adenocarcinoma (PDAC) patients involve KRAS mutations (KRASMUT), for which current treatment options are limited. Statins, commonly used to lower cholesterol, have demonstrated certain selective toxicity towards KRAS-transformed cells, prompting the question of whether statins could achieve selective uptake specifically in KRASMUT cells. To investigate this, we synthesized statin-dye conjugates by attaching a fluorescent dye (Cy5.5) to two statins: simvastatin and pravastatin, aiming to assess whether selective uptake indeed occurs. Our findings revealed that these conjugates exhibited markedly enhanced uptake in KRASMUT cells compared to KRAS wild-type (KRASWT) cells. Given the magnitude of the selective uptake, we realized that the uptake of these conjugates itself is of considerable intrinsic interests. We evaluated the uptake of these conjugates in both KRASMUT and KRASWT cells and examined their potential to selectively target KRASMUT pancreatic cancer cells (PCCs) using an engineered PDAC tumor model co-cultured with PCCs and cancer-associated fibroblasts (CAFs). Our findings indicate that KRASMUT cancer cells exhibited higher uptake of statin-Cy5.5 conjugates via enhanced macropinocytosis compared to KRASWT cancer cells and CAFs. We also found enhanced uptake of the statin-Cy5.5 conjugate in MCF10A cells with PTEN deficiency, a condition known to elevate macropinocytosis, compared to control MCF10A cells with wild-type PTEN. Notably, in the PCC and CAF co-culture model, the pravastatin-Cy5.5 conjugate selectively killed KRASMUT PCCs without affecting the KRASWT CAFs. These findings highlight the potential of stain-drug conjugates as targeted delivery vehicles for KRASMUT cancer therapy.

cancer biology↗

bioRxiv2024

A chemically defined and xeno-free hydrogel system for regenerative medicine.

Biofabricated scaffolds facilitate bona fide cellular interactions, cell type specification, and the formation of three-dimensional tissue architecture from human pluripotent stem cells (hPSCs). However, xenogenic biomaterials are poorly defined, and synthetic biomaterials remain underdeveloped and understudied, hindering regulatory approval for clinical use and preventing the translation of lab-grown therapies. Here, we describe a protein screen-based hydrogel system biofabricated from clinical-grade human components. We show that "Alphagel", a base hydrogel comprising human embryonic matrices, supports the trilineage differentiation of hPSCs into neural, cardiac, and liver tissue. Alphagel is also shown to be biocompatible and biodegradable in vivo. Further, upon adding select proteins from maturing human foetal liver to Alphagel, we show that the resulting hydrogel (termed "Hepatogel") enhances the differentiation of hPSC-derived hepatocytes (H-iHeps) compared with Matrigel. Importantly, when injected into mice livers, Hepatogel significantly improves the retention of H-iHeps compared to standard aqueous cell injections. Altogether, our results provide proof of concept that customisable and organ-specific hydrogel systems are a valuable tool for developing clinically translatable therapies for regenerative medicine and tissue engineering.

bioengineering↗

bioRxiv2024

Spatially Resolved Tumor Ecosystems and Cell States in Gastric Adenocarcinoma Progression and Evolution

Gastric cancer (GC) is a major cause of global cancer mortality with high heterogeneity levels. To explore geospatial interactions in tumor ecosystems, we integrated 1,563 spatial transcriptomic regions-of-interest (ROIs) with 152,423 single-cell expression profiles across 130 GC samples from 70 patients. We observed pervasive expression-based intratumor heterogeneity, recapitulating tumor progression through spatially localized and functionally ordered subgroups with specific immune microenvironments and immune checkpoint profiles. Evolutionary phylogenetic analysis revealed two different evolutionary trajectories (branched evolution and diaspora evolution) associated with distinct molecular subtypes, clinical prognoses, stromal neighborhoods including VWF+ ACKR1+ endothelial cells, and genetic drivers such as SOX9. Spatial analysis of tumor-stromal interfaces across multiple GCs highlighted new ecosystem states not attributable to mere tumor/stroma admixture, landmarked by increased GREM1 expression. Our results provide insights into how the cellular ecosystems of individual GCs are sculpted by tumor intrinsic and extrinsic selective pressures, culminating in individualized patient-specific cancer cartographies.

cancer biology↗

bioRxiv2024

Spatially resolved niche and tumor microenvironmental alterations in gastric cancer peritoneal metastases

Peritoneal metastases (PM) in gastric cancer (GC) portend a poor prognosis, yet our understanding of tumor microenvironmental (TME) characteristics associated with GCPM remain limited. Here, we analyzed intrinsic genomic alterations and transcriptomic programs predictive of GCPM in a prospective cohort of 248 patients, identifying CDH1, PIGR, and ELF3 mutations as predictors. By inspecting the spatial dynamics of the TME, we find that tumor compartment infiltration of pro-tumorigenic cell types such as inflammatory cancer-associated fibroblasts (CAFs) predict peritoneal recurrence. Next, in a cross-sectional study of 205 samples from 55 patients, distinct pathways and immune compositions in GCPM relative to liver metastases highlight the TMEs significance in transcoelomic metastases. Notably, several putative therapeutic targets exhibited distinct expression patterns between PTs and PMs. We also observed increased immune infiltration in GCPMs treated with systemic immunotherapy and intraperitoneal chemotherapy. Our findings highlight transcriptomic variations and niche reprogramming in the GCPM peritoneal environment, revealing roles of myeloid dendritic cells, effector memory CD8+ T cells, and CAFs in metastatic progression. Statement of significanceComprehensive molecular profiling of gastric cancer primary and peritoneal tumors unveils crucial insights into the distinct molecular and immune landscape of peritoneal metastases. Identifying predictive markers and therapeutic targets emphasizes the significance of tumor microenvironment alterations in guiding future therapies for gastric cancer peritoneal metastasis.

cancer biology↗

bioRxiv2023

Lysine vitcylation is a novel vitamin C-derived protein modification that enhances STAT1-mediated immune response

Vitamin C (vitC) is a vital nutrient for health and also used as a therapeutic agent in diseases such as cancer. However, the mechanisms underlying vitCs effects remain elusive. Here we report that vitC directly modifies lysine without enzymes to form vitcyl-lysine, termed "vitcylation", in a dose-, pH-, and sequence-dependent manner across diverse proteins in cells. We further discover that vitC vitcylates K298 site of STAT1, which impairs its interaction with the phosphatase PTPN2, preventing STAT1 Y701 dephosphorylation and leading to increased STAT1-mediated IFN pathway activation in tumor cells. As a result, these cells have increased MHC/HLA class-I expression and activate immune cells in co-cultures. Tumors collected from vitC-treated tumor-bearing mice have enhanced vitcylation, STAT1 phosphorylation and antigen presentation. The identification of vitcylation as a novel PTM and the characterization of its effect in tumor cells opens a new avenue for understanding vitC in cellular processes, disease mechanisms, and therapeutics.

biochemistry↗

bioRxiv2021

Temporal and spatial topography of cell proliferation in cancer

Proliferation is a fundamental trait of cancer cells but is poorly characterized in tumors by classical histologic methods. We use multiplexed tissue imaging to quantify the abundance of multiple cell cycle regulating proteins at single-cell level and develop robust multivariate proliferation metrics. Across cancers, the proliferative architecture is organized at two distinct spatial scales: large domains, and local niches enriched for specific immune lineages. A subset of tumor cells express cell cycle regulators in canonical patterns consistent with unrestrained proliferation, a phenomenon we refer to as "cell cycle coherence". By contrast, the cell cycles of other tumor cell populations are skewed toward a specific phase or characterized by non-canonical (incoherent) marker combinations. Coherence varies across space, with changes in oncogene activity, and with therapeutic intervention, and is associated with aggressive behavior. Multivariate measures capture clinically significant features of cancer proliferation, a fundamental step in enabling more precise use of anti-cancer therapies.

systems biology↗

bioRxiv2021

Activation of Sarm1 produces cADPR to increase intra-axonal calcium and promote axon degeneration in CIPN

Cancer patients frequently develop chemotherapy-induced peripheral neuropathy (CIPN), a painful and long-lasting disorder with profound somatosensory deficits. There are no effective therapies to prevent or treat this disorder. Pathologically, CIPN is characterized by a "dying-back" axonopathy that begins at intra-epidermal nerve terminals of sensory neurons and progresses in a retrograde fashion. Calcium dysregulation constitutes a critical event in CIPN, but it is not known how chemotherapies such as paclitaxel alter intra-axonal calcium and cause degeneration. Here, we demonstrate that paclitaxel triggers Sarm1-dependent cADPR production in distal axons, promoting intra-axonal calcium flux from both intracellular and extracellular calcium stores. Genetic or pharmacologic antagonists of cADPR signaling prevent paclitaxel-induced axon degeneration and allodynia symptoms, without mitigating the anti-neoplastic efficacy of paclitaxel. Our data demonstrate that cADPR is a calcium modulating factor that promotes paclitaxel-induced axon degeneration and suggest that targeting cADPR signaling provides a potential therapeutic approach for treating CIPN. HIGHLIGHTSO_LIPaclitaxel induces intra-axonal calcium flux C_LIO_LISarm1-dependent cADPR production promotes axonal calcium elevation and degeneration C_LIO_LIAntagonizing cADPR signaling pathway protects against paclitaxel-induced peripheral neuropathy in vitro and in vivo C_LI

neuroscience↗

bioRxiv2021

Targeting EGFR in glioblastoma with a novel brain-penetrant small molecule EGFR-TKI

Epidermal growth factor receptor (EGFR) is mutated or amplified in a majority of glioblastoma (GBM), and its mutation and focal amplification correlate with a more aggressive disease course. However, EGFR-directed tyrosine kinase inhibitors (TKIs) tested to date have yielded minimal clinical benefit. Here, we report a novel covalent-binding EGFR-TKI, CM93, as a potential drug to target adult GBMs with aberrant EGFR. CM93 has extraordinary brain exposure, with a brain-to-plasma ratio greater than 20-fold at estimated steady state. While all approved EGFR-TKIs are subject to extensive efflux transporter activity, CM93 does not inhibit the P-glycoprotein (P-gp) and breast cancer resistance protein (BCRP) efflux transporters in Caco-2 cells at expected clinically relevant plasma concentrations. Equally, CM93 demonstrates moderate absorption and permeation in Caco-2 cell monolayers with efflux ratios < 2, suggesting that it is not likely a substrate of an efflux transporter. Collectively, these in vitro data may account for the dramatic increase in brain exposure over plasma as noted above. Pre-clinical efficacy studies showed that CM93 is more effective than other EGFR-TKIs in blocking the proliferation of GBM tumor cells from both patient-derived and cultured human GBM cell lines with EGFR amplification and/or EGFRvIII mutation. In addition, CM93 administered as a single agent was able to attenuate the growth of orthotopic U251-EGFRvIII xenografts and extend the survival of tumor-bearing mice in a dose-dependent manner. Moreover, CM93 inhibited EGFR phosphorylation in GBM tumors derived from a novel genetically-engineered mouse (GEM) model of GBM with EGFRvIII expression both in vitro and in vivo. CM93 also extended the survival of mice bearing orthotopic allografts of GBM. Notably, mice maintained stable body weight during treatments with increasing doses of CM93 up to 75 mg/kg per day. Together, these data suggest that CM93 is a potential EGFR-TKI well suited for the treatment of adult GBM with mutant EGFR.

cancer biology↗

bioRxiv2020

Limited Environmental Serine Confers Sensitivity to PHGDH Inhibition in Brain Metastasis

A hallmark of metastasis is the adaptation of tumor cells to new environments. Although it is well established that the metabolic milieu of the brain is severely deprived of nutrients, particularly the amino acids serine and its catabolite glycine, how brain metastases rewire their metabolism to survive in the nutrient-limited environment of the brain is poorly understood. Here we demonstrate that cell-intrinsic de novo serine synthesis is a major determinant of brain metastasis. Whole proteome comparison of triple-negative breast cancer (TNBC) cells that differ in their capacity to colonize the brain reveals that 3-phosphoglycerate dehydrogenase (PHGDH), which catalyzes the rate-limiting step of glucose-derived serine synthesis, is the most significantly upregulated protein in cells that efficiently metastasize to the brain. Genetic silencing or pharmacological inhibition of PHGDH attenuated brain metastasis and improved overall survival in mice, whereas expression of catalytically active PHGDH in a non-brain trophic cell line promoted brain metastasis. Collectively, these findings indicate that nutrient availability determines serine synthesis pathway dependence in brain metastasis, and suggest that PHGDH inhibitors may be useful in the treatment of patients with cancers that have spread to the brain. Statement of SignificanceOur study highlights how limited serine and glycine availability within the brain microenvironment potentiates tumor cell sensitivity to serine synthesis inhibition. This finding underscores the importance of studying cancer metabolism in physiologically-relevant contexts, and provides a rationale for using PHGDH inhibitors to treat brain metastasis.

cancer biology↗

bioRxiv2019

Post-EMT: Cadherin-11 mediates cancer hijacking fibroblasts

Current prevailing knowledge on EMT (epithelial mesenchymal transition) deems epithelial cells acquire the characters of mesenchymal cells to be capable of invading and metastasizing on their own. One of the signature events of EMT is called "cadherin switch", e.g. the epithelial E-cadherin switching to the mesenchymal Cadherin-11. Here, we report the critical events after EMT that cancer cells utilize cadherin-11 to hijack the endogenous cadherin-11 positive fibroblasts. Numerous 3-D cell invasion assays with high-content live cell imaging methods reveal that cadherin-11 positive cancer cells adhere to and migrate back and forth dynamically on the cell bodies of fibroblasts. By adhering to fibroblasts for co-invasion through 3-D matrices, cancer cells acquire higher invasion speed and velocity, as well as significantly elevated invasion persistence, which are exclusive characteristics of fibroblast invasion. Silencing cadherin-11 in cancer cells or in fibroblasts, or in both, significantly decouples such physical co-invasion. Additional bioinformatics studies and PDX (patient derived xenograft) studies link such cadherin-11 mediated cancer hijacking fibroblasts to the clinical cancer progression in human such as triple-negative breast cancer patients. Further animal studies confirm cadherin-11 mediates cancer hijacking fibroblasts in vivo and promotes significant solid tumor progression and distant metastasis. Moreover, overexpression of cadherin-11 strikingly protects 4T1-luc cells from implant rejection against firefly luciferase in immunocompetent mice. Overall, our findings report and characterize the critical post-EMT event of cancer hijacking fibroblasts in cancer progression and suggest cadherin-11 can be a therapeutic target for solid tumors with stroma. Our studies hence provide significant updates on the "EMT" theory that EMT cancer cells can hijack fibroblasts to achieve full mesenchymal behaviors in vivo for efficient homing, growth, metastasis and evasion of immune surveillance. Our studies also reveal that cadherin-11 is the key molecule that helps link cancer cells to stromal fibroblasts in the "Seed & Soil" theory. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/729491v2_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@11317f1org.highwire.dtl.DTLVardef@88fffaorg.highwire.dtl.DTLVardef@5da692org.highwire.dtl.DTLVardef@62f6ed_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2017

Targeting neuronal activity-regulated neuroligin-3 dependency for high-grade glioma therapy

Neuronal activity promotes high-grade glioma (HGG) growth. An important mechanism mediating this neural regulation of brain cancer is activity-dependent cleavage and secretion of the synaptic molecule and glioma mitogen neuroligin-3 (Nlgn3), but the therapeutic potential of targeting Nlgn3 in glioma remains to be defined. We demonstrate a striking dependence of HGG growth on microenvironmental Nlgn3 and determine a targetable mechanism of secretion. Patient-derived orthotopic xenografts of pediatric glioblastoma, diffuse intrinsic pontine glioma and adult glioblastoma fail to grow in Nlgn3 knockout mice. Glioma exposure to Nlgn3 results in numerous signaling consequences, including early focal adhesion kinase activation upstream of PI3K-mTOR. Nlgn3 is cleaved from both neurons and oligodendrocyte precursor cells via the ADAM10 sheddase. Administration of ADAM10 inhibitors robustly blocks HGG xenograft growth. This work defines the therapeutic potential of and a promising strategy for targeting Nlgn3 secretion in the glioma microenvironment, which could prove transformative for treatment of HGG.

neuroscience↗

bioRxiv2017

Modeling Zika Virus Congenital Eye Disease: Differential Susceptibility of Fetal Retinal Progenitor Cells and iPSC-Derived Retinal Stem Cells to Zika Virus Infection

Zika virus (ZIKV) causes microcephaly and congenital eye disease that is characterized by macular pigment mottling, macular atrophy, and loss of foveal reflex. The cell and molecular basis of congenital ZIKV infection are not well understood. Here, we utilized a biologically relevant cell-based system on human fetal retinal pigment epithelial cells (FRPE) and iPSC-derived retinal stem cells (iRSCs) to model ZIKV-ocular cell injury processes. FRPEs were highly susceptible to ZIKV, resulting in apoptosis and decreased viability, whereas iRSCs showed reduced susceptibility. Transcriptomics and proteomics analyses of infected FRPE cells revealed the activation of innate immune and inflammatory response genes, and dysregulation of cell survival pathways, mitochondrial transmembrane potential, phagocytosis, and particle internalization. Nucleoside analogue drug treatment inhibited ZIKV replication and prevented apoptosis. In conclusion, ZIKV affects ocular cells of different developmental stages resulting in cellular injury and death, further providing molecular insight into the pathogenesis of congenital eye disease.

microbiology↗