Biology subjects

Bao, R.

Publications and source records attributed to Bao, R..

At least 19 recordsLinked to original sources

bioRxiv2026

The OxyR-Responsive TacAT Module Promotes Oxidative Stress Adaptation and In Vivo Fitness in K. pneumoniae

During infection, Klebsiella pneumoniae must withstand host-derived oxidative stress not only by detoxifying reactive oxygen species (ROS) but also by repairing oxidative damage to cellular physiology. How these detoxification and stress-adaptive responses are coordinated remains unclear. Here, we identify a plasmid-encoded tacAT locus as an OxyR-responsive regulatory module that supports peroxide tolerance and in vivo fitness in K. pneumoniae. Guided by the conservation of the OxyR DNA-binding domain and its consensus binding motif, we surveyed promoter-proximal regions of the K. pneumoniae CRK3022 chromosome and plasmids for candidate OxyR-responsive loci. This analysis identified tacAT, a putative type II toxin-antitoxin (TA) module, as the only plasmid-associated candidate. OxyR directly bound the tacAT promoter and contributed to tacAT induction during hydrogen peroxide (H?O?) stress. The TacAT complex exhibited DNA-binding and transcriptional regulatory activity, promoting the expression of genes linked to protein quality control and membrane/envelope homeostasis, including clpB, htpG, cadC, bhsA, and marA. Deletion of tacAT compromised survival under lethal peroxide challenge and attenuated bacterial dissemination, tissue pathology, and inflammatory responses in a murine bacteremia model. These findings define an OxyR-TacAT regulatory branch that connects peroxide sensing with stress-adaptive gene expression, revealing how a TA-associated module can be integrated into stress-adaptive programs during host-associated oxidative stress.

microbiology↗

bioRxiv2026

Promoter architecture decodes response regulator phosphorylation into distinct transcriptional logics in Pseudomonas aeruginosa

Two-component systems convert environmental signals into transcriptional responses, but how one response-regulator phosphorylation state produces different outputs at different promoters remains unclear. Here we show that promoter architecture determines how the ParR response regulator in Pseudomonas aeruginosa interprets phosphorylation. Phenotypic, transcriptomic, biochemical and promoter-engineering analyses showed that phosphorylation of the conserved ParR receiver residue Asp57 lowered DNA-occupancy thresholds across target promoters. Individual promoters, however, converted this shared increase in binding into activation, repression or phosphorylation-dependent sign switching. Chromosomally D57 ParR variants reproduced these behaviours at endogenous loci and altered antibiotic susceptibility, biofilm formation and virulence-associated phenotypes. Mapping and engineering of representative promoters identified a two-tier cis-regulatory code: half-site sequence compatibility determines productive ParR engagement, whereas spacer length determines regulatory sign and magnitude. Spacer swaps were sufficient to reprogram promoter logic between regulatory modes. These findings separate regulator state from promoter decoding and show how bacterial promoter architecture can diversify the outputs of a shared phosphorylation signal. ImportancePseudomonas aeruginosa is an opportunistic pathogen that survives antimicrobial treatment and adapts to diverse host environments by rapidly changing gene expression. How a single sensory pathway generates different, and sometimes opposing, responses across many genes has remained unclear. We show that the regulatory protein ParR does not impose one fixed transcriptional program. Instead, the DNA architecture of each target promoter determines whether the same phosphorylation signal activates, represses, or reverses gene expression. The sequence and spacing of ParR recognition sites form a compact regulatory code, and changing spacer length alone can reprogram promoter behavior. Different ParR states were also associated with changes in antibiotic susceptibility, biofilm formation, and virulence-associated phenotypes. Our findings explain how one bacterial signaling pathway can generate diverse physiological outcomes without additional regulators and provide a framework for understanding regulatory flexibility in Pseudomonas aeruginosa and for engineering genetic circuits with multiple outputs. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/740031v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@1b6ec28org.highwire.dtl.DTLVardef@4a3f2eorg.highwire.dtl.DTLVardef@79e528org.highwire.dtl.DTLVardef@b3aa77_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

Promoter architecture diversifies ParR-dependent transcription in Pseudomonas aeruginosa

Two-component systems convert environmental signals into transcriptional responses, but how one response-regulator phosphorylation state produces different outputs at different promoters remains unclear. Here we show that promoter architecture determines how the ParR response regulator in Pseudomonas aeruginosa interprets phosphorylation. Phenotypic, transcriptomic, biochemical and promoter-engineering analyses showed that phosphorylation of the conserved ParR receiver residue Asp57 lowered DNA-occupancy thresholds across target promoters. Individual promoters, however, converted this shared increase in binding into activation, repression or phosphorylation-dependent sign switching. Chromosomally D57 ParR variants reproduced these behaviours at endogenous loci and altered antibiotic susceptibility, biofilm formation and virulence-associated phenotypes. Mapping and engineering of representative promoters identified a two-tier cis-regulatory code: half-site sequence compatibility determines productive ParR engagement, whereas spacer length determines regulatory sign and magnitude. Spacer swaps were sufficient to reprogram promoter logic between regulatory modes. These findings separate regulator state from promoter decoding and show how bacterial promoter architecture can diversify the outputs of a shared phosphorylation signal. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/738673v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@1a0a26forg.highwire.dtl.DTLVardef@10836a8org.highwire.dtl.DTLVardef@3c6cd8org.highwire.dtl.DTLVardef@10dfefb_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsParR coordinates antibiotic resistance, biofilm formation and virulence-linked phenotypes in P. aeruginosa. Promoters convert ParR phosphorylation into activation, repression or sign switching. Half-site compatibility and spacer length form a cis-regulatory code for ParR output.

biochemistry↗

bioRxiv2026

Integrative multi-omic analysis identifies tumor-intrinsic p38 as a driver of immune exclusion in human epithelial cancers

Patients with tumors not responding to immune-checkpoint inhibition (ICI) often harbor a non-T cell-inflamed tumor microenvironment, characterized by the absence of IFN-{gamma}-associated CD8+ T cells and dendritic cell activation. While the role of p38 mitogen-activated protein kinases (MAPKs) in regulating dendritic and myeloid cells is established, the tumor-intrinsic immunomodulatory function of p38 remains underexplored. Here, we identify tumor cell-intrinsic p38 signaling as a target candidate associated with immune exclusion and reduced immunotherapy response. In human papillomavirus-negative head and neck squamous carcinoma (HNSCC), molecular analysis of 395 tumor tissues revealed a p38-centered network enriched in non-T cell-inflamed tumors. Multi-cancer single-cell RNA sequencing analysis of over 200,000 cells further identifies p38 activation as a potential immune-exclusion program across multiple epithelial tumor types, including HNSCC and lung squamous cell carcinoma (LUSC), supported by tissue validation in [~]250 human biospecimens using multispectral imaging and digital spatial profiling. Functional studies demonstrate that p38 knockdown or pharmacologic inhibition in HNSCC and LUSC cell lines increases T cell migration, with CXCL16 identified as a chemokine mediator in vitro; neutralization of CXCL16 attenuated this effect. Together, these findings identify tumor-intrinsic p38 activation as a driver of immune exclusion in epithelial cancers and support its potential as a therapeutic target to overcome immunotherapy resistance.

Cancer Biology↗

bioRxiv2026

CosMxScope: Scalable Reconstruction and Digital Pathology Integration of Imaging-Based Spatial Transcriptomics Data

Spatial transcriptomics technologies have transformed the capacity to quantify gene expression from human tissues, simultaneously capturing both the cell functional state and spatial organization at cellular and subcellular resolution. The CosMx Spatial Molecular Imager (SMI) is one of the leading platforms at single-cell spatial multi-modal omics profiling, capable of measuring thousands of RNA or protein targets per cell across whole slide sections. Data exported includes field-of-view (FOV) image tiles, subcellular transcript coordinates, and cell segmentation polygons, outputs that are rich in spatial information but not directly compatible with widely used digital pathology tools. Here we present CosMxScope, a lightweight open-source Python framework that bridges CosMx spatial outputs with histopathology visualization environments. CosMxScope provides functions for stitching FOV image tiles into reconstructed whole-slide images, converting cell segmentation polygons and transcript coordinates into GeoJSON objects which enabled further assessments within QuPath, and generating spatial visualization plots of cell types, transcript locations, and gene expression patterns. The framework is designed for practical use in translational research settings, enabling interactive exploration of spatial transcriptomic data alongside cell morphology. CosMxScope has been applied in multiple ongoing research projects involving CosMx profiling of human and mouse tissues, supporting pathology-based spatial analysis workflows. This open-source software is available at https://github.com/AivaraX-AI/CosMxScope.

bioinformatics↗

bioRxiv2026

Obscuration to Clarity: Bone Suppression for Enhanced Localization in Pneumothorax Segmentation of Chest Radiographs

Chest radiography (CXR) is a primary modality for assessing cardiopulmonary conditions, but its effectiveness is limited by anatomical obstructions (e.g., ribs, clavicles) that hinder accurate pneumothorax segmentation, boundary delineation, and severity estimation. While deep learning-based bone suppression improves soft-tissue visibility, its utility for precise pixel-wise localization remains underexplored. This study investigates the downstream application of bone suppression for pneumothorax segmentation, integrating it as a preprocessing step to mitigate bony obscuration. We evaluate its impact across CNN and Vision Transformer models on two public datasets, where models trained on bone-suppressed CXRs significantly outperform (p < 0.05) non-suppressed counterparts, achieving up to 17% improvement in Mean Average Surface Distance (MASD), 4.9% in Dice Similarity Coefficient (DSC), and 5.9% in Normalized Surface Dice (NSD), alongside a 9.5% gain in Matthews Correlation Coefficient (MCC). These results demonstrate bone suppression as an architecture-independent enhancement for pneumothorax localization, improving the reliability of automated CXR interpretation.

bioengineering↗

bioRxiv2025

Integrating Artificial Intelligence-Driven Digital Pathology and Genomics to Establish Patient-Derived Organoids as a Novel Alternative Model for Drug Response in Head and Neck Cancer

Patient-derived organoids (PDOs) are emerging as advanced 3D ex vivo novel alternative method (NAM) preclinical models, offering significant advantages over traditional cell lines and monolayer cultures for therapeutic development. In this study, we established PDOs from surgically resected fresh tissues of human papillomavirus (HPV)-negative head and neck squamous cell carcinoma (HNSCC) across anatomical sites, tumor T-categories, and sample types. These PDOs faithfully recapitulate the tumors pathology, mutational profile, and drug response. To enable rapid classification of PDO identity, we developed a new convolutional neural network (CNN) model, TransferNet-PDO, which accurately distinguished tumor versus normal PDOs in culture using digital histopathology images (AUC[≥]0.88). PDOs maintained stable cultures and were cryopreserved between passages 5 and 12. Immunohistochemistry (IHC) staining (PanCK, p63, Cytokeratin 13, Ki67) confirmed squamous phenotype and histologic aggression of the original tumor. For tumors harboring TP53 mutations by whole-exome sequencing (WES), PDOs retained the corresponding p53 functional status as confirmed by IHC (enhanced or loss of expression). Somatic mutational landscape revealed that PDOs preserved driver somatic mutations, copy number variations (CNVs), and clonal architecture including low-prevalence subclones. Drug sensitivity assessment of PDOs showed that cisplatin reduced cell viability, whereas cetuximab and lenvatinib had minimal effects. Chemoradiation led to greater tumor organoid killing compared to radiation or chemotherapy alone. This study presents an integrated HNSCC PDO platform combining tissue biobanking, organoid establishment, multi-omics characterization, functional drug screening, and AI-driven histopathologic classification, providing a comprehensive and scalable system for translational cancer research.

cancer biology↗

bioRxiv2025

Spatial Prior-Guided Boundary and Region-Aware 2D Lesion Segmentation in Neonatal Hypoxic Ischemic Encephalopathy

Segmenting acute and hyper-acute brain lesions in neona-tal hypoxic-ischemic encephalopathy (HIE) from diffusion-weighted MRI (DWI) is critical for prognosis and treatment planning but remains challenging due to severe class imbalance and lesion variability. We propose a computationally efficient 2D segmentation framework leveraging ADC and ZADC maps as a three-channel input to UNet++ with an Inception-v4 encoder and scSE attention for enhanced spatial-channel recalibration. To address class critical imbalance and lack of volumetric context in 2D methods, we introduce a novel boundary-and-region-aware weighted loss integrating Tversky, Log-Hausdorff, and Focal losses. Our method surpasses state-of-the-art 2D approaches and achieves competitive performance against computationally intensive 3D architectures, securing a Dice Similarity Coefficient (DSC) of 0.6060, Mean Average Surface Distance (MASD) of 2.6484, and Normalized Surface Distance (NSD) of 0.7477. These results establish a new benchmark for neonatal HIE lesion segmentation, demonstrating superior detection of both acute and hyper-acute lesions while mitigating the challenge of loss collapse. The code is available at Neonatal-HIE-SPARSeg.

bioinformatics↗

bioRxiv2025

CDKN2ALow cancer cells outcompete macrophages for microenvironmental zinc to drive immunotherapy resistance

Anti-PD1 therapies are primarily thought to rely on functional T cell responses; yet tumors with limited T cell infiltration can still benefit, suggesting alternative mechanisms contribute to therapeutic efficacy. Indeed, we found that myeloid-rich, T cell-poor tumor models respond to anti-Pd1, and this is dependent on a cancer cell-macrophage crosstalk mediated by cancer cell Cdkn2a expression. Mechanistically, we found that cancer cells with decreased Cdkn2a expression (Cdkn2aLow), which occurs in [~]50% of all human cancers, reorganize zinc compartmentalization by upregulating the zinc importer Slc39a9 at the plasma membrane. Increased cancer cell plasma membrane Slc39a9 leads to intracellular zinc accumulation in cancer cells and depletion of zinc in the tumor microenvironment (TME), resulting in zinc-starved tumor-associated macrophages (TAMs) with reduced phagocytic activity. Restoring zinc availability in TAMs--via dietary supplementation or Slc39a9 knockdown in cancer cells--reprograms TAMs to a pro-phagocytic state and sensitizes Cdkn2aLow tumors to anti-Pd1 therapy. Remarkably, Slc39a9 knockdown tumors respond to anti-Pd1 in Rag1-/- mice, and co-injection of zinc-replete macrophages is sufficient to drive an anti-Pd1 response in immunodeficient mice, demonstrating the T cell-independent nature of this response. Clinically, TAMs from CDKN2ALow cancer patients show reduced zinc and phagocytosis gene signatures. Moreover, patients with lower circulating zinc levels have significantly worse time-to-event outcomes than those with higher levels. Together, these findings uncover a previously unrecognized mechanism by which Cdkn2aLow cancer cells outcompete TAMs for zinc, impairing their function and limiting anti-Pd1 efficacy. They also provide evidence that macrophages alone, without T cells, can enhance anti-PD1 response through zinc-mediated reprogramming of phagocytosis.

cancer biology↗

bioRxiv2024

MALT1 protease inhibition restrains glioblastoma progression by reversing tumor-associated macrophage-dependent immunosuppression

MALT1 protease is an intracellular signaling molecule that promotes tumor progression via cancer cell-intrinsic and cancer cell-extrinsic mechanisms. MALT1 has been mostly studied in lymphocytes, and little is known about its role in tumor-associated macrophages. Here, we show that MALT1 plays a key role in glioblastoma (GBM)-associated macrophages. Mechanistically, GBM tumor cells induce a MALT1-NF-{kappa}B signaling axis within macrophages, leading to macrophage migration and polarization toward an immunosuppressive phenotype. Inactivation of MALT1 protease promotes transcriptional reprogramming that reduces migration and restores a macrophage "M1-like" phenotype. Preclinical in vivo analysis shows that MALT1 inhibitor treatment results in increased immuno-reactivity of GBM-associated macrophages and reduced GBM tumor growth. Further, the addition of MALT1 inhibitor to temozolomide reduces immunosuppression in the tumor microenvironment, which may enhance the efficacy of this standard-of-care chemotherapeutic. Together, our findings suggest that MALT1 protease inhibition represents a promising macrophage-targeted immunotherapeutic strategy for the treatment of GBM. Graphical abstract. O_FIG O_LINKSMALLFIG WIDTH=196 HEIGHT=200 SRC="FIGDIR/small/614808v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@18c969eorg.highwire.dtl.DTLVardef@f48f0dorg.highwire.dtl.DTLVardef@1dbbbb1org.highwire.dtl.DTLVardef@ff8237_HPS_FORMAT_FIGEXP M_FIG The effects of tumor cell-induced CARD9-BCL10-MALT1 (CBM) activation (left) and MALT1 protease inhibition (right) on GBM associated macrophages in the tumor microenvironment. Cartoon of cellular components of a GBM tumor with an immunosuppressive TME characterized by "M2-like macrophages" (left) and conversion to a more immune-reactive tumor microenvironment characterized by "M1-like macrophages and increased effector T-cells (right) as a result of MALT1 protease inhibition. C_FIG

cancer biology↗

bioRxiv2024

Immunocompetent murine model of Ewing sarcoma reveals role for TGFβ inhibition to enhance immune infiltrates in Ewing tumors during radiation

Ewing sarcoma (ES) is an aggressive cancer diagnosed in adolescents and young adults. The fusion oncoprotein (EWSR1::FLI1) that drives Ewing sarcoma is known to downregulate TGFBR2 expression (part of the TGF{beta} receptor). Because TGFBR2 is downregulated, it was thought that TGF{beta} likely plays an inconsequential role in Ewing biology. However, the expression of TGF{beta} in the Ewing tumor immune microenvironment (TIME) and functional impact of TGF{beta} in the TIME remains largely unknown given the historical lack of immunocompetent preclinical models. Here, we use single-cell RNAseq analysis of human Ewing tumors to show that immune cells, such as NK cells, are the largest source of TGF{beta} production in human Ewing tumors. We develop a humanized (immunocompetent) mouse model of ES and demonstrate distinct TME signatures and metastatic potential in these models as compared to tumors developed in immunodeficient mice. Using this humanized model, we study the effect of TGF{beta} inhibition on the Ewing TME during radiation therapy, a treatment that both enhances TGF{beta} activation and is used to treat aggressive ES. Utilizing a trivalent ligand TGF{beta} TRAP to inhibit TGF{beta}, we demonstrate that in combination with radiation, TGF{beta} inhibition both increases ES immune cell infiltration and decreases lung metastatic burden in vivo. The culmination of these data demonstrates the value of humanized models to address immunobiologic preclinical questions in Ewing sarcoma and suggests TGF{beta} inhibition as a promising intervention during radiation therapy to promote metastatic tumor control.

cancer biology↗

bioRxiv2023

Identification of tumor-intrinsic drivers of immune exclusion in acral melanoma

BackgroundAcral melanoma (AM) has distinct characteristics as compared to cutaneous melanoma and exhibits poor response to immune checkpoint inhibitors (ICI). Tumor-intrinsic mechanisms of immune exclusion have been identified in many cancers but less studied in AM. MethodsWe characterized clinically annotated tumors from patients diagnosed with AM at our institution in correlation with ICI response using whole transcriptome RNAseq, whole exome sequencing, CD8 immunohistochemistry, and multispectral immunofluorescence imaging. A defined interferon-{gamma}-associated T cell-inflamed gene signature was used to categorize tumors into non-T cell-inflamed and T cell-inflamed phenotypes. In combination with AM tumors from two published studies, we systematically assessed the immune landscape of AM and detected differential gene expression and pathway activation in a non-T cell-inflamed tumor microenvironment (TME). Two single-cell(sc) RNAseq AM cohorts and 11 bulk RNAseq cohorts of various tumor types were used for independent validation on pathways associated with lack of ICI response. In total, 892 specimens were included in this study. Results72.5% of AM tumors showed low expression of the T cell-inflamed gene signature, with 23.9% of total tumors categorized as the non-T cell-inflamed phenotype. Patients of low CD3+CD8+PD1+ intratumoral T cell density showed poor prognosis. We identified 11 oncogenic pathways significantly upregulated in non-T cell-inflamed relative to T cell-inflamed TME shared across all three acral cohorts (MYC, HGF, MITF, VEGF, EGFR, SP1, ERBB2, TFEB, SREBF1, SOX2, and CCND1). scRNAseq analysis revealed that tumor cell-expressing pathway scores were significantly higher in low vs high T cell-infiltrated AM tumors. We further demonstrated that the 11 pathways were enriched in ICI non-responders compared to responders across cancers, including acral melanoma, cutaneous melanoma, triple-negative breast cancer, and non-small cell lung cancer. Pathway activation was associated with low expression of interferon stimulated genes, suggesting suppression of antigen presentation. Across the 11 pathways, fatty acid synthase and CXCL8 were unifying downstream target molecules suggesting potential nodes for therapeutic intervention. ConclusionsA unique set of pathways is associated with immune exclusion and ICI resistance in AM. These data may inform immunotherapy combinations for immediate clinical translation.

cell biology↗

bioRxiv2023

Optical Control of G-Actin with a Photoswitchable Latrunculin

Actin is one of the most abundant proteins in eukaryotic cells and a key component of the cytoskeleton. A range of small molecules have emerged that interfere with actin dynamics by either binding to polymeric F-actin or monomeric G-actin to stabilize or destabilize filaments or prevent their formation and growth, respectively. Amongst these, the latrunculins, which bind to G-actin and affect polymerization, are widely used as tools to investigate actin-dependent cellular processes. Here, we report a photoswitchable version of latrunculin, termed opto-latrunculin (OptoLat), which binds to G-actin in a light-dependent fashion and affords optical control over actin polymerization. OptoLat can be activated with 390 - 490 nm pulsed light and rapidly relaxes to the inactive form in the dark. Light activated OptoLat induced depolymerization of F-actin networks in oligodendrocytes and budding yeast, as shown by fluorescence microscopy. Subcellular control of actin dynamics in human cancer cell lines was demonstrated by live cell imaging. Light-activated OptoLat also reduced microglia surveillance in organotypic mouse brain slices while ramification was not affected. Incubation in the dark did not alter the structural and functional integrity of microglia. Together, our data demonstrate that OptoLat is a useful tool for the elucidation of G-actin dependent dynamic processes in cells and tissues.

pharmacology and toxicology↗

bioRxiv2023

BOston Neonatal Brain Injury Dataset for HypoxicIschemic Encephalopathy (BONBID-HIE): Part I. MRI and Manual Lesion Annotation

Hypoxic ischemic encephalopathy (HIE) is a brain injury that occurs in 1 [~]5/1000 term neonates. Accurate identification and segmentation of HIE-related lesions in neonatal brain magnetic resonance images (MRIs) is the first step toward predicting prognosis, identifying high-risk patients, and evaluating treatment effects. It will lead to a more accurate estimation of prognosis, a better understanding of neurological symptoms, and a timely prediction of response to therapy. We release the first public dataset containing neonatal brain diffusion MRI and expert annotation of lesions from 133 patients diagnosed with HIE. HIE-related lesions in brain MRI are often diffuse (i.e., multi-focal), and small (over half the patients in our data having lesions occupying <1% of brain volume). Segmentation for HIE MRI data is remarkably different from, and arguably more challenging than, other segmentation tasks such as brain tumors with focal and relatively large lesions. We hope that this dataset can help fuel the development of MRI lesion segmentation methods for HIE and small diffuse lesions in general.

neuroscience↗

bioRxiv2022

Epigenetic silencing by SMYD3 represses tumor intrinsic interferon response in HPV-negative squamous cell carcinoma of the head and neck.

Cancers often display immune escape, but the mechanisms and potential for reversibility are incompletely understood. Epigenetic dysregulation has been implicated in the immune escape of various cancer types. We have identified the epigenetic modifier SET and MYND-domain containing protein 3 (SMYD3) as a mediator of immune escape in human papilloma virus (HPV)- negative head and neck squamous cell carcinoma (HNSCC), an aggressive disease with poor prognosis and low response to immunotherapy with pembrolizumab, a programmed-death-1 (PD-1) targeting antibody. SMYD3 loss increased the sensitivity of HNSCC cancer cells to IFN-{beta}, resulting in upregulation of type I IFN response and antigen presentation machinery genes. We found that SMYD3 regulates the transcription of Ubiquitin-Like PHD And RING Finger Domain- Containing Protein 1 (UHRF1), a key epigenetic reader of trimethylated lysine 9 on histone H3 (H3K9me3), which binds to H3K9me3-enriched promoters of key immune-related genes and silences their expression. SMYD3 further maintains the repression of immune-related genes through the deposition of H4K20me3 within the gene body regions of these genes. In an anti-PD-1 immune checkpoint resistant syngeneic mouse model of HPV-negative HNSCC, Smyd3 depletion induced influx of CD8+ T-cells, upregulated PD-L1 and MHC class I molecules, and increased sensitivity to anti-PD-1 therapy. SMYD3 overexpression was associated with decreased CD8 T-cell infiltration in tumor samples from patients with HPV-negative HNSCC, and was associated with poor response to pembrolizumab. Overall, these data highlight a previously unreported function of SMYD3 as a master epigenetic regulator of anti-tumor immune response in HPV-negative HNSCC and provide a rationale for translational approaches combining SMYD3 depletion strategies with checkpoint blockade to overcome anti-PD-1 resistance in this devastating disease.

cancer biology↗

bioRxiv2022

Microbial metabolite butyrate-prodrug polymeric micelles promote gut health and treat food allergies

The microbiome modulates host immunity and aids in maintenance of tolerance in the gut, where microbial and food-derived antigens are abundant. Modern lifestyle practices, including diet and antibiotic use, have depleted beneficial taxa, specifically butyrate-producing Clostridia. This depletion is associated with the rising incidence of food allergy, inflammatory bowel diseases, and other noncommunicable chronic diseases. Although butyrate is known to play important roles in regulating gut immunity and maintaining epithelial barrier function, its clinical translation is challenging due to its offensive odor and quick absorption in the upper gut. Here, we have developed two polymeric micelle systems, one with a neutral charge (NtL-ButM) and one with a negative charge (Neg-ButM) that release butyrate from their polymeric core in different regions of the gastrointestinal tract when administered intragastrically to mice. We show that these butyrate-containing micelles, used in combination, restore a barrier-protective response in mice treated with either dextran sodium sulfate or antibiotics. Moreover, butyrate micelle treatment protects peanut-allergic dysbiotic mice from an anaphylactic reaction to peanut challenge and rescues their antibiotic-induced dysbiosis by increasing the abundance of Clostridium Cluster XIVa. Butyrate micelle treatment also reduces the severity of colitis in a murine model. By restoring microbial and mucosal homeostasis, these butyrate-prodrug polymeric micelles may function as a new, antigen-agnostic approach for the treatment of allergic and inflammatory disease.

bioengineering↗

bioRxiv2022

Unlocking the microblogging potential for science and medicine

Microblogging platform Twitter allows researchers to showcase their work, receive constructive feedback, find jobs, and build scientific collaborations. While existing literature has analyzed the benefits of Twitter in the development and distribution of scientific knowledge, most of the studies only took into account a limited number of researchers, which affected the generalizability of derived results. Our study analyzed the activity of 6,000 biomedical scientists on Twitter using data-driven approaches, a third of whom were female. Furthermore, we estimated that up to a quarter of the members of the scientific community are engaged on Twitter. While the number of male scientists joining the microblogging platform every year has decreased, the number of female scientists has remained roughly the same. Scientists are very selective in who they are following as compared to the general public. We also found that the type of tweets and retweets one posts may affect the number of followers, specifically, that a moderate to high level of professionalism and a high level of positivity is correlated with followers count. Moreover, female scientists send fewer negative tweets as compared to male scientists (31.1% for females and 34.7% for males). Our analysis could provide insights and launch a conversation on the advantages and limitations of using Twitter for disseminating scientific information and engaging in constructive discussion and collaborations within the scientific community.

scientific communication and education↗

bioRxiv2022

BET inhibition sensitizes immunologically-cold Rb-deficient prostate cancer to immune checkpoint blockade

PurposeNon-T cell-inflamed immunologically "cold" tumor microenvironments (TME) are associated with poor responsiveness to immune checkpoint blockade (ICB), and can be sculpted by tumor cell genomics. Here we evaluated how Retinoblastoma (Rb) tumor suppressor loss of function (LOF), one of the most frequent alterations in human cancer and associated with lineage plasticity, poor prognosis and therapeutic outcomes, alters the TME, and whether therapeutic strategies targeting the molecular consequences of Rb loss enhance ICB efficacy. Experimental DesignWe performed bioinformatics analysis to elucidate the impact of endogenous Rb LOF on the immune TME in human primary and metastatic tumors. Next, we utilized isogenic murine models of Rb-deficient prostate cancer (PC) for in vitro and in vivo mechanistic studies to examine how Rb loss and bromodomain and extraterminal (BET) domain inhibition (BETi) reprograms the immune landscape, and evaluated in vivo therapeutic efficacy of BETi, singly and in combination with ICB and androgen deprivation therapy. ResultsRb loss was enriched in non-T cell-inflamed tumors, and Rb-deficient murine tumors demonstrated decreased immune infiltration in vivo. The BETi JQ1 increased immune infiltration into the TME through enhanced tumor cell STING/NF-{kappa}B activation and type I interferon (IFN) signaling within tumor cells, resulting in differential macrophage and T cell-mediated tumor growth inhibition and sensitization of Rb-deficient PC to ICB. ConclusionsBETi can reprogram the immunologically cold Rb-deficient TME via STING/NF-{kappa}B/IFN signaling to sensitize Rb-deficient PC to ICB. These data provide the mechanistic rationale to test combinations of BETi and ICB in clinical trials of Rb-deficient PC. STATEMENT OF TRANSLATIONAL RELEVANCERb LOF is one of the most common genomic alterations in human cancer, occurring in approximately 1/3 of advanced malignancies, Furthermore, loss of Rb correlates with enhanced aggressiveness and poor therapeutic outcomes. In this study, we demonstrate that loss of Rb is also associated with an immunosuppressive tumor microenvironment and lack of responsiveness to immune checkpoint blockade (ICB). As a strategy to overcome Rb LOF induced immunosuppression, we have demonstrated that BETi treatment drives STING/NF-{kappa}B signaling and type I interferon production within tumor cells, resulting in immune-mediated tumor control in Rb-deficient PC, which is accentuated by the combination with ICB and ADT. These findings provide a roadmap for maximizing the clinical translation of BET inhibitors into the clinic to treat aggressive-variant Rb-deficient PC.

cancer biology↗