Biology subjects

Wu, C.

Publications and source records attributed to Wu, C..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Hypoxia/HIF Signaling Negatively Regulates Bone Marrow Adiposity after Radiation Exposure

Radiation therapy is an essential cancer treatment, yet collateral damage to normal tissues remains a major clinical challenge. In bone, radiation-induced toxicity is characterized by loss of hematopoietic function, reduced bone volume, and increased marrow adipose tissue (MAT). Importantly, cancer patients who undergo radiotherapy exhibit significantly higher fracture risk compared to those receiving similar treatments without radiation exposure, underscoring the clinical consequences of bone microenvironment (BME) injury. The BME is inherently hypoxic resulting in the activation of by hypoxia-inducible factor (HIF) signaling. Here, we demonstrate that radiation induces a rapid and persistent accumulation of MAT, with adipocytes localizing preferentially to hypoxic regions of the marrow. To investigate the role of hypoxia/HIF signaling in this process, we generated aP2Cre;Hif-1 fl/fl;Hif-2fl/fl conditional knockout mice. Surprisingly, these mice exhibited increased MAT expansion following radiation compared to controls, suggesting that HIF deletion in aP2-expressing cells exacerbates radiation-induced adipogenesis. Analysis aP2CreRosa26tdTomato/+ mice revealed that most aP2-expressing cells did not give rise to mature adipocytes, macrophages, or endothelial cells, pointing instead to an uncharacterized stromal population that influences MAT formation. In contrast, conditional ablation of HIF transcription factors in LepRCre-expressing skeletal stem cells, which contain a subpopulation of skeletal progenitors which directly contribute to marrow adipocytes, had no effect on radiation-induced MAT expansion. Collectively, these findings identify a previously unrecognized population of adipocyte-regulatory cells whose HIF-dependent activity constrains stress-induced marrow adiposity. This work provides new mechanistic insight into how radiation disrupts the marrow microenvironment and expands MAT, advancing our understanding of the cellular and molecular drivers of radiation-induced bone fragility. One Sentence SummaryLoss of HIF signaling in aP2Cre expressing cells enhances radiation induced marrow adiposity.

developmental biology↗

bioRxiv2025

The Gene Encoding Ornithine Decarboxylase for Putrescine Biosynthesis Is Essential for the Viability of Fusobacterium nucleatum

Fusobacterium nucleatum is a Gram-negative anaerobe associated with periodontitis and colorectal cancer. It secretes putrescine, a polyamine that promotes biofilm formation by oral co-colonizers and enhances the proliferation of cancer cells. However, the physiological importance of putrescine for F. nucleatum itself remains unexplored. Here, we show that putrescine biosynthesis, mediated by the ornithine decarboxylase gene oda, is essential for F. nucleatum viability. Deletion of oda was only possible when a functional copy was provided in trans, and CRISPR interference of oda expression resulted in complete growth arrest. The essentiality of oda was conserved across multiple subspecies. Supplementation with exogenous putrescine enabled the isolation of a conditional oda mutant whose growth was strictly putrescine-dependent. Putrescine depletion caused filamentation, membrane disruption, detergent hypersensitivity, and lysis in hypoosmotic conditions, indicating a critical role in maintaining cell envelope integrity. RNA sequencing revealed broad transcriptional remodeling under putrescine-limited conditions, including upregulation of genes involved in lipid metabolism, osmoprotection, and cell wall remodeling. Notably, oda transcript levels increased when putrescine was depleted, suggesting a negative feedback mechanism. These findings demonstrate that putrescine is not only an extracellular communal metabolite but is also vital for the cellular integrity and survival of F. nucleatum under anaerobic conditions. IMPORTANCEFusobacterium nucleatum is a prominent member of the oral microbiota and has been linked to various human diseases, including periodontitis, preterm birth, and colorectal cancer. Despite its clinical significance, the metabolic requirements that support its growth and viability remain poorly understood. In this study, we identify the oda gene, which encodes ornithine decarboxylase, as essential for F. nucleatum survival due to its role in putrescine biosynthesis. We demonstrate that depletion of putrescine leads to severe growth and morphological defects, accompanied by widespread transcriptional changes. These findings reveal an underappreciated metabolic vulnerability and highlight the critical role of polyamine homeostasis in maintaining cellular integrity in this notorious anaerobe.

microbiology↗

bioRxiv2025

A Spatially Resolved Atlas of Alternative Polyadenylation Across 18 Human Tissues and 76 Disease States

Alternative polyadenylation (APA) is a key regulator of gene expression and cellular dynamics, yet systematic investigations of spatially resolved APA across diverse human tissues remain limited. Here, we developed SpatialAPA (https://github.com/Omicslab-Zhang/spatialAPA), a framework that benchmarks multiple APA identification methods and integrates spatial APA data with gene expression and cellular dynamics at spatial resolution. Applying SpatialAPA to 363 spatial transcriptomic data from 56 projects across 18 human tissues and 76 diseases, we constructed a spatially resolved APA atlas comprising 346,932 APA events across 52,175 genes. This atlas reveals organ-specific APA patterns and provides new insights into how APA regulates tissue homeostasis and disease progression beyond transcriptional control. To ensure cross-sample comparability, we applied batch correction, while spatial cell deconvolution uncovered cell-type-specific dynamics and interactions. In triple-negative breast cancer, integrated spatial and single-cell analyses identified TSPAN8-positive epithelial subpopulations whose distinct APA regulation and transcriptional programs drive differentiation and malignant progression. To facilitate community access, we developed an online platform (http://www.biomedical-web.com/spatialAPAdb/home) for exploring APA, gene expression, and cellular dynamics in health and disease. Together, this study establishes the first comprehensive spatial APA atlas, providing a valuable resource and analytical framework for investigating molecular mechanisms and therapeutic targets.

bioinformatics↗

bioRxiv2025

Type 1 Regulatory T cells induced by intestinal epithelial cells respond to food antigen

As the first-line barrier against food antigens, the intestinal epitheliums role in establishing peripheral immune tolerance to food remains completely unknown. Additionally, the specific types of regulatory T cells induced to maintain food tolerance--along with their antigen specificity--are still unclear. Here we found small intestinal FOXP3-IL-10+ Tr1 cells, but not Treg cells, can respond to food antigens presented by intestinal epithelial cells (IECs) in an antigen-specific manner. Through immunopeptidome analysis of MHCII-presented peptides, we demonstrate that IECs can present food-derived antigens. Importantly, these IEC-presented food antigens are exclusively recognized by the TCR repertoire of small intestinal Tr1 cells, not Treg cells. Furthermore, we show that T cells recognizing IEC-presented food antigens specifically differentiate into Tr1 cells in the siLP. These findings establish two key insights: first, that maintaining food tolerance represents a physiological function of Tr1 cells, and second, that IECs play a central role in maintaining food tolerance. Our work thus provides mechanistic understanding of how the intestinal epithelium contributes to immune tolerance through its antigen presentation capacity and subsequent Tr1 cell induction.

immunology↗

bioRxiv2025

AAV NRF2 Gene Therapy Preserves Retinal Structure and Function in Rodent Models of Oxidative Damage

Dry age-related macular degeneration is the most frequent cause of visual impairment in individuals over age 50 in developed countries. It is characterized by subretinal deposits of oxidized proteins and lipids and results in progressive loss of high acuity vision. One major risk factor is smoking, which causes oxidative stress in many tissues, including the eye. We previously showed that an adeno-associated viral vector expressing human NRF2 (AAV8/Best1-Nrf2), a transcription factor that regulates responses to oxidative damage, slowed degeneration in mouse models of another blinding disorder, retinitis pigmentosa, which also includes oxidative stress. Here, our AAV8/Best1-Nrf2 vector was tested in a model of oxidative stress wherein sodium iodate was injected systemically, as this is often used to model dry age-related macular degeneration. Sodium iodate causes acute oxidative damage to supporting cells of the retina, the retinal pigment epithelial cells, and ultimately leads to photoreceptor death. Subretinal injection of AAV8/Best1-Nrf2 led to protection of the retinal pigment epithelium and photoreceptors, as well as preservation of visual function, in rat and mouse sodium iodate models. AAV8/Best1-Nrf2 may serve as an effective gene-agnostic therapy for diseases with oxidative stress, including dry age-related macular degeneration. ETOCOxidative stress occurs in diseases that lead to vision loss, including age-related macular degeneration (AMD). AMD is commonly modeled by injection of sodium iodate (S.I.), an oxidizing agent. AAV-mediated delivery of Nrf2, a transcription factor that regulates oxidative stress, protects the eye from S.I. damage in rat and mouse models. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/663952v1_ufig1.gif" ALT="Figure 1"> View larger version (67K): org.highwire.dtl.DTLVardef@357e57org.highwire.dtl.DTLVardef@1f9986dorg.highwire.dtl.DTLVardef@186537corg.highwire.dtl.DTLVardef@1d31aad_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2025

The PTPN1 and PTPN2 phosphatases are Cooperative Regulators of Cancer Cell Immune Evasion

Immune evasion by cancer cells remains a major barrier to the success of immune checkpoint blockade (ICB). Here, we identify the phosphatases PTPN1 and PTPN2 as cooperative regulators of tumor immune resistance. Dual genetic ablation of PTPN1/2 in cancer cells enhances Type I and II interferon signaling, MHC-I and CXCL9 expression, and sensitizes tumor cells to cytotoxic T lymphocyte-mediated killing. The small-molecule inhibitor KQ791 phenocopies these effects and synergizes with anti-PD1 therapy to suppress tumor growth in murine models, including immunotherapy-refractory cancers. Mechanistically, PTPN1/2 loss augments STAT1/3/5 signaling and primes cancer cells for immunogenic cell death via IFN{gamma}/TNF-induced pathways. Moreover, PTPN1/2 inhibition enhances antigen release and cross-presentation, promoting robust antigen-specific CD8 T cell responses. These findings highlight PTPN1&2 as essential mediators of cancer immune evasion and support their inhibition as a strategy to broaden the effectiveness of immune checkpoint blockade in solid tumors.

cancer biology↗

bioRxiv2025

Deciphering gain-of-function from loss-of-function variants with AlphaMissense: A case study with the mechanosensitive PIEZO1 ion channel protein

Pathogenic missense mutations are commonly found in protein-coding regions of DNA, and often alter protein function. In the past decade, enormous experimental efforts have been undertaken through the development of functional assays, mutagenesis screenings, and computational prediction algorithms to characterize these variants. Indeed, most efforts have been focused towards identifying degrees of loss-of-function (LoF) effects on the three-dimensional structures of proteins, but gain-of-function (GoF) mutations remain poorly understood. Herein, we performed a case study of the PIEZO1 mechanosensitive ion channel protein whose GoF variants (n = 56) are implicated in hereditary xerocytosis (HX) and LoF variants (n = 6) in lymphatic dysplasia (LD), respectively. This study evaluated the abilities of AlphaMissense (AM) to decipher both mutation types, and benchmarked its performance against other algorithmic approaches, including Combined Annotation Dependent Depletion (CADD) v1.7, evolutionary model of variant effect (EVE), and Evolutionary Scale Modeling-1b (ESM-1B). We found that all approaches excelled in identifying LoF variants but were often ambiguous in their predictions for GoF PIEZO1 variants. ESM-1b was a notable exception that demonstrated balance sensitivity to both GoF and LoF variants as it likely identified certain sequential features not utilized in other approaches. Secondly, our findings suggest that GoF variants of HX do not significantly destabilize the PIEZO1 structure and are not generally identified by conventional signatures of damage from these algorithms. GoF variants are not synonymous with direct changes in changes in free energy upon mutations. Furthermore, we validated computational structure predictions of PIEZO1 against resolved cryo-EM structures, and provided biophysical data for variants located on unresolved residues of this ion channel. We formulated a weighted ensemble model that performed similarly to AM and outperformed all other traditional approaches evaluated in this study. Overall, this is the first study to directly evaluate the capabilities of pathogenicity prediction algorithms for deciphering GoF and LoF variants, and underscores the limitations present in current approaches.

biophysics↗

bioRxiv2025

The effects of gait speed on the responses to immediate and prolonged exposure to mediolateral optic flow perturbation in healthy young adults

BackgroundOptic flow is vital for locomotor control and is often perturbed to study the impact of optic flow on balance control. However, it remains unclear whether gait speed influences responses to such perturbations. This study aims to examine the effects of gait speed on gait parameters following immediate and prolonged exposure to mediolateral optic flow perturbations. MethodsTwenty-one young adults (23.43 {+/-} 4.19 years) walked on an instrumented treadmill, including 3 phases: baseline (3 min), perturbation with mediolateral optic flow (8 min), and post-perturbation (3 min). Trials were conducted at 0.6, 1.2, and 1.8 m/s. Ground reaction forces and 3D motion data were collected to calculate mediolateral margin of stability (MoS), mean step length (SL), step width (SW) and their variabilities. Three repeated-measures ANOVAs (Speed by Phase) were used to compare: baseline vs. early perturbation, early vs. late perturbation, and baseline vs. post-perturbation. ResultsThe responses to immediate and prolonged exposure to optic flow perturbation were speed dependent. Walking at slow speeds induced greater immediate responses in mediolateral gait parameters (SW and mediolateral MoS, both p < 0.001) compared to walking at faster speeds. During the perturbation phase, the adaptations were larger at faster vs. slower speeds for gait parameters in the direction of movement (SL, p = 0.007). ConclusionImmediate responses and adaptations to mediolateral optic flow perturbations are speed-dependent and larger at slower gait speeds. The responses to prolonged perturbation are interpreted as step-to-step adaptations that may inform future interventions and studies on gait speed selection.

neuroscience↗

bioRxiv2025

Predicting Spatial Transcriptomics from H&E Image by Pretrained Contrastive Alignment Learning

The intricate molecular landscape within tissues holds crucial information about cellular behavior and disease progression, yet capturing this complexity at a spatial level remains challenging. While Spatial transcriptomics (ST) offers valuable insights into gene expression patterns within their native tissue context, its widespread adoption is hindered by high costs and limited gene detection capabilities. Here we introduce CarHE (Contrastive Alignment of gene expRession for hematoxylin and eosin image), a method that overcomes these limitations by accurately predicting high-dimensional ST data (over 10,000 genes) solely from readily available H&E (Hematoxylin and Eosin) stained images. This novel pre-trained architecture employs contrastive learning through two mechanisms: cell-type-based transcriptomics information transfer and image-based histology information transfer. These mechanisms precisely align image features with spatial single-cell gene expressions, achieving prediction accuracies exceeding 0.7 (up to 1.7 folds compared to second best) across diverse tissue types and species. CarHEs superior performance extends to identifying subtle pathological features such as tertiary lymphoid structures in various cancers, including breast cancer, lung cancer, melanoma and ccRCC (clear cell renal cell carcinoma), and reconstructing 3D spatial transcriptomics from images alone, offering a cost-effective and robust alternative for large-scale spatial transcriptomics. We further validated CarHEs effectiveness by predicting DFS (Disease-Free Survival) from >1,600 lung cancer patients HE images, achieving a significantly higher AUC (Area Under the Receiver Operating Characteristic Curve) of 0.73 compared to state-of-the-art alternatives (0.58-0.64).

bioinformatics↗

bioRxiv2025

Fos labels a distinct excitatory neuron ensemble for memory retrieval

Experience-triggered expression of Fos has been extensively used as a marker representing memory engram. It is generally assumed that Fos-positive neurons are preferentially excited by the experience, yet this has not been directly examined. In this study, we tracked neuron activity and Fos expression in somatosensory cortex and dentate gyrus of hippocampus in mice, during electric shock-induced fear memory formation and retrieval. Contrary to the prevailing view, we found that calcium features fail to predict Fos for individual cells. Fos-positive neurons show no specific activation to stimuli during memory encoding, but their activities become stimuli-selective during retrieval. Surprisingly, inhibiting neurons that will express Fos during encoding does not affect the induction of memory-guided behavior upon their activation. Network simulation and voltage imaging further showed that connectivity to interneurons, not stimulus responsiveness, is a major factor determining Fos expression. Our results indicate that Fos labels excitatory neurons specific for memory retrieval.

neuroscience↗

bioRxiv2025

Evaluating the pathogenicity, stability, and stereochemical effects of variants of unknown significance in TREM2 using orthogonal structural analyses

Triggering receptor expressed on myeloid cells 2 (TREM2), an immune receptor expressed on the surface of microglia, has been identified through genome-wide association studies to be one of the risk factors in Alzheimers disease (AD). Several studies have also identified missense variants of TREM2 to be associated with frontotemporal dementia and Nasu-Hakola disease (NHD). To date, 51 novel missense variants of TREM2 have been identified in the literature, with the disease risk profiles of most variants still unknown. Assessing and classifying the pathogenicity of these variants is essential to investigate the disease mechanisms and develop effective treatments. Herein, we classified 32 missense variants involved in TREM2 using structural bioinformatic data with AlphaFold2. Using the protocol described in our previous work (Pillai et al., 2025), we determined the structural, stability, and potential functional effects of these variants. Our evaluations of the mutations were divided into those (i) implicated in NHD, (ii) located on the transmembrane domain, (iii) surface of the IgV-like domain, and (iii) buried in the receptor. Our analysis of variants involved in NHD suggests that, while V126G imposes the greatest effects, the T66M variant exerts significantly less effects on the TREM2 structures compared to the other remaining variants. Variants in the transmembrane domain of TREM2 did not impose significant alterations to the three-dimensional structure. Outside of known variants in the IgV-like domain, we identified 10 variants that imposed significant destabilizing effects to the structure and are of potential interest. Overall, the baseline biochemical data provided from this study may be informative to experimental efforts to better classify rare coding variants of TREM2 that are of unknown biological and clinical significance. HighlightsUsing our previously published protocol, we characterized the structure, stability, and functional effects of 27 unique variants of unknown biological significance in TREM2. Our analysis was divided into variants located on the transmembrane domain, surface of the IgV-like domain, buried in the IgV-like domain, and those leading to Nasu-Hakola disease. Excluding AD- and NHD-causing variants, we identified 10 TREM2 variants that cause significant destabilizing effects to the receptor. The in-silico data provided from this study serve as a baseline, and can guide future experimental efforts involving TREM2 variants. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/656054v1_ufig1.gif" ALT="Figure 1000"> View larger version (35K): org.highwire.dtl.DTLVardef@c426b1org.highwire.dtl.DTLVardef@1c859f1org.highwire.dtl.DTLVardef@88ea70org.highwire.dtl.DTLVardef@d777f4_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

PML1-Mediated Feedforward Loop Through PI3K and MAPK Axes Drives Endocrine Resistance

Treatment of estrogen receptor-positive (ER+) breast cancer is significantly hindered by endocrine resistance. We identified PML1 as a key therapeutic entity that can be targeted to overcome resistance. Endocrine-resistant breast cancer cells share three key characteristics: elevated PML1 protein levels, enhanced activity of PI3K, MAPK, or both signaling pathways, and reduced ER activity. We developed a PML1 gene signature that predicts poor prognosis and correlates strongly with PI3K, MAPK, and endocrine resistance gene signatures, as evident by cellular studies, scRNA-seq analysis, and spatial transcriptomics of endocrine therapy-treated tumors. This signature is present in endocrine-resistant breast cancer cells harboring the Y537S ER mutation. We consistently demonstrate high PML1 protein levels across cells resistant to various treatments, including 4-hydroxytamoxifen, fulvestrant, elacestrant, and CDK4/6 inhibitors. Furthermore, treatments with these therapeutic agents or knockdown of ESR1 mRNA also increase PML1 protein levels. Mechanistically, we show that ER inhibition through fulvestrant treatment activates PI3K and MAPK signaling, which enhance PML1 protein stability and synthesis. PML1 then drives a feedforward loop by stimulating the expression of cytokine and growth factor mRNAs, including CCL5 and HBEGF, further amplifying PI3K and MAPK signaling. Consequently, in endocrine-resistant cells, endocrine therapies, while inactivating ER, paradoxically reinforce this loop through increased PI3K/MAPK activation and PML1 protein accumulation, ultimately compromising therapeutic efficacy. Finally, we demonstrated that arsenic trioxide, an FDA-approved, PML-reducing drug, effectively disrupts this feedforward loop, offering a promising strategy for treating resistant metastatic breast cancer. STATEMENT OF SIGNIFICANCEEndocrine resistance remains a major obstacle in treating estrogen receptor-positive metastatic breast cancer. Our study identifies PML1 as a central mediator of this resistance, revealing how it maintains a self-reinforcing signaling network through PI3K and MAPK pathways by enhancing the production of cytokines and growth factors. The clinical significance of our findings is threefold: we establish PML1 as a biomarker for therapy resistance, demonstrate its mechanistic role in treatment failure, and show that FDA-approved arsenic trioxide can disrupt PML1-driven resistance. These insights provide a direct path to clinical translation, as combining arsenic trioxide with existing therapies could benefit patients with limited treatment options.

cancer biology↗

bioRxiv2025

FASN Inactivation-induced Progranulin (GRN) Expression Promotes Lysosome-dependent Cell Death to Suppress Leukemogenesis

Cancer cells rely on lipogenesis in addition to exogenous lipid uptake, and fatty acid synthase (FASN) is aberrantly overexpressed in myeloid leukemia. However, the precise role of FASN in leukemogenesis in vivo remains elusive. Here, we demonstrated that FASN is essential for leukemogenesis. Ablation of FASN impeded leukemic cell growth, survival, clonogenicity in vitro, and the leukemic burden in vivo. Conditional knockout of FASN barely affected hematopoiesis but significantly attenuated the leukemic progression of MLL-AF9 transplants. By screening a library of platensimycin derivatives, we identified compound MS-C19 as a potent FASN inhibitor. Pharmacological targeting of FASN by MS-C19 suppressed leukemic cell growth and clonogenicity in clinical AML blasts. Mechanistically, both MS-C19 treatment and FASN deficiency triggered the activation of lysosomal and inflammatory gene expression. Loss of FASN led to lysosomal membrane permeabilization and subsequent lysosome-associated cell death, but not lysosome biogenesis. We further identified that GRN, a lysosomal and neuroinflammatory gene, was potently transcribed by TFEB upon FASN loss. Depletion of GRN significantly reversed the inhibitory effects caused by FASN knockdown. Our work demonstrates that FASN is a therapeutic target for myeloid leukemia, and inactivation of FASN by the lead compound MS-C19 provides an alternative approach for leukemic intervention. Key PointsO_LIGenetic ablation of FASN induces apoptosis, impedes leukemia cell growth, and improves the survival of leukemic xenografts. C_LIO_LITargeting FASN by the compound MS-C19, a derivative of the natural microbe antibiotic platensimycin, reduces the cell survival of leukemic cell lines, the clinical leukemic blasts, and MLL-AF9 transformed murine leukemic cells. C_LIO_LIFASN inhibition induces lysosome-dependent cell death that relies on Progranulin (GRN) expression. C_LI

cancer biology↗

bioRxiv2025

Fluorescence recovery in the Super-Resolution regime reveals subcompartments of 53BP1 foci

We combine Lattice Structured Illumination Microscopy (diSIM with [~]60 nm resolution), Lattice Light-sheet microscopy and Fluorescence Recovery After Photobleaching (FRAP) to explore 53BP1 dynamics in Retinal Pigment Epithelial cells. 53BP1 forms liquid condensates during double-strand DNA repair, long-range DNA end-joining and heterochromatin maintenance. Our super-resolution movies reveal differences in 53BP1 foci contour: some foci are compact and stationary while others appear amorphous, dynamically changing shapes. To explore them, we developed FRAP in the Super-Resolution regime (FRAP-SR). 53BP1 foci with an amorphous loose contour display subcompartments that recover 53BP1-eGFP signals rapidly, indicating differential protein mobilities and 53BP1 functions within a single foci. In contrast, 53BP1-eGFP foci with a compact contour recover uniformly as single foci but show higher heterogeneity in 53BP1-eGFP recovery rates compared to foci that recover as multiple subcompartments. In cells released from aphidicolin, amorphous foci show faster 53BP1 recovery compared to compact foci. We discuss the conceptual implications of different 53BP1 mobilities, and how the FRAP-SR method transforms studies of dynamic 60-100 nm structures.

cell biology↗

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

Microbiota-derived secondary bile acids promote STING activation and antitumor activity

Microbiota metabolism generates diverse bile acids that are associated with health and disease, but the molecular targets and mechanisms of action for these metabolites have not been fully elucidated. Using deoxycholic acid (DCA) photoaffinity probes, with cholic acid (CA) probe as a comparator, we found many protein targets of microbiota-derived DCA in mammalian cells. Of note, we discovered that DCA binds the transmembrane domain of stimulator of interferon genes (STING), and enhances agonist-induced accumulation of higher-order STING species, type I interferon signaling and antitumor immunity. Moreover, DCA-producing microbiota species enhanced STING agonist-induced antitumor immunity primarily through the activation of natural killer (NK) cells. This reverse chemical microbiology approach revealed an unpredicted mechanism of action for DCA on STING activation and suggests that specific secondary bile acids and their associated microbiota species may promote NK activation and impact the efficacy of STING-targeted therapeutics.

immunology↗

bioRxiv2025

Inactivation of the Fusobacterium nucleatum Rnf complex reduces FadA-mediated amyloid formation and tumor development

The Gram-negative anaerobe Fusobacterium nucleatum is an oral oncobacterium that promotes colorectal cancer (CRC) development with the amyloid-forming cell surface adhesin FadA integral to CRC tumorigenesis. We describe here molecular genetic studies uncovering a novel mode of metabolic regulation of FadA-mediated tumor formation by a highly conserved respiratory enzyme known as the Rnf complex. First, we show that genetic disruption of Rnf, via rnfC deletion, significantly reduces the level of fadA transcript, accompanied by a near-complete abolishment of the precursor form of FadA (pFadA), reduced assembly of FadA at the mature cell pole, and severe defects in the osmotic stress-induced formation of FadA amyloids. We show further that the Rnf complex regulates three response regulators (CarR, ArlR, and S1), which modulate the expression of pFadA, without affecting fadA transcript. Consistent with our hypothesis that these response regulators control factors that process FadA, deletion of rnfC, carR, arlR, or s1 each impairs expression of the signal peptidase gene lepB, and FadA production is nearly abolished by CRISPR-induced depletion of lepB. Importantly, while rnfC deletion does not affect the ability of the mutant cells to adhere to CRC cells, rnfC deficiency significantly diminishes the fusobacterial invasion of CRC cells and formation of spheroid tumors in vitro. Evidently, the Rnf complex modulates the expression of the FadA adhesin and tumorigenesis through a gene regulatory network consisting of multiple response regulators, each controlling a signal peptidase that is critical for the post-translational processing of FadA and surface assembly of FadA amyloids. IMPORTANCEThe Rhodobacter nitrogen-fixation (Rnf) complex of Fusobacterium nucleatum plays an important role in the pathophysiology of this oral pathobiont, since genetic disruption of this conserved respiratory enzyme negatively impacts a wide range of metabolic pathways, as well as bacterial virulence in mice. Nonetheless, how Rnf deficiency weakens the virulence potential of F. nucleatum is not well understood. Here, we show that genetic disruption of the Rnf complex reduces surface assembly of adhesin FadA and FadA-mediated amyloid formation, via regulation of signal peptidase LepB by multiple response regulators. As FadA is critical in the carcinogenesis of colorectal cancer (CRC), the ability to invade CRC cells and promote spheroid tumor growth is strongly diminished in an Rnf-deficient mutant. Thus, this work uncovers a molecular linkage between the Rnf complex and LepB-regulated processing of FadA - likely via metabolic signaling - that maintains the virulence potential of this oncobacterium in various cellular niches.

microbiology↗

bioRxiv2025

Aging-dependent dysregulation of EXOSC2 is maintained in cancer as a dependency

Reprogramming of aged donor tissue cells into induced pluripotent stem cells (A-iPSC) preserved the epigenetic memory of aged-donor tissue, defined as genomic instability and poor tissue differentiation in our previous study. The unbalanced expression of RNA exosome subunits affects the RNA degradation complex function and is associated with geriatric diseases including premature aging and cancer progression. We hypothesized that the age-dependent progressive subtle dysregulation of EXOSC2 (exosome component 2) causes the aging traits (abnormal cell cycle and poor tissue differentiation). We used embryonic stem cells as a tool to study EXOSC2 function as the aging trait epigenetic memory determined in A-iPSC because these aging traits could not be studied in senesced aged cells or immortalized cancer cells. We found that the regulatory subunit of PP2A phosphatase, PPP2R5E, is a key target of EXOSC2 and this regulation is preserved in stem cells and cancer.

cell biology↗